Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq.

RNA sequencing technology combining short read and long read analysis can be used to detect chimeric RNAs in malignant cells. Here, we propose an integrated approach that uses k-mers to analyze indexed datasets. This approach is used to identify chimeric RNA in chronic myelomonocytic leukemia (CMML) cells, a myeloid malignancy that associates features of myelodysplastic and myeloproliferative neoplasms.

Kmerator Suite: design of specific -mer signatures and automatic metadata discovery in large RNA-seq datasets.

The huge body of publicly available RNA-sequencing (RNA-seq) libraries is a treasure of functional information allowing to quantify the expression of known or novel transcripts in tissues. However, transcript quantification commonly relies on alignment methods requiring a lot of computational resources and processing time, which does not scale easily to large datasets. -mer decomposition constitutes a new way to process RNA-seq data for the identification of transcriptional signatures, as -mers can be used to quantify accurately gene expression in a less resource-consuming way.

Joint segmentation and characterization of the dermis in 50 MHz ultrasound 2D and 3D images of the skin.

We propose a novel joint segmentation and characterization algorithm for the assessment of skin aging using 50 MHz high-frequency ultrasound images. The proposed segmentation method allows a fine determination of the envelope signal's statistics in the dermis as a function of depth. The sequence of statistical estimates obtained is then combined into a single aging score.

Sequential Emboli Detection From Ultrasound Outpatient Data.

This paper addresses the detection of emboli from signals acquired with a new miniaturized and portable transcranial Doppler ultrasound device. The use of this device enables outpatient monitoring but increases the number of artifacts. These artifacts usually come from the patient voice and motion and can be superimposed to emboli.

RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis.

RNA-Seq approach enables the detection and characterization of fusion or chimeric transcript associated to complex genome rearrangement. Until now, these events are classically identified at DNA level.Here we describe a complete procedure including a novel way of analyzing reads that combines genomic locations and local coverage to directly infer chimeric junctions with a high sensitivity and specificity, allowing identification of different classes of chimeric RNA events.

Segmentation of Skin Tumors in High-Frequency 3-D Ultrasound Images.

High-frequency 3-D ultrasound imaging is an informative tool for diagnosis, surgery planning and skin lesion examination. The purpose of this article was to describe a semi-automated segmentation tool providing easy access to the extent, shape and volume of a lesion. We propose an adaptive log-likelihood level-set segmentation procedure using non-parametric estimates of the intensity distribution.

Unusual growth rate during cystic echinococcosis.

Cystic echinococcosis is a world wild zoonosis caused by Echinococcus granulosus, leading to hepatic and lung cysts with a usually slight growth rate. We report the case of an 82year-old Algerian woman with hepatic and lung cystic echinococcosis with a 10-fold size increase in 6months.

Mutation of TP53 and alteration of p14(arf) expression in EGFR- and KRAS-mutated lung adenocarcinomas.

Background: In lung adenocarcinoma, inactivation of the tumor suppressor p53 may abrogate a safeguard mechanism preventing the development of tumors with activating mutations in EGFR or KRAS. To assess this hypothesis, we analyzed TP53 mutations and downregulation of p14(arf), a negative regulator of p53 activated by oncogenic signals, in a retrospective series of 96 patients with primary adenocarcinoma of the lung.

Patients And Methods: Mutations in TP53 (exons 4-9), KRAS (exon 1), and EGFR (exons 18-21) were identified by direct sequencing of DNA from formalin-fixed, paraffin-embedded resected tumors.

Completion pneumonectomy in patients with cancer: postoperative survival and mortality factors.

Objective: To describe postoperative complications and long-term outcomes of completion pneumonectomy and highlight prognostic factors.

Method: We retrospectively reviewed the records of 46 patients (38 men, 8 women) who underwent completion pneumonectomy for lung cancer between 1995 and 2009 in one of two thoracic surgery departments. Most were current or former smokers (n = 41; 89%) and did not undergo chemotherapy (n = 38; 83%) or radiotherapy (83%) before surgery.

Bronchial mucous gland adenoma revealed following acute pneumonia.

A 54-year old male, current smoker, was admitted to the emergency unit with lingular pneumonia. The follow-up chest CT and bronchoscopy showed an airway-blocking intrabronchial tumour. After surgical resection, pathological examination established the diagnosis of a bronchial mucous gland adenoma.

Dendritic cells infiltrating human non-small cell lung cancer are blocked at immature stage.

The efficacy of immune response to control human cancer remains controversial. It is particularly debated whether and to what extent the capacity of tumor-infiltrating dendritic cells (DC) to drive immunization can be turned off by transformed cells, leading to tumor-specific tolerance rather than immunization. To address this issue, we have characterized the DC isolated from human non-small cell lung cancer (NSCLC).

Preoperative chemotherapy does not increase complications after nonsmall cell lung cancer resection.

Background: Neoadjuvant chemotherapy before resection of nonsmall cell lung cancer seems to increase survival, mainly in the early stage. Risks of postoperative complications after chemotherapy and surgery remain controversial. Here we review our experience with patients treated in one thoracic surgery center.