bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of alternative approaches to modelling gas migration through a higher strength rock
Authors: Hoch A. R. , James M. 
Published: January 2013

AbstractThe Radioactive Waste Management Directorate of the UK Nuclear Decommissioning Authority has prepared a generic disposal system safety case (DSSC) that covers a range of possible host rock environments. In many of the waste packages considered in the DSSC, the formation of gases by chemical and microbial processes is likely to occur. In order to demonstrate safety, it is necessary to understand the rates at which the gases are generated and their subsequent migration from a disposal facility after closure. This paper is concerned with modelling gas migration through a fractured higher strength host rock. A first set of simulations compares alternative approaches to modelling gas migration through a fractured rock. The approaches differ in their representation of the interaction between the fractures and the rock matrix. As expected, the gross features of many of the simulations are very similar, with a single continuum approach in which the porosity is set equal to either the fracture porosity or the matrix porosity providing the bounding cases. Gas migration is slower for those simulations where the gas can access more of the rock matrix. A final simulation, with a heterogeneous permeability field, is compared with the other simulations, again showing a very similar evolution.
Sorption properties of aged cements
Authors: Baston G. M. N. , Cowper M. M. , Marshall T. A. 
Published: January 2013

AbstractSamples of artificially aged Nirex reference vault backfill (NRVB) were prepared by progressive leaching with deionized water, after which some of the samples underwent hydrothermal treatment. Compared to unaltered NRVB, X-ray diffraction (XRD) and differential scanning calorimetry (DSC) provided evidence for the ageing resulting in alteration of the mineralogy, in particular the absence of portlandite was observed. The specific surface area of NRVB initially increased due to leaching, but then decreased after further leaching.Sorption distribution ratios (RD values) of uranium(VI), neptunium(IV), tin and zirconium onto aged NRVB samples were measured using the batch sorption technique. For all four elements, there was little difference between RD values for aged NRVB and those for untreated material. The most probable explanation for these findings is that even though the ageing treatments altered the NRVB mineralogy, calcium silicate hydrate (C-S-H) phases are responsible for most of the radionuclide uptake and their transformation to more crystalline forms has little effect on the bulk sorption capacity of the aged material.
Viral latency locus augments B-cell response in vivo to induce chronic marginal zone enlargement, plasma cell hyperplasia, and lymphoma
Authors: Sin Sang-Hoon , Dittmer Dirk P. 
Published: January 2013

Key PointsKaposi sarcoma associated herpesvirus miRNAs and latent proteins drive B-cell proliferation. Viral miRNAs and latent proteins induce BCR and TLR hyper-responsivness in transgenic mice.
Genome-wide analysis of human hotspot intersected genes highlights the roles of meiotic recombination in evolution and disease
Authors: Zhou Tao , Hu Zhibin , Zhou Zuomin , Guo Xuejiang , Sha Jiahao 
Published: January 2013

Abstract

Background
Meiotic recombination events are not randomly located, but rather cluster at hotspot regions. Recently, the fine-scale mapping of genome-wide human recombination hotspots was performed. Here, we systematically analyzed the evolutionary and disease-associated features of hotspots that overlapped with protein-coding genes.

Results
In this study, we defined hotspot intersected genes as HI genes. We found that HI genes were prone to be located in the extracellular part and were functionally enriched in cell-to-cell communication. Tissue-specific genes and secreted protein encoding genes were overrepresented in HI genes, while housekeeping genes were underrepresented. Compared to slowly evolving housekeeping genes and random genes with lower recombination rates, HI genes evolved faster. The fact that brain and blood specific genes were overrepresented in HI genes indicates that they may be involved in the evolution of human intelligence and the immune system. We also found that genes related to disease were enriched in HI genes, especially genes with disease-associated chromosomal rearrangements. Hotspot sequence motifs were overrepresented in common sequences of HI genes and genes with disease-associated chromosomal rearrangements. We further listed repeat elements that were enriched both in hotspots and genes with disease-associated chromosomal rearrangements.

Conclusion
HI genes are evolving and may be involved in the generation of key features of human during evolution. Disease-associated genes may be by-products of meiotic recombination. In addition, hotspot sequence motifs and repeat elements showed the connection between meiotic recombination and genes with disease-associated chromosomal rearrangements at the sequence level. Our study will enable us to better understand the evolutionary and biological significance of human meiotic recombination.
Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes
Authors: Han Yujun , Qin Shanshan , Wessler Susan R 
Published: January 2013

Abstract

Background
Class 2 transposable elements (TEs) are the predominant elements in and around plant genes where they generate significant allelic diversity. Using the complete sequences of four grasses, we have performed a novel comparative analysis of class 2 TEs. To ensure consistent comparative analyses, we re-annotated class 2 TEs in Brachypodium distachyon, Oryza sativa (rice), Sorghum bicolor and Zea mays and assigned them to one of the five cut-and-paste superfamilies found in plant genomes (Tc1/mariner, PIF/Harbinger, hAT, Mutator, CACTA). We have focused on noncoding elements because of their abundance, and compared superfamily copy number, size and genomic distribution as well as correlation with the level of nearby gene expression.

Results
Our comparison revealed both unique and conserved features. First, the average length or size distribution of elements in each superfamily is largely conserved, with the shortest always being Tc1/mariner elements, followed by PIF/Harbinger, hAT, Mutator and CACTA. This order also holds for the ratio of the copy numbers of noncoding to coding elements. Second, with the exception of CACTAs, noncoding TEs are enriched within and flanking genes, where they display conserved distribution patterns, having the highest peak in the promoter region. Finally, our analysis of microarray data revealed that genes associated with Tc1/mariner and PIF/Harbinger noncoding elements have significantly higher expression levels than genes without class 2 TEs. In contrast, genes with CACTA elements have significantly lower expression than genes without class 2 TEs.

Conclusions
We have achieved the most comprehensive annotation of class 2 TEs to date in these four grass genomes. Comparative analysis of this robust dataset led to the identification of several previously unknown features of each superfamily related to copy number, element size, genomic distribution and correlation with the expression levels of nearby genes. These results highlight the importance of distinguishing TE superfamilies when assessing their impact on gene and genome evolution.
ANGUSTIFOLIA is a central component of tissue morphogenesis mediated by the atypical receptor-like kinase STRUBBELIG
Authors: Bai Yang , Vaddepalli Prasad , Fulton Lynette , Bhasin Hemal , Hülskamp Martin , Schneitz Kay 
Published: January 2013

AbstractBackgroundDuring plant tissue morphogenesis cells have to coordinate their behavior to allow the generation of the size, shape and cellular patterns that distinguish an organ. Despite impressive progress the underlying signaling pathways remain largely unexplored. InArabidopsis thaliana, the atypical leucine-rich repeat receptor-like kinase STRUBBELIG (SUB) is involved in signal transduction in several developmental processes including the formation of carpels, petals, ovules and root hair patterning. The threeSTRUBBELIG-LIKE MUTANT(SLM) genesDETORQUEO(DOQ),QUIRKY(QKY) andZERZAUST(ZET) are considered central elements ofSUB-mediated signal transduction pathways as corresponding mutants share most phenotypic aspects withsubmutants.ResultsHere we show thatDOQcorresponds to the previously identifiedANGUSTIFOLIAgene. The genetic analysis revealed that thedoq-1mutant exhibits all additional mutant phenotypes and conversely that otheranalleles show theslmphenotypes. We further provide evidence that SUB and AN physically interact and that AN is not required for subcellular localization of SUB.ConclusionsOur data suggest thatANis involved inSUBsignal transduction pathways. In addition, they reveal previously unreported functions ofANin several biological processes, such as ovule development, cell morphogenesis in floral meristems, and root hair patterning. Finally, SUB and AN may directly interact at the plasma membrane to mediate SUB-dependent signaling.
The maximum standardized uptake value of 18 F-FDG PET scan to determine prognosis of hormone-receptor positive metastatic breast cancer
Authors: Zhang Jian , Jia Zhen , Ragaz Joseph , Zhang Ying-Jian , Zhou Min , Zhang Yong-Ping , Li Gang , Wang Bi-Yun , Wang Zhong-Hua , Hu Xi-Chun 
Published: January 2013

Abstract

Background
Whether PET scan maximum standard uptake value (SUVmax) could differentiate luminal A from luminal B and help predict the survival of metastatic breast cancer (MBC) patients with luminal subtype is still unknown and need to be investigated.

Methods
305 MBC patients with luminal subtypes were screened with PET/CT. Eligible patients were prospectively followed up.

Results
In total, 134 patients were eligible for this study. SUVmax was significantly related to the number of metastatic sites and presence of visceral metastasis on univariate analysis. SUVmax could not effectively differentiate patients with luminal A from luminal B subtype. Although luminal subtype at diagnosis could predict the relapse-free interval, it could not predict progression-free survival (PFS) or overall survival (OS) after developing relapse. In contrast, SUVmax was predictive of both PFS and OS and this effect was maintained in multivariate COX regression model.

Conclusions
SUVmax of MBC did not correlate with molecular subtypes of primary tumor. While molecular subtype may be a valuable prognostic factor at primary diagnosis of breast cancer, the SUVmax, rather than molecular subtype, does have a potential to predict independently in multivariate analysis for the PFS and OS in patients with metastatic disease of luminal subtype.
Influence of the gel thickness on in vivo hyaline cartilage regeneration induced by double-network gel implanted at the bottom of a large osteochondral defect: Short-term results
Authors: Matsuda Hidetoshi , Kitamura Nobuto , Kurokawa Takayuki , Arakaki Kazunobu , Gong Jian Ping , Kanaya Fuminori , Yasuda Kazunori 
Published: January 2013

Abstract

Background
A double-network (DN) gel, which is composed of poly(2-acrylamido-2-methylpropanesulfonic acid) and poly(N,N’-dimethyl acrylamide), can induce hyaline cartilage regeneration in vivo in a large osteochondral defect. The purpose of this study was to clarify the influence of the thickness of the implanted DN gel on the induction ability of hyaline cartilage regeneration.

Methods
Thirty-eight mature rabbits were used in this study. We created an osteochondral defect having a diameter of 4.3-mm in the patellofemoral joint. The knees were randomly divided into 4 groups (Group I: 0.5-mm thick gel, Group II: 1.0-mm thick gel, Group III: 5.0-mm thick gel, and Group IV: untreated control). Animals in each group were further divided into 3 sub-groups depending on the gel implant position (2.0-, 3.0-, or 4.0-mm depth from the articular surface) in the defect. The regenerated tissues were evaluated with the Wayne’s gross and histological grading scales and real time PCR analysis of the cartilage marker genes at 4 weeks.

Results
According to the total Wayne’s score, when the depth of the final vacant space was set at 2.0 mm, the scores in Groups I, II, and III were significantly greater than that Group IV (p < 0.05), although there were no significant differences between Groups I and IV at a 3.0-mm deep vacant space. The expression levels of type-2 collagen in Groups II and III were significantly higher (p < 0.05) than that in Group IV.

Conclusions
The 1.0-mm thick DN gel sheet had the same ability to induce hyaline cartilage regeneration as the 5.0-mm thick DN gel plug. However, the induction ability of the 0.5-mm thick sheet was significantly lower when compared with the 1.0-mm thick gel sheet. The 1.0-mm DN gel sheet is a promising device to establish a cell-free cartilage regeneration strategy that minimizes bone loss from the gel implantation.
Oral health behavior of drug addicts in withdrawal treatment
Authors: Shekarchizadeh Hajar , Khami Mohammad R , Mohebbi Simin Z , Virtanen Jorma I 
Published: January 2013

AbstractBackgroundOral health behavior (OHB), one major factor contributing to proper oral health status, has been addressed insufficiently in addiction literature. The aim of our study was to investigate OHB and its determinants among drug addicts in withdrawal treatment.MethodsThrough a stratified cluster sampling method, we collected the data from 685 patients in withdrawal treatment in Tehran using self-administered questionnaires on OHB components and conducting interviews about patients’ characteristics and addiction history. The T-test, ANOVA, and a linear regression model served for statistical analysis.ResultsOf the patients, 48% reported brushing their teeth less than once a day, more than 90% used fluoride toothpaste almost or always, and 81% flossed their teeth rarely or never. Eating sugary products twice a day or more was reported by 57% of the patients and 85% of them were current smokers. Poor OHB was associated with male gender, lower education, being addicted mainly to crystalline heroin, starting drug abuse at a younger age, and having a longer history of addiction (p < .05).ConclusionPoor OHB was found among the participants in drug withdrawal treatment. Preventive strategies on oral health should be planned and be integrated into other health promotion programs for addicts along with their withdrawal treatment taking into account special groups at higher risk.
Treatment with a copper-selective chelator causes substantive improvement in cardiac function of diabetic rats with left-ventricular impairment
Authors: Lu Jun , Pontré Beau , Pickup Stephen , Choong Soon Y , Li Mingming , Xu Hong , Gamble Gregory D , Phillips Anthony RJ , Cowan Brett R , Young Alistair A , Cooper Garth JS 
Published: January 2013

Abstract

Background
Defective copper regulation is implicated as a causative mechanism of organ damage in diabetes. Treatment with trientine, a divalent-copper-selective chelator, improves arterial and renal structure/function in diabetes, wherein it also ameliorates left-ventricular (LV) hypertrophy. However, direct in vivo evidence that trientine can improve cardiac function in heart failure has hitherto been lacking.

Methods
To determine whether trientine treatment could improve in vivo outcome, we measured cardiac function in groups of trientine-treated diabetic (TETA-DIA), non-drug-treated diabetic (DIA) and sham-treated control (SHAM) rats, by using in vivo high-field cardiac magnetic-resonance imaging (cMRI) and an ex vivo isolated-perfused working heart method. Forty age-matched animals underwent a cMRI scan after which 12 were randomized to the SHAM group and 28 underwent streptozotocin-injection; of these, 25 developed stable diabetes, and 12 were then randomized to receive no treatment for 16 weeks (DIA) and the other 13 to undergo 8-weeks’ untreated diabetes followed by 8-weeks’ drug treatment (TETA-DIA). Animals were studied again by cMRI at 8 and 16 weeks following disease induction, and finally by measurement of ex vivo cardiac function.

Results
After eight weeks diabetes, rats (DIA/TETA-DIA) had developed significant impairment of LV function, as judged by impairment of ejection fraction (LVEF), cardiac output (CO), and LV mass (LVM)/body-mass (all P < 0.001), as well as other functional indexes. LVEF, CO (both P < 0.001) and the other indexes deteriorated further at 16 weeks in DIA, whereas trientine (TETA-DIA) improved cardiac function by elevating LVEF and CO (both P < 0.001), and also partially reversed the increase in LVM/body-mass (P < 0.05). In ex vivo hearts from DIA, the CO response to increasing preload pressure was deficient compared with SHAM (P < 0.001) whereas the preload-CO relationship was significantly improved in TETA-DIA animals (P < 0.001).

Conclusions
Trientine treatment significantly improved cardiac function in diabetic rats with substantive LV impairment. These results implicate impaired copper regulation in the pathogenesis of impaired cardiac function caused by diabetic cardiomyopathy, and support ongoing studies of trientine treatment in patients with heart failure.
Characterization of physicochemical properties of ivy nanoparticles for cosmetic application
Authors: Huang Yujian , Lenaghan Scott C , Xia Lijin , Burris Jason N , Stewart C Neal Jr , Zhang Mingjun 
Published: February 2013

Abstract

Background
Naturally occurring nanoparticles isolated from English ivy (Hedera helix) have previously been proposed as an alternative to metallic nanoparticles as sunscreen fillers due to their effective UV extinction property, low toxicity and potential biodegradability.

Methods
This study focused on analyzing the physicochemical properties of the ivy nanoparticles, specifically, those parameters which are crucial for use as sunscreen fillers, such as pH, temperature, and UV irradiation. The visual transparency and cytotoxicity of ivy nanoparticles were also investigated comparing them with other metal oxide nanoparticles.

Results
Results from this study demonstrated that, after treatment at 100°C, there was a clear increase in the UV extinction spectra of the ivy nanoparticles caused by the partial decomposition. In addition, the UVA extinction spectra of the ivy nanoparticles gradually reduced slightly with the decrease of pH values in solvents. Prolonged UV irradiation indicated that the influence of UV light on the stability of the ivy nanoparticle was limited and time-independent. Compared to TiO2 and ZnO nanoparticles, ivy nanoparticles showed better visual transparency. Methylthiazol tetrazolium assay demonstrated that ivy nanoparticles exhibited lower cytotoxicity than the other two types of nanoparticles. Results also suggested that protein played an important role in modulating the three-dimensional structure of the ivy nanoparticles.

Conclusions
Based on the results from this study it can be concluded that the ivy nanoparticles are able to maintain their UV protective capability at wide range of temperature and pH values, further demonstrating their potential as an alternative to replace currently available metal oxide nanoparticles in sunscreen applications.
Multi-channel acoustic recording and automated analysis of Drosophila courtship songs
Authors: Arthur Benjamin J , Sunayama-Morita Tomoko , Coen Philip , Murthy Mala , Stern David L 
Published: January 2013

Abstract

Background

Drosophila melanogaster has served as a powerful model system for genetic studies of courtship songs. To accelerate research on the genetic and neural mechanisms underlying courtship song, we have developed a sensitive recording system to simultaneously capture the acoustic signals from 32 separate pairs of courting flies as well as software for automated segmentation of songs.

Results
Our novel hardware design enables recording of low amplitude sounds in most laboratory environments. We demonstrate the power of this system by collecting, segmenting and analyzing over 18 hours of courtship song from 75 males from five wild-type strains of Drosophila melanogaster. Our analysis reveals previously undetected modulation of courtship song features and extensive natural genetic variation for most components of courtship song. Despite having a large dataset with sufficient power to detect subtle modulations of song, we were unable to identify previously reported periodic rhythms in the inter-pulse interval of song. We provide detailed instructions for assembling the hardware and for using our open-source segmentation software.

Conclusions
Analysis of a large dataset of acoustic signals from Drosophila melanogaster provides novel insight into the structure and dynamics of species-specific courtship songs. Our new system for recording and analyzing fly acoustic signals should therefore greatly accelerate future studies of the genetics, neurobiology and evolution of courtship song.
A (H1N1) pdm09 HA D222 variants associated with severity and mortality in patients during a second wave in Mexico
Authors: Vazquez-Perez Joel A , Isa Pavel , Kobasa Darwyn , Ormsby Christopher E , Ramírez-Gonzalez Jose E , Romero-Rodríguez Damaris P , Ranadheera Charlene , Li Yan , Bastien Nathalie , Embury-Hyatt Carissa , González-Duran Elizabeth , Barrera-Badillo Gisela , Ablanedo-Terrazas Yuria , Sevilla-Reyes Edgar E , Escalera-Zamudio Marina , Cobián-Güemes Ana G , Lopez Irma , Ortiz-Alcántara Joanna , Alpuche-Aranda Celia , Perez-Padilla Jose R , Reyes-Terán Gustavo 
Published: January 2013

Abstract

Background
Pandemic type A (H1N1) influenza arose in early 2009, probably in Mexico and the United States, and reappeared in North America in September for seven more months. An amino acid substitution in the hemagglutinin (HA), D222G, has been reported in a significant proportion of patients with a severe and fatal outcome. We studied the prevalence of HA222 substitutions in patients in Mexico during the second wave and its association with clinical outcome and pathogenicity in a mouse model.

Methods
The nucleotide sequences of hemagglutinin (HA) from viruses collected from 77 patients were determined including 50 severe and fatal cases and 27 ambulatory cases. Deep sequencing was done on 5 samples from severe or fatal cases in order to determine the quasispecies proportion. Weight loss and mortality due to infection with cultured influenza viruses were analyzed in a mouse model.

Results
Viruses from 14 out of 50 hospitalized patients (28%) had a non aspartic acid residue at the HA 222 position (nD222), while all 27 ambulatory patients had D222 (p = 0.0014). G222 was detected as sole species or in coexistence with N222 and D222 in 12 patients with severe disease including 8 who died. N222 in coexistence with D222 was detected in 1 patient who died and co-occurrence of A222 and V222, together with D222, was detected in another patient who died. The patients with a nD222 residue had higher mortality (71.4%), compared to the group with only D222 (22.2%, p = 0.0008). Four of the 14 viruses from hospitalized patients were cultured and intranasally infected into mice. Two viruses with G222 were lethal while a third virus, with G222, caused only mild illness in mice similar to the fourth virus that contained D222.

Conclusions
We confirm the elevated incidence of HA222 (H1N1)pdm09 variants in severe disease and mortality. Both clinical and mouse infection data support the idea that nD222 mutations contribute to increased severity of disease but additional determinants in disease outcome may be present.