bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing of bovine herpesvirus 4 v.test strain reveals important genome features
Authors: Palmeira Leonor , Machiels Bénédicte , Lété Céline , Vanderplasschen Alain , Gillet Laurent 
Published: August 2011

Abstract

Background
Bovine herpesvirus 4 (BoHV-4) is a useful model for the human pathogenic gammaherpesviruses Epstein-Barr virus and Kaposi's Sarcoma-associated Herpesvirus. Although genome manipulations of this virus have been greatly facilitated by the cloning of the BoHV-4 V.test strain as a Bacterial Artificial Chromosome (BAC), the lack of a complete genome sequence for this strain limits its experimental use.

Methods
In this study, we have determined the complete sequence of BoHV-4 V.test strain by a pyrosequencing approach.

Results
The long unique coding region (LUR) consists of 108,241 bp encoding at least 79 open reading frames and is flanked by several polyrepetitive DNA units (prDNA). As previously suggested, we showed that the prDNA unit located at the left prDNA-LUR junction (prDNA-G) differs from the other prDNA units (prDNA-inner). Namely, the prDNA-G unit lacks the conserved pac-2 cleavage and packaging signal in its right terminal region. Based on the mechanisms of cleavage and packaging of herpesvirus genomes, this feature implies that only genomes bearing left and right end prDNA units are encapsulated into virions.

Conclusions
In this study, we have determined the complete genome sequence of the BAC-cloned BoHV-4 V.test strain and identified genome organization features that could be important in other herpesviruses.
Using scenario tree modelling for targeted herd sampling to substantiate freedom from disease
Authors: Blickenstorfer Sarah , Schwermer Heinzpeter , Engels Monika , Reist Martin , Doherr Marcus G , Hadorn Daniela C 
Published: August 2011

AbstractBackgroundIn order to optimise the cost-effectiveness of active surveillance to substantiate freedom from disease, a new approach using targeted sampling of farms was developed and applied on the example of infectious bovine rhinotracheitis (IBR) and enzootic bovine leucosis (EBL) in Switzerland. Relevant risk factors (RF) for the introduction of IBR and EBL into Swiss cattle farms were identified and their relative risks defined based on literature review and expert opinions. A quantitative model based on the scenario tree method was subsequently used to calculate the required sample size of a targeted sampling approach (TS) for a given sensitivity. We compared the sample size with that of a stratified random sample (sRS) with regard to efficiency.ResultsThe required sample sizes to substantiate disease freedom were 1,241 farms for IBR and 1,750 farms for EBL to detect 0.2% herd prevalence with 99% sensitivity. Using conventional sRS, the required sample sizes were 2,259 farms for IBR and 2,243 for EBL. Considering the additional administrative expenses required for the planning of TS, the risk-based approach was still more cost-effective than a sRS (40% reduction on the full survey costs for IBR and 8% for EBL) due to the considerable reduction in sample size.ConclusionsAs the model depends on RF selected through literature review and was parameterised with values estimated by experts, it is subject to some degree of uncertainty. Nevertheless, this approach provides the veterinary authorities with a promising tool for future cost-effective sampling designs.
Optimality and evolution of transcriptionally regulated gene expression
Authors: Poelwijk Frank J , Heyning Philip D , de Vos Marjon GJ , Kiviet Daniel J , Tans Sander J 
Published: August 2011

Abstract

Background
How transcriptionally regulated gene expression evolves under natural selection is an open question. The cost and benefit of gene expression are the driving factors. While the former can be determined by gratuitous induction, the latter is difficult to measure directly.

Results
We addressed this problem by decoupling the regulatory and metabolic function of the Escherichia coli lac system, using an inducer that cannot be metabolized and a carbon source that does not induce. Growth rate measurements directly identified the induced expression level that maximizes the metabolism benefits minus the protein production costs, without relying on models. Using these results, we established a controlled mismatch between sensing and metabolism, resulting in sub-optimal transcriptional regulation with the potential to improve by evolution. Next, we tested the evolutionary response by serial transfer. Constant environments showed cells evolving to the predicted expression optimum. Phenotypes with decreased expression emerged several hundred generations later than phenotypes with increased expression, indicating a higher genetic accessibility of the latter. Environments alternating between low and high expression demands resulted in overall rather than differential changes in expression, which is explained by the concave shape of the cross-environmental tradeoff curve that limits the selective advantage of altering the regulatory response.

Conclusions
This work indicates that the decoupling of regulatory and metabolic functions allows one to directly measure the costs and benefits that underlie the natural selection of gene regulation. Regulated gene expression is shown to evolve within several hundreds of generations to optima that are predicted by these costs and benefits. The results provide a step towards a quantitative understanding of the adaptive origins of regulatory systems.
Randomized, Double-Blind, Controlled Trial of Early Endoscopic Ultrasound–Guided Celiac Plexus Neurolysis to Prevent Pain Progression in Patients With Newly Diagnosed, Painful, Inoperable Pancreatic Cancer
Authors: Wyse Jonathan M. , Carone Marco , Paquin Sarto C. , Usatii Mariana , Sahai Anand V. 
Published: August 2011

Purpose Celiac plexus neurolysis (CPN) is currently used as salvage therapy for morphine-resistant pancreatic cancer pain. Endoscopic ultrasound–guided CPN (EUS-CPN) can be performed early, at the time of EUS. We hypothesized that early EUS-CPN would reduce pain and morphine consumption, increase quality of life (QOL), and prolong survival. Patients and Methods Patients were eligible if referred for EUS for suspected pancreatic cancer with related pain. If EUS and EUS-guided fine-needle aspiration cytology confirmed inoperable adenocarcinoma, patients were randomly assigned to early EUS-CPN or conventional pain management. Pain scores (7-point Likert scale), morphine equivalent consumption, and QOL scores (Digestive Disease Questionnaire-15) were assessed at 1 and 3 months. Results Five hundred eighty eligible patients were seen between April 2006 and December 2008. Ninety-six patients were randomly assigned (48 patients per study arm). Pain relief was greater in the EUS-CPN group at 1 month and significantly greater at 3 months (difference in mean percent change in pain score = −28.9 [95% CI, −67.0 to 2.8], P = .09, and −60.7 [95% CI, −86.6 to −25.5], P = .01, respectively). Morphine consumption was similar in both groups at 1 month (difference in mean change in morphine consumption = −1.0 [95% CI, −47.7 to 49.2], P = .99), but tended toward lower consumption at 3 months in the neurolysis group (difference in mean change in morphine consumption = −49.5 [95% CI, −127.5 to 7.0], P = .10). There was no effect on QOL or survival. Conclusion Early EUS-CPN reduces pain and may moderate morphine consumption in patients with painful, inoperable pancreatic adenocarcinoma. EUS-CPN can be considered in all such patients at the time of diagnostic and staging EUS.
Adjunctive Oral Methylprednisolone in Pediatric Acute Pyelonephritis Alleviates Renal Scarring
Authors: Huang Ya-Yun , Chen Mei-Ju , Chiu Nan-Tsing , Chou Hsin-Hsu , Lin Kuang-Yen , Chiou Yuan-Yow 
Published: August 2011

OBJECTIVE:To determine if glucocorticoids can prevent renal scar formation after acute pyelonephritis in pediatric patients.METHODS:Patients younger than 16 years diagnosed with their first episode of acute pyelonephritis with a high risk of renal scar formation (ie, inflammatory volume ≥ 4.6 mL on technetium-99m–labeled dimercaptosuccinic acid scan [DMSA] or abnormal renal ultrasonography results) were randomly assigned to receive either antibiotics plus methylprednisolone sodium phosphate (1.6 mg/kg per day for 3 days [MPD group]) or antibiotics plus placebo (placebo group) every 6 hours for 3 days. Patients were reassessed by using DMSA 6 months after treatment. The primary outcome was the development of renal scars.RESULTS:A total of 84 patients were enrolled: 19 in the MPD group and 65 in the placebo group. Patient characteristics were similar between the 2 groups, including the acute inflammatory parameters and the initial DMSA result. Renal scarring was found in 33.3% of children treated with MPD and in 60.0% of those who received placebo (P &lt; .05). The median cortical defect volumes on follow-up DMSA were 0.0 mL (range: 0–4.5 mL) and 1.5 mL (range: 0–14.8 mL) for the MPD and placebo groups, respectively (P &lt; .01). Patients in the MPD group experienced faster defervescence after treatment than the placebo group.CONCLUSIONS:Adjunctive oral MPD therapy reduced the occurrence and/or severity of renal scarring after acute pyelonephritis in these hospitalized children who had a high risk of renal scar formation.
Idiopathic Inflammatory Myopathy Associated with Malignancy: A Retrospective Cohort of 151 Korean Patients with Dermatomyositis and Polymyositis
Authors: SO MIN WOOK , KOO BON SAN , KIM YONG-GIL , LEE CHANG-KEUN , YOO BIN 
Published: August 2011

Objective.To define the standardized incidence ratio (SIR) of malignancy and factors associated with malignancies in Korean patients with dermatomyositis (DM) and polymyositis (PM).Methods.The demographic, clinical, and laboratory features of 151 patients diagnosed with DM/PM were compared in patients with and without malignancies.Results.Malignancies were found in 23 of 98 patients with DM (23.5%) and in 2 of 53 with PM (3.8%). Lung cancer (8 patients) was the most common malignancy. Compared with the period-specific, sex-matched, and age-matched Korean population, the SIR for malignancy in patients with DM was 14.2 (95% CI 9.0–21.3). Univariate analysis showed that factors associated with malignancy included older age (p < 0.001), DM (p = 0.002), dysphagia (p < 0.001), the absence of interstitial lung disease (ILD; p = 0.001), and lower elevations in aspartate aminotransferase (p = 0.005) and lactate dehydrogenase concentrations (p < 0.001). Multivariate analysis showed that factors independently associated with malignancy included older age (per 10 years, OR 2.3, 95% CI 1.6–3.5, p < 0.001), DM (OR 5.9, 95% CI 1.3–26.2, p = 0.020), dysphagia (OR 2.6, 95% CI 1.2–6.6, p = 0.042), and the absence of ILD (OR 0.1, 95% CI 0.01–0.9, p = 0.040).Conclusion.DM was associated with a greater risk of concomitant malignancies, especially lung cancer, than PM. Independent factors associated with malignancies in patients with DM/PM were older age, the presence of dysphagia, and the absence of ILD.
Zonal cooperative inversion of partially co‐located data sets constrained by structural a priori information
Authors: Paasche Hendrik , Tronicke Jens , Dietrich Peter 
Published: August 2011

ABSTRACTIn many near‐surface geophysical studies it is now common practice to collect co‐located disparate geophysical data sets to explore subsurface structures. Reconstruction of physical parameter distributions underlying the available geophysical data sets usually requires the use of tomographic reconstruction techniques. To improve the quality of the obtained models, the information content of all data sets should be considered during the model generation process, e.g., by employing joint or cooperative inversion approaches. Here, we extend the zonal cooperative inversion methodology based on fuzzy c‐means cluster analysis and conventional single‐input data set inversion algorithms for the cooperative inversion of data sets with partially co‐located model areas. This is done by considering recent developments in fuzzy c‐means cluster analysis. Additionally, we show how supplementary a priori information can be incorporated in an automated fashion into the zonal cooperative inversion approach to further constrain the inversion. The only requirement is that this a priori information can be expressed numerically; e.g., by physical parameters or indicator variables. We demonstrate the applicability of the modified zonal cooperative inversion approach using synthetic and field data examples. In these examples, we cooperatively invert S‐ and P‐wave traveltime data sets with partially co‐located model areas using water saturation information expressed by indicator variables as additional a priori information. The approach results in a zoned multi‐parameter model, which is consistent with all available information given to the zonal cooperative inversion and outlines the major subsurface units. In our field example, we further compare the obtained zonal model to sparsely available borehole and direct‐push logs. This comparison provides further confidence in our zonal cooperative inversion model because the borehole and direct‐push logs indicate a similar zonation.
Management of early nasal polyposis using a steroid‐impregnated nasal dressing
Authors: More Yogesh , Willen Seth , Catalano Peter 
Published: August 2011

AbstractBackground:Oral corticosteroids are the mainstay of medical management of sinonasal polyposis. However, systemic steroid‐related side effects can be significant in both the short‐term and long‐term. Topical targeted steroids in optimal concentrations to the affected mucosa present an attractive alternative. The objective of this study was to compare the efficacy of steroid impregnated absorbable nasal dressing with oral steroids in the management of early nasal polyposis after endoscopic sinus surgery.Methods:A total of 21 symptomatic patients with nasal polyposis presenting with endoscopic findings of early polyposis received triamcinolone‐impregnated (20 mg/mL) nasal dressing (Nasopore; Stryker Canada). A control group of 20 similar patients were treated with a short course of oral steroids. Evaluation was based on Sinonasal Assessment Questionnaire (SNAQ‐11) and Perioperative Sinus Endoscopy (POSE) score at baseline, 4‐week, and 8‐week follow‐up intervals.Results:At baseline, 4 weeks, and 8 weeks mean SNAQ scores were 18.42, 8.76, and 9.42 in the study group and 19.35, 7.15, and 7.60 in the control group, respectively. Mean POSE scores were 12.14, 5.04, and 6.04 in the study group and 13.52, 5.01, and 5.52 in the control group, respectively. No significant difference was found between the groups at 4 and 8 weeks in either SNAQ (p = 0.129, p = 0.235) or POSE (p = 0.803, p = 0.795) scores.Conclusion:Triamcinolone‐impregnated absorbable nasal dressing is comparable to oral steroids in the management of early nasal polyposis after sinus surgery. © 2011 ARS‐AAOA, LLC.
A novel electro‐organic synthesis of aniline‐based copolymers at platinum electrodes
Authors: Saraswat Apoorv , Kant Sharma Laxmi , Srivastava Manish K. , Siddiqui I. R. , Singh R. K. P. 
Published: August 2011

AbstractA novel, efficient, and ecocompatible electro copolymerization of anilines at platinum electrode using acetonitrile as non‐aqueous solvent and lithiumperchlorate as supporting electrolyte was carried and described here. The progress and mechanistic study of copolymerization was done using cyclic voltammetry. The reaction proceeded smoothly and quantitatively at ambient temperature. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
The Five Whys Method: A Tool for Developing Problem Definitions in Collaboration with Children
Authors: Kohfeldt Danielle , Langhout Regina Day 
Published: August 2011

ABSTRACTParticipatory action research with young people (yPAR) involves youth and adults in a collaborative process of research, reflection, analysis and action. An important part of the research cycle is the identification of a problem definition. Yet, there is relatively little research addressing the process of how young people develop a problem definition on which to focus their analysis and intervention and what methods might exist to facilitate this process. This article draws upon a yPAR project with fifth‐grade working‐class young people, primarily young people of colour, to demonstrate how the Five Whys method for reflecting on lived experiences facilitated the development of problem definitions in line with second‐order change. The Five Whys method, when used within a participatory framework, offers both a context and a structure for young people to critically examine social problems they identify and to seek out root causes. The article highlights changes in the participant's formulation of problems in the context of using the Five Whys method, from a primarily individual level of analysis to a more structural level of analysis. It also outlines the subsequent changes in proposed actions to address the identified problems. Copyright © 2011 John Wiley & Sons, Ltd.
Syntheses and Antitumor Evaluation of C(6)‐Isobutyl‐ and C(6)‐Isobutenyl‐Substituted Pyrimidines, and Dihydropyrrolo[1,2‐c]pyrimidine‐1,3‐diones
Authors: Krištafor Svjetlana , Kraljević Tatjana Gazivoda , Ametamey Simon M. , Cetina Mario , Ratkaj Ivana , Haček Romana Tandara , Pavelić Sandra Kraljević , Raić‐Malić Silvana 
Published: August 2011

AbstractA growing body of evidence supports that pyrimidine derivatives, in which the sugar residues have been replaced by acyclic side chains, might be developed as promising anticancer agents that interfere with tumor cell proliferation, survival, and metastatic formation. In this work, we prepared novel pyrimidines bearing i‐Bu (i.e., 3, 4, and 7–9) and isobutenyl (i.e., 5 and 10) side chains at C(6) and examined their in vitro effects on tumor cell lines. The dihydropyrrolo[1,2‐c]pyrimidine‐1,3‐diones 6 and 11 were obtained as products of intramolecular cyclization, which occurred during the removal of Bn in 5 or MeO protecting groups in 10. Fluorination of 3 with diethylaminosulfur trifluoride (DAST) and then dehydrohalogenation of the resulting fluorinated derivative 4 afforded 6‐isobut‐2′‐enyl pyrimidine derivative 5 with a C(2′)C(3′) bond. For the preparation of 6‐isobut‐1′‐en‐1‐yl pyrimidine 10, a synthetic strategy involving acetylation of the 1,3‐diols was applied. Antitumor evaluation of compounds 3–11 showed that 2,4‐dimethoxypyrimidine containing 6‐[(1,3‐dibenzyloxy)‐2‐hydroxy]methyl side chain, 3, exerted a strong antiproliferative effect on the studied tumor cell lines. Additionally, it was shown that the mechanism of antiproliferative effect of 3 in HeLa cells include early G2/M arrest and apoptosis, as well as a p53‐independent S‐phase arrest upon prolonged treatment.
Construction and Activity of a Synthetic Basement Membrane with Active Laminin Peptides and Polysaccharides
Authors: Yamada Yuji , Hozumi Kentaro , Nomizu Motoyoshi 
Published: August 2011

AbstractCell‐adhesive peptides derived from extracellular matrix (ECM) proteins are potential candidates for incorporating cell‐binding activities into materials for tissue engineering. We have identified a number of cell adhesive peptides from laminins, which are major components of basement membrane ECM. Our goal is the development of synthetic basement membranes using the peptides on scaffolds. We review peptide–polysaccharide complexes, which were prepared by conjugation of the peptides to chitosan and alginate, and the biological activities of the resulting matrices. The peptide–polysaccharide matrices can also be used as a biomaterial for cell transplantation. These studies suggest that the peptide–polysaccharide complexes have the potential to mimic the multifunctional basement membrane and may be useful for tissue engineering.
Compressed error and erasure correcting codes via rank‐metric codes in random network coding
Authors: Chen Siguang , Wu Meng , Lu Weifeng 
Published: August 2011

SUMMARYThe error control of random network coding has recently received a lot of attention because its solution can increase robustness and reliability of data transmission. To achieve this, additional overhead is needed for error correction. In this paper, we design a compressed error and erasure correcting scheme to decrease the additional overhead of error correction. This scheme reduces the computation overhead dramatically by employing an efficient algorithm to detect and delete linearly dependent received packets in the destination node. It also simplifies the hardware operations when the scheme reduces the received matrix Y to form Ek(Y ) instead of E(Y ) in the decoding process. If at most r original packets get combined in k packets of one batch, the payload of one packet can increase from M − k to M − O(rlog qk) for the application of compressed code, where M is the packet length. In particular, the decoding complexity of compressed code is O(rm) operations in an extension field , which does not enhance the overall decoding complexity of the system. Finally, we also compare our scheme's performance with existing works. The numerical results and analyses illustrate the security and performance of our scheme. Copyright © 2011 John Wiley & Sons, Ltd.
Eremophilane‐Type Sesquiterpenoids from the Fermentation Broth of Plant Endophytic Fungus Pestalotiopsis photiniae Isolated from the Chinese Podocarpaceae Plant Podocarpus macrophyllus
Authors: Yang Xiao‐Long , Zhang Su , Zhu Hua‐Jie , Luo Du‐Qiang , Gao Xue‐Yan 
Published: August 2011

AbstractTwo new sesquiterpenoid esters, pestalotiopins B and C (1 and 2, resp.) related to the eremophilane class, together with one known compound, berkleasmin C (3), were isolated from the fermentation broth of the plant endophytic fungus Pestalotiopsis photiniae. Their structures and relative configurations were elucidated by extensive spectroscopic analysis including 1D‐ and 2D‐NMR (HSQC, HMBC, and NOESY), and MS experiments. Compound 1 has an interesting lactam structure, and this type of sesquiterpenoid with a lactam structure is reported for the first time.
Tuning of the pro‐oxidant and antioxidant activity of trolox through the controlled release from biodegradable poly(trolox ester) polymers
Authors: Wattamwar Paritosh P. , Hardas Sarita S. , Butterfield D. Allan , Anderson Kimberly W. , Dziubla Thomas D. 
Published: August 2011

AbstractIn a variety of biomedical applications (e.g., tissue engineering, drug delivery, etc.), the role of a bioactive material is to serve as a platform by which one can modulate the cellular response into a desired role. Of the methods by which one may achieve this control (e.g., shape, structure, binding, growth factor release), the control of the cellular redox state has been under evaluated. Ideally, the ability to tune the redox state of a cell provides an additional level of control over a variety of cellular responses including, cell differentiation, proliferation, and apoptosis. Yet, in order to achieve such control, it is important to know both the overall oxidative status of the cell and what molecular targets are being oxidized. In this work, poly (trolox ester) nanoparticles were evaluated for their ability to either inhibit or induce cellular oxidative stress in a dose‐dependent fashion. This polymer delivery form possessed a unique ability to suppress protein oxidation, a feature not seen in the free drug form, emphasizing the advantage of the delivery/dosage formulation has upon regulating cellular response. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2011.