24 research outputs found
Empirical Bayes models for multiple probe type microarrays at the probe level
<p>Abstract</p> <p>Background</p> <p>When analyzing microarray data a primary objective is often to find differentially expressed genes. With empirical Bayes and penalized t-tests the sample variances are adjusted towards a global estimate, producing more stable results compared to ordinary t-tests. However, for Affymetrix type data a clear dependency between variability and intensity-level generally exists, even for logged intensities, most clearly for data at the probe level but also for probe-set summarizes such as the MAS5 expression index. As a consequence, adjustment towards a global estimate results in an intensity-level dependent false positive rate.</p> <p>Results</p> <p>We propose two new methods for finding differentially expressed genes, Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW). Both methods use an empirical Bayes model taking the dependency between variability and intensity-level into account. A global covariance matrix is also used allowing for differing variances between arrays as well as array-to-array correlations. PLW is specially designed for Affymetrix type arrays (or other multiple-probe arrays). Instead of making inference on probe-set summaries, comparisons are made separately for each perfect-match probe and are then summarized into one score for the probe-set.</p> <p>Conclusion</p> <p>The proposed methods are compared to 14 existing methods using five spike-in data sets. For RMA and GCRMA processed data, PLW has the most accurate ranking of regulated genes in four out of the five data sets, and LMW consistently performs better than all examined moderated t-tests when used on RMA, GCRMA, and MAS5 expression indexes.</p
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Quantification of holmium:YAG and thulium:YAG laser-induced scleral Shrinkage for buckling procedures
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The importance of genetic testing as demonstrated by two cases of CACNA1F-associated retinal generation misdiagnosed as LCA
Purpose To describe in detail cases with an initial diagnosis of Leber congenital amaurosis that were later found to have a hemizygous mutation in the CACNA1F gene. Methods: The patients underwent a detailed ophthalmological evaluation and full-field electroretinography (ERG). Selective targeted capture and whole-exome next-generation sequencing (NGS) were used to find the disease-causing mutations. Results: Patient 1 presented at age 3 months with nystagmus, normal visual attention, and a normal fundus exam. ERG responses were severely decreased. Patient 2 presented with nystagmus, severe hyperopia, esotropia, and visual acuity of 20/360 oculus dexter (OD) and 20/270 oculus sinister (OS) at age 5 months. His fundus exam showed slightly increased pigmentation around the foveae. The scotopic ERG responses were severely decreased and photopic responses mildly decreased. Based on the initial presentation, both patients received the clinical diagnosis of Leber congenital amaurosis (LCA). However, genetic testing showed no mutations in known LCA genes. Instead, broader genetic testing using NGS showed point mutations in the CACNA1F gene, which is reported to be associated with type 2 congenital stationary night blindness (CSNB2). Conclusions: These two cases demonstrate the clinical overlap between LCA and CSNB in infants and young children. Genetic testing is an essential tool in these cases and provides a more accurate diagnosis and prognosis for patients with inherited retinal degenerative disorders
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Interstitial Laser Hyperthermia Model Development for Minimally Invasive Therapy of Breast Carcinoma
Background: This investigation describes the preclinical development of a laser fiberoptic interstitial delivery system for the thermal destruction of small breast cancers. We propose adaptation of this technology to stereotactic mammographic instrumentation currently employed for diagnostic core biopsy to thermally ablate a site of disease with maximal treatment efficacy, minimal observable surficial change, reduced patient trauma, and lowered overall treatment costs.
Study Design: Laser hyperthermia is a clinical modality that seeks to achieve tumor destruction through controlled tissue heating. The advantage of laser-induced hyperthermia over traditionally used heat sources such as ultrasound, microwave, or radiowave radiation lies in the ability to focus heat localization to the specific tumor tissue site. Neodymium:yttrium aluminum garnet (Nd:YAG) laser light transmitted through a fiberoptic cable to a diffusing quartz tip can induce such temperature increases leading to localized tissue destruction. Because breast cancer occurs with greatest frequency in the mature woman whose breast tissue has undergone glandular involution with fatty replacement, this study concentrates on determining the resultant laser energy heat distribution within fat and fibrofatty tissue. This investigation studied the time-temperature responses of ex vivo human breast and porcine fibrofatty tissue, which led to an in vivo subcutaneous porcine model for the practical demonstration of a laser hyperthermia treatment of small volumes of porcine mammary chain tissue.
Results: Spatial recordings of the resultant temperature fields through time exhibited similar, reproducible thermal profiles in both ex vivo human breast and subcutaneous porcine fat. In vivo laser-produced temperature fields in porcine subcutaneous fat were comparable to those in the ex vivo analyses, and showed a histologically, sharply defined, and controllable volume of necrosis with no injury to adjacent tissues or to overlying skin.
Conclusions: Interstitially placed, fiberoptically delivered Nd:YAG laser energy is capable of controlled tissue denaturation to a defined volume for the treatment of small breast cancers. It is hoped that this minimally invasive approach, with further investigation and refinement, may lead to the effective treatment of small, well-defined breast cancers that are commonly diagnosed through stereographic mammography and stereotactic core biopsy. The juxtaposition of such a localized treatment modality with these increasingly used diagnostic tools is of considerable promise
Update of laser hyperthermic treatment for primary breast cancer: ex-vivo and in-vivo models
The treatment of primary breast cancer in the last half century has progressively decreased in its disfiguring consequences while maintaining the same level of cure. Extending this philosophy beyond lumpectomy, we propose to treat small primary breast cancers by laser interstitial therapy with minimal possible cosmetic distortion. Our program to achieve that goal has made considerable progress in the preclinical instrument modification and development of physical, tissue, and live animal models. In anticipation of a clinical trial this report updates information presented in 1996