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Modelling Allelic and DNA Copy Number Variations using Continuous-index Hidden Markov Models

Popular Abstract in Swedish DNA i form av kromosomer finns i cellerna och innehåller information som styr flertalet av kroppens funktioner. Människor har vanligtvis 23 par kromosomer, där den ena kromosomen i ett par härstammar från personens mamma och den andra från dess pappa. DNA ser ut som en vriden stege där stegpinnarna består av nukleotidbaspar. I cancerceller kan det finnas bitar av kromIn human cells there are usually two copies of each chromosome, but in cancer cells abnormalities could exist. The differences consist of segments of chromosomes with an altered number of copies. There can be deletions as well as amplifications and the lengths of the segments can also vary. Localising the deviant regions is of great importance for increasing the knowledge of the disease. In this t

Determination of the isomeric fraction in a postaccelerated radioactive ion beam using the coupled decay-chain equations

A method based on the coupled decay-chain equations for extracting the isotopic and the isomeric composition of a postaccelerated radioactive ion beam is presented and demonstrated on a data set from a Coulomb excitation experiment. This is the first attempt of analyzing the content of a postaccelerated radioactive ion beam using this technique. The beam composition is required for an absolute nor

Effects of galectins and antibodies in HIV infection; Novel Assays

The high variability of the HIV envelope glycoproteins (Env), and their heavy glycan coating, contributes to the limited host immune control. Still, broadly neutralizing antibodies (bnAbs) are found in some chronically infected HIV-infected individuals, which has spurred the research on antibody-based vaccines. An important tool in detecting and studying bnAbs, are neutralization assays. Here we d

Main factors controlling microbial community structure and function after reclamation of a tailing pond with aided phytostabilization

Reclamation on bare tailing ponds has the potential to represent soil genesis in Technosols favoring the understanding of the changes of microbial communities and function. In this study we used phytostabilization aided with calcium carbonate and pig slurry/manure to reclaim an acidic bare tailing pond with the aim of investigating the effect of amending and different species on microbial communit

Mechanisms of microbial-host interaction during asymptomatic bacteriuria

Popular Abstract in Swedish Mer än hälften av alla kvinnor har haft en urinvägsinfektion. Infektionen uppkommer när bakterier når urinblåsan och börjar växa. Immunförsvaret känner igen bakterierna, reagerar med en inflammation och symptom som sveda, trängningar och smärtor i nedre magtrakten uppstår. Om bakterierna klättrar upp till njurarna sprider sig inflammationen dit och orsakar ryggsmärtor oUrinary tract infections (UTIs) present an interesting and relevant model for studying microbial adaptation. After establishing significant numbers, the bacteria either cause severe disease, or an asymptomatic carrier state resembling the normal flora at other mucosal sites. Patients with asymptomatic bacteriuria (ABU) are protected from re-infection if the strain that they carry outcompetes more

Protonation of the proximal histidine ligand in heme peroxidases.

The heme peroxidases have a histidine group as the axial ligand of iron. This ligand forms a hydrogen bond to an aspartate carboxylate group by the other nitrogen atom in the side chain. The aspartate is not present in the globins and it has been suggested that it gives an imidazolate character to the histidine ligand. Quantum chemical calculations have indicated that the properties of the heme si

All wurtzite (In,Ga)As-(Ga,Mn)As core-shell nanowires

Structural and magnetic properties of (In,Ga)As-(Ga,Mn)As core−shell nanowires grown by molecular beam epitaxy on GaAs(111)B substrate with gold catalyst have been investigated. (In,Ga)As core nanowires were grown at high temperature (500 °C) whereas (Ga,Mn)As shells were deposited on the {11̅00} side facets of the cores at much lower temperature (220 °C). High-resolution transmission electron mic

The uPA receptor in ovarian cancer. Regulation by EGF and the estrogen responsive membrane receptor GPR30. Soluble uPAR in diagnosis and prognosis.

Cell migration is the first step of the invasive process, which is part of the malignant phenotype, and the uPA receptor (uPAR) plays a central role in cell migration. We studied the role of EGF and estrogen on cell migration and uPAR expression in ovarian cancer cell lines. We also analyzed the diagnostic and prognostic value of cleaved forms of the uPAR in plasma from patients with ovarian tumor

Key Performance indicators used as measurement parameter for plant-wide feedback loops - work in progress

Feedback is a fundamental concept in automatic control. Feedback loops are used extensively in industrial applications today and there are work-procedures for designing traditional single parameter control loops. In the work procedure it is important to select control-parameters, manipulated parameters and control-strategies. A similar work-procedure could also be used for designing plant-wide con

Synthesis and production of polyhydroxyalkanoates by halophiles: current potential and future prospects

Biodegradable materials with plastic or elastomeric properties are in great demand for a variety of applications. Polyhydroxyalkanoates (PHAs), polyesters synthesized by microorganisms, possess such desired features. Industrial production of PHAs is currently achieved using recombinant Escherichia coli. Nevertheless, recent research on halophiles, salt requiring microorganisms, has shown a remarka

Nuclear-modification factor for open-heavy-flavor production at forward rapidity in Cu plus Cu collisions at root s(NN)=200 GeV

Background: Heavy-flavor production in p + p collisions is a good test of perturbative-quantum-chromodynamics (pQCD) calculations. Modification of heavy-flavor production in heavy-ion collisions relative to binary-collision scaling from p + p results, quantified with the nuclear-modification factor (R-AA), provides information on both cold-and hot-nuclear-matter effects. Midrapidity heavy-flavor R

Fine mapping and conditional analysis identify a new mutation in the autoimmunity susceptibility gene BLK that leads to reduced half-life of the BLK protein

Objectives To perform fine mapping of the autoimmunity susceptibility gene BLK and identify functional variants involved in systemic lupus erythematosus (SLE). Methods Genotyping of 1163 European SLE patients and 1482 controls and imputation were performed covering the BLK gene with 158 single-nucleotide polymorphisms. Logistic regression analysis was done using PLINK and conditional analyses usin

90Y Bremsstrahlung Imaging for Absorbed-Dose Assessment in High-Dose Radioimmunotherapy.

This feasibility study demonstrates (90)Y quantitative bremsstrahlung imaging of patients undergoing high-dose myeloablative (90)Y-ibritumomab treatment. METHODS: The study includes pretherapy (111)In SPECT/CT and planar whole-body (WB) imaging at 7 d and therapy (90)Y SPECT/CT at 6 d and (90)Y WB imaging at 1 d. Time-activity curves and organ-absorbed doses derived from (90)Y SPECT images were co

Focusing on the process diagnosis of anaerobic fermentation by a novel sensor system combining microbial fuel cell, gas flow meter and pH meter

Process diagnosis is essential to ensure anaerobic fermentation stable and efficient. Here, a novel sensor system combining microbial fuel cell (MFC), gas flow meter and pH meter was developed to evaluate its feasibility for probing the anaerobic process established on a model high-rate bioreactor. Repeated transient responses of electrical signal, proton concentration, and gas flow rate, were obs

Frequency tracking of atrial fibrillation using hidden Markov models.

A hidden Markov model (HMM) is employed to improve noise robustness when tracking the dominant frequency of atrial fibrillation (AF) in the electrocardiogram (ECG). Following QRST cancellation, a sequence of observed frequency states is obtained from the residual ECG, using the short-time Fourier transform. Based on the observed state sequence, the Viterbi algorithm retrieves the optimal state seq

M2K: II. A Triple-Planet System Orbiting HIP 57274

Doppler observations from Keck Observatory have revealed a triple-planet system orbiting the nearby K4V star, HIP 57274. The inner planet, HIP 57274b, is a super-Earth with M sin i = 11.6 M-circle plus (0.036 M-Jup), an orbital period of 8.135 +/- 0.004 days, and slightly eccentric orbit e = 0.19 +/- 0.1. We calculate a transit probability of 6.5% for the inner planet. The second planet has M sin