Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization.

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments are widely used to determine, within entire genomes, the occupancy sites of any protein of interest, including, for example, transcription factors, RNA polymerases, or histones with or without various modifications. In addition to allowing the determination of occupancy sites within one cell type and under one condition, this method allows, in principle, the establishment and comparison of occupancy maps in various cell types, tissues, and conditions. Such comparisons require, however, that samples be normalized. Widely used normalization methods that include a quantile normalization step perform well when factor occupancy varies at a subset of sites, but may miss uniform genome-wide increases or decreases in site occupancy. We describe a spike adjustment procedure (SAP) that, unlike commonly used normalization methods intervening at the analysis stage, entails an experimental step prior to immunoprecipitation. A constant, low amount from a single batch of chromatin of a foreign genome is added to the experimental chromatin. This "spike" chromatin then serves as an internal control to which the experimental signals can be adjusted. We show that the method improves similarity between replicates and reveals biological differences including global and largely uniform changes.

Iowa Airport Directory, 2003 ***NOTE*** This document is for historical viewing, the internal information is no longer current or accurate! ***NOTE*** Current information can be found at http://www.iowadot.gov/aviation/aircraftregistration/registration.aspx ***NOTE***

Iowa has 8 commercial service airports and 105 general aviation airports, of which three serve as reliever airports. ***NOTE*** This document is for historical viewing, the internal information is no longer current or accurate! ***NOTE*** Current information can be found at http://www.iowadot.gov/aviation/aircraftregistration/registration.aspx ***NOTE***

Giant extra-hepatic thrombosed portal vein aneurysm: a case report and review of the literature.

BACKGROUND: Extrahepatic Portal vein aneurysm (EPVA) is a rare finding that may be associated with different complications, e.g. thrombosis, rupture, portal hypertension and compression of adjacent structures. It is being diagnosed more frequently with the advent of modern cross-sectional imaging. Our review of the English literature disclosed 13 cases of thrombosed EPVA. CASE PRESENTATION: A 50-years-old woman presented with acute abdominal pain but no other symptom. She had no relevant medical history. Palpation of the right upper quadrant showed tenderness. Laboratory tests were unremarkable. A computed tomography showed portal vein aneurysm measuring 88 × 65 mm with thrombosis extending to the superior mesenteric and splenic vein. The patient was treated conservatively with anticoagulation therapy. She was released after two weeks and followed on an outpatient basis. At two months, she reported decreased abdominal pain and her physical examination was normal. A computed tomography was performed showing a decreased thrombosis size and extent, measuring 80 × 55 mm. CONCLUSIONS: Although rare, surgeons should be made aware of this entity. Complications are various. Conservative therapy should be chosen in first intent in most cases. We reported the case of the second largest thrombosed extra-hepatic PVA described in the literature, treated by anticoagulation therapy with a good clinical and radiological response.

Catheter entrapment in a pulmonary vein: a unique complication of pulmonary vein isolation.

Ablation strategies for the treatment of atrial fibrillation (AF) are associated with several potential complications. During electro-anatomic mapping of the left atrium (LA) before ablation, the ablation catheter was entrapped in the right inferior pulmonary vein (RIPV). After multiple unsuccessful gentle tractions, stronger maneuvers with rotation of the catheter slowly allowed its retrieval. Examination of the catheter showed a thin, translucent membrane covering its tip, suggesting complete stripping of a vein branch. Occlusion of the superior branch of the RIPV was confirmed by LA angiogram. During the following days, no pericardial effusion was noted, but the patient complained of light chest pain and mild hemoptysis, spontaneously resolving within 48 h. This case shows that catheter entrapment and mechanical disruption of a PV branch can be a rare potential complication of AF ablation. In this case, the outcome was spontaneously favorable and symptoms only included transient mild hemoptysis.

International registry on splanchnic vein thrombosis: description of the study population

Background: Splanchnic vein thrombosis (SVT) is an uncommon, butpotentially life-threatening disease. Aim of this ISTH based registryis to improve the knowledge on SVT by studying a large, international,unselected population.Methods: Consecutive patients with objectively diagnosed SVT areeligible for the registry. Information on clinical presentations, diagnosticapproaches, risk factors, therapeutic approaches, and recurrencesof SVT, bleedings and deaths at a 2 year follow up are enteredon a website database (www.svt.altervista.org). We planned a samplesize of 500 patients, including all sites of thrombosis.Results: As of December 31st, 2010, 429 patients with SVT (85.8%of the planned sample) have been enrolled at 25 centres from sevencountries. The mean age is 52.6 years (range 16-85 years); 62.2% aremales, 67.8% are Caucasians, and 31.2% Asians. SVT occurred inmultiple vein segments in 36.4% of patients, 40.5% of patients hadisolated portal vein thrombosis, 11.9% of patients had mesentericvein thrombosis, 7.5% had supra-hepatic vein thrombosis, and 3.6%had splenic vein thrombosis. Abdominal pain was the most commonsymptom occurring in 56.6% of the patients; 9.5% of patients hadgastrointestinal bleeding at the time of diagnosis; 25.4% of patientswith SVT were asymptomatic. Mean time between onset of symptomsand diagnosis was 7.4 days. Objective diagnosis was obtained withabdominal CT in 79.9% of patients. Most common risk factors atthe time of diagnosis included cancer (24.1%), cirrhosis (23.1%), andhematological disorders (15.4%); in 15.9% of patients SVT was idiopathic.Most patients were treated with anticoagulant drugs: 30.8%with parenteral drugs only, 56.9% with parenteral drugs followed byvitamin K antagonists.Conclusions: SVT is a major challenge for experts in thrombosis andhemostasis. Large collaborative studies are necessary to improve theunderstanding and the management of this heterogeneous disease.

Bitumens in the late Variscan hydrothermal vein-type uranium deposit of Pribram, Czech Republic: Sources, radiation-induced alteration, and relation to mineralization

The late Variscan (275-278 Ma) Pribram uranium deposit is one of the largest known accumulations of uraniferous bitumens in hydrothermal veins. The deposit extends along the northwestern boundary of the Central Bohemian pluton (345-335 Ma) with low-grade metamorphosed Late Proterozoic and unmetamorphosed Cambrian rocks. From a net uranium production of 41,742 metric tons (t), more than 6,000 t were extracted from bitumen-uraninite ores during 43 years of exploration and mining. Three morphological varieties of solid bitumen are recognized: globular, asphaltlike, and cokelike. While the globular bitumen is uranium free, the other two types are uraniferous. The amount of bitumen in ore veins gradually decreases toward the contact with the plutonic body and increases with depth. Two types of bitumen microtextures are recognized using high-resolution transmission electron microscopy: amorphous and microporous, the former being less common in uraniferous samples. A lower Raman peak area ratio (1,360/1,575 cm(-1)) in mineralized bitumens (0.9) compared with uranium-free samples (2.0) indicates a lower degree of microtextural organization in the latter The H/C and O/C atomic ratios in uranium-free bitumens (0.9-1.1 and 0.09, respectively) are higher than those in mineralized samples (H/C = 0.3-0.8, O/C = 0.03-0.09). The chloroform extractable matter yield is Very low in uranium-free bitumens (0.30-0.35% of the total organic carbon,TOC) and decreases with uranium content increase. The extracted solid uraniferous bitumen infrared spectra show depletion in aliphatic CH2 and CH3 groups compared to uranium-free samples. The concentration of oxygen-bearing functional groups relative to aromatic bonds in the IR spectra of uranium-free and mineralized bitumen, however, do not differ significantly. C-13 NMR confirmed than the aromaticity of a uraniferous sample is higher (F-ar = 0.61) than in the uranium-free bitumen (F-ar = 0.51). Pyrolysates from uraniferous and nonuraniferous bitumens do not differ significantly, being predominantly cresol, alkylphenols, alkylbenzenes, and alkylnaphthalenes. The liquid pyrolysate yield decreases significantly with increasing uranium content. The delta(13)C Values of bulk uranium-free bitumens and low-grade uraniferous, asphaltlike bitumens range from -43.6 to 52.3 per mil. High-grade, cokelike, uraniferous bitumens are more C-13 depleted (54.5 to -58.4 parts per thousand). In contrast to the very light isotopic ratios of the high-grade uraniferous cokelike bitumen bulk carbon, the individual n-alkanes and isoprenoids (pristane and phytane) extracted from the same sample are significantly C-13 enriched. The isotopic composition of the C13-24 n-alkanes extracted from the high-grade uraniferous sample (delta(13)C = -28.0 to 32.6 parts per thousand) are heavier compared with the same compounds in a uranium-free sample (delta(13)C = 31.9 to 33.8 parts per thousand). It is proposed that the bitumen source was the isotopically light (delta(13)C = 35.8 to 30.2 parts per thousand) organic matter of the Upper Proterozoic host rocks that were pyrolyzed during intrusion of the Central Bohemian pluton. The C-13- depleted pyrolysates were mobilized from the innermost part of the contact-metamorphic aureole, accumulated in structural traps in less thermally influenced parts of the sedimentary complex and were later extracted by hydrothermal fluids. Bitumens at the Pribram deposit are younger than the main part of the uranium mineralization and were formed through water-washing and radiation-induced polymerization of both the gaseous and liquid pyrolysates. Direct evidence for pyrolysate reduction of uranium in the hydrothermal system is difficult to obtain as the chemical composition of the original organic fluid phase was modified during water-washing and radiolytic alteration. However, indirect evidence-e.g., higher O/C atomic ratios in uranium-free bitumens (0.1) relative to the Upper Proterozoic source rocks (0.02-0.05), isotopically very light carbon in associated whewellite (delta(13)C = 31.7 to -28.4 parts per thousand), and the striking absence of bitumens in the pre-uranium, hematite stage of the mineralization-indicates that oxidation of organic fluids may have contributed to lowering of aO(2) and uraninite precipitation.

Internal test sets studies in a group of antimalarials

Topological indices have been applied to build QSAR models for a set of 20 antimalarial cyclic peroxy cetals. In order to evaluate the reliability of the proposed linear models leave-n-out and Internal Test Sets (ITS) approaches have been considered. The proposed procedure resulted in a robust and consensued prediction equation and here it is shown why it is superior to the employed standard cross-validation algorithms involving multilinear regression models

The effect of counterpoise correction and relaxation energy term to the internal rotation barriers: application to the BF3 ...NH3 and C2H4 ...SO2 dimers

The relevance of the fragment relaxation energy term and the effect of the basis set superposition error on the geometry of the BF3⋯NH3 and C2H4⋯SO2 van der Waals dimers have been analyzed. Second-order Møller-Plesset perturbation theory calculations with the d95(d,p) basis set have been used to calculate the counterpoise-corrected barrier height for the internal rotations. These barriers have been obtained by relocating the stationary points on the counterpoise-corrected potential energy surface of the processes involved. The fragment relaxation energy can have a large influence on both the intermolecular parameters and barrier height. The counterpoise correction has proved to be important for these systems

A gating mutation in the internal pore of ASIC1a.

Using a substituted cysteine accessibility scan, we have investigated the structures that form the internal pore of the acid-sensing ion channel 1a. We have identified the amino acid residues Ala-22, Ile-33, and Phe-34 in the amino terminus and Arg-43 in the first transmembrane helix, which when mutated into cysteine, were modified by intracellular application of MTSET, resulting in channel inhibition. The inhibition of the R43C mutant by internal MTSET requires opening of the channel. In addition, binding of Cd2+ ions to R43C slows the channel inactivation. This indicates that the first transmembrane helix undergoes conformational changes during channel inactivation. The effect of Cd2+ on R43C can be obtained with Cd2+ applied at either the extracellular or the intracellular side, indicating that R43C is located in the channel pore. The block of the A22C, I33C, and F34C mutants by MTSET suggests that these residues in the amino terminus of the channel also participate to the internal pore.

Relève en médecine interne générale: enjeux et perspectives [Perspectives and challenges to guarantee training and renewal in general internal medicine]

Training new doctors in general internal medicine represents a challenge. This requires to define future needs, which result from interest that are not necessarily convergent between patients, doctors, insurers and politicians. Problems related to medical demography in Switzerland, with the ageing of the population, the increase in health care costs and the place of Switzerland within the European Community require the implementation of specific objectives to train new physicians in general internal medicine. The success of these opportunities depends on social factors, political choices and choices from physician's association. In this article we will approach these challenges by formulating some proposals--nonexhaustive--in order to guarantee sufficient renewal in general internal medicine.

The Four Different Types of Internal Hernia Occurring After Laparascopic Roux-en-Y Gastric Bypass Performed for Morbid Obesity: Are There Any Multidetector Computed Tomography (MDCT) Features Permitting Their Distinction?

BACKGROUND: Four different types of internal hernias (IH) are known to occur after laparoscopic Roux-en-Y gastric bypass (LRYGBP) performed for morbid obesity. We evaluate multidetector row helical computed tomography (MDCT) features for their differentiation. METHODS: From a prospectively collected database including 349 patients with LRYGBP, 34 acutely symptomatic patients (28 women, mean age 32.6), operated on for IH immediately after undergoing MDCT, were selected. Surgery confirmed 4 (11.6%) patients with transmesocolic, 10 (29.4%) with Petersen's, 15 (44.2%) with mesojejunal, and 5 (14.8%) with jejunojejunal IH. In consensus, 2 radiologists analyzed 13 MDCT features to distinguish the four types of IH. Statistical significance was calculated (p < 0.05, Fisher's exact test, chi-square test). RESULTS: MDCT features of small bowel obstruction (SBO) (n = 25, 73.5%), volvulus (n = 22, 64.7%), or a cluster of small bowel loops (SBL) (n = 27, 79.4%) were inconsistently present and overlapped between the four IH. The following features allowed for IH differentiation: left upper quadrant clustered small bowel loops (p < 0.0001) and a mesocolic hernial orifice (p = 0.0003) suggested transmesocolic IH. SBL abutting onto the left abdominal wall (p = 0.0021) and left abdominal shift of the superior mesenteric vessels (SMV) (p = 0.0045) suggested Petersen's hernia. The SMV predominantly shifted towards the right anterior abdominal wall in mesojejunal hernia (p = 0.0033). Location of the hernial orifice near the distal anastomosis (p = 0.0431) and jejunojejunal suture widening (p = 0.0005) indicated jejunojejunal hernia. CONCLUSIONS: None of the four IH seems associated with a higher risk of SBO. Certain MDCT features, such as the position of clustered SBL and hernial orifice, help distinguish between the four IH and may permit straightforward surgery.