Experimental design, analysis of variance and slide quality assessment in gene expression arrays

A microarray experiment is a sequence of complicated molecular biology procedures relying on various laboratory tools, instrumentation and experimenter's skills. This paper discusses statistical models for distinguishing small changes in gene expression from the noise in the system. It describes methods for assigning statistical confidence to gene expression values derived from a single array slide. Some of the theory is discussed in the context of practical applications via software usage.     

Phase I and pharmacologic study of OSI-774, an epidermal growth factor receptor tyrosine kinase inhibitor, in patients with advanced solid malignancies.

PURPOSE: To assess the feasibility of administering OSI-774, to recommend a dose on a protracted, continuous daily schedule, to characterize its pharmacokinetic behavior, and to acquire preliminary evidence of anticancer activity. PATIENTS AND METHODS: Patients with advanced solid malignancies were treated with escalating doses of OSI-774 in three study parts (A to C) to evaluate progressively longer treatment intervals. Part A patients received OSI-774 25 to 100 mg once daily, for 3 days each week, for 3 weeks every 4 weeks. Part B patients received OSI-774 doses ranging from 50 to 200 mg given once daily for 3 weeks every 4 weeks to establish the maximum tolerated dose (MTD). In part C, patients received this MTD on a continuous, uninterrupted schedule. The pharmacokinetics of OSI-774 and its O-demethylated metabolite, OSI-420, were characterized. RESULTS: Forty patients received a total of 123 28-day courses of OSI-774. No severe toxicities precluded dose escalation of OSI-774 from 25 to 100 mg/d in part A. In part B, the incidence of severe diarrhea and/or cutaneous toxicity was unacceptably high at OSI-774 doses exceeding 150 mg/d. Uninterrupted, daily administration of OSI-774 150 mg/d represented the MTD on a protracted daily schedule. The pharmacokinetics of OSI-774 were dose independent; repetitive daily treatment did not result in drug accumulation (at 150 mg/d [average]: minimum steady-state plasma concentration, 1.20 +/- 0.62 microg/mL; clearance rate, 6.33 +/- 6.41 L/h; elimination half-life, 24.4 +/- 14.6 hours; volume of distribution, 136. 4 +/- 93.1 L; area under the plasma concentration-time curve for OSI-420 relative to OSI-774, 0.12 +/- 0.12 microg/h/mL). CONCLUSION: The recommended dose for disease-directed studies of OSI-774 administered orally on a daily, continuous, uninterrupted schedule is 150 mg/d. OSI-774 was well tolerated, and several patients with epidermoid malignancies demonstrated either antitumor activity or relatively long periods of stable disease. The precise contribution of OSI-774 to these effects is not known.     

1-(11)C]Acetate as a quantitative perfusion tracer in myocardial PET.

Our objective was to investigate the properties of [1-(11)C]acetate as a quantitative perfusion tracer for myocardial PET studies. METHODS: We determined the flow dependence of the effective acetate extraction by a comparison with [(13)N]ammonia in 24 patients at rest (n = 8) and under pharmacologic vasodilation (n = 16). Furthermore, we compared the statistical quality of the perfusion values derived with both tracers. Quantification was based on an irreversible 2-compartment model for [(13)N]ammonia and a reversible 1-compartment model for [1-(11)C]acetate. Area-conserving polar maps were used to determine the correlation between the unidirectional uptake parameters of both tracers on a pixel-by-pixel basis for the whole left ventricular myocardium. RESULTS: A fit of a generalized Renkin-Crone formula to the data yielded the unidirectional acetate extraction fraction E(f) = 1 - 0.64e(-1.20/f). An extraction correction based on this formula led to good quantitative agreement of perfusion values derived with [(13)N]ammonia and [1-(11)C]acetate over the whole observed flow range (average difference of flow values, 3%; correlation coefficient, 0.96). This agreement proved the applicability of acetate as a quantitative perfusion tracer even under stress conditions. An analysis of the statistical properties of the parameter estimates showed, moreover, that statistical errors were reduced by a factor of nearly 2 in comparison with ammonia. CONCLUSION: [1-(11)C]acetate allows accurate quantification of myocardial perfusion with PET at rest as well as under stress conditions. The use of acetate leads to distinctly improved statistical accuracy for the perfusion estimates in comparison with ammonia. This accuracy facilitates the generation of reliable parametric polar maps, which are especially useful for clinical application of myocardial perfusion quantification.     

Fluorine-18 radiolabeling of low-density lipoproteins: a potential approach for characterization and differentiation of metabolism of native and oxidized low-density lipoproteins in vivo

Oxidative modification of low-density lipoprotein (LDL) is regarded as a crucial event in atherogenesis. Assessing the metabolic fate of oxidized LDL (oxLDL) in vivo with radiotracer techniques is hindered by the lack of suitable sensitive and specific radiolabeling methods. We evaluated an improved methodology based on the radiolabeling of native LDL (nLDL) and oxLDL with the positron emitter fluorine-18 (¹⁸F) by conjugation with N-succinimidyl-4-[¹⁸F]fluorobenzoate ([¹⁸F]SFB). We investigated whether radiolabeling of LDL induces adverse structural modifications. Results suggest that radiolabeling of both nLDL and oxLDL using [¹⁸F]SFB causes neither additional oxidative structural modifications of LDL lipids and proteins nor alteration of their biological activity and functionality, respectively. Thus, radiolabeling of LDL using [¹⁸F]SFB could prove to be a promising approach for studying the kinetics of oxLDL in vivo.     

MRI Characteristics of Ependymoblastoma: Results from 22 Centrally Reviewed Cases

BACKGROUND AND PURPOSE:Ependymoblastoma is a malignant embryonal tumor that develops in early childhood and has a dismal prognosis. Categorized by the World Health Organization as a subgroup of CNS-primitive neuroectodermal tumor, ependymoblastoma is histologically defined by “ependymoblastic rosettes.” Because it is so rare, little is known about specific MR imaging characteristics of ependymoblastoma. We systematically analyzed and discussed MR imaging features of ependymoblastoma in a series of 22 consecutive patients.MATERIALS AND METHODS:Ependymoblastoma cases were obtained from the database of the German multicenter HIT trials between 2002 and 2013. All cases within this study were centrally reviewed for histopathology, MR imaging findings, and multimodal therapy. For systematic analysis of initial MR imaging scans at diagnosis, we applied standardized criteria for reference image evaluation of pediatric brain tumors.RESULTS:Ependymoblastomas are large tumors with well-defined tumor margins, iso- to hyperintense signal on T2WI, and diffusion restriction. Contrast enhancement is variable, with a tendency to mild or moderate enhancement. Subarachnoid spread is common in ependymoblastoma but can be absent initially. There was a male preponderance (1.75:1 ratio) for ependymoblastoma in our cohort. Mean age at diagnosis was 2.1 years.CONCLUSIONS:With this study, we add the largest case collection to the limited published database of MR imaging findings in ependymoblastoma, together with epidemiologic data. However, future studies are needed to systematically compare MR imaging findings of ependymoblastoma with other CNS-primitive neuroectodermal tumors and ependymoma, to delineate imaging criteria that might help distinguish these pediatric brain tumor entities.

According to the 2007 World Health Organization Classification of Tumors of the CNS, ependymoblastoma (EBL) is a grade IV embryonal tumor that can be categorized as a subgroup of primitive neuroectodermal tumor (PNET).¹ The group of CNS-PNET can be further subdivided into CNS-neuroblastoma, CNS-ganglioneuroblastoma, NOS (not otherwise specified), and medulloepithelioma. EBLs are highly aggressive tumors that occur mainly in young children, with rapid growth and craniospinal dissemination. The MR imaging appearance of EBL has been described in the literature as a large, well-demarcated but heterogeneous mass with variable contrast enhancement.² Most of the tumors are located supratentorially, followed by infratentorial and spinal sites.³ Locations outside the CNS are exceptionally rare, with published cases of congenital sacrococcygeal or ovarian tumors.^4,5First described by Bailey and Cushing^6,7 in 1926 as an ependymal-derived entity, the exact definition of EBL has since generated some controversy among neuropathologists. Rubinstein⁸ later characterized EBLs as primitive neuroepithalial tumors of high cellularity that show numerous and characteristic “ependymoblastic rosettes.”We want to contribute to this ongoing discussion with the first systematic analysis of imaging characteristics of EBL. Differentiation from other primitive embryonal tumors (such as other CNS-PNET variants and medulloblastoma) by means of diagnostic imaging is challenging. Due to the rarity of this tumor, a systematic analysis of MR imaging features of EBL has not yet been performed. To determine specific diagnostic features, we report on imaging characteristics of 22 consecutive EBL cases that were collected from the prospective German Society of Pediatric Oncology and Hematology multicenter trials HIT91, HIT-SKK92, and HIT2000 (HIT is a German abbreviation for brain tumor), with central review for neuropathology, neuroradiology, and therapy.^3,9,10     

Solitary fibrous tumor of the vulva: a case report

Solitary fibrous tumors of the genital tract female are extremely rare. We reported a case of solitary fibrous tumor originating in the vulva of a 37-year-old woman. The histological analysis revealed a conjunctiva tumourous proliferation, with variable cellularity, the morphology feature and the immunohistochemistry profile of which entailed us to infer on a solitary fibrous tumor. No recurrence was observed 16 months after surgery with flap reconstruction. Because of their possible pejorative evolution, it is very important to know these tumors. A long term follow-up must be advised.     

Hurt eczematiforme column (chronicle) of the breast after implementation of a surgical clip

We report a case of atopic dermatitis in relation with a surgical titanium clip. Such a complication has only been reported once in the literature. We advocate to ask the patients about query atopic manifestations especially contact dermatitis to metal before any procedure involving metallic implants.