bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation
Authors: Martin Natalia , Patel Satyakam , Segre Julia A.
Published: December 2004

Mammalian epidermis provides a permeability barrier between an organism and its environment. Under homeostatic conditions, epidermal cells produce structural proteins, which are cross-linked in an orderly fashion to form a cornified envelope (CE). However, under genetic or environmental stress, specific genes are induced to rapidly build a temporary barrier. Small proline-rich (SPRR) proteins are the primary constituents of the CE. Under stress the entire family of 14 Sprr genes is upregulated. The Sprr genes are clustered within the larger epidermal differentiation complex on mouse chromosome 3, human chromosome 1q21. The clustering of the Sprr genes and their upregulation under stress suggest that these genes may be coordinately regulated. To identify enhancer elements that regulate this stress response activation of the Sprr locus, we utilized bioinformatic tools and classical biochemical dissection. Long-range comparative sequence analysis identified conserved noncoding sequences (CNSs). Clusters of epidermal-specific DNaseI-hypersensitive sites (HSs) mapped to specific CNSs. Increased prevalence of these HSs in barrier-deficient epidermis provides in vivo evidence of the regulation of the Sprr locus by these conserved sequences. Individual components of these HSs were cloned, and one was shown to have strong enhancer activity specific to conditions when the Sprr genes are coordinately upregulated.
MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues
Authors: Barad Omer , Meiri Eti , Avniel Amir , Aharonov Ranit , Barzilai Adi , Bentwich Isaac , Einav Uri , Gilad Shlomit , Hurban Patrick , Karov Yael , Lobenhofer Edward K. , Sharon Eilon , Shiboleth Yoel M. , Shtutman Marat , Bentwich Zvi , Einat Paz
Published: December 2004

MicroRNAs (MIRs) are a novel group of conserved short ∼22 nucleotide-long RNAs with important roles in regulating gene expression. We have established a MIR-specific oligonucleotide microarray system that enables efficient analysis of the expression of the human MIRs identified so far. We show that the 60-mer oligonucleotide probes on the microarrays hybridize with labeled cRNA of MIRs, but not with their precursor hairpin RNAs, derived from amplified, size-fractionated, total RNA of human origin. Signal intensity is related to the location of the MIR sequences within the 60-mer probes, with location at the 5′ region giving the highest signals, and at the 3′ end, giving the lowest signals. Accordingly, 60-mer probes harboring one MIR copy at the 5′ end gave signals of similar intensity to probes containing two or three MIR copies. Mismatch analysis shows that mutations within the MIR sequence significantly reduce or eliminate the signal, suggesting that the observed signals faithfully reflect the abundance of matching MIRs in the labeled cRNA. Expression profiling of 150 MIRs in five human tissues and in HeLa cells revealed a good overall concordance with previously published results, but also with some differences. We present novel data on MIR expression in thymus, testes, and placenta, and have identified MIRs highly enriched in these tissues. Taken together, these results highlight the increased sensitivity of the DNA microarray over other methods for the detection and study of MIRs, and the immense potential in applying such microarrays for the study of MIRs in health and disease.
High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12
Authors: Honisch Christiane , Raghunathan Anu , Cantor Charles R. , Palsson Bernhard Ø. , van den Boom Dirk
Published: December 2004

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis of base-specific cleavage products is an efficient, highly accurate tool for the detection of single base sequence variations. We describe the first application of this comparative sequencing strategy for automated high-throughput mutation detection in microbial genomes. The method was applied to identify DNA sequence changes that occurred in Escherichia coli K-12 MG1655 during laboratory adaptive evolution to new optimal growth phenotypes. Experiments were based on a genome-scale in silico model of E. coli metabolism and growth. This model computes several phenotypic functions and predicts optimal growth rates. To identify mutations underlying a 40-d adaptive laboratory evolution on glycerol, we resequenced 4.4% of the E. coli-K12 MG1655 genome in several clones picked at the end of the evolutionary process. The 1.54-Mb screen was completed in 13.5 h. This resequencing study is the largest reported by MALDI-TOF mass spectrometry to date. Ten mutations in 40 clones and three deviations from the reference sequence were detected. Mutations were predominantly found within the glycerol kinase gene. Functional characterization of the most prominent mutation shows its metabolic impact on the process of adaptive evolution. All sequence changes were independently confirmed by genotyping and Sanger-sequencing. We demonstrate that comparative sequencing by base-specific cleavage and MALDI-TOF mass spectrometry is an automated, fast, and highly accurate alternative to capillary sequencing.
The mouse genome: Experimental examination of gene predictions and transcriptional start sites
Authors: Dike Sujit , Balija Vivekanand S. , Nascimento Lidia U. , Xuan Zhenyu , Ou Jacqueline , Zutavern Theresa , Palmer Lance E. , Hannon Greg , Zhang Michael Q. , McCombie W. Richard
Published: December 2004

The completion of the mouse and other mammalian genome sequences will provide necessary, but not sufficient, knowledge for an understanding of much of mouse biology at the molecular level. As a requisite next step in this process, the genes in mouse and their structure must be elucidated. In particular, knowledge of the transcriptional start site of these genes will be necessary for further study of their regulatory regions. To assess the current state of mouse genome annotation to support this activity, we identified several hundred gene predictions in mouse with varying levels of supporting evidence and tested them using RACE–PCR. Modifications were made to the procedure allowing pooling of RNA samples, resulting in a scaleable procedure. The results illustrate potential errors or omissions in the current 5′ end annotations in 58% of the genes detected. In testing experimentally unsupported gene predictions, we were able to identify 58 that are not usually annotated as genes but produced spliced transcripts (∼25% success rate). In addition, in many genes we were able to detect novel exons not predicted by any gene prediction algorithms. In 19.8% of the genes detected in this study, multiple transcript species were observed. These data show an urgent need to provide direct experimental validation of gene annotations. Moreover, these results show that direct validation using RACE–PCR can be an important component of genome-wide validation. This approach can be a useful tool in the ongoing efforts to increase the quality of gene annotations, especially transcriptional start sites, in complex genomes.
Unemployment in Europe: A Comparative Analysis of Regional Disparities in Germany, Italy and the UK
Authors: Taylor Jim , Bradley Steve
Published: December 2004

This paper investigates spatial disparities in unemployment in three Member States of the EU. It attempts to identify the factors responsible for the persistence of regional unemployment disparities in Germany, Italy and the UK during 1984‐94. The empirical results indicate that a substantial proportion of the variation in unemployment rates between NUTS2 level regions can be explained by regional disparities in three key variables: unit labour costs, the industry mix and employment density. The findings are consistent with the view that regional unemployment disparities are explained primarily by regional disparities in economic competitiveness.

ZUSAMMENFASSUNO

Dieser Artikel untersucht die räumlichen Unterschiede in der Höhe der Arbeitslosigkeit in drei Mitgliedsstaaten der EU. Er basiert auf dem Versuch, die Faktoren zu bestimmen, die im Zeitraum zwischen 1984 und 1994 für die Persistenz von regionalen Unterschieden der Höhe der Arbeitslosigkeit in Deutschland, Italien und Grossbritannien verantwortlich waren. Die empirischen Ergeb‐nisse zeigen, dass ein wesentlicher Teil der Unterschiede in der Höhe der Arbeitslosigkeit zwischen NUTS2 Regionen durch eine regional unterschiedliche Ausprägung von drei wichtigen Variablen erklärt werden kann: Lohnstückkosten, Wirtschaftsstruktur und Zahl der Arbeitsplätze pro Quadratkilometer. Die Ergebnisse bestätigen die Ansicht, dass die regional unterschiedlich hohe Arbeitslosigkeit hauptsächlich durch Unterschiede der regionalen Wettbewerbsfähigkeit zu cr‐klüren ist.

Ce document examine les disparités géographiques du chǒmage dans trois États membres de l'Union Européenne. Nous essayerons d'identifier les facteurs responsables de la persistance des disparités en chǒmage régional en Ailemagne, en Italie el au Royaume‐Uni pendant la période 1984‐94. Les résultats empiriques indiquent qu'une proportion importante de la variation du taux de chǒmage entre les régions de la catégorie NUTS2 peut s'expliquer par des disparités régionales en trois variables prépondérantes: le coǔt unitaire d'emploi, la structure industrielle et la densité d'emploi. Les résultats coïncident avec l'avis que les disparités du chǒmage régional s'expliquent surtout par les disparités régionales en compétitivitééconomique.
Life‐Cycle Happiness in a Discounted Utility Model
Authors: Shmanske Stephen
Published: December 2004

A discrete time, discounted utility model with a finite horizon is analyzed. Utility is separable and additive in the natural logarithms of the choice variables, consumption and leisure, and an exogenous ‘memory' series. Happiness is defined as the discounted value of the utility over the remaining lifespan. Simulations of the model show how happiness grows as the high consumption years get closer, peaks, then declines in later life as the remaining lifespan shortens, even though year by year utility may continue to rise. Simulations also show how the peak year for happiness depends on the subjective, personal discount rate, the rate of wage growth, the effect of a liquidity constraint, the effect of memories, and other parameters in the model. The model also illustrates those aspects of the life cycle characterized by the ‘slackers’, the ‘mid‐life crisis’, and the ‘golden years’.

Ein diskretes, abdiskontiertes Nutzenmodell mit einem endlichen Zeithorizont wird analysiert. Nutzen wird als zerlegbar und additiv in den natürlichen Logarithmen der Wahlvanablen Konsum und Freizeit und in den exogenen Zeitreihen für ‘Erinnerungen’ angenommen. Gluck ist definiert als abdiskontierter Wert des Nutzens der verbleibenden Lebenszeit. Simulationen zeigen, wie das Glück bei der Annäherung an die Jahre erhöhten Konsums ansteigt, einen Hohepunkt erreicht, um dann in der verbleibenden Lebenszeit wieder abzunehmen, obwohl der Nutzen Jahr fur Jahr weiterhin zunehmen kann. Die Simulationen zeigen auch, wie der Höhepunkt des Glücks vom persönlichen Diskontsatz, der Zuwachsrate des Einkommens, Liquiditatsbeschrankungen, Erinnerungen und anderen Parametern abhangt. Das Modell veranschaulicht aber auch jene Aspekte der Lebenszeit, die üblicherweise als ‘Slackers’, ‘Mid‐life Crisis' und ‘Goldene Jahre’ bezeichnet werden

Analyse d'un modèle d'utilité d'escompte à temps discret et à horizon limité. L'utilité est séparable et additive dans les logarithmes naturels des variables de choix, la consomption et les loisirs, et une série exogène de ‘mémoire’. On définit le bonheur comme la valeur d'escompte de l'utilité pendant la durée de la vie qui reste. Des simulations du modèle montrent comment le bonheur s'augmente au fur et à mesure que les année de grande consomption s'approchent, atteint son comble, puis baisse dans la dernière partie de la vie pendant que la durée de la vie qui reste se réduit, quoique, année par année, l'utilité puisse continuer à s'augmenter. Les simulations montrent aussi comment l'année du point culminant de bonheur dépend du taux d'escompte subjectif et personnel, du taux d'augmentation de salaire, de l'effet d'une contrainte de liquidité, de l'effet des souvenirs, et d'autres paramètres du modèle. Le modèle illustre aussi les aspects du cycle de vie caractérisés par les fainéants, la crise de ‘mid‐life’ et les années ‘dorées’.
Review article: diagnosis and investigation of gastro‐oesophageal reflux disease in Japanese patients
Authors: Kusano M.
Published: December 2004

Gastro‐oesophageal reflux disease (GERD) encompasses a wide range of disorders defined by either reflux‐related symptoms or by complications of gastro‐oesophageal reflux. The most characteristic GERD symptoms are heartburn and acid regurgitation. Patients with these symptoms are in most cases easily identifiable and diagnosis is made on the basis of symptoms alone. For patients with a decreased frequency of heartburn, diagnosis is more difficult, and endoscopy is the single best test for diagnosis of GERD. A major difference between the West and Asia is the frequency of endoscopic investigation. In Japan, the earlier high prevalence of stomach cancers resulted in the increased use of endoscopy as an investigational tool for dyspeptic symptoms and today endoscopy continues to be widely available as a diagnostic tool. However, the overall sensitivity of endoscopy for the diagnosis of GERD is less than 50% since not all patients will have oesophagitis at the time of endoscopy. Ambulatory pH monitoring is therefore a frequently used diagnostic tool as it allows correlation between reflux events and symptoms, and is especially useful in patients with atypical or extraoesophageal symptoms. Oesophageal manometry is also an excellent test to evaluate oesophageal function and to measure sphincter pressure and while it may not provide an unequivocal diagnosis of GERD it is a useful tool with which to evaluate oesophageal function.
Review article: treatment for gastro‐oesophageal reflux disease – lifestyle advice and medication
Authors: Kinoshita Y.
Published: December 2004

Management of gastro‐oesophageal reflux disease (GERD) is aimed at reducing oesophageal acid exposure to achieve symptom relief. Therapy has traditionally included advice to the patient on diet and lifestyle management. Recent evidence suggests, however, that some specific dietary modifications may be applicable to the Japanese patient. For example, ingestion of Japanese sweet cakes or rice cakes should be avoided by the Japanese patient with GERD as these foods may provoke heartburn. Pharmacological therapy is, however, usually also required for effective symptom relief. While antacids and histamine H2‐receptor antagonists have a role in treating mild GERD, effective relief of many cases of oesophagitis is usually only achieved by using proton‐pump inhibitors such as lansoprazole, omeprazole and rabeprazole. In the Japanese population, variation in the genetic polymorphism of CYP2C19 (a cytochrome P450 isoenzyme) leads to considerable inter‐individual unpredictability in the activity of lansoprazole and omeprazole due to inter‐individual differences in the extent to which these agents are metabolized. Consequently, rabeprazole, which does not undergo hepatic biotransformation by CYP2C19, offers significant advantages over the other PPIs as a result of its more predictable activity. This, coupled with its more rapid onset of action, leads to a more efficient and less variable acid‐suppressing effect.
Review article: the patient with gastro‐oesophageal reflux disease – lifestyle advice and medication
Authors: Holtmann G. , Adam B. , Liebregts T.
Published: December 2004

Gastro‐oesophageal reflux disease (GERD) is a highly prevalent disorder in all Western countries. Interestingly, prevalence rates appear to be increasing in these countries, with a remarkable increase of GERD‐related lethal and nonlethal complications. However, these complications are rare on a global scale. This review aims to summarize the current concepts of genetic, lifestyle and environmental factors that need to be considered whilst caring for patients with these disorders. GERD is defined by the augmented exposure of oesophageal mucosa to acidic content, and is associated with specific symptoms or mucosal lesions. A number of factors may contribute to the manifestation of GERD. Although recent studies emphasize the role of genetic factors, there are many other risk factors that play a pivotal role in the development of GERD and GERD complications. Some nutritional factors are believed to aggravate acidic reflux either by delaying gastric emptying or diminishing the pressure of the lower oesophageal sphincters. Patients are often advised to sleep with their heads elevated, but this advice is not easy to follow and has not been proven effective with regard to long‐term outcome. Other lifestyle modifications include changes to the patient's diet, which are important but not frequently sufficient. Thus, medication is usually necessary for symptom control. Proton pump inhibitors are now mainstream treatment for the reduction of acid secretion in patients with severe manifestations and 4‐week healing rates are approaching 90%.
HISTOACRYL BLUE VERSUS SUTURED LEFT COLONIC ANASTOMOSIS: EXPERIMENTAL STUDY
Authors: Ozmen M. Mahir , Ozalp Necdet , Zulfikaroglu Baris , Abbasoglu Latif , Kacar Ayper , Seckin Selda , Koc Mahmut
Published: December 2004

Background:  Cyanoacrylates have been advocated as a protective seal in colonic anastomosis to prevent leakage. In order to assess the effects of n‐butyl‐2‐cyanoacrylate on left colonic anastomosis it was compared to the sutured anastomosis in the rat.

Methods:  Forty male Wistar albino rats were divided into two groups of 20 each. On days 3 and 7, 10 animals in each goup were killed. The comparisons between n‐butyl‐2‐cyanoacrylate and sutured groups were made with respect to outcome measures including anastomotic leakage, anastomotic stricture, peritonitis and wound infections, and adhesion formation, anastomotic bursting pressure, histological appearance of the anastomotic area.

Results:  Although the adhesion formation was significantly more extensive in the n‐butyl‐2‐cyanoacrylate group on day 3 (P < 0.001), there was no significant difference between the groups on day 7. The more inflammatory reaction also occurred in the n‐butyl‐2‐cyanoacrylate group. The mean ± SD anastomotic bursting pressure was significantly higher in the suture group than in the n‐butyl‐2‐cyanoacrylate group (63 ± 14 mmHg vs 43 ± 8 mmHg) on day 3. The bursting pressure was also found to be higher on day 7 in the suture group (187 ± 26 mmHg vs 49 ± 12 mmHg, P < 0.0001). The suture group had a significantly higher bursting pressure on day 7 compared to day 3 (P < 0.05).

Conclusions:  Left colonic anastomosis with n‐butyl‐2‐cyanoacrylate in rats does not improve the healing process; on the contrary, it has a negative influence during the first week. As a consequence, the routine use of n‐butyl‐2‐cyanoacrylate in colonic anastomosis in the clinical situation does not appear to be justifiable.
Prevention of adhesions by sodium chromoglycate, dexamethasone, saline and aprotinin after pelvic surgery
Authors: Kucukozkan Tuncay , Ersoy Bayezit , Uygur Dilek , Gundogdu Cemal
Published: December 2004

Background:  The purpose of the present paper was to assess the efficacy of saline, sodium chromoglycate, dexamethasone and aprotinin, in single or in combined use in reducing postoperative pelvic adhesion formation in a rabbit model.

Methods:  A standard lesion was performed to induce adhesion formation. Forty‐five rabbits were divided into nine study groups. Group 1 was the non‐treatment group. In group 2, 3 cm3 of the rabbits’ own serum was instilled i.p. In group 3, 5 mg/kg sodium chromoglycate and 3 cm3 of the rabbits’ own serum were administered i.p. The group 4 rabbits were instilled with 5 mg/kg sodium chromoglycate, 3 cm3 rabbits’ own serum and 1 mg/kg dexamethasone i.p. The group 5 rabbits were injected with 5000 units aprotinin i.m. 2 h before operation and 5 mg/kg sodium chromoglycate, 3 cm3 of rabbit serum, 1 mg dexamethasone and 5000 units aprotinin instilled i.p. In group 6, 3 cm3 saline was instilled i.p. Groups 7, 8 and 9 were a repeat of groups 4, 5 and 6 with the exception of replacement of the rabbit serum by 3 cm3 saline. Animals were evaluated for adhesions 10 days after operation.

Results:  Macroscopic adhesion scores of all the groups (2−9) were significantly less than scores of the control group (group 1). The macroscopic adhesion scores of group 9 and group 8 were significantly less compared to that of group 7.

Conclusion:  Intraperitoneal instillation of saline and sodium chromoglycate decreased pelvic adhesion formation significantly in a rabbit model. Addition of aprotinin and dexamethasone to these agents gave a further advantage in decreasing pelvic adhesion formation.
Prospective trial of intraoperative radiation treatment for breast cancer
Authors: Joseph David J. , Bydder Sean , Jackson Lee R. , Corica Tammy , Hastrich Diana J. , Oliver David J. , Minchin David E. , Haworth Annette , Saunders Christobel M.
Published: December 2004

Background:  A new device, Intrabeam, is available for intraoperative radiotherapy. We have prospectively examined its feasibility and tolerability in delivering adjuvant breast cancer treatment.

Methods:  Thirty‐five patients undergoing breast‐conserving surgery received targeted tumour bed irradiation consisting of 5 Gy (at 10 mm) in a single fraction. This single intraoperative treatment was used to replace the external beam radiotherapy ‘boost’ that would usually be given in 10 daily treatments following 5 weeks of whole breast irradiation. Patients later completed external beam radiotherapy as usual. Potential toxicities were prospectively assessed fortnightly prior to external beam radiotherapy, weekly during it, and 3 monthly subsequently.

Results:  The intraoperative radiotherapy was able to be delivered without difficulty, either at time of initial cancer surgery or as a second procedure. When performed as a separate procedure the median operating time was 56 min. The treatment was well tolerated, with only one patient experiencing any grade 3 or 4 toxicities − this was acute grade three itch. There was an overall early breast infection rate of 17%. No unexpected toxicities were seen.

Conclusions:  This simple and well‐tolerated treatment delivers a useful radiation dose to the area of highest risk of tumour recurrence. The early infection rate is similar to that reported in the literature, for treatments without intraoperative radiotherapy. Whether such a treatment may adequately replace the entire adjuvant radiation therapy treatment for low‐risk patients is now being studied in a randomized trial.
Role of intraoperative frozen section in the management of thyroid nodules
Authors: Wong Zarina , Muthu Carl , Craik Jan , Carter Jim , Harman C. Richard
Published: December 2004

Background:  The role of intraoperative frozen section in the management of thyroid nodules is controversial. Its potential benefit is to facilitate one‐stage total thyroidectomy. Most literature on this topic originates from overseas tertiary referral centres with a high percentage of cancer cases and a fully resourced frozen section service. The aim of the present study was to review all patients undergoing frozen section at a typical general surgical department in New Zealand (North Shore Hospital, Auckland) to see how often frozen section altered surgical strategy.

Methods:  A retrospective review of all frozen sections between November 1999 and June 2003 was performed. Patient records, operation notes and pathology reports were reviewed.

Results:  Forty‐seven sequential frozen sections were included in the study. Thirteen patients had thyroid carcinoma (five follicular, three Hurthle cell, and five papillary). In only one patient did the result of an intraoperative frozen section result in a total thyroidectomy being performed instead of a thyroid lobectomy. The reason for this was the rare condition of Riedel's thyroiditis. In no patients did frozen section detect a cancer that was not diagnosed on preoperative fine‐needle aspirate biopsy.

Conclusion:  The present review found little benefit in performing intraoperative frozen section in this setting. As a diagnostic test the cost of frozen section (NZ $200 for each frozen section) needs to be weighed against its low clinical benefit.
Surgical management of lung cancer in Western Australia in 1996 and its outcomes
Authors: Mina Kym , Byrne Michael J. , Ryan Gerard , Fritschi Lin , Newman Mark , Joseph David , Harper Chris , Bayliss Evan , Kolybaba Marlene , Jamrozik Konrad
Published: December 2004

Background:  All cases of lung cancer diagnosed in Western Australia in 1996 in which surgery was the primary treatment, were reviewed. Reported herein are the characteristics of the patients, the treatment outcomes and a comparison of the management undertaken with that recommended by international guidelines.

Methods:  All patients with a new diagnosis of lung cancer in Western Australia in the calendar year of 1996 were identified using two different population‐based registration systems: the Western Australian (WA) Cancer Registry and the WA Hospital Morbidity Data System. A structured questionnaire on the diagnosis and management was completed for each case. Date of death was determined through the WA Cancer Registry.

Results:  Six hundred and sixty‐eight patients with lung cancer were identified; 132 (20%) were treated with surgery. Lobectomy was the most frequently performed procedure (71%), followed by pneumonectomy (19%). Major complications affected 23% of patients. Postoperative mortality was 6% (3% lobectomy, 12% pneumonectomy). At 5 years the absolute survival was as follows for stage I, II, IIIA, IIIB, respectively: 51%, 45%, 12%, 5%.

Conclusions:  Investigations and choice of surgery in WA in 1996 reflect current international guidelines. The survival of patients with resectable lung cancer remains unsatisfactory.
Stability and instability of regulation of intracellular calcium
Authors: Eisner D. A. , Diaz M. E. , Li Y. , O'Neill S. C. , Trafford A. W.
Published: December 2004

[Ca2+]i is used as a signal in many tissues. In this review we discuss the mechanisms that regulate [Ca2+]i and, importantly, what determines their stability. Brief mention is made of the effects of feedback gain and delays on stability. The control of cytoplasmic Ca concentration is shown to be generally stable as Ca pumping is essentially an instantaneous function of [Ca2+]i. In contrast, regulation of the Ca content of intracellular stores may be less stable. One example of this is instability in the control of sarcoplasmic reticulum (SR) Ca content in cardiac muscle. An increase of SR Ca content increases the systolic Ca transient amplitude. This in turn decreases Ca influx into the cell and increases efflux, thereby restoring SR Ca to control levels. This feedback system has an inherent delay and is potentially unstable if the gain is increased beyond a certain level. This instability produces Ca transients of alternating amplitude and may contribute to the clinical syndrome of pulsus alternans.
Stress Intensity Factors Due to Residual Stresses in T-Plate Welds
Authors: O’Dowd Noel P. , Nikbin Kamran M. , Lee Hyeong Y. , Wimpory Robert C. , Biglari Farid R.
Published: December 2004

Residual stress distributions in ferritic steel T-plate weldments have been obtained using the neutron diffraction method. It is shown that the transverse residual stress distribution for two plates of different yield strength are of similar shape and magnitude when normalized appropriately and peak stresses are on the order of the material yield strength. The resultant linear elastic stress intensity factors for these stress distributions have been obtained using the finite element method. It has been shown that the use of the recommended residual stress distributions in UK structural integrity procedures leads to a conservative assessment. The stress intensity factors for the welded T-plate have been shown to be very similar to those obtained using a smooth edge cracked plate subjected to the same local stress field.
The Performance of Pressure Vessel Using Concentric Double Cylindrical High Explosive
Authors: Hamada Toru , Nakamura Yuichi , Itoh Shigeru
Published: December 2004

The detonation pressure from the steady detonation of high explosives is a characteristic. Nevertheless, in materials processing using high explosives, there are cases when the detonation pressure does not match the intended pressure. In this investigation, as a new method of generating the overdriven detonation effectively, a double cylindrical high explosive set up using two kinds of explosives was developed, and its basic performance is analyzed. The concentric double cylindrical high explosive set up was composed of a high velocity explosive and a low velocity explosive, and the overdriven detonation was performed in the low velocity explosive. In this experiment, the ion gap was set up in the high velocity explosive and low velocity explosive respectively, and the detonation velocity was measured. The detonation pressure was also measured by setting up a manganin gauge (Kyowa Electric Instrument Co., Ltd.,) at the position where the generation of the overdriven detonation phenomenon was expected. Furthermore, the overdriven detonation process of the concentric double cylindrical high explosive was continually observed by numerical analysis and the framing photography. From the experimental results, the very high pressure region including the mach stem was observed in the low velocity explosive, and the overdriven detonation phenomenon was confirmed. The maximum pressure value of the concentric double cylindrical high explosive set up was 2.3 times higher than the Chapman-Jouguet pressure of the single explosive.
A New Approach to Evaluate Fracture Toughness of Structural Materials
Authors: Wang J. A. , Liu K. C.
Published: December 2004

A new method, designated as Spiral Notch Torsion Test (SNTT), is developed recently to measure the intrinsic fracture toughness KIC of structural materials. The SNTT overcomes many of the limitations inherent in traditional techniques and makes it possible to standardize fracture toughness testing. It is uniquely suitable for testing a wide variety of materials used extensively in pressure vessel and piping structural components and weldments, including others such as ceramics, their composites, and concrete. The SNTT system operates by applying pure torsion to uniform cylindrical specimens with a notch line that spirals around the specimen at a 45 deg pitch. The KIC values are obtained with the aid of a three-dimensional finite-element computer code, TOR3D-KIC, developed at Oak Ridge National Laboratory (ORNL). The fundamental mechanism of SNTT approach is also described in the paper.
A Re-Autofrettage Procedure for Mitigation of Bauschinger Effect in Thick Cylinders
Authors: Parker Anthony P.
Published: December 2004

A manufacturing procedure for enhancing residual stresses and thereby improving fatigue lifetime and fracture resistance of pressure vessels is proposed. The procedure involves initial autofrettage; one or more “heat soak plus autofrettage” sequences and an optional final heat soak. Stresses are calculated numerically for traditional, single autofrettage and compared with those created by the new procedure. The loss of bore compressive hoop stress due to Bauschinger effect is predicted to be significantly reduced. Associated fatigue lifetime calculations indicate that life may be improved by a factor of between 2 and 30, depending upon tube geometry and the ratio of cyclic pressure to yield strength. Repeated overload plus heat soak cycles may also be of benefit in other engineering design scenarios.
Limit Load of Anisotropic Components Using the M-Beta Multiplier Method
Authors: Indermohan H. , Reinhardt W. D. , Seshadri R.
Published: December 2004

The mβ-multiplier method is based on Mura’s extended variational theorems in plasticity, and has been applied previously to isotropic components containing notches and cracks. Lower bound limit loads rapidly converge to inelastic analysis results when the method is used in conjunction with elastic modulus adjustment procedures. In this paper, the mβ-multiplier method is applied to pressure components exhibiting anisotropy. Specifically, the method is applied to the limit load determination of a heat exchanger tubesheet, wherein the tubesheet is modeled as an equivalent solid plate with anisotropic properties. Results are presented for a finite element model where plasticity is represented with Hill’s yield criterion, and a model using a fourth order yield criterion that accounts for compressibility of the tubesheet.
Corrosion Fatigue Behavior of Low-Alloy Pressure Vessel Steels in High Temperature Water Under Multi-Factor Conditions
Authors: Wu Xinqiang , Katada Yasuyuki
Published: December 2004

The corrosion fatigue resistance of pressure vessel steels in simulated light water reactor coolant water is greatly influenced by the mechanical factor such as strain rate, environmental factor such as temperature and dissolved oxygen (DO) concentration in water, and material factor such as sulfur content in steels. In most of previous work, the mechanical or environmental conditions were usually fixed as a constant throughout an individual test. However, these factors may change frequently during actual operations in power plants. So, it is of great interest to investigate the effects of change of the above factors on fatigue resistance of components materials in service environments and to develop appropriate methods for evaluating the environmental effects on fatigue damage. The present work was to investigate the low cycle fatigue (LCF) behavior of low-alloy pressure vessel steels in high temperature water. Special attention was paid on the influence of strain rate change in an individual LCF test on fatigue resistance of the steels. The alternate sequence of strain rate in a test was also considered. Moreover, the influence of DO, temperature and sulfur content in the steels was investigated. The detailed cracking and fractographic features were examined to assist the understanding of underlying corrosion fatigue mechanisms.
Influence of Crack Orientation and Crosshead Speed on the Fracture Toughness of PVC Pipe Materials
Authors: El-Bagory Tarek M. , El-Fadaly Mohamed S. , Younan Maher Y. A. , Abdel-Latif Lotfi A.
Published: December 2004

In many modern engineering applications, designers and manufacturers of Polyvinyl chloride (PVC) pipes are interested in the evaluation of fracture toughness under several operation conditions. The aim of the present work is to investigate the fracture toughness of commercial amorphous thermoplastic PVC materials used in piping applications. The experimental work is carried out using three different specimens’ types: Taper Double Cantilever Beam (TDCB), Three Point Bend (TPB), and Compact Tension (CT). Tests are conducted on specimens with thickness (17, 20, 22, and 26 mm), longitudinal and transverse extrusion orientations, at different crosshead speeds (50–500 mm/min) to calculate the fracture toughness of PVC pipe materials. The experimental work has revealed that the crosshead speed has a significant effect on the fracture toughness at low speed rates. This effect, however, becomes insignificant at high rates since, the fracture behavior becomes brittle. The stress intensity factor KQ is approximately the same in both longitudinal and transverse orientations. The fracture toughness decreases as the specimen thickness increases.
Colorimetric Method for Identifying Plant Essential Oil Components That Affect Biofilm Formation and Structure
Authors: Niu C. , Gilbert E. S.
Published: December 2004

The specific biofilm formation (SBF) assay, a technique based on crystal violet staining, was developed to locate plant essential oils and their components that affect biofilm formation. SBF analysis determined that cinnamon, cassia, and citronella oils differentially affected growth-normalized biofilm formation by
Escherichia coli
. Examination of the corresponding essential oil principal components by the SBF assay revealed that cinnamaldehyde decreased biofilm formation compared to biofilms grown in Luria-Bertani broth, eugenol did not result in a change, and citronellol increased the SBF. To evaluate these results, two microscopy-based assays were employed. First, confocal laser scanning microscopy (CLSM) was used to examine
E. coli
biofilms cultivated in flow cells, which were quantitatively analyzed by COMSTAT, an image analysis program. The overall trend for five parameters that characterize biofilm development corroborated the findings of the SBF assay. Second, the results of an assay measuring growth-normalized adhesion by direct microscopy concurred with the results of the SBF assay and CLSM imaging. Viability staining indicated that there was reduced toxicity of the essential oil components to cells in biofilms compared to the toxicity to planktonic cells but revealed morphological damage to
E. coli
after cinnamaldehyde exposure. Cinnamaldehyde also inhibited the swimming motility of
E. coli
. SBF analysis of three
Pseudomonas
species exposed to cinnamaldehyde, eugenol, or citronellol revealed diverse responses. The SBF assay could be useful as an initial step for finding plant essential oils and their components that affect biofilm formation and structure.
Inactivation of Viruses in Bubbling Processes Utilized for Personal Bioaerosol Monitoring
Authors: Agranovski I. E. , Safatov A. S. , Borodulin A. I. , Pyankov O. V. , Petrishchenko V. A. , Sergeev A. N. , Agafonov A. P. , Ignatiev G. M. , Sergeev A. A. , Agranovski V.
Published: December 2004

A new personal bioaerosol sampler has recently been developed and evaluated for sampling of viable airborne bacteria and fungi under controlled laboratory conditions and in the field. The operational principle of the device is based on the passage of air through porous medium immersed in liquid. This process leads to the formation of bubbles within the filter as the carrier gas passes through and thus provides effective mechanisms for aerosol removal. As demonstrated in previous studies, the culturability of sampled bacterium and fungi remained high for the entire 8-h sampling period. The present study is the first step of the evaluation of the new sampler for monitoring of viable airborne viruses. It focuses on the investigation of the inactivation rate of viruses in the bubbling process during 4 h of continuous operation. Four microbes were used in this study, influenza, measles, mumps, and vaccinia viruses. It was found that the use of distilled water as the collection fluid was associated with a relatively high decay rate. A significant improvement was achieved by utilizing virus maintenance fluid prepared by using Hank's solution with appropriate additives. The survival rates of the influenza, measles, and mumps viruses were increased by 1.4 log, 0.83 log, and 0.82 log, respectively, after the first hour of operation compared to bubbling through the sterile water. The same trend was observed throughout the entire 4-h experiment. There was no significant difference observed only for the robust vaccinia virus.
Chitinase Gene Sequences Retrieved from Diverse Aquatic Habitats Reveal Environment-Specific Distributions
Authors: LeCleir Gary R. , Buchan Alison , Hollibaugh James T.
Published: December 2004

Chitin is an abundant biopolymer whose degradation is mediated primarily by bacterial chitinases. We developed a degenerate PCR primer set to amplify a ∼900-bp fragment of family 18, group I chitinase genes and used it to retrieve these gene fragments from environmental samples. Clone libraries of presumptive chitinase genes were created for nine water and six sediment samples from 10 aquatic environments including freshwater and saline lakes, estuarine water and sediments, and the central Arctic Ocean. Putative chitinase sequences were also retrieved from the Sargasso Sea metagenome sequence database. We were unable to obtain PCR product with these primers from an alkaline, hypersaline lake (Mono Lake, California). In total, 108 partial chitinase gene sequences were analyzed, with a minimum of 5 and a maximum of 13 chitinase sequences obtained from each library. All chitinase sequences were novel compared to previously identified sequences. Intralibrary sequence diversity was low, while we found significant differences between libraries from different water column samples and between water column and sediment samples. However, identical sequences were retrieved from samples collected at widely distributed locations that did not necessarily represent similar environments, suggesting homogeneity of chitinoclastic communities between some environments.
Genetic and Biochemical Characterization of Field-Evolved Resistance to
Bacillus thuringiensis
Toxin Cry1Ac in the Diamondback Moth,
Plutella xylostella
Authors: Sayyed Ali H. , Raymond Ben , Ibiza-Palacios M. Sales , Escriche Baltasar , Wright Denis J.
Published: December 2004

The long-term usefulness of
Bacillus thuringiensis
Cry toxins, either in sprays or in transgenic crops, may be compromised by the evolution of resistance in target insects. Managing the evolution of resistance to
B. thuringiensis
toxins requires extensive knowledge about the mechanisms, genetics, and ecology of resistance genes. To date, laboratory-selected populations have provided information on the diverse genetics and mechanisms of resistance to
B. thuringiensis
, highly resistant field populations being rare. However, the selection pressures on field and laboratory populations are very different and may produce resistance genes with distinct characteristics. In order to better understand the genetics, biochemical mechanisms, and ecology of field-evolved resistance, a diamondback moth (
Plutella xylostella
) field population (Karak) which had been exposed to intensive spraying with
B. thuringiensis
subsp.
kurstaki
was collected from Malaysia. We detected a very high level of resistance to Cry1Ac; high levels of resistance to
B. thuringiensis
subsp.
kurstaki
Cry1Aa, Cry1Ab, and Cry1Fa; and a moderate level of resistance to Cry1Ca. The toxicity of Cry1Ja to the Karak population was not significantly different from that to a standard laboratory population (LAB-UK). Notable features of the Karak population were that field-selected resistance to
B. thuringiensis
subsp.
kurstaki
did not decline at all in unselected populations over 11 generations in laboratory microcosm experiments and that resistance to Cry1Ac declined only threefold over the same period. This finding may be due to a lack of fitness costs expressed by resistance strains, since such costs can be environmentally dependent and may not occur under ordinary laboratory culture conditions. Alternatively, resistance in the Karak population may have been near fixation, leading to a very slow increase in heterozygosity. Reciprocal genetic crosses between Karak and LAB-UK populations indicated that resistance was autosomal and recessive. At the highest dose of Cry1Ac tested, resistance was completely recessive, while at the lowest dose, it was incompletely dominant. A direct test of monogenic inheritance based on a backcross of F
1
progeny with the Karak population suggested that resistance to Cry1Ac was controlled by a single locus. Binding studies with
125
I-labeled Cry1Ab and Cry1Ac revealed greatly reduced binding to brush border membrane vesicles prepared from this field population.
Comparison of Two Alternative Dominant Selectable Markers for Wine Yeast Transformation
Authors: Cebollero Eduardo , Gonzalez Ramon
Published: December 2004

Genetic improvement of industrial yeast strains is restricted by the availability of selectable transformation markers. Antibiotic resistance markers have to be avoided for public health reasons, while auxotrophy markers are generally not useful for wine yeast strain transformation because most industrialSaccharomyces cerevisiaestrains are prototrophic. For this work, we performed a comparative study of the usefulness of two alternative dominant selectable markers in both episomic and centromeric plasmids. Even though the selection for sulfite resistance conferred byFZF1-4resulted in a larger number of transformants for a laboratory strain, thep-fluoro-dl-phenylalanine resistance conferred byARO4-OFPresulted in a more suitable selection marker for all industrial strains tested. Both episomic and centromeric constructions carrying this marker resulted in transformation frequencies close to or above 103transformants per μg of DNA for the three wine yeast strains tested.
Diagnostic Real-Time PCR for Detection of
Salmonella
in Food
Authors: Malorny Burkhard , Paccassoni Elisa , Fach Patrick , Bunge Cornelia , Martin Annett , Helmuth Reiner
Published: December 2004

A robust 5′ nuclease (TaqMan) real-time PCR was developed and validated in-house for the specific detection of
Salmonella
in food. The assay used specifically designed primers and a probe target within the
ttrRSBCA
locus, which is located near the
Salmonella
pathogenicity island 2 at centisome 30.5. It is required for tetrathionate respiration in
Salmonella
. The assay correctly identified all 110
Salmonella
strains and 87 non-
Salmonella
strains tested. An internal amplification control, which is coamplified with the same primers as the
Salmonella
DNA, was also included in the assay. The detection probabilities were 70% when a
Salmonella
cell suspension containing 10
3
CFU/ml was used as a template in the PCR (5 CFU per reaction) and 100% when a suspension of 10
4
CFU/ml was used. A pre-PCR sample preparation protocol including a preenrichment step in buffered peptone water followed by DNA extraction-purification was applied when 110 various food samples (chicken rinses, minced meat, fish, and raw milk) were investigated for
Salmonella
. The diagnostic accuracy was shown to be 100% compared to the traditional culture method. The overall analysis time of the PCR method was approximately 24 h, in contrast to 4 to 5 days of analysis time for the traditional culture method. This methodology can contribute to meeting the increasing demand of quality assurance laboratories for standard diagnostic methods. Studies are planned to assess the interlaboratory performance of this diagnostic PCR method.