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Search Results: 1 - 10 of 325396 matches for " Laney S Light "
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Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage
Josyf C Mychaleckyj, Emily A Farber, Jessica Chmielewski, Jamie Artale, Laney S Light, Donald W Bowden, Xuanlin Hou, Santica M Marcovina
Journal of Translational Medicine , 2011, DOI: 10.1186/1479-5876-9-91
Abstract: We isolated DNA from 120 Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial buffy coats sampling a range of storage times up to 9 years and other factors that could influence DNA yield. We performed TaqMan SNP and GWA genotyping to test whether the DNA retained integrity for high quality genetic analysis.We tested two QIAGEN automated protocols for DNA isolation, preferring the Compromised Blood Protocol despite similar yields. We isolated DNA from all 120 specimens (yield range 1.1-312 ug per 8.5 ml ACD tube of whole blood) with only 3/120 samples yielding < 10 ug DNA. Age of participant at blood draw was negatively associated with yield (mean change -2.1 ug/year). DNA quality was very good based on gel electrophoresis QC, TaqMan genotyping of 6 SNPs (genotyping no-call rate 1.1% in 702 genotypes), and excellent quality GWA genotyping data (maximum per sample genotype missing rate 0.64%).When collected as a long term clinical trial or biobank specimen for DNA, buffy coats can be stored for up to 9 years in a -80degC frozen state and still produce high yields of DNA suitable for GWA analysis and other genetic testing.The Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial is registered with ClinicalTrials.gov, number NCT00000620.Clinical trials and prospective observational cohort studies are complex to design and costly to implement, hence there is a strong desire to maximize overall clinical and scientific return on investment. A common strategy is to include blood specimen collection at a baseline or early participant study visit to enable future ancillary studies or analysis of secondary biomarker outcomes. The blood specimens may be processed to produce aliquots of sera, plasma, or blood cell pack that are stored frozen for future use. For genetics studies, DNA is more stable under long-term freezer storage, but in many existing or completed studies, the study protocol required the extraction and storage of buffy coats (aliqu
Optimized coupling of cold atoms into a fiber using a blue-detuned hollow-beam funnel
Jerome Poulin,Philip S. Light,Raman Kashyap,Andre N. Luiten
Physics , 2011, DOI: 10.1103/PhysRevA.84.053812
Abstract: We theoretically investigate the process of coupling cold atoms into the core of a hollow-core photonic-crystal optical fiber using a blue-detuned Laguerre-Gaussian beam. In contrast to the use of a red-detuned Gaussian beam to couple the atoms, the blue-detuned hollow-beam can confine cold atoms to the darkest regions of the beam thereby minimizing shifts in the internal states and making the guide highly robust to heating effects. This single optical beam is used as both a funnel and guide to maximize the number of atoms into the fiber. In the proposed experiment, Rb atoms are loaded into a magneto-optical trap (MOT) above a vertically-oriented optical fiber. We observe a gravito-optical trapping effect for atoms with high orbital momentum around the trap axis, which prevents atoms from coupling to the fiber: these atoms lack the kinetic energy to escape the potential and are thus trapped in the laser funnel indefinitely. We find that by reducing the dipolar force to the point at which the trapping effect just vanishes, it is possible to optimize the coupling of atoms into the fiber. Our simulations predict that by using a low-power (2.5 mW) and far-detuned (300 GHz) Laguerre-Gaussian beam with a 20-{\mu}m radius core hollow-fiber it is possible to couple 11% of the atoms from a MOT 9 mm away from the fiber. When MOT is positioned further away, coupling efficiencies over 50% can be achieved with larger core fibers.
Management of Parapneumonic Effusions
Richard Light
Journal of Clinical and Analytical Medicine , 2010, DOI: 10.4328
Abstract: Pleural effusions associated with pneumonia (parapneumonic effusions) are one of the most common causes of exudative pleural effusions in the world [1]. Approximately 20 to 40% of patients hospitalized with pneumonia will have an accompanying pleural effusion [1]. The presence of a pleural effusion is associated with worse outcomes in patients with pneumonia. In one study of patients hospitalized with pneumonia the mortality risk was 6.5 times higher if the patient had bilateral pleural effusion and 3.7 times higher if the effusion was unilateral than if the patient had no pleural effusion [2]. At least part of the increased mortality with parapneumonic effusions is due to mismanagement of the pleural effusion. The likelihood of developing a pleural effusion with a bacterial pneumonia is dependent upon the organism responsible for the pneumonia. The distribution of organisms responsible for parapneumonic effusions is quite different from the distribution of organisms responsible for pneumonia in general. Organisms responsible for community and hospital acquired pneumonia with complicated parapneumonic effusions also differed considerably in a recent multicenter study from the United Kingdom [3]. For the 336 patients with community acquired pneumonias with parapneumonic effusions in whom the responsible bacteria were identified, the most common organisms were Strept. Milleri group 32%, anaerobes 16%, Strep. pneumoniae 13% and Staph. aueus 11%. For the 60 patients with hospital-acquired pneumonia, the most common organisms were multiple resistant Staph. aureus 28%, other Staph. 18%, Enterobacteriacea 15% and Enterococci 13% [3]. These numbers should be kept in mind when selecting antibiotics for patients with parapneumonic effusions.
Morphological Cues for Lexical Semantics
Marc Light
Computer Science , 1996,
Abstract: Most natural language processing tasks require lexical semantic information. Automated acquisition of this information would thus increase the robustness and portability of NLP systems. This paper describes an acquisition method which makes use of fixed correspondences between derivational affixes and lexical semantic information. One advantage of this method, and of other methods that rely only on surface characteristics of language, is that the necessary input is currently available.
Classification in Feature-based Default Inheritance Hierarchies
Marc Light
Computer Science , 1996,
Abstract: Increasingly, inheritance hierarchies are being used to reduce redundancy in natural language processing lexicons. Systems that utilize inheritance hierarchies need to be able to insert words under the optimal set of classes in these hierarchies. In this paper, we formalize this problem for feature-based default inheritance hierarchies. Since the problem turns out to be NP-complete, we present an approximation algorithm for it. We show that this algorithm is efficient and that it performs well with respect to a number of standard problems for default inheritance. A prototype implementation has been tested on lexical hierarchies and it has produced encouraging results. The work presented here is also relevant to other types of default hierarchies.
Laser frequency comb techniques for precise astronomical spectroscopy
Michael T. Murphy,Clayton R. Locke,Philip S. Light,Andre N. Luiten,Jon S. Lawrence
Physics , 2012, DOI: 10.1111/j.1365-2966.2012.20656.x
Abstract: Precise astronomical spectroscopic analyses routinely assume that individual pixels in charge-coupled devices (CCDs) have uniform sensitivity to photons. Intra-pixel sensitivity (IPS) variations may already cause small systematic errors in, for example, studies of extra-solar planets via stellar radial velocities and cosmological variability in fundamental constants via quasar spectroscopy, but future experiments requiring velocity precisions approaching ~1 cm/s will be more strongly affected. Laser frequency combs have been shown to provide highly precise wavelength calibration for astronomical spectrographs, but here we show that they can also be used to measure IPS variations in astronomical CCDs in situ. We successfully tested a laser frequency comb system on the Ultra-High Resolution Facility spectrograph at the Anglo-Australian Telescope. By modelling the 2-dimensional comb signal recorded in a single CCD exposure, we find that the average IPS deviates by <8 per cent if it is assumed to vary symmetrically about the pixel centre. We also demonstrate that series of comb exposures with absolutely known offsets between them can yield tighter constraints on symmetric IPS variations from ~100 pixels. We discuss measurement of asymmetric IPS variations and absolute wavelength calibration of astronomical spectrographs and CCDs using frequency combs.
Large parathyroid adenoma presenting as a femoral fracture in a young male  [PDF]
Duncan Light, Chakri Munipalle, Vijay Kurup
Case Reports in Clinical Medicine (CRCM) , 2013, DOI: 10.4236/crcm.2013.28120
Abstract: Parathyroid adenoma classically presents symptoms of hypercalcaemia. Here, we present a case of a rare presentation of a parathyroid adenoma in a young male patient with a pathological fracture.
Evolutionary history of mammalian sucking lice (Phthiraptera: Anoplura)
Jessica E Light, Vincent S Smith, Julie M Allen, Lance A Durden, David L Reed
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-292
Abstract: This study represents the first phylogenetic hypothesis of sucking louse relationships using molecular data and we find significant conflict between phylogenies constructed using molecular and morphological data. We also find that multiple families and genera of sucking lice are not monophyletic and that extensive taxonomic revision will be necessary for this group. Based on our divergence dating analyses, sucking lice diversified in the late Cretaceous, approximately 77 Ma, and soon after the Cretaceous-Paleogene boundary (ca. 65 Ma) these lice proliferated rapidly to parasitize multiple mammalian orders and families.The diversification time of sucking lice approximately 77 Ma is in agreement with mammalian evolutionary history: all modern mammal orders are hypothesized to have diverged by 75 Ma thus providing suitable habitat for the colonization and radiation of sucking lice. Despite the concordant timing of diversification events early in the association between anoplurans and mammals, there is substantial conflict between the host and parasite phylogenies. This conflict is likely the result of a complex history of host switching and extinction events that occurred throughout the evolutionary association between sucking lice and their mammalian hosts. It is unlikely that there are any ectoparasite groups (including lice) that tracked the early and rapid radiation of eutherian mammals.Lice (Insecta: Phthiraptera) are obligate, permanent ectoparasites of birds and mammals, entirely dependent upon their vertebrate hosts for survival. Four phthirapteran suborders are recognized: the chewing louse suborders Amblycera, Ischnocera, and Rhynchophthirina, and the sucking louse suborder Anoplura [1]. As a group, chewing lice parasitize birds and mammals, and all have chewing mouthparts that they use to feed upon the skin (feathers, fur, and dander) and sometimes the blood of their hosts [2]. Sucking lice, in contrast, parasitize only eutherian mammals and they are morphol
Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients
Melissa S Doud, Michael Light, Gisela Gonzalez, Giri Narasimhan, Kalai Mathee
Human Genomics , 2010, DOI: 10.1186/1479-7364-4-3-147
Abstract: Cystic fibrosis (CF) is an autorecessive disease affecting one in 3,500 Caucasian live births in the USA [1]. CF results from a mutation in the gene that encodes the CF transmembrane conductance regulator (CFTR) protein [2,3]. A defect in the CFTR protein leads to a malfunctioning cyclic AMP-activated chloride channel in secretory epithelia [4]. This defect in the lung leads to the inability to secrete chloride and to the excess re-absorption of sodium [4]. Thus, there is decreased fluid secretion and the mucus becomes immobilised and adheres to the epithelial cells. Overproduction of mucus in the airway results in congestion of the respiratory tract and increases susceptibility to bronchopulmonary infection. CF patients often suffer from infections with Staphylococcus aureus, Haemophilus influenzae, Pseudomonas aeruginosa and Burkholderia cenocepacia [5]. These chronic infections by highly adapted lung microbes cause inflammation and, eventually, lung damage; therefore, lung disease is the major cause of morbidity and mortality among these patients [6,7].It has also been estimated that less than 1 per cent of eubacteria in the environment can be cultured [8,9]. Thus, these identification methods will fail to detect all pathogens that might be causing the lung infection. Fortunately, with the advent of molecular techniques, culturing for identification purposes can be circumvented [10]. Recent molecular studies using terminal restriction fragment length analysis and sequencing have shown that the lung community is complex. Achromobacter (Alcaligenes) xylosoxidans, Rhodotorula mucilaginosa, Abiotrophia spp, Bacteroides gracilis, Eubacterium brachy, Mycobacterium mucilaginosus, Mycoplasma salivarium, Porphyromonas salivae, Ralstonia spp, Staphylococcus hominis, Streptococcus anginosus, Treponema vincentii, Veillonella spp, Burkholderia gladioli, Stenotrophomonas maltophilia and Pandoraea atypical have all been demonstrated to be members of this polymicrobial infection
Not All Distraction Is Bad: Working Memory Vulnerability to Implicit Socioemotional Distraction Correlates with Negative Symptoms and Functional Impairment in Psychosis
Quintino R. Mano,Gregory G. Brown,Heline Mirzakhanian,Khalima Bolden,Kristen S. Cadenhead,Gregory A. Light
Schizophrenia Research and Treatment , 2014, DOI: 10.1155/2014/320948
Abstract: This study investigated implicit socioemotional modulation of working memory (WM) in the context of symptom severity and functional status in individuals with psychosis ( ). A delayed match-to-sample task was modified wherein task-irrelevant facial distracters were presented early and briefly during the rehearsal of pseudoword memoranda that varied incrementally in load size (1, 2, or 3 syllables). Facial distracters displayed happy, sad, or emotionally neutral expressions. Implicit socioemotional modulation of WM was indexed by subtracting task accuracy on nonfacial geometrical distraction trials from facial distraction trials. Results indicated that the amount of implicit socioemotional modulation of high WM load accuracy was significantly associated with negative symptoms ( , ), role functioning ( , ), social functioning ( , ), and global assessment of functioning ( , ). Specifically, greater attentional distraction of high WM load was associated with less severe symptoms and functional impairment. This study demonstrates the importance of the WM-socioemotional interface in influencing clinical and psychosocial functional status in psychosis. 1. Introduction Attentional impairments are commonly observed in psychosis [1]. A classic view of attentional distraction is that it reflects cognitive impairment, that is, reduced ability to accurately maintain information in the presence of task-irrelevant stimuli. Yet, there are real-world situations wherein attentional distraction is adaptive. Consider a dyadic social encounter wherein the communicatee’s changing facial expressions appropriately disrupt the communicator’s thoughts. Here, attentional distraction adaptively permits the communicator to modulate ongoing cognition and attend to changing facial expressions in the communicatee. In other words, effective and reciprocal social encounters are those that demonstrate flexibility whereby communicators are sensitive to the facial expressions of the communicatee and are capable of modulating ongoing thoughts to attend to the communicatee. The present study aimed to capture the adaptability of this everyday challenge and gather proof of concept evidence by examining implicit socioemotional modulation of working memory (WM) in relation to symptom severity and functional status in individuals with psychosis. We reasoned that individuals with relatively severe psychosis have a WM system that is less sensitive to the moment-to-moment modulation of socioemotional stimuli. Though individuals with psychosis have general cognitive impairments, the WM construct was
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