bluuebunny/crossref_metadata_2025 huggingface dataset:
Transnationalism and media groups in independent television production in the UK and Spain
Authors: Fernández-Quijada David
Published: April 2013

In recent years, the growth and consolidation of the independent television production industry has stirred up a great deal of media group interest in entering this market. Through an original sample of prime-time television programmes in the UK and Spain and in-depth interviews with practitioners, this article offers an empirically grounded analysis of the presence of media groups and the strategies developed in this industry, with a particular focus on synergies at the transnational level. The results show that production markets are dominated by national media groups, that there are few pan-European synergies, and that regulation plays a key role in defining this market.
Application of evidential networks in quantitative analysis of railway accidents
Authors: Aguirre Felipe , Sallak Mohamed , Schön Walter , Belmonte Fabien
Published: April 2013

Currently, a high percentage of accidents in railway systems are accounted to human factors. As a consequence, safety engineers try to take into account this factor in risk assessment. However, human reliability data are very difficult to quantify, thus, qualitative methods are often used in railway system’s risk assessments. Modeling of human errors through probabilistic approaches has shown some limitation concerning the quantification of qualitative aspects of human factors. The proposed article presents an original method to account for the human factor by using evidential networks and fault tree analysis.
Dart-throwing motion in patients with scapholunate instability: a dynamic four-dimensional computed tomography study
Authors: Garcia-Elias M. , Alomar Serrallach X. , Monill Serra J.
Published: April 2013

When the normal wrist rotates along the ‘dart-throwing’ plane, the proximal row remains still, with most motion occurring at the midcarpal joint. Whether this behaviour is maintained when the scapholunate ligaments are torn is not known. If this is the case, patients having a scapholunate ligament repair could benefit from early dart-throwing exercises without the risk of pulling the sutures apart. Using dynamic computer tomography, we analysed the carpal behaviour of six normal wrists and six wrists with scapholunate instability during dart-throwing motion. In the normal wrists, the scaphoid and lunate did not flex or extend, but translated along the frontal plane an average 5.9 and 5.6 mm, respectively. When the scapholunate ligaments were torn, the scaphoid shifted towards the radial styloid considerably more than the lunate (12.8 mm versus 4.8 mm; p = 0.005), inducing a scapholunate gap. Based on these findings, we cannot recommend dart-throwing exercises after scapholunate ligament repair, unless the joint is stabilized with wires or screws.
Dynamic Duos
Authors: Reagan-Porras Laura L.
Published: April 2013

How can mentors maximize their positive relationships with “at-risk” youth? Youth mentoring program evaluations at the Boys & Girls Club of McAllen Metro (BGCMM) yield a framework that illuminates the content of relating inside mentoring relationships. The mentoring model identified is established primarily by qualitative methods with a phenomenological approach and supported by young adult alumni findings from a Harris Poll Interactive Survey. The case review of mentoring program evaluations is significant in that it fills a gap in the mentoring literature regarding the content of mentor-mentee relating. The summary of evaluation findings is also important because the inquiry occurs with 98 percent Latino youth population between the ages of 8 and 17. (The regional success of youth mentoring programs is meaningful to the nation in large part because South Texas is the one location where Latinos comprise a demographic majority). Given the academic achievement gap of Latino students, nationally with Latino high school drop-out rates approaching 50 percent and the overrepresentation of minority populations incarcerated, this simple replicable strategy for the successful mentoring program design and evaluation is timely. The interactionist sociological analysis examines what happens inside the mentor-mentee relationship as it is perceived to be impactful by the youth themselves with their definitions. The mentoring model informed by the case review is a practical tool in planning, implementing, and facilitating effective dyads between mentor and mentee that can inform mentor training and program evaluations.
A very unusual metastatic pattern exhibited by a mixed non-seminomatous germ cell tumour: a case report and review of literature
Authors: Osman Elsawi , Gomha Mohamed , Aldayel Adel
Published: April 2013

It is a known fact that the retroperitoneum is the commonest metastatic site for testicular germ cell tumours. Contrary to this we are hereby reporting a case of an advanced testicular non-seminomatous germ cell tumour (NSGCT) presenting with a huge anterior abdominal wall metastatic mass and no evidence of retroperitoneal lymphadenopathy. A 36 year-old gentleman who underwent bilateral orchidopexies as a child, presented with a huge anterior abdominal wall mass engulfing the external genitalia. Incisional biopsy showed a yolk sac tumour. He was treated primarily with immediate chemotherapy with a dramatically good response. This was followed by right radical orchidectomy. Unfortunately, a few months later he developed recurrences into the anterior abdominal wall as well as brain metastasis. We conclude with two main messages. Firstly, previous inguino-scrotal procedures can significantly alter the lymphatic drainage from the testicles. Secondly, primary chemotherapy before orchidectomy can have a very favourable outcome in selected patients.
Discovering motifs that induce sequencing errors
Authors: Allhoff Manuel , Schönhuth Alexander , Martin Marcel , Costa Ivan G , Rahmann Sven , Marschall Tobias
Published: April 2013

Background

Elevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS). Beyond routinely handled generic sources of errors, certain base calling errors relate to specific sequence patterns. Statistically principled ways to associate sequence patterns with base calling errors have not been previously described. Extant approaches either incur decisive losses in power, due to relating errors with individual genomic positions rather than motifs, or do not properly distinguish between motif-induced and sequence-unspecific sources of errors.

Results

Here, for the first time, we describe a statistically rigorous framework for the discovery of motifs that induce sequencing errors. We apply our method to several datasets from Illumina GA IIx, HiSeq 2000, and MiSeq sequencers. We confirm previously known error-causing sequence contexts and report new more specific ones.

Conclusions

Checking for error-inducing motifs should be included into SNP calling pipelines to avoid false positives. To facilitate filtering of sets of putative SNPs, we provide tracks of error-prone genomic positions (in BED format).

Availability

http://discovering-cse.googlecode.com
An optimized algorithm for detecting and annotating regional differential methylation
Authors: Li Sheng , Garrett-Bakelman Francine E , Akalin Altuna , Zumbo Paul , Levine Ross , To Bik L , Lewis Ian D , Brown Anna L , D'Andrea Richard J , Melnick Ari , Mason Christopher E
Published: April 2013

Background

DNA methylation profiling reveals important differentially methylated regions (DMRs) of the genome that are altered during development or that are perturbed by disease. To date, few programs exist for regional analysis of enriched or whole-genome bisulfate conversion sequencing data, even though such data are increasingly common. Here, we describe an open-source, optimized method for determining empirically based DMRs (eDMR) from high-throughput sequence data that is applicable to enriched whole-genome methylation profiling datasets, as well as other globally enriched epigenetic modification data.

Results

Here we show that our bimodal distribution model and weighted cost function for optimized regional methylation analysis provides accurate boundaries of regions harboring significant epigenetic modifications. Our algorithm takes the spatial distribution of CpGs into account for the enrichment assay, allowing for optimization of the definition of empirical regions for differential methylation. Combined with the dependent adjustment for regional p-value combination and DMR annotation, we provide a method that may be applied to a variety of datasets for rapid DMR analysis. Our method classifies both the directionality of DMRs and their genome-wide distribution, and we have observed that shows clinical relevance through correct stratification of two Acute Myeloid Leukemia (AML) tumor sub-types.

Conclusions

Our weighted optimization algorithm eDMR for calling DMRs extends an established DMR R pipeline (methylKit) and provides a needed resource in epigenomics. Our method enables an accurate and scalable way of finding DMRs in high-throughput methylation sequencing experiments. eDMR is available for download at http://code.google.com/p/edmr/.
Joint genotype inference with germline and somatic mutations
Authors: Bareke Eric , Saillour Virginie , Spinella Jean-François , Vidal Ramon , Healy Jasmine , Sinnett Daniel , Csűrös Miklós
Published: April 2013

The joint sequencing of related genomes has become an important means to discover rare variants. Normal-tumor genome pairs are routinely sequenced together to find somatic mutations and their associations with different cancers. Parental and sibling genomes revealde novogermline mutations and inheritance patterns related to Mendelian diseases.

Acute lymphoblastic leukemia (ALL) is the most common paediatric cancer and the leading cause of cancer-related death among children. With the aim of uncovering the full spectrum of germline and somatic genetic alterations in childhood ALL genomes, we conducted whole-exome re-sequencing on a unique cohort of over 120 exomes of childhood ALL quartets, each comprising a patient's tumor and matched-normal material, and DNA from both parents. We developed a general probabilistic model for such quartet sequencing reads mapped to the reference human genome. The model is used to infer joint genotypes at homologous loci across a normal-tumor genome pair and two parental genomes.

We describe the algorithms and data structures for genotype inference, model parameter training. We implemented the methods in an open-source software package (QUADGT) that uses the standard file formats of the 1000 Genomes Project. Our method's utility is illustrated on quartets from the ALL cohort.
Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing
Authors: Ueno Saneyoshi , Klopp Christophe , Leplé Jean Charles , Derory Jérémy , Noirot Céline , Léger Valérie , Prince Elodie , Kremer Antoine , Plomion Christophe , Le Provost Grégoire
Published: April 2013

Background

In temperate regions, the time lag between vegetative bud burst and bud set determines the duration of the growing season of trees (i.e. the duration of wood biomass production). Dormancy, the period during which the plant is not growing, allows trees to avoid cold injury resulting from exposure to low temperatures. An understanding of the molecular machinery controlling the shift between these two phenological states is of key importance in the context of climatic change. The objective of this study was to identify genes upregulated during endo- and ecodormancy, the two main stages of bud dormancy. Sessile oak is a widely distributed European white oak species. A forcing test on young trees was first carried out to identify the period most likely to correspond to these two stages. Total RNA was then extracted from apical buds displaying endo- and ecodormancy. This RNA was used for the generation of cDNA libraries, and in-depth transcriptome characterization was performed with 454 FLX pyrosequencing technology.

Results

Pyrosequencing produced a total of 495,915 reads. The data were cleaned, duplicated reads removed, and sequences were mapped onto the oak UniGene data. Digital gene expression analysis was performed, with bothRstatistics and the R-Bioconductor packages (edgeR and DESeq), on 6,471 contigs with read numbers ≥ 5 within any contigs. The number of sequences displaying significant differences in expression level (read abundance) between endo- and ecodormancy conditions ranged from 75 to 161, depending on the algorithm used. 13 genes displaying significant differences between conditions were selected for further analysis, and 11 of these genes, including those for glutathione-S-transferase (GST) and dehydrin xero2 (XERO2) were validated by quantitative PCR.

Conclusions

The identification and functional annotation of differentially expressed genes involved in the “response to abscisic acid”, “response to cold stress” and “response to oxidative stress” categories constitutes a major step towards characterization of the molecular network underlying vegetative bud dormancy, an important life history trait of long-lived organisms.
High throughput transcriptome analysis of lipid metabolism in Syrian hamster liver in absence of an annotated genome
Authors: Schmucki Roland , Berrera Marco , Küng Erich , Lee Serene , Thasler Wolfgang E , Grüner Sabine , Ebeling Martin , Certa Ulrich
Published: April 2013

Background

Whole transcriptome analyses are an essential tool for understanding disease mechanisms. Approaches based on next-generation sequencing provide fast and affordable data but rely on the availability of annotated genomes. However, there are many areas in biomedical research that require non-standard animal models for which genome information is not available. This includes the Syrian hamsterMesocricetus auratusas an important model for dyslipidaemia because it mirrors many aspects of human disease and pharmacological responses. We show that complementary use of two independent next generation sequencing technologies combined with mapping to multiple genome databases allows unambiguous transcript annotation and quantitative transcript imaging. We refer to this approach as “triple match sequencing” (TMS).

Results

Contigs assembled from a normalized Roche 454 hamster liver library comprising 1.2 million long reads were used to identify 10’800 unique transcripts based on homology to RefSeq database entries from human, mouse, and rat. For mRNA quantification we mapped 82 million SAGE tags (SOLiD) from the same RNA source to the annotated hamster liver transcriptome contigs. We compared the liver transcriptome of hamster with equivalent data from human, rat, minipig, and cynomolgus monkeys to highlight differential gene expression with focus on lipid metabolism. We identify a cluster of five genes functionally related to HDL metabolism that is expressed in human, cynomolgus, minipig, and hamster but lacking in rat as a non-responder species for lipid lowering drugs.

Conclusions

The TMS approach is suited for fast and inexpensive transcript profiling in cells or tissues of species where a fully annotated genome is not available. The continuously growing number of well annotated reference genomes will further empower reliable transcript identification and thereby raise the utility of the method for any species of interest.
Cell-type specificity of lung cancer associated with low-dose soil heavy metal contamination in Taiwan: An ecological study
Authors: Huang Hsien-Hung , Huang Jing-Yang , Lung Chia-Chi , Wu Chih-Lung , Ho Chien-Chang , Sun Yi-Hua , Ko Pei-Chieh , Su Shih-Yung , Chen Shih-Chang , Liaw Yung-Po
Published: April 2013

Background

Numerous studies have examined the association between heavy metal contamination (including arsenic [As], cadmium [Cd], chromium [Cr], copper [Cu], mercury [Hg], nickel [Ni], lead [Pb], and zinc [Zn]) and lung cancer. However, data from previous studies on pathological cell types are limited, particularly regarding exposure to low-dose soil heavy metal contamination. The purpose of this study was to explore the association between soil heavy metal contamination and lung cancer incidence by specific cell type in Taiwan.

Methods

We conducted an ecological study and calculated the annual averages of eight soil heavy metals (i.e., As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn) by using data from the Taiwan Environmental Protection Administration from1982 to 1986. The age-standardized incidence rates of lung cancer according to two major pathological types (adenocarcinoma [AC] and squamous cell carcinoma [SCC]) were obtained from the National Cancer Registry Program conducted in Taiwan from 2001 to 2005. A geographical information system was used to plot the maps of soil heavy metal concentration and lung cancer incidence rates. Poisson regression models were used to obtain the adjusted relative ratios (RR) and 95% confidence intervals (CI) for the lung cancer incidence associated with soil heavy metals.

Results

For males, the trend test for lung SCC incidence caused by exposure to Cr, Cu, Hg, Ni, and Zn showed a statistically significant dose–response relationship. However, for lung AC, only Cu and Ni had a significant dose–response relationship. As for females, those achieving a statistically significant dose–response relationship for the trend test were Cr (P = 0.02), Ni (P = 0.02), and Zn (P= 0.02) for lung SCC, and Cu (P < 0.01) and Zn (P = 0.02) for lung AC.

Conclusion

The current study suggests that a dose–response relationship exists between low-dose soil heavy metal concentration and lung cancer occurrence by specific cell-type; however, the relevant mechanism should be explored further.
Highly potent silver-organoalkoxysilane antimicrobial porous nanomembrane
Authors: Umar Sirajo , Liu Yuanfeng , Wu Yiguang , Li Guangtao , Ding Jiabo , Xiong Runsong , Chen Jinchun
Published: April 2013

We used a simple electrospinning technique to fabricate a highly potent silver-organoalkoxysilane antimicrobial composite from AgNO3-polyvinylpyrrolidone (PVP)/3-aminopropyltrimethoxysilane (APTMS)/tetraethoxysilane (TEOS) solution. Spectroscopic and microscopic analyses of the composite showed that the fibers contain an organoalkoxysilane ‘skeleton,’ 0.18 molecules/nm2 surface amino groups, and highly dispersed and uniformly distributed silver nanoparticles (5 nm in size). Incorporation of organoalkoxysilanes is highly beneficial to the antimicrobial mat as (1) amino groups of APTMS are adhesive and biocidal to microorganisms, (2) polycondensation of APTMS and TEOS increases the membrane’s surface area by forming silicon bonds that stabilize fibers and form a composite mat with membranous structure and high porosity, and (3) the organoalkoxysilanes are also instrumental to the synthesis of the very small-sized and highly dispersed silver metal particles in the fiber mat. Antimicrobial property of the composite was evaluated by disk diffusion, minimum inhibition concentration (MIC), kinetic, and extended use assays on bacteria (Escherichia coli, Bacillus anthracis, Staphylococcus aureus, and Brucella suis), a fungus (Aspergillus niger), and the Newcastle disease virus. The membrane shows quick and sustained broad-spectrum antimicrobial activity. Only 0.3 mg of fibers is required to achieve MIC against all the test organisms. Bacteria are inhibited within 30 min of contact, and the fibers can be used repeatedly. The composite is silver efficient and environment friendly, and its membranous structure is suitable for many practical applications as in air filters, antimicrobial linen, coatings, bioadhesives, and biofilms.
On fractional differential inclusions with anti-periodic type integral boundary conditions
Authors: Ahmad Bashir , Ntouyas Sotiris K , Alsaedi Ahmed
Published: April 2013

This paper investigates the existence of solutions for fractional differential inclusions of order

q
∈
(
2
,
3
]

with anti-periodic type integral boundary conditions by means of some standard fixed point theorems for inclusions. Our results include the cases when the multivalued map involved in the problem has convex as well as non-convex values. The paper concludes with an illustrative example.

MSC:34A60, 34A08.
Tolerability and outcomes of radiotherapy or chemoradiotherapy for rectal cancer in elderly patients aged 70 years and older
Authors: Cai Xin , Wu Hongbin , Peng Junjie , Zhu Ji , Cai Sanjun , Cai Gang , Zhang Zhen
Published: April 2013

Purpose

To assess the safety and outcomes of radiotherapy (RT) or chemoradiotherapy (CRT) in elderly patients (≥70) with rectal cancer.

Methods

Elderly patients aged 70 and older with rectal cancer, who were treated with RT or CRT at a single institution, were retrospectively analyzed. Performance status (KPS and ECOG score) and comorbidity (Charlson comorbidity index) were calculated, and their correlation with treatment toxicity and overall survival were studied. Risk factors for overall survival were investigated using univariate and multivariate survival analysis.

Results

A total of 126 patients with locally advanced disease, local recurrence or synchronous metastasis were included, with a 3-year OS rate of 48.1%. Scheduled dosage of radiation was delivered to 69% of patients. Grade 3 toxicities occurred more often in patients treated with CRT versus RT. The occurrence of grade 3 toxicities was not related to KPS score, ECOG score, number of comorbidities, and Charlson score. Multivariate analysis found that only age and Charlson score were independent prognostic factors for predicting patients’ 3-year OS. The 3-year OS rate was significantly higher in patients with Charlson score <4 vs Charlson score ≥4 (71.1% vs. 26.4%, P=0.0003).

Conclusions

Although toxicities may be significant, elderly patients with rectal cancer of varied stages can be safely treated with RT or CRT with careful monitoring and frequent modification of treatment. Except for patients’ age, Charlson comorbidity index may be helpful in assessing patients’ outcomes in elderly patients with rectal cancer.
Electrochemical DNA biosensor based on the BDD nanograss array electrode
Authors: Jin Huali , Wei Min , Wang Jinshui
Published: April 2013

Background

The development of DNA biosensor has attracted considerable attention due to their potential applications, including gene analysis, clinical diagnostics, forensic study and more medical applications. Using electroactive daunomycin as an indicator, the hybridization detection was measured by differential pulse voltammetry in this study.

Results

Electrochemical DNA biosensor was developed based on the BDD film electrode (fBDD) and BDD nanograss array electrode (nBDD). In comparison with fBDD and AuNPs/CA/fBDD electrode, the lower semicircle diameter of electrochemical impedance spectroscopy obtained on nBDD and AuNPs/CA/nBDD electrode indicated that the presence of nanograss array improved the reactive site, reduced the interfacial resistance, and made the electron transfer easier. Using electroactive daunomycin as an indicator, the hybridization detection was measured by differential pulse voltammetry.

Conclusions

The experimental results demonstrated that the prepared AuNPs/CA/nBDD electrode was suitable for DNA hybridization with favorable performance of faster response, higher sensitivity, lower detection limit and satisfactory selectivity, reproducibility and stability.
The acute and long‐term management of anaphylaxis: protocol for a systematic review
Authors: Dhami Sangeeta , Panesar Sukhmeet S , Rader Tamara , Muraro Antonella , Roberts Graham , Worm Margitta , Sheikh Aziz ,   EAACI Food Allergy and Anaphylaxis Guidelines group
Published: April 2013

Background

The European Academy of Allergy and Clinical Immunology is in the process of developing its Guideline for Food Allergy and Anaphylaxis, and this systematic review is one of seven inter‐linked evidence syntheses that are being undertaken in order to provide a state‐of‐the‐art synopsis of the current evidence base in relation to epidemiology, prevention, diagnosis and clinical management and impact on quality of life, which will be used to inform clinical recommendations.

The aims of this systematic review will be to assess the effectiveness of interventions for the acute management of anaphylaxis, and pharmacological and non‐pharmacological approaches for the long‐term management of anaphylaxis.

Methods

A highly sensitive search strategy has been developed, and validated study design filters will be applied to retrieve all articles pertaining to the management of anaphylaxis from electronic bibliographic databases. We will systematically review the literature on the acute management of anaphylaxis by assessing the effectiveness of epinephrine, H1‐antihistamines (versus placebo), systemic glucocorticosteroids, methylxanthines or any other treatments for the emergency management of people experiencing anaphylaxis. The main interventions that have been studied in the context of long‐term management are anaphylaxis management plans and allergen‐specific immunotherapy.

Discussion

There is at present little in the way of robust evidence to guide decisions on the acute and/or long‐term management of anaphylaxis. Given the risk of death and the considerable morbidity associated with anaphylaxis these evidence gaps need to be filled wherever possible; this systematic review will make a start in this area.
Characterization of x-type high-molecular-weight glutenin promoters (x-HGP) from different genomes in Triticeae
Authors: Jiang Qian-Tao , Zhao Quan-Zhi , Wang Xiu-Ying , Wang Chang-Shui , Zhao Shan , Cao Xue , Lan Xiu-Jin , Lu Zhen-Xiang , Zheng You-Liang , Wei Yu-Ming
Published: April 2013

The sequences of x-type high-molecular-weight glutenin promoter (x-HGP) from 21 diploid Triticeae species were cloned and sequenced. The lengths of x-HGP varied from 897 to 955 bp, and there are 329 variable sites including 105 singleton sites and 224 polymorphic sites. Genetic distances of pairwise X-HGP sequences ranged from 0.30 to 16.40% within 21 species and four outgroup species of Hordeum. All five recognized regulatory elements emerged and showed higher conservation in the x-HGP of 21 Triticeae species. Most variations were distributed in the regions among or between regulatory elements. A 22 bp and 50 bp insertions which were the copy of adjacent region with minor change, were found in the x-HGP of Ae. speltoides and Ps. Huashanica, and could be regarded as genome specific indels. The phylogeny of media-joining network and neighbour-joining tree both supported the topology were composed of three sperate clusters. Especially, the cluster I comprising the x-HGP sequences of Aegilops, Triticum, Henrardia, Agropyron and Taeniatherum was highly supporting by both network and NJ tree. As conferring to higher level and temporal and spatial expression, x-HGP can used as the source of promoter for constructing transgenic plants which allow endosperm-specific expression of exogenous gene on higher level. In addition, the x-HGP has enough conservation and variation; so it should be valuable in phylogenetic analyses of Triticeae family members.
Hepatic excretory function in sepsis: implications from biophotonic analysis of transcellular xenobiotic transport in a rodent model
Authors: Gonnert Falk A , Recknagel Peter , Hilger Ingrid , Claus Ralf A , Bauer Michael , Kortgen Andreas
Published: April 2013

Introduction

Hepatobiliary elimination of endo- and xenobiotics is affected by different variables including hepatic perfusion, hepatocellular energy state and functional integrity of transporter proteins, all of which are altered during sepsis. A particular impairment of hepatocellular transport at the canalicular pole resulting in an accumulation of potentially hepatotoxic compounds would have major implications for critical care pharmacology and diagnostics.

Methods

Hepatic transcellular transport, that is, uptake and hepatobiliary excretion, was studied in a rodent model of severe polymicrobial sepsis by two different biophotonic techniques to obtain insights into the handling of potentially toxic endo- and xenobiotics in sepsis. Direct and indirect in vivo imaging of the liver was performed by intravital multifluorescence microscopy and non-invasive whole-body near-infrared (NIRF) imaging after administration of two different, primarily hepatobiliary excreted xenobiotics, the organic anionic dyes indocyanine green (ICG) and DY635. Subsequent quantitative data analysis enabled assessment of hepatic uptake and fate of these model substrates under conditions of sepsis.

Results

Fifteen hours after sepsis induction, animals displayed clinical and laboratory signs of multiple organ dysfunction, including moderate liver injury, cholestasis and an impairment of sinusoidal perfusion. With respect to hepatocellular transport of both dyes, excretion into bile was significantly delayed for both dyes and resulted in net accumulation of potentially cytotoxic xenobiotics in the liver parenchyma (for example, specific dye fluorescence in liver at 30 minutes in sham versus sepsis: ICG: 75% versus 89%; DY635 20% versus 40% of maximum fluorescence; P < 0.05). Transcutaneous assessment of ICG fluorescence by whole body NIRF imaging revealed a significant increase of ICG fluorescence from the 30th minute on in the bowel region of the abdomen in sham but not in septic animals, confirming a sepsis-associated failure of canalicular excretion.

Conclusions

Hepatocytes accumulate organic anions under conditions of sepsis-associated organ dysfunction. These results have potential implications for monitoring liver function, critical care pharmacology and the understanding of drug-induced liver injury in the critically ill.
Geometrical considerations in the acquisition of borehole interferometric data for imaging near-vertical features: Design of field experiments
Authors: Brand Emma , Hurich Charles , Deemer Sharon
Published: April 2013

Seismic interferometry applied to walkaway vertical seismic profile data has significant potential for imaging the steeply dipping structures often encountered in hard-rock minerals exploration. Using the interferometry process, surface shots can be redatumed to the borehole receivers resulting in virtual shot gathers. The virtual shot gathers can then be processed using a standard common midpoint (CMP) processing flow. Carrying out this procedure for a subvertical borehole results in a geometry that is optimal for imaging structures that are near vertical. Field acquisition parameters play a critical role in recovering reliable virtual source images. We evaluated the major factors that play a role in designing a field acquisition program with the objective of providing guidance to field practitioners. The major issue to be considered is insuring that correlation gathers created in the interferometry process have a stationary phase component that when summed produces events with correct timing and cancellation of nonstationary components. Consistent with previous work, the ray-tracing-based analysis identified the surface source spacing, surface source aperture, and dominant frequency as the most critical parameters. The analysis indicated that because of the high apparent velocities typically encountered in hard rock terrains, a surface source spacing of 20 m and an aperture of 1000 m will result in stationary phase components and avoid spatial alias in the correlation gathers for frequencies as high as 80 Hz. However, closer spacing of the surface sources provided more traces in the correlation gathers resulting in fewer artifacts during summation. These results were further verified by acoustic wave modeling that provided data from more complex targets that were processed through a complete interferometry and CMP flow. The analysis indicated that with care in designing field acquisition parameters, seismic interferometry is realizable within the terrain and access restrictions imposed by many mining camps.
Singular-value decomposition analysis of source illumination in seismic interferometry by multidimensional deconvolution
Authors: Minato Shohei , Matsuoka Toshifumi , Tsuji Takeshi
Published: April 2013

We have developed a method to analytically evaluate the relationship between the source-receiver configuration and the retrieved wavefield in seismic interferometry performed by multidimensional deconvolution (MDD). The MDD method retrieves the wavefield with the desired source-receiver configuration from the observed wavefield without source information. We used a singular-value decomposition (SVD) approach to solve the inverse problem of MDD. By introducing SVD into MDD, we obtained quantities that revealed the characteristics of the MDD inverse problem and interpreted the effect of the initial source-receiver configuration for a survey design. We numerically simulated the wavefield with a 2D model and investigated the rank of the incident field matrix of the MDD inverse problem. With a source array of identical length, a sparse and a dense source distribution resulted in an incident field matrix of the same rank and retrieved the same wavefield. Therefore, the optimum source distribution can be determined by analyzing the rank of the incident field matrix of the inverse problem. In addition, the introduction of scatterers into the model improved the source illumination and effectively increased the rank, enabling MDD to retrieve a better wavefield. We found that the ambiguity of the wavefield inferred from the model resolution matrix was a good measure of the amount of illumination of each receiver by the sources. We used the field data recorded at the two boreholes from the surface sources to support our results of the numerical modeling. We evaluated the rank of incident field matrix with the dense and sparse source distribution. We discovered that these two distributions resulted in an incident field matrix of almost the same rank and retrieved almost the same wavefield as the numerical modeling. This is crucial information for designing seismic experiments using the MDD-based approach.
Regulated recycling of mutant CFTR partially restored by pharmacological treatment
Authors: Holleran John P. , Zeng Jianxin , Frizzell Raymond A. , Watkins Simon C.
Published: April 2013

Efficient trafficking of the cystic fibrosis transmembrane conductance regulator (CFTR) to and from the cell surface is essential for maintaining channel density at the plasma membrane (PM) and ensuring proper physiological activity. The most common mutation, F508del, exhibits reduced surface expression and impaired function despite treatment with currently available pharmacological small molecules, called correctors. To gain more detailed insight into whether CFTR enters compartments that allow corrector stabilization in the cell periphery, we investigated the peripheral trafficking itineraries and kinetics of WT and F508del in living cells using high-speed fluorescence microscopy together with fluorogen activating protein detection. We directly visualized internalization and accumulation of CFTR WT from the PM to a perinuclear compartment which colocalized with the endosomal recycling compartment (ERC) markers, Rab11 and EHD1, reaching steady-state distribution by 25 minutes. Stimulation by protein kinase A (PKA) depleted this intracellular pool and redistributed CFTR channels to the cell surface, elicited by reduced endocytosis and active translocation to the PM. Corrector or temperature rescue of F508del also resulted in targeting to the ERC and exhibited subsequent PKA stimulated trafficking to the PM. Corrector treatment (24 hr) lead to persistent residence of F508del in the ERC, while thermally destabilized F508del was targeted to lysosomal compartments by 3 hours. Acute addition of individual correctors, C4 or C18, acted on peripheral trafficking steps to partially block lysosomal targeting of thermally destabilized F508del. Taken together, corrector treatment redirects F508del trafficking from a degradative pathway to a regulated recycling route, and proteins which mediate this process become potential targets for improving efficacy of current and future correctors.
FE65 regulates and interacts with the Bloom syndrome protein in dynamic nuclear spheres – potential relevance to Alzheimer's disease
Authors: Schrötter Andreas , Mastalski Thomas , Nensa Fabian M. , Neumann Martin , Loosse Christina , Pfeiffer Kathy , Magraoui Fouzi El , Platta Harald W. , Erdmann Ralf , Theiss Carsten , Uszkoreit Julian , Eisenacher Martin , Meyer Helmut E. , Marcus Katrin , Müller Thorsten
Published: April 2013

The intracellular domain of the amyloid precursor protein (AICD) is generated following cleavage of the precursor by the γ-secretase complex and is involved in membrane to nucleus signaling, for which the binding of AICD to the adapter protein FE65 is essential. Here we show that FE65 knockdown causes a down regulation of the protein BLM and the MCM protein family and that elevated nuclear levels of FE65 result in stabilization of the BLM protein in nuclear mobile spheres. These spheres are able to grow and fuse, and potentially correspond to the nuclear domain 10. BLM plays a role in DNA replication and repair mechanisms and FE65 was also shown to play a role in the cell's response to DNA damage. A set of proliferation assays in our work revealed that FE65 knockdown cells exhibit reduced cell replication in HEK293T cells. On the basis of these results, we hypothesize that nuclear FE65 levels (nuclear FE65/BLM containing spheres) may regulate cell cycle re-entry in neurons due to increased interaction of FE65 with BLM and/or an increase in MCM protein levels. Thus, FE65 interactions with BLM and MCM proteins may contribute to the neuronal cell cycle re-entry observed in Alzheimer disease brains.
Pulmonary embolism due to popliteal vein aneurysm: approach and surgical treatment – a case report
Authors: Maggiore C , Rizzo L , Capotondi C , Dito R , Taurino M
Published: April 2013

Pulmonary embolism is the first presentation in 70–80% in patients with aneurysm of popliteal vein. We present a case of young man admitted in our hospital with respiratory distress, tachycardia and D-dimer >3000 mg/dL. The observation of pulmonary embolism required the placement of a caval temporary filter before the surgical treatment. The use of temporary filter is recommended in symptomatic patients for thromboembolic phenomena, and when ultrasound detects the presence of floating thrombus.
Local Investigation of outcomes Based on Ultrasound Examinations for Suspected Inguinal Hernia Performed by Sonographers and Radiologists
Authors: Cummings Janet , Edwards Hazel
Published: April 2013

Inguinal hernia is the most common surgical repair performed in England with more than 73,000 cases in 2007. The majority of inguinal hernias are diagnosed clinically, but ultrasound is fast becoming the imaging modality of choice for diagnosing occult hernia, due to its non-invasive nature and lack of radiation. At the Norfolk and Norwich University Hospitals NHS Foundation Trust, ultrasound of the groin was performed only by radiologists, but recently sonographers have also begun examining patients for inguinal hernia. This study investigates the accuracy of ultrasound diagnosis of hernia and compares the performances of radiologists and sonographers over a nine-month period involving 124 patients. Our results indicate that both professional groups have a high detection rate and that there is no significant difference in accuracy. An incidental finding was that many general practitioner referrals diagnosed with an inguinal hernia did not proceed to surgery. Since many ultrasound departments are experiencing demand versus capacity issues, it may be that further investigation into the value of diagnosis when surgery is unlikely is warranted.
Ultrasound and Colour Doppler of Placental Chorioangioma with Oligohydramnios
Authors: Mandava Anitha , Rajaram Nirmala , Nagasundari K , Kota Kusuma Kumar
Published: April 2013

Chorioangioma is the most common benign tumour of the placenta. Smaller lesions are asymptomatic but larger lesions are associated with adverse prognosis. Antenatal ultrasonography with colour Doppler is the primary modality in diagnosing these lesions and their complications. Chorioangiomas are generally associated with polyhydramnios but can rarely present with oligohydramnios. We report a case of a large chorioangioma, which led to oligohydramnios, compromised fetal blood flow and reduced fetal growth. A live infant weighing 830 g was delivered by Caesarean section at 34 weeks but survived for only two days.
Osmanlı Maârifi’nde Okutulan Mûsikî Kitapları
Authors: Özdent Erhan
Published: April 2013

Osmanlı Maârifi’nde müzik kitaplarının yayınlanması on dokuzuncu asrın Osmanlı Maârifi’nde müzik kitaplarının yayınlanması on dokuzuncu asrın sonlarında başlamıştır. Bunun öncesinde münferit kitaplar yazılmışgeneline yayılamamıştır. Bu döneme kadar müzik eğitiminde olması ders kitaplarının müfredata girmesini geciktirmiştir. Ancak eğitimde zamanın olması ders kitaplarının müfredata girmesini geciktirmiştir. Ancak eğitimde zamanın getirdiği yenilikler ve pedagojik anlayışgöstermiştir. Yayınlanan ilk ders kitapları Batı mûsikîsi temelinin verGenellikle Batı’da basılmış olan eserlerden ilham alınarak ya da birebir aynısınıGenellikle Batı’da basılmış olan eserlerden ilham alınarak ya da birebir aynısınınTürkçe’ye çevrilerek yayınlandığı bu sağlanmasına yönelik atılmış önemli bir adımdır. Derslerde ağırlıklı olarak notasağlanmasına yönelik atılmış önemli bir adımdır. Derslerde ağırlıklı olarak notaeğitiminin verilmesi müzik kitaplarının yazımında Batı müziği temelinin esas eğitiminin verilmesi müzik kitaplarının yazımında Batı müziği temelinin esas alınmasını zorunlu kılmıştır. Bunun yanında Türk mûsikîsini anlatan kitaplar da az alınmasını zorunlu kılmıştır. Bunun yanında Türk mûsikîsini anlatan kitaplar da az değildir. Bu makale Osmanlı Maârifi’nde okutulanedinmektedir
Başbakanlık Osmanlı Arşivi Mâbeyn-i Hümâyûn Evrakları Dosya Tasnifinde Bulunan İki Saz Eseri
Authors: Toker Hikmet , Aydemir Murat
Published: April 2013

Türk mûsikîsi, kuruluşundan bu yana Osmanlı saray hayatı içinde kendine T daima yer bulmuştur. Bu durum sarayda birçok musiki topluluğunun kurulmasını daima yer bulmuştur. Bu durum sarayda birçok musiki topluluğunun kurulmasını sağlamıştır. Görevi saray sakinleri ve sultan için Türk musikisi icrâ etmek olan sağlamıştır. Görevi saray sakinleri ve sultan için Türk musikisi icrâ etmek olan Sazendegân-ı Hâssa bu toplulukların en kurumun üyelerinden Neyzen Salih Dede ve İsmet Ağa’ya ait iki saz eserini kurumun üyelerinden Neyzen Salih Dede ve İsmet Ağa’ya ait iki saz eserini incelemektedir. Bu eserler ¨Başbakanlık Osmanlı Arşivi MâbeynTasnifinde¨ bulunmuştur. Üzerlerindeki notlardan ve içinde bulundutarihinden Sultan II. Abdülhamit’e sunuldukları anlaşılmaktadır. tarihinden Sultan II. Abdülhamit’e sunuldukları anlaşılmaktadır. Hicaz-aşiran makamında bestelenen vkaydedilen bu eserler elle yazılmıştır. Bu eserlerden birinin değişik zamanlarda kaydedilen bu eserler elle yazılmıştır. Bu eserlerden birinin değişik zamanlarda basılan üç değişik notası tespit edilmiş ve elimizde bulunan karşılaştırılarak nüshalar arası farklılıklar tespit edilmiştir. Diğer eserin her hangi karşılaştırılarak nüshalar arası farklılıklar tespit edilmiştir. Diğer eserin her hangi nüshasına rastlanılmamıştır. Bu eser yeniden yazılmış ve orijinal nüshada bulunmayan hâne başlangıçları, usul ve mâkâm isimleri belirtilmiştir
Muğam Tonallıqlarının Transpozisiya Problemləri
Authors: İsmayilov Şamil
Published: April 2013

Makalede muğam tonlarının göçürülmesi meselelerinden bahs olunmaktadır. Müellif orta asır Şark musiki risaleleri ve muasır bedii pratik esasında transpozisyon kaidelerinin müeyyenleşmiş kanuna uygunluklarını tayin etmiştir. Bu kaidelerin icrada ve muğam numunelerinin notaya alınmasında zaruriliği nazara alınmalıdır. Bu makale, musikişinaslara, icracılara ve muğam sanatı eğitimiyle uğraşan hocalara sunulmuştur.
Yeniçeri Müziği ve Batı Müziği Üzerindeki Türk Etkileri
Authors: Schmidt-Jones Catherine
Published: April 2013

Osmanlı İmparatorluğu'nun Batı müziği üzerindeki birincil etkisi -buna birinci Viyana ekolünün bestecileri üzerindeki çok büyük etkisi de dahil olmak üzere- Osmanlı askeri bandoları üzerinden olmuştur. Bu etkinin en uzun süreli olanı Batı Avrupa ve Amerika bando gelenekleri üzerinde olmuştur. Osmanlı İmparatorluğu ile Batı Avrupa arasındaki temel etkileşim askeri rekabettir. Bu nedenle Osmanlı devri Türk Müziğinin Batı Müziği üzerindeki etkisinin (Osmanlı Askeri Bandosu) mehterhane üzerinden olması şaşırtmamalıdır. Bu makale hem bu müzikal etkileri, hem de bu etkileri yaratan veya sınırlayan tarihi, müzikal ve sosyal etkileri araştırmayı amaçlamaktadır. Müziği bu konu için kritik olan Wolfğang Amadeus Mozart kendi müziğinde iki tür Türklük tanımlamıştır. İlk olarak "Türk Müziği" basitçe belirli vurmalı çalgıların kullanıldığı müzik anlamına gelirken, ikinci olarak ise "alaturka" (Türk Biçiminde, Türk Stilinde) melodik, armonik ve ritmik açıdan Türk Müziğini taklit eden müzik anlamında kullanılmıştır [1]. Mehterhanenin Batı Müziği üzerindeki etkileri iki geniş kategoride incelenebileceğinden Türk Müziği ve alaturka arasındaki bu ayrım önemlidir. Alaturkanın etkisi kısa sürmüş ve sınırlı olmuştur. Daha çok Batı müziğinin klasik dönemini etkilemiştir. Türk Müziği ise pek yaygın kabul görmese de özellikle askeri ve bando müziği üzerinde çok derin ve uzun süreli etki yapmıştır.