Towards the in silico identification of class II restricted T-cell epitopes:a partial least squares iterative self-consistent algorithm for affinity prediction

Motivation: The immunogenicity of peptides depends on their ability to bind to MHC molecules. MHC binding affinity prediction methods can save significant amounts of experimental work. The class II MHC binding site is open at both ends, making epitope prediction difficult because of the multiple binding ability of long peptides. Results: An iterative self-consistent partial least squares (PLS)-based additive method was applied to a set of 66 pep- tides no longer than 16 amino acids, binding to DRB1*0401. A regression equation containing the quantitative contributions of the amino acids at each of the nine positions was generated. Its predictability was tested using two external test sets which gave r pred =0.593 and r pred=0.655, respectively. Furthermore, it was benchmarked using 25 known T-cell epitopes restricted by DRB1*0401 and we compared our results with four other online predictive methods. The additive method showed the best result finding 24 of the 25 T-cell epitopes. Availability: Peptides used in the study are available from http://www.jenner.ac.uk/JenPep. The PLS method is available commercially in the SYBYL molecular modelling software package. The final model for affinity prediction of peptides binding to DRB1*0401 molecule is available at http://www.jenner.ac.uk/MHCPred. Models developed for DRB1*0101 and DRB1*0701 also are available in MHC- Pred

Oxidiative lipidomics coming of age:advances in analysis of oxidized phospholipids in physiology and pathology

Significance: Oxidized phospholipids are now well-recognized as markers of biological oxidative stress and bioactive molecules with both pro-inflammatory and anti-inflammatory effects. While analytical methods continue to be developed for studies of generic lipid oxidation, mass spectrometry (MS) has underpinned the advances in knowledge of specific oxidized phospholipids by allowing their identification and characterization, and is responsible for the expansion of oxidative lipidomics. Recent Advances: Studies of oxidized phospholipids in biological samples, both from animal models and clinical samples, have been facilitated by the recent improvements in MS, especially targeted routines that depend on the fragmentation pattern of the parent molecular ion and improved resolution and mass accuracy. MS can be used to identify selectively individual compounds or groups of compounds with common features, which greatly improves the sensitivity and specificity of detection. Application of these methods have enabled important advances in understanding the mechanisms of inflammatory diseases such as atherosclerosis, steatohepatitis, leprosy and cystic fibrosis, and offer potential for developing biomarkers of molecular aspects of the diseases. Critical Issues and Future Directions: The future in this field will depend on development of improved MS technologies, such as ion mobility, novel enrichment methods and databases and software for data analysis, owing to the very large amount of data generated in these experiments. Imaging of oxidized phospholipids in tissue MS is an additional exciting direction emerging that can be expected to advance understanding of physiology and disease.

Researching Framework for Simulating/Implementating P Systems

Researching simulation/implementation of membranes systems is very recent. Present literature gathers new publications frequently about software/hardware, data structures and algorithms for implementing P system evolution. In this context, this work presents a framework which goal is to make tasks of researchers of this field easier. Hence, it establishes the set of cooperating classes that form a reusable and flexible design for the customizable evaluation with new data structures and algorithms. Moreover, it includes customizable services for correcting, monitoring and logging the evolution and edition, recovering, automatic generating, persistence and visualizing P systems.

The Latest Prague Contributions to Written Cultural Heritage Processing

* The following text has been originally published in the Proceedings of the Language Recourses and Evaluation Conference held in Lisbon, Portugal, 2004, under the title of "Towards Intelligent Written Cultural Heritage Processing - Lexical processing". I present here a revised contribution of the aforementioned paper and I add here the latest efforts done in the Center for Computational Linguistic in Prague in the field under discussion.

An Adaptive Quadrilateral Mesh in Curved Domains

An nonlinear elliptic system for generating adaptive quadrilateral meshes in curved domains is presented. The presented technique has been implemented in the C++ language with the help of the standard template library. The software package writes the converged meshes in the GMV and the Matlab formats. Grid generation is the first very important step for numerically solving partial differential equations. Thus, the presented C++ grid generator is extremely important to the computational science community.

Linking design and manufacturing domains via web-based and enterprise integration technologies

The manufacturing industry faces many challenges such as reducing time-to-market and cutting costs. In order to meet these increasing demands, effective methods are need to support the early product development stages by bridging the gap of communicating early design ideas and the evaluation of manufacturing performance. This paper introduces methods of linking design and manufacturing domains using disparate technologies. The combined technologies include knowledge management supporting for product lifecycle management systems, Enterprise Resource Planning (ERP) systems, aggregate process planning systems, workflow management and data exchange formats. A case study has been used to demonstrate the use of these technologies, illustrated by adding manufacturing knowledge to generate alternative early process plan which are in turn used by an ERP system to obtain and optimise a rough-cut capacity plan. Copyright © 2010 Inderscience Enterprises Ltd.

Risk Factors of Central Venous Catheter Related Infections in Intensive Care Patients

2002 Mathematics Subject Classification: 62P10.

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences

Motivation: In any macromolecular polyprotic system - for example protein, DNA or RNA - the isoelectric point - commonly referred to as the pI - can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge - and thus the electrophoretic mobility - of the ampholyte sums to zero. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Peptide fractionation according to their pI is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Therefore accurate theoretical prediction of pI would expedite such analysis. While such pI calculation is widely used, it remains largely untested, motivating our efforts to benchmark pI prediction methods. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of pI calculation methods. We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. The machine-learning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. In general, learning-based pI prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction. Contact: yperez@ebi.ac.uk Availability and Implementation: The software and data are freely available at https://github.com/ypriverol/pIR. Supplementary information: Supplementary data are available at Bioinformatics online.

Design Optimization of Submerged Jet Nozzles for Enhanced Mixing

The purpose of this thesis was to identify the optimal design parameters for a jet nozzle which obtains a local maximum shear stress while maximizing the average shear stress on the floor of a fluid filled system. This research examined how geometric parameters of a jet nozzle, such as the nozzle's angle, height, and orifice, influence the shear stress created on the bottom surface of a tank. Simulations were run using a Computational Fluid Dynamics (CFD) software package to determine shear stress values for a parameterized geometric domain including the jet nozzle. A response surface was created based on the shear stress values obtained from 112 simulated designs. A multi-objective optimization software utilized the response surface to generate designs with the best combination of parameters to achieve maximum shear stress and maximum average shear stress. The optimal configuration of parameters achieved larger shear stress values over a commercially available design.

Evaluating and Selecting a Property Management System

In his study - Evaluating and Selecting a Property Management System - by Galen Collins, Assistant Professor, School of Hotel and Restaurant Management, Northern Arizona University, Assistant Professor Collins states briefly at the outset: “Computerizing a property requires a game plan. Many have selected a Property Management System without much forethought and have been unhappy with the final results. The author discusses the major factors that must be taken into consideration in the selection of a PMS, based on his personal experience.” Although, this article was written in the year 1988 and some information contained may be dated, there are many salient points to consider. “Technological advances have encouraged many hospitality operators to rethink how information should be processed, stored, retrieved, and analyzed,” offers Collins. “Research has led to the implementation of various cost-effective applications addressing almost every phase of operations,” he says in introducing the computer technology germane to many PMS functions. Professor Collins talks about the Request for Proposal, its conditions and its relevance in negotiating a PMS system. The author also wants the system buyer to be aware [not necessarily beware] of vendor recommendations, and not to rely solely on them. Exercising forethought will help in avoiding the drawback of purchasing an inadequate PMS system. Remember, the vendor is there first and foremost to sell you a system. This doesn’t necessarily mean that the adjectives unreliable and unethical are on the table, but do be advised. Professor Collins presents a graphic outline for the Weighted Average Approach to Scoring Vendor Evaluations. Among the elements to be considered in evaluating a PMS system, and there are several analyzed in this essay, Professor Collins advises that a perspective buyer not overlook the service factor when choosing a PMS system. Service is an important element to contemplate. “In a hotel environment, the special emphasis should be on service. System downtime can be costly and aggravating and will happen periodically,” Collins warns. Professor Collins also examines the topic of PMS system environment; of which the importance of such a factor should not be underestimated. “The design of the computer system should be based on the physical layout of the property and the projected workloads. The heart of the system, housed in a protected, isolated area, can support work stations strategically located throughout the property,” Professor Collins provides. A Property Profile Description is outlined in Table 1. The author would also point out that ease-of-operation is another significant factor to think about. “A user-friendly software package allows the user to easily move through the program without encountering frustrating obstacles,” says Collins. “Programs that require users to memorize abstract abbreviations, codes, and information to carry out standard routines should be avoided,” he counsels.

Optimization of three-dimensional branching networks of microchannels for thermal management of microelectronics

The aim of this work is to present a methodology to develop cost-effective thermal management solutions for microelectronic devices, capable of removing maximum amount of heat and delivering maximally uniform temperature distributions. The topological and geometrical characteristics of multiple-story three-dimensional branching networks of microchannels were developed using multi-objective optimization. A conjugate heat transfer analysis software package and an automatic 3D microchannel network generator were developed and coupled with a modified version of a particle-swarm optimization algorithm with a goal of creating a design tool for 3D networks of optimized coolant flow passages. Numerical algorithms in the conjugate heat transfer solution package include a quasi-ID thermo-fluid solver and a steady heat diffusion solver, which were validated against results from high-fidelity Navier-Stokes equations solver and analytical solutions for basic fluid dynamics test cases. Pareto-optimal solutions demonstrate that thermal loads of up to 500 W/cm2 can be managed with 3D microchannel networks, with pumping power requirements up to 50% lower with respect to currently used high-performance cooling technologies.

Computational fluid dynamics (CFD) based approach to consequence assessment of accidental release of hydrocarbon during storage and transportation

This thesis investigated the risk of accidental release of hydrocarbons during transportation and storage. Transportation of hydrocarbons from an offshore platform to processing units through subsea pipelines involves risk of release due to pipeline leakage resulting from corrosion, plastic deformation caused by seabed shakedown or damaged by contact with drifting iceberg. The environmental impacts of hydrocarbon dispersion can be severe. Overall safety and economic concerns of pipeline leakage at subsea environment are immense. A large leak can be detected by employing conventional technology such as, radar, intelligent pigging or chemical tracer but in a remote location like subsea or arctic, a small chronic leak may be undetected for a period of time. In case of storage, an accidental release of hydrocarbon from the storage tank could lead pool fire; further it could escalate to domino effects. This chain of accidents may lead to extremely severe consequences. Analyzing past accident scenarios it is observed that more than half of the industrial domino accidents involved fire as a primary event, and some other factors for instance, wind speed and direction, fuel type and engulfment of the compound. In this thesis, a computational fluid dynamics (CFD) approach is taken to model the subsea pipeline leak and the pool fire from a storage tank. A commercial software package ANSYS FLUENT Workbench 15 is used to model the subsea pipeline leakage. The CFD simulation results of four different types of fluids showed that the static pressure and pressure gradient along the axial length of the pipeline have a sharp signature variation near the leak orifice at steady state condition. Transient simulation is performed to obtain the acoustic signature of the pipe near leak orifice. The power spectral density (PSD) of acoustic signal is strong near the leak orifice and it dissipates as the distance and orientation from the leak orifice increase. The high-pressure fluid flow generates more noise than the low-pressure fluid flow. In order to model the pool fire from the storage tank, ANSYS CFX Workbench 14 is used. The CFD results show that the wind speed has significant contribution on the behavior of pool fire and its domino effects. The radiation contours are also obtained from CFD post processing, which can be applied for risk analysis. The outcome of this study will be helpful for better understanding of the domino effects of pool fire in complex geometrical settings of process industries. The attempt to reduce and prevent risks is discussed based on the results obtained from the numerical simulations of the numerical models.

Physical oceanography during SONNE cruise SO248 (BacGeoPac)

The data presented here were collected during the cruise SO248 (Project BacGeoPac) with the RV Sonne from Auckland, New Zealand to Dutch Harbor, Alaska/USA. The cruise lasted from May 1, 2016 to June 3, 2016 and 19 vertical CTD-hauls were conducted. The CTD system used during this cruise was a Sea-Bird Electronics Inc. SBE 911plus probe (SN 09-1266). The CTD was attached to a SBE 32 Carousel Water Sampler (SN 32-1119) containing 24 20-liter Ocean Test Equipment Inc. bottles. The system was equipped with double temperature (SBE 3) and conductivity sensors (SBE 4), a pressure sensor (Digiquartz) an oxygen (Aanderaa Optode 4831F) and, an altimeter (Bentos) and a chlorophyll fluorometer combined with a turbidity sensor (FluoroWetlabECO _AFL FL). The sensors were pre-calibrated by the manufacturers. The data were recorded with the Seasave V 7.23.2 software and processed using the SeaBird SBE Data Processing and the ManageCTD-software. The data were processed in the following way: Data obtained during adaptation of the CTD to ambient water conditions were removed manually. The "wildedit", "loopedit", "despike", "binavg" routines were applied. The data were also visually checked and a double sensor check was conducted. The accuracy of the double sensors derived from 56 data sets were: Temperature T = 0.0007 °C; Conductivity: C = 0,0071 mS/cm; Salinity S = 0.0081 psu. The salinity data (S by unsing pss78) were converted to absolute Salinity (SA) by using the TEOS 10 toolbox. The ship position data were derived from the shipboard GPS-system linked to the CTD data. The time zone is given in UTC. The oxygen CTD data were validated by additional measurements of 98 water samples using the Winkler titration method.

Variability of marine climate on the North Icelandic Shelf in a 1357-year proxy archive based on growth increments in the bivalve Arctica islandica

A multicentennial and absolutely-dated shell-based chronology for the marine environment of the North Icelandic Shelf has been constructed using annual growth increments in the shell of the long-lived bivalve clam Arctica islandica. The region from which the shells were collected is close to the North Atlantic Polar Front and is highly sensitive to the varying influences of Atlantic and Arctic water masses. A strong common environmental signal is apparent in the increment widths, and although the correlations between the growth increment indices and regional sea surface temperatures are significant at the 95% confidence level, they are low (r ~ 0.2), indicating that a more complex combination of environmental forcings is driving growth. Remarkable longevities of individual animals are apparent in the increment-width series used in the chronology, with several animals having lifetimes in excess of 300 years and one, at 507 years, being the longest-lived non-colonial animal so far reported whose age at death can be accurately determined. The sample depth is at least three shells after AD 1175, and the time series has been extended back to AD 649 with a sample depth of one or two by the addition of two further series, thus providing a 1357-year archive of dated shell material. The statistical and spectral characteristics of the chronology are investigated by using two different methods of removing the age-related trend in shell growth. Comparison with other proxy archives from the same region reveals several similarities in variability on multidecadal timescales, particularly during the period surrounding the transition from the Medieval Climate Anomaly to the Little Ice Age.

Finite element modeling of straightening of thin-walled seamless tubes of austenitic stainless steel

During this thesis work a coupled thermo-mechanical finite element model (FEM) was builtto simulate hot rolling in the blooming mill at Sandvik Materials Technology (SMT) inSandviken. The blooming mill is the first in a long line of processes that continuously or ingotcast ingots are subjected to before becoming finished products. The aim of this thesis work was twofold. The first was to create a parameterized finiteelement (FE) model of the blooming mill. The commercial FE software package MSCMarc/Mentat was used to create this model and the programing language Python was used toparameterize it. Second, two different pass schedules (A and B) were studied and comparedusing the model. The two pass series were evaluated with focus on their ability to healcentreline porosity, i.e. to close voids in the centre of the ingot. This evaluation was made by studying the hydrostatic stress (σm), the von Mises stress (σeq)and the plastic strain (εp) in the centre of the ingot. From these parameters the stress triaxiality(Tx) and the hydrostatic integration parameter (Gm) were calculated for each pass in bothseries using two different transportation times (30 and 150 s) from the furnace. The relationbetween Gm and an analytical parameter (Δ) was also studied. This parameter is the ratiobetween the mean height of the ingot and the contact length between the rolls and the ingot,which is useful as a rule of thumb to determine the homogeneity or penetration of strain for aspecific pass. The pass series designed with fewer passes (B), many with greater reduction, was shown toachieve better void closure theoretically. It was also shown that a temperature gradient, whichis the result of a longer holding time between the furnace and the blooming mill leads toimproved void closure.