bluuebunny/crossref_metadata_2025_split huggingface dataset:
Presenilin-1 regulates the constitutive turnover of the fibronectin matrix in endothelial cells
Authors: De Gasperi Rita , Gama Sosa Miguel A , Elder Gregory A 
Published: December 2012

Abstract

Background
Presenilin-1 (PS1) is a transmembrane protein first discovered because of its association with familial Alzheimer’s disease. Mice with null mutations in PS1 die shortly after birth exhibiting multiple CNS and non-CNS abnormalities. One of the most prominent features in the brains of PS1−/− embryos is a vascular dysgenesis that leads to multiple intracerebral hemorrhages. The molecular and cellular basis for the vascular dysgenesis in PS1−/− mice remains incompletely understood. Because the extracellular matrix plays key roles in vascular development we hypothesized that an abnormal extracellular matrix might be present in endothelial cells lacking PS1 and examined whether the lack of PS1 affects expression of fibronectin a component of the extracellular matrix known to be essential for vascular development.

Results
We report that primary as well as continuously passaged PS1−/− endothelial cells contain more fibronectin than wild type cells and that the excess fibronectin in PS1−/− endothelial cells is incorporated into a fibrillar network. Supporting the in vivo relevance of this observation fibronectin expression was increased in microvascular preparations isolated from E14.5 to E18.5 PS1−/− embryonic brain. Reintroduction of PS1 into PS1−/− endothelial cells led to a progressive decrease in fibronectin levels showing that the increased fibronectin in PS1−/− endothelial cells was due to loss of PS1. Increases in fibronectin protein in PS1−/− endothelial cells could not be explained by increased levels of fibronectin RNA nor based on metabolic labeling studies by increased protein synthesis. Rather we show based on the rate of turnover of exogenously added biotinylated fibronectin that increased fibronectin in PS1−/− endothelial cells results from a slower degradation of the fibronectin fibrillar matrix on the cell surface.

Conclusions
These studies show that PS1 regulates the constitutive turnover of the fibronectin matrix in endothelial cells. These studies provide molecular clues that may help to explain the origin of the vascular dysgenesis that develops in PS1−/− embryonic mice.
Genetic diversity and molecular typing of Listeria monocytogenes in China
Authors: Wang Yan , Zhao Ailan , Zhu Renfa , Lan Ruiting , Jin Dong , Cui Zhigang , Wang Yonglu , Li Zhenchuan , Wang Yiting , Xu Jianguo , Ye Changyun 
Published: December 2012

Abstract

Background

Listeria monocytogenes can cause invasive diseases in humans and farm animals and is frequently isolated from dairy products and poultry. Listeriosis is uncommon in China but L. monocytogenes has been isolated from foods and food processing environments in China. However little is known of genetic diversity of Chinese L. monocytogenes isolates and their relationships with global isolates.

Results
Two hundred and twelve isolates of L. monocytogenes from food sources from 12 provinces/cities in China were analysed by serotyping, Pulsed Field Gel Electrophoresis (PFGE) and Multi-locus Sequence Typing (MLST). The predominant serotypes are 1/2a, 1/2b and 1/2c accounting for 90.1% of the isolates. PFGE divided the isolates into 61 pulse types (PTs). Twenty nine PTs were represented by more than one isolates with PT GX6A16.0004 containing the most number of isolates. MLST differentiated the isolates into 36 STs, among which 15 were novel. The 3 most common STs were ST9 (29.1%), ST8 (10.7%) and ST87 (9.2%), accounting for 49.0% of the isolates.

Conclusions
STs prevalent in other parts of the world are also prevalent in China including 7 STs (ST1-ST3, ST5, ST6, ST8, ST9) which caused maternal fetal infections or outbreaks, suggesting that these STs potentially can also cause severe human infections or outbreaks in China. Surveillance of these STs will provide important information for prevention of listeriosis. This study also enhances our understanding of genetic diversity of L. monocytogenes in China.
Genome-wide association Scan of dental caries in the permanent dentition
Authors: Wang Xiaojing , Shaffer John R , Zeng Zhen , Begum Ferdouse , Vieira Alexandre R , Noel Jacqueline , Anjomshoaa Ida , Cuenco Karen T , Lee Myoung-Keun , Beck James , Boerwinkle Eric , Cornelis Marilyn C , Hu Frank B , Crosslin David R , Laurie Cathy C , Nelson Sarah C , Doheny Kimberly F , Pugh Elizabeth W , Polk Deborah E , Weyant Robert J , Crout Richard , McNeil Daniel W , Weeks Daniel E , Feingold Eleanor , Marazita Mary L 
Published: December 2012

Abstract

Background
Over 90% of adults aged 20 years or older with permanent teeth have suffered from dental caries leading to pain, infection, or even tooth loss. Although caries prevalence has decreased over the past decade, there are still about 23% of dentate adults who have untreated carious lesions in the US. Dental caries is a complex disorder affected by both individual susceptibility and environmental factors. Approximately 35-55% of caries phenotypic variation in the permanent dentition is attributable to genes, though few specific caries genes have been identified. Therefore, we conducted the first genome-wide association study (GWAS) to identify genes affecting susceptibility to caries in adults.

Methods
Five independent cohorts were included in this study, totaling more than 7000 participants. For each participant, dental caries was assessed and genetic markers (single nucleotide polymorphisms, SNPs) were genotyped or imputed across the entire genome. Due to the heterogeneity among the five cohorts regarding age, genotyping platform, quality of dental caries assessment, and study design, we first conducted genome-wide association (GWA) analyses on each of the five independent cohorts separately. We then performed three meta-analyses to combine results for: (i) the comparatively younger, Appalachian cohorts (N = 1483) with well-assessed caries phenotype, (ii) the comparatively older, non-Appalachian cohorts (N = 5960) with inferior caries phenotypes, and (iii) all five cohorts (N = 7443). Top ranking genetic loci within and across meta-analyses were scrutinized for biologically plausible roles on caries.

Results
Different sets of genes were nominated across the three meta-analyses, especially between the younger and older age cohorts. In general, we identified several suggestive loci (P-value ≤ 10E-05) within or near genes with plausible biological roles for dental caries, including RPS6KA2 and PTK2B, involved in p38-depenedent MAPK signaling, and RHOU and FZD1, involved in the Wnt signaling cascade. Both of these pathways have been implicated in dental caries. ADMTS3 and ISL1 are involved in tooth development, and TLR2 is involved in immune response to oral pathogens.

Conclusions
As the first GWAS for dental caries in adults, this study nominated several novel caries genes for future study, which may lead to better understanding of cariogenesis, and ultimately, to improved disease predictions, prevention, and/or treatment.
Simultaneous determination of phagocytosis of Plasmodium falciparum-parasitized and non-parasitized red blood cells by flow cytometry
Authors: Gallo Valentina , Skorokhod Oleksii A , Schwarzer Evelin , Arese Paolo 
Published: December 2012

Abstract

Background
Severe falciparum malaria anaemia (SMA) is a frequent cause of mortality in children and pregnant women. The most important determinant of SMA appears to be the loss of non-parasitized red blood cells (np-RBCs) in excess of loss of parasitized (p-) RBCs at schizogony. Based on data from acute SMA where excretion of haemoglobin in urine and increased plasma haemoglobin represented respectively less than 1% and 0.5% of total Hb loss, phagocytosis appears to be the predominant mechanism of removal of np- and p-RBC.
Estimates indicate that np-RBCs are cleared in approximately 10-fold excess compared to p-RBCs. An even larger removal of np-RBCs has been described in vivax malaria anaemia. Estimates were based on two single studies both performed on neurosyphilitic patients who underwent malaria therapy. As the share of np-RBC removal is likely to vary between wide limits, it is important to assess the contribution of both np- and p-RBC populations to overall RBC loss, and disclose the mechanism of such variability. As available methods do not discriminate between the removal of np- vs p-RBCs, the purpose of this study was to set up a system allowing the simultaneous determination of phagocytosis of p- and np-RBC in the same sample.

Methods and Results
Phagocytosis of p- and np-RBCs was quantified in the same sample using double-labelled target cells and the human phagocytic cell-line THP-1, pre-activated by TNF and IFNγ to enhance their phagocytic activity. Target RBCs were double-labelled with fluorescent carboxyfluorescein-succinimidyl ester (CF-SE) and the DNA label ethidium bromide (EB). EB, a DNA label, allowed to discriminate p-RBCs that contain parasitic DNA from the np-RBCs devoid of DNA. FACS analysis of THP-1 cells fed with double-labelled RBCs showed that p- and np-RBCs were phagocytosed in different proportions in relation to parasitaemia.

Conclusions
The assay allowed the analysis of phagocytosis rapidly and with low subjective error, and the differentiation between phagocytosed p- and np-RBCs in the same sample. The presented method may help to analyse the factors or conditions that modulate the share of np-RBC removal in vitro and in vivo and lead to a better understanding of the pathogenesis of SMA.
Existence and multiplicity of solutions for some second-order systems on time scales with impulsive effects
Authors: Zhou Jianwen , Wang Yanning , Li Yongkun 
Published: December 2012

AbstractIn this paper, we present a recent approach via variational methods and critical point theory to obtain the existence of solutions for the nonautonomous second-order system on time scales with impulsive effects{uΔ2(t)+A(σ(t))u(σ(t))+∇F(σ(t),u(σ(t)))=0,Δ-a.e. t∈[0,T]Tκ;u(0)−u(T)=uΔ(0)−uΔ(T)=0,(ui)Δ(tj+)−(ui)Δ(tj−)=Iij(ui(tj)),i=1,2,…,N,j=1,2,…,p,wheret0=0<t1<t2<⋯<tp<tp+1=T,tj∈[0,T]T(j=0,1,2,…,p+1),u(t)=(u1(t),u2(t),…,uN(t))∈RN,A(t)=[dlm(t)]is a symmetricN×Nmatrix-valued function defined on[0,T]Twithdlm∈L∞([0,T]T,R)for alll,m=1,2,…,N,Iij:R→R(i=1,2,…,N,j=1,2,…,p) are continuous andF:[0,T]T×RN→R. Finally, two examples are presented to illustrate the feasibility and effectiveness of our results.MSC:34B37, 34N05.
Determination of stanozolol and 3′-hydroxystanozolol in rat hair, urine and serum using liquid chromatography tandem mass spectrometry
Authors: Deshmukh Nawed IK , Zachar Gergely , Petróczi Andrea , Székely Andrea D , Barker James , Naughton Declan P 
Published: December 2012

Abstract

Background
Anabolic androgenic steroids, such as stanozolol, are typically misused by athletes during preparation for competition. Out-of-competition testing presents a unique challenge in the current anti-doping detection system owing to logistic reasons. Analysing hair for the presence of a prohibited drug offers a feasible solution for covering the wider window in out-of-competition testing. To assist in vivo studies aiming to establish a relationship between drug levels detected in hair, urine and blood, sensitive methods for the determination of stanozolol and its major metabolite 3′-hydroxystanozolol were developed in pigmented hair, urine and serum, using brown Norway rats as a model system and liquid chromatography tandem mass spectrometry (LC-MS/MS).

Results
For method development, spiked drug free rat hair, blood and urine samples were used. The newly developed method was then applied to hair, urine and serum samples from five brown Norway rats after treatment (intraperitoneal) with stanozolol for six consecutive days at 5.0 mg/kg/day. The assay for each matrix was linear within the quantification range with determination coefficient (r2) values above 0.995. The respective assay was capable of detecting 0.125 pg/mg stanozolol and 0.25 pg/mg 3′-hydroxystanozolol with 50 mg hair; 0.063 ng/mL stanozolol and 0.125 ng/mL 3′-hydroxystanozolol with 100 μL of urine or serum. The accuracy, precision and extraction recoveries of the assays were satisfactory for the detection of both compounds in all three matrices. The average concentrations of stanozolol and 3′-hydroxystanozolol, were as follows: hair = 70.18 ± 22.32 pg/mg and 13.01 ± 3.43 pg/mg; urine = 4.34 ± 6.54 ng/mL and 9.39 ± 7.42 ng/mL; serum = 7.75 ± 3.58 ng/mL and 7.16 ± 1.97 ng/mL, respectively.

Conclusions
The developed methods are sensitive, specific and reproducible for the determination of stanozolol and 3′-hydroxystanozolol in rat hair, urine and serum. These methods can be used for in vivo studies further investigating stanozolol metabolism, but also could be extended for doping testing. Owing to the complementary nature of these tests, with urine and serum giving information on recent drug use and hair providing retrospective information on habitual use, it is suggested that blood or urine tests could accompany hair analysis and thus avoid false doping results.
The association between depression, socio-economic factors and dietary intake in mothers having primary school children living in Rey, South of Tehran, Iran
Authors: Payab Moloud , Motlagh Ahmad-reza Dorosty , Eshraghian Mohammadreza , Rostami Reza , Siassi Fereydoun , Abbasi Behnood , Ahmadi Mehrnaz , Karimi Tina , Mahjouri Mohammad Yoosef , Seifirad Soroush 
Published: December 2012

Abstract
Background
According to the WHO report released in 2000, about 121 million people worldwide suffer from depression. The present study aimed to explore factors influencing depression in mothers from Rey, South of Tehran, Iran; who had elementary school children.

Methods
The cross-sectional survey was conducted in spring 2010. Four hundred thirty mothers, who had elementary school children, were selected through a two stage cluster sampling. Beck Depression Inventory (BDI) was used to assess depression in the mothers and a 24-hour food recall was used to collect information regarding their dietary intake. General information regarding economic condition and socio-economic status were also gathered using a questionnaire. The data was analyzed using chi-square, one-way analysis of variance and simple regression tests.

Results
In our study, 51.4% of the mothers suffered from depression. There was an inverse correlation between the educational level of the mothers and the heads of household, their occupational status, their marital status, their socio-economic condition and depression. Conversely, any increase in the family size worsened the depression. The daily intake of different macronutrients, except for fat, was lower in individuals of depressed group.

Conclusion
The present study emphasized the fact that more attention should be paid to the educational level and economic condition of the family in order to reduce maternal depression. Family size also plays an important role in this regard.
Ghrelin and adipokines as circulating markers of disease activity in patients with Takayasu arteritis
Authors: Yilmaz Hatice , Gerdan Vedat , Kozaci Didem , Solmaz Dilek , Akar Servet , Can Gercek , Gulcu Aytac , Goktay Yigit , Sari Ismail , Birlik Merih , Akkoc Nurullah , Onen Fatos 
Published: December 2012

Abstract
Introduction
The current markers of disease activity in Takayasu arteritis (TA) are insufficient for proper assessment. We investigated circulating levels of unacylated and acylated ghrelin, leptin and adiponectin and their relationships with disease activity in patients with TA.

Methods
This study included 31 patients with TA and 32 sex-, age- and body mass index-matched healthy controls. Disease activity was assessed in TA patients using various tools, including Kerr's criteria, disease extent index-Takayasu, physician's global assessment, radiological parameters, and laboratory markers. Plasma unacylated and acylated ghrelin, and serum leptin and adiponectin levels were measured using an enzyme-linked immunosorbent assay.

Results
Unacylated and acylated ghrelin levels were found to be significantly lower in TA patients than that in healthy controls. Patients with active disease had lower unacylated ghrelin levels than those with inactive disease and had lower acylated ghrelin levels than healthy controls. Ghrelin levels were negatively correlated with various parameters of disease activity. The leptin/ghrelin ratio was significantly higher in TA patients than controls. It was positively correlated with disease activity. There was a positive correlation between unacylated and acylated ghrelin and a negative correlation between leptin and ghrelin. There was no statistical difference in adiponectin levels between TA patients and controls. The radiological activity markers were positively correlated with other parameters of disease activity.

Conclusions
This study suggests that plasma unacylated and acylated ghrelin levels may be useful in monitoring disease activity and planning treatment strategies for patients with TA. The serum leptin level and leptin/ghrelin ratio may also be used to help assess the disease activity.
Microevolutionary analysis of Clostridium difficile genomes to investigate transmission
Authors: Didelot Xavier , Eyre David W , Cule Madeleine , Ip Camilla LC , Ansari M Azim , Griffiths David , Vaughan Alison , O'Connor Lily , Golubchik Tanya , Batty Elizabeth M , Piazza Paolo , Wilson Daniel J , Bowden Rory , Donnelly Peter J , Dingle Kate E , Wilcox Mark , Walker A Sarah , Crook Derrick W , A Peto Tim E , Harding Rosalind M 
Published: December 2012

Abstract
Background
The control of Clostridium difficile infection is a major international healthcare priority, hindered by a limited understanding of transmission epidemiology for these bacteria. However, transmission studies of bacterial pathogens are rapidly being transformed by the advent of next generation sequencing.

Results
Here we sequence whole C. difficile genomes from 486 cases arising over four years in Oxfordshire. We show that we can estimate the times back to common ancestors of bacterial lineages with sufficient resolution to distinguish whether direct transmission is plausible or not. Time depths were inferred using a within-host evolutionary rate that we estimated at 1.4 mutations per genome per year based on serially isolated genomes. The subset of plausible transmissions was found to be highly associated with pairs of patients sharing time and space in hospital. Conversely, the large majority of pairs of genomes matched by conventional typing and isolated from patients within a month of each other were too distantly related to be direct transmissions.

Conclusions
Our results confirm that nosocomial transmission between symptomatic C. difficile cases contributes far less to current rates of infection than has been widely assumed, which clarifies the importance of future research into other transmission routes, such as from asymptomatic carriers. With the costs of DNA sequencing rapidly falling and its use becoming more and more widespread, genomics will revolutionize our understanding of the transmission of bacterial pathogens.
Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing
Authors: Cardoso-Moreira Margarida , Arguello J Roman , Clark Andrew G 
Published: December 2012

Abstract
Background
The detailed study of breakpoints associated with copy number variants (CNVs) can elucidate the mutational mechanisms that generate them and the comparison of breakpoints across species can highlight differences in genomic architecture that may lead to lineage-specific differences in patterns of CNVs. Here, we provide a detailed analysis of Drosophila CNV breakpoints and contrast it with similar analyses recently carried out for the human genome.

Results
By applying split-read methods to a total of 10x coverage of 454 shotgun sequence across nine lines of D. melanogaster and by re-examining a previously published dataset of CNVs detected using tiling arrays, we identified the precise breakpoints of more than 600 insertions, deletions, and duplications. Contrasting these CNVs with those found in humans showed that in both taxa CNV breakpoints fall into three classes: blunt breakpoints; simple breakpoints associated with microhomology; and breakpoints with additional nucleotides inserted/deleted and no microhomology. In both taxa CNV breakpoints are enriched with non-B DNA sequence structures, which may impair DNA replication and/or repair. However, in contrast to human genomes, non-allelic homologous-recombination (NAHR) plays a negligible role in CNV formation in Drosophila. In flies, non-homologous repair mechanisms are responsible for simple, recurrent, and complex CNVs, including insertions of de novo sequence as large as 60 bp.

Conclusions
Humans and Drosophila differ considerably in the importance of homology-based mechanisms for the formation of CNVs, likely as a consequence of the differences in the abundance and distribution of both segmental duplications and transposable elements between the two genomes.
Ray Meta: scalable de novo metagenome assembly and profiling
Authors: Boisvert Sébastien , Raymond Frédéric , Godzaridis Élénie , Laviolette François , Corbeil Jacques 
Published: December 2012

AbstractaVoluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net.
Improvement in Thermal Stability of Anion-exchange Membranes for Fuel Cell Applications by Controlling Water State
Authors: Jung Hyangmi , Ohashi Hidenori , Tamaki Takanori , Yamaguchi Takeo 
Published: December 2012

Abstract
In this study, hydroxide ion mobility is reduced by controlling water movement in the membrane to improve its stability. The water movement was decreased by structuring the water with pore-filling membranes synthesized by confining an anion-exchange polymer in nanopores of a porous substrate. Compared with bare films of the same polymer, the pore-filling membranes showed higher stability subsequent to immersion in water at 100 °C.
Near-infrared-absorbing π-Extended Squarylium-based Dyes with Dicyanovinylene Substitution for Dye-sensitized Solar Cell Applications
Authors: Nakao Hidekazu , Maeda Takeshi , Nakazumi Hiroyuki 
Published: December 2012

Abstract
Novel π-extended squarylium dyes with dicyanovinylene substitution were synthesized through the Stille-type Pd-catalyzed cross-coupling reaction of a precursory iodinated squarylium dye with tributylstannyl squarate. Dye-sensitized solar cells (DSSCs) based on the squarylium dyes displayed remarkable performances in a wide wavelength range from the visible to the near-infrared region around 800 nm. The power conversion efficiencies of the DSSCs based on In-CN-In-S-OH and In-CN-In-S-In-COOH reached 3.5% and 2.1%, respectively.