bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling
Authors: Borgos Sven EF , Bordel Sergio , Sletta Håvard , Ertesvåg Helga , Jakobsen Øyvind , Bruheim Per , Ellingsen Trond E , Nielsen Jens , Valla Svein 
Published: March 2013

Abstract

Background
Alginate is an industrially important polysaccharide, currently produced commercially by harvesting of marine brown sea-weeds. The polymer is also synthesized as an exo-polysaccharide by bacteria belonging to the genera Pseudomonas and Azotobacter, and these organisms may represent an alternative alginate source in the future. The current work describes an attempt to rationally develop a biological system tuned for very high levels of alginate production, based on a fundamental understanding of the system through metabolic modeling supported by transcriptomics studies and carefully controlled fermentations.

Results
Alginate biosynthesis in Pseudomonas fluorescens was studied in a genomics perspective, using an alginate over-producing strain carrying a mutation in the anti-sigma factor gene mucA. Cells were cultivated in chemostats under nitrogen limitation on fructose or glycerol as carbon sources, and cell mass, growth rate, sugar uptake, alginate and CO2 production were monitored. In addition a genome scale metabolic model was constructed and samples were collected for transcriptome analyses. The analyses show that polymer production operates in a close to optimal way with respect to stoichiometric utilization of the carbon source and that the cells increase the uptake of carbon source to compensate for the additional needs following from alginate synthesis. The transcriptome studies show that in the presence of the mucA mutation, the alg operon is upregulated together with genes involved in energy generation, genes on both sides of the succinate node of the TCA cycle and genes encoding ribosomal and other translation-related proteins. Strains expressing a functional MucA protein (no alginate production) synthesize cellular biomass in an inefficient way, apparently due to a cycle that involves oxidation of NADPH without ATP production. The results of this study indicate that the most efficient way of using a mucA mutant as a cell factory for alginate production would be to use non-growing conditions and nitrogen deprivation.

Conclusions
The insights gained in this study should be very useful for a future efficient production of microbial alginates.
Consumer-centric resource accounting in the cloud
Authors: Mihoob Ahmed , Molina-Jimenez Carlos , Shrivastava Santosh 
Published: March 2013

Abstract
“Pay only for what you use” principle underpins the charging policies of widely used cloud services that are on offer. Ideally for these services, consumers should be in a position to verify the charges billed to them. However, unlike traditional utility services such as gas and electricity, no consumer–trusted metering services are available for cloud services, so consumers have no choice but to rely on the usage data made available by the providers. In light of this, the paper proposes the notion of Consumer–centric Resource Accounting Models for cloud resources. An accounting model is strongly consumer–centric if all the data that the model requires for calculating billing charges can be collected independently by the consumer (or a trusted third party, TTP); in effect, this means that a consumer (or a TTP) should be in a position to run their own measurement service. With this view in mind, the accounting models of some widely used cloud services are examined and possible sources of difficulties in data collection are identified, including causes that could lead to discrepancies between the metering data collected by the consumer and the provider. The paper goes on to suggest how cloud service providers can improve their accounting models to make them consumer-centric.
Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
Authors: Brunner Alayne L , Beck Andrew H , Edris Badreddin , Sweeney Robert T , Zhu Shirley X , Li Rui , Montgomery Kelli , Varma Sushama , Gilks Thea , Guo Xiangqian , Foley Joseph W , Witten Daniela M , Giacomini Craig P , Flynn Ryan A , Pollack Jonathan R , Tibshirani Robert , Chang Howard Y , van de Rijn Matt , West Robert B 
Published: March 2013

Abstract
Background
Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type-specific biomarkers. However, despite the potential importance of long non-coding RNAs to the cancer field, no comprehensive survey of long non-coding RNA expression across various cancers has been reported.

Results
We performed a sequencing-based transcriptional survey of both known long non-coding RNAs and novel intergenic transcripts across a panel of 64 archival tumor samples comprising 17 diagnostic subtypes of adenocarcinomas, squamous cell carcinomas and sarcomas. We identified hundreds of transcripts from among the known 1,065 long non-coding RNAs surveyed that showed variability in transcript levels between the tumor types and are therefore potential biomarker candidates. We discovered 1,071 novel intergenic transcribed regions and demonstrate that these show similar patterns of variability between tumor types. We found that many of these differentially expressed cancer transcripts are also expressed in normal tissues. One such novel transcript specifically expressed in breast tissue was further evaluated using RNA in situ hybridization on a panel of breast tumors. It was shown to correlate with low tumor grade and estrogen receptor expression, thereby representing a potentially important new breast cancer biomarker.

Conclusions
This study provides the first large survey of long non-coding RNA expression within a panel of solid cancers and also identifies a number of novel transcribed regions differentially expressed across distinct cancer types that represent candidate biomarkers for future research.
The Critic’s Byzantine Ploy: Voltairean Confusion in Postsecularist Narratives
Authors: Krallis Dimitris 
Published: March 2013

The debate on blasphemy generated by the publication of the Muhammad cartoons and the attendant conversation on the posited injury experienced by the offended religious subject has recently touched the world of Byzantium. The present essay takes on an elegant recent postsecularist engagement with Byzantine iconoclasm and argues that by appropriating elements of Byzantine Aristotelian theology in order to undergird a postsecularist argument, the modern critic dehistoricizes ideas that were firmly rooted in East Roman social, political, and cultural contexts in a manner that ultimately reinforces a reading of Byzantine culture firmly rooted in the most regressive Enlightenment distortions of the Byzantine experience.
Furthermore, a properly historical engagement with Byzantium contributes to a critical approach on assumptions regarding the nature of the “modern” and its effect on religion. Ultimately, a return to the Byzantine contexts that engender iconoclast theology and politics is also a call for a properly historicized study of Muslim injury, a study that leaves aside quasi-transcendental notions of uniquely Muslim personal injury for a return to the tangible world of modern ideas and political contestation.
A magnetic pulse does not affect homing pigeon navigation: a GPS tracking experiment
Authors: Holland Richard , Filannino Caterina , Gagliardo Anna 
Published: March 2013

Summary
The cues by which homing pigeons are able to return to a home loft after displacement to unfamiliar release sites remain debated. A number of experiments in which migratory birds have been treated with a magnetic pulse have produced a disruption in their orientation, which argues that a ferrimagnetic sense is used for navigation in birds. One previous experiment has also indicated an effect of magnetic pulses on homing pigeon navigation, although with inconsistent results. Previous studies have shown that some magnetic-related information is transmitted by the trigeminal nerve to the brain in some bird species including the homing pigeon. The function of this information is still unclear. It has been suggested that this information is important for navigation. Previous studies with trigeminal nerve lesioned pigeons have clearly shown that the lack of trigeminally mediated information, even if magnetic, is not crucial for homing performance in homing pigeons. However, this result does not completely exclude the possibility that other ferrimagnetic receptors in the homing pigeon play role in navigation. Additionally, recent studies on homing pigeons suggested the existence of a ferrimagnetic sense in a novel location presumably located in the inner ear (lagena). In the current study, we tested whether any ferrimagnetic magnetoreceptors, irrespective of their location in the bird's head, are involved in pigeons' homing. To do this, we treated homing pigeons with a strong magnetic pulse before release, tracked birds with GPS-loggers and analyzed whether this treatment affected homing performance. In the single previous magnetic pulse experiment on homing pigeons only initial orientation at a release site was considered and the results were inconsistent.We observed no effect of the magnetic pulse at any of the sites used, either in initial orientation, homing performance, tortuosity or track efficiency, which does not support a role for the ferrimagnetic sense in homing pigeon navigation, at least not in this geographic area, where magnetic field variations are in the region of 200 nT intensity and 0.8° inclination.
Internet-delivered eye movement desensitization and reprocessing (iEMDR): an open trial
Authors: Spence Jay , Titov Nickolai , Johnston Luke , Dear Blake F , Wootton Bethany , Terides Matthew , Zou Judy 
Published: March 2013

Recent research indicates internet-delivered cognitive behavioural therapy (iCBT) can reduce symptoms of post traumatic stress disorder (PTSD). This study examined the efficacy of an internet-delivered treatment protocol that combined iCBT and internet-delivered eye movement desensitization and reprocessing (iEMDR), in an uncontrolled trial. Eleven of the 15 participants completed post-treatment questionnaires. Large effect sizes were found from pre-treatment to 3-month follow-up (d = 1.03 – 1.61) on clinician-assessed and self-reported measures of PTSD, anxiety and distress, with moderate effect sizes (d = 0.59 – 0.70) found on measures of depression and disability. At post-treatment, 55% of the participants no longer met criteria for PTSD and this was sustained at follow-up. Symptom worsening occurred in 3 of 15 (20%) of the sample from pre- to post-treatment; however, these participants reported overall symptom improvement by follow-up. Future research directions for iEMDR are discussed.
The Effect of Asperity Inclination and Orientation on the Shear Behavior of Rock Joints
Authors: Khosravi Ali , Sadaghiani Mohammad H. , Khosravi Mohammad , Meehan Christopher L. 
Published: March 2013

Abstract
This study investigates the effect of asperity inclination angle and asperity orientation on the shear behavior of rock joints under constant normal loading conditions. The effects of these two rock joint characteristics were investigated by creating artificial rock joints having a regular pattern of triangular asperities that were oriented at different angles in the plane of shear. Large-scale direct shear tests were conducted over a range of normal stresses, on 0.30 × 0.30 m gypsum blocks containing well-mated joints with different asperity orientation and inclination angle characteristics. Experimental results illustrate the importance of considering both the asperity orientation with respect to the loading direction and the applied normal stress when predicting the shear behavior of rock joints. In general, higher normal stresses increased the stiffness of the rock joints in shearing, while a reduction in the shear strength of the rock joints was observed when increasing the asperity orientation angle. The dilation curves indicated the occurrence of both dilation and lateral displacement during shearing. Two different techniques are used to quantify the condition of the joint surfaces: the first approach utilizes the concept of fractal dimension, and the second utilizes the concept of potential contact area. These approaches can be applied in a useful fashion within the framework of existing shear failure criterion for oriented rock joints.
One Stage Conversion of an Infected Fused Knee to Total Knee Replacement - A Surgical Challenge
Authors: Ravikumar Mukartihal , Kendoff Daniel , Citak Mustafa , Luck Stefan , Gehrke Thorsten , Zahar Akos 
Published: March 2013

Background and Purpose:
Two-stage revision arthroplasty is a common technique for the treatment of infected total knee replacement. Few reports have addressed the conversion of a fused knee into a total knee replacement. However, there is no case reported of converting an infected fused knee into a hinge knee using a one-stage procedure.

Methods:
We report on a 51-year old male patient with an infected fused knee after multiple surgeries.

Results and Interpretation:
A one-stage conversion of septic fused knee into total knee arthroplasty by a rotational hinge prosthesis was performed. The case highlights that with profound preoperative assessment, meticulous surgical technique, combined antibiotic treatment and the right implant, one-stage revision in a surgical challenge may have a role as a treatment option with good functional outcome.
Blue toe syndrome as the initial manifestation of ANCA-associated vasculitis
Authors: Marinchev Liubomir , Hristova Maria , Baleva Marta , Kolarov Zlatimir 
Published: March 2013

Abstract
The blue (or purple) toe syndrome describes the development of a blue or violaceous discoloration in one or more toes in the absence of obvious trauma, serious cold-induced injury or disorders producing generalized cyanosis. The presence of blue toe syndrome requires the clinician to search for primary systemic vasculitides, as well as for malignancy, underlying infection, thrombosis, cardiovascular pathology and other diseases. An accurate diagnosis is critical because many of the causes threaten life or limb, but the patient’s medical history, accompanying non-dermatologic findings on physical examination and the use of discriminatory laboratory tests are usually more important than the nature of the cutaneous abnormalities. We describe the case of a 53-year-old Caucasian male patient presenting with blue toe syndrome as the initial manifestation of ANCA-associated vasculitis.
Predicting Macroeconomic Indicators in the Czech Republic Using Econometric Models and Exponential Smoothing Techniques
Authors: Simionescu Bratu Mihaela 
Published: March 2013

Abstract
Econometric modeling and exponential smoothing techniques are two quantitative forecasting methods with good results in practice, but the objective of the research was to find out which of the two techniques are better for short run predictions. Therefore, for inflation, unemployment and interest rate in the Czech Republic various accuracy indicators were calculated for the predictions based on these methods. Short run forecasts on a horizon of 3 months were made for December 2011-February 2012, the econometric models being updated. For the Czech Republic, the exponential smoothing techniques provided more accurate forecasts than the econometric models (VAR(2) models, ARMA procedure and models with lagged variables). One explication for the better performance of smoothing techniques would be that in the chosen countries the short run predictions were more influenced by the recent evolution of the indicators.
Toxicity of a plant based mosquito repellent/killer
Authors: Singh Bhoopendra , Singh Prakash Raj , Mohanty Manoj Kumar 
Published: March 2013

ABSTRACT
The mission to make humans less attractive to mosquitoes has fuelled decades of scientific research on mosquito behaviour and control. The search for the perfect topical insect repellent/killer continues. This analysis was conducted to review and explore the scientific information on toxicity produced by the ingredients/contents of a herbal product. In this process of systemic review the following methodology was applied. By doing a MEDLINE search with key words of selected plants, plant based insect repellents/ killers pertinent articles published in journals and authentic books were reviewed. The World Wide Web and the Extension Toxicity Network database (IPCS-ITOX) were also searched for toxicology data and other pertinent information. Repellents do not all share a single mode of action and surprisingly little is known about how repellents act on their target insects. Moreover, different mosquito species may react differently to the same repellent. After analysis of available data and information on the ingredient, of the product in relation to medicinal uses, acute and chronic toxicity of the selected medicinal plants, it can be concluded that the ingredients included in the herbal product can be used as active agents against mosquitoes. If the product which contains the powder of the above said plants is applied with care and safety, it is suitable fo use as a mosquito repellent/killer.
Antioxidant and hepatoprotective effect of Garcinia indica fruit rind in ethanolinduced hepatic damage in rodents
Authors: Panda Vandana , Ashar Hardik , Srinath Sudhamani 
Published: March 2013

ABSTRACT
The protective effects of aqueous extracts of the fruit rind of Garcinia indica (GIE) on ethanol-induced hepatotoxicity and the probable mechanisms involved in this protection were investigated in rats. Liver damage was induced in rats by administering ethanol (5 g/kg, 20% w/v p.o.) once daily for 21 days. GIE at 400 mg/kg and 800 mg/kg and the reference drug silymarin (200 mg/kg) were administered orally for 28 days to ethanol treated rats, this treatment beginning 7 days prior to the commencement of ethanol administration. Levels of marker enzymes (aspartate aminotransferase (AST), alanine aminotransferase (ALT) and alkaline phosphatase (ALP)), triglyceride (sTG), albumin (Alb) and total protein (TP) were evaluated in serum. Antioxidant parameters (reduced glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and glutathione reductase (GR)), hepatic triglycerides (hTG) and the lipid peroxidation marker malondialdehyde (MDA) were determined in liver. GIE and silymarin elicited significant hepatoprotective activity by attenuating the ethanol-elevated levels of AST, ALT, ALP, sTG, hTG and MDA and restored the ethanol-depleted levels of GSH, SOD, CAT, GPx, GR, Alb and TP. GIE 800 mg/kg demonstrated greater hepatoprotection than GIE 400 mg/kg. The present findings indicate that hepatoprotective effects of GIE in ethanol-induced oxidative damage may be due to an augmentation of the endogenous antioxidants and inhibition of lipid peroxidation in liver.
Distribution of the ymoA and ystA genes and enterotoxins Yst production by Yersinia enterocolitica strains isolated from humans and pigs
Authors: Bancerz-Kisiel A. , Szczerba-Turek A. , Platt-Samoraj A. , Szweda W. 
Published: March 2013

AbstractYersinia (Y.) enterocoliticais the third etiological agent of human diarrhea in terms of the number of confirmed clinical cases.One of the important virulence markers is theystgene which encodes the production of enterotoxins Yst (Yersiniastable toxins). However, not all strains withystgenes produce enterotoxins, what seems to be caused by theymoAgene encoding the production of the YmoA protein inhibiting the expression of various genes. The purpose of our study was to evaluate the distribution of theymoAandystAgenes and Yst production byY. enterocoliticaisolated from humans and pigs. All the studied strains obtained from pigs had theystAgene which indicates that they belong to the group of strains commonly regarded as pathogenic, but the ability to produce YstA was detected in only 14 out of 96 examined strains. The fragments ofystAgene were also detected in allY.enterocoliticastrains isolated from human cases of diarrhea. Amplification of a fragment of theymoAgene was detected in all the studied strains, both from humans and pigs, based on the presence of a 330 bp band. Thus no correlation was identified between the occurrence of theymoAandystAgenes and the production of a specific type of enterotoxin.
Use of rapid human respiratory syncytial virus strip tests for detection of bovine respiratory syncytial virus in experimentally vaccinated calves
Authors: Socha W. , Rola J. 
Published: March 2013

AbstractThree different rapid strip tests: TRU RSV, BinaxNOW RSV and RSV Respi-strip were compared with RT-PCR and ELISA BRSV Ag for the ability to detect bovine respiratory syncytial virus (BRSV) in nasal swabs collected from calves experimentally vaccinated with live vaccine Rispoval RS-PI3. The reference strains of BRSV (375 and A51908) were detected by ELISA BRSV Ag whereas the strains of human respiratory syncytial virus (HRSV) and bovine parainfluenza virus type 3 (BPIV-3) were not. All rapid strip tests as well as RT-PCR reacted positively both to HRSV and BRSV reference strains and negatively to BPIV-3. The detection limit for RT-PCR was 39.1 TCID50 (strain 375 of BRSV), whereas for each of the rapid tests it was approximately 156 TCID50 and 312 TCID50 for antigen ELISA. Diagnostic sensitivity in detecting BRSV in nasal swabs for TRU RSV and RSV Respi-strip tests was 33% and 50% for BinaxNOW RSV. Diagnostic specificity of TRU RSV was 100%, whereas for both BinaxNOW and Respi-strip it was 87%. We concluded that TRU RSV could be used as a supportive rapid test for BRSV screening in nasal swabs taken directly on a farm. However, due to the small group of animals used in the experiment, the results should be regarded as preliminary and the study should be repeated on a larger number of animals.
The low doses effect of experimental zearalenone (ZEN) intoxication on the presence of Ca2+ in selected ovarian cells from pre-pubertal bitches
Authors: Gajęcka M. , Przybylska-Gornowicz B. 
Published: March 2013

Abstract
The objective of this study was to determine the effect of 42-day ZEN intoxication on the presence of Ca2+ in selected ovarian cells from beagle bitches, using the potassium pyroantimonate (PPA) method. Samples were collected from 30 clinically healthy, pre-pubertal, genetically homogeneous animals. The bitches were divided into three groups of 10 animals each: experimental group I - 50 μg ZEN/kg BW (100% NOAEL) administered once daily per os; experimental group II - 75 μg ZEN/kg BW (150% NOAEL) administered once daily per os; control group - placebo containing no ZEN administered per os. An electron microscopic analysis revealed that cells died due to apoptosis, depending on the ZEN dose and the type of cells exposed to intoxication. Lower ZEN doses led to apoptosis-like changes in the cells. Cell death was a consequence of excess Ca2+ accumulation in the mitochondria, followed by cell dysfunction and a decrease in or the absence of mitochondrial metabolic activity in oocytes, follicle cells and interstitial cells in experimental bitches.