A comparison of immunohistochemical assays and FISH in detecting the ALK translocation in diagnostic histological and cytological lung tumor material.

Introduction: Detection of the ALK rearrangement in a solid tumor gives these patients the option of crizotinib as an oral form of anticancer treatment. The current test of choice is fluorescence in situ hybridization (FISH), but various cheaper and more convenient immunohistochemical (IHC) assays have been proposed as alternatives. 
Methods: Fifteen FISH-positive cases from patients, seven with data on crizotinib therapy and clinical response, were evaluated for the presence of ALK protein using three different commercially available antibodies: D5F3, using the proprietary automated system (Ventana), ALK1 (Dako), and 5A4 (Abcam). A further 14 FISH-negative and three uncertain (<15% rearrangement detected) cases were also retrieved. Of the total 32 specimens, 17 were excisions and 15 were computed tomography-guided biopsies or cytological specimens. All three antibodies were applied to all cases. Antibodies were semiquantitatively scored on intensity, and the proportion of malignant cells stained was documented. Cutoffs were set by receiver operating curve analysis for positivity to optimize correct classification. 
Results: All three IHC assays were 100% specific but sensitivity did vary: D5F3 86%, ALK 79%, 5A4 71%. Intensity was the most discriminating measure overall, with a combination of proportion and intensity not improving the test. No FISH-negative IHC-positive cases were seen. Two FISH-positive cases were negative with all three IHC assays. One of these had been treated with crizotinib and had failed to show clinical response. The other harbored a second driving mutation in the EGFR gene.
Conclusions: IHC with all three antibodies is especially highly specific (100%) although variably sensitive (71%-86%), specifically in cases with scanty material. D5F3 assay was most sensitive in these latter cases. Occasional cases are IHC-positive but FISH-negative, suggesting either inaccuracy of one assay or occasional tumors with ALK rearrangement that do not express high levels of ALK protein.

Diagnostic Tests and their Application in the Management of Soil- and Water-borne Oomycete Pathogen Species

Oomycete diseases cause significant losses across a broad range of crop and aquaculture commodities worldwide. These losses can be greatly reduced by disease management practices steered by accurate and early diagnoses of pathogen presence. Determinations of disease potential can help guide optimal crop rotation regimes, varietal selections, targeted control measures, harvest timings and crop post-harvest handling. Pathogen detection prior to infection can also reduce the incidence of disease epidemics. Classical methods for the isolation of oomycete pathogens are normally deployed only after disease symptom appearance. These processes are often-time consuming, relying on culturing the putative pathogen(s) and the availability of expert taxonomic skills for accurate identification; a situation that frequently results in either delayed application, or routine ‘blanket’ over-application of control measures. Increasing concerns about pesticides in the environment and the food chain, removal or restriction of their usage combined with rising costs have focussed interest in the development and improvement of disease management systems. To be effective, these require timely, accurate and preferably quantitatve diagnoses. A wide range of rapid diagnostic tools, from point of care immunodiagnostic kits to next generation nucleotide sequencing have potential application in oomycete disease management. Here we review currently-available as well as promising new technologies in the context of commercial agricultural production systems, considering the impacts of specific biotic and abiotic and other important factors such as speed and ease of access to information and cost effectiveness

Monitoring Infection Risk for Air and Soil Borne Fungal Plant Pathogens using Antibody and DNA Techniques and Mathematical Models describing Environmental Parameters

Economic losses resulting from disease development can be reduced by accurate and early detection of plant pathogens. Early detection can provide the grower with useful information on optimal crop rotation patterns, varietal selections, appropriate control measures, harvest date and post harvest handling. Classical methods for the isolation of pathogens are commonly used only after disease symptoms. This frequently results in a delay in application of control measures at potentially important periods in crop production. This paper describes the application of both antibody and DNA based systems to monitor infection risk of air and soil borne fungal pathogens and the use of this information with mathematical models describing risk of disease associated with environmental parameters.

Pancreatic pseudocyst: case report and short literature review

We report a case of pancreatic pseudocyst secondary to acute necrotizing pancreatitis treated with open cystogastrostomy. Following a literature review, we stress the enormous benefits offered by modern diagnostic techniques, and especially imaging techniques, for the diagnosis and monitoring of this disease. Treatment should be delayed for at least six weeks, following which the drainage by open surgery offers the best results and lowest morbidity and mortality, followed by laparoscopy and endoscopy, indicated in particular cases and in patients where open surgery is contraindicated.

Yellow Perch Population Assessment in Southwestern Lake Michigan, Including Evaluation of Sampling Techniques and the Identification Factors that Determine Yellow Perch Year-Class Strength April 1, 1996 - March 31, 1997

F-123-R; issued June 1, 1997; two different reports were issued from the Center for Aquatic Ecology with report number 1997 (9)

Indications for and limits of conservative surgery in breast cancer

Improvements in diagnostic techniques and, above all, breast cancer screening campaigns - essential for early diagnosis - have enabled the objectives of conservative surgery to be pursued: disease control, no or low incidence of recurrences and an excellent esthetic result. However, to reach these objectives, it is essential to ensure a careful evaluation of the medical history of every patient, a detailed clinical examination and the correct interpretation of imaging. Particular attention should be paid to all factors influencing the choice of treatment and/or possible local recurrence: age, site, tumor volume, genetic predisposition, pregnancy, previous radiotherapy, pathological features, and surgical margins. The decision to undertake conservative treatment thus requires a multidisciplinary approach involving pathologists, surgeons and oncological radiologists, as well, of course, as the patient herself.

Yellow Perch population assessment in Southwestern Lake Michigan, including evaluation of sampling techniques and identification of the factors that determine Yellow Perch year-class strength April 1, 2004 - March 31, 2005

ID: 8528; Annual Report to Division of Fisheries, Illinois Department of Natural Resources; F-123-R-11

Yellow Perch Population Assessment in Southwestern Lake Michigan, Including Evaluation of Sampling Techniques and Identification of factors that Determine Yellow Perch Year-Class Strength April 1, 2005 - March 31, 2006

Annual Report, Federal Aid Project F-123-R-12, April 1, 2005 - March 31, 2006

Yellow Perch Population Assessment in Southwestern Lake Michigan, Including Evaluation of Sampling Techniques and the Identification Factors that Determine Yellow Perch Year-Class Strength April 1,1997 - March 31, 1998

ID: 8827; issued June 1, 1998

Yellow Perch Population Assessment in Southwestern Lake Michigan, Including Evaluation of Sampling Techniques and the identification Factors that Determine Yellow Perch Year-Class Strength April 1, 1998 - March 31, 1999

ID: 8863; issued June 1, 1999

Yellow Perch Population Assessment in Southwestern Lake Michigan, Including Evaluation of Sampling Techniques and Identification of the Factors that Determine Yellow Perch Year-Class Strength April 1, 2007 – March 31, 2008

Division of Fisheries, Illinois Department of Natural Resources Grant/Contract No: F-123 R-14

Yellow perch population assessment in southwestern Lake Michigan, including evaluation of sampling techniques and identification of the factors that determine yellow perch year-class strength April 1, 2006 – March 31, 2007

Division of Fisheries, Illinois Department of Natural Resources Grant/Contract No: F-123 R-13

Yellow Perch Population Assessment in Southwestern Lake Michigan, Including Evaluation of Sampling Techniques and Identification of the Factors that Determine Yellow Perch Year-Class Strength April 1, 2008 – June 30, 2009

Division of Fisheries, Illinois Department of Natural Resources Grant/Contract No: Federal Aid Project F-123 R-15

JERICO Next. Rules and procedures for TNA. D8.9

The JERICO-NEXT Trans National Access (TNA) activity is built on the successful experience of the previous FP7 JERICO project, G.A. 262584 (Sparnocchia et al., 2014, 2016). However, it will involve a greater number of observatories distributed, as before, in coastal and shelf seas all around Europe, including some dedicated to biological observation (see D7.1 for a detailed description). A limited number of supporting facilities (calibration and research laboratories) and one item of special equipment are also included in the TNA service catalogue. This document relates to WP8 - Outreach, communication and engagement, and in particular to Task 8.8: Implementing Transnational Access to coastal observatories. It describes the procedures adopted for providing TNA during the three planned Calls for proposals, one per year from May 2016 until 2018. These procedures are a review and update of those already used by JERICO. Updates of this report prior to the next Call are possible and will depend on new needs that may emerge while conducting the first Call.