Human Papillomavirus Vaccine Frequency for University of Kansas Medical Center Pediatric Patients

Background. Human papillomavirus (HPV) vaccination is recommendedfor all adolescents aged 11 to 12 years, but coveragein Kansas is exceptionally poor. To understand local coverage, receiptof the 3-dose HPV vaccine series among pediatric patients atthe University of Kansas Medical Center (KUMC) was evaluated. Methods. All patients aged 11 to 12 years who were seen by aKUMC primary care provider (family medicine and pediatrics)in 2013 were included in the retrospective chart review. Recordswere reviewed through December 31, 2014 to capture the numberof HPV doses received, and receipt of other recommendedvaccines (tetanus-diphtheria-pertussis and meningococcal conjugate).Pearson’s chi-squared tests were used to evaluate relationshipsbetween HPV vaccination and patient characteristics. Results. Of the 261 eligible females and 243 eligible males, 71.2%received ≥ 1 HPV vaccine dose, 55.2% received ≥ 2 doses, and39.3% completed the HPV vaccine series (3 doses). Although vaccineinitiation was slightly lower in males compared to females(67.1% vs. 75.1%, p = 0.047), no difference in vaccine completionwas seen between males and females (37.0% vs. 41.7%, p = 0.319).Over 80% of patients received other concurrently recommendedvaccines (Tdap: 81.7%, meningococcal: 81.3%). HPV series completionoccurred more often among Spanish-speaking femalescompared to English-speaking females (59.5% vs 37.7%; p < 0.01).Conclusions. The proportion of adolescents who received theHPV vaccination at KUMC is substantially higher than nationaland state estimates, but there is room for improvement forboth initiation and series completion. KS J Med 2016;9(1):1-5

A fully automatic gridding method for cDNA microarray images

<p>Abstract</p> <p>Background</p> <p>Processing cDNA microarray images is a crucial step in gene expression analysis, since any errors in early stages affect subsequent steps, leading to possibly erroneous biological conclusions. When processing the underlying images, accurately separating the sub-grids and spots is extremely important for subsequent steps that include segmentation, quantification, normalization and clustering.</p> <p>Results</p> <p>We propose a parameterless and fully automatic approach that first detects the sub-grids given the entire microarray image, and then detects the locations of the spots in each sub-grid. The approach, first, detects and corrects rotations in the images by applying an affine transformation, followed by a polynomial-time optimal multi-level thresholding algorithm used to find the positions of the sub-grids in the image and the positions of the spots in each sub-grid. Additionally, a new validity index is proposed in order to find the correct number of sub-grids in the image, and the correct number of spots in each sub-grid. Moreover, a refinement procedure is used to correct possible misalignments and increase the accuracy of the method.</p> <p>Conclusions</p> <p>Extensive experiments on real-life microarray images and a comparison to other methods show that the proposed method performs these tasks fully automatically and with a very high degree of accuracy. Moreover, unlike previous methods, the proposed approach can be used in various type of microarray images with different resolutions and spot sizes and does not need any parameter to be adjusted.</p

Molecular epidemiology of Giardia infections in the genomic era

Giardia duodenalis is a major gastrointestinal parasite of humans and animals across the globe. It is also of interest from an evolutionary perspective as it possesses many features that are unique among the eukaryotes, including its distinctive binucleate cell structure. While genomic analysis of a small number of isolates has provided valuable insights, efforts to understand the epidemiology of the disease and the population biology of the parasite have been limited by the molecular tools currently available. We review these tools and assess the impact of affordable and rapid genome sequencing systems increasingly being deployed in diagnostic settings. While these technologies have direct implications for public and veterinary health, they will also improve our understanding of the unique biology of this fascinating parasite

Manipulation of the Spin Memory of Electrons in n-GaAs

We report on the optical manipulation of the electron spin relaxation time in a GaAs based heterostructure. Experimental and theoretical study shows that the average electron spin relaxes through hyperfine interaction with the lattice nuclei, and that the rate can be controlled by the electron-electron interactions. This time has been changed from 300 ns down to 5 ns by variation of the laser frequency. This modification originates in the optically induced depletion of n-GaAs layer

Low-temperature spin relaxation in n-type GaAs

Low-temperature electron spin relaxation is studied by the optical orientation method in bulk n-GaAs with donor concentrations from 10^14 cm^{-3} to 5x10^17 cm^{-3}. A peculiarity related to the metal-to-insulator transition (MIT) is observed in the dependence of the spin lifetime on doping near n_D = 2x10^16 cm^{-3}. In the metallic phase, spin relaxation is governed by the Dyakonov-Perel mechanism, while in the insulator phase it is due to anisotropic exchange interaction and hyperfine interactio

M3G: Maximum Margin Microarray Gridding

<p>Abstract</p> <p>Background</p> <p>Complementary DNA (cDNA) microarrays are a well established technology for studying gene expression. A microarray image is obtained by laser scanning a hybridized cDNA microarray, which consists of thousands of spots representing chains of cDNA sequences, arranged in a two-dimensional array. The separation of the spots into distinct cells is widely known as microarray image gridding.</p> <p>Methods</p> <p>In this paper we propose M³G, a novel method for automatic gridding of cDNA microarray images based on the maximization of the margin between the rows and the columns of the spots. Initially the microarray image rotation is estimated and then a pre-processing algorithm is applied for a rough spot detection. In order to diminish the effect of artefacts, only a subset of the detected spots is selected by matching the distribution of the spot sizes to the normal distribution. Then, a set of grid lines is placed on the image in order to separate each pair of consecutive rows and columns of the selected spots. The optimal positioning of the lines is determined by maximizing the margin between these rows and columns by using a maximum margin linear classifier, effectively facilitating the localization of the spots.</p> <p>Results</p> <p>The experimental evaluation was based on a reference set of microarray images containing more than two million spots in total. The results show that M³G outperforms state of the art methods, demonstrating robustness in the presence of noise and artefacts. More than 98% of the spots reside completely inside their respective grid cells, whereas the mean distance between the spot center and the grid cell center is 1.2 pixels.</p> <p>Conclusions</p> <p>The proposed method performs highly accurate gridding in the presence of noise and artefacts, while taking into account the input image rotation. Thus, it provides the potential of achieving perfect gridding for the vast majority of the spots.</p

Nanoscale Mapping of the 3D Strain Tensor in a Germanium Quantum Well Hosting a Functional Spin Qubit Device

A strained Ge quantum well, grown on a SiGe/Si virtual substrate and hosting two electrostatically defined hole spin qubits, is nondestructively investigated by synchrotron-based scanning X-ray diffraction microscopy to determine all its Bravais lattice parameters. This allows rendering the three-dimensional spatial dependence of the six strain tensor components with a lateral resolution of approximately 50 nm. Two different spatial scales governing the strain field fluctuations in proximity of the qubits are observed at 1 μm, respectively. The short-ranged fluctuations have a typical bandwidth of 2 × 10-4 and can be quantitatively linked to the compressive stressing action of the metal electrodes defining the qubits. By finite element mechanical simulations, it is estimated that this strain fluctuation is increased up to 6 × 10-4 at cryogenic temperature. The longer-ranged fluctuations are of the 10-3 order and are associated with misfit dislocations in the plastically relaxed virtual substrate. From this, energy variations of the light and heavy-hole energy maxima of the order of several 100 μeV and 1 meV are calculated for electrodes and dislocations, respectively. These insights over material-related inhomogeneities may feed into further modeling for optimization and design of large-scale quantum processors manufactured using the mainstream Si-based microelectronics technology

Molecular characterisation of Giardia duodenalis from human and companion animal sources in the United Kingdom using an improved triosephosphate isomerase molecular marker

Giardia duodenalis is a protozoan parasite known for its ability to cause gastrointestinal disease in human and non-human mammals. In the UK, the full impact of this parasite has yet to be fully explored, due to the limited testing which has been undertaken in humans and the low-resolution assemblage-typing methods currently available. Rather than being primarily a travel-associated condition, a recent study has highlighted that an endemic Giardia cycle is present in the UK, although the source of human disease is unclear in the majority of cases. This study focussed on the improvement of one of the commonly used assemblage-typing assays, a nested topoisomerase phosphate (tpi) PCR, to increase the amplification success rate across both human and companion animal samples. After comparing published primers to full Giardia reference genomes, this marker protocol was optimised and then deployed to test a substantial number of human (n ​= ​79) and companion animal (n ​= ​174) samples to gain an insight into the molecular epidemiology of Giardia in the UK. One assemblage A1 and eleven assemblage A2 genotypes were detected in humans, along with and 25 assemblage B genotypes. Assemblage A1 genotypes, known to be human-infective, were found in three feline and one canine sample, while one feline sample contained assemblage A2. Additionally, four feline samples contained assemblage B, which is recognised as potentially human-infective. This study demonstrates the presence of potentially human-infective Giardia genotypes circulating in the companion animal population, notably with 17.4% (8/46) of feline-derived Giardia strains being potentially zoonotic. Using a modified tpi-based genotyping assay, this work highlights the potential for domestic pets to be involved in the endemic transmission of giardiasis in the UK and underlines the need for appropriate hygiene measures to be observed when interacting with both symptomatic and asymptomatic animals. It also serves to underline the requirement for further studies to assess the zoonotic risk of Giardia associated with companion animals in high-income countries