bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of the Upgraded Tangent Linear and Adjoint of the Weather Research and Forecasting (WRF) Model
Authors: Zhang Xin , Huang Xiang-Yu , Pan Ning 
Published: February 2013

Abstract
The authors propose a new technique for parallelizations of tangent linear and adjoint codes, which were applied in the redevelopment for the Weather Research and Forecasting (WRF) model with its Advanced Research WRF dynamic core using the automatic differentiation engine. The tangent linear and adjoint codes of the WRF model (WRFPLUS) now have the following improvements: A complete check interface ensures that developers write accurate tangent linear and adjoint codes with ease and efficiency. A new technique based on the nature of duality that existed among message passing interface communication routines was adopted to parallelize the WRFPLUS model. The registry in the WRF model was extended to automatically generate the tangent linear and adjoint codes of the required communication operations. This approach dramatically speeds up the software development cycle of the parallel tangent linear and adjoint codes and leads to improved parallel efficiency. Module interfaces were constructed for coupling tangent linear and adjoint codes of the WRF model with applications such as four-dimensional variational data assimilation, forecast sensitivity to observation, and others.
The genomic signature of trait-associated variants
Authors: Kindt Alida S D , Navarro Pau , Semple Colin A M , Haley Chris S 
Published: February 2013

Abstract

Background
Genome-wide association studies have identified thousands of SNP variants associated with hundreds of phenotypes. For most associations the causal variants and the molecular mechanisms underlying pathogenesis remain unknown. Exploration of the underlying functional annotations of trait-associated loci has thrown some light on their potential roles in pathogenesis. However, there are some shortcomings of the methods used to date, which may undermine efforts to prioritize variants for further analyses. Here, we introduce and apply novel methods to rigorously identify annotation classes showing enrichment or depletion of trait-associated variants taking into account the underlying associations due to co-location of different functional annotations and linkage disequilibrium.

Results
We assessed enrichment and depletion of variants in publicly available annotation classes such as genic regions, regulatory features, measures of conservation, and patterns of histone modifications. We used logistic regression to build a multivariate model that identified the most influential functional annotations for trait-association status of genome-wide significant variants. SNPs associated with all of the enriched annotations were 8 times more likely to be trait-associated variants than SNPs annotated with none of them. Annotations associated with chromatin state together with prior knowledge of the existence of a local expression QTL (eQTL) were the most important factors in the final logistic regression model. Surprisingly, despite the widespread use of evolutionary conservation to prioritize variants for study we find only modest enrichment of trait-associated SNPs in conserved regions.

Conclusion
We established odds ratios of functional annotations that are more likely to contain significantly trait-associated SNPs, for the purpose of prioritizing GWAS hits for further studies. Additionally, we estimated the relative and combined influence of the different genomic annotations, which may facilitate future prioritization methods by adding substantial information.
Negative transcriptional control of ERBB2 gene by MBP-1 and HDAC1: diagnostic implications in breast cancer
Authors: Contino Flavia , Mazzarella Claudia , Ferro Arianna , Lo Presti Mariavera , Roz Elena , Lupo Carmelo , Perconti Giovanni , Giallongo Agata , Feo Salvatore 
Published: February 2013

Abstract

Background
The human ERBB2 gene is frequently amplified in breast tumors, and its high expression is associated with poor prognosis. We previously reported a significant inverse correlation between Myc promoter-binding protein-1 (MBP-1) and ERBB2 expression in primary breast invasive ductal carcinoma (IDC). MBP-1 is a transcriptional repressor of the c-MYC gene that acts by binding to the P2 promoter; only one other direct target of MBP-1, the COX2 gene, has been identified so far.

Methods
To gain new insights into the functional relationship linking MBP-1 and ERBB2 in breast cancer, we have investigated the effects of MBP-1 expression on endogenous ERBB2 transcript and protein levels, as well as on transcription promoter activity, by transient-transfection of SKBr3 cells. Reporter gene and chromatin immunoprecipitation assays were used to dissect the ERBB2 promoter and identify functional MBP-1 target sequences. We also investigated the relative expression of MBP-1 and HDAC1 in IDC and normal breast tissues by immunoblot analysis and immunohistochemistry.

Results
Transfection experiments and chromatin immunoprecipitation assays in SKBr3 cells indicated that MBP-1 negatively regulates the ERBB2 gene by binding to a genomic region between nucleotide −514 and −262 of the proximal promoter; consistent with this, a concomitant recruitment of HDAC1 and loss of acetylated histone H4 was observed. In addition, we found high expression of MBP-1 and HDAC1 in normal tissues and a statistically significant inverse correlation with ErbB2 expression in the paired tumor samples.

Conclusions
Altogether, our in vitro and in vivo data indicate that the ERBB2 gene is a novel MBP-1 target, and immunohistochemistry analysis of primary tumors suggests that the concomitant high expression of MBP-1 and HDAC1 may be considered a diagnostic marker of cancer progression for breast IDC.
Targeting of interleukin-13 receptor α2 for treatment of head and neck squamous cell carcinoma induced by conditional deletion of TGF-β and PTEN signaling
Authors: Hall Bradford , Nakashima Hideyuki , Sun Zhi-Jun , Sato Yuki , Bian Yansong , Husain Syed R , Puri Raj K , Kulkarni Ashok B 
Published: February 2013

Abstract

Background
The sixth leading class of cancer worldwide is head and neck cancer, which typically arise within the squamous epithelium of the oral mucosa. Human head and neck squamous cell carcinoma (HNSCC) is known to be difficult to treat and has only a 50% five-year survival rate. With HNSCC, novel therapeutics are needed along with a means of rapidly screening anti-cancer agents in vivo, such as mouse models.

Methods
In order to develop new animal models of cancer to test safety and efficacy of novel therapeutic agents for human HNSCC, tumors resembling clinical cases of human HNSCC were induced in the head and neck epithelium of a genetically engineered mouse model. This mouse model was generated by conditional deletion of two tumor suppressors, Transforming Growth Factor-β Receptor 1 (TGFβRI) and Phosphatase and Tensin homolog (PTEN), in the oral epithelium. We discovered that the tumors derived from these Tgfbr1/Pten double conditional knockout (2cKO) mice over-expressed IL-13Rα2, a high affinity receptor for IL-13 that can function as a tumor antigen. To demonstrate a proof-of-concept that targeted therapy against IL-13Rα2 expression would have any antitumor efficacy in this spontaneous tumor model, these mice were treated systemically with IL-13-PE, a recombinant immunotoxin consisting of IL-13 fused to the Pseudomonas exotoxin A.

Results

Tgfbr1/Pten 2cKO mice when treated with IL-13-PE displayed significantly increased survival when compared to the untreated control mice. The untreated mice exhibited weight loss, particularly with the rapid onset of tongue tumors, but the treated mice gained weight while on IL-13-PE therapy and showed no clinical signs of toxicity due to the immunotoxin. Expression of IL-13Rα2 in tumors was significantly decreased with IL-13-PE treatment as compared to the controls and the number of myeloid-derived suppressor cells (MDSC) was also significantly reduced in the spleens of the IL-13-PE treated mice.

Conclusions
Our study demonstrates that the Tgfbr1/Pten 2cKO mouse model of human HNSCC is a useful model for assessing antitumor activity of new cancer therapeutic agents, and that IL-13-PE has therapeutic potential to treat human head and neck cancer.
Prognostic significance of miR-194 in endometrial cancer
Authors: Zhai Haiyan , Karaayvaz Mihriban , Dong Peixin , Sakuragi Noriaki , Ju Jingfang 
Published: February 2013

Abstract
Endometrial cancer (EC) is the leading malignant tumor occurring in the female genital tract and some subtypes are highly invasive and metastatic. miRNAs are small non-coding RNAs that have a broad impact on cancer progression. In particular, miR-194 regulates epithelial to mesenchymal transition (EMT) by suppressing the expression of BMI-1 in EC. In this retrospective study, the clinical significance of miR-194 was investigated in archival EC specimens. We extracted total RNA from thirty-two EC samples and quantified the expression level of miR-194. We discovered that the expression level of miR-194 was significantly (P = 0.03) lower in type I EC patients with more advanced stage. In addition, patients with higher miR-194 levels have better prognosis than those with lower miR-194 levels (P = 0.0067; Cut-off value of miR-194 = 0.3). These results indicate that miR-194 has potential to serve as prognostic biomarker for EC patients.
The Influence of Varying Cell Sizes on the Tensile Behaviour of Open-Cell Foams
Authors: Sieber T. , Liedke T. , Mühlich U. , Ballani F. 
Published: February 2013

Abstract
The aim of this paper is to study the mechanical tensile properties of open-cell foam structures on the cell size variation by numerical simulations. For this purpose, random Laguerre tessellations were used, which allow the creation of foam structures with strongly varying cell sizes. First, a model was fitted to real open-cell foams based on x-ray computed tomography (XCT) scans by parameter optimization. Two more virtual foam models with different cell size variations were produced according to the first fitted one. Tensile properties of the model realizations were computed by finite-element analysis using beam elements. The numerical results were presented and discussed.
Potential Sources of Bisphenol A in the Neonatal Intensive Care Unit
Authors: Duty Susan M. , Mendonca Kaitlin , Hauser Russ , Calafat Antonia M. , Ye Xiaoyun , Meeker John D. , Ackerman Robin , Cullinane Judi , Faller Josephine , Ringer Steven 
Published: February 2013

OBJECTIVES:
To determine whether nutritional intake and medical devices are bisphenol A (BPA) exposure sources among premature infants in the NICU.

METHODS:
Mothers and their premature infants cared for in the NICU for the past 3 days were recruited for this exposure assessment study. Forty-three mothers contributed 1 nutrition sample (breast milk or formula) to characterize the infant’s intake. Two urine samples (before and after feeding) were collected from each of 55 infants. Medical device use was categorized as “low” or “high” based on the number and invasiveness of devices used. BPA urinary concentrations used as a biomarker to estimate BPA exposure were measured by online solid-phase extraction, high performance liquid chromatography, isotope dilution, tandem mass spectrometry. Nonparametric equivalence tests, intraclass correlations, and hierarchical linear mixed-effects models were conducted.

RESULTS:
Breast milk and formula samples did not differ in total BPA concentration nor did infants’ median urinary concentration of total BPA before or after feedings. However, the median urinary total BPA concentration among infants who required the use of 4 or more medical devices in the past 3 days was significantly higher (36.6 µg/L) than among infants who required the use of 0 to 3 devices (13.9 µg/L). The calculated BPA exposures are lower than the US Environmental Protection Agency reference dose, but considerably higher (16- to 32-fold) than among infants or children from the general population.

CONCLUSIONS:
The number of medical devices used in the past 3 days, but not nutritional intake, was positively associated with exposure to BPA.
Childhood and Adolescent Television Viewing and Antisocial Behavior in Early Adulthood
Authors: Robertson Lindsay A. , McAnally Helena M. , Hancox Robert J. 
Published: February 2013

OBJECTIVE:
To investigate whether excessive television viewing throughout childhood and adolescence is associated with increased antisocial behavior in early adulthood.

METHODS:
We assessed a birth cohort of 1037 individuals born in Dunedin, New Zealand, in 1972–1973, at regular intervals from birth to age 26 years. We used regression analysis to investigate the associations between television viewing hours from ages 5 to 15 years and criminal convictions, violent convictions, diagnosis of antisocial personality disorder, and aggressive personality traits in early adulthood.

RESULTS:
Young adults who had spent more time watching television during childhood and adolescence were significantly more likely to have a criminal conviction, a diagnosis of antisocial personality disorder, and more aggressive personality traits compared with those who viewed less television. The associations were statistically significant after controlling for sex IQ, socioeconomic status, previous antisocial behavior, and parental control. The associations were similar for both sexes, indicating that the relationship between television viewing and antisocial behavior is similar for male and female viewers.

CONCLUSIONS:
Excessive television viewing in childhood and adolescence is associated with increased antisocial behavior in early adulthood. The findings are consistent with a causal association and support the American Academy of Pediatrics recommendation that children should watch no more than 1 to 2 hours of television each day.
A Semi-Implicit Approach for Integrated Reservoir and Surface Network Simulation
Authors: Liang Jialing , Rubin Barry 
Published: February 2013

Abstract
Conventionally, methods of coupling reservoirs and surface networks are categorized into implicit and explicit approaches. The term implicit coupling indicates the two simulators solve unknowns together, simultaneously or iteratively. While explicit coupling indicates the two simulators solve unknowns sequentially and exchange their boundary conditions at the last coupled time tn.
The explicit approach is straightforward to implement in existing reservoir and surface network models and is widely used. Explicit coupling does have drawbacks, however; as well rate and pressure oscillations are often observed.
In this paper, a new semi-implicit method for coupled simulation is presented. This technique stabilizes and improves the accuracy of the coupled model. The semi-implicit coupling overcomes the problems found in explicit coupling methods without requiring the complexity of a fully implicit coupled model.
The new approach predicts inflow performance relationship (IPR) curves at the next coupled time tn+1 by simultaneously conducting well tests for all wells in the reservoir before actually taking the required timestep. All wells first simultaneously flow to the next coupled time tn+1 with the well rates unchanged from the last coupled timestep. The timestep is rewound, and all well rates are reduced by a uniform fraction and then simultaneously flow again to tn+1. By extrapolating the resulting well pressures, the well’s shut-in pressures at time tn+1 are determined and thus straight line IPRs are produced. The new IPR curves better approximates each well’s drainage region at tn+1 and each well’s shut-in pressure at tn+1 which helps to stabilize the explicitly coupled model.
The new coupling technique normally does not require iteration between the reservoir and surface network and normally has the stability and accuracy characteristics of an implicitly coupled approach. Since the well tests already account for individual well drainage regions, explicit knowledge of the well drainage region is not required. Due to the stabilized IPR, the approach has also been found to reduce the overall computational time when compared with explicit coupling.
Applications of the new approach are presented which show significant improvements over explicit coupling in both stability and accuracy.
Magnetic resonance spectroscopy (MRS) of vertebral column – an additional tool for evaluation of aggressiveness of vertebral haemangioma like lesion
Authors: Jeromel Miran , Podobnik Janez 
Published: February 2013

Abstract
Background. Most vertebral haemangioma are asymptomatic and discovered incidentally. Sometimes the symptomatic lesions present with radiological signs of aggressiveness and their appearance resemble other aggressive lesions (e.g. solitary plasmacytoma).
Case report. We present a patient with large symptomatic aggressive haemangioma like lesion in 12th thoracic vertebra in which a magnetic resonance spectroscopy (MRS) was used to analyse fat content within the lesion. The lesion in affected vertebrae showed low fat content with 33% of fat fraction (%FF). The fat content in non-affected (1st lumbar) vertebra was as expected for patient’s age (68%). Based on MRS data, the lesion was characterized as an aggressive haemangioma. The diagnosis was confirmed with biopsy, performed during the treatment - percutaneous vertebroplasty.
Conclusions. The presented case shows that MRS can be used as an additional tool for evaluation of aggressiveness of vertebral haemangioma like lesions.
New cases of pathogens imported with ornamental fish
Authors: Sobecka Ewa , Łuczak Ewa , Marcinkiewicz Michał 
Published: February 2013

Abstract
The global trade in live ornamental fish carries with it the potential threat of unwanted movement of pathogens. The live ornamental fish, when released into the natural environment of their destination countries, may disseminate their parasites, threatening local fish and causing economic loss in fish aquaculture. This study was aimed to explain the reasons for deterioration of health and premature death of ornamental fish: Nannostomus spp. from Colombia and Symphysodon spp. Some specimens of Symphysodon aequifasciatus Pellegrin, 1904 were captured from their natural habitats in the Amazon River basin and shipped to Poland by air mail. The hybrids of Symphysodon spp. originated from an aquarium in Poland (shared with S. aequifasciatus). The third discus fish species, Symphysodon discus Heckel, 1840 came from a fish farm in Thailand and represents an Asian breeding line. All the studied fish were infected with pathogens. Nannostomus spp. housed a single parasite species on its skin, namely Artystone minima. This isopod species was not recorded in Poland and probably in Europe before. The examined fish of the genus Symphysodon yielded 13 pathogens. Five of them Philodina sp., Ichthyobodo necator, Hexamita symphysodonis, Sciadicleithrum variabilum and Eustrongylides sp. were not earlier recorded in this host species in Poland. The findings of Ichthyophonus hoferi and Myxobolus sp. are new host records for Symphysodon spp. fish. Hybrid fish and S. aequifasciatus are reported here as hosts of Entamoeba sp. for the first time.
Comparison Between Currently Used Blood Samples And New Saliva Dna Collection Method For Quality Of Genomic Dna And Genotyping
Authors: Aftenie Loredana Mariana , Franciuc Irina , Martinescu Alina , Honcea Adina 
Published: February 2013

Abstract
Obtaining blood biospecimens presents logistical and financial challenges. As a result, saliva biospecimen collection is becoming more frequent because of the ease of collection and lower cost. This article describes an assessment of two different methods for collecting samples: whole blood and whole saliva samples used further for DNA extraction and HLA genotyping in immunogenic disease on a group of patients registered at our Molecular Genetics Laboratory Faculty of Medicine “Ovidius” University Constanţa. Our data show that only 81% of the requested participants delivered a blood sample, whereas 19% delivered a saliva sample because they refuse the first sampling method. Analysis of purified genomic DNA by Nano Photometer and agarose gel electrophoresis revealed that blood and saliva samples resulted in DNA with the best quality. PCR analysis showed that DNA from 100% of the blood samples and 93% of the saliva samples could be subsequently amplified. Our study shows that the response rate of self-collection saliva samples had to be considering for the patients that have a low response rate of blood sampling. The quality of genomic DNA from saliva samples was comparable with blood samples as assessed by purity, concentration, yield and PCR amplification. We conclude that the use of saliva samples is a good alternative to blood samples to obtain genomic DNA of high quality and it will considerably increase the participant’s response rate for genetic studies.
The Incidence Of Hepatic Steatosis Recently Found In Patients With Diabetes Mellitus Type 2 Newly Discovered
Authors: Cojocaru Cristina , Circo E. 
Published: February 2013

Abstract
The nonalcoholic hepatic steatos is represents one of the most frequent disorders in patients with diabetes mellitus type 2. The obesity and especially the abdominal adipose tissue distribution represent factors of higher risk for nonalcoholic hepatic steatosis. The echographic examination and FirboScan are very important in identification of this disorder. The study consisted in analysis of the clinical and paraclinical results in order to identify the SHNA (The nonalcoholic hepatic steatosis) incidence. It must be mentioned the fact that the absence of the abdominal obesity and increased transaminases do not exclude SHNA(The nonalcoholic hepatic steatosis).
Mineral Concentrations in Bottled Water Products: Implications for Canadians’ Mineral Intakes
Authors: Bertinato Jesse , Taylor Jessica 
Published: February 2013

Purpose: The popularity of bottled water products (BWPs) is growing in Canada. Concentrations of minerals with important implications for health were compared in different types of BWPs. Methods: One sample of each brand and type of plain BWP (purified, remineralized, spring, mineral, and artesian), flavoured BWP, and nutrient-enriched BWP sold in major stores in Ottawa, Ontario, was purchased to allow determination of mineral concentrations by flame atomic absorption or emission spectroscopy. A total of 124 BWPs representing 37 brands were analyzed. Results: In general, spring and mineral water contained higher amounts of magnesium and calcium than did purified, remineralized, artesian, flavoured, or nutrient-enriched water. Most plain BWPs contained little sodium and potassium, whereas 15% to 35% of flavoured and nutrient-enriched products had considerably higher concentrations. Only magnesium and calcium concentrations were highly correlated (r=0.76, p<0.001). Calculation of the percentage of Dietary Reference Intakes that could be supplied by each product revealed that, if they are consumed habitually, many products can contribute substantially to recommended intakes of these minerals. Conclusions: Mineral concentrations in most types of BWP varied, but distinct differences between types of products were identified. Consumers should be aware of the mineral content of BWPs because some could influence intakes of certain minerals significantly.