The Four Pillars for De-Risking Fluid Loss Potential Along Fault Damage Zone: A Framework for Well Designs and Drilling Operations

ABSTRACT:

Fluid loss along faults can pose significant operational challenges from drilling & completing wells to maintaining containment during fluid injection. While faults and fractures can be ubiquitous in the subsurface, not all of them pose the same threats to hydrocarbon extraction activities. During a drilling campaign in semi-consolidated deepwater clastics, a generic link between faults, fluid loss events, fluid circulation pressure and the fault strength parameters was established. In order to reduce the risks of fault-induced fluid loss along any proposed well path in future drilling campaigns, we developed and successfully implemented an integrated screening method that incorporates the observed correlation. The de-risking framework includes four elements (Geological, Geometrical, Mechanical and Dynamic considerations): Geological consideration highlighted the lithological influence on fault zone architecture and the confidence level on fault presences; Meanwhile, the placement of a well path relative to fault(s) will affect the exposure to potential leak paths; Thirdly, mechanical threshold of a fault will change the safe operation margin; And lastly, dynamic interaction between fluid and the fault zone during operation can alter fluid loss potential. Our proposed framework provides subsurface geoscientists and well engineers an efficient tool to quickly rank the integrated threats of fault-induced lost circulation to improve well design, optimize drilling and completion strategy along with appropriate level of mitigation and recovery measures. Unlike typical fault stability analyses that are primarily based on static fault zone architecture and/or stress-based slip potential, the integration and incorporation of engineering activities offers the missing link to de -risk and mitigate the threats posed by along fault fluid migration potential. With minor modifications, this framework can be extended for risk assessments related to containments, caprock or seal integrity evaluations related to other activities such as exploration, enhanced oil recovery or carbon capture and sequestration.

WHO informal consultation on revision of guidelines on evaluation of similar biotherapeutic products, virtual meeting, 30 June – 2 July 2021

The WHO informal consultation was held to promote the revision of WHO guidelines on evaluation of similar biotherapeutic products (SBPs) adopted by the Expert Committee on Biological Standardization (ECBS) in 2009. It was agreed in the past consultations that the evaluation principles in the guidelines are still valid, but a review was recommended to provide more clarity and case-by-case flexibility. The opportunity was therefore taken to review the experience and identify areas where the current guidance could be more permissive without compromising its basic principles, and where additional explanation could be provided regarding the possibility of reducing the amount of data needed for regulatory approval. The meeting participants applauded the leading role taken by the WHO in providing a much-needed streamlined approach for development and evaluation of SBPs which will provide efficient and cost-effective product development and increase patient access to treatments. It was recognized that the principles as currently described in the draft WHO guidelines are based on sound science and experience gained over the last fifteen years of biosimilar approvals. However, since these guidelines when finalised will constitute the global standard for biosimilar evaluation and assist national regulatory authorities in establishing revised guidance and regulatory practice in this complex area, it was felt that further revision and clarity on certain perspectives in specific areas was necessary to dispel uncertainties arising in the current revised version. This report describes the principles in the draft guidelines, including topics discussed and consensus reached.

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WHO guidelines serve as a basis for the development of national regulatory framework for biosimilars.

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Revision of guidelines is to provide more flexibility and clarification on data required for regulatory approval.

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Revised guidelines would contribute to improving consistency on regulatory decision and patient access to treatments.

Electronic search programs are effective in identifying patients with minimal trauma fractures

We assessed two electronic search tools that screen medical records for documented fractures. Both programs reliably identified patients with any fracture but missed individuals with minimal trauma fracture to different degrees. A hybrid tool combining the methodology of both tools is likely to improve the identification of those with osteoporosis.

PURPOSE

Most patients who suffer a minimal trauma fracture remain undiagnosed, placing them at high risk of refracture. Case finding can be improved by electronic search tools that screen medical records for documented fractures. Here, we assessed the efficacy of two new programs, AES and XRAIT, in identifying patients with minimal trauma fracture.

METHODS

Each tool was applied to search the electronic medical record and/or radiology reports at two tertiary hospitals in Sydney, Australia, from 1 July to 31 December 2018. Samples of the extracted reports were then manually reviewed to determine the sensitivity of each program in detecting minimal trauma fractures.

RESULTS

At the two centers, AES detected 872 and 1364 cases, whereas XRAIT identified 1414 and 2180 patients with fractures, respectively. The true positive rate for "any fracture" was similar for both instruments (77-88%). However, the ability to detect "minimal trauma fractures" differed between programs and centers (53-75% accuracy), with each tool identifying separate subsets of patients. Concordance between both tools was less than half of the combined total number of minimal trauma fractures (43-45%). Considering the total number of minimal trauma fractures detected by both tools combined, AES correctly identified 52-55% of cases while XRAIT identified 88-93% of cases.

CONCLUSION

Both programs reliably identified patients with any fracture but missed individuals with minimal trauma fracture to different degrees. Hybrid tools combining the methodology of XRAIT and AES are likely to improve the identification of patients who require investigation and treatment for osteoporosis.

Systematic Review and Meta-analysis of Histological Gastric Biopsy Aspects According to the Updated Sydney System in Children

OBJECTIVES

A descriptive and comparative study of gastric histological aspects according to the updated Sydney classification (USC), obtained from Helicobacter pylori-positive versus H pylori-negative children referred for upper gastrointestinal endoscopy.

METHODS

The Prisma method was used to perform a systematic review and meta-analysis. Selection criteria were based on following key words USC, H pylori, children, endoscopy, or biopsy. Publication biases were assessed according to the Newcastle-Ottawa Scale, and a meta-regression analysis was done. The study was registered on the PROSPERO platform.

RESULTS

Between 1994 and 2017, 1238 references were found; 97 studies were retained for the systematic review with a total number of 25,867 children; 75 studies were selected for the meta-analysis concerning 5990 H pylori-infected and 17,782 uninfected children.H pylori-positive versus H pylori-negative children, according to the USC, showed significantly higher relative risk for gastric antral and corpus chronic inflammation, presence of neutrophils, and of lymphoid follicles, and gastric mucosa atrophy, whereas, intestinal metaplasia showed a significantly higher RR only in antral biopsies. The meta-regression analysis showed that H pylori-positive versus H pylori-negative children had significantly higher risk only for corpus activity according to age, recurrent abdominal pain, and geographical area of low H pylori prevalence.

CONCLUSIONS

H pylori infection in children was associated with higher relative risk for gastric antral and corpus chronic inflammation, presence of neutrophils, lymphoid follicles, and rare gastric mucosa atrophy, whereas, rare intestinal metaplasia was only significantly higher in the antral area.

Determining the lipid specificity of insoluble protein transmembrane domains

While the specificity of protein-lipid interactions is a key feature in the function of biological membranes, studying the specifics of these interactions is challenging because most membrane proteins are insoluble in water due to the hydrophobic nature of their transmembrane domains (TMDs). Here, we introduce a method that overcomes this solubility limitation and identifies the affinity profile of protein TMDs to specific lipid formulations. Using 5 human TMDs as a sample group, our results demonstrate that TMDs are highly selective and that these specific lipid-TMD interactions can involve either a single lipid, or the combination of multiple lipid species.

Use of Infliximab Biosimilar Versus Originator in a Pediatric United Kingdom Inflammatory Bowel Disease Induction Cohort

OBJECTIVES

The aim of the study was to summarize short-term effectiveness, safety, and cost of using infliximab biosimilar (IFX-B) drugs, (Inflectra [Hospira] and Remsima [NAAP]) compared to originator infliximab (IFX-O) (Remicade [MSD]) in biologic naive pediatric inflammatory bowel disease in the United Kingdom.

METHODS

Prospective audit of patients starting anti-tumour necrosis factor (TNF) therapy. Disease severity, response to treatment, and remission rate was measured by Pediatric Crohn's Disease Activity Index (PCDAI) and/or Physician Global Assessment.

RESULTS

Between March 2015 and February 2016, 278 patients (175 IFX-O, 82 IFX-B, and 21 Adalimumab) were started on anti-TNF therapy. This was compared with collected data on 398 patients started on IFX-O from 2011 to 2015. At initiation, median PCDAI was 36 (20,48) (n = 42) in the IFX-O group and 28 (20,40) (n = 29) in the IFX-B group, (P = 0.08). Immunosuppression rates were similar: 150/175 (86%) for IFX-O and 65/82 (79%) for IFX-B (P > 0.05). Post induction, median PCDAI score was 5 (0,11) (n = 19) and 0 (0,8) (n = 15) in the IFX-O and IFX-B groups, respectively (P = 0.35). There was no difference in response to treatment using Physician Global Assessment 85% (n = 28) in IFX-O group and 86% (n = 19) in IFX-B group (P > 0.05). Adverse events at initiation and post induction were not different between both groups (P > 0.05). Using conservative calculations, £875,000 would have been saved for a 1-year period with universal adoption of biosimilars in patients who were instead treated with IFX-O.

CONCLUSIONS

IFX-B is likely as effective as IFX-O in treating IBD in comparable pediatric populations. Sites should adopt infliximab biosimilar for new starts due to cost reduction with no difference in other parameters.

Accuracy in Diagnosis of Celiac Disease Without Biopsies in Clinical Practice

BACKGROUND & AIMS

The guidelines of the European Society of Pediatric Gastroenterology, Hepatology, and Nutrition allow for diagnosis of celiac disease without biopsies in children with symptoms and levels of immunoglobulin A against tissue-transglutaminase (TGA-IgA) 10-fold or more the upper limit of normal (ULN), confirmed by detection of endomysium antibodies (EMA) and positivity for HLA-DQ2/DQ8. We performed a large, international prospective study to validate this approach.

METHODS

We collected data from consecutive pediatric patients (18 years or younger) on a gluten-containing diet who tested positive for TGA-IgA from November 2011 through May 2014, seen at 33 pediatric gastroenterology units in 21 countries. Local centers recorded symptoms; measurements of total IgA, TGA, and EMA; and histopathology findings from duodenal biopsies. Children were considered to have malabsorption if they had chronic diarrhea, weight loss (or insufficient gain), growth failure, or anemia. We directly compared central findings from 16 antibody tests (8 for TGA-IgA, 1 for TGA-IgG, 6 for IgG against deamidated gliadin peptides, and 1 for EMA, from 5 different manufacturers), 2 HLA-DQ2/DQ8 tests from 2 manufacturers, and histopathology findings from the reference pathologist. Final diagnoses were based on local and central results. If all local and central results were concordant for celiac disease, cases were classified as proven celiac disease. Patients with only a low level of TGA-IgA (threefold or less the ULN) but no other results indicating celiac disease were classified as no celiac disease. Central histo-morphometry analyses were performed on all other biopsies and cases were carefully reviewed in a blinded manner. Inconclusive cases were regarded as not having celiac disease for calculation of diagnostic accuracy. The primary aim was to determine whether the nonbiopsy approach identifies children with celiac disease with a positive predictive value (PPV) above 99% in clinical practice. Secondary aims included comparing performance of different serological tests and to determine whether the suggested criteria can be simplified.

RESULTS

Of 803 children recruited for the study, 96 were excluded due to incomplete data, low level of IgA, or poor-quality biopsies. In the remaining 707 children (65.1% girls; median age, 6.2 years), 645 were diagnosed with celiac disease, 46 were found not to have celiac disease, and 16 had inconclusive results. Findings from local laboratories of TGA-IgA 10-fold or more the ULN, a positive result from the test for EMA, and any symptom identified children with celiac disease (n = 399) with a PPV of 99.75 (95% confidence interval [CI], 98.61-99.99); the PPV was 100.00 (95% CI, 98.68-100.00) when only malabsorption symptoms were used instead of any symptom (n = 278). Inclusion of HLA analyses did not increase accuracy. Findings from central laboratories differed greatly for patients with lower levels of antibodies, but when levels of TGA-IgA were 10-fold or more the ULN, PPVs ranged from 99.63 (95% CI, 98.67-99.96) to 100.00 (95% CI, 99.23-100.00).

CONCLUSIONS

Children can be accurately diagnosed with celiac disease without biopsy analysis. Diagnosis based on level of TGA-IgA 10-fold or more the ULN, a positive result from the EMA tests in a second blood sample, and the presence of at least 1 symptom could avoid risks and costs of endoscopy for more than half the children with celiac disease worldwide. HLA analysis is not required for accurate diagnosis. Clinical Trial Registration no: DRKS00003555.

Surgical Management of Crohn Disease in Children: Guidelines From the Paediatric IBD Porto Group of ESPGHAN

The incidence of Crohn disease (CD) has been increasing and surgery needs to be contemplated in a substantial number of cases. The relevant advent of biological treatment has changed but not eliminated the need for surgery in many patients. Despite previous publications on the indications for surgery in CD, there was a need for a comprehensive review of existing evidence on the role of elective surgery and options in pediatric patients affected with CD. We present an expert opinion and critical review of the literature to provide evidence-based guidance to manage these patients. Indications, surgical options, risk factors, and medications in pre- and perioperative period are reviewed in the light of available evidence. Risks and benefits of surgical options are addressed. An algorithm is proposed for the management of postsurgery monitoring, timing for follow-up endoscopy, and treatment options.

IFPA meeting 2015 workshop report I: placental mitochondrial function, transport systems and epigenetics

Workshops are an important part of the IFPA annual meeting as they allow for discussion of specialized topics. At IFPA meeting 2015 there were twelve themed workshops, three of which are summarized in this report. These workshops covered areas of placental regulation and nutrient handling: 1) placental epigenetics; 2) placental mitochondrial function; 3) placental transport systems.

Incidental Adrenal Nodules and Masses: The Imaging Approach

Adrenal nodules are detected with increasing frequency. The National Institute of Health (NIH), American College of Radiology (ACR), and the American Association of Clinical Endocrinologists and American Association of Endocrine Surgeons (AACE/AAES) have produced guidelines for the management of incidental adrenal nodules. This review provides a summary of the consensus radiologic approach to these nodules.

Transthoracic fine-needle aspiration biopsy of the lungs using a C-arm cone-beam CT system: diagnostic accuracy and post-procedural complications

OBJECTIVE

The purpose of our study was to evaluate the diagnostic accuracy of transthoracic fine-needle aspiration biopsy (TFNAB) using a C-arm cone-beam CT (CBCT) system and to assess risk factors for immediate post-procedural complications in patients with lung lesions.

METHODS

From October 2007 to April 2009, 94 TFNAB procedures using a C-arm system were studied in 91 patients with pulmonary lesions a chest CT scans. We retrospectively reviewed the patients' radiological and histopathological findings. We evaluated the lesion size, lesion abutted to pleura and presence or absence of emphysema along the needle path, lesion depth, visibility of target lesion and patient's position. Pneumothorax and pulmonary haemorrhage were assessed after TFNAB. Overall diagnostic accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were analysed.

RESULTS

In 94 TFNAB procedures, 58 lesions were malignant and 36 were benign. The sensitivity, specificity, PPV, NPV and overall diagnostic accuracy rate of TFNAB were 93.1%, 100%, 100%, 90% and 97.9%, respectively. Pneumothorax was developed in 24 procedures. None of the parameters showed significant impact on the frequency of the pneumothorax. Overall haemorrhage occurred in 43 procedures. The incidence of overall haemorrhage was higher in patients with smaller lesions, longer pleural distance and pleural abutted lesions (p<0.05). Differences in visibility at projection radiographs were statistically significant between patients with or without perilesional haemorrhage (p<0.05).

CONCLUSION

Transthoracic fine-needle aspiration biopsy using a C-arm CBCT system is feasible for imaging guidance of lung lesion and early detection of the procedural-related complications.

Increased de novo copy number variants in the offspring of older males

The offspring of older fathers have an increased risk of neurodevelopmental disorders, such as schizophrenia and autism. In light of the evidence implicating copy number variants (CNVs) with schizophrenia and autism, we used a mouse model to explore the hypothesis that the offspring of older males have an increased risk of de novo CNVs. C57BL/6J sires that were 3- and 12-16-months old were mated with 3-month-old dams to create control offspring and offspring of old sires, respectively. Applying genome-wide microarray screening technology, 7 distinct CNVs were identified in a set of 12 offspring and their parents. Competitive quantitative PCR confirmed these CNVs in the original set and also established their frequency in an independent set of 77 offspring and their parents. On the basis of the combined samples, six de novo CNVs were detected in the offspring of older sires, whereas none were detected in the control group. Two of the CNVs were associated with behavioral and/or neuroanatomical phenotypic features. One of the de novo CNVs involved Auts2 (autism susceptibility candidate 2), and other CNVs included genes linked to schizophrenia, autism and brain development. This is the first experimental demonstration that the offspring of older males have an increased risk of de novo CNVs. Our results support the hypothesis that the offspring of older fathers have an increased risk of neurodevelopmental disorders such as schizophrenia and autism by generation of de novo CNVs in the male germline.

Herpes simplex virus pneumonia: high-resolution CT findings

The purpose of this study was to evaluate the high-resolution computed tomographic (HRCT) findings of five adult patients (either immunocompromised or immunocompetent) with herpes simplex virus (HSV) pneumonia. We retrospectively assessed HRCT images of 5 patients (all male patients, age range 39-70 years; mean 62 years) with HSV pneumonia. The specific pathological findings that allowed for a definite diagnosis of HSV pneumonia included the presence of intranuclear inclusion bodies on haematoxylin and eosin staining, or positive immunohistochemical staining. High-resolution CT scans (HiSpeed Advantage or LightSpeed QX/i, GE Healthcare) using 1- or 1.25-mm collimation at 10-mm intervals without intravenous contrast medium injection were assessed, in particular for the presence and distribution of parenchymal abnormalities including ground-glass attenuation, airspace consolidation, nodules and interlobular septal thickening. In two patients, pathological specimens were obtained from open lung biopsy or bronchoscopic biopsy, and were correlated with HRCT findings. Three HRCT patterns of pulmonary abnormalities were identified in our series of HSV pneumonia: predominant areas of diffuse or multifocal ground-glass attenuation, predominant areas of multifocal peribronchial consolidations, and a mixed pattern of both. Histopathologically, areas of ground-glass attenuation seen on HRCT corresponded to diffuse alveolar damage in one patient who underwent open lung biopsy. No specific differences in HRCT findings were seen between the immunocompromised and the immunocompetent patients. In patients suspected of having an acute lower respiratory infection, whether immunocompromised or immunocompetent, a possibility of HSV pneumonia can be included in differential diagnoses when diffuse or multifocal areas of ground-glass attenuation and/or consolidations are seen on HRCT.

Application of structure–metabolism relationships in the identification of a selective endothelin A antagonist, BMS-193884, with favourable pharmacokinetic properties

1. Based on binding affinity, 2'-amino-N-(3,4-dimethyl-5-isoxazolyl)-4'-(2-methylpropyl)[1,1'-biphenyl]-2-sulfonamide (2) was identified as an initial lead in a programme to identify selective endothelin (ET) receptor antagonists. However, the compound was extensively metabolized in preclinical animal species and human in vitro systems due to oxidative biotransformation. 2. To optimize this structural class, the site of metabolism of 2 was determined. This allowed for focussed structure-activity and structure-metabolism studies aimed at finding more metabolically stable analogues that maintained potency. New analogues were screened for their ET binding characteristics and their stability in rat and human liver microsomes. 3. The use of the microsomal stability screen was tested by the determination of the pharmacokinetic parameters of select analogues. A good correlation was found between reduced rates of rat microsomal metabolism and reduced clearance in the rat. 4. N-(3,4-dimethyl-5-isoxazolyl)-4'-(2-oxazolyl)[1,1'-biphenyl]-2-sulfonamide (3) was identified as an analogue with improved in vitro properties and further studies revealed that the compound had improved pharmacokinetic properties. 5. N-[[2'-[[(3,4-dimethyl-5-isoxazolyl)amino]sulfonyl]-4-(2-oxazolyl)[1,1'-biphenyl]-2-yl]methyl]acetamide (4) was subsequently identified as a compound with superior in vitro properties compared with compound 3, but when tested in vivo it had a substantially increased rate of clearance. Further studies demonstrated that the clearance of this closely related structural analogue was not dictated by metabolic processes, but was mediated by transport-mediated direct biliary excretion. 6. The utility of screening for in vitro liver microsomal stability as part of the lead optimization process for compounds with metabolic liabilities was shown. It was also shown that relatively small molecular changes can dramatically change the disposition of closely related analogues and care must be used when screening for a single property.

Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay

Virology laboratories historically have used direct fluorescent-antibody assay (DFA) and culture to detect six or seven respiratory viruses. Following the discovery of five new human respiratory viruses since 2000, there is an increasing need for diagnostic tests to detect these emerging viruses. We have developed a new test that can detect 20 different respiratory virus types/subtypes in a single 5-h test. The assay employs multiplex PCR using 14 virus-specific primer pairs, followed by a multiplexed target-specific primer extension (TSPE) reaction using 21 primers for specific respiratory virus types and subtypes. TSPE products were sorted and identified by using a fluid microsphere-based array (Universal Array; TmBioscience Corporation, Toronto, Canada) and the Luminex x-MAP system. The assay detected influenza A and B viruses; influenza A virus subtypes H1, H3, and H5 (including subtype H5N1 of the Asian lineage); parainfluenza virus types 1, 2, 3, and 4; respiratory syncytial virus types A and B; adenovirus; metapneumovirus; rhinovirus; enterovirus; and coronaviruses OC43, 229E, severe acute respiratory syndrome coronavirus, NL63, and HKU1. In a prospective evaluation using 294 nasopharyngeal swab specimens, DFA/culture detected 119 positives and the respiratory virus panel (RVP) test detected 112 positives, for a sensitivity of 97%. The RVP test detected an additional 61 positive specimens that either were not detected by DFA/culture or were positive for viruses not tested for by DFA/culture. After resolution of discordant results by using a second unique PCR assay and by using a combined reference standard of positivity, the RVP test detected 180 of 183 true positives, for a sensitivity of 98.5%, whereas DFA and culture detected only 126 of 183 true positives, for a sensitivity of 68.8%. The RVP test should improve the capabilities of hospital and public health laboratories for diagnosing viral respiratory tract infections and should assist public health agencies in identifying etiologic agents in respiratory tract infection outbreaks.

Abilities of APTIMA, AMPLICOR, and ProbeTec assays to detect Chlamydia trachomatis and Neisseria gonorrhoeae in PreservCyt ThinPrep Liquid-based Pap samples

Infections with Chlamydia trachomatis and Neisseria gonorrhoeae are often asymptomatic. Liquid-based Pap (L-Pap) screening may provide samples for testing by commercial assays. Women attending a health clinic or a street youth clinic had a PreservCyt ThinPrep sample and a cervical swab (CS) collected. The L-Pap sample was tested for cytopathology; then 1 ml was transferred to an L-Pap specimen transfer tube for testing by the Gen-Probe APTIMA assays (APTIMA Combo 2 [AC2], APTIMA C. trachomatis [ACT], and APTIMA N. gonorrhoeae [AGC]). The residual L-Pap sample was tested for C. trachomatis and N. gonorrhoeae using Roche AMPLICOR (AMP) and Becton Dickinson ProbeTec (PT). The CS was tested by AC2. A patient was considered infected if two specimens were positive or if a single specimen was positive in two tests. The prevalence of infection was 10% (29/290) for C. trachomatis and 2.4% (7/290) for N. gonorrhoeae. Most of the positive patients had specimens that were reactive in all assays (20/29 for C. trachomatis; 6/7 for N. gonorrhoeae). Four patients had double infections. The sensitivities and specificities of the various tests for the specimens tested were as follows. For C. trachomatis on L-Pap, sensitivity and specificity were 100 and 98.1%, respectively, for ACT, 93.1 and 98.8% for AC2, 86.2 and 91.2% for AMP, and 72.4 and 92.7% for PT. For N. gonorrhoeae on L-Pap, sensitivity and specificity were 100% for both AGC and AC2, 85.7 and 100% for AMP, and 85.7 and 100% for PT. For AC2 with CSs, sensitivity and specificity were 93.1 and 98.5%, respectively, for C. trachomatis, and both were 100% for N. gonorrhoeae. There were significant differences in sensitivity and specificity (P < 0.001). The APTIMA assays were more sensitive and specific than AMP or PT for detecting women's C. trachomatis and/or N. gonorrhoeae infections by testing ThinPrep samples.

Serial magnetic resonance imaging in a rat pup filament stroke model

Neonatal stroke is increasingly recognized in preterm and term infants but the ability to study this condition has been limited by the technical challenges in developing suitable animal models. In the current study we report the use of transient filament middle cerebral artery occlusion for 1.5 h in 10-day-old rat pups in which we were able to perform serial magnetic resonance imaging (MRI) studies. Serial MRI was performed immediately after the onset of stroke until 28 days after injury in an 11.7 T scanner using diffusion weighted and T2-weighted images. At 28 days the rat pups were sacrificed and standard histological stains were performed to validate stroke area. Serial behavioral assessments were also performed on the day of each imaging study. The anatomical distribution of stroke was similar to that expected from occlusion of the middle cerebral artery in adult models and represents a specific model of neonatal stroke in contrast to the commonly used model of carotid artery occlusion with 8% hypoxia. The initial stroke volume from MR measurements was 39% of the ipsilateral hemisphere at 0 h post-occlusion, reached a maximum at 24 h (44%) and then decreased in size (17%) with subsequent cavitation by 28 days. Infarction was more visible early with diffusion weighted imaging whereas T2-mapping provided more accurate infarct volumes at later time points. Despite the relatively large infarct volume, we saw little evidence of behavioral neurological deficit suggesting that this may also serve as a model of developmental plasticity and recovery.

Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens

The emergence of a novel coronavirus (CoV) as the cause of severe acute respiratory syndrome (SARS) catalyzed the development of rapid diagnostic tests. Stool samples have been shown to be appropriate for diagnostic testing for SARS CoV, although it has been recognized to be a heterogeneous and difficult sample that contains amplification inhibitors. Limited information on the efficiency of extraction methods for the purification and concentration of SARS CoV RNA from stool samples is available. Our study objectives were to determine the optimal extraction method for SARS CoV RNA detection and to examine the effect of increased specimen volume for the detection of SARS CoV RNA in stool specimens. We conducted a multicenter evaluation of four automated and four manual extraction methods using dilutions of viral lysate in replicate mock stool samples, followed by quantitation of SARS CoV RNA using real-time reverse transcriptase PCR. The sensitivities of the manual methods ranged from 50% to 100%, with the Cortex Biochem Magazorb method, a magnetic bead isolation method, allowing detection of all 12 positive samples. The sensitivities of the automated methods ranged from 75% to 100%. The bioMérieux NucliSens automated extractor and miniMag extraction methods each had a sensitivity of 100%. Examination of the copy numbers detected and the generation of 10-fold dilutions of the extracted material indicated that a number of extraction methods retained inhibitory substances that prevented optimal amplification. Increasing the volume of sample input did improve detection. This information could be useful for the extraction of other RNA viruses from stool samples and demonstrates the need to evaluate extraction methods for different specimen types.

Benign localized fibrous tumour of the pleura: CT features with histopathological correlations

AIM

To assess the CT features of benign localized fibrous tumour of the pleura, with histopathological correlations.

MATERIALS AND METHODS

CT and histopathological findings of 18 patients with surgically resected benign localized fibrous tumour of the pleura were retrospectively assessed.

RESULTS

Tumours were pleura or fissure based, semilunar, lentiform or oval in shape, classified according to their homogeneous, slightly heterogeneous or heterogeneous enhancement pattern. Of the 18 tumours, 5 (28%) demonstrated > or = 55 HU increment or higher attenuation than muscles on contrast-enhanced CT, and histopathologically showed a haemangiopericytoma-like pattern with rich vascularity.

CONCLUSION

CT analysis of the shape of a mass and the enhancement pattern can be helpful in the diagnosis of benign localized fibrous tumour of the pleura.

Helicobacter pylori infection in pediatrics

This review summarizes the literature on Helicobacter pylori infection in childhood between April 2005 and March 2006, and includes guidelines of the Canadian Helicobacter Study Group Consensus Conference, noninvasive tests, optimum therapy regimens and problems with resistance, and reviews on immune mechanisms in the gastric mucosa that may lead to the development of an effective vaccine.

Detection of severe acute respiratory syndrome coronavirus in stool specimens by commercially available real-time reverse transcriptase PCR assays

Three commercially available real-time reverse transcriptase PCR assays (the Artus RealArt HPA coronavirus LightCycler, the Artus RealArt HPA coronavirus Rotor-Gene, and the EraGen severe acute respiratory syndrome coronavirus POL assay) and three RNA extraction methodologies were evaluated for the detection of severe acute respiratory syndrome coronavirus RNA from 91 stool specimens. The assays' sensitivities were highest (58% to 75%) for specimens obtained 8 to 21 days after symptom onset. The assays were less sensitive when specimens were obtained less than 8 days or more than 21 days after the onset of symptoms. All assays were 100% specific.

Increased DNA methylation at the AXIN1 gene in a monozygotic twin from a pair discordant for a caudal duplication anomaly

The AXIN1 gene has been implicated in caudal duplication anomalies. Its coding region was sequenced in both members of a monozygotic (MZ) twin pair discordant for a caudal duplication anomaly, but no mutation was found. Using bisulfite sequencing, we examined methylation at the promoter region of the AXIN1 gene in these twins and in twin and age-matched singleton controls. Methylation of the promoter region in peripheral blood mononucleated cells was variable among individuals, including MZ pairs. In the MZ pair discordant for the caudal duplication, this region of the affected twin was significantly more methylated than that of the unaffected twin (P < .0001), which was significantly more methylated than those of the controls (P = .02). We have confirmed that this CpG island does function as a promoter in vitro and that its activity is inversely proportional to the extent of methylation. This finding raises the possibility that hypermethylation of the AXIN1 promoter, by mechanisms as yet undetermined, is associated with the malformation. This case may be paradigmatic for some cases of MZ discordance.

Studies in NZB IL-10 knockout mice of the requirement of IL-10 for progression of B-cell lymphoma

NZB mice develop an age-related malignant expansion of a subset of B cells, B-1 cells, with autocrine production of IL-10. IL-10, a pleiotropic cytokine with anti-inflammatory properties, is a potent growth and survival factor for malignant B cells. To further examine the in vivo requirement for IL-10 in the development and expansion of malignant B-1 clones in NZB mice, we developed a strain of homozygous IL-10 knockout (KO) mice on an NZB background. The NZB IL-10 KO mice develop peritoneal B-1 cells with approximately the same frequency as heterozygous and wild-type littermates. In contrast, the development of malignant B-1 cells in the peripheral blood and spleen, observed in wild-type NZB, rarely occurred in the NZB IL-10 KO. Phenotypic analysis of surface marker expression in splenic B cells indicated that, in contrast to the NZB with malignant B-1 splenic lymphoma, the surface marker expression of NZB IL-10 KO splenic B cells indicated that the majority of the B cells were typical B-2 cells. In the absence of IL-10, spontaneously activated B cells and antiapoptotic gene expression were reduced and lymphoma incidence was decreased. These results indicate that IL-10 is a critical factor for the progression of this B-cell malignant disease.