Aerospace Software Engineering for Advanced Systems Architectures (L’Ingenierie des Logiciels Pour les Architectures des Systemes Aerospatiaux)

DTIC Science & Technology

1993-11-01

Eliezer N. Solomon Steve Sedrel Westinghouse Electronic Systems Group P.O. Box 746, MS 432, Baltimore, Maryland 21203-0746, USA SUMMARY The United States...subset of the Joint Intergrated Avionics NewAgentCollection which has four Working Group (JIAWG), Performance parameters: Acceptor, of type Task._D...Published Noember 1993 Distribution and Availability on Back Cover SAGARD-CP54 ADVISORY GROUP FOR AERSACE RESEARCH & DEVELOPMENT 7 RUE ANCELLE 92200

Evaluation of repetitive element polymerase chain reaction for surveillance of methicillin-resistant Staphylococcus aureus at a large academic medical center and community hospitals.

PubMed

Wang, Shu-Hua; Stevenson, Kurt B; Hines, Lisa; Mediavilla, José R; Khan, Yosef; Soni, Ruchi; Dutch, Wendy; Brandt, Eric; Bannerman, Tammy; Kreiswirth, Barry N; Pancholi, Preeti

2015-01-01

Repetitive element polymerase chain reaction (rep-PCR) typing has been used for methicillin-resistant Staphylococcus aureus (MRSA) strain characterization. The goal of this study was to determine if a rapid commercial rep-PCR system, DiversiLab™ (DL; bioMérieux, Durham, NC, USA), could be used for MRSA surveillance at a large medical center and community hospitals. A total of 1286 MRSA isolates genotyped by the DL system were distributed into 84 distinct rep-PCR patterns: 737/1286 (57%) were clustered into 6 major rep-PCR patterns. A subset of 220 isolates was further typed by pulsed-field gel electrophoresis (PFGE), spa typing, and SCCmec typing. The 220 isolates were distributed into 80 rep-PCR patterns, 94 PFGE pulsotypes, 27 spa, and 3 SCCmec types. The DL rep-PCR system is sufficient for surveillance, but the DL system alone cannot be used to compare data to other institutions until a standardized nomenclature is established and the DL MRSA reference library is expanded. Copyright © 2015 Elsevier Inc. All rights reserved.

Global Land Carbon Uptake from Trait Distributions

NASA Astrophysics Data System (ADS)

Butler, E. E.; Datta, A.; Flores-Moreno, H.; Fazayeli, F.; Chen, M.; Wythers, K. R.; Banerjee, A.; Atkin, O. K.; Kattge, J.; Reich, P. B.

2016-12-01

Historically, functional diversity in land surface models has been represented through a range of plant functional types (PFTs), each of which has a single value for all of its functional traits. Here we expand the diversity of the land surface by using a distribution of trait values for each PFT. The data for these trait distributions is from a sub-set of the global database of plant traits, TRY, and this analysis uses three leaf traits: mass based nitrogen and phosphorus content and specific leaf area, which influence both photosynthesis and respiration. The data are extrapolated into continuous surfaces through two methodologies. The first, a categorical method, classifies the species observed in TRY into satellite estimates of their plant functional type abundances - analogous to how traits are currently assigned to PFTs in land surface models. Second, a Bayesian spatial method which additionally estimates how the distribution of a trait changes in accord with both climate and soil covariates. These two methods produce distinct patterns of diversity which are incorporated into a land surface model to estimate how the range of trait values affects the global land carbon budget.

The ESO Nearby Abell Cluster Survey. VI. Spatial distribution and kinematics of early- and late-type galaxies

NASA Astrophysics Data System (ADS)

de Theije, P. A. M.; Katgert, P.

1999-01-01

Analysis of the data obtained in the ESO Nearby Abell Cluster Survey (ENACS) has shown that the space distribution and kinematics of galaxies with detectable emission lines in their spectra differ significantly from those of galaxies without emission lines. This result, and details of the kinematics, were considered as support for the idea that at least the spirals with emission lines are on orbits that are not isotropic. This might indicate that this subset of late-type galaxies either has `first approach'-orbits towards the dense core of their respective clusters, or has orbits that `avoid' the core. The galaxies with emission lines are essentially all late-type galaxies. On the other hand, the emission-line galaxies represent only about a third of the late-type galaxies, the majority of which do not show detectable emission lines. The galaxies without emission lines are therefore a mix of early- and late-type galaxies. In this paper we attempt to separate early- and late-type galaxies, and we study possible differences in distribution and kinematics of the two galaxy classes. For only about 10% of the galaxies in the ENACS, the morphology is known from imaging. Here, we describe our classification on the basis of the ENACS spectrum. The significant information in each spectrum is compressed into 15 Principal Components, which are used as input for an Artificial Neural Network. The latter is `trained' with 150 of the 270 galaxies for which a morphological type is available from Dressler, and subsequently used to classify each galaxy. This yields a classification for two-thirds of the ENACS galaxies. The Artificial Neural Network has two output classes: early-type (E+S0) and late-type (S+I) galaxies. We do not distinguish E and S0 galaxies, because these cannot be separated very robustly on the basis of the spectrum. The success rate of the classification is estimated from the sample of 120 galaxies with Dressler morphologies which were not used to train the ANN. The success rate is higher for early-type than for late-type galaxies (78+/-6% vs. {63+/-6%}). The weighted average success rate, irrespective of type, is {73+/-4%}. The success rate is somewhat larger for the training set, and highest for the galaxies with emission lines. Of the 3798 galaxies that were classified from their spectrum {57+/-7%} are of early type, and {43+/-7%} of late type. Using a subset of these 3798 galaxies, we constructed a composite cluster of 2594 galaxies, 399 of which have emission lines and are therefore almost exclusively spirals and irregulars. The kinematics and spatial distribution of the late-type galaxies without emission lines resemble much more those of the early-type galaxies than those of the late-type galaxies with emission lines. Yet, the late-type galaxies without emission lines may have a somewhat larger velocity dispersion and a slightly less centrally concentrated distribution than the early-type galaxies. Only the late-type galaxies with emission lines appear to have a considerably larger global velocity dispersion and a much less concentrated projected density profile than the other galaxies. Thus, the suggestion of fairly radial, and possibly `first approach' orbits applies only to spirals with emission lines. The early-type galaxies with emission lines (among which the AGN), may also have a large velocity dispersion and be concentrated towards the cluster centre. Based on observations collected at the European Southern Observatory (La Silla, Chile)

Implementation of an Object-Oriented Flight Simulator D.C. Electrical System on a Hypercube Architecture

DTIC Science & Technology

1991-12-01

abstract data type is, what an object-oriented design is and how to apply "software engineering" principles to the design of both of them. I owe a great... Program (ASVP), a research and development effort by two aerospace contractors to redesign and implement subsets of two existing flight simulators in...effort addresses how to implement a simulator designed using the SEI OOD Paradigm on a distributed, parallel, multiple instruction, multiple data (MIMD

Target Detection Routine (TADER). User’s Guide.

DTIC Science & Technology

1987-09-01

o System range capability subset (one record - omitted for standoff SLAR and penetrating system) o System inherent detection probability subset ( IELT ...records, i.e., one per element type) * System capability modifier subset/A=1, E=1 ( IELT records) o System capability modifier subset/A=1, E=2 ( IELT ...records) s System capability modifier subset/A=2, E=1 ( IELT records) o System capability modifier subset/A=2, E=2 ( IELT records) Unit Data Set (one set

Association of the proprotein convertase subtilisin/kexin-type 2 (PCSK2) gene with type 2 diabetes in an African American population

PubMed Central

Leak, Tennille S.; Keene, Keith L.; Langefeld, Carl D.; Gallagher, Carla J.; Mychaleckyj, Josyf C.; Freedman, Barry I.; Bowden, Donald W.; Rich, Stephen S.; Sale, Michèle M.

2009-01-01

In a genome-wide scan for type 2 diabetes (T2DM) in African American (AA) families, ordered subsets analysis (OSA) provided evidence for linkage to chromosome 20p in a subset with later age at diagnosis (max. LOD 2.57, P = 0.008). The proprotein convertase subtilisin/kexin-type 2 (PCSK2) gene is within the LOD-1 interval of this linkage peak. Twenty-nine single nucleotide polymorphisms (SNPs) were genotyped across this gene in 380 unrelated AA individuals with T2DM and end-stage renal disease (T2DM-ESRD), 278 AA controls, 96 European Americans (EA) and 120 Yoruba Nigerian (YRI) controls. In addition, 22 ancestry-informative markers (AIMs) were genotyped in all AA subjects, 120 YRI, and 96 EA controls. ADMIXMAP was used to model the distributions of admixture and generate score tests of allelic and haplotypic association. Association with T2DM was observed among 4 SNPs: rs2021785 (admixture-adjusted Pa = 0.00014), rs1609659 (Pa = 0.028), rs4814597 (Pa = 0.039) and rs2269023 (Pa = 0.043). None of the PCSK2 SNPs were associated with age at T2DM diagnosis. A variant in the PCKS2 gene, rs2021785, appears to play a role in susceptibility to T2DM in this AA population. PMID:17618154

Discovery of Remote Globular Cluster Satellites of M87

NASA Astrophysics Data System (ADS)

Sparkman, Lea; Guo, Rachel; Toloba, Elisa; Guhathakurta, Puragra; Peng, Eric W.; Ferrarese, Laura; Cote, Patrick; NGVS Collaboration

2016-01-01

We present the discovery of several tens of globular clusters (GCs) in the outer regions of the giant elliptical M87, the brightest galaxy in the Virgo Cluster. These M87 GC satellites were discovered in the course of Keck/DEIMOS spectroscopic follow up of GC candidates that were identified in the Next Generation Virgo cluster Survey (NGVS). Specifically, the primary targets of this Keck spectroscopic campaign were GC satellites of early-type dwarf (dE) galaxies. However, we found that our sample contained a subset of GCs for which M87 is the most likely host. This subset is consistent with having an r^-1 power-law surface density distribution and a radial velocity distribution both centered on M87. The remote M87 GC satellites span the radial range 140 to 900 kpc, out to about a third of the Virgo Cluster's virial radius (for comparison, M87's effective radius is only 8 kpc). These M87 GC satellites are probably former satellites of other Virgo Cluster galaxies that have subsequently been cannibalized by M87.This research was supported by the National Science Foundation and the UC Santa Cruz Science Internship Program.

Spatial Downscaling of Alien Species Presences using Machine Learning

NASA Astrophysics Data System (ADS)

Daliakopoulos, Ioannis N.; Katsanevakis, Stelios; Moustakas, Aristides

2017-07-01

Large scale, high-resolution data on alien species distributions are essential for spatially explicit assessments of their environmental and socio-economic impacts, and management interventions for mitigation. However, these data are often unavailable. This paper presents a method that relies on Random Forest (RF) models to distribute alien species presence counts at a finer resolution grid, thus achieving spatial downscaling. A sufficiently large number of RF models are trained using random subsets of the dataset as predictors, in a bootstrapping approach to account for the uncertainty introduced by the subset selection. The method is tested with an approximately 8×8 km2 grid containing floral alien species presence and several indices of climatic, habitat, land use covariates for the Mediterranean island of Crete, Greece. Alien species presence is aggregated at 16×16 km2 and used as a predictor of presence at the original resolution, thus simulating spatial downscaling. Potential explanatory variables included habitat types, land cover richness, endemic species richness, soil type, temperature, precipitation, and freshwater availability. Uncertainty assessment of the spatial downscaling of alien species’ occurrences was also performed and true/false presences and absences were quantified. The approach is promising for downscaling alien species datasets of larger spatial scale but coarse resolution, where the underlying environmental information is available at a finer resolution than the alien species data. Furthermore, the RF architecture allows for tuning towards operationally optimal sensitivity and specificity, thus providing a decision support tool for designing a resource efficient alien species census.

Muon tomography imaging improvement using optimized limited angle data

NASA Astrophysics Data System (ADS)

Bai, Chuanyong; Simon, Sean; Kindem, Joel; Luo, Weidong; Sossong, Michael J.; Steiger, Matthew

2014-05-01

Image resolution of muon tomography is limited by the range of zenith angles of cosmic ray muons and the flux rate at sea level. Low flux rate limits the use of advanced data rebinning and processing techniques to improve image quality. By optimizing the limited angle data, however, image resolution can be improved. To demonstrate the idea, physical data of tungsten blocks were acquired on a muon tomography system. The angular distribution and energy spectrum of muons measured on the system was also used to generate simulation data of tungsten blocks of different arrangement (geometry). The data were grouped into subsets using the zenith angle and volume images were reconstructed from the data subsets using two algorithms. One was a distributed PoCA (point of closest approach) algorithm and the other was an accelerated iterative maximal likelihood/expectation maximization (MLEM) algorithm. Image resolution was compared for different subsets. Results showed that image resolution was better in the vertical direction for subsets with greater zenith angles and better in the horizontal plane for subsets with smaller zenith angles. The overall image resolution appeared to be the compromise of that of different subsets. This work suggests that the acquired data can be grouped into different limited angle data subsets for optimized image resolution in desired directions. Use of multiple images with resolution optimized in different directions can improve overall imaging fidelity and the intended applications.

Particle size distributions in chondritic meteorites: Evidence for pre-planetesimal histories

NASA Astrophysics Data System (ADS)

Simon, J. I.; Cuzzi, J. N.; McCain, K. A.; Cato, M. J.; Christoffersen, P. A.; Fisher, K. R.; Srinivasan, P.; Tait, A. W.; Olson, D. M.; Scargle, J. D.

2018-07-01

Magnesium-rich silicate chondrules and calcium-, aluminum-rich refractory inclusions (CAIs) are fundamental components of primitive chondritic meteorites. It has been suggested that concentration of these early-formed particles by nebular sorting processes may lead to accretion of planetesimals, the planetary bodies that represent the building blocks of the terrestrial planets. In this case, the size distributions of the particles may constrain the accretion process. Here we present new particle size distribution data for Northwest Africa 5717, a primitive ordinary chondrite (ungrouped 3.05) and the well-known carbonaceous chondrite Allende (CV3). Instead of the relatively narrow size distributions obtained in previous studies (Ebel et al., 2016; Friedrich et al., 2015; Paque and Cuzzi, 1997, and references therein), we observed broad size distributions for all particle types in both meteorites. Detailed microscopic image analysis of Allende shows differences in the size distributions of chondrule subtypes, but collectively these subpopulations comprise a composite "chondrule" size distribution that is similar to the broad size distribution found for CAIs. Also, we find accretionary 'dust' rims on only a subset (∼15-20%) of the chondrules contained in Allende, which indicates that subpopulations of chondrules experienced distinct histories prior to planetary accretion. For the rimmed subset, we find positive correlation between rim thickness and chondrule size. The remarkable similarity between the size distributions of various subgroups of particles, both with and without fine grained rims, implies a common size sorting process. Chondrite classification schemes, astrophysical disk models that predict a narrow chondrule size population and/or a common localized formation event, and conventional particle analysis methods must all be critically reevaluated. We support the idea that distinct "lithologies" in NWA 5717 are nebular aggregates of chondrules. If ≥cm-sized aggregates of chondrules can form it will have implications for planet formation and suggests the sticking stage is where the preferential size physics is operating.

Particle Size Distributions in Chondritic Meteorites: Evidence for Pre-Planetesimal Histories

NASA Technical Reports Server (NTRS)

Simon, J. I.; Cuzzi, J. N.; McCain, K. A.; Cato, M. J.; Christoffersen, P. A.; Fisher, K. R.; Srinivasan, P.; Tait, A. W.; Olson, D. M.; Scargle, J. D.

2018-01-01

Magnesium-rich silicate chondrules and calcium-, aluminum-rich refractory inclusions (CAIs) are fundamental components of primitive chondritic meteorites. It has been suggested that concentration of these early-formed particles by nebular sorting processes may lead to accretion of planetesimals, the planetary bodies that represent the building blocks of the terrestrial planets. In this case, the size distributions of the particles may constrain the accretion process. Here we present new particle size distribution data for Northwest Africa 5717, a primitive ordinary chondrite (ungrouped 3.05) and the well-known carbonaceous chondrite Allende (CV3). Instead of the relatively narrow size distributions obtained in previous studies (Ebel et al., 2016; Friedrich et al., 2015; Paque and Cuzzi, 1997, and references therein), we observed broad size distributions for all particle types in both meteorites. Detailed microscopic image analysis of Allende shows differences in the size distributions of chondrule subtypes, but collectively these subpopulations comprise a composite "chondrule" size distribution that is similar to the broad size distribution found for CAIs. Also, we find accretionary 'dust' rims on only a subset (approximately 15-20 percent) of the chondrules contained in Allende, which indicates that subpopulations of chondrules experienced distinct histories prior to planetary accretion. For the rimmed subset, we find positive correlation between rim thickness and chondrule size. The remarkable similarity between the size distributions of various subgroups of particles, both with and without fine grained rims, implies a common size sorting process. Chondrite classification schemes, astrophysical disk models that predict a narrow chondrule size population and/or a common localized formation event, and conventional particle analysis methods must all be critically reevaluated. We support the idea that distinct "lithologies" in NWA 5717 are nebular aggregates of chondrules. If greater than or equal to centimeter-sized aggregates of chondrules can form it will have implications for planet formation and suggests the sticking stage is where the preferential size physics is operating.

Distributed processor allocation for launching applications in a massively connected processors complex

DOEpatents

Pedretti, Kevin

2008-11-18

A compute processor allocator architecture for allocating compute processors to run applications in a multiple processor computing apparatus is distributed among a subset of processors within the computing apparatus. Each processor of the subset includes a compute processor allocator. The compute processor allocators can share a common database of information pertinent to compute processor allocation. A communication path permits retrieval of information from the database independently of the compute processor allocators.

On sample size and different interpretations of snow stability datasets

NASA Astrophysics Data System (ADS)

Schirmer, M.; Mitterer, C.; Schweizer, J.

2009-04-01

Interpretations of snow stability variations need an assessment of the stability itself, independent of the scale investigated in the study. Studies on stability variations at a regional scale have often chosen stability tests such as the Rutschblock test or combinations of various tests in order to detect differences in aspect and elevation. The question arose: ‘how capable are such stability interpretations in drawing conclusions'. There are at least three possible errors sources: (i) the variance of the stability test itself; (ii) the stability variance at an underlying slope scale, and (iii) that the stability interpretation might not be directly related to the probability of skier triggering. Various stability interpretations have been proposed in the past that provide partly different results. We compared a subjective one based on expert knowledge with a more objective one based on a measure derived from comparing skier-triggered slopes vs. slopes that have been skied but not triggered. In this study, the uncertainties are discussed and their effects on regional scale stability variations will be quantified in a pragmatic way. An existing dataset with very large sample sizes was revisited. This dataset contained the variance of stability at a regional scale for several situations. The stability in this dataset was determined using the subjective interpretation scheme based on expert knowledge. The question to be answered was how many measurements were needed to obtain similar results (mainly stability differences in aspect or elevation) as with the complete dataset. The optimal sample size was obtained in several ways: (i) assuming a nominal data scale the sample size was determined with a given test, significance level and power, and by calculating the mean and standard deviation of the complete dataset. With this method it can also be determined if the complete dataset consists of an appropriate sample size. (ii) Smaller subsets were created with similar aspect distributions to the large dataset. We used 100 different subsets for each sample size. Statistical variations obtained in the complete dataset were also tested on the smaller subsets using the Mann-Whitney or the Kruskal-Wallis test. For each subset size, the number of subsets were counted in which the significance level was reached. For these tests no nominal data scale was assumed. (iii) For the same subsets described above, the distribution of the aspect median was determined. A count of how often this distribution was substantially different from the distribution obtained with the complete dataset was made. Since two valid stability interpretations were available (an objective and a subjective interpretation as described above), the effect of the arbitrary choice of the interpretation on spatial variability results was tested. In over one third of the cases the two interpretations came to different results. The effect of these differences were studied in a similar method as described in (iii): the distribution of the aspect median was determined for subsets of the complete dataset using both interpretations, compared against each other as well as to the results of the complete dataset. For the complete dataset the two interpretations showed mainly identical results. Therefore the subset size was determined from the point at which the results of the two interpretations converged. A universal result for the optimal subset size cannot be presented since results differed between different situations contained in the dataset. The optimal subset size is thus dependent on stability variation in a given situation, which is unknown initially. There are indications that for some situations even the complete dataset might be not large enough. At a subset size of approximately 25, the significant differences between aspect groups (as determined using the whole dataset) were only obtained in one out of five situations. In some situations, up to 20% of the subsets showed a substantially different distribution of the aspect median. Thus, in most cases, 25 measurements (which can be achieved by six two-person teams in one day) did not allow to draw reliable conclusions.

A Single HIV-1 Cluster and a Skewed Immune Homeostasis Drive the Early Spread of HIV among Resting CD4+ Cell Subsets within One Month Post-Infection

PubMed Central

Avettand-Fenoël, Véronique; Nembot, Georges; Mélard, Adeline; Blanc, Catherine; Lascoux-Combe, Caroline; Slama, Laurence; Allegre, Thierry; Allavena, Clotilde; Yazdanpanah, Yazdan; Duvivier, Claudine; Katlama, Christine; Goujard, Cécile; Seksik, Bao Chau Phung; Leplatois, Anne; Molina, Jean-Michel; Meyer, Laurence; Autran, Brigitte; Rouzioux, Christine

2013-01-01

Optimizing therapeutic strategies for an HIV cure requires better understanding the characteristics of early HIV-1 spread among resting CD4+ cells within the first month of primary HIV-1 infection (PHI). We studied the immune distribution, diversity, and inducibility of total HIV-DNA among the following cell subsets: monocytes, peripheral blood activated and resting CD4 T cells, long-lived (naive [TN] and central-memory [TCM]) and short-lived (transitional-memory [TTM] and effector-memory cells [TEM]) resting CD4+T cells from 12 acutely-infected individuals recruited at a median 36 days from infection. Cells were sorted for total HIV-DNA quantification, phylogenetic analysis and inducibility, all studied in relation to activation status and cell signaling. One month post-infection, a single CCR5-restricted viral cluster was massively distributed in all resting CD4+ subsets from 88% subjects, while one subject showed a slight diversity. High levels of total HIV-DNA were measured among TN (median 3.4 log copies/million cells), although 10-fold less (p = 0.0005) than in equally infected TCM (4.5), TTM (4.7) and TEM (4.6) cells. CD3−CD4+ monocytes harbored a low viral burden (median 2.3 log copies/million cells), unlike equally infected resting and activated CD4+ T cells (4.5 log copies/million cells). The skewed repartition of resting CD4 subsets influenced their contribution to the pool of resting infected CD4+T cells, two thirds of which consisted of short-lived TTM and TEM subsets, whereas long-lived TN and TCM subsets contributed the balance. Each resting CD4 subset produced HIV in vitro after stimulation with anti-CD3/anti-CD28+IL-2 with kinetics and magnitude varying according to subset differentiation, while IL-7 preferentially induced virus production from long-lived resting TN cells. In conclusion, within a month of infection, a clonal HIV-1 cluster is massively distributed among resting CD4 T-cell subsets with a flexible inducibility, suggesting that subset activation and skewed immune homeostasis determine the conditions of viral dissemination and early establishment of the HIV reservoir. PMID:23691172

Northeast Artificial Intelligence Consortium Annual Report - 1988. Volume 4. Distributed AI for Communications Network Management

DTIC Science & Technology

1989-10-01

apiots to rerlliii their los1 ’ at act ions iii Ilie rouist ’lirt iii of thle plain. Th’lis fast piece of iiiforiat liolu is plrovidied tlioiigli Ow 1use of...maximum compatible sets and delete subsets otherwise for every plan fragment pf, for g,. tile first goal in goals, if p.f- does not exceed resource... deletes an non-default assumption. 4.5.3.2 Data Structures The MATMS is a frame-based system in which there are five basic types of objects: beliefs

75 FR 13342 - Pipeline Safety: Workshop on Distribution Pipeline Construction

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-19

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration [Docket ID... natural gas distribution construction. Natural gas distribution pipelines are subject to a unique subset... distribution pipeline construction practices. This workshop will focus solely on natural gas distribution...

Label-free haemogram using wavelength modulated Raman spectroscopy for identifying immune-cell subset

NASA Astrophysics Data System (ADS)

Ashok, Praveen C.; Praveen, Bavishna B.; Campbell, Elaine C.; Dholakia, Kishan; Powis, Simon J.

2014-03-01

Leucocytes in the blood of mammals form a powerful protective system against a wide range of dangerous pathogens. There are several types of immune cells that has specific role in the whole immune system. The number and type of immune cells alter in the disease state and identifying the type of immune cell provides information about a person's state of health. There are several immune cell subsets that are essentially morphologically identical and require external labeling to enable discrimination. Here we demonstrate the feasibility of using Wavelength Modulated Raman Spectroscopy (WMRS) with suitable machine learning algorithms as a label-free method to distinguish between different closely lying immune cell subset. Principal Component Analysis (PCA) was performed on WMRS data from single cells, obtained using confocal Raman microscopy for feature reduction, followed by Support Vector Machine (SVM) for binary discrimination of various cell subset, which yielded an accuracy >85%. The method was successful in discriminating between untouched and unfixed purified populations of CD4+CD3+ and CD8+CD3+ T lymphocyte subsets, and CD56+CD3- natural killer cells with a high degree of specificity. It was also proved sensitive enough to identify unique Raman signatures that allow clear discrimination between dendritic cell subsets, comprising CD303+CD45+ plasmacytoid and CD1c+CD141+ myeloid dendritic cells. The results of this study clearly show that WMRS is highly sensitive and can distinguish between cell types that are morphologically identical.

Estimating the spatial distribution of artificial groundwater recharge using multiple tracers.

PubMed

Moeck, Christian; Radny, Dirk; Auckenthaler, Adrian; Berg, Michael; Hollender, Juliane; Schirmer, Mario

2017-10-01

Stable isotopes of water, organic micropollutants and hydrochemistry data are powerful tools for identifying different water types in areas where knowledge of the spatial distribution of different groundwater is critical for water resource management. An important question is how the assessments change if only one or a subset of these tracers is used. In this study, we estimate spatial artificial infiltration along an infiltration system with stage-discharge relationships and classify different water types based on the mentioned hydrochemistry data for a drinking water production area in Switzerland. Managed aquifer recharge via surface water that feeds into the aquifer creates a hydraulic barrier between contaminated groundwater and drinking water wells. We systematically compare the information from the aforementioned tracers and illustrate differences in distribution and mixing ratios. Despite uncertainties in the mixing ratios, we found that the overall spatial distribution of artificial infiltration is very similar for all the tracers. The highest infiltration occurred in the eastern part of the infiltration system, whereas infiltration in the western part was the lowest. More balanced infiltration within the infiltration system could cause the elevated groundwater mound to be distributed more evenly, preventing the natural inflow of contaminated groundwater. Dedicated to Professor Peter Fritz on the occasion of his 80th birthday.

Two Opsin 3-Related Proteins in the Chicken Retina and Brain: A TMT-Type Opsin 3 Is a Blue-Light Sensor in Retinal Horizontal Cells, Hypothalamus, and Cerebellum.

PubMed

Kato, Mutsuko; Sugiyama, Takashi; Sakai, Kazumi; Yamashita, Takahiro; Fujita, Hirofumi; Sato, Keita; Tomonari, Sayuri; Shichida, Yoshinori; Ohuchi, Hideyo

2016-01-01

Opsin family genes encode G protein-coupled seven-transmembrane proteins that bind a retinaldehyde chromophore in photoreception. Here, we sought potential as yet undescribed avian retinal photoreceptors, focusing on Opsin 3 homologs in the chicken. We found two Opsin 3-related genes in the chicken genome: one corresponding to encephalopsin/panopsin (Opn3) in mammals, and the other belonging to the teleost multiple tissue opsin (TMT) 2 group. Bioluminescence imaging and G protein activation assays demonstrated that the chicken TMT opsin (cTMT) functions as a blue light sensor when forced-expressed in mammalian cultured cells. We did not detect evidence of light sensitivity for the chicken Opn3 (cOpn3). In situ hybridization demonstrated expression of cTMT in subsets of differentiating cells in the inner retina and, as development progressed, predominant localization to retinal horizontal cells (HCs). Immunohistochemistry (IHC) revealed cTMT in HCs as well as in small numbers of cells in the ganglion and inner nuclear layers of the post-hatch chicken retina. In contrast, cOpn3-IR cells were found in distinct subsets of cells in the inner nuclear layer. cTMT-IR cells were also found in subsets of cells in the hypothalamus. Finally, we found differential distribution of cOpn3 and cTMT proteins in specific cells of the cerebellum. The present results suggest that a novel TMT-type opsin 3 may function as a photoreceptor in the chicken retina and brain.

Expression and Secretion of TNF-α in Mouse Taste Buds: A Novel Function of a Specific Subset of Type II Taste Cells

PubMed Central

Feng, Pu; Zhao, Hang; Chai, Jinghua; Huang, Liquan; Wang, Hong

2012-01-01

Taste buds are chemosensory structures widely distributed on the surface of the oral cavity and larynx. Taste cells, exposed to the oral environment, face great challenges in defense against potential pathogens. While immune cells, such as T-cells and macrophages, are rarely found in taste buds, high levels of expression of some immune-response-associated molecules are observed in taste buds. Yet, the cellular origins of these immune molecules such as cytokines in taste buds remain to be determined. Here, we show that a specific subset of taste cells selectively expresses high levels of the inflammatory cytokine tumor necrosis factor-α (TNF-α). Based on immuno-colocalization experiments using taste-cell-type markers, the TNF-α-producing cells are predominantly type II taste cells expressing the taste receptor T1R3. These cells can rapidly increase TNF-α production and secretion upon inflammatory challenges, both in vivo and in vitro. The lipopolysaccharide (LPS)-induced TNF-α expression in taste cells was completely eliminated in TLR2−/−/TLR4−/− double-gene-knockout mice, which confirms that the induction of TNF-α in taste buds by LPS is mediated through TLR signaling pathways. The taste-cell-produced TNF-α may contribute to local immune surveillance, as well as regulate taste sensation under normal and pathological conditions. PMID:22905218

Expression and secretion of TNF-α in mouse taste buds: a novel function of a specific subset of type II taste cells.

PubMed

Feng, Pu; Zhao, Hang; Chai, Jinghua; Huang, Liquan; Wang, Hong

2012-01-01

Taste buds are chemosensory structures widely distributed on the surface of the oral cavity and larynx. Taste cells, exposed to the oral environment, face great challenges in defense against potential pathogens. While immune cells, such as T-cells and macrophages, are rarely found in taste buds, high levels of expression of some immune-response-associated molecules are observed in taste buds. Yet, the cellular origins of these immune molecules such as cytokines in taste buds remain to be determined. Here, we show that a specific subset of taste cells selectively expresses high levels of the inflammatory cytokine tumor necrosis factor-α (TNF-α). Based on immuno-colocalization experiments using taste-cell-type markers, the TNF-α-producing cells are predominantly type II taste cells expressing the taste receptor T1R3. These cells can rapidly increase TNF-α production and secretion upon inflammatory challenges, both in vivo and in vitro. The lipopolysaccharide (LPS)-induced TNF-α expression in taste cells was completely eliminated in TLR2(-/-)/TLR4(-/-) double-gene-knockout mice, which confirms that the induction of TNF-α in taste buds by LPS is mediated through TLR signaling pathways. The taste-cell-produced TNF-α may contribute to local immune surveillance, as well as regulate taste sensation under normal and pathological conditions.

NKT Cell Subsets Can Exert Opposing Effects in Autoimmunity, Tumor Surveillance and Inflammation

PubMed Central

Viale, Rachael; Ware, Randle; Maricic, Igor; Chaturvedi, Varun; Kumar, Vipin

2014-01-01

The innate-like natural killer T (NKT) cells are essential regulators of immunity. These cells comprise at least two distinct subsets and recognize different lipid antigens presented by the MHC class I like molecules CD1d. The CD1d-dependent recognition pathway of NKT cells is highly conserved from mouse to humans. While most type I NKT cells can recognize αGalCer and express a semi-invariant T cell receptor (TCR), a major population of type II NKT cells reactive to sulfatide utilizes an oligoclonal TCR. Furthermore TCR recognition features of NKT subsets are also distinctive with almost parallel as opposed to perpendicular footprints on the CD1d molecules for the type I and type II NKT cells respectively. Here we present a view based upon the recent studies in different clinical and experimental settings that while type I NKT cells are more often pathogenic, they may also be regulatory. On the other hand, sulfatide-reactive type II NKT cells mostly play an inhibitory role in the control of autoimmune and inflammatory diseases. Since the activity and cytokine secretion profiles of NKT cell subsets can be modulated differently by lipid ligands or their analogs, novel immunotherapeutic strategies are being developed for their differential activation for potential intervention in inflammatory diseases. PMID:25288922

Long High Redshift GRB and Xrt/swift Lightcurves

NASA Astrophysics Data System (ADS)

Arkhangelskaja, Irene

At February of 2010 the volume of Swift GRB subset with known redshift consisted of more than 150 bursts. Long GRB redshift distribution analysis has shown that confidence level of single peak approximation of this distribution is only ˜60%. Moreover, more than 40% of GRB are in very heavy tails outside 3σ level for this fit. More detailed analysis of long GRB redshift distribution reveals that at 97% confidence level at least two subgroups could be separated with following parameters: = 0.9 ± 0.1 and = 2.7 ± 0.2. It allows to make conclusion that Swift long GRB sources subset is not uniform. In the presented article attention is paid on the measure of discrepancy of long GRB with z>3 and subset of other long GRB with known redshifts. XRT/Swift lightcurves for these groups of GRB were considered and it have shown that at least 90% XRT/Swift lightcurves for GRB with z>3 are more complicated and have got a number of maxima.

Acoustic and Categorical Dissimilarity of Musical Timbre: Evidence from Asymmetries Between Acoustic and Chimeric Sounds

PubMed Central

Siedenburg, Kai; Jones-Mollerup, Kiray; McAdams, Stephen

2016-01-01

This paper investigates the role of acoustic and categorical information in timbre dissimilarity ratings. Using a Gammatone-filterbank-based sound transformation, we created tones that were rated as less familiar than recorded tones from orchestral instruments and that were harder to associate with an unambiguous sound source (Experiment 1). A subset of transformed tones, a set of orchestral recordings, and a mixed set were then rated on pairwise dissimilarity (Experiment 2A). We observed that recorded instrument timbres clustered into subsets that distinguished timbres according to acoustic and categorical properties. For the subset of cross-category comparisons in the mixed set, we observed asymmetries in the distribution of ratings, as well as a stark decay of inter-rater agreement. These effects were replicated in a more robust within-subjects design (Experiment 2B) and cannot be explained by acoustic factors alone. We finally introduced a novel model of timbre dissimilarity based on partial least-squares regression that compared the contributions of both acoustic and categorical timbre descriptors. The best model fit (R2 = 0.88) was achieved when both types of descriptors were taken into account. These findings are interpreted as evidence for an interplay of acoustic and categorical information in timbre dissimilarity perception. PMID:26779086

An Active RBSE Framework to Generate Optimal Stimulus Sequences in a BCI for Spelling

NASA Astrophysics Data System (ADS)

Moghadamfalahi, Mohammad; Akcakaya, Murat; Nezamfar, Hooman; Sourati, Jamshid; Erdogmus, Deniz

2017-10-01

A class of brain computer interfaces (BCIs) employs noninvasive recordings of electroencephalography (EEG) signals to enable users with severe speech and motor impairments to interact with their environment and social network. For example, EEG based BCIs for typing popularly utilize event related potentials (ERPs) for inference. Presentation paradigm design in current ERP-based letter by letter typing BCIs typically query the user with an arbitrary subset characters. However, the typing accuracy and also typing speed can potentially be enhanced with more informed subset selection and flash assignment. In this manuscript, we introduce the active recursive Bayesian state estimation (active-RBSE) framework for inference and sequence optimization. Prior to presentation in each iteration, rather than showing a subset of randomly selected characters, the developed framework optimally selects a subset based on a query function. Selected queries are made adaptively specialized for users during each intent detection. Through a simulation-based study, we assess the effect of active-RBSE on the performance of a language-model assisted typing BCI in terms of typing speed and accuracy. To provide a baseline for comparison, we also utilize standard presentation paradigms namely, row and column matrix presentation paradigm and also random rapid serial visual presentation paradigms. The results show that utilization of active-RBSE can enhance the online performance of the system, both in terms of typing accuracy and speed.

Heating-Induced Evaporation of Nine Different Secondary Organic Aerosol Types

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolesar, Katheryn R.; Li, Ziyue; Wilson, Kevin R.

The volatility of the compounds comprising organic aerosol (OA) determines their distribution between the gas and particle phases. However, there is a disconnect between volatility distributions as typically derived from secondary OA (SOA) growth experiments and the effective particle volatility as probed in evaporation experiments. Specifically, the evaporation experiments indicate an overall much less volatile SOA. This raises questions regarding the use of traditional volatility distributions in the simulation and prediction of atmospheric SOA concentrations. Here, we present results from measurements of thermally induced evaporation of SOA for nine different SOA types (i.e., distinct volatile organic compound and oxidant pairs)more » encompassing both anthropogenic and biogenic compounds and O 3 and OH to examine the extent to which the low effective volatility of SOA is a general phenomenon or specific to a subset of SOA types. The observed extents of evaporation with temperature were similar for all the SOA types and indicative of a low effective volatility. Furthermore, minimal variations in the composition of all the SOA types upon heating-induced evaporation were observed. These results suggest that oligomer decomposition likely plays a major role in controlling SOA evaporation, and since the SOA formation time scale in these measurements was less than a minute, the oligomer-forming reactions must be similarly rapid. Overall, these results emphasize the importance of accounting for the role of condensed phase reactions in altering the composition of SOA when assessing particle volatility.« less

Numerical simulations of imaging satellites with optical interferometry

NASA Astrophysics Data System (ADS)

Ding, Yuanyuan; Wang, Chaoyan; Chen, Zhendong

2015-08-01

Optical interferometry imaging system, which is composed of multiple sub-apertures, is a type of sensor that can break through the aperture limit and realize the high resolution imaging. This technique can be utilized to precisely measure the shapes, sizes and position of astronomical objects and satellites, it also can realize to space exploration and space debris, satellite monitoring and survey. Fizeau-Type optical aperture synthesis telescope has the advantage of short baselines, common mount and multiple sub-apertures, so it is feasible for instantaneous direct imaging through focal plane combination.Since 2002, the researchers of Shanghai Astronomical Observatory have developed the study of optical interferometry technique. For array configurations, there are two optimal array configurations proposed instead of the symmetrical circular distribution: the asymmetrical circular distribution and the Y-type distribution. On this basis, two kinds of structure were proposed based on Fizeau interferometric telescope. One is Y-type independent sub-aperture telescope, the other one is segmented mirrors telescope with common secondary mirror.In this paper, we will give the description of interferometric telescope and image acquisition. Then we will mainly concerned the simulations of image restoration based on Y-type telescope and segmented mirrors telescope. The Richardson-Lucy (RL) method, Winner method and the Ordered Subsets Expectation Maximization (OS-EM) method are studied in this paper. We will analyze the influence of different stop rules too. At the last of the paper, we will present the reconstruction results of images of some satellites.

Heating-Induced Evaporation of Nine Different Secondary Organic Aerosol Types

DOE PAGES

Kolesar, Katheryn R.; Li, Ziyue; Wilson, Kevin R.; ...

2015-09-22

The volatility of the compounds comprising organic aerosol (OA) determines their distribution between the gas and particle phases. However, there is a disconnect between volatility distributions as typically derived from secondary OA (SOA) growth experiments and the effective particle volatility as probed in evaporation experiments. Specifically, the evaporation experiments indicate an overall much less volatile SOA. This raises questions regarding the use of traditional volatility distributions in the simulation and prediction of atmospheric SOA concentrations. Here, we present results from measurements of thermally induced evaporation of SOA for nine different SOA types (i.e., distinct volatile organic compound and oxidant pairs)more » encompassing both anthropogenic and biogenic compounds and O 3 and OH to examine the extent to which the low effective volatility of SOA is a general phenomenon or specific to a subset of SOA types. The observed extents of evaporation with temperature were similar for all the SOA types and indicative of a low effective volatility. Furthermore, minimal variations in the composition of all the SOA types upon heating-induced evaporation were observed. These results suggest that oligomer decomposition likely plays a major role in controlling SOA evaporation, and since the SOA formation time scale in these measurements was less than a minute, the oligomer-forming reactions must be similarly rapid. Overall, these results emphasize the importance of accounting for the role of condensed phase reactions in altering the composition of SOA when assessing particle volatility.« less

A Preliminary Analysis of LANDSAT-4 Thematic Mapper Radiometric Performance

NASA Technical Reports Server (NTRS)

Justice, C.; Fusco, L.; Mehl, W.

1985-01-01

The NASA raw (BT) product, the radiometrically corrected (AT) product, and the radiometrically and geometrically corrected (PT) product of a TM scene were analyzed examine the frequency distribution of the digital data; the statistical correlation between the bands; and the variability between the detectors within a band. The analyses were performed on a series of image subsets from the full scence. Results are presented from one 1024 c 1024 pixel subset of Realfoot Lake, Tennessee which displayed a representative range of ground conditions and cover types occurring within the full frame image. From this cursory examination of one of the first seven channel TM data sets, it would appear that the radiometric performance of the system is most satisfactory and largely meets pre-launch specifications. Problems were noted with Band 5 Detector 3 and Band 2 Detector 4. Differences were observed between forward and reverse scan detector responses both for the BT and AT products. No systematic variations were observed between odd and even detectors.

Evaluation of spatial, radiometric and spectral thematic mapper performance for coastal studies

NASA Technical Reports Server (NTRS)

Klemas, V. (Principal Investigator)

1983-01-01

An area along the southeastern shore of the Chesapeake Bay was subsetted from TM imagery. The subsetted image was then enhanced and classified using an ERDAS 400 system. Results obtained were compared with a chart showing the distribution of both Zolsters marina and Rupplia martime in the Vaucluse Shores and which supports a large community of SAV. Radiative transfer models describing the irradiance reflectance of a water column containing SAV are being refined. Radiative transfer theory was used to model upwelling radiance for an orbiting sensor viewing an estuarine environment. Upwelling radiance was calculated for a clear maritime atmosphere, an optically shallow estuary of either clear or turbid water, and one of three bottom types: vegetation, sand, or mud using TM bands 1, 2, and 3 and MSS bands 4 and 5. A spectral quality index was defined similar to the equation for apparent contrast and used to evaluate the relative effectiveness of TM and MSS bands in detecting submerged vegetation.

Mapping of NKp46+ Cells in Healthy Human Lymphoid and Non-Lymphoid Tissues

PubMed Central

Tomasello, Elena; Yessaad, Nadia; Gregoire, Emilie; Hudspeth, Kelly; Luci, Carmelo; Mavilio, Domenico; Hardwigsen, Jean; Vivier, Eric

2012-01-01

Understanding Natural Killer (NK) cell anatomical distribution is key to dissect the role of these unconventional lymphocytes in physiological and disease conditions. In mouse, NK cells have been detected in various lymphoid and non-lymphoid organs, while in humans the current knowledge of NK cell distribution at steady state is mainly restricted to lymphoid tissues. The translation to humans of findings obtained in mice is facilitated by the identification of NK cell markers conserved between these two species. The Natural Cytotoxicity Receptor (NCR) NKp46 is a marker of the NK cell lineage evolutionary conserved in mammals. In mice, NKp46 is also present on rare T cell subsets and on a subset of gut Innate Lymphoid Cells (ILCs) expressing the retinoic acid receptor-related orphan receptor γt (RORγt) transcription factor. Here, we documented the distribution and the phenotype of human NKp46+ cells in lymphoid and non-lymphoid tissues isolated from healthy donors. Human NKp46+ cells were found in splenic red pulp, in lymph nodes, in lungs, and gut lamina propria, thus mirroring mouse NKp46+ cell distribution. We also identified a novel cell subset of CD56dimNKp46low cells that includes RORγt+ ILCs with a lineage−CD94−CD117brightCD127bright phenotype. The use of NKp46 thus contributes to establish the basis for analyzing quantitative and qualitative changes of NK cell and ILC subsets in human diseases. PMID:23181063

Effects of selective type I and II adrenal steroid agonists on immune cell distribution.

PubMed

Miller, A H; Spencer, R L; hassett, J; Kim, C; Rhee, R; Ciurea, D; Dhabhar, F; McEwen, B; Stein, M

1994-11-01

Adrenal steroids exert their effects through two distinct adrenal steroid receptor subtypes; the high affinity type I, or mineralocorticoid, receptor and the lower affinity type II, or glucocorticoid, receptor. Adrenal steroids have well known effects on immune cell distribution, and although both type I and II receptors are expressed in immune cells and tissues, few data exist on the relative effects mediated through these two receptor subtypes. Accordingly, we administered selective type I and II adrenal steroid receptor agonists to young adult male Sprague-Dawley rats for 7 days and then measured immune cell distribution in the peripheral blood and spleen. Results were compared with those of similar studies using the naturally occurring glucocorticoid of the rat, corticosterone, which binds both type I and II receptors. The majority of the well characterized effects of adrenal steroids on peripheral blood immune cells (increased neutrophils and decreased lymphocytes and monocytes) were reproduced by the type II receptor agonist, RU28362. RU28362 decreased the numbers of all lymphocyte subsets [T-cells, B-cells, and natural killer (NK) cells] to very low absolute levels. The largest relative decrease (i.e. in percentage) was seen in B-cells, whereas NK cells exhibited the least relative decrease and actually showed a 2-fold increase in relative percentage during RU28362 treatment. Similar to RU28362, the type I receptor agonist, aldosterone, significantly reduced the number of lymphocytes and monocytes. In contrast to RU28362, however, aldosterone significantly decreased the number of neutrophils. Moreover, aldosterone decreased the number of T-helper cells and NK cells, while having no effect on the number of B-cells or T-suppressor/cytotoxic cells. Corticosterone at physiologically relevant concentrations had potent effects on immune cell distribution, which were indistinguishable from those of the type II receptor agonist, RU28362. Taken together, these results indicate that effects of adrenal steroids on immune cell distribution are dependent on the receptor subtype involved as well as the specific cell type targeted. These factors allow for varied and complex effects of adrenal steroids on the immune system under physiological conditions.

Generalized Lotka—Volterra systems connected with simple Lie algebras

NASA Astrophysics Data System (ADS)

Charalambides, Stelios A.; Damianou, Pantelis A.; Evripidou, Charalambos A.

2015-06-01

We devise a new method for producing Hamiltonian systems by constructing the corresponding Lax pairs. This is achieved by considering a larger subset of the positive roots than the simple roots of the root system of a simple Lie algebra. We classify all subsets of the positive roots of the root system of type An for which the corresponding Hamiltonian systems are transformed, via a simple change of variables, to Lotka-Volterra systems. For some special cases of subsets of the positive roots of the root system of type An, we produce new integrable Hamiltonian systems.

Evolution of nuclear rDNA ITS sequences in the Cladophora albida/sericea clade (Chlorophyta).

PubMed

Bakker, F T; Olsen, J L; Stam, W T

1995-06-01

Ribosomal DNA ITS sequences were compared among 13 different species and biogeographic isolates from the monophyletic "albida/sericea clade" in the green algal genus Cladophora. Six distinct ITS sequence types were found, characterized by multiple insertions and deletions and high levels of nucleotide substitution. Conserved domains within the ITS regions indicate the presence of ITS secondary structure. Low transition/transversion ratios among the six types and nearly symmetrical tree-length frequency distributions indicate some saturation, and low phylogenetic signal. Although branching order among five of the six ITS sequence types could not be resolved, estimates of ITS sequence divergence as compared with 18S divergence in a subset of the taxa suggests that the origin of the different ITS types is probably in the mid-Miocene (12 Ma ago) but that biogeographic isolates within a single ITS type (including both Pacific and Atlantic representatives) have probably dispersed on a time scale of thousands rather than millions of years.

HZETRN radiation transport validation using balloon-based experimental data

NASA Astrophysics Data System (ADS)

Warner, James E.; Norman, Ryan B.; Blattnig, Steve R.

2018-05-01

The deterministic radiation transport code HZETRN (High charge (Z) and Energy TRaNsport) was developed by NASA to study the effects of cosmic radiation on astronauts and instrumentation shielded by various materials. This work presents an analysis of computed differential flux from HZETRN compared with measurement data from three balloon-based experiments over a range of atmospheric depths, particle types, and energies. Model uncertainties were quantified using an interval-based validation metric that takes into account measurement uncertainty both in the flux and the energy at which it was measured. Average uncertainty metrics were computed for the entire dataset as well as subsets of the measurements (by experiment, particle type, energy, etc.) to reveal any specific trends of systematic over- or under-prediction by HZETRN. The distribution of individual model uncertainties was also investigated to study the range and dispersion of errors beyond just single scalar and interval metrics. The differential fluxes from HZETRN were generally well-correlated with balloon-based measurements; the median relative model difference across the entire dataset was determined to be 30%. The distribution of model uncertainties, however, revealed that the range of errors was relatively broad, with approximately 30% of the uncertainties exceeding ± 40%. The distribution also indicated that HZETRN systematically under-predicts the measurement dataset as a whole, with approximately 80% of the relative uncertainties having negative values. Instances of systematic bias for subsets of the data were also observed, including a significant underestimation of alpha particles and protons for energies below 2.5 GeV/u. Muons were found to be systematically over-predicted at atmospheric depths deeper than 50 g/cm2 but under-predicted for shallower depths. Furthermore, a systematic under-prediction of alpha particles and protons was observed below the geomagnetic cutoff, suggesting that improvements to the light ion production cross sections in HZETRN should be investigated.

Definition of Drosophila hemocyte subsets by cell-type specific antigens.

PubMed

Kurucz, Eva; Váczi, B; Márkus, R; Laurinyecz, Barbara; Vilmos, P; Zsámboki, J; Csorba, Kinga; Gateff, Elisabeth; Hultmark, D; Andó, I

2007-01-01

We analyzed the heterogeneity of Drosophila hemocytes on the basis of the expression of cell-type specific antigens. The antigens characterize distinct subsets which partially overlap with those defined by morphological criteria. On the basis of the expression or the lack of expression of blood cell antigens the following hemocyte populations have been defined: crystal cells, plasmatocytes, lamellocytes and precursor cells. The expression of the antigens and thus the different cell types are developmentally regulated. The hemocytes are arranged in four main compartments: the circulating blood cells, the sessile tissue, the lymph glands and the posterior hematopoietic tissue. Each hemocyte compartment has a specific and characteristic composition of the various cell types. The described markers represent the first successful attempt to define hemocyte lineages by immunological markers in Drosophila and help to define morphologically, functionally, spatially and developmentally distinct subsets of hemocytes.

The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells.

PubMed

Rubio, María E; Matsui, Ko; Fukazawa, Yugo; Kamasawa, Naomi; Harada, Harumi; Itakura, Makoto; Molnár, Elek; Abe, Manabu; Sakimura, Kenji; Shigemoto, Ryuichi

2017-11-01

The neurotransmitter receptor subtype, number, density, and distribution relative to the location of transmitter release sites are key determinants of signal transmission. AMPA-type ionotropic glutamate receptors (AMPARs) containing GluA3 and GluA4 subunits are prominently expressed in subsets of neurons capable of firing action potentials at high frequencies, such as auditory relay neurons. The auditory nerve (AN) forms glutamatergic synapses on two types of relay neurons, bushy cells (BCs) and fusiform cells (FCs) of the cochlear nucleus. AN-BC and AN-FC synapses have distinct kinetics; thus, we investigated whether the number, density, and localization of GluA3 and GluA4 subunits in these synapses are differentially organized using quantitative freeze-fracture replica immunogold labeling. We identify a positive correlation between the number of AMPARs and the size of AN-BC and AN-FC synapses. Both types of AN synapses have similar numbers of AMPARs; however, the AN-BC have a higher density of AMPARs than AN-FC synapses, because the AN-BC synapses are smaller. A higher number and density of GluA3 subunits are observed at AN-BC synapses, whereas a higher number and density of GluA4 subunits are observed at AN-FC synapses. The intrasynaptic distribution of immunogold labeling revealed that AMPAR subunits, particularly GluA3, are concentrated at the center of the AN-BC synapses. The central distribution of AMPARs is absent in GluA3-knockout mice, and gold particles are evenly distributed along the postsynaptic density. GluA4 gold labeling was homogenously distributed along both synapse types. Thus, GluA3 and GluA4 subunits are distributed at AN synapses in a target-cell-dependent manner.

Investigating Evolutionary Conservation of Dendritic Cell Subset Identity and Functions

PubMed Central

Vu Manh, Thien-Phong; Bertho, Nicolas; Hosmalin, Anne; Schwartz-Cornil, Isabelle; Dalod, Marc

2015-01-01

Dendritic cells (DCs) were initially defined as mononuclear phagocytes with a dendritic morphology and an exquisite efficiency for naïve T-cell activation. DC encompass several subsets initially identified by their expression of specific cell surface molecules and later shown to excel in distinct functions and to develop under the instruction of different transcription factors or cytokines. Very few cell surface molecules are expressed in a specific manner on any immune cell type. Hence, to identify cell types, the sole use of a small number of cell surface markers in classical flow cytometry can be deceiving. Moreover, the markers currently used to define mononuclear phagocyte subsets vary depending on the tissue and animal species studied and even between laboratories. This has led to confusion in the definition of DC subset identity and in their attribution of specific functions. There is a strong need to identify a rigorous and consensus way to define mononuclear phagocyte subsets, with precise guidelines potentially applicable throughout tissues and species. We will discuss the advantages, drawbacks, and complementarities of different methodologies: cell surface phenotyping, ontogeny, functional characterization, and molecular profiling. We will advocate that gene expression profiling is a very rigorous, largely unbiased and accessible method to define the identity of mononuclear phagocyte subsets, which strengthens and refines surface phenotyping. It is uniquely powerful to yield new, experimentally testable, hypotheses on the ontogeny or functions of mononuclear phagocyte subsets, their molecular regulation, and their evolutionary conservation. We propose defining cell populations based on a combination of cell surface phenotyping, expression analysis of hallmark genes, and robust functional assays, in order to reach a consensus and integrate faster the huge but scattered knowledge accumulated by different laboratories on different cell types, organs, and species. PMID:26082777

Listeria arpJ gene modifies T helper type 2 subset differentiation.

PubMed

Kanoh, Makoto; Maruyama, Saho; Shen, Hua; Matsumoto, Akira; Shinomiya, Hiroto; Przybilla, Karin; Gouin, Edith; Cossart, Pascale; Goebel, Werner; Asano, Yoshihiro

2015-07-15

Although the T-cell subset differentiation pathway has been characterized extensively from the view of host gene regulation, the effects of genes of the pathogen on T-cell subset differentiation during infection have yet to be elucidated. Especially, the bacterial genes that are responsible for this shift have not yet been determined. Utilizing a single-gene-mutation Listeria panel, we investigated genes involved in the host-pathogen interaction that are required for the initiation of T-cell subset differentiation in the early phase of pathogen infection. We demonstrate that the induction of T helper types 1 and 2 (Th1 and Th2) subsets are separate phenomena and are mediated by distinct Listeria genes. We identified several candidate Listeria genes that appear to be involved in the host-Listeria interaction. Among them, arpJ is the strongest candidate gene for inhibiting Th2 subset induction. Furthermore, the analysis utilizing arpJ-deficient Listeria monocytogenes (Lm) revealed that the tumor necrosis factor (TNF) superfamily (Tnfsf) 9-TNF receptor superfamily (Tnfrsf) 9 interaction inhibits the Th2 response during Lm infection. arpJ is the candidate gene for inhibiting Th2 T-cell subset induction. The arpJ gene product influences the expression of Tnfsf/Tnfrsf on antigen-presenting cells and inhibits the Th2 T-cell subset differentiation during Listeria infection. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Evaluation of volatile organic compounds in two Mojave Desert basins-Mojave River and Antelope Valley-in San Bernardino, Los Angeles, and Kern Counties, California, June-October 2002

USGS Publications Warehouse

Densmore, Jill N.; Belitz, Kenneth; Wright, Michael T.; Dawson, Barbara J.; Johnson, Tyler D.

2005-01-01

The California Aquifer Susceptibility Assessment of the Ground-Water Ambient Monitoring and Assessment Program was developed to assess water quality and susceptibility of ground-water resources to contamination from surficial sources. This study focuses on the Mojave River and the Antelope Valley ground-water basins in southern California. Volatile organic compound (VOC) data were evaluated in conjunction with tritium data to determine a potential correlation with aquifer type, depth to top of perforations, and land use to VOC distribution and occurrence in the Mojave River and the Antelope Valley Basins. Detection frequencies for VOCs were compiled and compared to assess the distribution in each area. Explanatory variables were evaluated by comparing detection frequencies for VOCs and tritium and the number of compounds detected. Thirty-three wells were sampled in the Mojave River Basin (9 in the floodplain aquifer, 15 in the regional aquifer, and 9 in the sewered subset of the regional aquifer). Thirty-two wells were sampled in the Antelope Valley Basin. Quality-control samples also were collected to identify, quantify, and document bias and variability in the data. Results show that VOCs generally were detected slightly more often in the Antelope Valley Basin samples than in the Mojave River Basin samples. VOCs were detected more frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Tritium was detected more frequently in the Mojave River Basin samples than in the Antelope Valley Basin samples, and it was detected more frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Most of the samples collected in both basins for this study contained old water (water recharged prior to 1952). In general, in these desert basins, tritium need not be present for VOCs to be present. When VOCs were detected, young water (water recharge after 1952) was slightly more likely to be contaminated than old water. Trihalomethanes (THMs) were detected less frequently in the Mojave River Basin samples than in the Antelope Valley Basin samples. The THMs that were detected in the Mojave River Basin were detected more frequently in the floodplain aquifer than in the regional aquifer and sewered subset. Solvents were detected more frequently in the Mojave River samples than in the Antelope Valley samples. In the Mojave River Basin samples, solvents were detected less frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Benzene, toluene, ethylbenzene and xylene (BTEX) were not detected in either study area. Methyl tert-butyl ether (MTBE) was detected in one sample from both the Mojave River and Antelope Valley Basins. The most frequently detected compound (detected in more than 10 percent of the wells) in the Mojave River Basin was chloroform. The two most frequently detected compounds in the Antelope Valley Basin were chloroform and tetrachloroethylene (PCE). In the Mojave River Basin, aquifer type and land use within 1,640 ft (500 m) of the well head were not statistically correlated with the number of VOCs detected, although VOCs were detected more frequently in the floodplain aquifer than in the regional aquifer and the sewered subset. Depth to the top of the perforations was an explanatory factor for the number of VOCs detected in the Mojave River Basin; the detection frequency was greater for shallow wells than for deep wells. In the Antelope Valley Basin, neither aquifer type, depth to the top of the perforations, nor land use within 1,640 ft of the well head were explanatory factors for the number of VOCs detected. Although aquifer type and depth to top of the perforations did explain the presence of tritium in the Mojave River Basin, land use within 1,640 ft of the well head was not a statistically significant explanatory factor for the presence of tritium in this basin. Aquifer type, depth to the top of the perfora

Predicting fundamental and realized distributions based on thermal niche: A case study of a freshwater turtle

NASA Astrophysics Data System (ADS)

Rodrigues, João Fabrício Mota; Coelho, Marco Túlio Pacheco; Ribeiro, Bruno R.

2018-04-01

Species distribution models (SDM) have been broadly used in ecology to address theoretical and practical problems. Currently, there are two main approaches to generate SDMs: (i) correlative, which is based on species occurrences and environmental predictor layers and (ii) process-based models, which are constructed based on species' functional traits and physiological tolerances. The distributions estimated by each approach are based on different components of species niche. Predictions of correlative models approach species realized niches, while predictions of process-based are more akin to species fundamental niche. Here, we integrated the predictions of fundamental and realized distributions of the freshwater turtle Trachemys dorbigni. Fundamental distribution was estimated using data of T. dorbigni's egg incubation temperature, and realized distribution was estimated using species occurrence records. Both types of distributions were estimated using the same regression approaches (logistic regression and support vector machines), both considering macroclimatic and microclimatic temperatures. The realized distribution of T. dorbigni was generally nested in its fundamental distribution reinforcing theoretical assumptions that the species' realized niche is a subset of its fundamental niche. Both modelling algorithms produced similar results but microtemperature generated better results than macrotemperature for the incubation model. Finally, our results reinforce the conclusion that species realized distributions are constrained by other factors other than just thermal tolerances.

Psychophysics of the McGurk and Other Audiovisual Speech Integration Effects

PubMed Central

Jiang, Jintao; Bernstein, Lynne E.

2011-01-01

When the auditory and visual components of spoken audiovisual nonsense syllables are mismatched, perceivers produce four different types of perceptual responses, auditory correct, visual correct, fusion (the so-called McGurk effect), and combination (i.e., two consonants are reported). Here, quantitative measures were developed to account for the distribution of types of perceptual responses to 384 different stimuli from four talkers. The measures included mutual information, the presented acoustic signal versus the acoustic signal recorded with the presented video, and the correlation between the presented acoustic and video stimuli. In Experiment 1, open-set perceptual responses were obtained for acoustic /bA/ or /lA/ dubbed to video /bA, dA, gA, vA, zA, lA, wA, ΔA/. The talker, the video syllable, and the acoustic syllable significantly influenced the type of response. In Experiment 2, the best predictors of response category proportions were a subset of the physical stimulus measures, with the variance accounted for in the perceptual response category proportions between 17% and 52%. That audiovisual stimulus relationships can account for response distributions supports the possibility that internal representations are based on modality-specific stimulus relationships. PMID:21574741

Data on correlations between T cell subset frequencies and length of partial remission in type 1 diabetes.

PubMed

Narsale, Aditi; Moya, Rosita; Robertson, Hannah Kathryn; Davies, Joanna Davida

2016-09-01

Partial remission in patients newly diagnosed with type 1 diabetes is a period of good glucose control that can last from several weeks to over a year. The clinical significance of the remission period is that patients might be more responsive to immunotherapy if treated within this period. This article provides clinical data that indicates the level of glucose control and insulin-secreting β-cell function of each patient in the study at baseline (within 3 months of diagnosis), and at 3, 6, 9, 12, 18 and 24 months post-baseline. The relative frequency of immune cell subsets in the PBMC of each patient and the association between the frequency of immune cell subsets measured and length of remission is also shown. These data support the findings reported in the accompanying publication, "A pilot study showing associations between frequency of CD4+ memory cell subsets at diagnosis and duration of partial remission in type 1 diabetes" (Moya et al., 2016) [1], where a full interpretation, including biological relevance of the study can be found.

Comparison of Campylobacter jejuni isolates from human, food, veterinary and environmental sources in Iceland using PFGE, MLST and fla-SVR sequencing.

PubMed

Magnússon, S H; Guðmundsdóttir, S; Reynisson, E; Rúnarsson, A R; Harðardóttir, H; Gunnarson, E; Georgsson, F; Reiersen, J; Marteinsson, V Th

2011-10-01

Campylobacter jejuni isolates from various sources in Iceland were genotyped with the aim of assessing the genetic diversity, population structure, source distribution and campylobacter transmission routes to humans. A collection of 584 Campylobacter isolates were collected from clinical cases, food, animals and environment in Iceland in 1999-2002, during a period of national Campylobacter epidemic in Iceland. All isolates were characterized by pulse field gel electrophoresis (PFGE), and selected subset of 52 isolates representing the diversity of the identified PFGE types was further genotyped using multilocus sequence typing (MLST) and fla-SVR sequencing to gain better insight into the population structure. The results show a substantial diversity within the Icelandic Campylobacter population. Majority of the human Campylobacter infections originated from domestic chicken and cattle isolates. MLST showed the isolates to be distributed among previously reported and common sequence type complexes in the MLST database. The genotyping of Campylobacter from various sources has not previously been reported from Iceland, and the results of the study gave a valuable insight into the population structure of Camp. jejuni in Iceland, source distribution and transmission routes to humans. The geographical isolation of Iceland in the north Atlantic provides new information on Campylobacter population dynamics on a global scale. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology No claim to Icelandic Government works.

Flood Extent Delineation by Thresholding Sentinel-1 SAR Imagery Based on Ancillary Land Cover Information

NASA Astrophysics Data System (ADS)

Liang, J.; Liu, D.

2017-12-01

Emergency responses to floods require timely information on water extents that can be produced by satellite-based remote sensing. As SAR image can be acquired in adverse illumination and weather conditions, it is particularly suitable for delineating water extent during a flood event. Thresholding SAR imagery is one of the most widely used approaches to delineate water extent. However, most studies apply only one threshold to separate water and dry land without considering the complexity and variability of different dry land surface types in an image. This paper proposes a new thresholding method for SAR image to delineate water from other different land cover types. A probability distribution of SAR backscatter intensity is fitted for each land cover type including water before a flood event and the intersection between two distributions is regarded as a threshold to classify the two. To extract water, a set of thresholds are applied to several pairs of land cover types—water and urban or water and forest. The subsets are merged to form the water distribution for the SAR image during or after the flooding. Experiments show that this land cover based thresholding approach outperformed the traditional single thresholding by about 5% to 15%. This method has great application potential with the broadly acceptance of the thresholding based methods and availability of land cover data, especially for heterogeneous regions.

Morphological and physiological analysis of type-5 and other bipolar cells in the Mouse Retina.

PubMed

Hellmer, C B; Zhou, Y; Fyk-Kolodziej, B; Hu, Z; Ichinose, T

2016-02-19

Retinal bipolar cells are second-order neurons in the visual system, which initiate multiple image feature-based neural streams. Among more than ten types of bipolar cells, type-5 cells are thought to play a role in motion detection pathways. Multiple subsets of type-5 cells have been reported; however, detailed characteristics of each subset have not yet been elucidated. Here, we found that they exhibit distinct morphological features as well as unique voltage-gated channel expression. We have conducted electrophysiological and immunohistochemical analysis of retinal bipolar cells. We defined type-5 cells by their axon terminal ramification in the inner plexiform layer between the border of ON/OFF sublaminae and the ON choline acetyltransferase (ChAT) band. We found three subsets of type-5 cells: XBCs had the widest axon terminals that stratified at a close approximation of the ON ChAT band as well as exhibiting large voltage-gated Na(+) channel activity, type-5-1 cells had compact terminals and no Na(+) channel activity, and type-5-2 cells contained umbrella-shaped terminals as well as large voltage-gated Na(+) channel activity. Hyperpolarization-activated cyclic nucleotide-gated (HCN) currents were also evoked in all type-5 bipolar cells. We found that XBCs and type-5-2 cells exhibited larger HCN currents than type-5-1 cells. Furthermore, the former two types showed stronger HCN1 expression than the latter. Our previous observations (Ichinose et al., 2014) match the current study: low temporal tuning cells that we named 5S corresponded to 5-1 in this study, while high temporal tuning 5f cells from the previous study corresponded to 5-2 cells. Taken together, we found three subsets of type-5 bipolar cells based on their morphologies and physiological features. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

Wild-type MIC distributions of four fluoroquinolones active against Mycobacterium tuberculosis in relation to current critical concentrations and available pharmacokinetic and pharmacodynamic data.

PubMed

Angeby, K A; Jureen, P; Giske, C G; Chryssanthou, E; Sturegård, E; Nordvall, M; Johansson, A G; Werngren, J; Kahlmeter, G; Hoffner, S E; Schön, T

2010-05-01

To describe wild-type distributions of the MIC of fluoroquinolones for Mycobacterium tuberculosis in relation to current critical concentrations used for drug susceptibility testing and pharmacokinetic/pharmacodynamic (PK/PD) data. A 96-stick replicator on Middlebrook 7H10 medium was used to define the MICs of ciprofloxacin, ofloxacin, moxifloxacin and levofloxacin for 90 consecutive clinical strains and 24 drug-resistant strains. The MICs were compared with routine BACTEC 460 susceptibility results and with MIC determinations in the BACTEC MGIT 960 system in a subset of strains using ofloxacin as a class representative. PK/PD data for each drug were reviewed in relation to the wild-type MIC distribution. The wild-type MICs of ciprofloxacin, ofloxacin, moxifloxacin and levofloxacin were distributed from 0.125 to 1, 0.25 to 1, 0.032 to 0.5 and 0.125 to 0.5 mg/L, respectively. The MIC data correlated well with the BACTEC 960 MGIT and BACTEC 460 results. PD indices were the most favourable for levofloxacin, followed by moxifloxacin, ofloxacin and ciprofloxacin. We propose S (susceptible)

Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014.

PubMed

Becker, Laura; Kaase, Martin; Pfeifer, Yvonne; Fuchs, Stephan; Reuss, Annicka; von Laer, Anja; Sin, Muna Abu; Korte-Berwanger, Miriam; Gatermann, Sören; Werner, Guido

2018-01-01

By using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing K. pneumoniae isolated from hospitalized patients in Germany between 2008 and 2014. We selected a representative subset of 107 carbapenemase-producing K. pneumoniae clinical isolates possessing the four most prevalent carbapenemase types in Germany (KPC-2, KPC-3, OXA-48, NDM-1). Isolates were processed via illumina NGS. Data were analysed using different SNP-based mapping and de-novo assembly approaches. Relevant information was extracted from NGS data (antibiotic resistance determinants, wzi gene/ cps type, virulence genes). NGS data from the present study were also compared with 238 genome data from two previous international studies on K. pneumoniae. NGS-based analyses revealed a preferred prevalence of KPC-2-producing ST258 and KPC-3-producing ST512 isolates. OXA-48, being the most prevalent carbapenemase type in Germany, was associated with various K. pneumoniae strain types; most of them possessing IncL/M plasmid replicons suggesting a preferred dissemination of bla OXA-48 via this well-known plasmid type. Clusters ST15, ST147, ST258, and ST512 demonstrated an intermingled subset structure consisting of German and other European K. pneumoniae isolates. ST23 being the most frequent MLST type in Asia was found only once in Germany. This latter isolate contained an almost complete set of virulence genes and a K1 capsule suggesting occurrence of a hypervirulent ST23 strain producing OXA-48 in Germany. Our study results suggest prevalence of "classical" K. pneumonaie strain types associated with widely distributed carbapenemase genes such as ST258/KPC-2 or ST512/KPC-3 also in Germany. The finding of a supposed hypervirulent and OXA-48-producing ST23 K. pneumoniae isolates outside Asia is highly worrisome and requires intense molecular surveillance.

Figuring fact from fiction: unbiased polling of memory T cells.

PubMed

Gerlach, Carmen; Loughhead, Scott M; von Andrian, Ulrich H

2015-05-07

Immunization generates several memory T cell subsets that differ in their migratory properties, anatomic distribution, and, hence, accessibility to investigation. In this issue, Steinert et al. demonstrate that what was believed to be a minor memory cell subset in peripheral tissues has been dramatically underestimated. Thus, current models of protective immunity require revision. Copyright © 2015 Elsevier Inc. All rights reserved.

The U.S. glulam beam and lamstock market and implications for Alaska lumber.

Treesearch

Joseph A. Roos; Allen M. Brackley; Daisuke Sasatani

2009-01-01

In this study, glulam beam manufacturers in the United States and Canada were surveyed regarding their lamstock usage and glulam beam distribution channels. The respondents were divided into three subsets to measure regional comparisons: U.S. West, U.S. Central and South, and Canada. They were further divided into subsets based on annual sales figures. The research...

Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification

PubMed Central

2012-01-01

Background Previous studies on tumor classification based on gene expression profiles suggest that gene selection plays a key role in improving the classification performance. Moreover, finding important tumor-related genes with the highest accuracy is a very important task because these genes might serve as tumor biomarkers, which is of great benefit to not only tumor molecular diagnosis but also drug development. Results This paper proposes a novel gene selection method with rich biomedical meaning based on Heuristic Breadth-first Search Algorithm (HBSA) to find as many optimal gene subsets as possible. Due to the curse of dimensionality, this type of method could suffer from over-fitting and selection bias problems. To address these potential problems, a HBSA-based ensemble classifier is constructed using majority voting strategy from individual classifiers constructed by the selected gene subsets, and a novel HBSA-based gene ranking method is designed to find important tumor-related genes by measuring the significance of genes using their occurrence frequencies in the selected gene subsets. The experimental results on nine tumor datasets including three pairs of cross-platform datasets indicate that the proposed method can not only obtain better generalization performance but also find many important tumor-related genes. Conclusions It is found that the frequencies of the selected genes follow a power-law distribution, indicating that only a few top-ranked genes can be used as potential diagnosis biomarkers. Moreover, the top-ranked genes leading to very high prediction accuracy are closely related to specific tumor subtype and even hub genes. Compared with other related methods, the proposed method can achieve higher prediction accuracy with fewer genes. Moreover, they are further justified by analyzing the top-ranked genes in the context of individual gene function, biological pathway, and protein-protein interaction network. PMID:22830977

PD-1 is a marker for abnormal distribution of naïve/memory T cell subsets in HIV-1 infection

PubMed Central

Breton, Gaëlle; Chomont, Nicolas; Takata, Hiroshi; Fromentin, Rémi; Ahlers, Jeffrey; Filali-Mouhim, Abdelali; Riou, Catherine; Boulassel, Mohamed-Rachid; Routy, Jean-Pierre; Yassine-Diab, Bader; Sékaly, Rafick-Pierre

2013-01-01

Chronic activation of T cells is a hallmark of HIV-1 infection and plays an important role in disease progression. We previously showed that the engagement of the inhibitory receptor PD-1 on HIV-1 specific CD4+ and CD8+ T cells leads to their functional exhaustion in vitro. However, little is known about the impact of PD-1 expression on the turnover and maturation status of T cells during the course of the disease. Here, we show that PD-1 is up regulated on all T cell subsets including naïve, central memory and transitional memory T cells in HIV-1 infected subjects. PD-1 is expressed at similar levels on most CD4+ T cells during the acute and the chronic phase of disease and identifies cells that have recently entered the cell cycle. In contrast, PD-1 expression dramatically increased in CD8+ T cells during the transition from acute to chronic infection and this was associated with reduced levels of cell proliferation. The failure to down regulate expression of PD-1 in most T cells during chronic HIV-1 infection was associated to persistent alterations in the distribution of T cell subsets and was associated with impaired responses to IL-7. Our findings identify PD-1 as a marker for aberrant distribution of T cell subsets in HIV-1 infection. PMID:23918986

Introducing the Qplex: a novel arena for quantum theory

NASA Astrophysics Data System (ADS)

Appleby, Marcus; Fuchs, Christopher A.; Stacey, Blake C.; Zhu, Huangjun

2017-07-01

We reconstruct quantum theory starting from the premise that, as Asher Peres remarked, "Unperformed experiments have no results." The tools of quantum information theory, and in particular the symmetric informationally complete (SIC) measurements, provide a concise expression of how exactly Peres's dictum holds true. That expression is a constraint on how the probability distributions for outcomes of different, hypothetical and mutually exclusive experiments ought to mesh together, a type of constraint not foreseen in classical thinking. Taking this as our foundational principle, we show how to reconstruct the formalism of quantum theory in finite-dimensional Hilbert spaces. The central variety of mathematical entity in our reconstruction is the qplex, a very particular type of subset of a probability simplex. Along the way, by closely studying the symmetry properties of qplexes, we derive a condition for the existence of a d-dimensional SIC.

Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics

PubMed Central

Vu Manh, Thien-Phong; Elhmouzi-Younes, Jamila; Urien, Céline; Ruscanu, Suzana; Jouneau, Luc; Bourge, Mickaël; Moroldo, Marco; Foucras, Gilles; Salmon, Henri; Marty, Hélène; Quéré, Pascale; Bertho, Nicolas; Boudinot, Pierre; Dalod, Marc; Schwartz-Cornil, Isabelle

2015-01-01

Mononuclear phagocytes are organized in a complex system of ontogenetically and functionally distinct subsets, that has been best described in mouse and to some extent in human. Identification of homologous mononuclear phagocyte subsets in other vertebrate species of biomedical, economic, and environmental interest is needed to improve our knowledge in physiologic and physio-pathologic processes, and to design intervention strategies against a variety of diseases, including zoonotic infections. We developed a streamlined approach combining refined cell sorting and integrated comparative transcriptomics analyses which revealed conservation of the mononuclear phagocyte organization across human, mouse, sheep, pigs and, in some respect, chicken. This strategy should help democratizing the use of omics analyses for the identification and study of cell types across tissues and species. Moreover, we identified conserved gene signatures that enable robust identification and universal definition of these cell types. We identified new evolutionarily conserved gene candidates and gene interaction networks for the molecular regulation of the development or functions of these cell types, as well as conserved surface candidates for refined subset phenotyping throughout species. A phylogenetic analysis revealed that orthologous genes of the conserved signatures exist in teleost fishes and apparently not in Lamprey. PMID:26150816

Coaggregation-Mediated Interactions of Streptococci and Actinomyces Detected in Initial Human Dental Plaque

PubMed Central

Palmer, Jr., Robert J.; Gordon, Sharon M.; Cisar, John O.; Kolenbrander, Paul E.

2003-01-01

Streptococci and actinomyces that initiate colonization of the tooth surface frequently coaggregate with each other as well as with other oral bacteria. These observations have led to the hypothesis that interbacterial adhesion influences spatiotemporal development of plaque. To assess the role of such interactions in oral biofilm formation in vivo, antibodies directed against bacterial surface components that mediate coaggregation interactions were used as direct immunofluorescent probes in conjunction with laser confocal microscopy to determine the distribution and spatial arrangement of bacteria within intact human plaque formed on retrievable enamel chips. In intrageneric coaggregation, streptococci such as Streptococcus gordonii DL1 recognize receptor polysaccharides (RPS) borne on other streptococci such as Streptococcus oralis 34. To define potentially interactive subsets of streptococci in the developing plaque, an antibody against RPS (anti-RPS) was used together with an antibody against S. gordonii DL1 (anti-DL1). These antibodies reacted primarily with single cells in 4-h-old plaque and with mixed-species microcolonies in 8-h-old plaque. Anti-RPS-reactive bacteria frequently formed microcolonies with anti-DL1-reactive bacteria and with other bacteria distinguished by general nucleic acid stains. In intergeneric coaggregation between streptococci and actinomyces, type 2 fimbriae of actinomyces recognize RPS on the streptococci. Cells reactive with antibody against type 2 fimbriae of Actinomyces naeslundii T14V (anti-type-2) were much less frequent than either subset of streptococci. However, bacteria reactive with anti-type-2 were seen in intimate association with anti-RPS-reactive cells. These results are the first direct demonstration of coaggregation-mediated interactions during initial plaque accumulation in vivo. Further, these results demonstrate the spatiotemporal development and prevalence of mixed-species communities in early dental plaque. PMID:12754239

Different subsets of natural killer T cells may vary in their roles in health and disease

PubMed Central

Kumar, Vipin; Delovitch, Terry L

2014-01-01

Natural killer T cells (NKT) can regulate innate and adaptive immune responses. Type I and type II NKT cell subsets recognize different lipid antigens presented by CD1d, an MHC class-I-like molecule. Most type I NKT cells express a semi-invariant T-cell receptor (TCR), but a major subset of type II NKT cells reactive to a self antigen sulphatide use an oligoclonal TCR. Whereas TCR-α dominates CD1d-lipid recognition by type I NKT cells, TCR-α and TCR-β contribute equally to CD1d-lipid recognition by type II NKT cells. These variable modes of NKT cell recognition of lipid–CD1d complexes activate a host of cytokine-dependent responses that can either exacerbate or protect from disease. Recent studies of chronic inflammatory and autoimmune diseases have led to a hypothesis that: (i) although type I NKT cells can promote pathogenic and regulatory responses, they are more frequently pathogenic, and (ii) type II NKT cells are predominantly inhibitory and protective from such responses and diseases. This review focuses on a further test of this hypothesis by the use of recently developed techniques, intravital imaging and mass cytometry, to analyse the molecular and cellular dynamics of type I and type II NKT cell antigen-presenting cell motility, interaction, activation and immunoregulation that promote immune responses leading to health versus disease outcomes. PMID:24428389

The distribution of HIV DNA and RNA in cell subsets differs in gut and blood of HIV-positive patients on ART: implications for viral persistence.

PubMed

Yukl, Steven A; Shergill, Amandeep K; Ho, Terence; Killian, Maudi; Girling, Valerie; Epling, Lorrie; Li, Peilin; Wong, Lisa K; Crouch, Pierre; Deeks, Steven G; Havlir, Diane V; McQuaid, Kenneth; Sinclair, Elizabeth; Wong, Joseph K

2013-10-15

Even with optimal antiretroviral therapy, human immunodeficiency virus (HIV) persists in plasma, blood cells, and tissues. To develop new therapies, it is essential to know what cell types harbor residual HIV. We measured levels of HIV DNA, RNA, and RNA/DNA ratios in sorted subsets of CD4+ T cells (CCR7+, transitional memory, and effector memory) and non-CD4+ T leukocytes from blood, ileum, and rectum of 8 ART-suppressed HIV-positive subjects. Levels of HIV DNA/million cells in CCR7+ and effector memory cells were higher in the ileum than blood. When normalized by cell frequencies, most HIV DNA and RNA in the blood were found in CCR7+ cells, whereas in both gut sites, most HIV DNA and RNA were found in effector memory cells. HIV DNA and RNA were observed in non-CD4+ T leukocytes at low levels, particularly in gut tissues. Compared to the blood, the ileum had higher levels of HIV DNA and RNA in both CD4+ T cells and non-CD4+ T leukocytes, whereas the rectum had higher HIV DNA levels in both cell types but lower RNA levels in CD4+ T cells. Future studies should determine whether different mechanisms allow HIV to persist in these distinct reservoirs, and the degree to which different therapies can affect each reservoir.

'Dressed for success' C-type lectin receptors for the delivery of glyco-vaccines to dendritic cells.

PubMed

Unger, Wendy W J; van Kooyk, Yvette

2011-02-01

Current strategies in immunotherapy for the treatment of tumors or autoimmunity focus on direct in vivo targeting of antigens to dendritic cells (DC), as these cells are the key regulators of immune responses. Multiple DC subsets can be distinguished in both humans and mice, based on phenotype and location. Moreover, recent data show that these subsets have distinct functions. All these features have implications for the design of DC-targeting vaccines. In this review we integrate recent knowledge on the different DC subsets in human and mice and how DC-expressed C-type lectin receptors (CLR) can be exploited for the induction of either antigen-specific immunity or tolerance. Copyright © 2010 Elsevier Ltd. All rights reserved.

Partition dataset according to amino acid type improves the prediction of deleterious non-synonymous SNPs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Jing; Li, Yuan-Yuan; Shanghai Center for Bioinformation Technology, Shanghai 200235

2012-03-02

Highlights: Black-Right-Pointing-Pointer Proper dataset partition can improve the prediction of deleterious nsSNPs. Black-Right-Pointing-Pointer Partition according to original residue type at nsSNP is a good criterion. Black-Right-Pointing-Pointer Similar strategy is supposed promising in other machine learning problems. -- Abstract: Many non-synonymous SNPs (nsSNPs) are associated with diseases, and numerous machine learning methods have been applied to train classifiers for sorting disease-associated nsSNPs from neutral ones. The continuously accumulated nsSNP data allows us to further explore better prediction approaches. In this work, we partitioned the training data into 20 subsets according to either original or substituted amino acid type at the nsSNPmore » site. Using support vector machine (SVM), training classification models on each subset resulted in an overall accuracy of 76.3% or 74.9% depending on the two different partition criteria, while training on the whole dataset obtained an accuracy of only 72.6%. Moreover, the dataset was also randomly divided into 20 subsets, but the corresponding accuracy was only 73.2%. Our results demonstrated that partitioning the whole training dataset into subsets properly, i.e., according to the residue type at the nsSNP site, will improve the performance of the trained classifiers significantly, which should be valuable in developing better tools for predicting the disease-association of nsSNPs.« less

Whole genome sequencing: an efficient approach to ensuring food safety

NASA Astrophysics Data System (ADS)

Lakicevic, B.; Nastasijevic, I.; Dimitrijevic, M.

2017-09-01

Whole genome sequencing is an effective, powerful tool that can be applied to a wide range of public health and food safety applications. A major difference between WGS and the traditional typing techniques is that WGS allows all genes to be included in the analysis, instead of a well-defined subset of genes or variable intergenic regions. Also, the use of WGS can facilitate the understanding of contamination/colonization routes of foodborne pathogens within the food production environment, and can also afford efficient tracking of pathogens’ entry routes and distribution from farm-to-consumer. Tracking foodborne pathogens in the food processing-distribution-retail-consumer continuum is of the utmost importance for facilitation of outbreak investigations and rapid action in controlling/preventing foodborne outbreaks. Therefore, WGS likely will replace most of the numerous workflows used in public health laboratories to characterize foodborne pathogens into one consolidated, efficient workflow.

Functional diversity of human vaginal APC subsets in directing T cell responses

PubMed Central

Duluc, Dorothée; Gannevat, Julien; Anguiano, Esperanza; Zurawski, Sandra; Carley, Michael; Boreham, Muriel; Stecher, Jack; Dullaers, Melissa; Banchereau, Jacques; Oh, SangKon

2012-01-01

Human vaginal mucosa is the major entry site of sexually transmitted pathogens and thus has long been attractive as a site for mounting mucosal immunity. It is also known as a tolerogenic microenvironment. Here, we demonstrate that immune responses in the vagina are orchestrated by the functional diversity of four major antigen-presenting cell (APC) subsets. Langerhans cells (LCs) and CD14− lamina propria (LP)-DCs polarize CD4+ and CD8+ T cells toward Th2, whereas CD14+ LP-DCs and macrophages polarize CD4+ T cells toward Th1. Both LCs and CD14− LP-DCs are potent inducers of Th22. Due to their functional specialties and the different expression levels of pattern-recognition receptors on the APC subsets, microbial products do not bias them to elicit common types of immune responses (Th1 or Th2). To evoke desired types of adaptive immune responses in the human vagina, antigens may need to be targeted to proper APC subsets with right adjuvants. PMID:23131784

The expanding universe of T-cell subsets: Th1, Th2 and more.

PubMed

Mosmann, T R; Sad, S

1996-03-01

Since their discovery nearly ten years ago, T helper 1 (Th1) and Th2 subsets have been implicated in the regulation of many immune responses. In this article, Tim Mosmann and Subash Sad discuss the increasing number of T-cell subsets defined by cytokine patterns; the differentiation pathways of CD4+ and CD8+ T cells; the contribution of other cell types to these patterns; and the cytokine interactions during infection and pregnancy.

Comparing species distribution models constructed with different subsets of environmental predictors

USGS Publications Warehouse

Bucklin, David N.; Basille, Mathieu; Benscoter, Allison M.; Brandt, Laura A.; Mazzotti, Frank J.; Romañach, Stephanie S.; Speroterra, Carolina; Watling, James I.

2014-01-01

Our results indicate that additional predictors have relatively minor effects on the accuracy of climate-based species distribution models and minor to moderate effects on spatial predictions. We suggest that implementing species distribution models with only climate predictors may provide an effective and efficient approach for initial assessments of environmental suitability.

Beneficial Effects of cART Initiated during Primary and Chronic HIV-1 Infection on Immunoglobulin-Expression of Memory B-Cell Subsets

PubMed Central

Pensieroso, Simone; Tolazzi, Monica; Chiappetta, Stefania; Nozza, Silvia; Lazzarin, Adriano; Tambussi, Giuseppe; Scarlatti, Gabriella

2015-01-01

Introduction During HIV-1 infection the B-cell compartment undergoes profound changes towards terminal differentiation, which are only partially restored by antiretroviral therapy (cART). Materials and Methods To investigate the impact of infection as early as during primary HIV-1 infection (PHI) we assessed distribution of B-cell subsets in 19 PHI and 25 chronic HIV-1-infected (CHI) individuals before and during 48 weeks of cART as compared to healthy controls (n = 23). We also analysed Immunoglobulin-expression of memory B-cell subsets to identify alterations in Immunoglobulin-maturation. Results Determination of B-cell subsets at baseline showed that total and Naive B-cells were decreased whereas Activated Memory (AM), Tissue-like Memory (TLM) B-cells and Plasma cells were increased in both PHI and CHI patients. After 4 weeks of cART total B-cells increased, while AM, TLM B-cells and Plasma cells decreased, although without reaching normal levels in either group of individuals. This trend was maintained until week 48, though only total B-cells normalized in both PHI and CHI. Resting Memory (RM) B-cells were preserved since baseline. This subset remained stable in CHI, while was expanded by an early initiation of cART during PHI. Untreated CHI patients showed IgM-overexpression at the expenses of switched (IgM-IgD-) phenotypes of the memory subsets. Interestingly, in PHI patients a significant alteration of Immunoglobulin-expression was evident at BL in TLM cells, and after 4 weeks, despite treatment, in AM and RM subsets. After 48 weeks of therapy, Immunoglobulin-expression of AM and RM almost normalized, but remained perturbed in TLM cells in both groups. Conclusions In conclusion, aberrant activated and exhausted B-cell phenotypes rose already during PHI, while most of the alterations in Ig-expression seen in CHI appeared later, despite 4 weeks of effective cART. After 48 weeks of cART B-cell subsets distribution improved although without full normalization, while Immunoglobulin-expression normalized among AM and RM, remaining perturbed in TLM B-cells of PHI and CHI. PMID:26474181

Beneficial Effects of cART Initiated during Primary and Chronic HIV-1 Infection on Immunoglobulin-Expression of Memory B-Cell Subsets.

PubMed

Pogliaghi, Manuela; Ripa, Marco; Pensieroso, Simone; Tolazzi, Monica; Chiappetta, Stefania; Nozza, Silvia; Lazzarin, Adriano; Tambussi, Giuseppe; Scarlatti, Gabriella

2015-01-01

During HIV-1 infection the B-cell compartment undergoes profound changes towards terminal differentiation, which are only partially restored by antiretroviral therapy (cART). To investigate the impact of infection as early as during primary HIV-1 infection (PHI) we assessed distribution of B-cell subsets in 19 PHI and 25 chronic HIV-1-infected (CHI) individuals before and during 48 weeks of cART as compared to healthy controls (n = 23). We also analysed Immunoglobulin-expression of memory B-cell subsets to identify alterations in Immunoglobulin-maturation. Determination of B-cell subsets at baseline showed that total and Naive B-cells were decreased whereas Activated Memory (AM), Tissue-like Memory (TLM) B-cells and Plasma cells were increased in both PHI and CHI patients. After 4 weeks of cART total B-cells increased, while AM, TLM B-cells and Plasma cells decreased, although without reaching normal levels in either group of individuals. This trend was maintained until week 48, though only total B-cells normalized in both PHI and CHI. Resting Memory (RM) B-cells were preserved since baseline. This subset remained stable in CHI, while was expanded by an early initiation of cART during PHI. Untreated CHI patients showed IgM-overexpression at the expenses of switched (IgM-IgD-) phenotypes of the memory subsets. Interestingly, in PHI patients a significant alteration of Immunoglobulin-expression was evident at BL in TLM cells, and after 4 weeks, despite treatment, in AM and RM subsets. After 48 weeks of therapy, Immunoglobulin-expression of AM and RM almost normalized, but remained perturbed in TLM cells in both groups. In conclusion, aberrant activated and exhausted B-cell phenotypes rose already during PHI, while most of the alterations in Ig-expression seen in CHI appeared later, despite 4 weeks of effective cART. After 48 weeks of cART B-cell subsets distribution improved although without full normalization, while Immunoglobulin-expression normalized among AM and RM, remaining perturbed in TLM B-cells of PHI and CHI.

NKT cell subsets as key participants in liver physiology and pathology

PubMed Central

Bandyopadhyay, Keya; Marrero, Idania; Kumar, Vipin

2016-01-01

Natural killer T (NKT) cells are innate-like lymphocytes that generally recognize lipid antigens and are enriched in microvascular compartments of the liver. NKT cells can be activated by self- or microbial-lipid antigens and by signaling through toll-like receptors. Following activation, NKT cells rapidly secrete pro-inflammatory or anti-inflammatory cytokines and chemokines, and thereby determine the milieu for subsequent immunity or tolerance. It is becoming clear that two different subsets of NKT cells—type I and type II—have different modes of antigen recognition and have opposing roles in inflammatory liver diseases. Here we focus mainly on the roles of both NKT cell subsets in the maintenance of immune tolerance and inflammatory diseases in liver. Furthermore, how the differential activation of type I and type II NKT cells influences other innate cells and adaptive immune cells to result in important consequences for tissue integrity is discussed. It is crucial that better reagents, including CD1d tetramers, be used in clinical studies to define the roles of NKT cells in liver diseases in patients. PMID:26972772

DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less

DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

DOE PAGES

Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.

2017-01-16

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less

Pathological Heterogeneity of Frontotemporal Lobar Degeneration with Ubiquitin-Positive Inclusions Delineated by Ubiquitin Immunohistochemistry and Novel Monoclonal Antibodies

PubMed Central

Sampathu, Deepak M.; Neumann, Manuela; Kwong, Linda K.; Chou, Thomas T.; Micsenyi, Matthew; Truax, Adam; Bruce, Jennifer; Grossman, Murray; Trojanowski, John Q.; Lee, Virginia M.-Y.

2006-01-01

Frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U) is a common neuropathological subtype of frontotemporal dementia. Although this subtype of frontotemporal dementia is defined by the presence of ubiquitin-positive but tau- and α-synuclein-negative inclusions, it is unclear whether all cases of FTLD-U have the same underlying pathogenesis. Examination of tissue sections from FTLD-U brains stained with anti-ubiquitin antibodies revealed heterogeneity in the morphological characteristics of pathological inclusions among subsets of cases. Three types of FTLD-U were delineated based on morphology and distribution of ubiquitin-positive inclusions. To address the hypothesis that FTLD-U is pathologically heterogeneous, novel monoclonal antibodies (mAbs) were generated by immunization of mice with high molecular mass (Mr > 250 kd) insoluble material prepared by biochemical fractionation of FTLD-U brains. Novel mAbs were identified that immunolabeled all of the ubiquitin-positive inclusions in one subset of FTLD-U cases, whereas other mAbs stained the ubiquitin-positive inclusions in a second subset of cases. These novel mAbs did not stain inclusions in other neurodegenerative disorders, including tauopathies and α-synucleinopathies. Therefore, ubiquitin immunohistochemistry and the immunostaining properties of the novel mAbs generated here suggest that FTLD-U is pathologically he-terogeneous. Identification of the disease proteins recognized by these mAbs will further advance understanding of molecular substrates of FTLD-U neurodegenerative pathways. PMID:17003490

Large contribution of human papillomavirus in vaginal neoplastic lesions: a worldwide study in 597 samples.

PubMed

Alemany, L; Saunier, M; Tinoco, L; Quirós, B; Alvarado-Cabrero, I; Alejo, M; Joura, E A; Maldonado, P; Klaustermeier, J; Salmerón, J; Bergeron, C; Petry, K U; Guimerà, N; Clavero, O; Murillo, R; Clavel, C; Wain, V; Geraets, D T; Jach, R; Cross, P; Carrilho, C; Molina, C; Shin, H R; Mandys, V; Nowakowski, A M; Vidal, A; Lombardi, L; Kitchener, H; Sica, A R; Magaña-León, C; Pawlita, M; Quint, W; Bravo, I G; Muñoz, N; de Sanjosé, S; Bosch, F X

2014-11-01

This work describes the human papillomavirus (HPV) prevalence and the HPV type distribution in a large series of vaginal intraepithelial neoplasia (VAIN) grades 2/3 and vaginal cancer worldwide. We analysed 189 VAIN 2/3 and 408 invasive vaginal cancer cases collected from 31 countries from 1986 to 2011. After histopathological evaluation of sectioned formalin-fixed paraffin-embedded samples, HPV DNA detection and typing was performed using the SPF-10/DNA enzyme immunoassay (DEIA)/LiPA25 system (version 1). A subset of 146 vaginal cancers was tested for p16(INK4a) expression, a cellular surrogate marker for HPV transformation. Prevalence ratios were estimated using multivariate Poisson regression with robust variance. HPV DNA was detected in 74% (95% confidence interval (CI): 70-78%) of invasive cancers and in 96% (95% CI: 92-98%) of VAIN 2/3. Among cancers, the highest detection rates were observed in warty-basaloid subtype of squamous cell carcinomas, and in younger ages. Concerning the type-specific distribution, HPV16 was the most frequently type detected in both precancerous and cancerous lesions (59%). p16(INK4a) overexpression was found in 87% of HPV DNA positive vaginal cancer cases. HPV was identified in a large proportion of invasive vaginal cancers and in almost all VAIN 2/3. HPV16 was the most common type detected. A large impact in the reduction of the burden of vaginal neoplastic lesions is expected among vaccinated cohorts. Copyright © 2014 Elsevier Ltd. All rights reserved.

Different subsets of natural killer T cells may vary in their roles in health and disease.

PubMed

Kumar, Vipin; Delovitch, Terry L

2014-07-01

Natural killer T cells (NKT) can regulate innate and adaptive immune responses. Type I and type II NKT cell subsets recognize different lipid antigens presented by CD1d, an MHC class-I-like molecule. Most type I NKT cells express a semi-invariant T-cell receptor (TCR), but a major subset of type II NKT cells reactive to a self antigen sulphatide use an oligoclonal TCR. Whereas TCR-α dominates CD1d-lipid recognition by type I NKT cells, TCR-α and TCR-β contribute equally to CD1d-lipid recognition by type II NKT cells. These variable modes of NKT cell recognition of lipid-CD1d complexes activate a host of cytokine-dependent responses that can either exacerbate or protect from disease. Recent studies of chronic inflammatory and autoimmune diseases have led to a hypothesis that: (i) although type I NKT cells can promote pathogenic and regulatory responses, they are more frequently pathogenic, and (ii) type II NKT cells are predominantly inhibitory and protective from such responses and diseases. This review focuses on a further test of this hypothesis by the use of recently developed techniques, intravital imaging and mass cytometry, to analyse the molecular and cellular dynamics of type I and type II NKT cell antigen-presenting cell motility, interaction, activation and immunoregulation that promote immune responses leading to health versus disease outcomes. © 2014 John Wiley & Sons Ltd.

Modeling Hawaiian Ecosystem Degradation due to Invasive Plants under Current and Future Climates

PubMed Central

Vorsino, Adam E.; Fortini, Lucas B.; Amidon, Fred A.; Miller, Stephen E.; Jacobi, James D.; Price, Jonathan P.; Gon, Sam 'Ohukani'ohi'a; Koob, Gregory A.

2014-01-01

Occupation of native ecosystems by invasive plant species alters their structure and/or function. In Hawaii, a subset of introduced plants is regarded as extremely harmful due to competitive ability, ecosystem modification, and biogeochemical habitat degradation. By controlling this subset of highly invasive ecosystem modifiers, conservation managers could significantly reduce native ecosystem degradation. To assess the invasibility of vulnerable native ecosystems, we selected a proxy subset of these invasive plants and developed robust ensemble species distribution models to define their respective potential distributions. The combinations of all species models using both binary and continuous habitat suitability projections resulted in estimates of species richness and diversity that were subsequently used to define an invasibility metric. The invasibility metric was defined from species distribution models with <0.7 niche overlap (Warrens I) and relatively discriminative distributions (Area Under the Curve >0.8; True Skill Statistic >0.75) as evaluated per species. Invasibility was further projected onto a 2100 Hawaii regional climate change scenario to assess the change in potential habitat degradation. The distribution defined by the invasibility metric delineates areas of known and potential invasibility under current climate conditions and, when projected into the future, estimates potential reductions in native ecosystem extent due to climate-driven invasive incursion. We have provided the code used to develop these metrics to facilitate their wider use (Code S1). This work will help determine the vulnerability of native-dominated ecosystems to the combined threats of climate change and invasive species, and thus help prioritize ecosystem and species management actions. PMID:24805254

Modeling Hawaiian ecosystem degradation due to invasive plants under current and future climates.

PubMed

Vorsino, Adam E; Fortini, Lucas B; Amidon, Fred A; Miller, Stephen E; Jacobi, James D; Price, Jonathan P; Gon, Sam 'ohukani'ohi'a; Koob, Gregory A

2014-01-01

Occupation of native ecosystems by invasive plant species alters their structure and/or function. In Hawaii, a subset of introduced plants is regarded as extremely harmful due to competitive ability, ecosystem modification, and biogeochemical habitat degradation. By controlling this subset of highly invasive ecosystem modifiers, conservation managers could significantly reduce native ecosystem degradation. To assess the invasibility of vulnerable native ecosystems, we selected a proxy subset of these invasive plants and developed robust ensemble species distribution models to define their respective potential distributions. The combinations of all species models using both binary and continuous habitat suitability projections resulted in estimates of species richness and diversity that were subsequently used to define an invasibility metric. The invasibility metric was defined from species distribution models with <0.7 niche overlap (Warrens I) and relatively discriminative distributions (Area Under the Curve >0.8; True Skill Statistic >0.75) as evaluated per species. Invasibility was further projected onto a 2100 Hawaii regional climate change scenario to assess the change in potential habitat degradation. The distribution defined by the invasibility metric delineates areas of known and potential invasibility under current climate conditions and, when projected into the future, estimates potential reductions in native ecosystem extent due to climate-driven invasive incursion. We have provided the code used to develop these metrics to facilitate their wider use (Code S1). This work will help determine the vulnerability of native-dominated ecosystems to the combined threats of climate change and invasive species, and thus help prioritize ecosystem and species management actions.

Using abiotic variables to predict importance of sites for species representation.

PubMed

Albuquerque, Fabio; Beier, Paul

2015-10-01

In systematic conservation planning, species distribution data for all sites in a planning area are used to prioritize each site in terms of the site's importance toward meeting the goal of species representation. But comprehensive species data are not available in most planning areas and would be expensive to acquire. As a shortcut, ecologists use surrogates, such as occurrences of birds or another well-surveyed taxon, or land types defined from remotely sensed data, in the hope that sites that represent the surrogates also represent biodiversity. Unfortunately, surrogates have not performed reliably. We propose a new type of surrogate, predicted importance, that can be developed from species data for a q% subset of sites. With species data from this subset of sites, importance can be modeled as a function of abiotic variables available at no charge for all terrestrial areas on Earth. Predicted importance can then be used as a surrogate to prioritize all sites. We tested this surrogate with 8 sets of species data. For each data set, we used a q% subset of sites to model importance as a function of abiotic variables, used the resulting function to predict importance for all sites, and evaluated the number of species in the sites with highest predicted importance. Sites with the highest predicted importance represented species efficiently for all data sets when q = 25% and for 7 of 8 data sets when q = 20%. Predicted importance requires less survey effort than direct selection for species representation and meets representation goals well compared with other surrogates currently in use. This less expensive surrogate may be useful in those areas of the world that need it most, namely tropical regions with the highest biodiversity, greatest biodiversity loss, most severe lack of inventory data, and poorly developed protected area networks. © 2015 Society for Conservation Biology.

Population analysis of Vibrio parahaemolyticus originating from different geographical regions demonstrates a high genetic diversity.

PubMed

Urmersbach, Sara; Alter, Thomas; Koralage, Madura Sanjeevani Gonsal; Sperling, Lisa; Gerdts, Gunnar; Messelhäusser, Ute; Huehn, Stephan

2014-03-08

Vibrio parahaemolyticus is frequently isolated from environmental and seafood samples and associated with gastroenteritis outbreakes in American, European, Asian and African countries. To distinguish between different lineages of V. parahaemolyticus various genotyping techniques have been used, incl. multilocus sequence typing (MLST). Even though some studies have already applied MLST analysis to characterize V. parahaemolyticus strain sets, these studies have been restricted to specific geographical areas (e.g. U.S. coast, Thailand and Peru), have focused exclusively on pandemic or non-pandemic pathogenic isolates or have been based on a limited strain number. To generate a global picture of V. parahaemolyticus genotype distribution, a collection of 130 environmental and seafood related V. parahaemolyticus isolates of different geographical origins (Sri Lanka, Ecuador, North Sea and Baltic Sea as well as German retail) was subjected to MLST analysis after modification of gyrB and recA PCRs. The V. parahaemolyticus population was composed of 82 unique Sequence Types (STs), of which 68 (82.9%) were new to the pubMLST database. After translating the in-frame nucleotide sequences into amino acid sequences, less diversity was detectable: a total of 31 different peptide Sequence Types (pSTs) with 19 (61.3%) new pSTs were generated from the analyzed isolates. Most STs did not show a global dissemination, but some were supra-regionally distributed and clusters of STs were dependent on geographical origin. On peptide level no general clustering of strains from specific geographical regions was observed, thereby the most common pSTs were found on all continents (Asia, South America and Europe) and rare pSTs were restricted to distinct countries or even geographical regions. One lineage of pSTs associated only with strains from North and Baltic Sea strains was identified. Our study reveals a high genetic diversity in the analyzed V. parahaemolyticus strain set as well as for geographical strain subsets, with a high proportion of newly discovered alleles and STs. Differences between the subsets were identified. Our data support the postulated population structure of V. parahaemolyticus which follows the 'epidemic' model of clonal expansion. Application of peptide based AA-MLST allowed the identification of reliable relationships between strains.

A Simple Joint Estimation Method of Residual Frequency Offset and Sampling Frequency Offset for DVB Systems

NASA Astrophysics Data System (ADS)

Kwon, Ki-Won; Cho, Yongsoo

This letter presents a simple joint estimation method for residual frequency offset (RFO) and sampling frequency offset (STO) in OFDM-based digital video broadcasting (DVB) systems. The proposed method selects a continual pilot (CP) subset from an unsymmetrically and non-uniformly distributed CP set to obtain an unbiased estimator. Simulation results show that the proposed method using a properly selected CP subset is unbiased and performs robustly.

Imbalance of Circulating Monocyte Subsets and PD-1 Dysregulation in Q Fever Endocarditis: The Role of IL-10 in PD-1 Modulation

PubMed Central

Ka, Mignane B.; Gondois-Rey, Françoise; Capo, Christian; Textoris, Julien; Million, Mathieu; Raoult, Didier; Olive, Daniel; Mege, Jean-Louis

2014-01-01

Q fever endocarditis, a severe complication of Q fever, is associated with a defective immune response, the mechanisms of which are poorly understood. We hypothesized that Q fever immune deficiency is related to altered distribution and activation of circulating monocyte subsets. Monocyte subsets were analyzed by flow cytometry in peripheral blood mononuclear cells from patients with Q fever endocarditis and controls. The proportion of classical monocytes (CD14+CD16− monocytes) was similar in patients and controls. In contrast, the patients with Q fever endocarditis exhibited a decrease in the non-classical and intermediate subsets of monocytes (CD16+ monocytes). The altered distribution of monocyte subsets in Q fever endocarditis was associated with changes in their activation profile. Indeed, the expression of HLA-DR, a canonical activation molecule, and PD-1, a co-inhibitory molecule, was increased in intermediate monocytes. This profile was not restricted to CD16+ monocytes because CD4+ T cells also overexpressed PD-1. The mechanism leading to the overexpression of PD-1 did not require the LPS from C. burnetii but involved interleukin-10, an immunosuppressive cytokine. Indeed, the incubation of control monocytes with interleukin-10 led to a higher expression of PD-1 and neutralizing interleukin-10 prevented C. burnetii-stimulated PD-1 expression. Taken together, these results show that the immune suppression of Q fever endocarditis involves a cross-talk between monocytes and CD4+ T cells expressing PD-1. The expression of PD-1 may be useful to assess chronic immune alterations in Q fever endocarditis. PMID:25211350

Distribution of cyclophilin B-binding sites in the subsets of human peripheral blood lymphocytes.

PubMed

Denys, A; Allain, F; Foxwell, B; Spik, G

1997-08-01

Cyclophilin B (CyPB) is a cyclosporin A (CsA)-binding protein, mainly associated with the secretory pathway and released in biological fluids. We have recently demonstrated that both free CyPB and CyPB-CsA complex specifically bind to peripheral blood T lymphocytes and are internalized. These results suggest that CyPB might promote the targeting of the drug into sensitive cells. Peripheral blood lymphocytes are subdivided in several populations according to their biological functions and sensitivity to CsA. We have investigated the binding of CyPB to these different subsets using a CyPB derivatized by fluorescein through its single cysteine which retains its binding properties. We have confirmed that only T cells were involved in the interaction with CyPB. The ligand binding was found to be heterogeneously distributed on the different T-cell subsets and surface-bound CyPB was mainly associated with the CD4-positive cells. No significant difference was noted between the CD45RA and CD45RO subsets, demonstrating that CyPB-binding sites were equally distributed between native and memory T cells. CD3 stimulation of T lymphocytes led to a decrease in the CyPB-binding capacity, that may be explained by a down-regulation of the CyPB-receptor expression upon T-cell activation. Finally, we demonstrated that CyPB-receptor-positive cells, isolated on CyPB sulphydryl-coupled affinity matrices, are more sensitive to CyPB-complexed CsA than mixed peripheral blood lymphocytes, suggesting that CyPB potentiates CsA activity through the binding of the complex. Taken together, our results demonstrate that CyPB-binding sites are mainly associated with resting cells of the helper T lymphocyte, and that CyPB might modulate the distribution of CsA through the drug targeting to sensitive cells.

Expanding the tools for identifying mononuclear phagocyte subsets in swine: Reagents to porcine CD11c and XCR1.

PubMed

Deloizy, Charlotte; Bouguyon, Edwige; Fossum, Even; Sebo, Peter; Osicka, Radim; Bole, Angélique; Pierres, Michel; Biacchesi, Stéphane; Dalod, Marc; Bogen, Bjarne; Bertho, Nicolas; Schwartz-Cornil, Isabelle

2016-12-01

Pig is a domestic species of major importance in the agro-economy and in biomedical research. Mononuclear phagocytes (MNP) are organized in subsets with specialized roles in the orchestration of the immune response and new tools are awaited to improve MNP subset identification in the pig. We cloned pig CD11c cDNA and generated a monoclonal antibody to pig CD11c which showed a pattern of expression by blood and skin MNP subsets similar to humans. We also developed a porcine XCL1-mCherry dimer which specifically reacted with the XCR1-expressing dendritic cell subset of the type 1 lineage in blood and skin. These original reagents will allow the efficient identification of pig MNP subsets to study their role in physiological and pathological processes and also to target these cells in novel intervention and vaccine strategies for veterinary applications and preclinical evaluations. Copyright © 2016 Elsevier Ltd. All rights reserved.

FLASH_SSF_Aqua-FM3-MODIS_Version3C

Atmospheric Science Data Center

2018-04-04

... Tool:  CERES Order Tool  (netCDF) Subset Data:  CERES Search and Subset Tool (HDF4 & netCDF) ... Cloud Layer Area Cloud Infared Emissivity Cloud Base Pressure Surface (Radiative) Flux TOA Flux Surface Types TOT ... Radiance SW Filtered Radiance LW Flux Order Data:  Earthdata Search:  Order Data Guide Documents:  ...

FLASH_SSF_Terra-FM1-MODIS_Version3C

Atmospheric Science Data Center

2018-04-04

... Tool:  CERES Order Tool  (netCDF) Subset Data:  CERES Search and Subset Tool (HDF4 & netCDF) ... Cloud Layer Area Cloud Infrared Emissivity Cloud Base Pressure Surface (Radiative) Flux TOA Flux Surface Types TOT ... Radiance SW Filtered Radiance LW Flux Order Data:  Earthdata Search:  Order Data Guide Documents:  ...

Circulating B cells in type 1 diabetics exhibit fewer maturation-associated phenotypes.

PubMed

Hanley, Patrick; Sutter, Jennifer A; Goodman, Noah G; Du, Yangzhu; Sekiguchi, Debora R; Meng, Wenzhao; Rickels, Michael R; Naji, Ali; Luning Prak, Eline T

2017-10-01

Although autoantibodies have been used for decades as diagnostic and prognostic markers in type 1 diabetes (T1D), further analysis of developmental abnormalities in B cells could reveal tolerance checkpoint defects that could improve individualized therapy. To evaluate B cell developmental progression in T1D, immunophenotyping was used to classify circulating B cells into transitional, mature naïve, mature activated, and resting memory subsets. Then each subset was analyzed for the expression of additional maturation-associated markers. While the frequencies of B cell subsets did not differ significantly between patients and controls, some T1D subjects exhibited reduced proportions of B cells that expressed transmembrane activator and CAML interactor (TACI) and Fas receptor (FasR). Furthermore, some T1D subjects had B cell subsets with lower frequencies of class switching. These results suggest circulating B cells exhibit variable maturation phenotypes in T1D. These phenotypic variations may correlate with differences in B cell selection in individual T1D patients. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Infants can use distributional cues to form syntactic categories.

PubMed

Gerken, LouAnn; Wilson, Rachel; Lewis, William

2005-05-01

Nearly all theories of language development emphasize the importance of distributional cues for segregating words and phrases into syntactic categories like noun, feminine or verb phrase. However, questions concerning whether such cues can be used to the exclusion of referential cues have been debated. Using the headturn preference procedure, American children aged 1;5 were briefly familiarized with a partial Russian gender paradigm, with a subset of the paradigm members withheld. During test, infants listened on alternate trials to previously withheld grammatical items and ungrammatical items with incorrect gender markings on previously heard stems. Across three experiments, infants discriminated new grammatical from ungrammatical items, but like adults in previous studies, were only able to do so when a subset of familiarization items was double marked for gender category. The results suggest that learners can use distributional cues to category structure, to the exclusion of referential cues, from relatively early in the language learning process.

Modeling Hawaiian ecosystem degradation due to invasive plants under current and future climates

USGS Publications Warehouse

Vorsino, Adam E.; Fortini, Lucas B.; Amidon, Fred A.; Miller, Stephen E.; Jacobi, James D.; Price, Jonathan P.; `Ohukani`ohi`a Gon, Sam; Koob, Gregory A.

2014-01-01

Occupation of native ecosystems by invasive plant species alters their structure and/or function. In Hawaii, a subset of introduced plants is regarded as extremely harmful due to competitive ability, ecosystem modification, and biogeochemical habitat degradation. By controlling this subset of highly invasive ecosystem modifiers, conservation managers could significantly reduce native ecosystem degradation. To assess the invasibility of vulnerable native ecosystems, we selected a proxy subset of these invasive plants and developed robust ensemble species distribution models to define their respective potential distributions. The combinations of all species models using both binary and continuous habitat suitability projections resulted in estimates of species richness and diversity that were subsequently used to define an invasibility metric. The invasibility metric was defined from species distribution models with 0.8; True Skill Statistic >0.75) as evaluated per species. Invasibility was further projected onto a 2100 Hawaii regional climate change scenario to assess the change in potential habitat degradation. The distribution defined by the invasibility metric delineates areas of known and potential invasibility under current climate conditions and, when projected into the future, estimates potential reductions in native ecosystem extent due to climate-driven invasive incursion. We have provided the code used to develop these metrics to facilitate their wider use (Code S1). This work will help determine the vulnerability of native-dominated ecosystems to the combined threats of climate change and invasive species, and thus help prioritize ecosystem and species management actions.

Adenovirus-specific T-cell Subsets in Human Peripheral Blood and After IFN-γ Immunomagnetic Selection.

PubMed

Qian, Chongsheng; Wang, Yingying; Cai, Huili; Laroye, Caroline; De Carvalho Bittencourt, Marcelo; Clement, Laurence; Stoltz, Jean-François; Decot, Véronique; Reppel, Loïc; Bensoussan, Danièle

2016-01-01

Adoptive antiviral cellular immunotherapy by infusion of virus-specific T cells (VSTs) is becoming an alternative treatment for viral infection after hematopoietic stem cell transplantation. The T memory stem cell (TSCM) subset was recently described as exhibiting self-renewal and multipotency properties which are required for sustained efficacy in vivo. We wondered if such a crucial subset for immunotherapy was present in VSTs. We identified, by flow cytometry, TSCM in adenovirus (ADV)-specific interferon (IFN)-γ+ T cells before and after IFN-γ-based immunomagnetic selection, and analyzed the distribution of the main T-cell subsets in VSTs: naive T cells (TN), TSCM, T central memory cells (TCM), T effector memory cell (TEM), and effector T cells (TEFF). In this study all of the different T-cell subsets were observed in the blood sample from healthy donor ADV-VSTs, both before and after IFN-γ-based immunomagnetic selection. As the IFN-γ-based immunomagnetic selection system sorts mainly the most differentiated T-cell subsets, we observed that TEM was always the major T-cell subset of ADV-specific T cells after immunomagnetic isolation and especially after expansion in vitro. Comparing T-cell subpopulation profiles before and after in vitro expansion, we observed that in vitro cell culture with interleukin-2 resulted in a significant expansion of TN-like, TCM, TEM, and TEFF subsets in CD4IFN-γ T cells and of TCM and TEM subsets only in CD8IFN-γ T cells. We demonstrated the presence of all T-cell subsets in IFN-γ VSTs including the TSCM subpopulation, although this was weakly selected by the IFN-γ-based immunomagnetic selection system.

ROTATING STARS FROM KEPLER OBSERVED WITH GAIA DR1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davenport, James R. A.

2017-01-20

Astrometric data from the recent Gaia Data Release 1 have been matched against the sample of stars from Kepler with known rotation periods. A total of 1299 bright rotating stars were recovered from the subset of Gaia sources with good astrometric solutions, most with temperatures above 5000 K. From these sources, 894 were selected as lying near the main sequence using their absolute G -band magnitudes. These main-sequence stars show a bimodality in their rotation period distribution, centered roughly around a 600 Myr rotation isochrone. This feature matches the bimodal period distribution found in cooler stars with Kepler , butmore » was previously undetected for solar-type stars due to sample contamination by subgiants. A tenuous connection between the rotation period and total proper motion is found, suggesting that the period bimodality is due to the age distribution of stars within ∼300 pc of the Sun, rather than a phase of rapid angular momentum loss. This work emphasizes the unique power for understanding stellar populations that is created by combining temporal monitoring from Kepler with astrometric data from Gaia .« less

White Matter Connectivity of the Thalamus Delineates the Functional Architecture of Competing Thalamocortical Systems

PubMed Central

O'Muircheartaigh, Jonathan; Keller, Simon S.; Barker, Gareth J.; Richardson, Mark P.

2015-01-01

There is an increasing awareness of the involvement of thalamic connectivity on higher level cortical functioning in the human brain. This is reflected by the influence of thalamic stimulation on cortical activity and behavior as well as apparently cortical lesion syndromes occurring as a function of small thalamic insults. Here, we attempt to noninvasively test the correspondence of structural and functional connectivity of the human thalamus using diffusion-weighted and resting-state functional MRI. Using a large sample of 102 adults, we apply tensor independent component analysis to diffusion MRI tractography data to blindly parcellate bilateral thalamus according to diffusion tractography-defined structural connectivity. Using resting-state functional MRI collected in the same subjects, we show that the resulting structurally defined thalamic regions map to spatially distinct, and anatomically predictable, whole-brain functional networks in the same subjects. Although there was significant variability in the functional connectivity patterns, the resulting 51 structural and functional patterns could broadly be reduced to a subset of 7 similar core network types. These networks were distinct from typical cortical resting-state networks. Importantly, these networks were distributed across the brain and, in a subset, map extremely well to known thalamocortico-basal-ganglial loops. PMID:25899706

Emerging concepts and future challenges in innate lymphoid cell biology

PubMed Central

Artis, David

2016-01-01

Innate lymphoid cells (ILCs) are innate immune cells that are ubiquitously distributed in lymphoid and nonlymphoid tissues and enriched at mucosal and barrier surfaces. Three major ILC subsets are recognized in mice and humans. Each of these subsets interacts with innate and adaptive immune cells and integrates cues from the epithelium, the microbiota, and pathogens to regulate inflammation, immunity, tissue repair, and metabolic homeostasis. Although intense study has elucidated many aspects of ILC development, phenotype, and function, numerous challenges remain in the field of ILC biology. In particular, recent work has highlighted key new questions regarding how these cells communicate with their environment and other cell types during health and disease. This review summarizes new findings in this rapidly developing field that showcase the critical role ILCs play in directing immune responses through their ability to interact with a variety of hematopoietic and nonhematopoietic cells. In addition, we define remaining challenges and emerging questions facing the field. Finally, this review discusses the potential application of basic studies of ILC biology to the development of new treatments for human patients with inflammatory and infectious diseases in which ILCs play a role. PMID:27811053

Early- versus late-onset obsessive-compulsive disorder: investigating genetic and clinical correlates.

PubMed

Hemmings, Sîan M J; Kinnear, Craig J; Lochner, Christine; Niehaus, Dana J H; Knowles, James A; Moolman-Smook, Johanna C; Corfield, Valerie A; Stein, Dan J

2004-09-30

There is increasing evidence that obsessive-compulsive disorder (OCD) is mediated by genetic factors. Although the precise mechanism of inheritance is unclear, recent evidence has pointed towards the involvement of the serotonergic and dopaminergic systems in the disorder's development. Furthermore, early-onset OCD appears to be a subtype that exhibits distinct clinical features and that is associated with greater familial loading. In the present investigation, South African OCD patients (n=252) were stratified according to age of onset and were clinically assessed. Additionally, selected variants in genes encoding serotonergic and dopaminergic components were investigated in a Caucasian OCD subset (n=180). This subgroup was further stratified to evaluate the role that these candidate genes may play in the genetically homogeneous Afrikaner subset (n=80). Analysis of the clinical data revealed an association between early age of onset and an increased frequency of tics, Tourette's disorder, and trichotillomania (TTM). The genetic studies yielded statistically significant results when the allelic distributions of genetic variants in the dopamine receptor type 4 gene (DRD4) were analysed in the Caucasian OCD cohort. These data support a role for the dopaminergic system, which may be relevant to the development of early-onset OCD.

Cellular protein quality control and the evolution of aggregates in spinocerebellar ataxia type 3 (SCA3).

PubMed

Seidel, K; Meister, M; Dugbartey, G J; Zijlstra, M P; Vinet, J; Brunt, E R P; van Leeuwen, F W; Rüb, U; Kampinga, H H; den Dunnen, W F A

2012-10-01

A characteristic of polyglutamine diseases is the increased propensity of disease proteins to aggregate, which is thought to be a major contributing factor to the underlying neurodegeneration. Healthy cells contain mechanisms for handling protein damage, the protein quality control, which must be impaired or inefficient to permit proteotoxicity under pathological conditions. We used a quantitative analysis of immunohistochemistry of the pons of eight patients with the polyglutamine disorder spinocerebellar ataxia type 3. We employed the anti-polyglutamine antibody 1C2, antibodies against p62 that is involved in delivering ubiquitinated protein aggregates to autophagosomes, antibodies against the chaperones HSPA1A and DNAJB1 and the proteasomal stress marker UBB⁺¹. The 1C2 antibody stained neuronal nuclear inclusions (NNIs), diffuse nuclear staining (DNS), granular cytoplasmic staining (GCS) and combinations, with reproducible distribution. P62 always co-localized with 1C2 in NNI. DNS and GCS co-stained with a lower frequency. UBB⁺¹ was present in a subset of neurones with NNI. A subset of UBB⁺¹-containing neurones displayed increased levels of HSPA1A, while DNAJB1 was sequestered into the NNI. Based on our results, we propose a model for the aggregation-associated pathology of spinocerebellar ataxia type 3: GCS and DNS aggregation likely represents early stages of pathology, which progresses towards formation of p62-positive NNI. A fraction of NNI exhibits UBB⁺¹ staining, implying proteasomal overload at a later stage. Subsequently, the stress-inducible HSPA1A is elevated while DNAJB1 is recruited into NNIs. This indicates that the stress response is only induced late when all endogenous protein quality control systems have failed. © 2011 The Authors. Neuropathology and Applied Neurobiology © 2011 British Neuropathological Society.

Sulcal set optimization for cortical surface registration.

PubMed

Joshi, Anand A; Pantazis, Dimitrios; Li, Quanzheng; Damasio, Hanna; Shattuck, David W; Toga, Arthur W; Leahy, Richard M

2010-04-15

Flat mapping based cortical surface registration constrained by manually traced sulcal curves has been widely used for inter subject comparisons of neuroanatomical data. Even for an experienced neuroanatomist, manual sulcal tracing can be quite time consuming, with the cost increasing with the number of sulcal curves used for registration. We present a method for estimation of an optimal subset of size N(C) from N possible candidate sulcal curves that minimizes a mean squared error metric over all combinations of N(C) curves. The resulting procedure allows us to estimate a subset with a reduced number of curves to be traced as part of the registration procedure leading to optimal use of manual labeling effort for registration. To minimize the error metric we analyze the correlation structure of the errors in the sulcal curves by modeling them as a multivariate Gaussian distribution. For a given subset of sulci used as constraints in surface registration, the proposed model estimates registration error based on the correlation structure of the sulcal errors. The optimal subset of constraint curves consists of the N(C) sulci that jointly minimize the estimated error variance for the subset of unconstrained curves conditioned on the N(C) constraint curves. The optimal subsets of sulci are presented and the estimated and actual registration errors for these subsets are computed. Copyright 2009 Elsevier Inc. All rights reserved.

Clustering, Seriation, and Subset Extraction of Confusion Data

ERIC Educational Resources Information Center

Brusco, Michael J.; Steinley, Douglas

2006-01-01

The study of confusion data is a well established practice in psychology. Although many types of analytical approaches for confusion data are available, among the most common methods are the extraction of 1 or more subsets of stimuli, the partitioning of the complete stimulus set into distinct groups, and the ordering of the stimulus set. Although…

Immune Reactions against Gene Gun Vaccines Are Differentially Modulated by Distinct Dendritic Cell Subsets in the Skin

PubMed Central

Deressa, Tekalign; Strandt, Helen; Florindo Pinheiro, Douglas; Mittermair, Roberta; Pizarro Pesado, Jennifer; Thalhamer, Josef; Hammerl, Peter; Stoecklinger, Angelika

2015-01-01

The skin accommodates multiple dendritic cell (DC) subsets with remarkable functional diversity. Immune reactions are initiated and modulated by the triggering of DC by pathogen-associated or endogenous danger signals. In contrast to these processes, the influence of intrinsic features of protein antigens on the strength and type of immune responses is much less understood. Therefore, we investigated the involvement of distinct DC subsets in immune reactions against two structurally different model antigens, E. coli beta-galactosidase (betaGal) and chicken ovalbumin (OVA) under otherwise identical conditions. After epicutaneous administration of the respective DNA vaccines with a gene gun, wild type mice induced robust immune responses against both antigens. However, ablation of langerin+ DC almost abolished IgG1 and cytotoxic T lymphocytes against betaGal but enhanced T cell and antibody responses against OVA. We identified epidermal Langerhans cells (LC) as the subset responsible for the suppression of anti-OVA reactions and found regulatory T cells critically involved in this process. In contrast, reactions against betaGal were not affected by the selective elimination of LC, indicating that this antigen required a different langerin+ DC subset. The opposing findings obtained with OVA and betaGal vaccines were not due to immune-modulating activities of either the plasmid DNA or the antigen gene products, nor did the differential cellular localization, size or dose of the two proteins account for the opposite effects. Thus, skin-borne protein antigens may be differentially handled by distinct DC subsets, and, in this way, intrinsic features of the antigen can participate in immune modulation. PMID:26030383

Oral Challenge with Wild-Type Salmonella Typhi Induces Distinct Changes in B Cell Subsets in Individuals Who Develop Typhoid Disease.

PubMed

Toapanta, Franklin R; Bernal, Paula J; Fresnay, Stephanie; Magder, Laurence S; Darton, Thomas C; Jones, Claire; Waddington, Claire S; Blohmke, Christoph J; Angus, Brian; Levine, Myron M; Pollard, Andrew J; Sztein, Marcelo B

2016-06-01

A novel human oral challenge model with wild-type Salmonella Typhi (S. Typhi) was recently established by the Oxford Vaccine Group. In this model, 104 CFU of Salmonella resulted in 65% of participants developing typhoid fever (referred here as typhoid diagnosis -TD-) 6-9 days post-challenge. TD was diagnosed in participants meeting clinical (oral temperature ≥38°C for ≥12h) and/or microbiological (S. Typhi bacteremia) endpoints. Changes in B cell subpopulations following S. Typhi challenge remain undefined. To address this issue, a subset of volunteers (6 TD and 4 who did not develop TD -NoTD-) was evaluated. Notable changes included reduction in the frequency of B cells (cells/ml) of TD volunteers during disease days and increase in plasmablasts (PB) during the recovery phase (>day 14). Additionally, a portion of PB of TD volunteers showed a significant increase in activation (CD40, CD21) and gut homing (integrin α4β7) molecules. Furthermore, all BM subsets of TD volunteers showed changes induced by S. Typhi infections such as a decrease in CD21 in switched memory (Sm) CD27+ and Sm CD27- cells as well as upregulation of CD40 in unswitched memory (Um) and Naïve cells. Furthermore, changes in the signaling profile of some BM subsets were identified after S. Typhi-LPS stimulation around time of disease. Notably, naïve cells of TD (compared to NoTD) volunteers showed a higher percentage of cells phosphorylating Akt suggesting enhanced survival of these cells. Interestingly, most these changes were temporally associated with disease onset. This is the first study to describe differences in B cell subsets directly related to clinical outcome following oral challenge with wild-type S. Typhi in humans.

A subset of thalamocortical projections to the retrosplenial cortex possesses two vesicular glutamate transporter isoforms, VGluT1 and VGluT2, in axon terminals and somata.

PubMed

Oda, Satoko; Funato, Hiromasa; Sato, Fumi; Adachi-Akahane, Satomi; Ito, Masanori; Takase, Kenkichi; Kuroda, Masaru

2014-06-15

Vesicular glutamate transporter isoforms, VGluT1-VGluT3, accumulate glutamate into synaptic vesicles and are considered to be important molecules in glutamatergic transmission. Among them, VGluT2 mRNA is expressed predominantly throughout the dorsal thalamus, whereas VGluT1 mRNA is expressed in a few thalamic nuclei. In the thalamic nuclei that project to the retrosplenial cortex (RSC), VGluT1 mRNA is expressed strongly in the anterodorsal thalamic nucleus (AD), is expressed moderately in the anteroventral and laterodorsal thalamic nuclei, and is not expressed in the anteromedial thalamic nucleus. Thus, it has been strongly suggested that a subset of thalamocortical projections to RSC possesses both VGluT1 and VGluT2. In this study, double-labeled neuronal somata showing both VGluT1 and VGluT2 immunolabelings were found exclusively in the ventral region of AD (vAD). Many double-labeled axon terminals were also found in two major targets of vAD, the rostral part of the reticular thalamic nucleus and layers Ia and III-IV of the retrosplenial granular b cortex (RSGb). Some were also found in layer Ia of the retrosplenial granular a cortex (RSGa). These axon terminals contain significant amounts of both VGluTs. Because the subset of thalamocortical projections to RSC has a unique molecular basis in the glutamatergic transmission system, it might play an important role in the higher cognitive functions processed in the RSC. Furthermore, double-labeled axon terminals of a different type were distributed in RSGb and RSGa. Because they are small and the immunoreactivity of VGluT2 is significantly weaker than that of VGluT1, they seemed to be a subset of corticocortical terminals. Copyright © 2013 Wiley Periodicals, Inc.

Expression of Glutamate and Inhibitory Amino Acid Vesicular Transporters in the Rodent Auditory Brainstem

PubMed Central

Ito, Tetsufumi; Bishop, Deborah C.; Oliver, Douglas L.

2011-01-01

Glutamate is the main excitatory neurotransmitter in the auditory system, but associations between glutamatergic neuronal populations and the distribution of their synaptic terminations have been difficult. Different subsets of glutamatergic terminals employ one of three vesicular glutamate transporters (VGLUT) to load synaptic vesicles. Recently, VGLUT1 and VGLUT2 terminals were found to have different patterns of organization in the inferior colliculus suggesting that there are different types of glutamatergic neurons in the brainstem auditory system with projections to the colliculus. To positively identify VGLUT-expressing neurons as well as inhibitory neurons in the auditory brainstem, we used in situ hybridization to identify the mRNA for VGLUT1, VGLUT2, and VIAAT (the vesicular inhibitory amino acid transporter used by GABAergic and glycinergic terminals). Similar expression patterns were found in subsets of glutamatergic and inhibitory neurons in the auditory brainstem and thalamus of adult rats and mice. Four patterns of gene expression were seen in individual neurons. 1) VGLUT2 expressed alone was the prevalent pattern. 2) VGLUT1 co-expressed with VGLUT2 was seen in scattered neurons in most nuclei but was common in the medial geniculate body and ventral cochlear nucleus. 3) VGLUT1 expressed alone was found only in granule cells. 4) VIAAT expression was common in most nuclei but dominated in some. These data show that the expression of the VGLUT1/2 and VIAAT genes can identify different subsets of auditory neurons. This may facilitate the identification of different components in auditory circuits. PMID:21165977

Documentation for the machine-readable version of OAO 2 filter photometry of 531 stars of diverse types

NASA Technical Reports Server (NTRS)

Warren, W. H., Jr.

1982-01-01

A magnetic tape version of the ultraviolet photometry of 531 stars observed with the Wisconsin Experiment Package aboard the Orbiting Astronomical Observatory (OAO 2) is described. The data were obtained with medium band interference filters and were reduced to a uniform magnitude system. They represent a subset of partially reduced data currently on file at the National Space Science Data Center. The document is intended to enable users of the tape file to read and process data without problems or guesswork. For technical details concerning the observations, instrumentation limitations, and interpretation of the data the reference publication should be consulted. This document was designed for distribution with any machine-readable version of the OAO 2 photometric data.

Visual feature extraction from voxel-weighted averaging of stimulus images in 2 fMRI studies.

PubMed

Hart, Corey B; Rose, William J

2013-11-01

Multiple studies have provided evidence for distributed object representation in the brain, with several recent experiments leveraging basis function estimates for partial image reconstruction from fMRI data. Using a novel combination of statistical decomposition, generalized linear models, and stimulus averaging on previously examined image sets and Bayesian regression of recorded fMRI activity during presentation of these data sets, we identify a subset of relevant voxels that appear to code for covarying object features. Using a technique we term "voxel-weighted averaging," we isolate image filters that these voxels appear to implement. The results, though very cursory, appear to have significant implications for hierarchical and deep-learning-type approaches toward the understanding of neural coding and representation.

CCR6+ Th cell distribution differentiates systemic lupus erythematosus patients based on anti-dsDNA antibody status.

PubMed

Zhong, Wei; Jiang, Zhenyu; Wu, Jiang; Jiang, Yanfang; Zhao, Ling

2018-01-01

Systemic lupus erythematosus (SLE) disease has been shown to be associated with the generation of multiple auto-antibodies. Among these, anti-dsDNA antibodies (anti-DNAs) are specific and play a pathogenic role in SLE. Indeed, anti-DNA + SLE patients display a worse disease course. The generation of these pathogenic anti-DNAs has been attributed to the interaction between aberrant T helper (Th) cells and autoimmune B cells. Thus, in this study we have investigated whether CCR6 + Th cells have the ability to differentiate SLE patients based on anti-DNA status, and if their distribution has any correlation with disease activity. We recruited 25 anti-DNA + and 25 anti-DNA - treatment-naive onset SLE patients, matched for various clinical characteristics in our nested matched case-control study. CCR6 + Th cells and their additional subsets were analyzed in each patient by flow cytometry. Anti-DNA + SLE patients specifically had a higher percentage of Th cells expressing CCR6 and CXCR3. Further analysis of CCR6 + Th cell subsets showed that anti-DNA + SLE patients had elevated proportions of Th9, Th17, Th17.1 and CCR4/CXCR3 double-negative (DN) cells. However, the proportions of CCR6 - Th subsets, including Th1 and Th2 cells, did not show any association with anti-DNA status. Finally, we identified a correlation between CCR6 + Th subsets and clinical indicators, specifically in anti-DNA + SLE patients. Our data indicated that CCR6 + Th cells and their subsets were elevated and correlated with disease activity in anti-DNA + SLE patients. We speculated that CCR6 + Th cells may contribute to distinct disease severity in anti-DNA + SLE patients.

Frequency and distribution of incidental findings deemed appropriate for S modifier designation on low-dose CT in a lung cancer screening program.

PubMed

Reiter, Michael J; Nemesure, Allison; Madu, Ezemonye; Reagan, Lisa; Plank, April

2018-06-01

To describe the frequency, distribution and reporting patterns of incidental findings receiving the Lung-RADS S modifier on low-dose chest computed tomography (CT) among lung cancer screening participants. This retrospective investigation included 581 individuals who received baseline low-dose chest CT for lung cancer screening between October 2013 and June 2017 at a single center. Incidental findings resulting in assignment of Lung-RADS S modifier were recorded as were incidental abnormalities detailed within the body of the radiology report only. A subset of 60 randomly selected CTs was reviewed by a second (blinded) radiologist to evaluate inter-rater variability of Lung-RADS reporting. A total of 261 (45%) participants received the Lung-RADS S modifier on baseline CT with 369 incidental findings indicated as potentially clinically significant. Coronary artery calcification was most commonly reported, accounting for 182 of the 369 (49%) findings. An additional 141 incidentalomas of the same types as these 369 findings were described in reports but were not labelled with the S modifier. Therefore, as high as 69% (402 of 581) of participants could have received the S modifier if reporting was uniform. Inter-radiologist concordance of S modifier reporting in a subset of 60 participants was poor (42% agreement, kappa = 0.2). Incidental findings are commonly identified on chest CT for lung cancer screening, yet reporting of the S modifier within Lung-RADS is inconsistent. Specific guidelines are necessary to better define potentially clinically significant abnormalities and to improve reporting uniformity. Copyright © 2018 Elsevier B.V. All rights reserved.

A NEAR-INFRARED STUDY OF THE STAR-FORMING REGION RCW 34

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van der Walt, D. J.; De Villiers, H. M.; Czanik, R. J.

2012-07-15

We report the results of a near-infrared imaging study of a 7.8 Multiplication-Sign 7.8 arcmin{sup 2} region centered on the 6.7 GHz methanol maser associated with the RCW 34 star-forming region using the 1.4 m IRSF telescope at Sutherland. A total of 1283 objects were detected simultaneously in J, H, and K for an exposure time of 10,800 s. The J - H, H - K two-color diagram revealed a strong concentration of more than 700 objects with colors similar to what is expected of reddened classical T Tauri stars. The distribution of the objects on the K versus Jmore » - K color-magnitude diagram is also suggestive that a significant fraction of the 1283 objects is made up of lower mass pre-main-sequence stars. We also present the luminosity function for the subset of about 700 pre-main-sequence stars and show that it suggests ongoing star formation activity for about 10{sup 7} years. An examination of the spatial distribution of the pre-main-sequence stars shows that the fainter (older) part of the population is more dispersed over the observed region and the brighter (younger) subset is more concentrated around the position of the O8.5V star. This suggests that the physical effects of the O8.5V star and the two early B-type stars on the remainder of the cloud out of which they formed could have played a role in the onset of the more recent episode of star formation in RCW 34.« less

Descriptive Characteristics of Concussions in National Football League Games, 2010-2011 to 2013-2014.

PubMed

Clark, Michael D; Asken, Breton M; Marshall, Stephen W; Guskiewicz, Kevin M

2017-03-01

Despite a high reported incidence rate of concussion, little is known about the on-field characteristics of injurious head impacts in National Football League (NFL) games. To characterize on-field features (location, player position, and time during game) and biomechanical features (anticipation status, closing distance, impact location and type) associated with concussions in NFL games over a 4-season period (2010-2011 to 2013-2014). Descriptive epidemiology study. We analyzed video of a subset of reported, in-game concussions for the 2010-2011 to 2013-2014 seasons. These videos represented a sample of injuries that were diagnosed and reported on the same day and that could be clearly associated with an in-game collision as captured on video. We determined anticipation status, closing distance, impact location on the injured player's helmet, and impact type (helmet-to-helmet, helmet-to-body, or helmet-to-ground). Associations between these variables were analyzed by use of descriptive statistics and tests of association. A total of 871 diagnosed concussions were reported as occurring during NFL preseason, regular season, and postseason games for the 2010-2011, 2011-2012, 2012-2013, and 2013-2014 seasons. A total of 1324 games were played during this period, giving a concussion incidence rate of 0.658 per game (95% CI, 0.61-0.70). From the video-reviewed subset (n = 429; 49.3%), the majority of injurious impacts occurred with good anticipation (57.3%) and <10 yards of closing distance (59.0%). An association was found between anticipation status and play type ([Formula: see text] = 27.398, P < .001), largely because injuries occurring on pass plays were more likely to be poorly anticipated than injuries during run plays (43.0% vs 21.4%; [Formula: see text] = 14.78, P < .001). Kick returns had the greatest proportion of well-anticipated impacts (78%) and the greatest proportion of impacts with ≥10 yards of closing distance (80%). The type of impact was approximately equally divided between helmet-to-helmet, helmet-to-body, and helmet-to-ground types. The impact location was broadly distributed over the helmet of the injured player. In-game concussions in the NFL occurred through a diverse variety of mechanisms, surprisingly tended to be well-anticipated, and, also surprisingly, occurred with <10 yards of closing distance. The impacts causing concussion were broadly distributed over the helmet. More concussions occurred during the second half of game play, but we do not have evidence to explain this finding.

Threshold quantum state sharing based on entanglement swapping

NASA Astrophysics Data System (ADS)

Qin, Huawang; Tso, Raylin

2018-06-01

A threshold quantum state sharing scheme is proposed. The dealer uses the quantum-controlled-not operations to expand the d-dimensional quantum state and then uses the entanglement swapping to distribute the state to a random subset of participants. The participants use the single-particle measurements and unitary operations to recover the initial quantum state. In our scheme, the dealer can share different quantum states among different subsets of participants simultaneously. So the scheme will be very flexible in practice.

Correlations in star networks: from Bell inequalities to network inequalities

NASA Astrophysics Data System (ADS)

Tavakoli, Armin; Olivier Renou, Marc; Gisin, Nicolas; Brunner, Nicolas

2017-07-01

The problem of characterizing classical and quantum correlations in networks is considered. Contrary to the usual Bell scenario, where distant observers share a physical system emitted by one common source, a network features several independent sources, each distributing a physical system to a subset of observers. In the quantum setting, the observers can perform joint measurements on initially independent systems, which may lead to strong correlations across the whole network. In this work, we introduce a technique to systematically map a Bell inequality to a family of Bell-type inequalities bounding classical correlations on networks in a star-configuration. Also, we show that whenever a given Bell inequality can be violated by some entangled state ρ, then all the corresponding network inequalities can be violated by considering many copies of ρ distributed in the star network. The relevance of these ideas is illustrated by applying our method to a specific multi-setting Bell inequality. We derive the corresponding network inequalities, and study their quantum violations.

Tools, Services & Support of NASA Salinity Mission Data Archival Distribution through PO.DAAC

NASA Astrophysics Data System (ADS)

Tsontos, V. M.; Vazquez, J.

2017-12-01

The Physical Oceanography Distributed Active Center (PO.DAAC) serves as the designated NASA repository and distribution node for all Aquarius/SAC-D and SMAP sea surface salinity (SSS) mission data products in close collaboration with the projects. In addition to these official mission products, that by December 2017 will include the Aquarius V5.0 end-of-mission data, PO.DAAC archives and distributes high-value, principal investigator led satellite SSS products, and also datasets from NASA's "Salinity Processes in the Upper Ocean Regional Study" (SPURS 1 & 2) field campaigns in the N. Atlantic salinity maximum and high rainfall E. Tropical Pacific regions. Here we report on the status of these data holdings at PO.DAAC, and the range of data services and access tools that are provided in support of NASA salinity. These include user support and data discovery services, OPeNDAP and THREDDS web services for subsetting/extraction, and visualization via LAS and SOTO. Emphasis is placed on newer capabilities, including PODAAC's consolidated web services (CWS) and advanced L2 subsetting tool called HiTIDE.

A parallel decision tree-based method for user authentication based on keystroke patterns.

PubMed

Sheng, Yong; Phoha, Vir V; Rovnyak, Steven M

2005-08-01

We propose a Monte Carlo approach to attain sufficient training data, a splitting method to improve effectiveness, and a system composed of parallel decision trees (DTs) to authenticate users based on keystroke patterns. For each user, approximately 19 times as much simulated data was generated to complement the 387 vectors of raw data. The training set, including raw and simulated data, is split into four subsets. For each subset, wavelet transforms are performed to obtain a total of eight training subsets for each user. Eight DTs are thus trained using the eight subsets. A parallel DT is constructed for each user, which contains all eight DTs with a criterion for its output that it authenticates the user if at least three DTs do so; otherwise it rejects the user. Training and testing data were collected from 43 users who typed the exact same string of length 37 nine consecutive times to provide data for training purposes. The users typed the same string at various times over a period from November through December 2002 to provide test data. The average false reject rate was 9.62% and the average false accept rate was 0.88%.

The Influence of Host Galaxies in Type Ia Supernova Cosmology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uddin, Syed A.; Mould, Jeremy; Lidman, Chris

We use a sample of 1338 spectroscopically confirmed and photometrically classified Type Ia supernovae (SNe Ia) sourced from Carnegie Supernova Project, Center for Astrophysics Supernova Survey, Sloan Digital Sky Survey-II, and SuperNova Legacy Survey SN samples to examine the relationships between SNe Ia and the galaxies that host them. Our results provide confirmation with improved statistical significance that SNe Ia, after standardization, are on average more luminous in massive hosts (significance >5 σ ), and decline more rapidly in massive hosts (significance >9 σ ) and in hosts with low specific star formation rates (significance >8 σ ). We studymore » the variation of these relationships with redshift and detect no evolution. We split SNe Ia into pairs of subsets that are based on the properties of the hosts and fit cosmological models to each subset. Including both systematic and statistical uncertainties, we do not find any significant shift in the best-fit cosmological parameters between the subsets. Among different SN Ia subsets, we find that SNe Ia in hosts with high specific star formation rates have the least intrinsic scatter ( σ {sub int} = 0.08 ± 0.01) in luminosity after standardization.« less

The Influence of Host Galaxies in Type Ia Supernova Cosmology

NASA Astrophysics Data System (ADS)

Uddin, Syed A.; Mould, Jeremy; Lidman, Chris; Ruhlmann-Kleider, Vanina; Zhang, Bonnie R.

2017-10-01

We use a sample of 1338 spectroscopically confirmed and photometrically classified Type Ia supernovae (SNe Ia) sourced from Carnegie Supernova Project, Center for Astrophysics Supernova Survey, Sloan Digital Sky Survey-II, and SuperNova Legacy Survey SN samples to examine the relationships between SNe Ia and the galaxies that host them. Our results provide confirmation with improved statistical significance that SNe Ia, after standardization, are on average more luminous in massive hosts (significance >5σ), and decline more rapidly in massive hosts (significance >9σ) and in hosts with low specific star formation rates (significance >8σ). We study the variation of these relationships with redshift and detect no evolution. We split SNe Ia into pairs of subsets that are based on the properties of the hosts and fit cosmological models to each subset. Including both systematic and statistical uncertainties, we do not find any significant shift in the best-fit cosmological parameters between the subsets. Among different SN Ia subsets, we find that SNe Ia in hosts with high specific star formation rates have the least intrinsic scatter (σ int = 0.08 ± 0.01) in luminosity after standardization.

EXPLORING THE VARIABLE SKY WITH LINEAR. II. HALO STRUCTURE AND SUBSTRUCTURE TRACED BY RR LYRAE STARS TO 30 kpc

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sesar, Branimir; Ivezic, Zeljko; Morgan, Dylan M.

We present a sample of {approx}5000 RR Lyrae stars selected from the recalibrated LINEAR data set and detected at heliocentric distances between 5 kpc and 30 kpc over {approx}8000 deg{sup 2} of sky. The coordinates and light curve properties, such as period and Oosterhoff type, are made publicly available. We analyze in detail the light curve properties and Galactic distribution of the subset of {approx}4000 type ab RR Lyrae (RRab) stars, including a search for new halo substructures and the number density distribution as a function of Oosterhoff type. We find evidence for the Oosterhoff dichotomy among field RR Lyraemore » stars, with the ratio of the type II and I subsamples of about 1:4, but with a weaker separation than for globular cluster stars. The wide sky coverage and depth of this sample allow unique constraints for the number density distribution of halo RRab stars as a function of galactocentric distance: it can be described as an oblate ellipsoid with an axis ratio q = 0.63 and with either a single or a double power law with a power-law index in the range -2 to -3. Consistent with previous studies, we find that the Oosterhoff type II subsample has a steeper number density profile than the Oosterhoff type I subsample. Using the group-finding algorithm EnLink, we detected seven candidate halo groups, only one of which is statistically spurious. Three of these groups are near globular clusters (M53/NGC 5053, M3, M13), and one is near a known halo substructure (Virgo Stellar Stream); the remaining three groups do not seem to be near any known halo substructures or globular clusters and seem to have a higher ratio of Oosterhoff type II to Oosterhoff type I RRab stars than what is found in the halo. The extended morphology and the position (outside the tidal radius) of some of the groups near globular clusters are suggestive of tidal streams possibly originating from globular clusters. Spectroscopic follow-up of detected halo groups is encouraged.« less

Exploring the Variable Sky with LINEAR. II. Halo Structure and Substructure Traced by RR Lyrae Stars to 30 kpc

NASA Astrophysics Data System (ADS)

Sesar, Branimir; Ivezić, Željko; Stuart, J. Scott; Morgan, Dylan M.; Becker, Andrew C.; Sharma, Sanjib; Palaversa, Lovro; Jurić, Mario; Wozniak, Przemyslaw; Oluseyi, Hakeem

2013-08-01

We present a sample of ~5000 RR Lyrae stars selected from the recalibrated LINEAR data set and detected at heliocentric distances between 5 kpc and 30 kpc over ~8000 deg2 of sky. The coordinates and light curve properties, such as period and Oosterhoff type, are made publicly available. We analyze in detail the light curve properties and Galactic distribution of the subset of ~4000 type ab RR Lyrae (RRab) stars, including a search for new halo substructures and the number density distribution as a function of Oosterhoff type. We find evidence for the Oosterhoff dichotomy among field RR Lyrae stars, with the ratio of the type II and I subsamples of about 1:4, but with a weaker separation than for globular cluster stars. The wide sky coverage and depth of this sample allow unique constraints for the number density distribution of halo RRab stars as a function of galactocentric distance: it can be described as an oblate ellipsoid with an axis ratio q = 0.63 and with either a single or a double power law with a power-law index in the range -2 to -3. Consistent with previous studies, we find that the Oosterhoff type II subsample has a steeper number density profile than the Oosterhoff type I subsample. Using the group-finding algorithm EnLink, we detected seven candidate halo groups, only one of which is statistically spurious. Three of these groups are near globular clusters (M53/NGC 5053, M3, M13), and one is near a known halo substructure (Virgo Stellar Stream); the remaining three groups do not seem to be near any known halo substructures or globular clusters and seem to have a higher ratio of Oosterhoff type II to Oosterhoff type I RRab stars than what is found in the halo. The extended morphology and the position (outside the tidal radius) of some of the groups near globular clusters are suggestive of tidal streams possibly originating from globular clusters. Spectroscopic follow-up of detected halo groups is encouraged.

Clinical relevance and suppressive capacity of human MDSC subsets.

PubMed

Lang, Stephan; Bruderek, Kirsten; Kaspar, Cordelia; Höing, Benedikt; Kanaan, Oliver; Dominas, Nina; Hussain, Timon; Droege, Freya; Eyth, Christian Peter; Hadaschik, Boris; Brandau, Sven

2018-06-18

Myeloid-derived suppressor cells (MDSC) are a heterogeneous group of pathologically expanded myeloid cells with immunosuppressive activity. In human disease three major MDSC subpopulations can be defined as monocytic M-MDSC, granulocytic PMN-MDSC and early stage e-MDSC, which lack myeloid lineage markers of the former two subsets. It was the purpose of this study to determine and compare the immunosuppressive capacity and clinical relevance of each of these subsets in patients with solid cancer. The frequency of MDSC subsets in the peripheral blood was determined by flow cytometry in a cohort of 49 patients with advanced head and neck cancer (HNC) and 22 patients with urological cancers. Sorted and purified MDSC subsets were tested in vitro for their T cell suppressive capacity. Frequency of circulating MDSC was correlated with overall survival of HNC patients. A high frequency of PMN-MDSC most strongly correlated with poor overall survival in HNC. T cell suppressive activity was higher in PMN-MDSC compared with M-MDSC and e-MDSC. A subset of CD66b+/CD11b+/CD16+ mature PMN-MDSC displayed high expression and activity of arginase I, and was superior to the other subsets in suppressing proliferation and cytokine production of T cells in both cancer types. High levels of this CD11b+/CD16+ PMN-MDSC, but not other PMN-MDSC subsets, strongly correlated with adverse outcome in HNC. A subset of mature CD11b+/CD16+ PMN-MDSC was identified as the MDSC subset with the strongest immunosuppressive activity and the highest clinical relevance. Copyright ©2018, American Association for Cancer Research.

Redefining Myeloid Cell Subsets in Murine Spleen

PubMed Central

Hey, Ying-Ying; Tan, Jonathan K. H.; O’Neill, Helen C.

2016-01-01

Spleen is known to contain multiple dendritic and myeloid cell subsets, distinguishable on the basis of phenotype, function and anatomical location. As a result of recent intensive flow cytometric analyses, splenic dendritic cell (DC) subsets are now better characterized than other myeloid subsets. In order to identify and fully characterize a novel splenic subset termed “L-DC” in relation to other myeloid cells, it was necessary to investigate myeloid subsets in more detail. In terms of cell surface phenotype, L-DC were initially characterized as a CD11bhiCD11cloMHCII−Ly6C−Ly6G− subset in murine spleen. Their expression of CD43, lack of MHCII, and a low level of CD11c was shown to best differentiate L-DC by phenotype from conventional DC subsets. A complete analysis of all subsets in spleen led to the classification of CD11bhiCD11cloMHCII−Ly6CloLy6G− cells as monocytes expressing CX3CR1, CD43 and CD115. Siglec-F expression was used to identify a specific eosinophil population, distinguishable from both Ly6Clo and Ly6Chi monocytes, and other DC subsets. L-DC were characterized as a clear subset of CD11bhiCD11cloMHCII−Ly6C−Ly6G− cells, which are CD43+, Siglec-F− and CD115−. Changes in the prevalence of L-DC compared to other subsets in spleens of mutant mice confirmed the phenotypic distinction between L-DC, cDC and monocyte subsets. L-DC development in vivo was shown to occur independently of the BATF3 transcription factor that regulates cDC development, and also independently of the FLT3L and GM-CSF growth factors which drive cDC and monocyte development, so distinguishing L-DC from these commonly defined cell types. PMID:26793192

Expression of GAD67 and Dlx5 in the taste buds of mice genetically lacking Mash1.

PubMed

Kito-Shingaki, Ayae; Seta, Yuji; Toyono, Takashi; Kataoka, Shinji; Kakinoki, Yasuaki; Yanagawa, Yuchio; Toyoshima, Kuniaki

2014-06-01

It has been reported that a subset of type III taste cells express glutamate decarboxylase (GAD)67, which is a molecule that synthesizes gamma-aminobutyric acid (GABA), and that Mash1 could be a potential regulator of the development of GABAnergic neurons via Dlx transcription factors in the central nervous system. In this study, we investigated the expression of GAD67 and Dlx in the embryonic taste buds of the soft palate and circumvallate papilla using Mash1 knockout (KO)/GAD67-GFP knock-in mice. In the wild-type animal, a subset of type III taste cells contained GAD67 in the taste buds of the soft palate and the developing circumvallate papilla, whereas GAD67-expressing taste bud cells were missing from Mash1 KO mice. A subset of type III cells expressed mRNA for Dlx5 in the wild-type animals, whereas Dlx5-expressing cells were not evident in the apical part of the circumvallate papilla and taste buds in the soft palate of Mash1 KO mice. Our results suggest that Mash1 is required for the expression of GAD67 and Dlx5 in taste bud cells. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Discovering biclusters in gene expression data based on high-dimensional linear geometries

PubMed Central

Gan, Xiangchao; Liew, Alan Wee-Chung; Yan, Hong

2008-01-01

Background In DNA microarray experiments, discovering groups of genes that share similar transcriptional characteristics is instrumental in functional annotation, tissue classification and motif identification. However, in many situations a subset of genes only exhibits consistent pattern over a subset of conditions. Conventional clustering algorithms that deal with the entire row or column in an expression matrix would therefore fail to detect these useful patterns in the data. Recently, biclustering has been proposed to detect a subset of genes exhibiting consistent pattern over a subset of conditions. However, most existing biclustering algorithms are based on searching for sub-matrices within a data matrix by optimizing certain heuristically defined merit functions. Moreover, most of these algorithms can only detect a restricted set of bicluster patterns. Results In this paper, we present a novel geometric perspective for the biclustering problem. The biclustering process is interpreted as the detection of linear geometries in a high dimensional data space. Such a new perspective views biclusters with different patterns as hyperplanes in a high dimensional space, and allows us to handle different types of linear patterns simultaneously by matching a specific set of linear geometries. This geometric viewpoint also inspires us to propose a generic bicluster pattern, i.e. the linear coherent model that unifies the seemingly incompatible additive and multiplicative bicluster models. As a particular realization of our framework, we have implemented a Hough transform-based hyperplane detection algorithm. The experimental results on human lymphoma gene expression dataset show that our algorithm can find biologically significant subsets of genes. Conclusion We have proposed a novel geometric interpretation of the biclustering problem. We have shown that many common types of bicluster are just different spatial arrangements of hyperplanes in a high dimensional data space. An implementation of the geometric framework using the Fast Hough transform for hyperplane detection can be used to discover biologically significant subsets of genes under subsets of conditions for microarray data analysis. PMID:18433477

Rapid activation of spleen dendritic cell subsets following lymphocytic choriomeningitis virus infection of mice: analysis of the involvement of type 1 IFN.

PubMed

Montoya, Maria; Edwards, Matthew J; Reid, Delyth M; Borrow, Persephone

2005-02-15

In this study, we report the dynamic changes in activation and functions that occur in spleen dendritic cell (sDC) subsets following infection of mice with a natural murine pathogen, lymphocytic choriomeningitis virus (LCMV). Within 24 h postinfection (pi), sDCs acquired the ability to stimulate naive LCMV-specific CD8+ T cells ex vivo. Conventional (CD11chigh CD8+ and CD4+) sDC subsets rapidly up-regulated expression of costimulatory molecules and began to produce proinflammatory cytokines. Their tendency to undergo apoptosis ex vivo simultaneously increased, and in vivo the number of conventional DCs in the spleen decreased markedly, dropping approximately 2-fold by day 3 pi. Conversely, the number of plasmacytoid (CD11clowB220+) DCs in the spleen increased, so that they constituted almost 40% of sDCs by day 3 pi. Type 1 IFN production was up-regulated in plasmacytoid DCs by 24 h pi. Analysis of DC activation and maturation in mice unable to respond to type 1 IFNs implicated these cytokines in driving infection-associated phenotypic activation of conventional DCs and their enhanced tendency to undergo apoptosis, but also indicated the existence of type 1 IFN-independent pathways for the functional maturation of DCs during LCMV infection.

MODIS Interactive Subsetting Tool (MIST)

NASA Astrophysics Data System (ADS)

McAllister, M.; Duerr, R.; Haran, T.; Khalsa, S. S.; Miller, D.

2008-12-01

In response to requests from the user community, NSIDC has teamed with the Oak Ridge National Laboratory Distributive Active Archive Center (ORNL DAAC) and the Moderate Resolution Data Center (MrDC) to provide time series subsets of satellite data covering stations in the Greenland Climate Network (GC-NET) and the International Arctic Systems for Observing the Atmosphere (IASOA) network. To serve these data NSIDC created the MODIS Interactive Subsetting Tool (MIST). MIST works with 7 km by 7 km subset time series of certain Version 5 (V005) MODIS products over GC-Net and IASOA stations. User- selected data are delivered in a text Comma Separated Value (CSV) file format. MIST also provides online analysis capabilities that include generating time series and scatter plots. Currently, MIST is a Beta prototype and NSIDC intends that user requests will drive future development of the tool. The intent of this poster is to introduce MIST to the MODIS data user audience and illustrate some of the online analysis capabilities.

The SIMRAND methodology: Theory and application for the simulation of research and development projects

NASA Technical Reports Server (NTRS)

Miles, R. F., Jr.

1986-01-01

A research and development (R&D) project often involves a number of decisions that must be made concerning which subset of systems or tasks are to be undertaken to achieve the goal of the R&D project. To help in this decision making, SIMRAND (SIMulation of Research ANd Development Projects) is a methodology for the selection of the optimal subset of systems or tasks to be undertaken on an R&D project. Using alternative networks, the SIMRAND methodology models the alternative subsets of systems or tasks under consideration. Each path through an alternative network represents one way of satisfying the project goals. Equations are developed that relate the system or task variables to the measure of reference. Uncertainty is incorporated by treating the variables of the equations probabilistically as random variables, with cumulative distribution functions assessed by technical experts. Analytical techniques of probability theory are used to reduce the complexity of the alternative networks. Cardinal utility functions over the measure of preference are assessed for the decision makers. A run of the SIMRAND Computer I Program combines, in a Monte Carlo simulation model, the network structure, the equations, the cumulative distribution functions, and the utility functions.

Dopaminergic neurons encode a distributed, asymmetric representation of temperature in Drosophila.

PubMed

Tomchik, Seth M

2013-01-30

Dopaminergic circuits modulate a wide variety of innate and learned behaviors in animals, including olfactory associative learning, arousal, and temperature-preference behavior. It is not known whether distinct or overlapping sets of dopaminergic neurons modulate these behaviors. Here, I have functionally characterized the dopaminergic circuits innervating the Drosophila mushroom body with in vivo calcium imaging and conditional silencing of genetically defined subsets of neurons. Distinct subsets of PPL1 dopaminergic neurons innervating the vertical lobes of the mushroom body responded to decreases in temperature, but not increases, with rapidly adapting bursts of activity. PAM neurons innervating the horizontal lobes did not respond to temperature shifts. Ablation of the antennae and maxillary palps reduced, but did not eliminate, the responses. Genetic silencing of dopaminergic neurons innervating the vertical mushroom body lobes substantially reduced behavioral cold avoidance, but silencing smaller subsets of these neurons had no effect. These data demonstrate that overlapping dopaminergic circuits encode a broadly distributed, asymmetric representation of temperature that overlays regions implicated previously in learning, memory, and forgetting. Thus, diverse behaviors engage overlapping sets of dopaminergic neurons that encode multimodal stimuli and innervate a single anatomical target, the mushroom body.

The MODIS reprojection tool

USGS Publications Warehouse

Dwyer, John L.; Schmidt, Gail L.; Qu, J.J.; Gao, W.; Kafatos, M.; Murphy , R.E.; Salomonson, V.V.

2006-01-01

The MODIS Reprojection Tool (MRT) is designed to help individuals work with MODIS Level-2G, Level-3, and Level-4 land data products. These products are referenced to a global tiling scheme in which each tile is approximately 10° latitude by 10° longitude and non-overlapping (Fig. 9.1). If desired, the user may reproject only selected portions of the product (spatial or parameter subsetting). The software may also be used to convert MODIS products to file formats (generic binary and GeoTIFF) that are more readily compatible with existing software packages. The MODIS land products distributed by the Land Processes Distributed Active Archive Center (LP DAAC) are in the Hierarchical Data Format - Earth Observing System (HDF-EOS), developed by the National Center for Supercomputing Applications at the University of Illinois at Urbana Champaign for the NASA EOS Program. Each HDF-EOS file is comprised of one or more science data sets (SDSs) corresponding to geophysical or biophysical parameters. Metadata are embedded in the HDF file as well as contained in a .met file that is associated with each HDF-EOS file. The MRT supports 8-bit, 16-bit, and 32-bit integer data (both signed and unsigned), as well as 32-bit float data. The data type of the output is the same as the data type of each corresponding input SDS.

mtDNA control-region sequence variation suggests multiple independent origins of an "Asian-specific" 9-bp deletion in sub-Saharan Africans.

PubMed Central

Soodyall, H.; Vigilant, L.; Hill, A. V.; Stoneking, M.; Jenkins, T.

1996-01-01

The intergenic COII/tRNA(Lys) 9-bp deletion in human mtDNA, which is found at varying frequencies in Asia, Southeast Asia, Polynesia, and the New World, was also found in 81 of 919 sub-Saharan Africans. Using mtDNA control-region sequence data from a subset of 41 individuals with the deletion, we identified 22 unique mtDNA types associated with the deletion in Africa. A comparison of the unique mtDNA types from sub-Saharan Africans and Asians with the 9-bp deletion revealed that sub-Saharan Africans and Asians have sequence profiles that differ in the locations and frequencies of variant sites. Both phylogenetic and mismatch-distribution analysis suggest that 9-bp deletion arose independently in sub-Saharan Africa and Asia and that the deletion has arisen more than once in Africa. Within Africa, the deletion was not found among Khoisan peoples and was rare to absent in western and southwestern African populations, but it did occur in Pygmy and Negroid populations from central Africa and in Malawi and southern African Bantu-speakers. The distribution of the 9-bp deletion in Africa suggests that the deletion could have arisen in central Africa and was then introduced to southern Africa via the recent "Bantu expansion." PMID:8644719

Irisin plasma concentration in PCOS and healthy subjects is related to body fat content and android fat distribution.

PubMed

Pukajło, Katarzyna; Łaczmański, Łukasz; Kolackov, Katarzyna; Kuliczkowska-Płaksej, Justyna; Bolanowski, Marek; Milewicz, Andrzej; Daroszewski, Jacek

2015-01-01

Irisin (Ir), a recently identified adipo-myokine, cleaved and secreted from the protein FNDC5 in response to physical activity, has been postulated to induce the differentiation of a subset of white adipocytes into brown fat and to mediate the beneficial effects on metabolic homeostasis. Metabolic syndrome (MS), a cluster of factors leading to impaired energy homeostasis, affects a significant proportion of subjects suffering from polycystic ovary syndrome (PCOS). The aim of our study was to investigate the relationship between Ir plasma concentrations and metabolic disturbances. The study group consisted of 179 PCOS patients and a population of 122 healthy controls (both groups aged 25-35 years). A subset of 90 subjects with MS was isolated. A positive association between Ir plasma level and MS in the whole group and in controls was found. In subjects with high adipose body content (>40%), Ir was higher than in lean persons (<30%). Our results showed a significant positive association between Ir concentration and android type of adipose tissue in the whole study group and in the control group. Understanding the role of Ir in increased energy expenditure may lead to the development of new therapeutics for obesity and obesity-related diseases.

Expression of the vesicular glutamate transporter vGluT2 in a subset of cones of the mouse retina.

PubMed

Wässle, Heinz; Regus-Leidig, Hanna; Haverkamp, Silke

2006-06-01

Cone photoreceptors have a continuous release of glutamate that is modulated by light. Vesicular glutamate transporters (vGluT) play an essential role for sustaining this release by loading synaptic vesicles in the cone synapse, the so-called cone pedicle. In the present study mouse retinas were immunostained for vGluT1 and vGluT2. vGluT1 was localized to all cone pedicles and rod spherules, whereas vGluT2 was found in only 10% of the cone pedicles. The vGluT2-expressing cones were characterized in more detail. They are distributed in a regular array, suggesting they are a distinct type. Their proportion does not differ between dorsal (L-cone-dominated) and ventral (S-cone-dominated) retina, and they are not the genuine blue cones of the mouse retina. During development, vGluT1 and vGluT2 expression in cones starts at around P0 and right from the beginning vGluT2 is only expressed in a subset of cones. Bipolar cells contact the vGluT2-expressing cones and other cones nonselectively. The possible functional role of vGluT2 expression in a small fraction of cones is discussed.

Human papilloma virus genotypes in women from Nayarit, Mexico, with squamous intraepithelial lesions and cervical cancer.

PubMed

Ortega-Cervantes, Laura; Aguilar-Lemarroy, Adriana; Rojas-García, Aurora Elizabeth; Barrón-Vivanco, Briscia Socorro; Vallejo-Ruiz, Verónica; León, David Cantú-De; Hernández, Yael Yvette Bernal; Jáuregui-Martínez, Armando; Medina-Díaz, Irma Martha

2016-07-01

In Mexico cervical cancer (CC) is the most common cause of death from neoplasia in women. Study aimed to analyze the current distribution of Human papillomavirus (HPV) types in women from Nayarit, Mexico, with Squamous intraepithelial lesions (SIL) and Cervical cancer (CC). Between January 2011 and July 2013, cervical samples were collected from female residents of the Mexican state of Nayarit and were analyzed by means of a LINEAR ARRAY® HPV genotyping test. Data analyses were performed using Stata ver. 8.0 statistical software. Of the samples analyzed, 91.2%, HPV DNA was detected. Of these positive samples, 82% were High-risk (HR) viral types. The most prevalent HPV genotypes identified were 16, 58, 31, 18, and 70. Forty two percent of participants had a single infection, while 23 and 26% of participants were infected with two or more HPV genotypes, respectively. HPV 16 was the most prevalent genotype identified and was frequently present as a co-infection with HPV types 18, 51, 52, 59, 66, or 70. Women <20 years of age were most often infected with HPV, and the HPV Quadrivalent vaccine (types 16, 18, 6, and 11), currently available in Mexico, no confers protection against a subset of the HPV genotypes identified in the present study (58, 31, 70, and 35). Thus, it is important evaluate the geographical distribution of specific HPV genotypes in all health of center across Mexico in order to implement a successful vaccination program and to diagnose CC in its early stages.

Human papilloma virus genotypes in women from Nayarit, Mexico, with squamous intraepithelial lesions and cervical cancer

PubMed Central

Ortega-Cervantes, Laura; Aguilar-Lemarroy, Adriana; Rojas-García, Aurora Elizabeth; Barrón-Vivanco, Briscia Socorro; Vallejo-Ruiz, Verónica; León, David Cantú-De; Hernández, Yael Yvette Bernal; Jáuregui-Martínez, Armando; Medina-Díaz, Irma Martha

2016-01-01

Objective In Mexico cervical cancer (CC) is the most common cause of death from neoplasia in women. Study aimed to analyze the current distribution of Human papillomavirus (HPV) types in women from Nayarit, Mexico, with Squamous intraepithelial lesions (SIL) and Cervical cancer (CC). Methodology Between January 2011 and July 2013, cervical samples were collected from female residents of the Mexican state of Nayarit and were analyzed by means of a LINEAR ARRAY® HPV genotyping test. Data analyses were performed using Stata ver. 8.0 statistical software. Results Of the samples analyzed, 91.2%, HPV DNA was detected. Of these positive samples, 82% were High-risk (HR) viral types. The most prevalent HPV genotypes identified were 16, 58, 31, 18, and 70. Forty two percent of participants had a single infection, while 23 and 26% of participants were infected with two or more HPV genotypes, respectively. HPV 16 was the most prevalent genotype identified and was frequently present as a co-infection with HPV types 18, 51, 52, 59, 66, or 70. Conclusion Women <20 years of age were most often infected with HPV, and the HPV Quadrivalent vaccine (types 16, 18, 6, and 11), currently available in Mexico, no confers protection against a subset of the HPV genotypes identified in the present study (58, 31, 70, and 35). Thus, it is important evaluate the geographical distribution of specific HPV genotypes in all health of center across Mexico in order to implement a successful vaccination program and to diagnose CC in its early stages. PMID:27610056

A global look into human T cell subsets before and after cryopreservation using multiparametric flow cytometry and two-dimensional visualization analysis.

PubMed

Lemieux, Jennifer; Jobin, Christine; Simard, Carl; Néron, Sonia

2016-07-01

The cryopreservation of human lymphocytes is an essential step for the achievement of several cellular therapies. Besides, T cells are considered as promising actors in cancer therapy for their cytotoxic and regulatory properties. Consequently, the development of tools to monitor the impact of freezing and thawing processes on their fine distribution may be an asset to achieve quality control in cellular therapy. In this study, the phenotypes of freshly isolated human mononuclear cells were compared to those observed following one cycle of cryopreservation and rest periods 0h, 1h and 24h after thawing but before staining. T cells were scrutinized for their distribution according to naive, memory effector, regulatory and helper subsets. Flow cytometry analyses were done using eight-color antibody panels as proposed by the Human Immunophenotyping Consortium. Data were further analyzed by using conventional directed gating and clustering software, namely SPADE and viSNE. Overall, SPADE and viSNE tools were very efficient to monitor the outcome of PBMC populations and T cell subsets. T cells were more sensitive to cryopreservation than other cells. Our results indicated that submitting the thawed cells to a 1h rest period improved the detection of some cell markers when compared to fresh samples. In contrast, cells submitted to a 24h rest period, or to none, were less representative of fresh sample distribution. The heterogeneity of PBMC, as well as the effects of freeze-thaw cycle on their distribution, can be easily monitored by using SPADE and viSNE. Copyright © 2016 Elsevier B.V. All rights reserved.

Applications of self-organizing neural networks in virtual screening and diversity selection.

PubMed

Selzer, Paul; Ertl, Peter

2006-01-01

Artificial neural networks provide a powerful technique for the analysis and modeling of nonlinear relationships between molecular structures and pharmacological activity. Many network types, including Kohonen and counterpropagation, also provide an intuitive method for the visual assessment of correspondence between the input and output data. This work shows how a combination of neural networks and radial distribution function molecular descriptors can be applied in various areas of industrial pharmaceutical research. These applications include the prediction of biological activity, the selection of screening candidates (cherry picking), and the extraction of representative subsets from large compound collections such as combinatorial libraries. The methods described have also been implemented as an easy-to-use Web tool, allowing chemists to perform interactive neural network experiments on the Novartis intranet.

Collagen XIX Is Expressed by Interneurons and Contributes to the Formation of Hippocampal Synapses

PubMed Central

Su, Jianmin; Gorse, Karen; Ramirez, Francesco; Fox, Michael A.

2010-01-01

Extracellular matrix (ECM) molecules contribute to the formation and maintenance of synapses in the mammalian nervous system. We previously discovered a family of nonfibrillar collagens that organize synaptic differentiation at the neuromuscular junction (NMJ). Although many NMJ-organizing cues contribute to central nervous system (CNS) synaptogenesis, whether similar roles for collagens exist at central synapses remained unclear. In the present study we discovered that col19a1, the gene encoding nonfibrillar collagen XIX, is expressed by subsets of hippocampal neurons. Colocalization with the interneuron-specific enzyme glutamate decarboxylase 67 (Gad67), but not other cell-type-specific markers, suggests that hippocampal expression of col19a1 is restricted to interneurons. However, not all hippocampal interneurons express col19a1 mRNA; subsets of neuropeptide Y (NPY)-, somatostatin (Som)-, and calbindin (Calb)-immunoreactive interneurons express col19a1, but those containing parvalbumin (Parv) or calretinin (Calr) do not. To assess whether collagen XIX is required for the normal formation of hippocampal synapses, we examined synaptic morphology and composition in targeted mouse mutants lacking collagen XIX. We show here that subsets of synaptotagmin 2 (Syt2)-containing hippocampal nerve terminals appear malformed in the absence of collagen XIX. The presence of Syt2 in inhibitory hippocampal synapses, the altered distribution of Gad67 in collagen XIX-deficient subiculum, and abnormal levels of gephyrin in collagen XIX-deficient hippocampal extracts all suggest inhibitory synapses are affected by the loss of collagen XIX. Together, these data not only reveal that collagen XIX is expressed by central neurons, but show for the first time that a nonfibrillar collagen is necessary for the formation of hippocampal synapses. PMID:19937713

Solving large tomographic linear systems: size reduction and error estimation

NASA Astrophysics Data System (ADS)

Voronin, Sergey; Mikesell, Dylan; Slezak, Inna; Nolet, Guust

2014-10-01

We present a new approach to reduce a sparse, linear system of equations associated with tomographic inverse problems. We begin by making a modification to the commonly used compressed sparse-row format, whereby our format is tailored to the sparse structure of finite-frequency (volume) sensitivity kernels in seismic tomography. Next, we cluster the sparse matrix rows to divide a large matrix into smaller subsets representing ray paths that are geographically close. Singular value decomposition of each subset allows us to project the data onto a subspace associated with the largest eigenvalues of the subset. After projection we reject those data that have a signal-to-noise ratio (SNR) below a chosen threshold. Clustering in this way assures that the sparse nature of the system is minimally affected by the projection. Moreover, our approach allows for a precise estimation of the noise affecting the data while also giving us the ability to identify outliers. We illustrate the method by reducing large matrices computed for global tomographic systems with cross-correlation body wave delays, as well as with surface wave phase velocity anomalies. For a massive matrix computed for 3.7 million Rayleigh wave phase velocity measurements, imposing a threshold of 1 for the SNR, we condensed the matrix size from 1103 to 63 Gbyte. For a global data set of multiple-frequency P wave delays from 60 well-distributed deep earthquakes we obtain a reduction to 5.9 per cent. This type of reduction allows one to avoid loss of information due to underparametrizing models. Alternatively, if data have to be rejected to fit the system into computer memory, it assures that the most important data are preserved.

Human papillomavirus prevalence, distribution and correlation to histopathological parameters in a large Swedish cohort of men with penile carcinoma.

PubMed

Kirrander, Peter; Kolaric, Aleksandra; Helenius, Gisela; Windahl, Torgny; Andrén, Ove; Stark, Jennifer Rider; Lillsunde-Larsson, Gabriella; Elgh, Fredrik; Karlsson, Mats

2011-08-01

• To analyse the overall and type-specific human papillomavirus (HPV) prevalence and distribution in penile carcinoma and determine the correlation to histopathological parameters. • In this retrospective study, we analysed HPV status in 241 patients with penile carcinoma, treated at Örebro University Hospital, Örebro, Sweden, between 1984 and 2008. Age and date at diagnosis was recorded. • The tumour specimens were categorized according to the UICC 2002 TNM classification. A subset of patients was operatively staged with regard to lymph node status. • A commercially available Real Time PCR was used to detect 13 different types of HPV (6,11,16,18,31,33,35,45,51,52,56,58 and 59). • We excluded 25 patients due to low DNA quality. Of the remaining 216, 179 (82.9%) tumour specimens were HPV infected. The majority of cases positive for HPV (70.4%) were infected by a single-type. The most frequent type was HPV 16 followed by HPV 18. • No significant association between HPV status and pathological tumour stage, grade or lymph node status was found. • The HPV prevalence found is higher than in most other studies, further strengthening HPV as an etiological agent in penile carcinoma. Furthermore, the high prevalence of HPV 16 and 18 raises the question of what potential impact current HPV vaccines that target these specific HPV types might have on penile carcinoma. No significant association between HPV status and histopathological parameters was found in the present study. Additional investigations are needed to draw final conclusions on the prognostic value of HPV status in penile carcinoma. © 2010 THE AUTHORS. BJU INTERNATIONAL © 2010 BJU INTERNATIONAL.

A Survey of Ca II H and K Chromospheric Emission in Southern Solar-Type Stars

NASA Astrophysics Data System (ADS)

Henry, Todd J.; Soderblom, David R.; Donahue, Robert A.; Baliunas, Sallie L.

1996-01-01

More than 800 southern stars within 50 pc have been observed for chromospheric emission in the cores of the Ca II H and K lines. Most of the sample targets were chosen to be G dwarfs on the basis of colors and spectral types. The bimodal distribution in stellar activity first noted in a sample of northern stars by Vaughan and Preston in 1980 is confirmed, and the percentage of active stars, about 30%, is remarkably consistent between the northern and southern surveys. This is especially compelling given that we have used an entirely different instrumental setup and stellar sample than used in the previous study. Comparisons to the Sun, a relatively inactive star, show that most nearby solar-type stars have a similar activity level, and presumably a similar age. We identify two additional subsamples of stars -- a very active group, and a very inactive group. The very active group may be made up of young stars near the Sun, accounting for only a few percent of the sample, and appears to be less than ~0.1 Gyr old. Included in this high-activity tail of the distribution, however, is a subset of very close binaries of the RS CVn or W UMa types. The remaining members of this population may be undetected close binaries or very young single stars. The very inactive group of stars, contributting ~5%--10% to the total sample, may be those caught in a Maunder Minimum type phase. If the observations of the survey stars are considered to be a sequence of snapshots of the Sun during its life, we might expect that the Sun will spend about 10% of the remainder of its main sequence life in a Maunder Minimum phase.

The role of complement receptor positive and complement receptor negative B cells in the primary and secondary immune response to thymus independent type 2 and thymus dependent antigens.

PubMed

Lindsten, T; Yaffe, L J; Thompson, C B; Guelde, G; Berning, A; Scher, I; Kenny, J J

1985-05-01

Both complement receptor positive (CR+) and complement receptor negative (CR-) B cells have been shown to be involved in the primary immune response to PC-Hy (phosphocholine conjugated hemocyanin), a thymus dependent (TD) antigen which preferentially induces antibody secretion in Lyb-5+ B cells during a primary adoptive transfer assay. CR+ and CR- B cells also responded in a primary adoptive transfer assay to TNP-Ficoll, a thymus independent type 2 (TI-2) antigen which activates only Lyb-5+ B cells. When the secondary immune response to PC-Hy and TNP-Ficoll were analyzed, it was found that most of the immune memory to both antigens was present in the CR- B cell subset. The CR- B cell subset also dominated the secondary immune response to PC-Hy in immune defective (CBA/N X DBA/2N)F1 male mice. These data indicate that CR- B cells dominate the memory response in both the Lyb-5+ and Lyb-5- B cell subsets of normal and xid immune defective mice and suggest that Lyb-5+ and Lyb-5- B cells can be subdivided into CR+ and CR- subsets.

Host compatibility rather than vector–host-encounter rate determines the host range of avian Plasmodium parasites

PubMed Central

Medeiros, Matthew C. I.; Hamer, Gabriel L.; Ricklefs, Robert E.

2013-01-01

Blood-feeding arthropod vectors are responsible for transmitting many parasites between vertebrate hosts. While arthropod vectors often feed on limited subsets of potential host species, little is known about the extent to which this influences the distribution of vector-borne parasites in some systems. Here, we test the hypothesis that different vector species structure parasite–host relationships by restricting access of certain parasites to a subset of available hosts. Specifically, we investigate how the feeding patterns of Culex mosquito vectors relate to distributions of avian malaria parasites among hosts in suburban Chicago, IL, USA. We show that Plasmodium lineages, defined by cytochrome b haplotypes, are heterogeneously distributed across avian hosts. However, the feeding patterns of the dominant vectors (Culex restuans and Culex pipiens) are similar across these hosts, and do not explain the distributions of Plasmodium parasites. Phylogenetic similarity of avian hosts predicts similarity in their Plasmodium parasites. This effect was driven primarily by the general association of Plasmodium parasites with particular host superfamilies. Our results suggest that a mosquito-imposed encounter rate does not limit the distribution of avian Plasmodium parasites across hosts. This implies that compatibility between parasites and their avian hosts structure Plasmodium host range. PMID:23595266

Quality Assurance in Distance Education: The Challenges to Be Addressed

ERIC Educational Resources Information Center

Stella, Antony; Gnanam, A.

2004-01-01

Integration of technology in all forms of education has narrowed down the gap between the on- and off-campus students and has resulted in the use of the more broad-based term "distributed learning". Consequently, distance learning is seen as a subset of distributed learning, focusing on students who may be separated in time and space from their…

How do we choose the best model? The impact of cross-validation design on model evaluation for buried threat detection in ground penetrating radar

NASA Astrophysics Data System (ADS)

Malof, Jordan M.; Reichman, Daniël.; Collins, Leslie M.

2018-04-01

A great deal of research has been focused on the development of computer algorithms for buried threat detection (BTD) in ground penetrating radar (GPR) data. Most recently proposed BTD algorithms are supervised, and therefore they employ machine learning models that infer their parameters using training data. Cross-validation (CV) is a popular method for evaluating the performance of such algorithms, in which the available data is systematically split into ܰ disjoint subsets, and an algorithm is repeatedly trained on ܰ-1 subsets and tested on the excluded subset. There are several common types of CV in BTD, which vary principally upon the spatial criterion used to partition the data: site-based, lane-based, region-based, etc. The performance metrics obtained via CV are often used to suggest the superiority of one model over others, however, most studies utilize just one type of CV, and the impact of this choice is unclear. Here we employ several types of CV to evaluate algorithms from a recent large-scale BTD study. The results indicate that the rank-order of the performance of the algorithms varies substantially depending upon which type of CV is used. For example, the rank-1 algorithm for region-based CV is the lowest ranked algorithm for site-based CV. This suggests that any algorithm results should be interpreted carefully with respect to the type of CV employed. We discuss some potential interpretations of performance, given a particular type of CV.

Aggregation of carbon dioxide sequestration storage assessment units

USGS Publications Warehouse

Blondes, Madalyn S.; Schuenemeyer, John H.; Olea, Ricardo A.; Drew, Lawrence J.

2013-01-01

The U.S. Geological Survey is currently conducting a national assessment of carbon dioxide (CO2) storage resources, mandated by the Energy Independence and Security Act of 2007. Pre-emission capture and storage of CO2 in subsurface saline formations is one potential method to reduce greenhouse gas emissions and the negative impact of global climate change. Like many large-scale resource assessments, the area under investigation is split into smaller, more manageable storage assessment units (SAUs), which must be aggregated with correctly propagated uncertainty to the basin, regional, and national scales. The aggregation methodology requires two types of data: marginal probability distributions of storage resource for each SAU, and a correlation matrix obtained by expert elicitation describing interdependencies between pairs of SAUs. Dependencies arise because geologic analogs, assessment methods, and assessors often overlap. The correlation matrix is used to induce rank correlation, using a Cholesky decomposition, among the empirical marginal distributions representing individually assessed SAUs. This manuscript presents a probabilistic aggregation method tailored to the correlations and dependencies inherent to a CO2 storage assessment. Aggregation results must be presented at the basin, regional, and national scales. A single stage approach, in which one large correlation matrix is defined and subsets are used for different scales, is compared to a multiple stage approach, in which new correlation matrices are created to aggregate intermediate results. Although the single-stage approach requires determination of significantly more correlation coefficients, it captures geologic dependencies among similar units in different basins and it is less sensitive to fluctuations in low correlation coefficients than the multiple stage approach. Thus, subsets of one single-stage correlation matrix are used to aggregate to basin, regional, and national scales.

Cellular and humoral immune reactions in chronic active liver disease. II. Lymphocyte subsets and viral antigens in liver biopsies of patients with acute and chronic hepatitis B.

PubMed Central

Eggink, H F; Houthoff, H J; Huitema, S; Wolters, G; Poppema, S; Gips, C H

1984-01-01

The characteristics and distribution of the inflammatory infiltrate in liver biopsies of 25 patients with hepatitis B viral (HBV) infection were studied in relation to the distribution and expression of HBV antigens. Mononuclear subsets were characterized with monoclonal (OKT, OKM, Leu) antibodies to surface antigens. For the demonstration of viral antigens directly conjugated antibodies to surface (HBsAg), core (HBcAg) and 'e' (HBeAg) antigen were used. For the study of mutual relations all methods were performed on serial cut tissue sections. In chronic active hepatitis B (CAH-B, n = 12) OKT8+ lymphocytes of T cell origin were the only cell type present in areas with liver cell degeneration and T cell cytotoxicity appears to be the only immune mechanism. In chronic persistent hepatitis B (CPH-B, n = 7) the only conspicuous feature was the presence of many Leu 3+ lymphocytes of the helper/inducer population in the portal tracts. In acute hepatitis B (AHB, n = 6) OKT8+ cells of non-T origin (OKT1-,3-) and Leu 7+ cells of presumed natural killer (NK) potential predominated in the areas with liver cell necrosis, and non-T cell cytotoxicity appears to be the predominant immune mechanism. In none of these disease entities a positive spatial relation could be established between the cytotoxic cells and the demonstrable expression of HBV antigens in hepatocytes. It is concluded that differences in immunological reaction pattern may explain the different course in the three forms of HBV infection studied. Images Fig. 1 Fig. 2 PMID:6713726

"Small" data in a big data world: archiving terrestrial ecology data at ORNL DAAC

NASA Astrophysics Data System (ADS)

Santhana Vannan, S. K.; Beaty, T.; Boyer, A.; Deb, D.; Hook, L.; Shrestha, R.; Thornton, M.; Virdi, M.; Wei, Y.; Wright, D.

2016-12-01

The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC http://daac.ornl.gov), a NASA-funded data center, archives a diverse collection of terrestrial biogeochemistry and ecological dynamics observations and models in support of NASA's Earth Science program. The ORNL DAAC has been addressing the increasing challenge of publishing diverse small data products into an online archive while dealing with the enhanced need for integration and availability of these data to address big science questions. This paper will show examples of "small" diverse data holdings - ranging from the Daymet model output data to site-based soil moisture observation data. We define "small" by the data volume of these data products compared to petabyte scale observations. We will highlight the use of tools and services for visualizing diverse data holdings and subsetting services such as the MODIS land products subsets tool (at ORNL DAAC) that provides big MODIS data in small chunks. Digital Object Identifiers (DOI) and data citations have enhanced the availability of data. The challenge faced by data publishers now is to deal with the increased number of publishable data products and most importantly the difficulties of publishing small diverse data products into an online archive. This paper will also present our experiences designing a data curation system for these types of data. The characteristics of these data will be examined and their scientific value will be demonstrated via data citation metrics. We will present case studies of leveraging specialized tools and services that have enabled small data sets to realize their "big" scientific potential. Overall, we will provide a holistic view of the challenges and potential of small diverse terrestrial ecology data sets from data curation to distribution.

Role of distinct CD4(+) T helper subset in pathogenesis of oral lichen planus.

PubMed

Wang, Hui; Zhang, Dunfang; Han, Qi; Zhao, Xin; Zeng, Xin; Xu, Yi; Sun, Zheng; Chen, Qianming

2016-07-01

Oral lichen planus (OLP) is one of the most common chronic inflammatory oral mucosal diseases with T-cell-mediated immune pathogenesis. In subepithelial and lamina propria of OLP local lesions, the presence of CD4(+) T helper (CD4(+) Th) cells appeared as the major lymphocytes. These CD4(+) T lymphocytes can differentiate into distinct Th cell types such as Th1, Th2, Treg, Th17, Th22, Th9, and Tfh within the context of certain cytokines environment. Growing evidence indicated that Th1/Th2 imbalance may greatly participate into the cytokine network of OLP immunopathology. In addition, Th1/Th2 imbalance can be regulated by the Treg subset and also greatly influenced by the emerging novel CD4(+) Th subset Th17. Furthermore, the presence of novel subsets Th22, Th9 and Tfh in OLP patients is yet to be clarified. All these Th subsets and their specific cytokines may play a critical role in determining the character, extent and duration of immune responses in OLP pathogenesis. Therefore, we review the roles of distinct CD4(+) Th subsets and their signature cytokines in determining disease severity and susceptibility of OLP and also reveal the novel therapeutic strategies based on T lymphocytes subsets in OLP treatment. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Autoreactive T effector memory differentiation mirrors β-cell function in type 1 diabetes.

PubMed

Yeo, Lorraine; Woodwyk, Alyssa; Sood, Sanjana; Lorenc, Anna; Eichmann, Martin; Pujol-Autonell, Irma; Melchiotti, Rossella; Skowera, Ania; Fidanis, Efthymios; Dolton, Garry M; Tungatt, Katie; Sewell, Andrew K; Heck, Susanne; Saxena, Alka; Beam, Craig A; Peakman, Mark

2018-05-31

In type 1 diabetes, cytotoxic CD8 T cells with specificity for β-cell autoantigens are found in the pancreatic islets where they are implicated in the destruction of insulin-secreting β cells. In contrast, the disease relevance of β-cell-reactive CD8 T cells that are detectable in the circulation, and their relationship to β-cell function, are not known. Here, we tracked multiple, circulating β-cell-reactive CD8 T cell subsets and measured β-cell function longitudinally for two years, starting immediately after diagnosis of type 1 diabetes. We found that change in β-cell-specific effector memory CD8 T cells expressing CD57 was positively correlated with C-peptide change in subjects below 12 years of age. Autoreactive CD57+ effector memory CD8 T cells bore the signature of enhanced effector function (higher expression of granzyme B, killer specific protein 37 and CD16, and reduced expression of CD28) compared with their CD57-negative counterparts, and network association modelling indicated that the dynamics of β-cell-reactive CD57+ effector memory CD8 T cell subsets were strongly linked. Thus, coordinated changes in circulating β-cell-specific CD8 T cells within the CD57+ effector memory subset calibrate to functional insulin reserve in type 1 diabetes, providing a tool for immune monitoring and a mechanism-based target for immunotherapy.

A novel subset of helper T cells promotes immune responses by secreting GM-CSF

PubMed Central

Zhang, J; Roberts, A I; Liu, C; Ren, G; Xu, G; Zhang, L; Devadas, S; Shi, Yufang

2013-01-01

Helper T cells are crucial for maintaining proper immune responses. Yet, they have an undefined relationship with one of the most potent immune stimulatory cytokines, granulocyte macrophage-colony-stimulating factor (GM-CSF). By depleting major cytokines during the differentiation of CD4+ T cells in vitro, we derived cells that were found to produce large amounts of GM-CSF, but little of the cytokines produced by other helper T subsets. By their secretion of GM-CSF, this novel subset of helper T cells (which we have termed ThGM cells) promoted the production of cytokines by other T-cell subtypes, including type 1 helper T cell (Th1), type 2 helper T cell (Th2), type 1 cytotoxic T cell (Tc1), type 2 cytotoxic T cell (Tc2), and naive T cells, as evidenced by the fact that antibody neutralization of GM-CSF abolished this effect. ThGM cells were found to be highly prone to activation-induced cell death (AICD). Inhibitors of TRAIL or granzymes could not block AICD in ThGM cells, whereas inhibition of FasL/Fas interaction partially rescued ThGM cells from AICD. Thus, ThGM cells are a novel subpopulation of T helper cells that produce abundant GM-CSF, exhibit exquisite susceptibility to apoptosis, and therefore play a pivotal role in the regulation of the early stages of immune responses. PMID:24076588

In vitro haematopoiesis of a novel dendritic-like cell present in murine spleen.

PubMed

Tan, Jonathan K H; O'Neill, Helen C

2010-12-01

Dendritic cells (DC) are important antigen presenting cells (APC) which induce and control the adaptive immune response. In spleen alone, multiple DC subsets can be distinguished by cell surface marker phenotype. Most of these have been shown to develop from progenitors in bone marrow and to seed lymphoid and tissue sites during development. This study advances in vitro methodology for haematopoiesis of dendritic-like cells from progenitors in spleen. Since spleen progenitors undergo differentiation in vitro to produce these cells, the possibility exists that spleen represents a specific niche for differentiation of this subset. The fact that an equivalent cell subset has been shown to exist in spleen also supports that hypothesis. Studies have been directed at investigating the specific functional role of this novel subset as an APC accessible to blood-borne antigen, as well as the conditions under which haematopoiesis is initiated in spleen, and the type of progenitor involved.

Type III Cells in Anterior Taste Fields Are More Immunohistochemically Diverse Than Those of Posterior Taste Fields in Mice.

PubMed

Wilson, Courtney E; Finger, Thomas E; Kinnamon, Sue C

2017-10-31

Activation of Type III cells in mammalian taste buds is implicated in the transduction of acids (sour) and salty stimuli. Several lines of evidence suggest that function of Type III cells in the anterior taste fields may differ from that of Type III cells in posterior taste fields. Underlying anatomy to support this observation is, however, scant. Most existing immunohistochemical data characterizing this cell type focus on circumvallate taste buds in the posterior tongue. Equivalent data from anterior taste fields-fungiform papillae and soft palate-are lacking. Here, we compare Type III cells in four taste fields: fungiform, soft palate, circumvallate, and foliate in terms of reactivity to four canonical markers of Type III cells: polycystic kidney disease 2-like 1 (PKD2L1), synaptosomal associated protein 25 (SNAP25), serotonin (5-HT), and glutamate decarboxylase 67 (GAD67). Our findings indicate that while PKD2L1, 5-HT, and SNAP25 are highly coincident in posterior taste fields, they diverge in anterior taste fields. In particular, a subset of taste cells expresses PKD2L1 without the synaptic markers, and a subset of SNAP25 cells lacks expression of PKD2L1. In posterior taste fields, GAD67-positive cells are a subset of PKD2L1 expressing taste cells, but anterior taste fields also contain a significant population of GAD67-only expressing cells. These differences in expression patterns may underlie the observed functional differences between anterior and posterior taste fields. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

An overview of the NASA Langley Atmospheric Data Center: Online tools to effectively disseminate Earth science data products

NASA Astrophysics Data System (ADS)

Parker, L.; Dye, R. A.; Perez, J.; Rinsland, P.

2012-12-01

Over the past decade the Atmospheric Science Data Center (ASDC) at NASA Langley Research Center has archived and distributed a variety of satellite mission and aircraft campaign data sets. These datasets posed unique challenges to the user community at large due to the sheer volume and variety of the data and the lack of intuitive features in the order tools available to the investigator. Some of these data sets also lack sufficient metadata to provide rudimentary data discovery. To meet the needs of emerging users, the ASDC addressed issues in data discovery and delivery through the use of standards in data and access methods, and distribution through appropriate portals. The ASDC is currently undergoing a refresh of its webpages and Ordering Tools that will leverage updated collection level metadata in an effort to enhance the user experience. The ASDC is now providing search and subset capability to key mission satellite data sets. The ASDC has collaborated with Science Teams to accommodate prospective science users in the climate and modeling communities. The ASDC is using a common framework that enables more rapid development and deployment of search and subset tools that provide enhanced access features for the user community. Features of the Search and Subset web application enables a more sophisticated approach to selecting and ordering data subsets by parameter, date, time, and geographic area. The ASDC has also applied key practices from satellite missions to the multi-campaign aircraft missions executed for Earth Venture-1 and MEaSUReS

Effect of Sampling Period on Flood Frequency Distributions in the Susquehanna Basin

NASA Astrophysics Data System (ADS)

Kargar, M.; Beighley, R. E.

2010-12-01

Flooding is a devastating natural hazard that claims many human lives and significantly impact regional economies each year. Given the magnitude of flooding impacts, significant resources are dedicated to the development of forecasting models for early warning and evacuation planning, construction of flood defenses (levees/dams) to limit flooding, and the design of civil infrastructure (bridges, culverts, storm sewers) to convey flood flows without failing. In all these cases, it is particularly important to understand the potential flooding risk in terms of both recurrence interval (i.e., return period) and magnitude. Flood frequency analysis (FFA) is a form of risk analysis used to extrapolate the return periods of floods beyond the gauged record. The technique involves using observed annual peak flow discharge data to calculate statistical information such as mean values, standard deviations, skewness, and recurrence intervals. Since discharge data for most catchments have been collected for periods of time less than 100 years, the estimation of the design discharge requires a degree of extrapolation. This study focuses on the assessment and modifications of flood frequency based discharges for sites with limited sampling periods. Here, limited sampling period is intended to capture two issues: (1) limited number of observations to adequately capture the flood frequency signal (i.e., minimum number of annual peaks needed) and (2) climate variability (i.e., sampling period contains primarily “wet” or “dry” periods only). Total of 34 gauges (more than 70 years of data) spread throughout the Susquehanna River basin (71,000 sq km) were used to investigate the impact of sampling period on flood frequency distributions. Data subsets ranging from 10 years to the total number of years available were created from the data for each gauging station. To estimate the flood frequency, the Log Pearson Type III distribution was fit to the logarithms of instantaneous annual peak flows following Bulletin 17B guidelines of the U.S. Interagency Advisory Committee on Water Data. The resulting flood frequencies from these subsets were compared to the results from the entire record at each gauge. Based on the analysis, the minimum number of years required to obtain a reasonable flood frequency distribution was determined for each gauge. In addition, a method to adjust flood frequency distribution at a given gauging station with limited data based on other locations with longer periods of records was developed.

Transcriptional Classification and Functional Characterization of Human Airway Macrophage and Dendritic Cell Subsets

PubMed Central

Patel, Vineet I.; Booth, J. Leland; Duggan, Elizabeth S.; Cate, Steven; White, Vicky L.; Hutchings, David; Kovats, Susan; Burian, Dennis M.; Dozmorov, Mikhail; Metcalf, Jordan P.

2016-01-01

The respiratory system is a complex network of many cell types, including subsets of macrophages and dendritic cells that work together to maintain steady-state respiration. Due to limitations in acquiring cells from healthy human lung, these subsets remain poorly characterized transcriptionally and phenotypically. We set out to systematically identify these subsets in human airways by developing a schema of isolating large numbers of cells by whole lung bronchoalveolar lavage. Six subsets of phagocytic antigen presenting (HLA-DR+) cells were consistently observed. Aside from alveolar macrophages, subsets of Langerin+, BDCA1− CD14+, BDCA1+ CD14+, BDCA1+ CD14−, and BDCA1− CD14− cells were identified. These subsets varied in their ability to internalize Escherichia coli, Staphylococcus aureus, and Bacillus anthracis particles. All subsets were more efficient at internalizing S. aureus and B. anthracis compared to E. coli. Alveolar macrophages and CD14+ cells were overall more efficient at particle internalization compared to the four other populations. Subsets were further separated into two groups based on their inherent capacities to upregulate surface CD83, CD86, and CCR7 expression levels. Whole genome transcriptional profiling revealed a clade of “true dendritic cells” consisting of Langerin+, BDCA1+ CD14+, and BDCA1+ CD14− cells. The dendritic cell clade was distinct from a macrophage/monocyte clade, as supported by higher mRNA expression levels of several dendritic cell-associated genes, including CD1, FLT3, CX3CR1, and CCR6. Each clade, and each member of both clades, were discerned by specific upregulated genes, which can serve as markers for future studies in healthy and diseased states. PMID:28031342

Automatic Nuclei Segmentation in H&E Stained Breast Cancer Histopathology Images

PubMed Central

Veta, Mitko; van Diest, Paul J.; Kornegoor, Robert; Huisman, André; Viergever, Max A.; Pluim, Josien P. W.

2013-01-01

The introduction of fast digital slide scanners that provide whole slide images has led to a revival of interest in image analysis applications in pathology. Segmentation of cells and nuclei is an important first step towards automatic analysis of digitized microscopy images. We therefore developed an automated nuclei segmentation method that works with hematoxylin and eosin (H&E) stained breast cancer histopathology images, which represent regions of whole digital slides. The procedure can be divided into four main steps: 1) pre-processing with color unmixing and morphological operators, 2) marker-controlled watershed segmentation at multiple scales and with different markers, 3) post-processing for rejection of false regions and 4) merging of the results from multiple scales. The procedure was developed on a set of 21 breast cancer cases (subset A) and tested on a separate validation set of 18 cases (subset B). The evaluation was done in terms of both detection accuracy (sensitivity and positive predictive value) and segmentation accuracy (Dice coefficient). The mean estimated sensitivity for subset A was 0.875 (±0.092) and for subset B 0.853 (±0.077). The mean estimated positive predictive value was 0.904 (±0.075) and 0.886 (±0.069) for subsets A and B, respectively. For both subsets, the distribution of the Dice coefficients had a high peak around 0.9, with the vast majority of segmentations having values larger than 0.8. PMID:23922958

Automatic nuclei segmentation in H&E stained breast cancer histopathology images.

PubMed

Veta, Mitko; van Diest, Paul J; Kornegoor, Robert; Huisman, André; Viergever, Max A; Pluim, Josien P W

2013-01-01

The introduction of fast digital slide scanners that provide whole slide images has led to a revival of interest in image analysis applications in pathology. Segmentation of cells and nuclei is an important first step towards automatic analysis of digitized microscopy images. We therefore developed an automated nuclei segmentation method that works with hematoxylin and eosin (H&E) stained breast cancer histopathology images, which represent regions of whole digital slides. The procedure can be divided into four main steps: 1) pre-processing with color unmixing and morphological operators, 2) marker-controlled watershed segmentation at multiple scales and with different markers, 3) post-processing for rejection of false regions and 4) merging of the results from multiple scales. The procedure was developed on a set of 21 breast cancer cases (subset A) and tested on a separate validation set of 18 cases (subset B). The evaluation was done in terms of both detection accuracy (sensitivity and positive predictive value) and segmentation accuracy (Dice coefficient). The mean estimated sensitivity for subset A was 0.875 (±0.092) and for subset B 0.853 (±0.077). The mean estimated positive predictive value was 0.904 (±0.075) and 0.886 (±0.069) for subsets A and B, respectively. For both subsets, the distribution of the Dice coefficients had a high peak around 0.9, with the vast majority of segmentations having values larger than 0.8.

Estimation of the lower and upper bounds on the probability of failure using subset simulation and random set theory

NASA Astrophysics Data System (ADS)

Alvarez, Diego A.; Uribe, Felipe; Hurtado, Jorge E.

2018-02-01

Random set theory is a general framework which comprises uncertainty in the form of probability boxes, possibility distributions, cumulative distribution functions, Dempster-Shafer structures or intervals; in addition, the dependence between the input variables can be expressed using copulas. In this paper, the lower and upper bounds on the probability of failure are calculated by means of random set theory. In order to accelerate the calculation, a well-known and efficient probability-based reliability method known as subset simulation is employed. This method is especially useful for finding small failure probabilities in both low- and high-dimensional spaces, disjoint failure domains and nonlinear limit state functions. The proposed methodology represents a drastic reduction of the computational labor implied by plain Monte Carlo simulation for problems defined with a mixture of representations for the input variables, while delivering similar results. Numerical examples illustrate the efficiency of the proposed approach.

Global meta-analysis reveals low consistency of biodiversity congruence relationships.

PubMed

Westgate, Martin J; Barton, Philip S; Lane, Peter W; Lindenmayer, David B

2014-05-21

Knowledge of the number and distribution of species is fundamental to biodiversity conservation efforts, but this information is lacking for the majority of species on earth. Consequently, subsets of taxa are often used as proxies for biodiversity; but this assumes that different taxa display congruent distribution patterns. Here we use a global meta-analysis to show that studies of cross-taxon congruence rarely give consistent results. Instead, species richness congruence is highest at extreme spatial scales and close to the equator, while congruence in species composition is highest at large extents and grain sizes. Studies display highest variance in cross-taxon congruence when conducted in areas with dissimilar areal extents (for species richness) or latitudes (for species composition). These results undermine the assumption that a subset of taxa can be representative of biodiversity. Therefore, researchers whose goal is to prioritize locations or actions for conservation should use data from a range of taxa.

Distributing Data from Desktop to Hand-Held Computers

NASA Technical Reports Server (NTRS)

Elmore, Jason L.

2005-01-01

A system of server and client software formats and redistributes data from commercially available desktop to commercially available hand-held computers via both wired and wireless networks. This software is an inexpensive means of enabling engineers and technicians to gain access to current sensor data while working in locations in which such data would otherwise be inaccessible. The sensor data are first gathered by a data-acquisition server computer, then transmitted via a wired network to a data-distribution computer that executes the server portion of the present software. Data in all sensor channels -- both raw sensor outputs in millivolt units and results of conversion to engineering units -- are made available for distribution. Selected subsets of the data are transmitted to each hand-held computer via the wired and then a wireless network. The selection of the subsets and the choice of the sequences and formats for displaying the data is made by means of a user interface generated by the client portion of the software. The data displayed on the screens of hand-held units can be updated at rates from 1 to

Performance Analysis of Relay Subset Selection for Amplify-and-Forward Cognitive Relay Networks

PubMed Central

Qureshi, Ijaz Mansoor; Malik, Aqdas Naveed; Zubair, Muhammad

2014-01-01

Cooperative communication is regarded as a key technology in wireless networks, including cognitive radio networks (CRNs), which increases the diversity order of the signal to combat the unfavorable effects of the fading channels, by allowing distributed terminals to collaborate through sophisticated signal processing. Underlay CRNs have strict interference constraints towards the secondary users (SUs) active in the frequency band of the primary users (PUs), which limits their transmit power and their coverage area. Relay selection offers a potential solution to the challenges faced by underlay networks, by selecting either single best relay or a subset of potential relay set under different design requirements and assumptions. The best relay selection schemes proposed in the literature for amplify-and-forward (AF) based underlay cognitive relay networks have been very well studied in terms of outage probability (OP) and bit error rate (BER), which is deficient in multiple relay selection schemes. The novelty of this work is to study the outage behavior of multiple relay selection in the underlay CRN and derive the closed-form expressions for the OP and BER through cumulative distribution function (CDF) of the SNR received at the destination. The effectiveness of relay subset selection is shown through simulation results. PMID:24737980

Participatory Equity and Student Outcomes in Living-Learning Programs of Differing Thematic Types

ERIC Educational Resources Information Center

Soldner, Matthew Edward

2011-01-01

This study evaluated participatory equity in varying thematic types of living-learning programs and, for a subset of student group x program type combinations found to be below equity, used latent mean modeling to determine whether statistically significant mean differences existed between the outcome scores of living-learning participants and…

Type II NKT Cells in Inflammation, Autoimmunity, Microbial Immunity, and Cancer

PubMed Central

Marrero, Idania; Ware, Randle; Kumar, Vipin

2015-01-01

Natural killer T cells (NKT) recognize self and microbial lipid antigens presented by non-polymorphic CD1d molecules. Two major NKT cell subsets, type I and II, express different types of antigen receptors (TCR) with distinct mode of CD1d/lipid recognition. Though type II NKT cells are less frequent in mice and difficult to study, they are predominant in human. One of the major subsets of type II NKT cells reactive to the self-glycolipid sulfatide is the best characterized and has been shown to induce a dominant immune regulatory mechanism that controls inflammation in autoimmunity and in anti-cancer immunity. Recently, type II NKT cells reactive to other self-glycolipids and phospholipids have been identified suggesting both promiscuous and specific TCR recognition in microbial immunity as well. Since the CD1d pathway is highly conserved, a detailed understanding of the biology and function of type II NKT cells as well as their interplay with type I NKT cells or other innate and adaptive T cells will have major implications for potential novel interventions in inflammatory and autoimmune diseases, microbial immunity, and cancer. PMID:26136748

Discrimination in lexical decision

PubMed Central

Feldman, Laurie Beth; Ramscar, Michael; Hendrix, Peter; Baayen, R. Harald

2017-01-01

In this study we present a novel set of discrimination-based indicators of language processing derived from Naive Discriminative Learning (ndl) theory. We compare the effectiveness of these new measures with classical lexical-distributional measures—in particular, frequency counts and form similarity measures—to predict lexical decision latencies when a complete morphological segmentation of masked primes is or is not possible. Data derive from a re-analysis of a large subset of decision latencies from the English Lexicon Project, as well as from the results of two new masked priming studies. Results demonstrate the superiority of discrimination-based predictors over lexical-distributional predictors alone, across both the simple and primed lexical decision tasks. Comparable priming after masked corner and cornea type primes, across two experiments, fails to support early obligatory segmentation into morphemes as predicted by the morpho-orthographic account of reading. Results fit well with ndl theory, which, in conformity with Word and Paradigm theory, rejects the morpheme as a relevant unit of analysis. Furthermore, results indicate that readers with greater spelling proficiency and larger vocabularies make better use of orthographic priors and handle lexical competition more efficiently. PMID:28235015

Evolution of drop size distribution in natural rain

NASA Astrophysics Data System (ADS)

D'Adderio, Leo Pio; Porcù, Federico; Tokay, Ali

2018-02-01

Both numerical modeling and laboratory experiments document the possibility of a raindrop size distribution (DSD) to evolve to an equilibrium stage (EDSD), where all the principal processes occur at steady rates. The aim of this work is to observe the temporal behavior of the DSD and to directly investigate the conditions favorable to the onset of the EDSD in natural rain. We exploited a large disdrometer dataset collected in the framework of the Ground Validation activities related to the NASA Global Precipitation Measurement mission. More than 200,000 one-minute data of two-dimensional video disdrometer (2DVD) are collected over USA to represent a wide range of precipitation types. The original data are averaged over 2 min and an automatic algorithm is used on a selected subset to identify samples with EDSD. Results show that the EDSD occurs mainly in convective events and lasts for very short time intervals (2 to 4 min). It is more frequent for rain rate between 20 and 40 mm h- 1 and it mostly occurs during sharp increase of precipitation rates.

Discrimination in lexical decision.

PubMed

Milin, Petar; Feldman, Laurie Beth; Ramscar, Michael; Hendrix, Peter; Baayen, R Harald

2017-01-01

In this study we present a novel set of discrimination-based indicators of language processing derived from Naive Discriminative Learning (ndl) theory. We compare the effectiveness of these new measures with classical lexical-distributional measures-in particular, frequency counts and form similarity measures-to predict lexical decision latencies when a complete morphological segmentation of masked primes is or is not possible. Data derive from a re-analysis of a large subset of decision latencies from the English Lexicon Project, as well as from the results of two new masked priming studies. Results demonstrate the superiority of discrimination-based predictors over lexical-distributional predictors alone, across both the simple and primed lexical decision tasks. Comparable priming after masked corner and cornea type primes, across two experiments, fails to support early obligatory segmentation into morphemes as predicted by the morpho-orthographic account of reading. Results fit well with ndl theory, which, in conformity with Word and Paradigm theory, rejects the morpheme as a relevant unit of analysis. Furthermore, results indicate that readers with greater spelling proficiency and larger vocabularies make better use of orthographic priors and handle lexical competition more efficiently.

Patterns of Genetic Structure and Linkage Disequilibrium in a Large Collection of Pea Germplasm

PubMed Central

Siol, Mathieu; Jacquin, Françoise; Chabert-Martinello, Marianne; Smýkal, Petr; Le Paslier, Marie-Christine; Aubert, Grégoire; Burstin, Judith

2017-01-01

Pea (Pisum sativum, L.) is a major pulse crop used both for animal and human alimentation. Owing to its association with nitrogen-fixing bacteria, it is also a valuable component for low-input cropping systems. To evaluate the genetic diversity and the scale of linkage disequilibrium (LD) decay in pea, we genotyped a collection of 917 accessions, gathering elite cultivars, landraces, and wild relatives using an array of ∼13,000 single nucleotide polymorphisms (SNP). Genetic diversity is broadly distributed across three groups corresponding to wild/landraces peas, winter types, and spring types. At a finer subdivision level, genetic groups relate to local breeding programs and type usage. LD decreases steeply as genetic distance increases. When considering subsets of the data, LD values can be higher, even if the steep decay remains. We looked for genomic regions exhibiting high level of differentiation between wild/landraces, winter, and spring pea, respectively. Two regions on linkage groups 5 and 6 containing 33 SNPs exhibit stronger differentiation between winter and spring peas than would be expected under neutrality. Interestingly, QTL for resistance to cold acclimation and frost resistance have been identified previously in the same regions. PMID:28611254

Hydraulic head interpolation using ANFIS—model selection and sensitivity analysis

NASA Astrophysics Data System (ADS)

Kurtulus, Bedri; Flipo, Nicolas

2012-01-01

The aim of this study is to investigate the efficiency of ANFIS (adaptive neuro fuzzy inference system) for interpolating hydraulic head in a 40-km 2 agricultural watershed of the Seine basin (France). Inputs of ANFIS are Cartesian coordinates and the elevation of the ground. Hydraulic head was measured at 73 locations during a snapshot campaign on September 2009, which characterizes low-water-flow regime in the aquifer unit. The dataset was then split into three subsets using a square-based selection method: a calibration one (55%), a training one (27%), and a test one (18%). First, a method is proposed to select the best ANFIS model, which corresponds to a sensitivity analysis of ANFIS to the type and number of membership functions (MF). Triangular, Gaussian, general bell, and spline-based MF are used with 2, 3, 4, and 5 MF per input node. Performance criteria on the test subset are used to select the 5 best ANFIS models among 16. Then each is used to interpolate the hydraulic head distribution on a (50×50)-m grid, which is compared to the soil elevation. The cells where the hydraulic head is higher than the soil elevation are counted as "error cells." The ANFIS model that exhibits the less "error cells" is selected as the best ANFIS model. The best model selection reveals that ANFIS models are very sensitive to the type and number of MF. Finally, a sensibility analysis of the best ANFIS model with four triangular MF is performed on the interpolation grid, which shows that ANFIS remains stable to error propagation with a higher sensitivity to soil elevation.

Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn's disease.

PubMed

Aldhous, Marian C; Abu Bakar, Suhaili; Prescott, Natalie J; Palla, Raquel; Soo, Kimberley; Mansfield, John C; Mathew, Christopher G; Satsangi, Jack; Armour, John A L

2010-12-15

The copy number variation in beta-defensin genes on human chromosome 8 has been proposed to underlie susceptibility to inflammatory disorders, but presents considerable challenges for accurate typing on the scale required for adequately powered case-control studies. In this work, we have used accurate methods of copy number typing based on the paralogue ratio test (PRT) to assess beta-defensin copy number in more than 1500 UK DNA samples including more than 1000 cases of Crohn's disease. A subset of 625 samples was typed using both PRT-based methods and standard real-time PCR methods, from which direct comparisons highlight potentially serious shortcomings of a real-time PCR assay for typing this variant. Comparing our PRT-based results with two previous studies based only on real-time PCR, we find no evidence to support the reported association of Crohn's disease with either low or high beta-defensin copy number; furthermore, it is noteworthy that there are disagreements between different studies on the observed frequency distribution of copy number states among European controls. We suggest safeguards to be adopted in assessing and reporting the accuracy of copy number measurement, with particular emphasis on integer clustering of results, to avoid reporting of spurious associations in future case-control studies.

Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn's disease

PubMed Central

Aldhous, Marian C.; Abu Bakar, Suhaili; Prescott, Natalie J.; Palla, Raquel; Soo, Kimberley; Mansfield, John C.; Mathew, Christopher G.; Satsangi, Jack; Armour, John A.L.

2010-01-01

The copy number variation in beta-defensin genes on human chromosome 8 has been proposed to underlie susceptibility to inflammatory disorders, but presents considerable challenges for accurate typing on the scale required for adequately powered case–control studies. In this work, we have used accurate methods of copy number typing based on the paralogue ratio test (PRT) to assess beta-defensin copy number in more than 1500 UK DNA samples including more than 1000 cases of Crohn's disease. A subset of 625 samples was typed using both PRT-based methods and standard real-time PCR methods, from which direct comparisons highlight potentially serious shortcomings of a real-time PCR assay for typing this variant. Comparing our PRT-based results with two previous studies based only on real-time PCR, we find no evidence to support the reported association of Crohn's disease with either low or high beta-defensin copy number; furthermore, it is noteworthy that there are disagreements between different studies on the observed frequency distribution of copy number states among European controls. We suggest safeguards to be adopted in assessing and reporting the accuracy of copy number measurement, with particular emphasis on integer clustering of results, to avoid reporting of spurious associations in future case–control studies. PMID:20858604

Expression of synaptogyrin-1 in T1R2-expressing type II taste cells and type III taste cells of rat circumvallate taste buds.

PubMed

Kotani, Takeshi; Toyono, Takashi; Seta, Yuji; Kitou, Ayae; Kataoka, Shinji; Toyoshima, Kuniaki

2013-09-01

Synaptogyrins are conserved components of the exocytic apparatus and function as regulators of Ca(2+)-dependent exocytosis. The synaptogyrin family comprises three isoforms: two neuronal (synaptogyrin-1 and -3) and one ubiquitous (synaptogyrin-2) form. Although the expression patterns of the exocytic proteins synaptotagmin-1, SNAP-25, synaptobrevin-2 and synaptophysin have been elucidated in taste buds, the function and expression pattern of synaptogyrin-1 in rat gustatory tissues have not been determined. Therefore, we examined the expression patterns of synaptogyrin-1 and several cell-specific markers of type II and III cells in rat gustatory tissues. Reverse transcription/polymerase chain reaction assays and immunoblot analysis revealed the expression of synaptogyrin-1 mRNA and its protein in circumvallate papillae. In fungiform, foliate and circumvallate papillae, the antibody against synaptogyrin-1 immunolabeled a subset of taste bud cells and intra- and subgemmal nerve processes. Double-labeling experiments revealed the expression of synaptogyrin-1 in most taste cells immunoreactive for aromatic L-amino acid decarboxylase and the neural cell adhesion molecule. A subset of synaptogyrin-1-immunoreactive taste cells also expressed phospholipase Cβ2, gustducin, or sweet taste receptor (T1R2). In addition, most synaptogyrin-1-immunoreactive taste cells expressed synaptobrevin-2. These results suggest that synaptogyrin-1 plays a regulatory role in transmission at the synapses of type III cells and is involved in exocytic function with synaptobrevin-2 in a subset of type II cells in rat taste buds.

Uncertainty Analysis via Failure Domain Characterization: Polynomial Requirement Functions

NASA Technical Reports Server (NTRS)

Crespo, Luis G.; Munoz, Cesar A.; Narkawicz, Anthony J.; Kenny, Sean P.; Giesy, Daniel P.

2011-01-01

This paper proposes an uncertainty analysis framework based on the characterization of the uncertain parameter space. This characterization enables the identification of worst-case uncertainty combinations and the approximation of the failure and safe domains with a high level of accuracy. Because these approximations are comprised of subsets of readily computable probability, they enable the calculation of arbitrarily tight upper and lower bounds to the failure probability. A Bernstein expansion approach is used to size hyper-rectangular subsets while a sum of squares programming approach is used to size quasi-ellipsoidal subsets. These methods are applicable to requirement functions whose functional dependency on the uncertainty is a known polynomial. Some of the most prominent features of the methodology are the substantial desensitization of the calculations from the uncertainty model assumed (i.e., the probability distribution describing the uncertainty) as well as the accommodation for changes in such a model with a practically insignificant amount of computational effort.

Housing is positively associated with invasive exotic plant species richness in New England, USA.

PubMed

Gavier-Pizarro, Gregorio I; Radeloff, Volker C; Stewart, Susan I; Huebner, Cynthia D; Keuler, Nicholas S

2010-10-01

Understanding the factors related to invasive exotic species distributions at broad spatial scales has important theoretical and management implications, because biological invasions are detrimental to many ecosystem functions and processes. Housing development facilitates invasions by disturbing land cover, introducing nonnative landscaping plants, and facilitating dispersal of propagules along roads. To evaluate relationships between housing and the distribution of invasive exotic plants, we asked (1) how strongly is housing associated with the spatial distribution of invasive exotic plants compared to other anthropogenic and environmental factors; (2) what type of housing pattern is related to the richness of invasive exotic plants; and (3) do invasive plants represent ecological traits associated with specific housing patterns? Using two types of regression analysis (best subset analysis and hierarchical partitioning analysis), we found that invasive exotic plant richness was equally or more strongly related to housing variables than to other human (e.g., mean income and roads) and environmental (e.g., topography and forest cover) variables at the county level across New England. Richness of invasive exotic plants was positively related to area of wildland-urban interface (WUI), low-density residential areas, change in number of housing units between 1940 and 2000, mean income, plant productivity (NDVI), and altitudinal range and rainfall; it was negatively related to forest area and connectivity. Plant life history traits were not strongly related to housing patterns. We expect the number of invasive exotic plants to increase as a result of future housing growth and suggest that housing development be considered a primary factor in plans to manage and monitor invasive exotic plant species.

Innate lymphoid cells: a paradigm for low SSI in cleft lip repair.

PubMed

Simmerman, Erika; Qin, Xu; Marshall, Brendan; Perry, Libby; Cai, Lei; Wang, Tailing; Yu, Jack; Akbari, Omid; Baban, Babak

2016-10-01

Cleft lip and palate reconstructions demonstrate significantly lower surgical site infection rates compared with clean-contaminated cases, prompting investigation into the pathophysiology causing this discrepancy. Recent studies have identified a new group of innate lymphocytes called innate lymphoid cells (ILCs), located in barrier surfaces of the skin, airways, and intestine. Our objectives were to explore for the first time the presence of ILCs in the vermillion of neonates and young children undergoing cleft lip reconstruction and characterize their composition by measuring the three classes of ILCs. Lip tissue samples were collected from 13 subjects undergoing vermillion resection during cleft lip reconstructive surgery. Preparative, transmission electron microscopy, and analytical flow cytometry were performed. The functionality of ILCs was tested in terms of their capacity to produce type 1 (IFN-γ/TNF-α), type 2 (IL-5/IL-13), and type 3 (IL-17/IL-22) cytokines. Data were analyzed using Student t test or the analysis of variance to establish significance (P < 0.05) among groups for all other data. All three classes of ILCs were detected and visualized in the tissue samples. In all samples, the level of ILC2 subset was significantly higher than the other two ILC subsets (P < 0.01), followed by the ILC1 subset, which was present in significantly higher levels than the ILC3 subset (P < 0.05). Our data place ILCs for the first time in the interface of oral mucosal immunity, tissue microenvironment, and homeostasis during and after tissue development, possibly explaining lower infection rates in cleft lip or palate reconstructions. Copyright © 2016 Elsevier Inc. All rights reserved.

Reduction in CD4 central memory T-cell subset in costimulation modulator abatacept-treated patients with recent-onset type 1 diabetes is associated with slower C-peptide decline.

PubMed

Orban, Tihamer; Beam, Craig A; Xu, Ping; Moore, Keith; Jiang, Qi; Deng, Jun; Muller, Sarah; Gottlieb, Peter; Spain, Lisa; Peakman, Mark

2014-10-01

We previously reported that continuous 24-month costimulation blockade by abatacept significantly slows the decline of β-cell function after diagnosis of type 1 diabetes. In a mechanistic extension of that study, we evaluated peripheral blood immune cell subsets (CD4, CD8-naive, memory and activated subsets, myeloid and plasmacytoid dendritic cells, monocytes, B lymphocytes, CD4(+)CD25(high) regulatory T cells, and invariant NK T cells) by flow cytometry at baseline and 3, 6, 12, 24, and 30 months after treatment initiation to discover biomarkers of therapeutic effect. Using multivariable analysis and lagging of longitudinally measured variables, we made the novel observation in the placebo group that an increase in central memory (CM) CD4 T cells (CD4(+)CD45R0(+)CD62L(+)) during a preceding visit was significantly associated with C-peptide decline at the subsequent visit. These changes were significantly affected by abatacept treatment, which drove the peripheral contraction of CM CD4 T cells and the expansion of naive (CD45R0(-)CD62L(+)) CD4 T cells in association with a significantly slower rate of C-peptide decline. The findings show that the quantification of CM CD4 T cells can provide a surrogate immune marker for C-peptide decline after the diagnosis of type 1 diabetes and that costimulation blockade may exert its beneficial therapeutic effect via modulation of this subset. © 2014 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

Mycobacterium leprae in Colombia described by SNP7614 in gyrA, two minisatellites and geography

PubMed Central

Cardona-Castro, Nora; Beltrán-Alzate, Juan Camilo; Romero-Montoya, Irma Marcela; Li, Wei; Brennan, Patrick J; Vissa, Varalakshmi

2013-01-01

New cases of leprosy are still being detected in Colombia after the country declared achievement of the WHO defined ‘elimination’ status. To study the ecology of leprosy in endemic regions, a combination of geographic and molecular tools were applied for a group of 201 multibacillary patients including six multi-case families from eleven departments. The location (latitude and longitude) of patient residences were mapped. Slit skin smears and/or skin biopsies were collected and DNA was extracted. Standard agarose gel electrophoresis following a multiplex PCR-was developed for rapid and inexpensive strain typing of M. leprae based on copy numbers of two VNTR minisatellite loci 27-5 and 12-5. A SNP (C/T) in gyrA (SNP7614) was mapped by introducing a novel PCR-RFLP into an ongoing drug resistance surveillance effort. Multiple genotypes were detected combining the three molecular markers. The two frequent genotypes in Colombia were SNP7614(C)/27-5(5)/12-5(4) [C54] predominantly distributed in the Atlantic departments and SNP7614 (T)/27-5(4)/12-5(5) [T45] associated with the Andean departments. A novel genotype SNP7614 (C)/27-5(6)/12-5(4) [C64] was detected in cities along the Magdalena river which separates the Andean from Atlantic departments; a subset was further characterized showing association with a rare allele of minisatellite 23-3 and the SNP type 1 of M. leprae. The genotypes within intra-family cases were conserved. Overall, this is the first large scale study that utilized simple and rapid assay formats for identification of major strain types and their distribution in Colombia. It provides the framework for further strain type discrimination and geographic information systems as tools for tracing transmission of leprosy. PMID:23291420

Results of the second national forest soil inventory in Germany - Interpretation of level and stock profiles for PCDD/F and PCB in terms of vegetation and humus type.

PubMed

Pandelova, Marchela; Henkelmann, Bernhard; Bussian, Bernd M; Schramm, Karl-Werner

2018-01-01

Polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and polychlorinated biphenyls (PCBs) were detected in 86 humic topsoil layers and in a subset of 11 randomly selected top mineral forest soils at the depths of 0-5cm and 5-10cm collected from different federal states of Germany. The distribution of these persistent organic pollutants (POPs) in humic topsoils with respect to vegetation cover (coniferous vs. deciduous vs. mixed), total organic carbon (TOC), altitude and latitude data was investigated. There is cross correlation between the contents and TOC while the correlation with latitude indicates higher abundances of POPs in central Germany where there is high population density accompanied with industrial activities. The calculated stocks suggest that humus type (mor, mull, or moder) in conjunction with forest type can explain the relative POPs abundances in different soil layers. Generally, humic topsoils show highest contents of POPs compare to the two mineral soils with a ratio of 100:10:1. However, the stock humic layers of coniferous stands contribute about 50% to the total stock, whereas at deciduous stands the stock is mainly located in the upper mineral soil layer (0-5cm). The soil-water distribution coefficients (Kd) were calculated to estimate the potential translocation in the different soil types. The Kd values vary among the PCBs and PCDD/Fs congeners and are most variable for humic topsoils. There is pronounced chemical abundance in the top mineral soils with increasing Kd and this points to non-water bound transport processes for superlipophilic compounds. Copyright © 2017 Elsevier B.V. All rights reserved.

Variability of oil and gas well productivities for continuous (unconventional) petroleum accumulations

USGS Publications Warehouse

Charpentier, Ronald R.; Cook, Troy A.

2013-01-01

Over the last decade, oil and gas well productivities were estimated using decline-curve analysis for thousands of wells as part of U.S. Geological Survey (USGS) studies of continuous (unconventional) oil and gas resources in the United States. The estimated ultimate recoveries (EURs) of these wells show great variability that was analyzed at three scales: within an assessment unit (AU), among AUs of similar reservoir type, and among groups of AUs with different reservoir types. Within a particular oil or gas AU (such as the Barnett Shale), EURs vary by about two orders of magnitude between the most productive wells and the least productive ones (excluding those that are dry and abandoned). The distributions of EURs are highly skewed, with most of the wells in the lower part of the range. Continuous AUs were divided into four categories based on reservoir type and major commodity (oil or gas): coalbed gas, shale gas, other low-permeability gas AUs (such as tight sands), and low-permeability oil AUs. Within each of these categories, there is great variability from AU to AU, as shown by plots of multiple EUR distributions. Comparing the means of each distribution within a category shows that the means themselves have a skewed distribution, with a range of approximately one to two orders of magnitude. A comparison of the three gas categories (coalbed gas, shale gas, and other low-permeability gas AUs) shows large overlap in the ranges of EUR distributions. Generally, coalbed gas AUs have lower EUR distributions, shale gas AUs have intermediate sizes, and the other low-permeability gas AUs have higher EUR distributions. The plot of EUR distributions for each category shows the range of variation among developed AUs in an appropriate context for viewing the historical development within a particular AU. The Barnett Shale is used as an example to demonstrate that dividing wells into groups by time allows one to see the changes in EUR distribution. Subdivision into groups can also be done by vertical versus horizontal wells, by length of horizontal completion, by distance to closest previously drilled well, by thickness of reservoir interval, or by any other variable for which one has or can calculate values for each well. The resulting plots show how one can subdivide the total range of productivity in shale-gas wells into smaller subsets that are more appropriate for use as analogs.

Cell-type specific differences in promoter activity of the ALS-linked C9orf72 mouse ortholog.

PubMed

Langseth, Abraham J; Kim, Juhyun; Ugolino, Janet E; Shah, Yajas; Hwang, Ho-Yon; Wang, Jiou; Bergles, Dwight E; Brown, Solange P

2017-07-18

A hexanucleotide repeat expansion in the C9orf72 gene is the most common cause of inherited forms of the neurodegenerative disease amyotrophic lateral sclerosis (ALS). Both loss-of-function and gain-of-function mechanisms have been proposed to underlie this disease, but the pathogenic pathways are not fully understood. To better understand the involvement of different cell types in the pathogenesis of ALS, we systematically analyzed the distribution of promoter activity of the mouse ortholog of C9orf72 in the central nervous system. We demonstrate that C9orf72 promoter activity is widespread in both excitatory and inhibitory neurons as well as in oligodendrocytes and oligodendrocyte precursor cells. In contrast, few microglia and astrocytes exhibit detectable C9orf72 promoter activity. Although at a gross level, the distribution of C9orf72 promoter activity largely follows overall cellular density, we found that it is selectively enriched in subsets of neurons and glial cells that degenerate in ALS. Specifically, we show that C9orf72 promoter activity is enriched in corticospinal and spinal motor neurons as well as in oligodendrocytes in brain regions that are affected in ALS. These results suggest that cell autonomous changes in both neurons and glia may contribute to C9orf72-mediated disease, as has been shown for mutations in superoxide dismutase-1 (SOD1).

[Does prenatal diagnosis modify neonatal management and early outcome of children with esophageal atresia type III?].

PubMed

Garabedian, C; Sfeir, R; Langlois, C; Bonnard, A; Khen-Dunlop, N; Gelas, T; Michaud, L; Auber, F; Piolat, C; Lemelle, J-L; Fouquet, V; Habonima, É; Becmeur, F; Polimerol, M-L; Breton, A; Petit, T; Podevin, G; Lavrand, F; Allal, H; Lopez, M; Elbaz, F; Merrot, T; Michel, J-L; Buisson, P; Sapin, E; Delagausie, P; Pelatan, C; Gaudin, J; Weil, D; de Vries, P; Jaby, O; Lardy, H; Aubert, D; Borderon, C; Fourcade, L; Geiss, S; Breaud, J; Pouzac, M; Echaieb, A; Laplace, C; Gottrand, F; Houfflin-Debarge, V

2015-11-01

Evaluate neonatal management and outcome of neonates with either a prenatal or a post-natal diagnosis of EA type III. Population-based study using data from the French National Register for EA from 2008 to 2010. We compared children with prenatal versus post-natal diagnosis in regards to prenatal, maternal and neonatal characteristics. We define a composite variable of morbidity (anastomotic esophageal leaks, recurrent fistula, stenosis) and mortality at 1 year. Four hundred and eight live births with EA type III were recorded with a prenatal diagnosis rate of 18.1%. Transfer after birth was lower in prenatal subset (32.4% versus 81.5%, P<0.001). Delay between birth and first intervention was not significantly different. Defect size (2cm vs 1.4cm, P<0.001), gastrostomy (21.6% versus 8.7%, P<0.001) and length in neonatal unit care were higher in prenatal subset (47.9 days versus 33.6 days, P<0.001). The composite variables were higher in prenatal diagnosis subset (38.7% vs 26.1%, P=0.044). Despite the excellent survival rate of EA, cases with antenatal detection have a higher morbidity related to the EA type (longer gap). Even if it does not modify neonatal management and 1-year outcome, prenatal diagnosis allows antenatal parental counseling and avoids post-natal transfer. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Interval timing under a behavioral microscope: Dissociating motivational and timing processes in fixed-interval performance.

PubMed

Daniels, Carter W; Sanabria, Federico

2017-03-01

The distribution of latencies and interresponse times (IRTs) of rats was compared between two fixed-interval (FI) schedules of food reinforcement (FI 30 s and FI 90 s), and between two levels of food deprivation. Computational modeling revealed that latencies and IRTs were well described by mixture probability distributions embodying two-state Markov chains. Analysis of these models revealed that only a subset of latencies is sensitive to the periodicity of reinforcement, and prefeeding only reduces the size of this subset. The distribution of IRTs suggests that behavior in FI schedules is organized in bouts that lengthen and ramp up in frequency with proximity to reinforcement. Prefeeding slowed down the lengthening of bouts and increased the time between bouts. When concatenated, latency and IRT models adequately reproduced sigmoidal FI response functions. These findings suggest that behavior in FI schedules fluctuates in and out of schedule control; an account of such fluctuation suggests that timing and motivation are dissociable components of FI performance. These mixture-distribution models also provide novel insights on the motivational, associative, and timing processes expressed in FI performance. These processes may be obscured, however, when performance in timing tasks is analyzed in terms of mean response rates.

Genomic gains and losses are similar in genetic and histologic subsets of rhabdomyosarcoma, whereas amplification predominates in embryonal with anaplasia and alveolar subtypes.

PubMed

Bridge, Julia A; Liu, Jian; Qualman, Stephen J; Suijkerbuijk, Ron; Wenger, Gail; Zhang, Ji; Wan, Xiaoying; Baker, K Scott; Sorensen, Poul; Barr, Frederic G

2002-03-01

In this investigation, we selected PAX3/FKHR and PAX7/FKHR fusion transcript-positive and -negative alveolar rhabdomyosarcomas (ARMSs) and embryonal rhabdomyosarcomas (ERMSs) with and without anaplastic features, to ascertain genomic imbalance differences and/or similarities within these histopathologic and genetic rhabdomyosarcoma (RMS) variants. Comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH) studies were performed on 45 rhabdomyosarcoma specimens consisting of 23 ARMSs and 22 ERMSs (12 ERMS cases were included from an earlier study). The anaplastic variant of RMS has not previously been subjected to CGH analysis. Overall, the most prominent imbalances were gain of chromosomes or chromosomal regions 2/2q (40%), 7/7q (31%), 8/8p (53%), 11/11q (31%), 12q13-15 (49%), 13q14 (22%), and 20/20p (31%), and loss of 1p36 (27%), 3p14-21 (22%), 9q21-22 (33%), 10q22-qter (18%), 16q (27%), 17p (22%), and 22 (22%). These gains and losses were distributed equally between ARMS and ERMS histologic subtypes (excluding 7/7q and 11/11q gain that were observed chiefly in ERMS), demonstrating that these entities are similar with respect to recurrent genomic imbalances. Moreover, genomic imbalances were also evenly distributed among the ARMS fusion transcript subtypes, providing evidence for a genetic kinship despite the absence of a fusion transcript in some cases. Genomic amplification was detected in 26% and 23% of the ARMS and ERMS cases, respectively (with nearly all of the latter subset exhibiting anaplastic features). One amplicon, involving 15q25-26, corresponds to the locus of the insulin-like growth factor type I receptor (IGF1R) gene. Amplification of IGF1R was confirmed molecularly in the cases exhibiting a 15q25-26 amplicon. In summary, these results indicate that genomic gains and losses involve alike chromosomes with similar frequencies within the histopathologic and genetic subtypes of rhabdomyosarcoma, that genomic amplification is frequent not only in the alveolar histologic subtype of rhabdomyosarcoma but also in ERMS with anaplasia, and that amplification of IGF1R possibly plays a role in the development or progression of a subset of rhabdomyosarcomas. Copyright 2002 Wiley-Liss, Inc.

Distinct alterations in the distribution of CD45RO+ T-cell subsets in HIV-2 compared with HIV-1 infection.

PubMed

Jaleco, A C; Covas, M J; Pinto, L A; Victorino, R M

1994-12-01

Some clinical studies indicate that disease progression in HIV-2-infected subjects may be slower than in HIV-1. We investigated whether there were differences in the distribution of CD45RO+ (memory) and CD45RA+ (naive) T-cell subsets between HIV-1 and HIV-2 infection. Analysis of lymphocyte subsets was performed by flow cytometry in peripheral blood mononuclear cells from healthy controls, HIV-1-(n = 49) and HIV-2-infected (n = 47) individuals divided into two groups: asymptomatic (ASY)/persistent generalized lymphadenopathy (PGL) and AIDS-related complex (ARC)/AIDS. Both HIV-1- and HIV-2-infected patients had significant reductions in the absolute number and percentage of CD4+ lymphocytes compared with seronegative individuals. No significant differences were found between HIV-2- and HIV-1-infected subjects in the same clinical stage. CD4+CD45RA+ cells were significantly reduced in HIV-1 and HIV-2 ARC/AIDS patients and mildly reduced in ASY/PGL HIV-1 and HIV-2 patients. There were no differences in the degree of reduction of CD4+CD45RO+ cells in ASY/PGL HIV-1 versus HIV-2 patients. However, in HIV-1-infected ARC/AIDS individuals the reduction in the percentage of this subset was more pronounced than in HIV-2 infection and this difference reached statistical significance. The increase in CD8+ lymphocytes (percentage and absolute number) was more pronounced in HIV-1 and the differences between HIV-1- and HIV-2-infected patients were statistically significant. CD8+CD45RO+ cells were significantly increased both in ASY/PGL and ARC/AIDS HIV-1-infected patients, whereas HIV-2-infected ASY/PGL patients had normal levels of these cells and HIV-2-infected ARC/AIDS patients had increases that were much less pronounced than that observed in HIV-1-infected ARC/AIDS patients. Significant differences in the absolute number and percentage of this subset between HIV-1- and HIV-2-infected individuals in similar clinical stages were found. HIV-2-infected individuals exhibit a lesser degree of depletion of memory CD4+ cells and a more limited expansion of CD8+CD45RO+ subset, which could be related to the putative lower immunopathogenicity of HIV-2.

Development of a New Molecular Subtyping Tool for Salmonella enterica Serovar Enteritidis Based on Single Nucleotide Polymorphism Genotyping Using PCR

PubMed Central

Kelly, Hilary; Dupras, Andrée Ann; Belanger, Sebastien; Devenish, John

2014-01-01

The lack of a sufficiently discriminatory molecular subtyping tool for Salmonella enterica serovar Enteritidis has hindered source attribution efforts and impeded regulatory actions required to disrupt its food-borne transmission. The underlying biological reason for the ineffectiveness of current molecular subtyping tools such as pulsed-field gel electrophoresis (PFGE) and phage typing appears to be related to the high degree of clonality of S. Enteritidis. By interrogating the organism's genome, we previously identified single nucleotide polymorphisms (SNP) distributed throughout the chromosome and have designed a highly discriminatory PCR-based SNP typing test based on 60 polymorphic loci. The application of the SNP-PCR method to DNA samples from S. Enteritidis strains (n = 55) obtained from a variety of sources has led to the differentiation and clustering of the S. Enteritidis isolates into 12 clades made up of 2 to 9 isolates per clade. Significantly, the SNP-PCR assay was able to further differentiate predominant PFGE types (e.g., XAI.0003) and phage types (e.g., phage type 8) into smaller subsets. The SNP-PCR subtyping test proved to be an accurate, precise, and quantitative tool for evaluating the relationships among the S. Enteritidis isolates tested in this study and should prove useful for clustering related S. Enteritidis isolates involved in outbreaks. PMID:25297333

Diagnosis of Chronic Kidney Disease Based on Support Vector Machine by Feature Selection Methods.

PubMed

Polat, Huseyin; Danaei Mehr, Homay; Cetin, Aydin

2017-04-01

As Chronic Kidney Disease progresses slowly, early detection and effective treatment are the only cure to reduce the mortality rate. Machine learning techniques are gaining significance in medical diagnosis because of their classification ability with high accuracy rates. The accuracy of classification algorithms depend on the use of correct feature selection algorithms to reduce the dimension of datasets. In this study, Support Vector Machine classification algorithm was used to diagnose Chronic Kidney Disease. To diagnose the Chronic Kidney Disease, two essential types of feature selection methods namely, wrapper and filter approaches were chosen to reduce the dimension of Chronic Kidney Disease dataset. In wrapper approach, classifier subset evaluator with greedy stepwise search engine and wrapper subset evaluator with the Best First search engine were used. In filter approach, correlation feature selection subset evaluator with greedy stepwise search engine and filtered subset evaluator with the Best First search engine were used. The results showed that the Support Vector Machine classifier by using filtered subset evaluator with the Best First search engine feature selection method has higher accuracy rate (98.5%) in the diagnosis of Chronic Kidney Disease compared to other selected methods.

Information Entropy of Influenza A Segment 7

NASA Astrophysics Data System (ADS)

Thompson, William A.; Fan, Shaohua; Weltman, Joel K.

2008-12-01

Information entropy (H) is a measure of uncertainty at each position within in a sequence of nucleotides.H was used to characterize a set of influenza A segment 7 nucleotide sequences. Nucleotide locations of high entropy were identified near the 5’ start of all of the sequences and the sequences were assigned to subsets according to synonymous nucleotide variants at those positions: either uracil at position six (U6), cytosine at position six (C6), adenine (A12) at position 12, guanine at position 12 (G12), adenine at position 15 (A15) or cytosine (C15) at position 15. H values were found to be correlated/corresponding (Kendall tau) along the lengths of the nucleotide segments of the subset pairs at each position. However, the H values of each subset of sequences were statistically distinguishable from those of the other member of the pair (Kolmogorov-Smirnov test). The joint probability of uncorrelated distributions of U6 and C6 sequences to viral subtypes and to viral host species was 34 times greater than for the A12:G12 subset pair and 214 times greater than for the A15:C15 pair. This result indicates that the high entropy position six of segment 7 is either a reporter or a sentinel location. The fact that not one of the H5N1 sequences in the dataset was a member of the C6 subset, but all 125 H5N1 sequences are members of the U6 subset suggests a non-random sentinel function.

Spectra of random operators with absolutely continuous integrated density of states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rio, Rafael del, E-mail: delrio@iimas.unam.mx, E-mail: delriomagia@gmail.com

2014-04-15

The structure of the spectrum of random operators is studied. It is shown that if the density of states measure of some subsets of the spectrum is zero, then these subsets are empty. In particular follows that absolute continuity of the integrated density of states implies singular spectra of ergodic operators is either empty or of positive measure. Our results apply to Anderson and alloy type models, perturbed Landau Hamiltonians, almost periodic potentials, and models which are not ergodic.

Performance observations based on a subset of the DICOM 3.0 draft standard

NASA Astrophysics Data System (ADS)

Moore, Stephen M.; Blaine, G. James; Jost, R. Gilbert

1993-09-01

The American College of Radiology (ACR) and the National Electrical Manufacturers Association (NEMA) are defining the Digital Imaging and Communications in Medicine (DICOM) V3.0 Standard. Previous authors have investigated the performance of the ACR- NEMA V1.0 and V2.0 Standards in point to point and network applications. This paper describes an early implementation of a subset of the DICOM V3.0 Standard and presents performance results for a combination of workstation types and network technologies.

On the Hardness of Subset Sum Problem from Different Intervals

NASA Astrophysics Data System (ADS)

Kogure, Jun; Kunihiro, Noboru; Yamamoto, Hirosuke

The subset sum problem, which is often called as the knapsack problem, is known as an NP-hard problem, and there are several cryptosystems based on the problem. Assuming an oracle for shortest vector problem of lattice, the low-density attack algorithm by Lagarias and Odlyzko and its variants solve the subset sum problem efficiently, when the “density” of the given problem is smaller than some threshold. When we define the density in the context of knapsack-type cryptosystems, weights are usually assumed to be chosen uniformly at random from the same interval. In this paper, we focus on general subset sum problems, where this assumption may not hold. We assume that weights are chosen from different intervals, and make analysis of the effect on the success probability of above algorithms both theoretically and experimentally. Possible application of our result in the context of knapsack cryptosystems is the security analysis when we reduce the data size of public keys.

Engineering Immunity: Modulating Dendritic Cell Subsets and Lymph Node Response to Direct Immune-polarization and Vaccine Efficacy

PubMed Central

Leleux, Jardin; Atalis, Alexandra; Roy, Krishnendu

2017-01-01

While successful vaccines have been developed against many pathogens, there are still many diseases and pathogenic infections that are highly evasive to current vaccination strategies. Thus, more sophisticated approaches to control the type and quality of vaccine-induced immune response must be developed. Dendritic cells (DCs) are the sentinels of the body and play a critical role in immune response generation and direction by bridging innate and adaptive immunity. It is now well recognized that DCs can be separated into many subgroups, each of which has a unique function. Better understanding of how various DC subsets, in lymphoid organs and in the periphery, can be targeted through controlled delivery; and how these subsets modulate and control the resulting immune response could greatly enhance our ability to develop new, effective vaccines against complex diseases. In this review, we provide an overview of DC subset biology and discuss current immunotherapeutic strategies that utilize DC targeting to modulate and control immune responses. PMID:26489733

A Negative Partition Relation

PubMed Central

Hajnal, A.

1971-01-01

If the continuum hypothesis is assumed, there is a graph G whose vertices form an ordered set of type ω12; G does not contain triangles or complete even graphs of form [[unk]0,[unk]0], and there is no independent subset of vertices of type ω12. PMID:16591893

Selective accumulation of langerhans-type dendritic cells in small airways of patients with COPD

PubMed Central

2010-01-01

Background Dendritic cells (DC) linking innate and adaptive immune responses are present in human lungs, but the characterization of different subsets and their role in COPD pathogenesis remain to be elucidated. The aim of this study is to characterize and quantify pulmonary myeloid DC subsets in small airways of current and ex-smokers with or without COPD. Methods Myeloid DC were characterized using flowcytometry on single cell suspensions of digested human lung tissue. Immunohistochemical staining for langerin, BDCA-1, CD1a and DC-SIGN was performed on surgical resection specimens from 85 patients. Expression of factors inducing Langerhans-type DC (LDC) differentiation was evaluated by RT-PCR on total lung RNA. Results Two segregated subsets of tissue resident pulmonary myeloid DC were identified in single cell suspensions by flowcytometry: the langerin+ LDC and the DC-SIGN+ interstitial-type DC (intDC). LDC partially expressed the markers CD1a and BDCA-1, which are also present on their known blood precursors. In contrast, intDC did not express langerin, CD1a or BDCA-1, but were more closely related to monocytes. Quantification of DC in the small airways by immunohistochemistry revealed a higher number of LDC in current smokers without COPD and in COPD patients compared to never smokers and ex-smokers without COPD. Importantly, there was no difference in the number of LDC between current and ex-smoking COPD patients. In contrast, the number of intDC did not differ between study groups. Interestingly, the number of BDCA-1+ DC was significantly lower in COPD patients compared to never smokers and further decreased with the severity of the disease. In addition, the accumulation of LDC in the small airways significantly correlated with the expression of the LDC inducing differentiation factor activin-A. Conclusions Myeloid DC differentiation is altered in small airways of current smokers and COPD patients resulting in a selective accumulation of the LDC subset which correlates with the pulmonary expression of the LDC-inducing differentiation factor activin-A. This study identified the LDC subset as an interesting focus for future research in COPD pathogenesis. PMID:20307269

Interference-mediated synaptonemal complex formation with embedded crossover designation

PubMed Central

Zhang, Liangran; Espagne, Eric; de Muyt, Arnaud; Zickler, Denise; Kleckner, Nancy E.

2014-01-01

Biological systems exhibit complex patterns at length scales ranging from the molecular to the organismic. Along chromosomes, events often occur stochastically at different positions in different nuclei but nonetheless tend to be relatively evenly spaced. Examples include replication origin firings, formation of chromatin loops along chromosome axes and, during meiosis, localization of crossover recombination sites (“crossover interference”). We present evidence in the fungus Sordaria macrospora that crossover interference is part of a broader pattern that includes synaptonemal complex (SC) nucleation. This pattern comprises relatively evenly spaced SC nucleation sites, among which a subset are crossover sites that show a classical interference distribution. This pattern ensures that SC forms regularly along the entire length of the chromosome as required for the maintenance of homolog pairing while concomitantly having crossover interactions locally embedded within the SC structure as required for both DNA recombination and structural events of chiasma formation. This pattern can be explained by a threshold-based designation and spreading interference process. This model can be generalized to give diverse types of related and/or partially overlapping patterns, in two or more dimensions, for any type of object. PMID:25380597

Everything you ever wanted to know about the ultraviolet spectra of star-forming galaxies but were afraid to ask

NASA Technical Reports Server (NTRS)

Kinney, A. L.; Bohlin, R.; Calzetti, D.; Panagia, N.; Wyse, R.

1993-01-01

We present ultraviolet spectra of 143 star-forming galaxies of different morphological types and activity classes including S0, Sa, Sb, Sc, Sd, irregular, starburst, blue compact, blue compact dwarf, Liner, and Seyfert 2 galaxies. These IUE spectra cover the wavelength range from 1200 to 3200 A and are taken in a large aperture (10 x 20 inch). The ultraviolet spectral energy distributions are shown for a subset of the galaxies, ordered by spectral index, and separated by type for normal galaxies, Liners, starburst galaxies, blue compact (BCG) and blue compact dwarf (BCDG) galaxies, and Seyfert 2 galaxies. The ultraviolet spectra of Liners are, for the most part, indistinguishable from the spectra of normal galaxies. Starburst galaxies have a large range of ultraviolet slope, from blue to red. The star-forming galaxies which are the bluest in the optical (BCG and BCDG), also have the 'bluest' average ultraviolet slope of beta = -1.75 +/- 0.63. Seyfert 2 galaxies are the only galaxies in the sample that consistently have detectable UV emission lines.

Characterization of Aquaporin 4 Protein Expression and Localization in Tissues of the Dogfish (Squalus acanthias)

PubMed Central

Cutler, Christopher P.; Harmon, Sheena; Walsh, Jonathon; Burch, Kia

2012-01-01

The role of aquaporin water channels such as aquaporin 4 (Aqp4) in elasmobranchs such as the dogfish Squalus acanthias is completely unknown. This investigation set out to determine the expression and cellular and sub-cellular localization of Aqp4 protein in dogfish tissues. Two polyclonal antibodies were generated (AQP4/1 and AQP4/2) and these showed somewhat different characteristics in Western blotting and immunohistochemistry. Western blots using the AQP4/1 antibody showed two bands (35.5 and 49.5 kDa) in most tissues in a similar fashion to mammals. Liver had an additional band of 57 kDa and rectal gland two further faint bands of 37.5 and 38.5 kDa. However, unlike in mammals, Aqp4 protein was ubiquitously expressed in all tissues including gill and liver. The AQP4/2 antibody appeared much less specific in Western blots. Both antibodies were used in immunohistochemistry and showed similar cellular localizations, although the AQP4/2 antibody had a more restricted sub-cellular distribution compared to AQP4/1 and therefore appeared to be more specific for Aqp4. In kidney a sub-set of tubules were stained which may represent intermediate tubule segments (In-III–In-VI). AQP4/1 and AQP4/2 antibodies localized to the same tubules segments in serial sections although the intensity and sub-cellular distribution were different. AQP4/2 showed a basal or basolateral membrane distribution whereas AQP4/1 was often distributed throughout the whole cell including the nuclear region. In rectal gland and cardiac stomach Aqp4 was localized to secretory tubules but again AQP/1 and AQP/2 exhibited different sub-cellular distributions. In gill, both antibodies stained large cells in the primary filament and secondary lamellae. Again AQP4/1 antibody stained most or all the cell including the nucleus, whereas AQP4/2 had a plasma membrane or plasma membrane and cytoplasmic distribution. Two types of large mitochondrial rich transport cells are known to exist in elasmobranchs, that express either Na, K-ATPase, or V-type ATPase ion transporters. Using Na, K-ATPase, and V-type ATPase antibodies, Aqp4 was colocalized with these proteins using the AQP4/1 antibody. Results show Aqp4 is expressed in both (and all) branchial Na, K-ATPase, and V-type ATPase expressing cells. PMID:22363294

Characterization of Aquaporin 4 Protein Expression and Localization in Tissues of the Dogfish (Squalus acanthias).

PubMed

Cutler, Christopher P; Harmon, Sheena; Walsh, Jonathon; Burch, Kia

2012-01-01

The role of aquaporin water channels such as aquaporin 4 (Aqp4) in elasmobranchs such as the dogfish Squalus acanthias is completely unknown. This investigation set out to determine the expression and cellular and sub-cellular localization of Aqp4 protein in dogfish tissues. Two polyclonal antibodies were generated (AQP4/1 and AQP4/2) and these showed somewhat different characteristics in Western blotting and immunohistochemistry. Western blots using the AQP4/1 antibody showed two bands (35.5 and 49.5 kDa) in most tissues in a similar fashion to mammals. Liver had an additional band of 57 kDa and rectal gland two further faint bands of 37.5 and 38.5 kDa. However, unlike in mammals, Aqp4 protein was ubiquitously expressed in all tissues including gill and liver. The AQP4/2 antibody appeared much less specific in Western blots. Both antibodies were used in immunohistochemistry and showed similar cellular localizations, although the AQP4/2 antibody had a more restricted sub-cellular distribution compared to AQP4/1 and therefore appeared to be more specific for Aqp4. In kidney a sub-set of tubules were stained which may represent intermediate tubule segments (In-III-In-VI). AQP4/1 and AQP4/2 antibodies localized to the same tubules segments in serial sections although the intensity and sub-cellular distribution were different. AQP4/2 showed a basal or basolateral membrane distribution whereas AQP4/1 was often distributed throughout the whole cell including the nuclear region. In rectal gland and cardiac stomach Aqp4 was localized to secretory tubules but again AQP/1 and AQP/2 exhibited different sub-cellular distributions. In gill, both antibodies stained large cells in the primary filament and secondary lamellae. Again AQP4/1 antibody stained most or all the cell including the nucleus, whereas AQP4/2 had a plasma membrane or plasma membrane and cytoplasmic distribution. Two types of large mitochondrial rich transport cells are known to exist in elasmobranchs, that express either Na, K-ATPase, or V-type ATPase ion transporters. Using Na, K-ATPase, and V-type ATPase antibodies, Aqp4 was colocalized with these proteins using the AQP4/1 antibody. Results show Aqp4 is expressed in both (and all) branchial Na, K-ATPase, and V-type ATPase expressing cells.

Distributed Wind Soft Costs: A Beginning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jimenez, Tony; Forsyth,Trudy; Preus, Robert

2016-06-14

Tony Jimenez presented this overview of distributed wind soft costs at the 2016 Small Wind Conference in Stevens Point, Wisconsin, on June 14, 2016. Soft costs are any non-hardware project costs, such as costs related to permitting fees, installer/developer profit, taxes, transaction costs, permitting, installation, indirect corporate costs, installation labor, and supply chain costs. This presentation provides an overview of soft costs, a distributed wind project taxonomy (of which soft costs are a subset), an alpha data set project demographics, data summary, and future work in this area.

Formal Semantics and Implementation of BPMN 2.0 Inclusive Gateways

NASA Astrophysics Data System (ADS)

Christiansen, David Raymond; Carbone, Marco; Hildebrandt, Thomas

We present the first direct formalization of the semantics of inclusive gateways as described in the Business Process Modeling Notation (BPMN) 2.0 Beta 1 specification. The formal semantics is given for a minimal subset of BPMN 2.0 containing just the inclusive and exclusive gateways and the start and stop events. By focusing on this subset we achieve a simple graph model that highlights the particular non-local features of the inclusive gateway semantics. We sketch two ways of implementing the semantics using algorithms based on incrementally updated data structures and also discuss distributed communication-based implementations of the two algorithms.

Taking a(c)count of eye movements: Multiple mechanisms underlie fixations during enumeration.

PubMed

Paul, Jacob M; Reeve, Robert A; Forte, Jason D

2017-03-01

We habitually move our eyes when we enumerate sets of objects. It remains unclear whether saccades are directed for numerosity processing as distinct from object-oriented visual processing (e.g., object saliency, scanning heuristics). Here we investigated the extent to which enumeration eye movements are contingent upon the location of objects in an array, and whether fixation patterns vary with enumeration demands. Twenty adults enumerated random dot arrays twice: first to report the set cardinality and second to judge the perceived number of subsets. We manipulated the spatial location of dots by presenting arrays at 0°, 90°, 180°, and 270° orientations. Participants required a similar time to enumerate the set or the perceived number of subsets in the same array. Fixation patterns were systematically shifted in the direction of array rotation, and distributed across similar locations when the same array was shown on multiple occasions. We modeled fixation patterns and dot saliency using a simple filtering model and show participants judged groups of dots in close proximity (2°-2.5° visual angle) as distinct subsets. Modeling results are consistent with the suggestion that enumeration involves visual grouping mechanisms based on object saliency, and specific enumeration demands affect spatial distribution of fixations. Our findings highlight the importance of set computation, rather than object processing per se, for models of numerosity processing.

Skin lesion computational diagnosis of dermoscopic images: Ensemble models based on input feature manipulation.

PubMed

Oliveira, Roberta B; Pereira, Aledir S; Tavares, João Manuel R S

2017-10-01

The number of deaths worldwide due to melanoma has risen in recent times, in part because melanoma is the most aggressive type of skin cancer. Computational systems have been developed to assist dermatologists in early diagnosis of skin cancer, or even to monitor skin lesions. However, there still remains a challenge to improve classifiers for the diagnosis of such skin lesions. The main objective of this article is to evaluate different ensemble classification models based on input feature manipulation to diagnose skin lesions. Input feature manipulation processes are based on feature subset selections from shape properties, colour variation and texture analysis to generate diversity for the ensemble models. Three subset selection models are presented here: (1) a subset selection model based on specific feature groups, (2) a correlation-based subset selection model, and (3) a subset selection model based on feature selection algorithms. Each ensemble classification model is generated using an optimum-path forest classifier and integrated with a majority voting strategy. The proposed models were applied on a set of 1104 dermoscopic images using a cross-validation procedure. The best results were obtained by the first ensemble classification model that generates a feature subset ensemble based on specific feature groups. The skin lesion diagnosis computational system achieved 94.3% accuracy, 91.8% sensitivity and 96.7% specificity. The input feature manipulation process based on specific feature subsets generated the greatest diversity for the ensemble classification model with very promising results. Copyright © 2017 Elsevier B.V. All rights reserved.

Hepatic dendritic cell subsets in the mouse.

PubMed

Jomantaite, Ieva; Dikopoulos, Nektarios; Kröger, Andrea; Leithäuser, Frank; Hauser, Hansjörg; Schirmbeck, Reinhold; Reimann, Jörg

2004-02-01

The CD11c(+) cell population in the non-parenchymal cell population of the mouse liver contains dendritic cells (DC), NK cells, B cells and T cells. In the hepatic CD11c(+) DC population from immunocompetent or immunodeficient [recombinase-activating gene-1 (RAG1)(-/-)] C57BL/6 mice (rigorously depleted of T cells, B cells and NK cells), we identified a B220(+) CD11c(int) subset of 'plasmacytoid' DC, and a B220(-) CD11c(+) DC subset. The latter DC population could be subdivided into a major, immature (CD40(lo) CD80(lo) CD86(lo) MHC class II(lo)) CD11c(int) subset, and a minor, mature (CD40(hi) CD80(hi) CD86(hi) MHC class II(hi)) CD11c(hi) subset. Stimulated B220(+) but not B220(-) DC produced type I interferon. NKT cell activation in vivo increased the number of liver B220(-) DC three- to fourfold within 18 h post-injection, and up-regulated their surface expression of activation marker, while it contracted the B220(+) DC population. Early in virus infection, the hepatic B220(+) DC subset expanded, and both, the B220(+) as well as B220(-) DC populations in the liver matured. In vitro, B220(-) but not B220(+) DC primed CD4(+) or CD8(+)T cells. Expression of distinct marker profiles and functions, and distinct early reaction to activation signals hence identify two distinct B220(+) and B220(-) subsets in CD11c(+) DC populations freshly isolated from the mouse liver.

Benchmarking of vertically-integrated CO2 flow simulations at the Sleipner Field, North Sea

NASA Astrophysics Data System (ADS)

Cowton, L. R.; Neufeld, J. A.; White, N. J.; Bickle, M. J.; Williams, G. A.; White, J. C.; Chadwick, R. A.

2018-06-01

Numerical modeling plays an essential role in both identifying and assessing sub-surface reservoirs that might be suitable for future carbon capture and storage projects. Accuracy of flow simulations is tested by benchmarking against historic observations from on-going CO2 injection sites. At the Sleipner project located in the North Sea, a suite of time-lapse seismic reflection surveys enables the three-dimensional distribution of CO2 at the top of the reservoir to be determined as a function of time. Previous attempts have used Darcy flow simulators to model CO2 migration throughout this layer, given the volume of injection with time and the location of the injection point. Due primarily to computational limitations preventing adequate exploration of model parameter space, these simulations usually fail to match the observed distribution of CO2 as a function of space and time. To circumvent these limitations, we develop a vertically-integrated fluid flow simulator that is based upon the theory of topographically controlled, porous gravity currents. This computationally efficient scheme can be used to invert for the spatial distribution of reservoir permeability required to minimize differences between the observed and calculated CO2 distributions. When a uniform reservoir permeability is assumed, inverse modeling is unable to adequately match the migration of CO2 at the top of the reservoir. If, however, the width and permeability of a mapped channel deposit are allowed to independently vary, a satisfactory match between the observed and calculated CO2 distributions is obtained. Finally, the ability of this algorithm to forecast the flow of CO2 at the top of the reservoir is assessed. By dividing the complete set of seismic reflection surveys into training and validation subsets, we find that the spatial pattern of permeability required to match the training subset can successfully predict CO2 migration for the validation subset. This ability suggests that it might be feasible to forecast migration patterns into the future with a degree of confidence. Nevertheless, our analysis highlights the difficulty in estimating reservoir parameters away from the region swept by CO2 without additional observational constraints.

The Effect of Distributed Practice Homework on Precalculus Achievement at a Military Academy.

DTIC Science & Technology

1996-04-08

This study investigated the main effect of distributive practice homework on achievement in Precalculus . This study also investigated the aptitude...achievement in Precalculus . The sample consisted of 351 United States Air Force Academy cadets (experimental n = 161, control n = 190), all in their first...achievement. A subset of the Math Anxiety Rating Scale developed by Alexander and Martray (1989) was used as the measure of mathematics anxiety. Precalculus

Reconstitution of lymphocyte subpopulations after hematopoietic stem cell transplantation: comparison of hematologic malignancies and donor types in event-free patients.

PubMed

Park, Borae G; Park, Chan-Jeoung; Jang, Seongsoo; Chi, Hyun-Sook; Kim, Dae-Young; Lee, Jung-Hee; Lee, Je-Hwan; Lee, Kyoo-Hyung

2015-12-01

The reconstitution of different immunocyte subsets after hematopoietic stem cell transplantation (HSCT), follows different timelines. We prospectively investigated changes in lymphocyte subsets after HSCT and their associations with primary diagnosis, conditioning regimen, and HSCT type in event-free patients. A total of 95 patients (48 with acute myeloid leukemia, 22 with acute lymphoid leukemia, and 25 with myelodysplastic syndrome) who underwent allogeneic HSCT (34 sibling matched, 37 unrelated matched, and 24 haploidentical HSCT) but did not experience any events such as relapse or death were enrolled in this study. Lymphocyte subpopulations (T cells, helper/inducer T cells, cytotoxic/suppressor T cells, memory T cells, regulatory T cells, natural killer (NK) cells, NK-T cells, and B cells) were quantified by flow cytometry of peripheral blood from recipients 7 days before and 1, 2, 3, 6, and 12 months after HSCT. Leukocyte counts recovered within 1 month after HSCT. However, the number of T and B lymphocytes recovered at 2 months after HSCT. NK cell counts recovered shortly after haploidentical HSCT. However, T lymphocytes and their subpopulations showed delayed recovery after haploidentical HSCT. Lymphocyte subsets showed different sequential patterns according to HSCT type but no differences were seen according to primary diagnosis or conditioning regimen. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multiclass cancer classification using a feature subset-based ensemble from microRNA expression profiles.

PubMed

Piao, Yongjun; Piao, Minghao; Ryu, Keun Ho

2017-01-01

Cancer classification has been a crucial topic of research in cancer treatment. In the last decade, messenger RNA (mRNA) expression profiles have been widely used to classify different types of cancers. With the discovery of a new class of small non-coding RNAs; known as microRNAs (miRNAs), various studies have shown that the expression patterns of miRNA can also accurately classify human cancers. Therefore, there is a great demand for the development of machine learning approaches to accurately classify various types of cancers using miRNA expression data. In this article, we propose a feature subset-based ensemble method in which each model is learned from a different projection of the original feature space to classify multiple cancers. In our method, the feature relevance and redundancy are considered to generate multiple feature subsets, the base classifiers are learned from each independent miRNA subset, and the average posterior probability is used to combine the base classifiers. To test the performance of our method, we used bead-based and sequence-based miRNA expression datasets and conducted 10-fold and leave-one-out cross validations. The experimental results show that the proposed method yields good results and has higher prediction accuracy than popular ensemble methods. The Java program and source code of the proposed method and the datasets in the experiments are freely available at https://sourceforge.net/projects/mirna-ensemble/. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identifying the Target Cell in Primary Simian Immunodeficiency Virus (SIV) Infection: Highly Activated Memory CD4+ T Cells Are Rapidly Eliminated in Early SIV Infection In Vivo

PubMed Central

Veazey, Ronald S.; Tham, Irene C.; Mansfield, Keith G.; DeMaria, MaryAnn; Forand, Amy E.; Shvetz, Daniel E.; Chalifoux, Laura V.; Sehgal, Prabhat K.; Lackner, Andrew A.

2000-01-01

It has recently been shown that rapid and profound CD4+ T-cell depletion occurs almost exclusively within the intestinal tract of simian immunodeficiency virus (SIV)-infected macaques within days of infection. Here we demonstrate (by three- and four-color flow cytometry) that this depletion is specific to a definable subset of CD4+ T cells, namely, those having both a highly and/or acutely activated (CD69+ CD38+ HLA-DR+) and memory (CD45RA− Leu8−) phenotype. Moreover, we demonstrate that this subset of helper T cells is found primarily within the intestinal lamina propria. Viral tropism for this particular cell type (which has been previously suggested by various studies in vitro) could explain why profound CD4+ T-cell depletion occurs in the intestine and not in peripheral lymphoid tissues in early SIV infection. Furthermore, we demonstrate that an acute loss of this specific subset of activated memory CD4+ T cells may also be detected in peripheral blood and lymph nodes in early SIV infection. However, since this particular cell type is present in such small numbers in circulation, its loss does not significantly affect total CD4+ T cell counts. This finding suggests that SIV and, presumably, human immunodeficiency virus specifically infect, replicate in, and eliminate definable subsets of CD4+ T cells in vivo. PMID:10590091

VisFlow - Web-based Visualization Framework for Tabular Data with a Subset Flow Model.

PubMed

Yu, Bowen; Silva, Claudio T

2017-01-01

Data flow systems allow the user to design a flow diagram that specifies the relations between system components which process, filter or visually present the data. Visualization systems may benefit from user-defined data flows as an analysis typically consists of rendering multiple plots on demand and performing different types of interactive queries across coordinated views. In this paper, we propose VisFlow, a web-based visualization framework for tabular data that employs a specific type of data flow model called the subset flow model. VisFlow focuses on interactive queries within the data flow, overcoming the limitation of interactivity from past computational data flow systems. In particular, VisFlow applies embedded visualizations and supports interactive selections, brushing and linking within a visualization-oriented data flow. The model requires all data transmitted by the flow to be a data item subset (i.e. groups of table rows) of some original input table, so that rendering properties can be assigned to the subset unambiguously for tracking and comparison. VisFlow features the analysis flexibility of a flow diagram, and at the same time reduces the diagram complexity and improves usability. We demonstrate the capability of VisFlow on two case studies with domain experts on real-world datasets showing that VisFlow is capable of accomplishing a considerable set of visualization and analysis tasks. The VisFlow system is available as open source on GitHub.

Promoter classifier: software package for promoter database analysis.

PubMed

Gershenzon, Naum I; Ioshikhes, Ilya P

2005-01-01

Promoter Classifier is a package of seven stand-alone Windows-based C++ programs allowing the following basic manipulations with a set of promoter sequences: (i) calculation of positional distributions of nucleotides averaged over all promoters of the dataset; (ii) calculation of the averaged occurrence frequencies of the transcription factor binding sites and their combinations; (iii) division of the dataset into subsets of sequences containing or lacking certain promoter elements or combinations; (iv) extraction of the promoter subsets containing or lacking CpG islands around the transcription start site; and (v) calculation of spatial distributions of the promoter DNA stacking energy and bending stiffness. All programs have a user-friendly interface and provide the results in a convenient graphical form. The Promoter Classifier package is an effective tool for various basic manipulations with eukaryotic promoter sequences that usually are necessary for analysis of large promoter datasets. The program Promoter Divider is described in more detail as a representative component of the package.

Tissue specific distribution of iNKT cells impacts their cytokine response

PubMed Central

Lee, You Jeong; Wang, Haiguang; Starrett, Gabriel J.; Phuong, Vanessa; Jameson, Stephen C.; Hogquist, Kristin A.

2015-01-01

Summary Three subsets of invariant natural killer T (iNKT) cells have been identified, NKT1, NKT2 and NKT17, which produce distinct cytokines when stimulated, but little is known about their localization. Here, we have defined the anatomic localization and systemic distribution of these subsets and measured their cytokine production. Thymic NKT2 cells that produced interleukin-4 (IL-4) at steady state were located in the medulla and conditioned medullary thymocytes. NKT2 cells were abundant in the mesenteric lymph node (LN) of BALB/c mice and produced IL-4 in the T cell zone that conditioned other lymphocytes. Intravenous injection of α-galactosylceramide activated NKT1 cells with vascular access, but not LN or thymic NKT cells, resulting in systemic interferon-γ and IL-4 production, while oral α-galactosylceramide activated NKT2 cells in the mesenteric LN, resulting in local IL-4 release. These finding indicate that the localization of iNKT cells governs their cytokine response both at steady state and upon activation. PMID:26362265

CMEs, the Tail of the Solar Wind Magnetic Field Distribution, and 11-yr Cosmic Ray Modulation at 1 AU. Revised

NASA Technical Reports Server (NTRS)

Cliver, E. W.; Ling, A. G.; Richardson, I. G.

2003-01-01

Using a recent classification of the solar wind at 1 AU into its principal components (slow solar wind, high-speed streams, and coronal mass ejections (CMEs) for 1972-2000, we show that the monthly-averaged galactic cosmic ray intensity is anti-correlated with the percentage of time that the Earth is imbedded in CME flows. We suggest that this correlation results primarily from a CME related change in the tail of the distribution function of hourly-averaged values of the solar wind magnetic field (B) between solar minimum and solar maximum. The number of high-B (square proper subset 10 nT) values increases by a factor of approx. 3 from minimum to maximum (from 5% of all hours to 17%), with about two-thirds of this increase due to CMEs. On an hour-to-hour basis, average changes of cosmic ray intensity at Earth become negative for solar wind magnetic field values square proper subset 10 nT.

Precipitable water: Its linear retrieval using leaps and bounds procedure and its global distribution from SEASAT SMMR data

NASA Technical Reports Server (NTRS)

Pandey, P. C.

1982-01-01

Eight subsets using two to five frequencies of the SEASAT scanning multichannel microwave radiometer are examined to determine their potential in the retrieval of atmospheric water vapor content. Analysis indicates that the information concerning the 18 and 21 GHz channels are optimum for water vapor retrieval. A comparison with radiosonde observations gave an rms accuracy of approximately 0.40 g sq cm. The rms accuracy of precipitable water using different subsets was within 10 percent. Global maps of precipitable water over oceans using two and five channel retrieval (average of two and five channel retrieval) are given. Study of these maps reveals the possibility of global moisture distribution associated with oceanic currents and large scale general circulation in the atmosphere. A stable feature of the large scale circulation is noticed. The precipitable water is maximum over the Bay of Bengal and in the North Pacific over the Kuroshio current and shows a general latitudinal pattern.

Efficient bootstrap estimates for tail statistics

NASA Astrophysics Data System (ADS)

Breivik, Øyvind; Aarnes, Ole Johan

2017-03-01

Bootstrap resamples can be used to investigate the tail of empirical distributions as well as return value estimates from the extremal behaviour of the sample. Specifically, the confidence intervals on return value estimates or bounds on in-sample tail statistics can be obtained using bootstrap techniques. However, non-parametric bootstrapping from the entire sample is expensive. It is shown here that it suffices to bootstrap from a small subset consisting of the highest entries in the sequence to make estimates that are essentially identical to bootstraps from the entire sample. Similarly, bootstrap estimates of confidence intervals of threshold return estimates are found to be well approximated by using a subset consisting of the highest entries. This has practical consequences in fields such as meteorology, oceanography and hydrology where return values are calculated from very large gridded model integrations spanning decades at high temporal resolution or from large ensembles of independent and identically distributed model fields. In such cases the computational savings are substantial.

Single-Molecule Tracking Photoactivated Localization Microscopy to Map Nano-Scale Structure and Dynamics in Living Spines

PubMed Central

MacGillavry, Harold D.; Blanpied, Thomas A.

2013-01-01

Super-resolution microscopy has rapidly become an indispensable tool in cell biology and neuroscience by enabling measurement in live cells of structures smaller than the classical limit imposed by diffraction. The most widely applied super-resolution method currently is localization microscopy, which takes advantage of the ability to determine the position of individual fluorescent molecules with nanometer accuracy even in cells. By iteratively measuring sparse subsets of photoactivatable fluorescent proteins, protein distribution in macromolecular structures can be accurately reconstructed. Moreover, the motion trajectories of individual molecules within cells can be measured, providing unique ability to measure transport kinetics, exchange rates, and binding affinities of even small subsets of molecules with high temporal resolution and great spatial specificity. This unit describes protocols to measure and quantify the distribution of scaffold proteins within single synapses of cultured hippocampal neurons, and to track and measure the diffusion of intracellular constituents of the neuronal plasma membrane. PMID:25429311

Data approximation using a blending type spline construction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dalmo, Rune; Bratlie, Jostein

2014-11-18

Generalized expo-rational B-splines (GERBS) is a blending type spline construction where local functions at each knot are blended together by C{sup k}-smooth basis functions. One way of approximating discrete regular data using GERBS is by partitioning the data set into subsets and fit a local function to each subset. Partitioning and fitting strategies can be devised such that important or interesting data points are interpolated in order to preserve certain features. We present a method for fitting discrete data using a tensor product GERBS construction. The method is based on detection of feature points using differential geometry. Derivatives, which aremore » necessary for feature point detection and used to construct local surface patches, are approximated from the discrete data using finite differences.« less

The Psychosomatic Disorders Pertaining to Dental Practice with Revised Working Type Classification

PubMed Central

2014-01-01

Psychosomatic disorders are defined as disorders characterized by physiological changes that originate partially from emotional factors. This article aims to discuss the psychosomatic disorders of the oral cavity with a revised working type classification. The author has added one more subset to the existing classification, i.e., disorders caused by altered perception of dentofacial form and function, which include body dysmorphic disorder. The author has also inserted delusional halitosis under the miscellaneous disorders classification of psychosomatic disorders and revised the already existing classification proposed for the psychosomatic disorders pertaining to dental practice. After the inclusion of the subset (disorders caused by altered perception of dentofacial form and function), the terminology "psychosomatic disorders of the oral cavity" is modified to "psychosomatic disorders pertaining to dental practice". PMID:24478896

The psychosomatic disorders pertaining to dental practice with revised working type classification.

PubMed

Shamim, Thorakkal

2014-01-01

Psychosomatic disorders are defined as disorders characterized by physiological changes that originate partially from emotional factors. This article aims to discuss the psychosomatic disorders of the oral cavity with a revised working type classification. The author has added one more subset to the existing classification, i.e., disorders caused by altered perception of dentofacial form and function, which include body dysmorphic disorder. The author has also inserted delusional halitosis under the miscellaneous disorders classification of psychosomatic disorders and revised the already existing classification proposed for the psychosomatic disorders pertaining to dental practice. After the inclusion of the subset (disorders caused by altered perception of dentofacial form and function), the terminology "psychosomatic disorders of the oral cavity" is modified to "psychosomatic disorders pertaining to dental practice".

[Nested species subsets of amphibians and reptiles in Thousand Island Lake].

PubMed

Wang, Xi; Wang, Yan-Ping; Ding, Ping

2012-10-01

Habitat fragmentation is a main cause for the loss of biological diversity. Combining line-transect methods to survey the amphibians and reptiles on 23 islands on Thousand Island Lake in Zhejiang province, along with survey data on nearby plant species and habitat variables collected by GIS, we used the"BINMATNEST (binary matrix nestedness temperature calculator)" software and the Spearman rank correlation to examine whether amphibians and reptiles followed nested subsets and their influencing factors. The results showed that amphibians and reptiles were significantly nested, and that the island area and habitat type were significantly associated with their nested ranks. Therefore, to effectively protect amphibians and reptiles in the Thousand Islands Lake area we should pay prior attention to islands with larger areas and more habitat types.

Stochastic associative memory

NASA Astrophysics Data System (ADS)

Baumann, Erwin W.; Williams, David L.

1993-08-01

Artificial neural networks capable of learning and recalling stochastic associations between non-deterministic quantities have received relatively little attention to date. One potential application of such stochastic associative networks is the generation of sensory 'expectations' based on arbitrary subsets of sensor inputs to support anticipatory and investigate behavior in sensor-based robots. Another application of this type of associative memory is the prediction of how a scene will look in one spectral band, including noise, based upon its appearance in several other wavebands. This paper describes a semi-supervised neural network architecture composed of self-organizing maps associated through stochastic inter-layer connections. This 'Stochastic Associative Memory' (SAM) can learn and recall non-deterministic associations between multi-dimensional probability density functions. The stochastic nature of the network also enables it to represent noise distributions that are inherent in any true sensing process. The SAM architecture, training process, and initial application to sensor image prediction are described. Relationships to Fuzzy Associative Memory (FAM) are discussed.

Comparative study of probability distribution distances to define a metric for the stability of multi-source biomedical research data.

PubMed

Sáez, Carlos; Robles, Montserrat; García-Gómez, Juan Miguel

2013-01-01

Research biobanks are often composed by data from multiple sources. In some cases, these different subsets of data may present dissimilarities among their probability density functions (PDF) due to spatial shifts. This, may lead to wrong hypothesis when treating the data as a whole. Also, the overall quality of the data is diminished. With the purpose of developing a generic and comparable metric to assess the stability of multi-source datasets, we have studied the applicability and behaviour of several PDF distances over shifts on different conditions (such as uni- and multivariate, different types of variable, and multi-modality) which may appear in real biomedical data. From the studied distances, we found information-theoretic based and Earth Mover's Distance to be the most practical distances for most conditions. We discuss the properties and usefulness of each distance according to the possible requirements of a general stability metric.

Rotating Radio Transients and Their Place Among Pulsars

NASA Technical Reports Server (NTRS)

Burke-Spolaor, S.

2012-01-01

Six years ago, the discovery of Rotating Radio Transients (RRATs) marked what appeared to be a new type of sparsely-emitting pulsar. Since 2006, more than 70 of these objects have been discovered in single-pulse searches of archival and new surveys. With a continual inflow of new information about the RRAT population in the form of new discoveries, multi-frequency follow ups, coherent timing solutions, and pulse rate statistics, a view is beginning to form of the place in the pulsar population RRATs hold. Here we review the properties of neutron stars discovered through single pulse searches. We first seek to clarify the definition of the term RRAT, emphasising that "the RRAT population" encompasses several phenomenologies. A large subset of RRATs appears to represent the tail of an extended distribution of pulsar nulling fractions and activity cycles; these objects present several key open questions remaining in this field.

Pupal habitat productivity of Anopheles gambiae complex mosquitoes in a rural village in western Kenya.

PubMed

Mutuku, Francis M; Bayoh, M Nabie; Gimnig, John E; Vulule, John M; Kamau, Luna; Walker, Edward D; Kabiru, Ephantus; Hawley, William A

2006-01-01

The productivity of larval habitats of the malaria vector Anopheles gambiae for pupae (the stage preceding adult metamorphosis) is poorly known, yet adult emergence from habitats is the primary determinant of vector density. To assess it, we used absolute sampling methods in four studies involving daily sampling for 25 days in 6 habitat types in a village in western Kenya. Anopheles gambiae s.s. comprised 82.5% of emergent adults and Anopheles arabiensis the remainder. Pupal production occurred from a subset of habitats, primarily soil burrow pits, and was discontinuous in time, even when larvae occupied all habitats continuously. Habitat stability was positively associated with pupal productivity. In a dry season, pupal productivity was distributed between burrow pits and pools in streambeds. Overall, these data support the notion that source reduction measures against recognizably productive habitats would be a useful component of an integrated management program for An. gambiae in villages.

The split personality of NKT cells in malignancy, autoimmune and allergic disorders

PubMed Central

Subleski, Jeff J; Jiang, Qun; Weiss, Jonathan M; Wiltrout, Robert H

2011-01-01

NKT cells are a heterogeneous subset of specialized, self-reactive T cells, with innate and adaptive immune properties, which allow them to bridge innate and adaptive immunity and profoundly influence autoimmune and malignant disease outcomes. NKT cells mediate these activities through their ability to rapidly express pro- and anti-inflammatory cytokines that influence the type and magnitude of the immune response. Not only do NKT cells regulate the functions of other cell types, but experimental evidence has found NKT cell subsets can modulate the functions of other NKT subsets. Depending on underlying mechanisms, NKT cells can inhibit or exacerbate autoimmunity and malignancy, making them potential targets for disease intervention. NKT cells can respond to foreign and endogenous antigenic glycolipid signals that are expressed during pathogenic invasion or ongoing inflammation, respectively, allowing them to rapidly react to and influence a broad array of diseases. In this article we review the unique development and activation pathways of NKT cells and focus on how these attributes augment or exacerbate autoimmune disorders and malignancy. We also examine the growing evidence that NKT cells are involved in liver inflammatory conditions that can contribute to the development of malignancy. PMID:21995570

Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection

PubMed Central

Carbo, Adria; Bassaganya-Riera, Josep; Pedragosa, Mireia; Viladomiu, Monica; Marathe, Madhav; Eubank, Stephen; Wendelsdorf, Katherine; Bisset, Keith; Hoops, Stefan; Deng, Xinwei; Alam, Maksudul; Kronsteiner, Barbara; Mei, Yongguo; Hontecillas, Raquel

2013-01-01

T helper (Th) cells play a major role in the immune response and pathology at the gastric mucosa during Helicobacter pylori infection. There is a limited mechanistic understanding regarding the contributions of CD4+ T cell subsets to gastritis development during H. pylori colonization. We used two computational approaches: ordinary differential equation (ODE)-based and agent-based modeling (ABM) to study the mechanisms underlying cellular immune responses to H. pylori and how CD4+ T cell subsets influenced initiation, progression and outcome of disease. To calibrate the model, in vivo experimentation was performed by infecting C57BL/6 mice intragastrically with H. pylori and assaying immune cell subsets in the stomach and gastric lymph nodes (GLN) on days 0, 7, 14, 30 and 60 post-infection. Our computational model reproduced the dynamics of effector and regulatory pathways in the gastric lamina propria (LP) in silico. Simulation results show the induction of a Th17 response and a dominant Th1 response, together with a regulatory response characterized by high levels of mucosal Treg) cells. We also investigated the potential role of peroxisome proliferator-activated receptor γ (PPARγ) activation on the modulation of host responses to H. pylori by using loss-of-function approaches. Specifically, in silico results showed a predominance of Th1 and Th17 cells in the stomach of the cell-specific PPARγ knockout system when compared to the wild-type simulation. Spatio-temporal, object-oriented ABM approaches suggested similar dynamics in induction of host responses showing analogous T cell distributions to ODE modeling and facilitated tracking lesion formation. In addition, sensitivity analysis predicted a crucial contribution of Th1 and Th17 effector responses as mediators of histopathological changes in the gastric mucosa during chronic stages of infection, which were experimentally validated in mice. These integrated immunoinformatics approaches characterized the induction of mucosal effector and regulatory pathways controlled by PPARγ during H. pylori infection affecting disease outcomes. PMID:24039925

Mid-infrared interferometry of Seyfert galaxies: Challenging the Standard Model

NASA Astrophysics Data System (ADS)

López-Gonzaga, N.; Jaffe, W.

2016-06-01

Aims: We aim to find torus models that explain the observed high-resolution mid-infrared (MIR) measurements of active galactic nuclei (AGN). Our goal is to determine the general properties of the circumnuclear dusty environments. Methods: We used the MIR interferometric data of a sample of AGNs provided by the instrument MIDI/VLTI and followed a statistical approach to compare the observed distribution of the interferometric measurements with the distributions computed from clumpy torus models. We mainly tested whether the diversity of Seyfert galaxies can be described using the Standard Model idea, where differences are solely due to a line-of-sight (LOS) effect. In addition to the LOS effects, we performed different realizations of the same model to include possible variations that are caused by the stochastic nature of the dusty models. Results: We find that our entire sample of AGNs, which contains both Seyfert types, cannot be explained merely by an inclination effect and by including random variations of the clouds. Instead, we find that each subset of Seyfert type can be explained by different models, where the filling factor at the inner radius seems to be the largest difference. For the type 1 objects we find that about two thirds of our objects could also be described using a dusty torus similar to the type 2 objects. For the remaining third, it was not possible to find a good description using models with high filling factors, while we found good fits with models with low filling factors. Conclusions: Within our model assumptions, we did not find one single set of model parameters that could simultaneously explain the MIR data of all 21 AGN with LOS effects and random variations alone. We conclude that at least two distinct cloud configurations are required to model the differences in Seyfert galaxies, with volume-filling factors differing by a factor of about 5-10. A continuous transition between the two types cannot be excluded.

A SOAP Web Service for accessing MODIS land product subsets

DOE Office of Scientific and Technical Information (OSTI.GOV)

SanthanaVannan, Suresh K; Cook, Robert B; Pan, Jerry Yun

2011-01-01

Remote sensing data from satellites have provided valuable information on the state of the earth for several decades. Since March 2000, the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor on board NASA s Terra and Aqua satellites have been providing estimates of several land parameters useful in understanding earth system processes at global, continental, and regional scales. However, the HDF-EOS file format, specialized software needed to process the HDF-EOS files, data volume, and the high spatial and temporal resolution of MODIS data make it difficult for users wanting to extract small but valuable amounts of information from the MODIS record. Tomore » overcome this usability issue, the NASA-funded Distributed Active Archive Center (DAAC) for Biogeochemical Dynamics at Oak Ridge National Laboratory (ORNL) developed a Web service that provides subsets of MODIS land products using Simple Object Access Protocol (SOAP). The ORNL DAAC MODIS subsetting Web service is a unique way of serving satellite data that exploits a fairly established and popular Internet protocol to allow users access to massive amounts of remote sensing data. The Web service provides MODIS land product subsets up to 201 x 201 km in a non-proprietary comma delimited text file format. Users can programmatically query the Web service to extract MODIS land parameters for real time data integration into models, decision support tools or connect to workflow software. Information regarding the MODIS SOAP subsetting Web service is available on the World Wide Web (WWW) at http://daac.ornl.gov/modiswebservice.« less

Earth Mover's Distance (EMD): A True Metric for Comparing Biomarker Expression Levels in Cell Populations.

PubMed

Orlova, Darya Y; Zimmerman, Noah; Meehan, Stephen; Meehan, Connor; Waters, Jeffrey; Ghosn, Eliver E B; Filatenkov, Alexander; Kolyagin, Gleb A; Gernez, Yael; Tsuda, Shanel; Moore, Wayne; Moss, Richard B; Herzenberg, Leonore A; Walther, Guenther

2016-01-01

Changes in the frequencies of cell subsets that (co)express characteristic biomarkers, or levels of the biomarkers on the subsets, are widely used as indices of drug response, disease prognosis, stem cell reconstitution, etc. However, although the currently available computational "gating" tools accurately reveal subset frequencies and marker expression levels, they fail to enable statistically reliable judgements as to whether these frequencies and expression levels differ significantly between/among subject groups. Here we introduce flow cytometry data analysis pipeline which includes the Earth Mover's Distance (EMD) metric as solution to this problem. Well known as an informative quantitative measure of differences between distributions, we present three exemplary studies showing that EMD 1) reveals clinically-relevant shifts in two markers on blood basophils responding to an offending allergen; 2) shows that ablative tumor radiation induces significant changes in the murine colon cancer tumor microenvironment; and, 3) ranks immunological differences in mouse peritoneal cavity cells harvested from three genetically distinct mouse strains.

Treatment of Primary Cutaneous CD4 Small/Medium T cell Lymphoproliferative Disorder with Intralesional Triamcinolone Acetonide.

DTIC Science & Technology

2018-02-15

12. REPORT TYPE 02/15/2018 Poster 4. TITLE AND SUBTITLE Treatment of Primary Cutaneous CD4+ Small/Medium T- cell Lymphoproliferative Disorder with...cutaneous CD4+ small/medium T- cell lymphoproliferative disorder (LPD) is a generally indolent cutaneous T- cell proliferation. Most cases follow a benign...lmmunohistochemistry showed diffuse CD3+ CD4+ T- cells without CD30, TIA1 or CD10. A subset of medium to large cells expressed BCL-6. Small subsets of B- cells and CDB

Exploratory subsetting of autism families based on savant skills improves evidence of genetic linkage to 15q11-q13.

PubMed

Nurmi, Erika L; Dowd, Michael; Tadevosyan-Leyfer, Ovsanna; Haines, Jonathan L; Folstein, Susan E; Sutcliffe, James S

2003-07-01

Autism displays a remarkably high heritability but a complex genetic etiology. One approach to identifying susceptibility loci under these conditions is to define more homogeneous subsets of families on the basis of genetically relevant phenotypic or biological characteristics that vary from case to case. The authors performed a principal components analysis, using items from the Autism Diagnostic Interview, which resulted in six clusters of variables, five of which showed significant sib-sib correlation. The utility of these phenotypic subsets was tested in an exploratory genetic analysis of the autism candidate region on chromosome 15q11-q13. When the Collaborative Linkage Study of Autism sample was divided, on the basis of mean proband score for the "savant skills" cluster, the heterogeneity logarithm of the odds under a recessive model at D15S511, within the GABRB3 gene, increased from 0.6 to 2.6 in the subset of families in which probands had greater savant skills. These data are consistent with the genetic contribution of a 15q locus to autism susceptibility in a subset of affected individuals exhibiting savant skills. Similar types of skills have been noted in individuals with Prader-Willi syndrome, which results from deletions of this chromosomal region.

Analysis of thematic mapper simulator data acquired during winter season over Pearl River, Mississippi, test site

NASA Technical Reports Server (NTRS)

Anderson, J. E.; Kalcic, M. T. (Principal Investigator)

1982-01-01

Digital processed aircraft-acquired thematic mapping simulator (TMS) data collected during the winter season over a forested site in southern Mississippi are presented to investigate the utility of TMS data for use in forest inventories and monitoring. Analyses indicated that TMS data are capable of delineating the mixed forest land cover type to an accuracy of 92.5 % correct. The accuracies associated with river bottom forest and pine forest were 95.5 and 91.5 % correct. The accuracies associated with river bottom forest and pine forest were 95.5 and 91.5 % correct, respectively. The figures reflect the performance for products produced using the best subset of channels for each forest cover type. It was found that the choice of channels (subsets) has a significant effect on the accuracy of classification produced, and that the same channels are not the most desirable for all three forest types studied. Both supervised and unsupervised spectral signature development techniques are evaluated; the unsupervised methods proved unacceptable for the three forest types considered.

T Helper 17 Cells Interplay with CD4+CD25highFoxp3+ Tregs in Regulation of Inflammations and Autoimmune Diseases

PubMed Central

Mai, Jietang; Wang, Hong; Yang#, Xiao-Feng

2010-01-01

Interleukin-17 (IL-17)-secreting T helper 17 cells (Th17) are a recently identified CD4+ T helper subset that has been implicated in various inflammatory and autoimmune diseases. Th17, along with CD4+CD25high Foxp3+ regulatory T cells (Tregs) and other newly emergent T helper subsets, Th9 and Tfh, have expanded the Th1-Th2 paradigm. Although this newly proposed six-subset paradigm significantly improved our understanding on the differentiation of CD4+ T helper cell subsets and the regulation of T helper cells in inflammation and autoimmunity, many questions remain to be answered. In this overview, we will briefly review the following issues: a) Old Th1-Th2 paradigm versus new multi-subset paradigm; b) Structural features of IL-17 family cytokines; c) Th17 cells; d) Effects of IL-17 on various cell types and tissues; e) IL-17 receptor and signaling pathways; f) Th17-mediated inflammations; and g) Protective mechanisms of IL-17 in infections. Lastly, we will look into the interaction of Th17 and Treg in autoimmune diseases and inflammation: Th17 cells interplay with Tregs. Regulation of autoimmunity and inflammation lies in the interplays of the different T helper subsets, therefore, better understanding of these subsets’ interactions with one another would greatly improve our approaches in developing therapy to combat inflammatory and autoimmune diseases. PMID:20515737

Automatic Target Recognition: Statistical Feature Selection of Non-Gaussian Distributed Target Classes

DTIC Science & Technology

2011-06-01

implementing, and evaluating many feature selection algorithms. Mucciardi and Gose compared seven different techniques for choosing subsets of pattern...122 THIS PAGE INTENTIONALLY LEFT BLANK 123 LIST OF REFERENCES [1] A. Mucciardi and E. Gose , “A comparison of seven techniques for

Integrating prediction, provenance, and optimization into high energy workflows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schram, M.; Bansal, V.; Friese, R. D.

We propose a novel approach for efficient execution of workflows on distributed resources. The key components of this framework include: performance modeling to quantitatively predict workflow component behavior; optimization-based scheduling such as choosing an optimal subset of resources to meet demand and assignment of tasks to resources; distributed I/O optimizations such as prefetching; and provenance methods for collecting performance data. In preliminary results, these techniques improve throughput on a small Belle II workflow by 20%.

Genetic Basis of Type 1 Diabetes: Similarities and Differences between East and West

PubMed Central

Ikegami, Hiroshi; Noso, Shinsuke; Babaya, Naru; Hiromine, Yoshihisa; Kawabata, Yumiko

2008-01-01

Type 1 diabetes is a multifactorial disease caused by a complex interaction of genetic and environmental factors. The genetic factors involved consist of multiple susceptibility genes, at least five of which, HLA, INS, CTLA4, PTPN22 and IL2RA/CD25, have been shown to be associated with type 1 diabetes in Caucasian (Western) populations, as has recently been confirmed by genome-wide association studies. It has been proposed, however, that the contribution of these genes to type 1 diabetes susceptibility may be different in Asian (Eastern) populations. HLA and INS genes are consistently associated with type 1 diabetes in both Caucasian and Asian populations, but apparent differences in disease-associated alleles and haplotypes are observed between Japanese and Caucasian subjects. The association of CTLA4 with type 1 diabetes is concentrated in a subset of patients with autoimmune thyroid disease (AITD) in both Japanese and Caucasian populations, while the association of PTPN22 with type 1 diabetes in Japanese and most Asian populations is not as clear as in Caucasians. IL2RA/CD25 genes seem to be similarly distributed in type 1 diabetes patients in the two populations, whereas genetic heterogeneity may exist regarding SUMO4, with an association of the M55V variant with type 1 diabetes observed in Asians, but not in Caucasians. Genome-wide association studies (GWA) are largely outstanding for Asian populations but they are now underway in Japan. This review reports on the discovered similarities and differences in susceptibility genes for type 1 diabetes between East and West and discusses the most recent observations made by the involved investigators. PMID:18795209

Comparison of Genetic Algorithm, Particle Swarm Optimization and Biogeography-based Optimization for Feature Selection to Classify Clusters of Microcalcifications

NASA Astrophysics Data System (ADS)

Khehra, Baljit Singh; Pharwaha, Amar Partap Singh

2017-04-01

Ductal carcinoma in situ (DCIS) is one type of breast cancer. Clusters of microcalcifications (MCCs) are symptoms of DCIS that are recognized by mammography. Selection of robust features vector is the process of selecting an optimal subset of features from a large number of available features in a given problem domain after the feature extraction and before any classification scheme. Feature selection reduces the feature space that improves the performance of classifier and decreases the computational burden imposed by using many features on classifier. Selection of an optimal subset of features from a large number of available features in a given problem domain is a difficult search problem. For n features, the total numbers of possible subsets of features are 2n. Thus, selection of an optimal subset of features problem belongs to the category of NP-hard problems. In this paper, an attempt is made to find the optimal subset of MCCs features from all possible subsets of features using genetic algorithm (GA), particle swarm optimization (PSO) and biogeography-based optimization (BBO). For simulation, a total of 380 benign and malignant MCCs samples have been selected from mammogram images of DDSM database. A total of 50 features extracted from benign and malignant MCCs samples are used in this study. In these algorithms, fitness function is correct classification rate of classifier. Support vector machine is used as a classifier. From experimental results, it is also observed that the performance of PSO-based and BBO-based algorithms to select an optimal subset of features for classifying MCCs as benign or malignant is better as compared to GA-based algorithm.

Female-biased dimorphism underlies a female-specific role for post-embryonic Ilp7 neurons in Drosophila fertility

PubMed Central

Castellanos, Monica C.; Tang, Jonathan C. Y.; Allan, Douglas W.

2013-01-01

In Drosophila melanogaster, much of our understanding of sexually dimorphic neuronal development and function comes from the study of male behavior, leaving female behavior less well understood. Here, we identify a post-embryonic population of Insulin-like peptide 7 (Ilp7)-expressing neurons in the posterior ventral nerve cord that innervate the reproductive tracts and exhibit a female bias in their function. They form two distinct dorsal and ventral subsets in females, but only a single dorsal subset in males, signifying a rare example of a female-specific neuronal subset. Female post-embryonic Ilp7 neurons are glutamatergic motoneurons innervating the oviduct and are required for female fertility. In males, they are serotonergic/glutamatergic neuromodulatory neurons innervating the seminal vesicle but are not required for male fertility. In both sexes, these neurons express the sex-differentially spliced fruitless-P1 transcript but not doublesex. The male fruitless-P1 isoform (fruM) was necessary and sufficient for serotonin expression in the shared dorsal Ilp7 subset, but although it was necessary for eliminating female-specific Ilp7 neurons in males, it was not sufficient for their elimination in females. By contrast, sex-specific RNA-splicing by female-specific transformer is necessary for female-type Ilp7 neurons in females and is sufficient for their induction in males. Thus, the emergence of female-biased post-embryonic Ilp7 neurons is mediated in a subset-specific manner by a tra- and fru-dependent mechanism in the shared dorsal subset, and a tra-dependent, fru-independent mechanism in the female-specific subset. These studies provide an important counterpoint to studies of the development and function of male-biased neuronal dimorphism in Drosophila. PMID:23981656

mtDNA variation in the Yanomami: evidence for additional New World founding lineages.

PubMed

Easton, R D; Merriwether, D A; Crews, D E; Ferrell, R E

1996-07-01

Native Americans have been classified into four founding haplogroups with as many as seven founding lineages based on mtDNA RFLPs and DNA sequence data. mtDNA analysis was completed for 83 Yanomami from eight villages in the Surucucu and Catrimani Plateau regions of Roraima in northwestern Brazil. Samples were typed for 15 polymorphic mtDNA sites (14 RFLP sites and 1 deletion site), and a subset was sequenced for both hypervariable regions of the mitochondrial D-loop. Substantial mitochondrial diversity was detected among the Yanomami, five of seven accepted founding haplotypes and three others were observed. Of the 83 samples, 4 (4.8%) were lineage B1, 1 (1.2%) was lineage B2, 31 (37.4%) were lineage C1, 29 (34.9%) were lineage C2, 2 (2.4%) were lineage D1, 6 (7.2%) were lineage D2, 7 (8.4%) were a haplotype we designated "X6," and 3 (3.6%) were a haplotype we designated "X7." Sequence analysis found 43 haplotypes in 50 samples. B2, X6, and X7 are previously unrecognized mitochondrial founding lineage types of Native Americans. The widespread distribution of these haplotypes in the New World and Asia provides support for declaring these lineages to be New World founding types.

mtDNA variation in the Yanomami: evidence for additional New World founding lineages.

PubMed Central

Easton, R. D.; Merriwether, D. A.; Crews, D. E.; Ferrell, R. E.

1996-01-01

Native Americans have been classified into four founding haplogroups with as many as seven founding lineages based on mtDNA RFLPs and DNA sequence data. mtDNA analysis was completed for 83 Yanomami from eight villages in the Surucucu and Catrimani Plateau regions of Roraima in northwestern Brazil. Samples were typed for 15 polymorphic mtDNA sites (14 RFLP sites and 1 deletion site), and a subset was sequenced for both hypervariable regions of the mitochondrial D-loop. Substantial mitochondrial diversity was detected among the Yanomami, five of seven accepted founding haplotypes and three others were observed. Of the 83 samples, 4 (4.8%) were lineage B1, 1 (1.2%) was lineage B2, 31 (37.4%) were lineage C1, 29 (34.9%) were lineage C2, 2 (2.4%) were lineage D1, 6 (7.2%) were lineage D2, 7 (8.4%) were a haplotype we designated "X6," and 3 (3.6%) were a haplotype we designated "X7." Sequence analysis found 43 haplotypes in 50 samples. B2, X6, and X7 are previously unrecognized mitochondrial founding lineage types of Native Americans. The widespread distribution of these haplotypes in the New World and Asia provides support for declaring these lineages to be New World founding types. PMID:8659527

Behçet syndrome: the vascular cluster.

PubMed

Yazıcı, Hasan; Seyahi, Emire

2016-11-17

Although skin-mucosa lesions are common in almost all patients with Behçet syndrome (BS), clinical properties may differ from one patient to another. Within BS, there are subsets with different organ involvement and hence probably different pathological pathways. These subsets can be described as a) solo skin-mucosa disease with no major organ involvement, b) eye disease, c) seronegative spondyloarthropathy-like disease (arthritis, enthesopathy, and folliculitis), d) Crohn-like disease, and finally the topic of this chapter: e) vascular disease. In the vascular disease subset, not surprisingly, several types of vascular involvement may be observed in the same individual. These subsets may make up the total clinical picture all at the same time or step by step with each relapse. Significant correlations exist between cerebral vascular thrombosis and pulmonary artery involvement, intracardiac thrombi and pulmonary artery involvement, Budd-Chiari syndrome, and inferior vena cava syndrome. Lower extremity vein thrombosis is often present in these associations and even precedes them. The recognition of these clusters is not only important in diagnosis and management but also in basic science, including genetic studies.

Alteration of Th17 and Treg cell subpopulations co-exist in patients affected with systemic sclerosis.

PubMed

Fenoglio, Daniela; Battaglia, Florinda; Parodi, Alessia; Stringara, Silvia; Negrini, Simone; Panico, Nicoletta; Rizzi, Marta; Kalli, Francesca; Conteduca, Giuseppina; Ghio, Massimo; De Palma, Raffaele; Indiveri, Francesco; Filaci, Gilberto

2011-06-01

Aim of the study has been to understand the relationship between TH17 and Treg cell subsets in patients affected with systemic sclerosis (SSc). Phenotypes and functions of Th17 and Treg cell subsets were analyzed in a series of 36 SSc patients. Th17 cell concentration in the peripheral blood was found to be increased in SSc patients with respect to healthy controls independently from type or stage of disease. After PBMC stimulation with a polyclonal stimulus or Candida albicans antigens the frequency of Th17 T cell clones was significantly higher in SSc patients with respect to controls suggesting the skewing of immune response in SSc patients toward Th17 cell generation/expansion. Concerning the Treg compartment, both CD4+CD25+ and CD8+CD28- Treg subsets showed quantitative and qualitative alteration in the peripheral blood of SSc patients. Collectively, these data highlight the existence of an imbalanced ratio between Th17 and Treg cell subsets in SSc patients. Copyright © 2011 Elsevier Inc. All rights reserved.

On the Impact of Local Taxes in a Set Cover Game

NASA Astrophysics Data System (ADS)

Escoffier, Bruno; Gourvès, Laurent; Monnot, Jérôme

Given a collection C of weighted subsets of a ground set E, the SET cover problem is to find a minimum weight subset of C which covers all elements of E. We study a strategic game defined upon this classical optimization problem. Every element of E is a player which chooses one set of C where it appears. Following a public tax function, every player is charged a fraction of the weight of the set that it has selected. Our motivation is to design a tax function having the following features: it can be implemented in a distributed manner, existence of an equilibrium is guaranteed and the social cost for these equilibria is minimized.

Implementation of a fully-balanced periodic tridiagonal solver on a parallel distributed memory architecture

NASA Technical Reports Server (NTRS)

Eidson, T. M.; Erlebacher, G.

1994-01-01

While parallel computers offer significant computational performance, it is generally necessary to evaluate several programming strategies. Two programming strategies for a fairly common problem - a periodic tridiagonal solver - are developed and evaluated. Simple model calculations as well as timing results are presented to evaluate the various strategies. The particular tridiagonal solver evaluated is used in many computational fluid dynamic simulation codes. The feature that makes this algorithm unique is that these simulation codes usually require simultaneous solutions for multiple right-hand-sides (RHS) of the system of equations. Each RHS solutions is independent and thus can be computed in parallel. Thus a Gaussian elimination type algorithm can be used in a parallel computation and the more complicated approaches such as cyclic reduction are not required. The two strategies are a transpose strategy and a distributed solver strategy. For the transpose strategy, the data is moved so that a subset of all the RHS problems is solved on each of the several processors. This usually requires significant data movement between processor memories across a network. The second strategy attempts to have the algorithm allow the data across processor boundaries in a chained manner. This usually requires significantly less data movement. An approach to accomplish this second strategy in a near-perfect load-balanced manner is developed. In addition, an algorithm will be shown to directly transform a sequential Gaussian elimination type algorithm into the parallel chained, load-balanced algorithm.

Identity and Diversity of Human Peripheral Th and T Regulatory Cells Defined by Single-Cell Mass Cytometry.

PubMed

Kunicki, Matthew A; Amaya Hernandez, Laura C; Davis, Kara L; Bacchetta, Rosa; Roncarolo, Maria-Grazia

2018-01-01

Human CD3 + CD4 + Th cells, FOXP3 + T regulatory (Treg) cells, and T regulatory type 1 (Tr1) cells are essential for ensuring peripheral immune response and tolerance, but the diversity of Th, Treg, and Tr1 cell subsets has not been fully characterized. Independent functional characterization of human Th1, Th2, Th17, T follicular helper (Tfh), Treg, and Tr1 cells has helped to define unique surface molecules, transcription factors, and signaling profiles for each subset. However, the adequacy of these markers to recapitulate the whole CD3 + CD4 + T cell compartment remains questionable. In this study, we examined CD3 + CD4 + T cell populations by single-cell mass cytometry. We characterize the CD3 + CD4 + Th, Treg, and Tr1 cell populations simultaneously across 23 memory T cell-associated surface and intracellular molecules. High-dimensional analysis identified several new subsets, in addition to the already defined CD3 + CD4 + Th, Treg, and Tr1 cell populations, for a total of 11 Th cell, 4 Treg, and 1 Tr1 cell subsets. Some of these subsets share markers previously thought to be selective for Treg, Th1, Th2, Th17, and Tfh cells, including CD194 (CCR4) + FOXP3 + Treg and CD183 (CXCR3) + T-bet + Th17 cell subsets. Unsupervised clustering displayed a phenotypic organization of CD3 + CD4 + T cells that confirmed their diversity but showed interrelation between the different subsets, including similarity between Th1-Th2-Tfh cell populations and Th17 cells, as well as similarity of Th2 cells with Treg cells. In conclusion, the use of single-cell mass cytometry provides a systems-level characterization of CD3 + CD4 + T cells in healthy human blood, which represents an important baseline reference to investigate abnormalities of different subsets in immune-mediated pathologies. Copyright © 2017 by The American Association of Immunologists, Inc.

Moderate physical activity of music aerobic exercise increases lymphocyte counts, specific subsets, and differentiation.

PubMed

Yeh, Shu-Hui; Lai, Hsiu-Ling; Hsiao, Chiu-Yueh; Lin, Li-Wei; Chuang, Yu-Kuan; Yang, Yu-Yeng; Yang, Kuender D

2014-09-01

Moderate physical activity has been shown to promote immunity. Different moderate physical activities may have different effects on immunity. This study investigated the impacts of a 12-week regular music aerobic exercise (MAE) program on leukocyte distribution, lymphocyte subsets, and lymphocyte polarization. The study used a case-control design with pretest and posttest. Forty-seven middle-age women were recruited for this study. Three participants dropped out, 22 completed the 12-week MAE program, and the other 22 participants who had heat-intolerance or limited schedule eligibility were enrolled as the control group without the MAE exercise. Results showed that the MAE exercise for 12 weeks didn't change red blood cells or total leukocytes but increased lymphocyte counts. The women in MAE group revealed significant increases (P ≤ 0.01) of CD3CD4, CD3CD8, and CD4CD25 cells, associated with Treg polarization showing enhanced FoxP3 but not T-bet, Gata-3, or RORγT expression (P < .01). The control group without exercise revealed insignificant change of lymphocyte subsets or lymphocyte polarization. This study shows that MAE increases specific lymphocyte subsets and enhances Treg cell differentiation. It is suggested to encourage moderate physical activity of music aerobic exercise to enhance lymphocyte function of middle-aged women.

Microbiota of the Small Intestine Is Selectively Engulfed by Phagocytes of the Lamina Propria and Peyer’s Patches

PubMed Central

Morikawa, Masatoshi; Tsujibe, Satoshi; Kiyoshima-Shibata, Junko; Watanabe, Yohei; Kato-Nagaoka, Noriko; Shida, Kan; Matsumoto, Satoshi

2016-01-01

Phagocytes such as dendritic cells and macrophages, which are distributed in the small intestinal mucosa, play a crucial role in maintaining mucosal homeostasis by sampling the luminal gut microbiota. However, there is limited information regarding microbial uptake in a steady state. We investigated the composition of murine gut microbiota that is engulfed by phagocytes of specific subsets in the small intestinal lamina propria (SILP) and Peyer’s patches (PP). Analysis of bacterial 16S rRNA gene amplicon sequences revealed that: 1) all the phagocyte subsets in the SILP primarily engulfed Lactobacillus (the most abundant microbe in the small intestine), whereas CD11bhi and CD11bhiCD11chi cell subsets in PP mostly engulfed segmented filamentous bacteria (indigenous bacteria in rodents that are reported to adhere to intestinal epithelial cells); and 2) among the Lactobacillus species engulfed by the SILP cell subsets, L. murinus was engulfed more frequently than L. taiwanensis, although both these Lactobacillus species were abundant in the small intestine under physiological conditions. These results suggest that small intestinal microbiota is selectively engulfed by phagocytes that localize in the adjacent intestinal mucosa in a steady state. These observations may provide insight into the crucial role of phagocytes in immune surveillance of the small intestinal mucosa. PMID:27701454

Microbiota of the Small Intestine Is Selectively Engulfed by Phagocytes of the Lamina Propria and Peyer's Patches.

PubMed

Morikawa, Masatoshi; Tsujibe, Satoshi; Kiyoshima-Shibata, Junko; Watanabe, Yohei; Kato-Nagaoka, Noriko; Shida, Kan; Matsumoto, Satoshi

2016-01-01

Phagocytes such as dendritic cells and macrophages, which are distributed in the small intestinal mucosa, play a crucial role in maintaining mucosal homeostasis by sampling the luminal gut microbiota. However, there is limited information regarding microbial uptake in a steady state. We investigated the composition of murine gut microbiota that is engulfed by phagocytes of specific subsets in the small intestinal lamina propria (SILP) and Peyer's patches (PP). Analysis of bacterial 16S rRNA gene amplicon sequences revealed that: 1) all the phagocyte subsets in the SILP primarily engulfed Lactobacillus (the most abundant microbe in the small intestine), whereas CD11bhi and CD11bhiCD11chi cell subsets in PP mostly engulfed segmented filamentous bacteria (indigenous bacteria in rodents that are reported to adhere to intestinal epithelial cells); and 2) among the Lactobacillus species engulfed by the SILP cell subsets, L. murinus was engulfed more frequently than L. taiwanensis, although both these Lactobacillus species were abundant in the small intestine under physiological conditions. These results suggest that small intestinal microbiota is selectively engulfed by phagocytes that localize in the adjacent intestinal mucosa in a steady state. These observations may provide insight into the crucial role of phagocytes in immune surveillance of the small intestinal mucosa.

Misleading prioritizations from modelling range shifts under climate change

Treesearch

Helen R. Sofaer; Catherine S. Jarnevich; Curtis H. Flather

2018-01-01

Conservation planning requires the prioritization of a subset of taxa and geographical locations to focus monitoring and management efforts. Integration of the threats and opportunities posed by climate change often relies on predictions from species distribution models, particularly for assessments of vulnerability or invasion risk for multiple taxa. We evaluated...

A probabilistic Sperner's theorem, with applications to the problem of retrieving information from a data base

NASA Technical Reports Server (NTRS)

Baumert, L. D.; Mceliece, R. J.; Rodemich, E. R.; Rumsey, H., Jr.

1978-01-01

The design of an optimal merged keycode data base information retrieval system is detailed. A probability distribution of n-bit binary words that minimized false drops was developed for the case where the set of desired records was a subset of tagged records.

Multiple-Matrix Sampling: A Technique for Maximizing the Effectiveness of Lengthy Survey Instruments.

ERIC Educational Resources Information Center

Shemick, John M.

1983-01-01

In a project to identify and verify professional competencies for beginning industrial education teachers, researchers found a 173-item questionnaire unwieldy. Using multiple-matrix sampling, they distributed subsets of items to respondents, resulting in adequate returns as well as duplication, postage, and time savings. (SK)

Flow cytometry analysis of T-cell subsets in cerebrospinal fluid of narcolepsy type 1 patients with long-lasting disease.

PubMed

Moresco, Monica; Lecciso, Mariangela; Ocadlikova, Darina; Filardi, Marco; Melzi, Silvia; Kornum, Birgitte Rahbek; Antelmi, Elena; Pizza, Fabio; Mignot, Emmanuel; Curti, Antonio; Plazzi, Giuseppe

2018-04-01

Type 1 narcolepsy (NT1) is a central hypersomnia linked to the destruction of hypocretin-producing neurons. A great body of genetic and epidemiological data points to likely autoimmune disease aetiology. Recent reports have characterized peripheral blood T-cell subsets in NT1, whereas data regarding the cerebrospinal fluid (CSF) immune cell composition are lacking. The current study aimed to characterize the T-cell and natural killer (NK) cell subsets in NT1 patients with long disease course. Immune cell subsets from CSF and peripheral blood mononuclear cell (PBMC) samples were analysed by flow cytometry in two age-balanced and sex-balanced groups of 14 NT1 patients versus 14 healthy controls. The frequency of CSF cell groups was compared with PBMCs. Non-parametric tests were used for statistical analyses. The NT1 patients did not show significant differences of CSF immune cell subsets compared to controls, despite a trend towards higher CD4 + terminally differentiated effector memory T cells. T cells preferentially displayed a memory phenotype in the CSF compared to PBMCs. Furthermore, a reduced frequency of CD4 + terminally differentiated effector memory T cells and an increased frequency of NK CD56 bright cells was observed in PBMCs from patients compared to controls. Finally, the ratio between CSF and peripheral CD4 + terminally differentiated effector memory T cells was two-fold increased in NT1 patients versus controls. Significant differences in PBMCs and in CSF/PBMC ratios of immune cell profile were found in NT1 patients compared to healthy controls. These differences might have arisen from the different HLA status, or be primary or secondary to hypocretin deficiency. Further functional studies in patients close to disease onset are required to understand NT1 pathophysiology. Copyright © 2017 Elsevier B.V. All rights reserved.

Oxytocin signaling in mouse taste buds.

PubMed

Sinclair, Michael S; Perea-Martinez, Isabel; Dvoryanchikov, Gennady; Yoshida, Masahide; Nishimori, Katsuhiko; Roper, Stephen D; Chaudhari, Nirupa

2010-08-05

The neuropeptide, oxytocin (OXT), acts on brain circuits to inhibit food intake. Mutant mice lacking OXT (OXT knockout) overconsume salty and sweet (i.e. sucrose, saccharin) solutions. We asked if OXT might also act on taste buds via its receptor, OXTR. Using RT-PCR, we detected the expression of OXTR in taste buds throughout the oral cavity, but not in adjacent non-taste lingual epithelium. By immunostaining tissues from OXTR-YFP knock-in mice, we found that OXTR is expressed in a subset of Glial-like (Type I) taste cells, and also in cells on the periphery of taste buds. Single-cell RT-PCR confirmed this cell-type assignment. Using Ca2+ imaging, we observed that physiologically appropriate concentrations of OXT evoked [Ca2+]i mobilization in a subset of taste cells (EC50 approximately 33 nM). OXT-evoked responses were significantly inhibited by the OXTR antagonist, L-371,257. Isolated OXT-responsive taste cells were neither Receptor (Type II) nor Presynaptic (Type III) cells, consistent with our immunofluorescence observations. We also investigated the source of OXT peptide that may act on taste cells. Both RT-PCR and immunostaining suggest that the OXT peptide is not produced in taste buds or in their associated nerves. Finally, we also examined the morphology of taste buds from mice that lack OXTR. Taste buds and their constituent cell types appeared very similar in mice with two, one or no copies of the OXTR gene. We conclude that OXT elicits Ca2+ signals via OXTR in murine taste buds. OXT-responsive cells are most likely a subset of Glial-like (Type I) taste cells. OXT itself is not produced locally in taste tissue and is likely delivered through the circulation. Loss of OXTR does not grossly alter the morphology of any of the cell types contained in taste buds. Instead, we speculate that OXT-responsive Glial-like (Type I) taste bud cells modulate taste signaling and afferent sensory output. Such modulation would complement central pathways of appetite regulation that employ circulating homeostatic and satiety signals.

Human papillomavirus prevalence and type distribution in penile carcinoma.

PubMed

Miralles-Guri, C; Bruni, L; Cubilla, A L; Castellsagué, X; Bosch, F X; de Sanjosé, S

2009-10-01

Penile carcinoma is an uncommon and potentially mutilating disease with a heterogeneous aetiology. Several risk factors have been established for its development. Human papillomavirus (HPV) infection seems to play an important role in the development of a subset of these carcinomas and its presence is thought to be related to the histological type. HPV prevalence in penile tumours is reported to be associated to a variety of morphological changes. Its determination will provide a better estimate for HPV related cancer burden and its preventable fraction. A systematic and comprehensive literature review of the major penile cancer studies published from 1986 until June 2008 evaluating the HPV prevalence among the different histological types was carried out. 31 studies including 1466 penile carcinomas were reviewed. Global HPV prevalence was 46.9%. Relative contribution was: HPV-16 (60.23%), HPV-18 (13.35%), HPV-6/11 (8.13%), HPV-31 (1.16%), HPV-45 (1.16%), HPV-33 (0.97%), HPV-52 (0.58%), other types (2.47%). Assessment of multiple infections contribution is limited due to study design. Basaloid and warty squamous cell carcinomas were the most frequent HPV-related histological types, but keratinising and non-keratinising subtypes also showed prevalence rates of around 50%. About half of the penile tumours were associated with HPV 16-18 with little presence of other genotypes. Research on the mechanisms behind penile carcinogenesis is warranted. Available HPV vaccines are likely to be effective in penile tumours.

Multi-Locus Sequence Typing of Bartonella henselae Isolates from Three Continents Reveals Hypervirulent and Feline-Associated Clones

PubMed Central

Arvand, Mardjan; Feil, Edward J.; Giladi, Michael; Boulouis, Henri-Jean; Viezens, Juliane

2007-01-01

Bartonella henselae is a zoonotic pathogen and the causative agent of cat scratch disease and a variety of other disease manifestations in humans. Previous investigations have suggested that a limited subset of B. henselae isolates may be associated with human disease. In the present study, 182 human and feline B. henselae isolates from Europe, North America and Australia were analysed by multi-locus sequence typing (MLST) to detect any associations between sequence type (ST), host species and geographical distribution of the isolates. A total of 14 sequence types were detected, but over 66% (16/24) of the isolates recovered from human disease corresponded to a single genotype, ST1, and this type was detected in all three continents. In contrast, 27.2% (43/158) of the feline isolates corresponded to ST7, but this ST was not recovered from humans and was restricted to Europe. The difference in host association of STs 1 (human) and 7 (feline) was statistically significant (P≤0.001). eBURST analysis assigned the 14 STs to three clonal lineages, which contained two or more STs, and a singleton comprising ST7. These groups were broadly consistent with a neighbour-joining tree, although splits decomposition analysis was indicative of a history of recombination. These data indicate that B. henselae lineages differ in their virulence properties for humans and contribute to a better understanding of the population structure of B. henselae. PMID:18094753

A global analysis of bird plumage patterns reveals no association between habitat and camouflage.

PubMed

Somveille, Marius; Marshall, Kate L A; Gluckman, Thanh-Lan

2016-01-01

Evidence suggests that animal patterns (motifs) function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types-mottled (irregular), scales, bars and spots (regular)-and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species' geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world's birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world's eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis.

Genetics Home Reference: mucopolysaccharidosis type III

MedlinePlus

... breakdown of a subset of GAGs called heparan sulfate. MPS IIIA is caused by mutations in the ... of these enzymes disrupts the breakdown of heparan sulfate. As a result, partially broken down heparan sulfate ...

New Developments in Uncertainty: Linking Risk Management, Reliability, Statistics and Stochastic Optimization

DTIC Science & Technology

2014-11-13

Cm) in a given set C ⊂ IRm . (5.7) Motivation for generalized regression comes from applications in which Y has the cost/loss orien- tation that we have...distribution. The corresponding probability measure on IRm is induced then by the multivariate distribution function FV1,...,Vm(v1, . . . , vm) = prob { (V1...could be generated by future observations of some variables V1, . . . , Vm, as above, in which case Ω would be a subset of IRm with elements ω = (v1

Threshold quantum cryptography

NASA Astrophysics Data System (ADS)

Tokunaga, Yuuki; Okamoto, Tatsuaki; Imoto, Nobuyuki

2005-01-01

We present the concept of threshold collaborative unitary transformation or threshold quantum cryptography, which is a kind of quantum version of threshold cryptography. Threshold quantum cryptography states that classical shared secrets are distributed to several parties and a subset of them, whose number is greater than a threshold, collaborates to compute a quantum cryptographic function, while keeping each share secretly inside each party. The shared secrets are reusable if no cheating is detected. As a concrete example of this concept, we show a distributed protocol (with threshold) of conjugate coding.

[Effect of G-CSF in vitro Stimulation on Distribution of Peripheral Lymphocyte Subsets in the Healthy Persons].

PubMed

Zhao, Sha-Sha; Fang, Shu; Zhu, Cheng-Ying; Wang, Li-Li; Gao, Chun-Ji

2018-02-01

To investigate the effect of granulocyte-colony stimulating factor (G-CSF) in vitro stimulation on the distribution of lymphocyte subset in healthy human. Peripheral blood mononuclear cells (PBMNCs) were collected from 8 healthy volunteers by density gradient centrifugation on Ficoll-Paque TM . In vitro 200 ng/ml G-CSF or 200 ng/ml G-CSF plus 10 µg/ml ConA directly act on PBMNCs, then the colleted cells were cultivated for 3 days. Lymphocyte subsets were stained with the corresponding fluoresce labeled antibodies and detected by flow cytometry. The levels of T cells in G-CSF group and G-CSF+ConA group were both higher than that in the control group (P<0.001, P<0.05). However, there were not significantly different in B cells and NK cells levels among the 3 groups. Furthermore, analysis of the effect of G-CSF on T cell subsets indicated that the levels of CD4 + T cells and CD8 + T cells in G-CSF group were both significantly higher than those in control group (P<0.01, P<0.05), Treg cells was not different between G-CSF and control group. Compared with the control group, the level of CD4 + T cells, CD8 + T cells and Treg cells in G-CSF+ConA group significantly increased (P<0.05, P<0.01, P<0.01). Analysis of G-CSF receptor (G-CSFR) expression showed that G-CSFR expression on T cells in G-CSF+ConA group dramatically increased, as compared with control group (P<0.01). The levels of CD4 + T cells and CD8 + T cells in healthy human peripheral blood can be increased by G-CSF stimulation. ConA can enhance the level of T cells and induce G-CSFR expression on T cells.

Altered distribution of peripheral blood dendritic cell subsets in patients with pulmonary paracoccidioidomycosis.

PubMed

Venturini, James; Cavalcante, Ricardo Souza; Moris, Daniela Vanessa; Golim, Márjorie de Assis; Levorato, Adriele Dandara; Reis, Karoline Hagatha Dos; Arruda, Maria Sueli Parreira de; Mendes, Rinaldo Poncio

2017-09-01

Paracoccidioidomycosis (PCM) is a systemic mycosis caused by fungi from the genus Paracoccidioides in Latin America. PCM-patients (PCM-p) are classified as having acute/subacute or chronic (CF) clinical forms. CF is responsible for 75%-90% of all cases, affects mainly adults over 30 years old and the clinical manifestation are associated mainly with lungs and mucosa of upper airdigestive tract. In addition, the CF patients exhibit fibrosis of the lungs, oral mucous membranes and adrenals, and pulmonary emphysema. Consequently, CF PCM-p with active disease, as well as those that have been apparently cured, seem to be an interesting model for studies aiming to understand the long-term host-fungi relationship and hypoxia. Dendritic cells (DCs) constitute a system that serve as a major link between innate and adaptive immunity composed of several subpopulations of cells including two main subsets: myeloid (mDCs) and plasmacytoid (pDCs). The present study aimed to access the distribution of PBDC subsets of CF PCM-p who were not treated (NT) or treated (apparently cured - AC). CF PCM-p were categorized into two groups, consisting of 9 NTs and 9 ACs. Twenty-one healthy individuals were used as the control group. The determination of the PBDC subsets was performed by FACS (fluorescence-activated cell sorting) and the dosage of serum TNF-α, IL1β, IL-18, CCL3, IL-10 and basic fibroblast growth factor (bFGF) by ELISA (enzyme-linked immunosorbent assay). A high count and percentage of mDCs was observed before treatment, along with a low count of pDCs in treated patients. Furthermore, the mDC:pDC ratio and serum levels of TNF-α was higher in both of the PCM-p groups than in the control group. In conclusion, our findings demonstrated that active PCM influences the distribution of mDCs and pDCs, and after treatment, PCM-p retained a lower count of pDCs associated with pro-inflammatory profile. Therefore, we identified new evidences of persistent immunological abnormalities in PCM-p after treatment. Even these patients showing fungal clearance after successful antifungal treatment; the hypoxia, triggered by the persistent pulmonary sequelae, possibly continues to interfere in the immune response. Copyright © 2017 Elsevier B.V. All rights reserved.

Higher Improvement in Patient-Reported Outcomes Can Be Achieved After Transforaminal Lumbar Interbody Fusion for Clinical and Radiographic Degenerative Spondylolisthesis Classification Type D Degenerative Lumbar Spondylolisthesis.

PubMed

Chen, Xi; Xu, Liang; Qiu, Yong; Chen, Zhong-Hui; Zhou, Qing-Shuang; Li, Song; Sun, Xu

2018-06-01

Clinical and radiographic degenerative spondylolisthesis (CARDS) classification defines a distinct subset of patients with kyphotic angulation at the involved segment (type D). Research using CARDS classification to investigate motion characteristics at involved segments or patient-related outcomes (PROs) following surgical intervention is sparse. We investigated the relationship between CARDS type D spondylolisthesis and dynamic instability and PROs in type D versus non-type D spondylolisthesis. We reviewed consecutive patients who received transforaminal lumbar interbody fusion for L4-5 spondylolisthesis between 2009 and 2015. Patients were assigned into type D and non-type D groups. Translational motion was determined by upright lumbar lateral radiography with supine sagittal magnetic resonance imaging or flexion and extension radiography. Demographics, radiographic parameters, and PROs were evaluated. Type D and non-type D groups comprised 34 and 163 patients, respectively. Compared with non-type D, type D group was characterized by lordotic angulation loss and higher degree of olisthesis on upright radiographs and demonstrated higher translational motion on upright lumbar lateral radiography with supine sagittal magnetic resonance imaging analysis. After surgery, mean reduction rate was significantly higher in type D group; type D had less slippage, but differences in slip angle and disc height were not significant. Preoperative Oswestry Disability Index and visual analog scale for back pain scores were higher in type D group. Type D spondylolisthesis and dynamic instability were associated with achieving minimal clinically important differences in PROs. CARDS type D spondylolisthesis is a distinct subset associated with dynamic instability and worse PROs. Higher improvement in PROs can be achieved in CARDS type D spondylolisthesis after surgery. Copyright © 2018 Elsevier Inc. All rights reserved.

The involvement of plasmacytoid cells in HIV infection and pathogenesis.

PubMed

Aiello, Alessandra; Giannessi, Flavia; Percario, Zulema A; Affabris, Elisabetta

2018-04-01

Plasmacytoid dendritic cells (pDCs) are a unique dendritic cell subset that are specialized in type I interferon (IFN) production. pDCs are key players in the antiviral immune response and serve as bridge between innate and adaptive immunity. Although pDCs do not represent the main reservoir of the Human Immunodeficiency Virus (HIV), they are a crucial subset in HIV infection as they influence viral transmission, target cell infection and antigen presentation. pDCs act as inflammatory and immunosuppressive cells, thus contributing to HIV disease progression. This review provides a state of art analysis of the interactions between HIV and pDCs and their potential roles in HIV transmission, chronic immune activation and immunosuppression. A thorough understanding of the roles of pDCs in HIV infection will help to improve therapeutic strategies to fight HIV infection, and will further increase our knowledge on this important immune cell subset. Copyright © 2018 Elsevier Ltd. All rights reserved.

A comparison of small-mammal communities in a desert riparian floodplain

USGS Publications Warehouse

Ellison, Laura E.; van Riper, Charles

1998-01-01

We compared small-mammal communities between inactive floodplain and actively flooded terraces of riparian habitat in the Verde Valley of central Arizona. We used species diversity, abundance, weight of adult males, number of juveniles, number of reproductively active individuals, longevity, residency status, and patterns of microhabitat use to compare the two communities. Although abundances of small mammals tended to be higher in the active floodplain, species diversity was greater in the inactive floodplain. Results were inconsistent with our initial prediction that actively flooded riparian habitat acts as a species source, whereas inactive floodplain acts as a sink or dispersal site for small mammals. Within each habitat type, we found evidence of significant microhabitat separation among the three most abundant small-mammal species (Peromyscus boylii, P. eremicus, and Neotoma albigula). Percent cover by annual and perennial grasses and shrubs, substrate, and frequency of shrubs, trees, and debris were significant determinants of small-mammal distribution within a habitat type. We found that the three most abundant species selected a nonrandom subset of available habitat. Nonrandom use of habitat and microhabitat separation were the two most important mechanisms structuring small-mammal communities in riparian habitat of central Arizona.

Enhancing the Discrimination Ability of a Gas Sensor Array Based on a Novel Feature Selection and Fusion Framework.

PubMed

Deng, Changjian; Lv, Kun; Shi, Debo; Yang, Bo; Yu, Song; He, Zhiyi; Yan, Jia

2018-06-12

In this paper, a novel feature selection and fusion framework is proposed to enhance the discrimination ability of gas sensor arrays for odor identification. Firstly, we put forward an efficient feature selection method based on the separability and the dissimilarity to determine the feature selection order for each type of feature when increasing the dimension of selected feature subsets. Secondly, the K-nearest neighbor (KNN) classifier is applied to determine the dimensions of the optimal feature subsets for different types of features. Finally, in the process of establishing features fusion, we come up with a classification dominance feature fusion strategy which conducts an effective basic feature. Experimental results on two datasets show that the recognition rates of Database I and Database II achieve 97.5% and 80.11%, respectively, when k = 1 for KNN classifier and the distance metric is correlation distance (COR), which demonstrates the superiority of the proposed feature selection and fusion framework in representing signal features. The novel feature selection method proposed in this paper can effectively select feature subsets that are conducive to the classification, while the feature fusion framework can fuse various features which describe the different characteristics of sensor signals, for enhancing the discrimination ability of gas sensors and, to a certain extent, suppressing drift effect.

Modeling Booklet Effects for Nonequivalent Group Designs in Large-Scale Assessment

ERIC Educational Resources Information Center

Hecht, Martin; Weirich, Sebastian; Siegle, Thilo; Frey, Andreas

2015-01-01

Multiple matrix designs are commonly used in large-scale assessments to distribute test items to students. These designs comprise several booklets, each containing a subset of the complete item pool. Besides reducing the test burden of individual students, using various booklets allows aligning the difficulty of the presented items to the assumed…

Network Access to Visual Information: A Study of Costs and Uses.

ERIC Educational Resources Information Center

Besser, Howard

This paper summarizes a subset of the findings of a study of digital image distribution that focused on the Museum Educational Site Licensing (MESL) project--the first large-scale multi-institutional project to explore digital delivery of art images and accompanying text/metadata from disparate sources. This Mellon Foundation-sponsored study…

Isotropic probability measures in infinite-dimensional spaces

NASA Technical Reports Server (NTRS)

Backus, George

1987-01-01

Let R be the real numbers, R(n) the linear space of all real n-tuples, and R(infinity) the linear space of all infinite real sequences x = (x sub 1, x sub 2,...). Let P sub in :R(infinity) approaches R(n) be the projection operator with P sub n (x) = (x sub 1,...,x sub n). Let p(infinity) be a probability measure on the smallest sigma-ring of subsets of R(infinity) which includes all of the cylinder sets P sub n(-1) (B sub n), where B sub n is an arbitrary Borel subset of R(n). Let p sub n be the marginal distribution of p(infinity) on R(n), so p sub n(B sub n) = p(infinity) (P sub n to the -1 (B sub n)) for each B sub n. A measure on R(n) is isotropic if it is invariant under all orthogonal transformations of R(n). All members of the set of all isotropic probability distributions on R(n) are described. The result calls into question both stochastic inversion and Bayesian inference, as currently used in many geophysical inverse problems.

The model of palliative care in the perinatal setting: a review of the literature

PubMed Central

2012-01-01

Background The notion of Palliative Care (PC) in neonatal and perinatal medicine has largely developed in recent decades. Our aim was to systematically review the literature on this topic, summarise the evolution of care and, based on the available data, suggest a current standard for this type of care. Methods Data sources included Medline, the Cochrane Library, CINAHL, and the bibliographies of the papers retrieved. Articles focusing on neonatal/perinatal hospices or PC were included. A qualitative analysis of the content was performed, and data on the lead author, country, year, type of article or design, and direct and indirect subjects were obtained. Results Among the 1558 articles retrieved, we did not find a single quantitative empirical study. To study the evolution of the model of care, we ultimately included 101 studies, most of which were from the USA. Fifty of these were comments/reflections, and only 30 were classifiable as clinical studies (half of these were case reports). The analysis revealed a gradual conceptual evolution of the model, which includes the notions of family-centered care, comprehensive care (including bereavement) and early and integrative care (also including the antenatal period). A subset of 27 articles that made special mention of antenatal aspects showed a similar distribution. In this subset, the results of the four descriptive clinical studies showed that, in the context of specific programmes, a significant number of couples (between 37 and 87%) opted for PC and to continue with the pregnancy when the foetus has been diagnosed with a lethal illness. Conclusions Despite the interest that PC has aroused in perinatal medicine, there are no evidence-based empirical studies to indicate the best model of care for this clinical setting. The very notion of PC has evolved to encompass perinatal PC, which includes, among other things, the idea of comprehensive care, and early and integrative care initiated antenatally. PMID:22409881

Effectiveness of a web-based automated cell distribution system.

PubMed

Niland, Joyce C; Stiller, Tracey; Cravens, James; Sowinski, Janice; Kaddis, John; Qian, Dajun

2010-01-01

In recent years, industries have turned to the field of operations research to help improve the efficiency of production and distribution processes. Largely absent is the application of this methodology to biological materials, such as the complex and costly procedure of human pancreas procurement and islet isolation. Pancreatic islets are used for basic science research and in a promising form of cell replacement therapy for a subset of patients afflicted with severe type 1 diabetes mellitus. Having an accurate and reliable system for cell distribution is therefore crucial. The Islet Cell Resource Center Consortium was formed in 2001 as the first and largest cooperative group of islet production and distribution facilities in the world. We previously reported on the development of a Matching Algorithm for Islet Distribution (MAID), an automated web-based tool used to optimize the distribution of human pancreatic islets by matching investigator requests to islet characteristics. This article presents an assessment of that algorithm and compares it to the manual distribution process used prior to MAID. A comparison was done using an investigator's ratio of the number of islets received divided by the number requested pre- and post-MAID. Although the supply of islets increased between the pre- versus post-MAID period, the median received-to-requested ratio remained around 60% due to an increase in demand post-MAID. A significantly smaller variation in the received-to-requested ratio was achieved in the post- versus pre-MAID period. In particular, the undesirable outcome of providing users with more islets than requested, ranging up to four times their request, was greatly reduced through the algorithm. In conclusion, this analysis demonstrates, for the first time, the effectiveness of using an automated web-based cell distribution system to facilitate efficient and consistent delivery of human pancreatic islets by enhancing the islet matching process.

Mycobacterium leprae in Colombia described by SNP7614 in gyrA, two minisatellites and geography.

PubMed

Cardona-Castro, Nora; Beltrán-Alzate, Juan Camilo; Romero-Montoya, Irma Marcela; Li, Wei; Brennan, Patrick J; Vissa, Varalakshmi

2013-03-01

New cases of leprosy are still being detected in Colombia after the country declared achievement of the WHO defined 'elimination' status. To study the ecology of leprosy in endemic regions, a combination of geographic and molecular tools were applied for a group of 201 multibacillary patients including six multi-case families from eleven departments. The location (latitude and longitude) of patient residences were mapped. Slit skin smears and/or skin biopsies were collected and DNA was extracted. Standard agarose gel electrophoresis following a multiplex PCR-was developed for rapid and inexpensive strain typing of Mycobacterium leprae based on copy numbers of two VNTR minisatellite loci 27-5 and 12-5. A SNP (C/T) in gyrA (SNP7614) was mapped by introducing a novel PCR-RFLP into an ongoing drug resistance surveillance effort. Multiple genotypes were detected combining the three molecular markers. The two frequent genotypes in Colombia were SNP7614(C)/27-5(5)/12-5(4) [C54] predominantly distributed in the Atlantic departments and SNP7614 (T)/27-5(4)/12-5(5) [T45] associated with the Andean departments. A novel genotype SNP7614 (C)/27-5(6)/12-5(4) [C64] was detected in cities along the Magdalena river which separates the Andean from Atlantic departments; a subset was further characterized showing association with a rare allele of minisatellite 23-3 and the SNP type 1 of M. leprae. The genotypes within intra-family cases were conserved. Overall, this is the first large scale study that utilized simple and rapid assay formats for identification of major strain types and their distribution in Colombia. It provides the framework for further strain type discrimination and geographic information systems as tools for tracing transmission of leprosy. Copyright © 2012 Elsevier B.V. All rights reserved.

TCGA's Testicular Germ Cell Tumor Study - TCGA

Cancer.gov

TCGA network researchers identify molecular characteristics that classify testicular germ cell tumor types, including a separate subset of seminomas defined by KIT mutations. This provides a set of candidate biomarkers for risk stratification and potential therapeutic targeting.

Dendritic cell subsets in type 1 diabetes: friend or foe?

PubMed

Morel, Penelope A

2013-12-06

Type 1 diabetes (T1D) is a T cell mediated autoimmune disease characterized by immune mediated destruction of the insulin-producing β cells in the islets of Langerhans. Dendritic cells (DC) have been implicated in the pathogenesis of T1D and are also used as immunotherapeutic agents. Plasmacytoid (p)DC have been shown to have both protective and pathogenic effects and a newly described merocytic DC population has been shown to break tolerance in the mouse model of T1D, the non-obese diabetic (NOD) mouse. We have used DC populations to prevent the onset of T1D in NOD mice and clinical trials of DC therapy in T1D diabetes have been initiated. In this review we will critically examine the recent published literature on the role of DC subsets in the induction and regulation of the autoimmune response in T1D.

A Novel Collection of snRNA-Like Promoters with Tissue-Specific Transcription Properties

PubMed Central

Garritano, Sonia; Gigoni, Arianna; Costa, Delfina; Malatesta, Paolo; Florio, Tullio; Cancedda, Ranieri; Pagano, Aldo

2012-01-01

We recently identified a novel dataset of snRNA-like trascriptional units in the human genome. The investigation of a subset of these elements showed that they play relevant roles in physiology and/or pathology. In this work we expand our collection of small RNAs taking advantage of a newly developed algorithm able to identify genome sequence stretches with RNA polymerase (pol) III type 3 promoter features thus constituting putative pol III binding sites. The bioinformatic analysis of a subset of these elements that map in introns of protein-coding genes in antisense configuration suggest their association with alternative splicing, similarly to other recently characterized small RNAs. Interestingly, the analysis of the transcriptional activity of these novel promoters shows that they are active in a cell-type specific manner, in accordance with the emerging body of evidence of a tissue/cell-specific activity of pol III. PMID:23109855

A novel collection of snRNA-like promoters with tissue-specific transcription properties.

PubMed

Garritano, Sonia; Gigoni, Arianna; Costa, Delfina; Malatesta, Paolo; Florio, Tullio; Cancedda, Ranieri; Pagano, Aldo

2012-01-01

We recently identified a novel dataset of snRNA-like trascriptional units in the human genome. The investigation of a subset of these elements showed that they play relevant roles in physiology and/or pathology. In this work we expand our collection of small RNAs taking advantage of a newly developed algorithm able to identify genome sequence stretches with RNA polymerase (pol) III type 3 promoter features thus constituting putative pol III binding sites. The bioinformatic analysis of a subset of these elements that map in introns of protein-coding genes in antisense configuration suggest their association with alternative splicing, similarly to other recently characterized small RNAs. Interestingly, the analysis of the transcriptional activity of these novel promoters shows that they are active in a cell-type specific manner, in accordance with the emerging body of evidence of a tissue/cell-specific activity of pol III.

Comparison of Different EHG Feature Selection Methods for the Detection of Preterm Labor

PubMed Central

Alamedine, D.; Khalil, M.; Marque, C.

2013-01-01

Numerous types of linear and nonlinear features have been extracted from the electrohysterogram (EHG) in order to classify labor and pregnancy contractions. As a result, the number of available features is now very large. The goal of this study is to reduce the number of features by selecting only the relevant ones which are useful for solving the classification problem. This paper presents three methods for feature subset selection that can be applied to choose the best subsets for classifying labor and pregnancy contractions: an algorithm using the Jeffrey divergence (JD) distance, a sequential forward selection (SFS) algorithm, and a binary particle swarm optimization (BPSO) algorithm. The two last methods are based on a classifier and were tested with three types of classifiers. These methods have allowed us to identify common features which are relevant for contraction classification. PMID:24454536

Isolation of mouse pancreatic alpha, beta, duct and acinar populations with cell surface markers.

PubMed

Dorrell, Craig; Grompe, Maria T; Pan, Fong Cheng; Zhong, Yongping; Canaday, Pamela S; Shultz, Leonard D; Greiner, Dale L; Wright, Chris V; Streeter, Philip R; Grompe, Markus

2011-06-06

Tools permitting the isolation of live pancreatic cell subsets for culture and/or molecular analysis are limited. To address this, we developed a collection of monoclonal antibodies with selective surface labeling of endocrine and exocrine pancreatic cell types. Cell type labeling specificity and cell surface reactivity were validated on mouse pancreatic sections and by gene expression analysis of cells isolated using FACS. Five antibodies which marked populations of particular interest were used to isolate and study viable populations of purified pancreatic ducts, acinar cells, and subsets of acinar cells from whole pancreatic tissue or of alpha or beta cells from isolated mouse islets. Gene expression analysis showed the presence of known endocrine markers in alpha and beta cell populations and revealed that TTR and DPPIV are primarily expressed in alpha cells whereas DGKB and GPM6A have a beta cell specific expression profile. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Evaluation of wavelength groups for discrimination of agricultural cover types. [remote sensing of environment in INDIANA

NASA Technical Reports Server (NTRS)

Kumar, R.

1978-01-01

Multispectral scanner data in twelve spectral channels, in the wavelength range 0.46 to 11.7 mm, acquired in July 1971 for three flightlines, were analyzed by applying automatic pattern recognition techniques. These twelve spectral channels were divided into four wavelength groups (W1, W2, W3 and W4), each consisting of three wavelength channels -- with respect to their estimated probability of correct classification (P sub c) in discriminating agricultural cover types. The same analysis was also done for the data acquired in August, to investigate the effect of time on these results. The effect of deletion of each of the wavelength groups on P sub C in the subsets of one to nine channels, is given. Values of P sub C for all possible combinations of wavelength groups, in the subsets of one to eleven channels are also given.

Improving Distributed Diagnosis Through Structural Model Decomposition

NASA Technical Reports Server (NTRS)

Bregon, Anibal; Daigle, Matthew John; Roychoudhury, Indranil; Biswas, Gautam; Koutsoukos, Xenofon; Pulido, Belarmino

2011-01-01

Complex engineering systems require efficient fault diagnosis methodologies, but centralized approaches do not scale well, and this motivates the development of distributed solutions. This work presents an event-based approach for distributed diagnosis of abrupt parametric faults in continuous systems, by using the structural model decomposition capabilities provided by Possible Conflicts. We develop a distributed diagnosis algorithm that uses residuals computed by extending Possible Conflicts to build local event-based diagnosers based on global diagnosability analysis. The proposed approach is applied to a multitank system, and results demonstrate an improvement in the design of local diagnosers. Since local diagnosers use only a subset of the residuals, and use subsystem models to compute residuals (instead of the global system model), the local diagnosers are more efficient than previously developed distributed approaches.

Impaired cognitive functioning in patients with tyrosinemia type I receiving nitisinone.

PubMed

Bendadi, Fatiha; de Koning, Tom J; Visser, Gepke; Prinsen, Hubertus C M T; de Sain, Monique G M; Verhoeven-Duif, Nanda; Sinnema, Gerben; van Spronsen, Francjan J; van Hasselt, Peter M

2014-02-01

To examine cognitive functioning in patients with tyrosinemia type I treated with nitisinone and a protein-restricted diet. We performed a cross-sectional study to establish cognitive functioning in children with tyrosinemia type I compared with their unaffected siblings. Intelligence was measured using age-appropriate Wechsler Scales. To assess cognitive development over time, we retrieved sequential IQ scores in a single-center subset of patients. We also evaluated whether plasma phenylalanine and tyrosine levels during treatment was correlated with cognitive development. Average total IQ score in 10 patients with tyrosinemia type I receiving nitisinone was significantly lower compared with their unaffected siblings (71 ± 13 vs 91 ± 13; P = .008). Both verbal and performance IQ subscores differed (77 ± 14 vs 95 ± 11; P < .05 and 70 ± 11 vs 87 ± 15; P < .05, respectively). Repeated IQ measurements in a single-center subset of 5 patients revealed a decline in average IQ score over time, from 96 ± 15 to 69 ± 11 (P < .001). No significant association was found between IQ score and either plasma tyrosine or phenylalanine concentration. Patients with tyrosinemia type I treated with nitisinone are at risk for impaired cognitive function despite a protein-restricted diet. Copyright © 2014 Mosby, Inc. All rights reserved.

In Silico Syndrome Prediction for Coronary Artery Disease in Traditional Chinese Medicine

PubMed Central

Lu, Peng; Chen, Jianxin; Zhao, Huihui; Gao, Yibo; Luo, Liangtao; Zuo, Xiaohan; Shi, Qi; Yang, Yiping; Yi, Jianqiang; Wang, Wei

2012-01-01

Coronary artery disease (CAD) is the leading causes of deaths in the world. The differentiation of syndrome (ZHENG) is the criterion of diagnosis and therapeutic in TCM. Therefore, syndrome prediction in silico can be improving the performance of treatment. In this paper, we present a Bayesian network framework to construct a high-confidence syndrome predictor based on the optimum subset, that is, collected by Support Vector Machine (SVM) feature selection. Syndrome of CAD can be divided into asthenia and sthenia syndromes. According to the hierarchical characteristics of syndrome, we firstly label every case three types of syndrome (asthenia, sthenia, or both) to solve several syndromes with some patients. On basis of the three syndromes' classes, we design SVM feature selection to achieve the optimum symptom subset and compare this subset with Markov blanket feature select using ROC. Using this subset, the six predictors of CAD's syndrome are constructed by the Bayesian network technique. We also design Naïve Bayes, C4.5 Logistic, Radial basis function (RBF) network compared with Bayesian network. In a conclusion, the Bayesian network method based on the optimum symptoms shows a practical method to predict six syndromes of CAD in TCM. PMID:22567030

Application of proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program (DASP) sample subset

PubMed Central

Metz, Thomas O.; Qian, Wei-Jun; Jacobs, Jon M.; Gritsenko, Marina A.; Moore, Ronald J.; Polpitiya, Ashoka D.; Monroe, Matthew E.; Camp, David G.; Mueller, Patricia W.; Smith, Richard D.

2009-01-01

Novel biomarkers of type 1 diabetes must be identified and validated in initial, exploratory studies before they can be assessed in proficiency evaluations. Currently, untargeted “-omics” approaches are under-utilized in profiling studies of clinical samples. This report describes the evaluation of capillary liquid chromatography (LC) coupled with mass spectrometry (MS) in a pilot proteomic analysis of human plasma and serum from a subset of control and type 1 diabetic individuals enrolled in the Diabetes Autoantibody Standardization Program with the goal of identifying candidate biomarkers of type 1 diabetes. Initial high-resolution capillary LC-MS/MS experiments were performed to augment an existing plasma peptide database, while subsequent LC-FTICR studies identified quantitative differences in the abundance of plasma proteins. Analysis of LC-FTICR proteomic data identified five candidate protein biomarkers of type 1 diabetes. Alpha-2-glycoprotein 1 (zinc), corticosteroid-binding globulin, and lumican were 2-fold up-regulated in type 1 diabetic samples relative to control samples, whereas clusterin and serotransferrin were 2-fold up-regulated in control samples relative to type 1 diabetic samples. Observed perturbations in the levels of all five proteins are consistent with the metabolic aberrations found in type 1 diabetes. While the discovery of these candidate protein biomarkers of type 1 diabetes is encouraging, follow up studies are required for validation in a larger population of individuals and for determination of laboratory-defined sensitivity and specificity values using blinded samples. PMID:18092746

Application of proteomics in the discovery of candidate protein biomarkers in a diabetes autoantibody standardization program sample subset.

PubMed

Metz, Thomas O; Qian, Wei-Jun; Jacobs, Jon M; Gritsenko, Marina A; Moore, Ronald J; Polpitiya, Ashoka D; Monroe, Matthew E; Camp, David G; Mueller, Patricia W; Smith, Richard D

2008-02-01

Novel biomarkers of type 1 diabetes must be identified and validated in initial, exploratory studies before they can be assessed in proficiency evaluations. Currently, untargeted "-omics" approaches are underutilized in profiling studies of clinical samples. This report describes the evaluation of capillary liquid chromatography (LC) coupled with mass spectrometry (MS) in a pilot proteomic analysis of human plasma and serum from a subset of control and type 1 diabetic individuals enrolled in the Diabetes Autoantibody Standardization Program, with the goal of identifying candidate biomarkers of type 1 diabetes. Initial high-resolution capillary LC-MS/MS experiments were performed to augment an existing plasma peptide database, while subsequent LC-FTICR studies identified quantitative differences in the abundance of plasma proteins. Analysis of LC-FTICR proteomic data identified five candidate protein biomarkers of type 1 diabetes. alpha-2-Glycoprotein 1 (zinc), corticosteroid-binding globulin, and lumican were 2-fold up-regulated in type 1 diabetic samples relative to control samples, whereas clusterin and serotransferrin were 2-fold up-regulated in control samples relative to type 1 diabetic samples. Observed perturbations in the levels of all five proteins are consistent with the metabolic aberrations found in type 1 diabetes. While the discovery of these candidate protein biomarkers of type 1 diabetes is encouraging, follow up studies are required for validation in a larger population of individuals and for determination of laboratory-defined sensitivity and specificity values using blinded samples.

Restoration of STORM images from sparse subset of localizations (Conference Presentation)

NASA Astrophysics Data System (ADS)

Moiseev, Alexander A.; Gelikonov, Grigory V.; Gelikonov, Valentine M.

2016-02-01

To construct a Stochastic Optical Reconstruction Microscopy (STORM) image one should collect sufficient number of localized fluorophores to satisfy Nyquist criterion. This requirement limits time resolution of the method. In this work we propose a probabalistic approach to construct STORM images from a subset of localized fluorophores 3-4 times sparser than required from Nyquist criterion. Using a set of STORM images constructed from number of localizations sufficient for Nyquist criterion we derive a model which allows us to predict the probability for every location to be occupied by a fluorophore at the end of hypothetical acquisition, having as an input parameters distribution of already localized fluorophores in the proximity of this location. We show that probability map obtained from number of fluorophores 3-4 times less than required by Nyquist criterion may be used as superresolution image itself. Thus we are able to construct STORM image from a subset of localized fluorophores 3-4 times sparser than required from Nyquist criterion, proportionaly decreasing STORM data acquisition time. This method may be used complementary with other approaches desined for increasing STORM time resolution.

Distinct pattern of lesion distribution in multiple sclerosis is associated with different circulating T-helper and helper-like innate lymphoid cell subsets.

PubMed

Gross, Catharina C; Schulte-Mecklenbeck, Andreas; Hanning, Uta; Posevitz-Fejfár, Anita; Korsukewitz, Catharina; Schwab, Nicholas; Meuth, Sven G; Wiendl, Heinz; Klotz, Luisa

2017-06-01

Distinct lesion topography in relapsing-remitting multiple sclerosis (RRMS) might be due to different antigen presentation and/or trafficking routes of immune cells into the central nervous system (CNS). To investigate whether distinct lesion patterns in multiple sclerosis (MS) might be associated with a predominance of distinct circulating T-helper cell subset as well as their innate counterparts. Flow cytometric analysis of lymphocytes derived from the peripheral blood of patients with exclusively cerebral (n = 20) or predominantly spinal (n = 12) disease manifestation. Patients with exclusively cerebral or preferential spinal lesion manifestation were associated with increased proportions of circulating granulocyte-macrophage colony-stimulating factor (GM-CSF) producing T H 1 cells or interleukin (IL)-17-producing T H 17 cells, respectively. In contrast, proportions of peripheral IL-17/IL-22-producing lymphoid tissue inducer (LTi), the innate counterpart of T H 17 cells, were enhanced in RRMS patients with exclusively cerebral lesion topography. Distinct T-helper and T-helper-like innate lymphoid cell (ILC) subsets are associated with different lesion topography in RRMS.

Research on allocation efficiency of the daisy chain allocation algorithm

NASA Astrophysics Data System (ADS)

Shi, Jingping; Zhang, Weiguo

2013-03-01

With the improvement of the aircraft performance in reliability, maneuverability and survivability, the number of the control effectors increases a lot. How to distribute the three-axis moments into the control surfaces reasonably becomes an important problem. Daisy chain method is simple and easy to be carried out in the design of the allocation system. But it can not solve the allocation problem for entire attainable moment subset. For the lateral-directional allocation problem, the allocation efficiency of the daisy chain can be directly measured by the area of its subset of attainable moments. Because of the non-linear allocation characteristic, the subset of attainable moments of daisy-chain method is a complex non-convex polygon, and it is difficult to solve directly. By analyzing the two-dimensional allocation problems with a "micro-element" idea, a numerical calculation algorithm is proposed to compute the area of the non-convex polygon. In order to improve the allocation efficiency of the algorithm, a genetic algorithm with the allocation efficiency chosen as the fitness function is proposed to find the best pseudo-inverse matrix.

Topographic specializations of catecholaminergic cells and ganglion cells and distribution of calcium binding proteins in the crepuscular rock cavy (Kerodon rupestris) retina.

PubMed

Oliveira, Francisco Gilberto; Nascimento-Júnior, Expedito Silva do; Cavalcante, Judney Cley; Guzen, Fausto Pierdoná; Cavalcante, Jeferson de Souza; Soares, Joacil Germano; Cavalcanti, José Rodolfo Lopes de Paiva; Freitas, Leandro Moura de; Costa, Miriam Stela Maris de Oliveira; Andrade-da-Costa, Belmira Lara da Silveira

2018-07-01

The rock cavy (Kerodon rupestris) is a crepuscular Hystricomorpha rodent that has been used in comparative analysis of retinal targets, but its retinal organization remains to be investigated. In order to better characterize its visual system, the present study analyzed neurochemical features related to the topographic organization of catecholaminergic cells and ganglion cells, as well the distribution of calcium-binding proteins in the outer and inner retina. Retinal sections and/or wholemounts were processed using tyrosine hydroxylase (TH), GABA, calbindin, parvalbumin and calretinin immunohistochemistry or Nissl staining. Two types of TH-immunoreactive (TH-IR) cells were found which differ in soma size, dendritic arborization, intensity of TH immunoreactivity and stratification pattern in the inner plexiform layer. The topographic distribution of all TH-IR cells defines a visual streak along the horizontal meridian in the superior retina. The ganglion cells are also distributed in a visual streak and the visual acuity estimated considering their peak density is 4.13 cycles/degree. A subset of TH-IR cells express GABA or calbindin. Calretinin is abundant in most of retinal layers and coexists with calbindin in horizontal cells. Parvalbumin is less abundant and expressed by presumed amacrine cells in the INL and some ganglion cells in the GCL. The topographic distribution of TH-IR cells and ganglion cells in the rock cavy retina indicate a suitable adaptation for using a broad extension of its inferior visual field in aspects that involve resolution, adjustment to ambient light intensity and movement detection without specialized eye movements. Copyright © 2017 Elsevier B.V. All rights reserved.

A Major Population of Functional KLRG1- ILC2s in Female Lungs Contributes to a Sex Bias in ILC2 Numbers.

PubMed

Kadel, Sapana; Ainsua-Enrich, Erola; Hatipoglu, Ibrahim; Turner, Sean; Singh, Simar; Khan, Sohaib; Kovats, Susan

2018-02-01

Humans show significant sex differences in the incidence and severity of respiratory diseases, including asthma and virus infection. Sex hormones contribute to the female sex bias in type 2 inflammation associated with respiratory diseases, consistent with recent reports that female lungs harbor greater numbers of GATA-3-dependent group 2 innate lymphoid cells (ILC2s). In this study, we determined whether sex hormone levels govern sex differences in the numbers, phenotype, and function of ILC2s in the murine lung and bone marrow (BM). Our data show that lungs of female mice harbor significantly greater ILC2 numbers in homeostasis, in part due to a major subset of ILC2s lacking killer-cell lectin like receptor G1 (KLRG1), a population largely absent in male lungs. The KLRG1 - ILC2s were capable of type 2 cytokine production and increased with age after sexual maturity, suggesting that a unique functional subset exists in females. Experiments with gonadectomized mice or mice bearing either global or lymphocyte restricted estrogen receptor α ( Esr1 ) deficiency showed that androgens rather than estrogens regulated numbers of the KLRG1 - ILC2 subset and ILC2 functional capacity in the lung and BM, as well as levels of GATA-3 expression in BM ILC2s. Furthermore, the frequency of BM PLZF + ILC precursors was higher in males and increased by excess androgens, suggesting that androgens act to inhibit the transition of ILC precursors to ILC2s. Taken together, these data show that a functional subset of KLRG1 - ILC2s in females contributes to the sex bias in lung ILC2s that is observed after reproductive age.

Diffuse Staining for Activated NOTCH1 Correlates With NOTCH1 Mutation Status and Is Associated With Worse Outcome in Adenoid Cystic Carcinoma.

PubMed

Sajed, Dipti P; Faquin, William C; Carey, Chris; Severson, Eric A; H Afrogheh, Amir; A Johnson, Carl; Blacklow, Stephen C; Chau, Nicole G; Lin, Derrick T; Krane, Jeffrey F; Jo, Vickie Y; Garcia, Joaquín J; Sholl, Lynette M; Aster, Jon C

2017-11-01

NOTCH1 is frequently mutated in adenoid cystic carcinoma (ACC). To test the idea that immunohistochemical (IHC) staining can identify ACCs with NOTCH1 mutations, we performed IHC for activated NOTCH1 (NICD1) in 197 cases diagnosed as ACC from 173 patients. NICD1 staining was positive in 194 cases (98%) in 2 major patterns: subset positivity, which correlated with tubular/cribriform histology; and diffuse positivity, which correlated with a solid histology. To determine the relationship between NICD1 staining and NOTCH1 mutational status, targeted exome sequencing data were obtained on 14 diffusely NICD1-positive ACC specimens from 11 patients and 15 subset NICD1-positive ACC specimens from 15 patients. This revealed NOTCH1 gain-of-function mutations in 11 of 14 diffusely NICD1-positive ACC specimens, whereas all subset-positive tumors had wild-type NOTCH1 alleles. Notably, tumors with diffuse NICD1 positivity were associated with significantly worse outcomes (P=0.003). To determine whether NOTCH1 activation is unique among tumors included in the differential diagnosis with ACC, we performed NICD1 IHC on a cohort of diverse salivary gland and head and neck tumors. High fractions of each of these tumor types were positive for NICD1 in a subset of cells, particularly in basaloid squamous cell carcinomas; however, sequencing of basaloid squamous cell carcinomas failed to identify NOTCH1 mutations. These findings indicate that diffuse NICD1 positivity in ACC correlates with solid growth pattern, the presence of NOTCH1 gain-of-function mutations, and unfavorable outcome, and suggest that staining for NICD1 can be helpful in distinguishing ACC with solid growth patterns from other salivary gland and head and neck tumors.

Abnormal B cell memory subsets dominate HIV-specific responses in infected individuals

PubMed Central

Kardava, Lela; Moir, Susan; Shah, Naisha; Wang, Wei; Wilson, Richard; Buckner, Clarisa M.; Santich, Brian H.; Kim, Leo J.Y.; Spurlin, Emily E.; Nelson, Amy K.; Wheatley, Adam K.; Harvey, Christopher J.; McDermott, Adrian B.; Wucherpfennig, Kai W.; Chun, Tae-Wook; Tsang, John S.; Li, Yuxing; Fauci, Anthony S.

2014-01-01

Recently, several neutralizing anti-HIV antibodies have been isolated from memory B cells of HIV-infected individuals. Despite extensive evidence of B cell dysfunction in HIV disease, little is known about the cells from which these rare HIV-specific antibodies originate. Accordingly, we used HIV envelope gp140 and CD4 or coreceptor (CoR) binding site (bs) mutant probes to evaluate HIV-specific responses in peripheral blood B cells of HIV-infected individuals at various stages of infection. In contrast to non-HIV responses, HIV-specific responses against gp140 were enriched within abnormal B cells, namely activated and exhausted memory subsets, which are largely absent in the blood of uninfected individuals. Responses against the CoRbs, which is a poorly neutralizing epitope, arose early, whereas those against the well-characterized neutralizing epitope CD4bs were delayed and infrequent. Enrichment of the HIV-specific response within resting memory B cells, the predominant subset in uninfected individuals, did occur in certain infected individuals who maintained low levels of plasma viremia and immune activation with or without antiretroviral therapy. The distribution of HIV-specific responses among memory B cell subsets was corroborated by transcriptional analyses. Taken together, our findings provide valuable insight into virus-specific B cell responses in HIV infection and demonstrate that memory B cell abnormalities may contribute to the ineffectiveness of the antibody response in infected individuals. PMID:24892810

Oligoclonal T cell expansions in patients with Behçet's disease

PubMed Central

DIRESKENELI, H; EKSIOGLU-DEMIRALP, E; KIBAROGLU, A; YAVUZ, S; ERGUN, T; AKOGLU, T

1999-01-01

Behçet's disease (BD) is a multisystem disorder with oral and genital ulcers, mucocutaneous, ocular, joint, vascular and central nervous system involvement. In this study, the peripheral T cell repertoire was analysed in patients with BD with MoAbs against T cell receptor (TCR) Vβ gene products in CD4+ and CD8+ T cell compartments, and these were compared with rheumatoid arthritis (RA) patients and healthy controls (HC). In the CD4+ T cell compartment, oligoclonal TCR Vβ expression was observed in 56% of BD (10/18), 71% of RA (5/7) patients and 21% (3/14) of HC. In the CD8+ T cell group 50% of BD (9/18), 57% of RA patients and 28% of HC (4/14) had an oligoclonal TCR repertoire. An increase of TCR Vβ5.1 subset was observed in five BD patients among CD8+ T cells. Other elevations of TCR Vβ subsets were heterogeneously distributed with one to three different Vβ subsets. Our results suggest an antigen-driven oligoclonal increase of T cells in BD. There was no overall increase in any Vβ group to suggest a superantigen effect. Analysis of the responsible antigens causing the increase in T cell subsets may give insights into the aetiopathogenesis of BD and immunomodulation of these T cells may lead to new treatments. PMID:10403931

Clonal origin of Epstein-Barr virus (EBV)-infected T/NK-cell subpopulations in EBV-positive T/NK-cell lymphoproliferative disorders of childhood.

PubMed

Ohga, Shouichi; Ishimura, Masataka; Yoshimoto, Goichi; Miyamoto, Toshihiro; Takada, Hidetoshi; Tanaka, Tamami; Ohshima, Koichi; Ogawa, Yoshiyasu; Imadome, Ken-Ichi; Abe, Yasunobu; Akashi, Koichi; Hara, Toshiro

2011-05-01

In Japan, chronic active Epstein-Barr virus infection (CAEBV) may manifest with infection of T-cells or NK-cells, clonal lymphoid proliferations, and overt lymphoid malignancy. These EBV-positive lymphoproliferative disorders (EBV(+)LPD) of childhood are related to, but distinct from the infectious mononucleosis-like CAEBV seen in Western populations. The clonal nature of viral infection within lymphoid subsets of patients with EBV(+)LPD of childhood is not well described. Viral distribution and clonotype were assessed within T-cell subsets, NK-cells, and CD34(+)stem cells following high purity cell sorting. Six Japanese patients with EBV(+)LPD of childhood (3 T-cell LPD and 3 NK-cell LPD) were recruited. Prior to immunochemotherapy, viral loads and clonal analyses of T-cell subsets, NK-cells, and CD34(+)stem cells were studied by high-accuracy cell sorting (>99.5%), Southern blotting and real-time polymerase chain reaction. Patient 1 had a monoclonal proliferation of EBV-infected γδT-cells and carried a lower copy number of EBV in αβT-cells. Patients 2 and 3 had clonal expansions of EBV-infected CD4(+)T-cells, and lower EBV load in NK-cells. Patients 4, 5 and 6 had EBV(+)NK-cell expansions with higher EBV load than T-cells. EBV-terminal repeats were determined as clonal bands in the minor targeted populations of 5 patients. The size of terminal repeats indicated the same clonotype in minor subsets as in the major subsets of four patients. EBV was not, however, detected in the bone marrow-derived CD34(+)stem cells of patients. A single EBV clonotype may infect multiple NK-cell and T-cell subsets of patients with EBV(+)LPD of childhood. CD34(+)stem cells are spared, suggesting infection of more differentiated elements. Copyright © 2011 Elsevier B.V. All rights reserved.

IL-23 (Interleukin-23)-Producing Conventional Dendritic Cells Control the Detrimental IL-17 (Interleukin-17) Response in Stroke.

PubMed

Gelderblom, Mathias; Gallizioli, Mattia; Ludewig, Peter; Thom, Vivien; Arunachalam, Priyadharshini; Rissiek, Björn; Bernreuther, Christian; Glatzel, Markus; Korn, Thomas; Arumugam, Thiruma Valavan; Sedlacik, Jan; Gerloff, Christian; Tolosa, Eva; Planas, Anna M; Magnus, Tim

2018-01-01

Inflammatory mechanisms can exacerbate ischemic tissue damage and worsen clinical outcome in patients with stroke. Both αβ and γδ T cells are established mediators of tissue damage in stroke, and the role of dendritic cells (DCs) in inducing the early events of T cell activation and differentiation in stroke is not well understood. In a murine model of experimental stroke, we defined the immune phenotype of infiltrating DC subsets based on flow cytometry of surface markers, the expression of ontogenetic markers, and cytokine levels. We used conditional DC depletion, bone marrow chimeric mice, and IL-23 (interleukin-23) receptor-deficient mice to further explore the functional role of DCs. We show that the ischemic brain was rapidly infiltrated by IRF4 + /CD172a + conventional type 2 DCs and that conventional type 2 DCs were the most abundant subset in comparison with all other DC subsets. Twenty-four hours after ischemia onset, conventional type 2 DCs became the major source of IL-23, promoting neutrophil infiltration by induction of IL-17 (interleukin-17) in γδ T cells. Functionally, the depletion of CD11c + cells or the genetic disruption of the IL-23 signaling abrogated both IL-17 production in γδ T cells and neutrophil infiltration. Interruption of the IL-23/IL-17 cascade decreased infarct size and improved neurological outcome after stroke. Our results suggest a central role for interferon regulatory factor 4-positive IL-23-producing conventional DCs in the IL-17-dependent secondary tissue damage in stroke. © 2017 American Heart Association, Inc.

Generalized Subset Designs in Analytical Chemistry.

PubMed

Surowiec, Izabella; Vikström, Ludvig; Hector, Gustaf; Johansson, Erik; Vikström, Conny; Trygg, Johan

2017-06-20

Design of experiments (DOE) is an established methodology in research, development, manufacturing, and production for screening, optimization, and robustness testing. Two-level fractional factorial designs remain the preferred approach due to high information content while keeping the number of experiments low. These types of designs, however, have never been extended to a generalized multilevel reduced design type that would be capable to include both qualitative and quantitative factors. In this Article we describe a novel generalized fractional factorial design. In addition, it also provides complementary and balanced subdesigns analogous to a fold-over in two-level reduced factorial designs. We demonstrate how this design type can be applied with good results in three different applications in analytical chemistry including (a) multivariate calibration using microwave resonance spectroscopy for the determination of water in tablets, (b) stability study in drug product development, and (c) representative sample selection in clinical studies. This demonstrates the potential of generalized fractional factorial designs to be applied in many other areas of analytical chemistry where representative, balanced, and complementary subsets are required, especially when a combination of quantitative and qualitative factors at multiple levels exists.

ChromBiSim: Interactive chromatin biclustering using a simple approach.

PubMed

Noureen, Nighat; Zohaib, Hafiz Muhammad; Qadir, Muhammad Abdul; Fazal, Sahar

2017-10-01

Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations. It displays the results in the forms of charts and heat maps in accordance with saving them in files which could be used for post analysis. ChromBiSim tested on multiple cell types produced in total 803 combinatorial patterns. It could be used to highlight variations among diseased versus normal cell types of any species. ChromBiSim is available at (http://sourceforge.net/projects/chrombisim) in C-sharp and python languages. Copyright © 2017 Elsevier Inc. All rights reserved.

RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities

PubMed Central

Rai, Richa; Chauhan, Sudhir Kumar; Singh, Vikas Vikram; Rai, Madhukar; Rai, Geeta

2016-01-01

Systemic lupus erythematosus (SLE) patients exhibit immense heterogeneity which is challenging from the diagnostic perspective. Emerging high throughput sequencing technologies have been proved to be a useful platform to understand the complex and dynamic disease processes. SLE patients categorised based on autoantibody specificities are reported to have differential immuno-regulatory mechanisms. Therefore, we performed RNA-seq analysis to identify transcriptomics of SLE patients with distinguished autoantibody specificities. The SLE patients were segregated into three subsets based on the type of autoantibodies present in their sera (anti-dsDNA+ group with anti-dsDNA autoantibody alone; anti-ENA+ group having autoantibodies against extractable nuclear antigens (ENA) only, and anti-dsDNA+ENA+ group having autoantibodies to both dsDNA and ENA). Global transcriptome profiling for each SLE patients subsets was performed using Illumina® Hiseq-2000 platform. The biological relevance of dysregulated transcripts in each SLE subsets was assessed by ingenuity pathway analysis (IPA) software. We observed that dysregulation in the transcriptome expression pattern was clearly distinct in each SLE patients subsets. IPA analysis of transcripts uniquely expressed in different SLE groups revealed specific biological pathways to be affected in each SLE subsets. Multiple cytokine signaling pathways were specifically dysregulated in anti-dsDNA+ patients whereas Interferon signaling was predominantly dysregulated in anti-ENA+ patients. In anti-dsDNA+ENA+ patients regulation of actin based motility by Rho pathway was significantly affected. The granulocyte gene signature was a common feature to all SLE subsets; however, anti-dsDNA+ group showed relatively predominant expression of these genes. Dysregulation of Plasma cell related transcripts were higher in anti-dsDNA+ and anti-ENA+ patients as compared to anti-dsDNA+ ENA+. Association of specific canonical pathways with the uniquely expressed transcripts in each SLE subgroup indicates that specific immunological disease mechanisms are operative in distinct SLE patients’ subsets. This ‘sub-grouping’ approach could further be useful for clinical evaluation of SLE patients and devising targeted therapeutics. PMID:27835693

Characterization of human invariant natural killer T subsets in health and disease using a novel invariant natural killer T cell-clonotypic monoclonal antibody, 6B11.

PubMed

Montoya, Carlos J; Pollard, David; Martinson, Jeffrey; Kumari, Kumud; Wasserfall, Clive; Mulder, Candice B; Rugeles, Maria T; Atkinson, Mark A; Landay, Alan L; Wilson, S Brian

2007-09-01

Identification of human CD1d-restricted T-cell receptor (TCR)-invariant natural killer T (iNKT) cells has been dependent on utilizing combinations of monoclonal antibodies or CD1d tetramers, which do not allow for the most specific analysis of this T-cell subpopulation. A novel monoclonal antibody (clone 6B11), specific for the invariant CDR3 loop of human canonical Valpha24Jalpha18 TCR alpha chain, was developed and used to specifically characterize iNKT cells. In healthy individuals studied for up to 1 year, a wide but stable frequency of circulating iNKT cells (range: 0.01-0.92%) was observed, with no differences in frequency by gender. Four stable iNKT cell subsets were characterized in peripheral blood based on the expression of CD4 and CD8, with CD8(+) iNKT cells being a phenotypic and functionally different subset from CD4(+) and double negative iNKT cells; in particular, LAG-3 was preferentially expressed on CD8(+) iNKT cells. In addition, a strong negative linear correlation between the frequency of total iNKT cells and percentage of the CD4(+) subset was observed. In terms of their potential association with disease, patients at risk for type 1 diabetes had significantly expanded frequencies of double negative iNKT cells when compared to matched controls and first-degree relatives. Moreover, peripheral blood CD4(+) iNKT cells were the highest producers of interleukin-4, while the production of interferon-gamma and tumour necrosis factor-alpha was similar amongst all iNKT cell subsets. These differences in iNKT cell subsets suggest that in humans the relative ratio of iNKT cell subsets may influence susceptibility vs. resistance to immune-mediated diseases.

Characterization of human invariant natural killer T subsets in health and disease using a novel invariant natural killer T cell-clonotypic monoclonal antibody, 6B11

PubMed Central

Montoya, Carlos J; Pollard, David; Martinson, Jeffrey; Kumari, Kumud; Wasserfall, Clive; Mulder, Candice B; Rugeles, Maria T; Atkinson, Mark A; Landay, Alan L; Wilson, S Brian

2007-01-01

Identification of human CD1d-restricted T-cell receptor (TCR)-invariant natural killer T (iNKT) cells has been dependent on utilizing combinations of monoclonal antibodies or CD1d tetramers, which do not allow for the most specific analysis of this T-cell subpopulation. A novel monoclonal antibody (clone 6B11), specific for the invariant CDR3 loop of human canonical Vα24Jα18 TCR α chain, was developed and used to specifically characterize iNKT cells. In healthy individuals studied for up to 1 year, a wide but stable frequency of circulating iNKT cells (range: 0·01–0·92%) was observed, with no differences in frequency by gender. Four stable iNKT cell subsets were characterized in peripheral blood based on the expression of CD4 and CD8, with CD8+ iNKT cells being a phenotypic and functionally different subset from CD4+ and double negative iNKT cells; in particular, LAG-3 was preferentially expressed on CD8+ iNKT cells. In addition, a strong negative linear correlation between the frequency of total iNKT cells and percentage of the CD4+ subset was observed. In terms of their potential association with disease, patients at risk for type 1 diabetes had significantly expanded frequencies of double negative iNKT cells when compared to matched controls and first-degree relatives. Moreover, peripheral blood CD4+ iNKT cells were the highest producers of interleukin-4, while the production of interferon-γ and tumour necrosis factor-α was similar amongst all iNKT cell subsets. These differences in iNKT cell subsets suggest that in humans the relative ratio of iNKT cell subsets may influence susceptibility vs. resistance to immune-mediated diseases. PMID:17662044

Antigen presenting capacity of murine splenic myeloid cells.

PubMed

Hey, Ying-Ying; Quah, Benjamin; O'Neill, Helen C

2017-01-11

The spleen is an important site for hematopoiesis. It supports development of myeloid cells from bone marrow-derived precursors entering from blood. Myeloid subsets in spleen are not well characterised although dendritic cell (DC) subsets are clearly defined in terms of phenotype, development and functional role. Recently a novel dendritic-like cell type in spleen named 'L-DC' was distinguished from other known dendritic and myeloid cells by its distinct phenotype and developmental origin. That study also redefined splenic eosinophils as well as resident and inflammatory monocytes in spleen. L-DC are shown to be distinct from known splenic macrophages and monocyte subsets. Using a new flow cytometric procedure, it has been possible to identify and isolate L-DC in order to assess their functional competence and ability to activate T cells both in vivo and in vitro. L-DC are readily accessible to antigen given intravenously through receptor-mediated endocytosis. They are also capable of CD8 + T cell activation through antigen cross presentation, with subsequent induction of cytotoxic effector T cells. L-DC are MHCII - cells and unable to activate CD4 + T cells, a property which clearly distinguishes them from conventional DC. The myeloid subsets of resident monocytes, inflammatory monocytes, neutrophils and eosinophils, were found to have varying capacities to take up antigen, but were uniformly unable to activate either CD4 + T cells or CD8 + T cells. The results presented here demonstrate that L-DC in spleen are distinct from other myeloid cells in that they can process antigen for CD8 + T cell activation and induction of cytotoxic effector function, while both L-DC and myeloid subsets remain unable to activate CD4 + T cells. The L-DC subset in spleen is therefore distinct as an antigen presenting cell.

Selection of organisms for the co-evolution-based study of protein interactions.

PubMed

Herman, Dorota; Ochoa, David; Juan, David; Lopez, Daniel; Valencia, Alfonso; Pazos, Florencio

2011-09-12

The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature. We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions. In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest.

Timing of Locomotor Recovery from Anoxia Modulated by the white Gene in Drosophila

PubMed Central

Xiao, Chengfeng; Robertson, R. Meldrum

2016-01-01

Locomotor recovery from anoxia follows the restoration of disordered ion distributions and neuronal excitability. The time taken for locomotor recovery after 30 sec anoxia (around 10 min) is longer than the time for the propagation of action potentials to be restored (<1 min) in Drosophila wild type. We report here that the white (w) gene modulates the timing of locomotor recovery. Wild-type flies displayed fast and consistent recovery of locomotion from anoxia, whereas mutants of w showed significantly delayed and more variable recovery. Genetic analysis including serial backcrossing revealed a strong association between the w locus and the timing of locomotor recovery, and haplo-insufficient function of w+ in promoting fast recovery. The locomotor recovery phenotype was independent of classic eye pigmentation, although both are associated with the w gene. Introducing up to four copies of mini-white (mw+) into w1118 was insufficient to promote fast and consistent locomotor recovery. However, flies carrying w+ duplicated to the Y chromosome showed wild-type-like fast locomotor recovery. Furthermore, Knockdown of w by RNA interference (RNAi) in neurons but not glia delayed locomotor recovery, and specifically, knockdown of w in subsets of serotonin neurons was sufficient to delay the locomotor recovery. These data reveal an additional role for w in modulating the timing of locomotor recovery from anoxia. PMID:27029736

Relative frequencies of DRB1*11 alleles and their DRB3 associations in five major population groups in a United States bone marrow registry.

PubMed

Tang, T F; Huang, A Y; Pappas, A; Slack, R; Ng, J; Hartzman, R J; Hurley, C K

2000-08-01

One hundred sixty-one individuals from each of five US population groups, Caucasians (CAU), African Americans (AFA), Asians/Pacific Islanders (API), Hispanics (HIS), and Native Americans (NAT), were randomly selected from a volunteer bone marrow registry database consisting of 14,452 HLA-DRB1*11 positive individuals. This sampling provided at least an 80% probability of detecting a rare allele that occurred at 1% in the DRB1*11 positive population. Samples were typed for DRB1*11 alleles by polymerase chain reaction-sequence specific oligonucleotide probe typing (PCR-SSOP). A total of 10 DRB1*11 alleles out of 27 possible alleles were detected. The distribution and diversity of DRB1*11 alleles varied among populations although DRB1*1101 was the predominant DRB1*11 allele in all populations. Caucasians were the least diversified; only four common alleles (DRB1*1101-*1104) were observed. As well as the four common alleles, other groups also carried one or two other less frequent alleles including DRB1*1105 (API), *1106 (API), *1110 (AFA), *1114 (HIS), *1115 (NAT), and *1117 (AFA). A subset (418) of these individuals were also typed for DRB3 alleles. Most (97.6%) showed a strong association of DRB1*11 with DRB3*0202.

Selection of organisms for the co-evolution-based study of protein interactions

PubMed Central

2011-01-01

Background The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature. Results We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions. Conclusions In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest. PMID:21910884

Recent Advances in Insect Olfaction, Specifically Regarding the Morphology and Sensory Physiology of Antennal Sensilla of the Female Sphinx Moth Manduca sexta

PubMed Central

SHIELDS, VONNIE D.C.; HILDEBRAND, JOHN G.

2008-01-01

The antennal flagellum of female Manduca sexta bears eight sensillum types: two trichoid, two basiconic, one auriculate, two coeloconic, and one styliform complex sensilla. The first type of trichoid sensillum averages 34 μm in length and is innervated by two sensory cells. The second type averages 26 μm in length and is innervated by either one or three sensory cells. The first type of basiconic sensillum averages 22 μm in length, while the second type averages 15 μm in length. Both types are innervated by three bipolar sensory cells. The auriculate sensillum averages 4 μm in length and is innervated by two bipolar sensory cells. The coeloconic type-A and type-B both average 2 μm in length. The former type is innervated by five bipolar sensory cells, while the latter type, by three bipolar sensory cells. The styliform complex sensillum occurs singly on each annulus and averages 38-40 μm in length. It is formed by several contiguous sensilla. Each unit is innervated by three bipolar sensory cells. A total of 2,216 sensilla were found on a single annulus (annulus 21) of the flagellum. Electrophysiological responses from type-A trichoid sensilla to a large panel of volatile odorants revealed three different subsets of olfactory receptor cells (ORCs). Two subsets responded strongly to only a narrow range of odorants, while the third responded strongly to a broad range of odorants. Anterograde labeling of ORCs from type-A trichoid sensilla revealed that their axons projected mainly to two large female glomeruli of the antennal lobe. PMID:11754510

Modification of composition and spatial distribution of intestinal microbiota following antibiotic therapy in immunocompetent defined flora C3H/HeN mice

USDA-ARS?s Scientific Manuscript database

Background: Luminal bacteria and/or their products play a pivotal role in the pathogenesis of chronic intestinal inflammation associated with inflammatory bowel diseases (IBD). While host responses to resident flora may initiate IBD, the subsets of bacteria responsible for mediating inflammation in ...

Dynamics in species composition of stream fish assemblages: environmental variability and nested subsets

Treesearch

Christopher M. Taylor; Melvin L. Warren

2001-01-01

Stream landscapes are highly variable in space and time and, like terrestrial landscapes, the resources they contain are patchily distributed. Organisms may disperse among patches to fulfill life-history requirements, but biotic and abiotic factors may limit patch or locality occupancy. Thus, the dynamics of immigration and extinction determine, in part, the local...

Response Latency as a Function of Hypothesis-Testing Strategies in Concept Identification

ERIC Educational Resources Information Center

Fink, Richard T.

1972-01-01

The ability of M. Levine's subset-sampling assumptions to account for the decrease in response latency following the trial of the last error was investigated by employing a distributed stimulus set composed of four binary dimensions and a procedure which required Ss to make an overt response in order to sample each dimension. (Author)

Estimation of Causal Mediation Effects for a Dichotomous Outcome in Multiple-Mediator Models using the Mediation Formula

PubMed Central

Nelson, Suchitra; Albert, Jeffrey M.

2013-01-01

Mediators are intermediate variables in the causal pathway between an exposure and an outcome. Mediation analysis investigates the extent to which exposure effects occur through these variables, thus revealing causal mechanisms. In this paper, we consider the estimation of the mediation effect when the outcome is binary and multiple mediators of different types exist. We give a precise definition of the total mediation effect as well as decomposed mediation effects through individual or sets of mediators using the potential outcomes framework. We formulate a model of joint distribution (probit-normal) using continuous latent variables for any binary mediators to account for correlations among multiple mediators. A mediation formula approach is proposed to estimate the total mediation effect and decomposed mediation effects based on this parametric model. Estimation of mediation effects through individual or subsets of mediators requires an assumption involving the joint distribution of multiple counterfactuals. We conduct a simulation study that demonstrates low bias of mediation effect estimators for two-mediator models with various combinations of mediator types. The results also show that the power to detect a non-zero total mediation effect increases as the correlation coefficient between two mediators increases, while power for individual mediation effects reaches a maximum when the mediators are uncorrelated. We illustrate our approach by applying it to a retrospective cohort study of dental caries in adolescents with low and high socioeconomic status. Sensitivity analysis is performed to assess the robustness of conclusions regarding mediation effects when the assumption of no unmeasured mediator-outcome confounders is violated. PMID:23650048

Estimation of causal mediation effects for a dichotomous outcome in multiple-mediator models using the mediation formula.

PubMed

Wang, Wei; Nelson, Suchitra; Albert, Jeffrey M

2013-10-30

Mediators are intermediate variables in the causal pathway between an exposure and an outcome. Mediation analysis investigates the extent to which exposure effects occur through these variables, thus revealing causal mechanisms. In this paper, we consider the estimation of the mediation effect when the outcome is binary and multiple mediators of different types exist. We give a precise definition of the total mediation effect as well as decomposed mediation effects through individual or sets of mediators using the potential outcomes framework. We formulate a model of joint distribution (probit-normal) using continuous latent variables for any binary mediators to account for correlations among multiple mediators. A mediation formula approach is proposed to estimate the total mediation effect and decomposed mediation effects based on this parametric model. Estimation of mediation effects through individual or subsets of mediators requires an assumption involving the joint distribution of multiple counterfactuals. We conduct a simulation study that demonstrates low bias of mediation effect estimators for two-mediator models with various combinations of mediator types. The results also show that the power to detect a nonzero total mediation effect increases as the correlation coefficient between two mediators increases, whereas power for individual mediation effects reaches a maximum when the mediators are uncorrelated. We illustrate our approach by applying it to a retrospective cohort study of dental caries in adolescents with low and high socioeconomic status. Sensitivity analysis is performed to assess the robustness of conclusions regarding mediation effects when the assumption of no unmeasured mediator-outcome confounders is violated. Copyright © 2013 John Wiley & Sons, Ltd.

Combined endeavor of Neutrosophic Set and Chan-Vese model to extract accurate liver image from CT scan.

PubMed

Siri, Sangeeta K; Latte, Mrityunjaya V

2017-11-01

Many different diseases can occur in the liver, including infections such as hepatitis, cirrhosis, cancer and over effect of medication or toxins. The foremost stage for computer-aided diagnosis of liver is the identification of liver region. Liver segmentation algorithms extract liver image from scan images which helps in virtual surgery simulation, speedup the diagnosis, accurate investigation and surgery planning. The existing liver segmentation algorithms try to extort exact liver image from abdominal Computed Tomography (CT) scan images. It is an open problem because of ambiguous boundaries, large variation in intensity distribution, variability of liver geometry from patient to patient and presence of noise. A novel approach is proposed to meet challenges in extracting the exact liver image from abdominal CT scan images. The proposed approach consists of three phases: (1) Pre-processing (2) CT scan image transformation to Neutrosophic Set (NS) and (3) Post-processing. In pre-processing, the noise is removed by median filter. The "new structure" is designed to transform a CT scan image into neutrosophic domain which is expressed using three membership subset: True subset (T), False subset (F) and Indeterminacy subset (I). This transform approximately extracts the liver image structure. In post processing phase, morphological operation is performed on indeterminacy subset (I) and apply Chan-Vese (C-V) model with detection of initial contour within liver without user intervention. This resulted in liver boundary identification with high accuracy. Experiments show that, the proposed method is effective, robust and comparable with existing algorithm for liver segmentation of CT scan images. Copyright © 2017 Elsevier B.V. All rights reserved.

Aggressive behavior and poor prognosis of endometrial stromal sarcomas with YWHAE-FAM22 rearrangement indicate the clinical importance to recognize this subset.

PubMed

Kruse, Arnold-Jan; Croce, Sabrina; Kruitwagen, Roy F P M; Riedl, Robert G; Slangen, Brigitte F M; Van Gorp, Toon; Van de Vijver, Koen K

2014-11-01

Although the World Health Organization (WHO) in 2003 defined endometrial stromal sarcomas (ESSs) in general have a good prognosis, considerable differences in clinical behavior and prognosis may exist between different patients with ESS. The ESSs of the type associated with YWHAE-NUTM2 (previously named YWHAE-FAM22) fusion have a more aggressive clinical behavior and poorer prognosis than conventional ESS. Recently, the WHO 2014 classification recognizes this subset of ESS as a separate entity and classifies these as high-grade ESSs. Recognition of this subset has therefore an important clinical impact. We performed a review of the literature to delineate the clinicopathologic features of ESS patients with an YWHAE-NUTM2 rearrangement, with the goal to recognize this subset of ESS. We report a case of a woman with WHO 2014-defined high-grade ESS. Furthermore, published English literature was reviewed for YWHAE-FAM22 ESS and uterus. Twenty patients were identified, with a median age of 50 (range, 28-67) years. There were no clinical features able to recognize YWHAE-NUTM2 ESS. However, they characteristically contain specific histopathological features. Furthermore, YWHAE-NUTM2 ESSs are strongly cyclin D1 positive in contrast to conventional low-grade ESSs. YWHAE-NUTM2 ESSs represent a subset of ESSs with an aggressive clinical behavior and poor prognosis. Specific histopathological features may indicate the presence of YWHAE-NUTM2 rearrangement, which subsequently can be confirmed by cyclin D1 immunostaining.

ADF/ADC Web Tools for Browsing and Visualizing Astronomical Catalogs and NASA Astrophysics Mission Metadata

NASA Astrophysics Data System (ADS)

Shaya, E.; Kargatis, V.; Blackwell, J.; Borne, K.; White, R. A.; Cheung, C.

1998-05-01

Several new web based services have been introduced this year by the Astrophysics Data Facility (ADF) at the NASA Goddard Space Flight Center. IMPReSS is a graphical interface to astrophysics databases that presents the user with the footprints of observations of space-based missions. It also aids astronomers in retrieving these data by sending requests to distributed data archives. The VIEWER is a reader of ADC astronomical catalogs and journal tables that allows subsetting of catalogs by column choices and range selection and provides database-like search capability within each table. With it, the user can easily find the table data most appropriate for their purposes and then download either the subset table or the original table. CATSEYE is a tool that plots output tables from the VIEWER (and soon AMASE), making exploring the datasets fast and easy. Having completed the basic functionality of these systems, we are enhancing the site to provide advanced functionality. These will include: market basket storage of tables and records of VIEWER output for IMPReSS and AstroBrowse queries, non-HTML table responses to AstroBrowse type queries, general column arithmetic, modularity to allow entrance into the sequence of web pages at any point, histogram plots, navigable maps, and overplotting of catalog objects on mission footprint maps. When completed, the ADF/ADC web facilities will provide astronomical tabled data and mission retrieval information in several hyperlinked environments geared for users at any level, from the school student to the typical astronomer to the expert datamining tools at state-of-the-art data centers.

Genome Sequences and Phylogenetic Analysis of K88- and F18-Positive Porcine Enterotoxigenic Escherichia coli

PubMed Central

Shepard, Sara M.; Danzeisen, Jessica L.; Isaacson, Richard E.; Seemann, Torsten; Achtman, Mark

2012-01-01

Porcine enterotoxigenic Escherichia coli (ETEC) continues to result in major morbidity and mortality in the swine industry via postweaning diarrhea. The key virulence factors of ETEC strains, their serotypes, and their fimbrial components have been well studied. However, most studies to date have focused on plasmid-encoded traits related to colonization and toxin production, and the chromosomal backgrounds of these strains have been largely understudied. Here, we generated the genomic sequences of K88-positive and F18-positive porcine ETEC strains and examined the phylogenetic distribution of clinical porcine ETEC strains and their plasmid-associated genetic content. The genomes of porcine ETEC strains UMNK88 and UMNF18 were both found to contain remarkable plasmid complements containing known virulence factors, potential novel virulence factors, and antimicrobial resistance-associated elements. The chromosomes of these strains also possessed several unique genomic islands containing hypothetical genes with similarity to classical virulence factors, although phage-associated genomic islands dominated the accessory genomes of these strains. Phylogenetic analysis of 78 clinical isolates associated with neonatal and porcine diarrhea revealed that a limited subset of porcine ETEC lineages exist that generally contain common toxin and fimbrial profiles, with many of the isolates belonging to the ST10, ST23, and ST169 multilocus sequencing types. These lineages were generally distinct from existing human ETEC database isolates. Overall, most porcine ETEC strains appear to have emerged from a limited subset of E. coli lineages that either have an increased propensity to carry plasmid-encoded virulence factors or have the appropriate ETEC core genome required for virulence. PMID:22081385

Assessing variability in the impacts of heat on health outcomes in New York City over time, season, and heat-wave duration.

PubMed

Sheridan, Scott C; Lin, Shao

2014-12-01

While the impacts of heat upon mortality and morbidity have been frequently studied, few studies have examined the relationship between heat, morbidity, and mortality across the same events. This research assesses the relationship between heat events and morbidity and mortality in New York City for the period 1991-2004. Heat events are defined based on oppressive weather types as determined by the Spatial Synoptic Classification. Morbidity data include hospitalizations for heat-related, respiratory, and cardiovascular causes; mortality data include these subsets as well as all-cause totals. Distributed-lag models assess the relationship between heat and health outcome for a cumulative 15-day period following exposure. To further refine analysis, subset analyses assess the differences between early- and late-season events, shorter and longer events, and earlier and later years. The strongest heat-health relationships occur with all-cause mortality, cardiovascular mortality, and heat-related hospital admissions. The impacts of heat are greater during longer heat events and during the middle of summer, when increased mortality is still statistically significant after accounting for mortality displacement. Early-season heat waves have increases in mortality that appear to be largely short-term displacement. The impacts of heat on mortality have decreased over time. Heat-related hospital admissions have increased during this time, especially during the earlier days of heat events. Given the trends observed, it suggests that a greater awareness of heat hazards may have led to increased short-term hospitalizations with a commensurate decrease in mortality.

Diffusion-plus-drift models for the mass leakage from centrifugal magnetospheres of magnetic hot-stars

NASA Astrophysics Data System (ADS)

Owocki, Stanley P.; Cranmer, Steven R.

2018-03-01

In the subset of luminous, early-type stars with strong, large-scale magnetic fields and moderate to rapid rotation, material from the star's radiatively driven stellar wind outflow becomes trapped by closed magnetic loops, forming a centrifugally supported, corotating magnetosphere. We present here a semi-analytic analysis of how this quasi-steady accumulation of wind mass can be balanced by losses associated with a combination of an outward, centrifugally driven drift in the region beyond the Kepler co-rotation radius, and an inward/outward diffusion near this radius. We thereby derive scaling relations for the equilibrium spatial distribution of mass, and the associated emission measure for observational diagnostics like Balmer line emission. We discuss the potential application of these relations for interpreting surveys of the emission line diagnostics for OB stars with centrifugally supported magnetospheres. For a specific model of turbulent field-line-wandering rooted in surface motions associated with the iron opacity bump, we estimate values for the associated diffusion and drift coefficients.

Assessment of ITS benefits : early results

DOT National Transportation Integrated Search

1995-08-01

The following text gives an overview of benefits : from many types of systems, with an emphasis on systems that have : realized benefits in real-world operation. Many of the benefits are : measured either system-wide or for a subset of the system, wh...

Integrated Task and Data Parallel Programming

NASA Technical Reports Server (NTRS)

Grimshaw, A. S.

1998-01-01

This research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers 1995 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.

Integrated Task And Data Parallel Programming: Language Design

NASA Technical Reports Server (NTRS)

Grimshaw, Andrew S.; West, Emily A.

1998-01-01

his research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers '95 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program m. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.

Accumulation of actin in subsets of pioneer growth cone filopodia in response to neural and epithelial guidance cues in situ

PubMed Central

1993-01-01

Directed outgrowth of neural processes must involve transmission of signals from the tips of filopodia to the central region of the growth cone. Here, we report on the distribution and dynamics of one possible element in this process, actin, in live growth cones which are reorienting in response to in situ guidance cues. In grasshopper embryonic limbs, pioneer growth cones respond to at least three types of guidance cues: a limb axis cue, intermediate target cells, and a circumferential band of epithelial cells. With time-lapse imaging of intracellularly injected rhodamine-phalloidin and rhodamine-actin, we monitored the distribution of actin during growth cone responses to these cues. In distal limb regions, accumulation of actin in filopodia and growth cone branches accompanies continued growth, while reduction of actin accompanies withdrawal. Where growth cones are reorienting to intermediate target cells, or along the circumferential epithelial band, actin selectively accumulates in the proximal regions of those filopodia that have contacted target cells or are extending along the band. Actin accumulations can be retrogradely transported along filopodia, and can extend into the central region of the growth cone. These results suggest that regulation and translocation of actin may be a significant element in growth cone steering. PMID:8227150

INFORM Lab: a testbed for high-level information fusion and resource management

NASA Astrophysics Data System (ADS)

Valin, Pierre; Guitouni, Adel; Bossé, Eloi; Wehn, Hans; Happe, Jens

2011-05-01

DRDC Valcartier and MDA have created an advanced simulation testbed for the purpose of evaluating the effectiveness of Network Enabled Operations in a Coastal Wide Area Surveillance situation, with algorithms provided by several universities. This INFORM Lab testbed allows experimenting with high-level distributed information fusion, dynamic resource management and configuration management, given multiple constraints on the resources and their communications networks. This paper describes the architecture of INFORM Lab, the essential concepts of goals and situation evidence, a selected set of algorithms for distributed information fusion and dynamic resource management, as well as auto-configurable information fusion architectures. The testbed provides general services which include a multilayer plug-and-play architecture, and a general multi-agent framework based on John Boyd's OODA loop. The testbed's performance is demonstrated on 2 types of scenarios/vignettes for 1) cooperative search-and-rescue efforts, and 2) a noncooperative smuggling scenario involving many target ships and various methods of deceit. For each mission, an appropriate subset of Canadian airborne and naval platforms are dispatched to collect situation evidence, which is fused, and then used to modify the platform trajectories for the most efficient collection of further situation evidence. These platforms are fusion nodes which obey a Command and Control node hierarchy.

Stress Prediction for Distributed Structural Health Monitoring Using Existing Measurements and Pattern Recognition.

PubMed

Lu, Wei; Teng, Jun; Zhou, Qiushi; Peng, Qiexin

2018-02-01

The stress in structural steel members is the most useful and directly measurable physical quantity to evaluate the structural safety in structural health monitoring, which is also an important index to evaluate the stress distribution and force condition of structures during structural construction and service phases. Thus, it is common to set stress as a measure in steel structural monitoring. Considering the economy and the importance of the structural members, there are only a limited number of sensors that can be placed, which means that it is impossible to obtain the stresses of all members directly using sensors. This study aims to develop a stress response prediction method for locations where there are insufficent sensors, using measurements from a limited number of sensors and pattern recognition. The detailed improved aspects are: (1) a distributed computing process is proposed, where the same pattern is recognized by several subsets of measurements; and (2) the pattern recognition using the subset of measurements is carried out by considering the optimal number of sensors and number of fusion patterns. The validity and feasibility of the proposed method are verified using two examples: the finite-element simulation of a single-layer shell-like steel structure, and the structural health monitoring of the space steel roof of Shenzhen Bay Stadium; for the latter, the anti-noise performance of this method is verified by the stress measurements from a real-world project.

Field size, length, and width distributions based on LACIE ground truth data. [large area crop inventory experiment

NASA Technical Reports Server (NTRS)

Pitts, D. E.; Badhwar, G.

1980-01-01

The development of agricultural remote sensing systems requires knowledge of agricultural field size distributions so that the sensors, sampling frames, image interpretation schemes, registration systems, and classification systems can be properly designed. Malila et al. (1976) studied the field size distribution for wheat and all other crops in two Kansas LACIE (Large Area Crop Inventory Experiment) intensive test sites using ground observations of the crops and measurements of their field areas based on current year rectified aerial photomaps. The field area and size distributions reported in the present investigation are derived from a representative subset of a stratified random sample of LACIE sample segments. In contrast to previous work, the obtained results indicate that most field-size distributions are not log-normally distributed. The most common field size observed in this study was 10 acres for most crops studied.

Short-term capture of the Earth-Moon system

NASA Astrophysics Data System (ADS)

Qi, Yi; de Ruiter, Anton

2018-06-01

In this paper, the short-term capture (STC) of an asteroid in the Earth-Moon system is proposed and investigated. First, the space condition of STC is analysed and five subsets of the feasible region are defined and discussed. Then, the time condition of STC is studied by parameter scanning in the Sun-Earth-Moon-asteroid restricted four-body problem. Numerical results indicate that there is a clear association between the distributions of the time probability of STC and the five subsets. Next, the influence of the Jacobi constant on STC is examined using the space and time probabilities of STC. Combining the space and time probabilities of STC, we propose a STC index to evaluate the probability of STC comprehensively. Finally, three potential STC asteroids are found and analysed.

Ocean Surface Topography Data Products and Tools

NASA Technical Reports Server (NTRS)

Case, Kelley E.; Bingham, Andrew W.; Berwin, Robert W.; Rigor, Eric M.; Raskin, Robert G.

2004-01-01

The Physical Oceanography Distributed Active Archiving Center (PO.DAAC), NASA's primary data center for archiving and distributing oceanographic data, is supporting the Jason and TOPEX/Poseidon satellite tandem missions by providing a variety of data products, tools, and distribution methods to the wider scientific and general community. PO.DAAC has developed several new data products for sea level residual measurements, providing a longterm climate data record from 1992 to the present These products provide compatible measurements of sea level residuals for the entire time series including the tandem TOPEX/Poseidon and Jason mission. Several data distribution tool. are available from NASA PO.DAAC. The Near-Real-Time Image Distribution Server (NEREIDS) provides quicklook browse images and binary data files The PO.DAAC Ocean ESIP Tool (POET) provides interactive, on-tine data subsetting and visualization for several altimetry data products.

Genetic hotels for the standard genetic code: evolutionary analysis based upon novel three-dimensional algebraic models.

PubMed

José, Marco V; Morgado, Eberto R; Govezensky, Tzipe

2011-07-01

Herein, we rigorously develop novel 3-dimensional algebraic models called Genetic Hotels of the Standard Genetic Code (SGC). We start by considering the primeval RNA genetic code which consists of the 16 codons of type RNY (purine-any base-pyrimidine). Using simple algebraic operations, we show how the RNA code could have evolved toward the current SGC via two different intermediate evolutionary stages called Extended RNA code type I and II. By rotations or translations of the subset RNY, we arrive at the SGC via the former (type I) or via the latter (type II), respectively. Biologically, the Extended RNA code type I, consists of all codons of the type RNY plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The Extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. Since the dimensions of remarkable subsets of the Genetic Hotels are not necessarily integer numbers, we also introduce the concept of algebraic fractal dimension. A general decoding function which maps each codon to its corresponding amino acid or the stop signals is also derived. The Phenotypic Hotel of amino acids is also illustrated. The proposed evolutionary paths are discussed in terms of the existing theories of the evolution of the SGC. The adoption of 3-dimensional models of the Genetic and Phenotypic Hotels will facilitate the understanding of the biological properties of the SGC.

Saltmarsh Boundary Modulates Dispersal of Mangrove Propagules: Implications for Mangrove Migration with Sea-Level Rise

PubMed Central

Peterson, Jennifer M.; Bell, Susan S.

2015-01-01

Few studies have empirically examined the suite of mechanisms that underlie the distributional shifts displayed by organisms in response to changing climatic condition. Mangrove forests are expected to move inland as sea-level rises, encroaching on saltmarsh plants inhabiting higher elevations. Mangrove propagules are transported by tidal waters and propagule dispersal is likely modified upon encountering the mangrove-saltmarsh ecotone, the implications of which are poorly known. Here, using an experimental approach, we record landward and seaward dispersal and subsequent establishment of mangrove propagules that encounter biotic boundaries composed of two types of saltmarsh taxa: succulents and grasses. Our findings revealed that propagules emplaced within saltmarsh vegetation immediately landward of the extant mangrove fringe boundary frequently dispersed in the seaward direction. However, propagules moved seaward less frequently and over shorter distances upon encountering boundaries composed of saltmarsh grasses versus succulents. We uniquely confirmed that the small subset of propagules dispersing landward displayed proportionately higher establishment success than those transported seaward. Although impacts of ecotones on plant dispersal have rarely been investigated in situ, our experimental results indicate that the interplay between tidal transport and physical attributes of saltmarsh vegetation influence boundary permeability to propagules, thereby directing the initial phase of shifting mangrove distributions. The incorporation of tidal inundation information and detailed data on landscape features, such as the structure of saltmarsh vegetation at mangrove boundaries, should improve the accuracy of models that are being developed to forecast mangrove distributional shifts in response to sea-level rise. PMID:25760867

Saltmarsh boundary modulates dispersal of mangrove propagules: implications for mangrove migration with sea-level rise.

PubMed

Peterson, Jennifer M; Bell, Susan S

2015-01-01

Few studies have empirically examined the suite of mechanisms that underlie the distributional shifts displayed by organisms in response to changing climatic condition. Mangrove forests are expected to move inland as sea-level rises, encroaching on saltmarsh plants inhabiting higher elevations. Mangrove propagules are transported by tidal waters and propagule dispersal is likely modified upon encountering the mangrove-saltmarsh ecotone, the implications of which are poorly known. Here, using an experimental approach, we record landward and seaward dispersal and subsequent establishment of mangrove propagules that encounter biotic boundaries composed of two types of saltmarsh taxa: succulents and grasses. Our findings revealed that propagules emplaced within saltmarsh vegetation immediately landward of the extant mangrove fringe boundary frequently dispersed in the seaward direction. However, propagules moved seaward less frequently and over shorter distances upon encountering boundaries composed of saltmarsh grasses versus succulents. We uniquely confirmed that the small subset of propagules dispersing landward displayed proportionately higher establishment success than those transported seaward. Although impacts of ecotones on plant dispersal have rarely been investigated in situ, our experimental results indicate that the interplay between tidal transport and physical attributes of saltmarsh vegetation influence boundary permeability to propagules, thereby directing the initial phase of shifting mangrove distributions. The incorporation of tidal inundation information and detailed data on landscape features, such as the structure of saltmarsh vegetation at mangrove boundaries, should improve the accuracy of models that are being developed to forecast mangrove distributional shifts in response to sea-level rise.

IFN-α and CD46 stimulation are associated with active lupus and skew natural T regulatory cell differentiation to type 1 regulatory T (Tr1) cells

PubMed Central

Le Buanec, Hélène; Gougeon, Marie-Lise; Mathian, Alexis; Lebon, Pierre; Dupont, Jean-Michel; Peltre, Gabriel; Hemon, Patrice; Schmid, Michel; Bizzini, Bernard; Künding, Thomas; Burny, Arsène; Bensussan, Armand; Amoura, Zahir; Gallo, Robert C.; Zagury, Daniel

2011-01-01

Immune suppressive activities exerted by regulatory T-cell subsets have several specific functions, including self-tolerance and regulation of adaptive immune reactions, and their dysfunction can lead to autoimmune diseases and contribute to AIDS and cancer. Two functionally distinct regulatory T-cell subsets are currently identified in peripheral tissues: thymus-developed natural T regulatory cells (nTregs) controlling self-tolerance and antiinflammatory IL-10–secreting type 1 regulatory T cells (Tr1) derived from Ag-stimulated T cells, which regulate inflammation-dependent adaptive immunity and minimize immunopathology. We establish herein that cell contact-mediated nTreg regulatory function is inhibited by inflammation, especially in the presence of the complement C3b receptor (CD46). Instead, as with other T-cell subsets, the latter inflammatory conditions of stimulation skew nTreg differentiation to Tr1 cells secreting IL-10, an effect potentiated by IFN-α. The clinical relevance of these findings was verified in a study of 152 lupus patients, in which we showed that lupus nTreg dysfunction is not due to intrinsic defects but is rather induced by C3b stimulation of CD46 and IFN-α and that these immune components of inflammation are directly associated with active lupus. These results provide a rationale for using anti–IFN-α Ab immunotherapy in lupus patients. PMID:22065791

Resilient Distributed Estimation Through Adversary Detection

NASA Astrophysics Data System (ADS)

Chen, Yuan; Kar, Soummya; Moura, Jose M. F.

2018-05-01

This paper studies resilient multi-agent distributed estimation of an unknown vector parameter when a subset of the agents is adversarial. We present and analyze a Flag Raising Distributed Estimator ($\\mathcal{FRDE}$) that allows the agents under attack to perform accurate parameter estimation and detect the adversarial agents. The $\\mathcal{FRDE}$ algorithm is a consensus+innovations estimator in which agents combine estimates of neighboring agents (consensus) with local sensing information (innovations). We establish that, under $\\mathcal{FRDE}$, either the uncompromised agents' estimates are almost surely consistent or the uncompromised agents detect compromised agents if and only if the network of uncompromised agents is connected and globally observable. Numerical examples illustrate the performance of $\\mathcal{FRDE}$.

Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks.

PubMed

Pellacani, Davide; Bilenky, Misha; Kannan, Nagarajan; Heravi-Moussavi, Alireza; Knapp, David J H F; Gakkhar, Sitanshu; Moksa, Michelle; Carles, Annaick; Moore, Richard; Mungall, Andrew J; Marra, Marco A; Jones, Steven J M; Aparicio, Samuel; Hirst, Martin; Eaves, Connie J

2016-11-15

The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines. Each genome-wide analysis contains profiles for six histone marks, methylated DNA, and RNA transcripts. Analysis of these datasets shows that each cell type has unique features, primarily within genomic regulatory regions, and that the cell lines group together. Analyses of the promoter and enhancer profiles place the luminal progenitors in between the basal cells and the non-progenitor luminal subset. Integrative analysis reveals networks of subset-specific transcription factors. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

The Cross-Entropy Based Multi-Filter Ensemble Method for Gene Selection.

PubMed

Sun, Yingqiang; Lu, Chengbo; Li, Xiaobo

2018-05-17

The gene expression profile has the characteristics of a high dimension, low sample, and continuous type, and it is a great challenge to use gene expression profile data for the classification of tumor samples. This paper proposes a cross-entropy based multi-filter ensemble (CEMFE) method for microarray data classification. Firstly, multiple filters are used to select the microarray data in order to obtain a plurality of the pre-selected feature subsets with a different classification ability. The top N genes with the highest rank of each subset are integrated so as to form a new data set. Secondly, the cross-entropy algorithm is used to remove the redundant data in the data set. Finally, the wrapper method, which is based on forward feature selection, is used to select the best feature subset. The experimental results show that the proposed method is more efficient than other gene selection methods and that it can achieve a higher classification accuracy under fewer characteristic genes.

Neural network-based distributed attitude coordination control for spacecraft formation flying with input saturation.

PubMed

Zou, An-Min; Kumar, Krishna Dev

2012-07-01

This brief considers the attitude coordination control problem for spacecraft formation flying when only a subset of the group members has access to the common reference attitude. A quaternion-based distributed attitude coordination control scheme is proposed with consideration of the input saturation and with the aid of the sliding-mode observer, separation principle theorem, Chebyshev neural networks, smooth projection algorithm, and robust control technique. Using graph theory and a Lyapunov-based approach, it is shown that the distributed controller can guarantee the attitude of all spacecraft to converge to a common time-varying reference attitude when the reference attitude is available only to a portion of the group of spacecraft. Numerical simulations are presented to demonstrate the performance of the proposed distributed controller.

Statistical detection of patterns in unidimensional distributions by continuous wavelet transforms

NASA Astrophysics Data System (ADS)

Baluev, R. V.

2018-04-01

Objective detection of specific patterns in statistical distributions, like groupings or gaps or abrupt transitions between different subsets, is a task with a rich range of applications in astronomy: Milky Way stellar population analysis, investigations of the exoplanets diversity, Solar System minor bodies statistics, extragalactic studies, etc. We adapt the powerful technique of the wavelet transforms to this generalized task, making a strong emphasis on the assessment of the patterns detection significance. Among other things, our method also involves optimal minimum-noise wavelets and minimum-noise reconstruction of the distribution density function. Based on this development, we construct a self-closed algorithmic pipeline aimed to process statistical samples. It is currently applicable to single-dimensional distributions only, but it is flexible enough to undergo further generalizations and development.

77 FR 43879 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Designation of a Longer Period for...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-26

... Proposed Rule Change Amending NYSE Arca Equities Rule 7.31(h) To Add a PL Select Order Type July 20, 2012...(h) to add a PL Select Order type. The proposed rule change was published for comment in the Federal... security at a specified, undisplayed price. The PL Select Order would be a subset of the PL Order that...

CD4+VEGFR1(HIGH) T cell as a novel Treg subset regulates inflammatory bowel disease in lymphopenic mice.

PubMed

Shin, Jin-Young; Yoon, Il-Hee; Lim, Jong-Hyung; Shin, Jun-Seop; Nam, Hye-Young; Kim, Yong-Hee; Cho, Hyoung-Soo; Hong, So-Hee; Kim, Jung-Sik; Lee, Won-Woo; Park, Chung-Gyu

2015-09-01

Regulatory T cells (Tregs) are a specialized subpopulation of T cells that control the immune response and thereby maintain immune system homeostasis and tolerance to self-antigens. Many subsets of CD4(+) Tregs have been identified, including Foxp3(+), Tr1, Th3, and Foxp3neg iT(R)35 cells. In this study, we identified a new subset of CD4(+)VEGFR1(high) Tregs that have immunosuppressive capacity. CD4(+)VEGFR1high T cells, which constitute approximately 1.0% of CD4(+) T cells, are hyporesponsive to T-cell antigen receptor stimulation. Surface marker and FoxP3 expression analysis revealed that CD4(+)VEGFR1(high) T cells are distinct from known Tregs. CD4(+)VEGFR1(high) T cells suppressed the proliferation of CD4(+)CD25(-) T cell as efficiently as CD4(+)CD25(high) natural Tregs in a contact-independent manner. Furthermore, adoptive transfer of CD4(+)VEGFR1(+) T cells from wild type to RAG-2-deficient C57BL/6 mice inhibited effector T-cell-mediated inflammatory bowel disease. Thus, we report CD4(+) VEGFR1(high) T cells as a novel subset of Tregs that regulate the inflammatory response in the intestinal tract.

Reducing seed dependent variability of non-uniformly sampled multidimensional NMR data

NASA Astrophysics Data System (ADS)

Mobli, Mehdi

2015-07-01

The application of NMR spectroscopy to study the structure, dynamics and function of macromolecules requires the acquisition of several multidimensional spectra. The one-dimensional NMR time-response from the spectrometer is extended to additional dimensions by introducing incremented delays in the experiment that cause oscillation of the signal along "indirect" dimensions. For a given dimension the delay is incremented at twice the rate of the maximum frequency (Nyquist rate). To achieve high-resolution requires acquisition of long data records sampled at the Nyquist rate. This is typically a prohibitive step due to time constraints, resulting in sub-optimal data records to the detriment of subsequent analyses. The multidimensional NMR spectrum itself is typically sparse, and it has been shown that in such cases it is possible to use non-Fourier methods to reconstruct a high-resolution multidimensional spectrum from a random subset of non-uniformly sampled (NUS) data. For a given acquisition time, NUS has the potential to improve the sensitivity and resolution of a multidimensional spectrum, compared to traditional uniform sampling. The improvements in sensitivity and/or resolution achieved by NUS are heavily dependent on the distribution of points in the random subset acquired. Typically, random points are selected from a probability density function (PDF) weighted according to the NMR signal envelope. In extreme cases as little as 1% of the data is subsampled. The heavy under-sampling can result in poor reproducibility, i.e. when two experiments are carried out where the same number of random samples is selected from the same PDF but using different random seeds. Here, a jittered sampling approach is introduced that is shown to improve random seed dependent reproducibility of multidimensional spectra generated from NUS data, compared to commonly applied NUS methods. It is shown that this is achieved due to the low variability of the inherent sensitivity of the random subset chosen from a given PDF. Finally, it is demonstrated that metrics used to find optimal NUS distributions are heavily dependent on the inherent sensitivity of the random subset, and such optimisation is therefore less critical when using the proposed sampling scheme.

Tachykinins Stimulate a Subset of Mouse Taste Cells

PubMed Central

Grant, Jeff

2012-01-01

The tachykinins substance P (SP) and neurokinin A (NKA) are present in nociceptive sensory fibers expressing transient receptor potential cation channel, subfamily V, member 1 (TRPV1). These fibers are found extensively in and around the taste buds of several species. Tachykinins are released from nociceptive fibers by irritants such as capsaicin, the active compound found in chili peppers commonly associated with the sensation of spiciness. Using real-time Ca2+-imaging on isolated taste cells, it was observed that SP induces Ca2+ -responses in a subset of taste cells at concentrations in the low nanomolar range. These responses were reversibly inhibited by blocking the SP receptor NK-1R. NKA also induced Ca2+-responses in a subset of taste cells, but only at concentrations in the high nanomolar range. These responses were only partially inhibited by blocking the NKA receptor NK-2R, and were also inhibited by blocking NK-1R indicating that NKA is only active in taste cells at concentrations that activate both receptors. In addition, it was determined that tachykinin signaling in taste cells requires Ca2+-release from endoplasmic reticulum stores. RT-PCR analysis further confirmed that mouse taste buds express NK-1R and NK-2R. Using Ca2+-imaging and single cell RT-PCR, it was determined that the majority of tachykinin-responsive taste cells were Type I (Glial-like) and umami-responsive Type II (Receptor) cells. Importantly, stimulating NK-1R had an additive effect on Ca2+ responses evoked by umami stimuli in Type II (Receptor) cells. This data indicates that tachykinin release from nociceptive sensory fibers in and around taste buds may enhance umami and other taste modalities, providing a possible mechanism for the increased palatability of spicy foods. PMID:22363709

Dense transient receptor potential cation channel, vanilloid family, type 2 (TRPV2) immunoreactivity defines a subset of motoneurons in the dorsal lateral nucleus of the spinal cord, the nucleus ambiguus and the trigeminal motor nucleus in rat.

PubMed

Lewinter, R D; Scherrer, G; Basbaum, A I

2008-01-02

The transient receptor potential cation channel, vanilloid family, type 2 (TRPV2) is a member of the TRPV family of proteins and is a homologue of the capsaicin/vanilloid receptor (transient receptor potential cation channel, vanilloid family, type 1, TRPV1). Like TRPV1, TRPV2 is expressed in a subset of dorsal root ganglia (DRG) neurons that project to superficial laminae of the spinal cord dorsal horn. Because noxious heat (>52 degrees C) activates TRPV2 in transfected cells this channel has been implicated in the processing of high intensity thermal pain messages in vivo. In contrast to TRPV1, however, which is restricted to small diameter DRG neurons, there is significant TRPV2 immunoreactivity in a variety of CNS regions. The present report focuses on a subset of neurons in the brainstem and spinal cord of the rat including the dorsal lateral nucleus (DLN) of the spinal cord, the nucleus ambiguus, and the motor trigeminal nucleus. Double label immunocytochemistry with markers of motoneurons, combined with retrograde labeling, established that these cells are, in fact, motoneurons. With the exception of their smaller diameter, these cells did not differ from other motoneurons, which are only lightly TRPV2-immunoreactive. As for the majority of DLN neurons, the densely-labeled populations co-express androgen receptor and follow normal DLN ontogeny. The functional significance of the very intense TRPV2 expression in these three distinct spinal cord and brainstem motoneurons groups remains to be determined.

Random or predictable?: Adoption patterns of chronic care management practices in physician organizations.

PubMed

Miake-Lye, Isomi M; Chuang, Emmeline; Rodriguez, Hector P; Kominski, Gerald F; Yano, Elizabeth M; Shortell, Stephen M

2017-08-24

Theories, models, and frameworks used by implementation science, including Diffusion of Innovations, tend to focus on the adoption of one innovation, when often organizations may be facing multiple simultaneous adoption decisions. For instance, despite evidence that care management practices (CMPs) are helpful in managing chronic illness, there is still uneven adoption by physician organizations. This exploratory paper leverages this natural variation in uptake to describe inter-organizational patterns in adoption of CMPs and to better understand how adoption choices may be related to one another. We assessed a cross section of national survey data from physician organizations reporting on the use of 20 CMPs (5 each for asthma, congestive heart failure, depression, and diabetes). Item response theory was used to explore patterns in adoption, first considering all 20 CMPs together and then by subsets according to disease focus or CMP type (e.g., registries, patient reminders). Mokken scale analysis explored whether adoption choices were linked by disease focus or CMP type and whether a consistent ordering of adoption choices was present. The Mokken scale for all 20 CMPs demonstrated medium scalability (H = 0.43), but no consistent ordering. Scales for subsets of CMPs sharing a disease focus had medium scalability (0.4 < H < 0.5), while subsets sharing a CMP type had strong scalability (H > 0.5). Scales for CMP type consistently ranked diabetes CMPs as most adoptable and depression CMPs as least adoptable. Within disease focus scales, patient reminders were ranked as the most adoptable CMP, while clinician feedback and patient education were ranked the least adoptable. Patterns of adoption indicate that innovation characteristics may influence adoption. CMP dissemination efforts may be strengthened by encouraging traditionally non-adopting organizations to focus on more adoptable practices first and then describing a pathway for the adoption of subsequent CMPs. Clarifying why certain CMPs are "less adoptable" may also provide insights into how to overcome CMP adoption constraints.

Distributional Analysis of the Transposed-Letter Neighborhood Effect on Naming Latency

ERIC Educational Resources Information Center

Johnson, Rebecca L.; Staub, Adrian; Fleri, Amanda M.

2012-01-01

Printed words that have a transposed-letter (TL) neighbor (e.g., angel has the TL neighbor angle) have been shown to be more difficult to process, in a range of paradigms, than words that do not have a TL neighbor. However, eye movement evidence suggests that this processing difficulty may occur on only a subset of trials. To investigate this…

A Scalable and Robust Multi-Agent Approach to Distributed Optimization

NASA Technical Reports Server (NTRS)

Tumer, Kagan

2005-01-01

Modularizing a large optimization problem so that the solutions to the subproblems provide a good overall solution is a challenging problem. In this paper we present a multi-agent approach to this problem based on aligning the agent objectives with the system objectives, obviating the need to impose external mechanisms to achieve collaboration among the agents. This approach naturally addresses scaling and robustness issues by ensuring that the agents do not rely on the reliable operation of other agents We test this approach in the difficult distributed optimization problem of imperfect device subset selection [Challet and Johnson, 2002]. In this problem, there are n devices, each of which has a "distortion", and the task is to find the subset of those n devices that minimizes the average distortion. Our results show that in large systems (1000 agents) the proposed approach provides improvements of over an order of magnitude over both traditional optimization methods and traditional multi-agent methods. Furthermore, the results show that even in extreme cases of agent failures (i.e., half the agents fail midway through the simulation) the system remains coordinated and still outperforms a failure-free and centralized optimization algorithm.

Isotropic probability measures in infinite dimensional spaces: Inverse problems/prior information/stochastic inversion

NASA Technical Reports Server (NTRS)

Backus, George

1987-01-01

Let R be the real numbers, R(n) the linear space of all real n-tuples, and R(infinity) the linear space of all infinite real sequences x = (x sub 1, x sub 2,...). Let P sub n :R(infinity) approaches R(n) be the projection operator with P sub n (x) = (x sub 1,...,x sub n). Let p(infinity) be a probability measure on the smallest sigma-ring of subsets of R(infinity) which includes all of the cylinder sets P sub n(-1) (B sub n), where B sub n is an arbitrary Borel subset of R(n). Let p sub n be the marginal distribution of p(infinity) on R(n), so p sub n(B sub n) = p(infinity)(P sub n to the -1(B sub n)) for each B sub n. A measure on R(n) is isotropic if it is invariant under all orthogonal transformations of R(n). All members of the set of all isotropic probability distributions on R(n) are described. The result calls into question both stochastic inversion and Bayesian inference, as currently used in many geophysical inverse problems.

Incomplete and inconsistent information provided to men making decisions for treatment of early-stage prostate cancer.

PubMed

Snow, Stephanie L; Panton, Rachel L; Butler, Lorna J; Wilke, Derek R; Rutledge, Robert D H; Bell, David G; Rendon, Ricardo A

2007-05-01

To determine whether there is a gap between what patients know about early-stage prostate cancer and what they need to know to make treatment decisions, and whether the information patients receive varies depending on their treating physician. Needs assessment was performed using a questionnaire consisting of 41 statements about early-stage prostate cancer. Statements were divided into six thematic subsets. Participants used a 5-point Likert scale to rate statements in terms of knowledge of the information and importance to a treatment decision. Information gaps were defined as significant difference between the importance and knowledge of an item. Descriptive statistics were used to describe demographic subscale scores. The information gap was analyzed by a paired t test for each thematic subset. One-way analyses of variance were used to detect any differences on the basis of treating physician. Questionnaires were distributed to 270 men (135 treated by radical prostatectomy, 135 by external beam radiotherapy). The return rate was 51% (138 questionnaires). A statistically significant information gap was found among all six thematic subsets, with five of the six P values less than 0.0001. Statistically significant variation was observed in the amount of information patients received from their treating physicians among four of the thematic subsets. There is an information gap between what early-stage prostate cancer patients need to know and the information they receive. Additionally there is a difference in the amount of information provided by different physicians.

Functional Differences between Human NKp44(-) and NKp44(+) RORC(+) Innate Lymphoid Cells.

PubMed

Hoorweg, Kerim; Peters, Charlotte P; Cornelissen, Ferry; Aparicio-Domingo, Patricia; Papazian, Natalie; Kazemier, Geert; Mjösberg, Jenny M; Spits, Hergen; Cupedo, Tom

2012-01-01

Human RORC(+) lymphoid tissue inducer cells are part of a rapidly expanding family of innate lymphoid cells (ILC) that participate in innate and adaptive immune responses as well as in lymphoid tissue (re) modeling. The assessment of a potential role for innate lymphocyte-derived cytokines in human homeostasis and disease is hampered by a poor characterization of RORC(+) innate cell subsets and a lack of knowledge on the distribution of these cells in adults. Here we show that functionally distinct subsets of human RORC(+) innate lymphoid cells are enriched for secretion of IL-17a or IL-22. Both subsets have an activated phenotype and can be distinguished based on the presence or absence of the natural cytotoxicity receptor NKp44. NKp44(+) IL-22 producing cells are present in tonsils while NKp44(-) IL-17a producing cells are present in fetal developing lymph nodes. Development of human intestinal NKp44(+) ILC is a programmed event that is independent of bacterial colonization and these cells colonize the fetal intestine during the first trimester. In the adult intestine, NKp44(+) ILC are the main ILC subset producing IL-22. NKp44(-) ILC remain present throughout adulthood in peripheral non-inflamed lymph nodes as resting, non-cytokine producing cells. However, upon stimulation lymph node ILC can swiftly initiate cytokine transcription suggesting that secondary human lymphoid organs may function as a reservoir for innate lymphoid cells capable of participating in inflammatory responses.

Systematic pan-cancer analysis reveals immune cell interactions in the tumor microenvironment

PubMed Central

Varn, Frederick S.; Wang, Yue; Mullins, David W.; Fiering, Steven; Cheng, Chao

2017-01-01

With the recent advent of immunotherapy, there is a critical need to understand immune cell interactions in the tumor microenvironment in both pan-cancer and tissue-specific contexts. Multi-dimensional datasets have enabled systematic approaches to dissect these interactions in large numbers of patients, furthering our understanding of the patient immune response to solid tumors. Using an integrated approach, we inferred the infiltration levels of distinct immune cell subsets in 23 tumor types from The Cancer Genome Atlas. From these quantities, we constructed a co-infiltration network, revealing interactions between cytolytic cells and myeloid cells in the tumor microenvironment. By integrating patient mutation data, we found that while mutation burden was associated with immune infiltration differences between distinct tumor types, additional factors likely explained differences between tumors originating from the same tissue. We concluded this analysis by examining the prognostic value of individual immune cell subsets as well as how co-infiltration of functionally discordant cell types associated with patient survival. In multiple tumor types, we found that the protective effect of CD8+ T cell infiltration was heavily modulated by co-infiltration of macrophages and other myeloid cell types, suggesting the involvement of myeloid-derived suppressor cells in tumor development. Our findings illustrate complex interactions between different immune cell types in the tumor microenvironment and indicate these interactions play meaningful roles in patient survival. These results demonstrate the importance of personalized immune response profiles when studying the factors underlying tumor immunogenicity and immunotherapy response. PMID:28126714

Evidence for Sexual Reproduction: Identification, Frequency, and Spatial Distribution of Venturia effusa (Pecan Scab) Mating Type Idiomorphs.

PubMed

Young, Carolyn A; Bock, Clive H; Charlton, Nikki D; Mattupalli, Chakradhar; Krom, Nick; Bowen, Joanna K; Templeton, Matthew; Plummer, Kim M; Wood, Bruce W

2018-05-10

Venturia effusa (syn. Fusicladium effusum), causal agent of pecan scab, is the most prevalent pathogen of pecan (Carya illinoinensis), causing severe yield losses in the southeastern United States. V. effusa is currently known only by its asexual (conidial) stage. However, the degree and distribution of genetic diversity observed within and among populations of V. effusa are typical of a sexually reproducing fungal pathogen, and comparable with other dothideomycetes with a known sexual stage, including the closely related apple scab pathogen, V. inaequalis. Using the mating type (MAT) idiomorphs from V. inaequalis, we identified a single MAT gene, MAT1-1-1, in a draft genome of V. effusa. The MAT1-1-1 locus is flanked by two conserved genes encoding a DNA lyase (APN2) and a hypothetical protein. The MAT locus spanning the flanking genes was amplified and sequenced from a subset of 14 isolates, of which 7 contained MAT1-1-1 and the remaining samples contained MAT1-2-1. A multiplex polymerase chain reaction screen was developed to amplify MAT1-1-1, MAT1-2-1, and a conserved reference gene encoding β-tubulin, and used to screen 784 monoconidial isolates of V. effusa collected from 11 populations of pecan across the southeastern United States. A hierarchical sampling protocol representing region, orchard, and tree allowed for analysis of MAT structure at different spatial scales. Analysis of this collection revealed the frequency of the MAT idiomorphs is in a 1:1 equilibrium of MAT1-1:MAT1-2. The apparent equilibrium of the MAT idiomorphs provides impetus for a renewed effort to search for the sexual stage of V. effusa. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Effect of species rarity on the accuracy of species distribution models for reptiles and amphibians in southern California

USGS Publications Warehouse

Franklin, J.; Wejnert, K.E.; Hathaway, S.A.; Rochester, C.J.; Fisher, R.N.

2009-01-01

Aim: Several studies have found that more accurate predictive models of species' occurrences can be developed for rarer species; however, one recent study found the relationship between range size and model performance to be an artefact of sample prevalence, that is, the proportion of presence versus absence observations in the data used to train the model. We examined the effect of model type, species rarity class, species' survey frequency, detectability and manipulated sample prevalence on the accuracy of distribution models developed for 30 reptile and amphibian species. Location: Coastal southern California, USA. Methods: Classification trees, generalized additive models and generalized linear models were developed using species presence and absence data from 420 locations. Model performance was measured using sensitivity, specificity and the area under the curve (AUC) of the receiver-operating characteristic (ROC) plot based on twofold cross-validation, or on bootstrapping. Predictors included climate, terrain, soil and vegetation variables. Species were assigned to rarity classes by experts. The data were sampled to generate subsets with varying ratios of presences and absences to test for the effect of sample prevalence. Join count statistics were used to characterize spatial dependence in the prediction errors. Results: Species in classes with higher rarity were more accurately predicted than common species, and this effect was independent of sample prevalence. Although positive spatial autocorrelation remained in the prediction errors, it was weaker than was observed in the species occurrence data. The differences in accuracy among model types were slight. Main conclusions: Using a variety of modelling methods, more accurate species distribution models were developed for rarer than for more common species. This was presumably because it is difficult to discriminate suitable from unsuitable habitat for habitat generalists, and not as an artefact of the effect of sample prevalence on model estimation. ?? 2008 The Authors.

The use of decision tree induction and artificial neural networks for recognizing the geochemical distribution patterns of LREE in the Choghart deposit, Central Iran

NASA Astrophysics Data System (ADS)

Zaremotlagh, S.; Hezarkhani, A.

2017-04-01

Some evidences of rare earth elements (REE) concentrations are found in iron oxide-apatite (IOA) deposits which are located in Central Iranian microcontinent. There are many unsolved problems about the origin and metallogenesis of IOA deposits in this district. Although it is considered that felsic magmatism and mineralization were simultaneous in the district, interaction of multi-stage hydrothermal-magmatic processes within the Early Cambrian volcano-sedimentary sequence probably caused some epigenetic mineralizations. Secondary geological processes (e.g., multi-stage mineralization, alteration, and weathering) have affected on variations of major elements and possible redistribution of REE in IOA deposits. Hence, the geochemical behaviors and distribution patterns of REE are expected to be complicated in different zones of these deposits. The aim of this paper is recognizing LREE distribution patterns based on whole-rock chemical compositions and automatic discovery of their geochemical rules. For this purpose, the pattern recognition techniques including decision tree and neural network were applied on a high-dimensional geochemical dataset from Choghart IOA deposit. Because some data features were irrelevant or redundant in recognizing the distribution patterns of each LREE, a greedy attribute subset selection technique was employed to select the best subset of predictors used in classification tasks. The decision trees (CART algorithm) were pruned optimally to more accurately categorize independent test data than unpruned ones. The most effective classification rules were extracted from the pruned tree to describe the meaningful relationships between the predictors and different concentrations of LREE. A feed-forward artificial neural network was also applied to reliably predict the influence of various rock compositions on the spatial distribution patterns of LREE with a better performance than the decision tree induction. The findings of this study could be effectively used to visualize the LREE distribution patterns as geochemical maps.

Evaluation of Sixth Edition of AJCC Staging System for Nasopharyngeal Carcinoma and Proposed Improvement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu Mengzhong; Tang Linglong; Zong Jingfeng

2008-03-15

Purpose: To evaluate the 6th edition of the International Union Against Cancer/American Joint Committee on Cancer staging system for nasopharyngeal carcinoma and to search for ways to improve the system. Methods and Materials: We performed a retrospective review of data from 749 biopsy-proven nonmetastatic nasopharyngeal carcinoma patients. All patients had undergone contrast-enhanced computed tomography and had received radiotherapy as their primary treatment. Results: The T stage, N stage, and stage group were significant, independent predictors for disease-specific death. No significant differences were found between Stage T2a and T1 in local failure-free survival or between Stage N3a and N2 in distantmore » failure-free survival. Survival curves of the different T/N subsets showed a better segregation when T2a and N3a were downstaged to T1 and N2, respectively. The hazard ratio of disease-specific deaths for patients with T2N0 disease was similar to that of patients with T1N0 disease; the same result was found for the T3N0 and T4N0 subsets. Downstaging the T2N0 subset to Stage I, T3N0 to Stage II, and T4N0 to Stage III resulted in a more balanced patient distribution, better hazard consistency among subgroups, and improved hazard discrimination between overall stages. Conclusion: Using the 6th edition of the American Joint Committee on Cancer staging system produced an acceptable distribution of patient numbers and segregation of survival curves among the different stage groups. The prognostic accuracy of the staging system could be improved by recategorization of the T, N, and group stage criteria.« less

Oral dendritic cells mediate antigen-specific tolerance by stimulating TH1 and regulatory CD4+ T cells.

PubMed

Mascarell, Laurent; Lombardi, Vincent; Louise, Anne; Saint-Lu, Nathalie; Chabre, Henri; Moussu, Hélène; Betbeder, Didier; Balazuc, Anne-Marie; Van Overtvelt, Laurence; Moingeon, Philippe

2008-09-01

A detailed characterization of oral antigen-presenting cells is critical to improve second-generation sublingual allergy vaccines. To characterize oral dendritic cells (DCs) within lingual and buccal tissues from BALB/c mice with respect to their surface phenotype, distribution, and capacity to polarize CD4(+) T-cell responses. In situ analysis of oral DCs was performed by immunohistology. Purified DCs were tested in vitro for their capacity to capture, process, and present the ovalbumin antigen to naive CD4(+) T cells. In vivo priming of ovalbumin-specific T cells adoptively transferred to BALB/c mice was analyzed by cytofluorometry in cervical lymph nodes after sublingual administration of mucoadhesive ovalbumin. Three subsets of oral DCs with a distinct tissue distribution were identified: (1) a minor subset of CD207(+) Langerhans cells located in the mucosa itself, (2) a major subpopulation of CD11b(+)CD11c(-) and CD11b(+)CD11c(+) myeloid DCs at the mucosal/submucosal interface, and (3) B220(+)120G8(+) plasmacytoid DCs found in submucosal tissues. Purified myeloid and plasmacytoid oral DCs capture and process the antigen efficiently and are programmed to elicit IFN-gamma and/or IL-10 production together with a suppressive function in naive CD4(+) T cells. Targeting the ovalbumin antigen to oral DCs in vivo by using mucoadhesive particles establishes tolerance in the absence of cell depletion through the stimulation of IFN-gamma and IL-10-producing CD4(+) regulatory T cells in cervical lymph nodes. The oral immune system is composed of various subsets of tolerogenic DCs organized in a compartmentalized manner and programmed to induce T(H)1/regulatory T-cell responses.

The Arecibo Pisces Perseus Supercluster Survey: Declination Strip 27

NASA Astrophysics Data System (ADS)

Ricci, Mariah; Miller, Brendan; APPSS Team; Undergraduate ALFALFA Team; ALFALFA Team

2018-01-01

The Arecibo Pisces Perseus Supercluster Survey (APPSS) is an HI survey measuring galaxy infall into the filament and clusters. Galaxies were selected for HI observations based on their location within the Pisces Perseus supercluster and SDSS and GALEX colors predictive of cold gas content. Most of the HI observations were conducted at Arecibo using the L Band Wide receiver, with some high-declination coverage provided by Green Bank. The observations provide increased sensitivity compared to ALFALFA blind survey data. For this project, we investigated a subset of 132 APPSS galaxies with declinations near 27 degrees. Using custom data reduction and analysis tools developed for the Undergraduate ALFALFA Team, we determined the following information for galaxies in our subset: systemic velocity, line width, integrated flux density, HI mass, and gas fraction (or corresponding limits for non-detections). We calculate our HI detection fraction and mean gas fraction as a function of stellar mass and compare to previous results. We investigate the distribution of systemic velocities for our galaxies with their location on the sky. Finally, we discuss several interesting sources from our subset of APPSS galaxies. This work has been supported by NSF grants AST-1211005, AST-1637299, and AST-1637339

Optimization of camera exposure durations for multi-exposure speckle imaging of the microcirculation

PubMed Central

Kazmi, S. M. Shams; Balial, Satyajit; Dunn, Andrew K.

2014-01-01

Improved Laser Speckle Contrast Imaging (LSCI) blood flow analyses that incorporate inverse models of the underlying laser-tissue interaction have been used to develop more quantitative implementations of speckle flowmetry such as Multi-Exposure Speckle Imaging (MESI). In this paper, we determine the optimal camera exposure durations required for obtaining flow information with comparable accuracy with the prevailing MESI implementation utilized in recent in vivo rodent studies. A looping leave-one-out (LOO) algorithm was used to identify exposure subsets which were analyzed for accuracy against flows obtained from analysis with the original full exposure set over 9 animals comprising n = 314 regional flow measurements. From the 15 original exposures, 6 exposures were found using the LOO process to provide comparable accuracy, defined as being no more than 10% deviant, with the original flow measurements. The optimal subset of exposures provides a basis set of camera durations for speckle flowmetry studies of the microcirculation and confers a two-fold faster acquisition rate and a 28% reduction in processing time without sacrificing accuracy. Additionally, the optimization process can be used to identify further reductions in the exposure subsets for tailoring imaging over less expansive flow distributions to enable even faster imaging. PMID:25071956

An enhanced data visualization method for diesel engine malfunction classification using multi-sensor signals.

PubMed

Li, Yiqing; Wang, Yu; Zi, Yanyang; Zhang, Mingquan

2015-10-21

The various multi-sensor signal features from a diesel engine constitute a complex high-dimensional dataset. The non-linear dimensionality reduction method, t-distributed stochastic neighbor embedding (t-SNE), provides an effective way to implement data visualization for complex high-dimensional data. However, irrelevant features can deteriorate the performance of data visualization, and thus, should be eliminated a priori. This paper proposes a feature subset score based t-SNE (FSS-t-SNE) data visualization method to deal with the high-dimensional data that are collected from multi-sensor signals. In this method, the optimal feature subset is constructed by a feature subset score criterion. Then the high-dimensional data are visualized in 2-dimension space. According to the UCI dataset test, FSS-t-SNE can effectively improve the classification accuracy. An experiment was performed with a large power marine diesel engine to validate the proposed method for diesel engine malfunction classification. Multi-sensor signals were collected by a cylinder vibration sensor and a cylinder pressure sensor. Compared with other conventional data visualization methods, the proposed method shows good visualization performance and high classification accuracy in multi-malfunction classification of a diesel engine.

An Enhanced Data Visualization Method for Diesel Engine Malfunction Classification Using Multi-Sensor Signals

PubMed Central

Li, Yiqing; Wang, Yu; Zi, Yanyang; Zhang, Mingquan

2015-01-01

The various multi-sensor signal features from a diesel engine constitute a complex high-dimensional dataset. The non-linear dimensionality reduction method, t-distributed stochastic neighbor embedding (t-SNE), provides an effective way to implement data visualization for complex high-dimensional data. However, irrelevant features can deteriorate the performance of data visualization, and thus, should be eliminated a priori. This paper proposes a feature subset score based t-SNE (FSS-t-SNE) data visualization method to deal with the high-dimensional data that are collected from multi-sensor signals. In this method, the optimal feature subset is constructed by a feature subset score criterion. Then the high-dimensional data are visualized in 2-dimension space. According to the UCI dataset test, FSS-t-SNE can effectively improve the classification accuracy. An experiment was performed with a large power marine diesel engine to validate the proposed method for diesel engine malfunction classification. Multi-sensor signals were collected by a cylinder vibration sensor and a cylinder pressure sensor. Compared with other conventional data visualization methods, the proposed method shows good visualization performance and high classification accuracy in multi-malfunction classification of a diesel engine. PMID:26506347

Feasibility study of developing and creating a standardized subset of bridge plans.

DOT National Transportation Integrated Search

2015-09-01

This study investigated sizes and geometry of existing bridges in Colorado and investigated standard bridge systems used by : other entities. The study proposed standard bridge types advancing the goals of SHRP 2 R19A & B, the rapidest ABC : construc...

Pseudomonas syringae Type III Effector HopBB1 Promotes Host Transcriptional Repressor Degradation to Regulate Phytohormone Responses and Virulence.

PubMed

Yang, Li; Teixeira, Paulo José Pereira Lima; Biswas, Surojit; Finkel, Omri M; He, Yijian; Salas-Gonzalez, Isai; English, Marie E; Epple, Petra; Mieczkowski, Piotr; Dangl, Jeffery L

2017-02-08

Independently evolved pathogen effectors from three branches of life (ascomycete, eubacteria, and oomycete) converge onto the Arabidopsis TCP14 transcription factor to manipulate host defense. However, the mechanistic basis for defense control via TCP14 regulation is unknown. We demonstrate that TCP14 regulates the plant immune system by transcriptionally repressing a subset of the jasmonic acid (JA) hormone signaling outputs. A previously unstudied Pseudomonas syringae (Psy) type III effector, HopBB1, interacts with TCP14 and targets it to the SCF COI1 degradation complex by connecting it to the JA signaling repressor JAZ3. Consequently, HopBB1 de-represses the TCP14-regulated subset of JA response genes and promotes pathogen virulence. Thus, HopBB1 fine-tunes host phytohormone crosstalk by precisely manipulating part of the JA regulon to avoid pleiotropic host responses while promoting pathogen proliferation. Copyright © 2017 Elsevier Inc. All rights reserved.

Dendritic Cell Subset Distributions in the Aorta in Healthy and Atherosclerotic Mice

PubMed Central

Lutz, Manfred B.; Zernecke, Alma

2014-01-01

Dendritic cells (DCs) can be sub-divided into various subsets that play specialized roles in priming of adaptive immune responses. Atherosclerosis is regarded as a chronic inflammatory disease of the vessel wall and DCs can be found in non-inflamed and diseased arteries. We here performed a systematic analyses of DCs subsets during atherogenesis. Our data indicate that distinct DC subsets can be localized in the vessel wall. In C57BL/6 and low density lipoprotein receptor-deficient (Ldlr −/−) mice, CD11c+ MHCII+ DCs could be discriminated into CD103− CD11b+F4/80+, CD11b+F4/80− and CD11b−F4/80− DCs and CD103+ CD11b−F4/80− DCs. Except for CD103− CD11b− F4/80− DCs, these subsets expanded in high fat diet-fed Ldlr −/− mice. Signal-regulatory protein (Sirp)-α was detected on aortic macrophages, CD11b+ DCs, and partially on CD103− CD11b− F4/80− but not on CD103+ DCs. Notably, in FMS-like tyrosine kinase 3-ligand-deficient (Flt3l −/−) mice, a specific loss of CD103+ DCs but also CD103− CD11b+ F4/80− DCs was evidenced. Aortic CD103+ and CD11b+ F4/80− CD103− DCs may thus belong to conventional rather than monocyte-derived DCs, given their dependence on Flt3L-signalling. CD64, postulated to distinguish macrophages from DCs, could not be detected on DC subsets under physiological conditions, but appeared in a fraction of CD103− CD11b+ F4/80− and CD11b+ F4/80+ cells in atherosclerotic Ldlr −/− mice. The emergence of CD64 expression in atherosclerosis may indicate that CD11b+ F4/80− DCs similar to CD11b+ F4/80+ DCs are at least in part derived from immigrated monocytes during atherosclerotic lesion formation. Our data advance our knowledge about the presence of distinct DC subsets and their accumulation characteristics in atherosclerosis, and may help to assist in future studies aiming at specific DC-based therapeutic strategies for the treatment of chronic vascular inflammation. PMID:24551105

Using machine learning to emulate human hearing for predictive maintenance of equipment

NASA Astrophysics Data System (ADS)

Verma, Dinesh; Bent, Graham

2017-05-01

At the current time, interfaces between humans and machines use only a limited subset of senses that humans are capable of. The interaction among humans and computers can become much more intuitive and effective if we are able to use more senses, and create other modes of communicating between them. New machine learning technologies can make this type of interaction become a reality. In this paper, we present a framework for a holistic communication between humans and machines that uses all of the senses, and discuss how a subset of this capability can allow machines to talk to humans to indicate their health for various tasks such as predictive maintenance.

geoknife: Reproducible web-processing of large gridded datasets

USGS Publications Warehouse

Read, Jordan S.; Walker, Jordan I.; Appling, Alison P.; Blodgett, David L.; Read, Emily K.; Winslow, Luke A.

2016-01-01

Geoprocessing of large gridded data according to overlap with irregular landscape features is common to many large-scale ecological analyses. The geoknife R package was created to facilitate reproducible analyses of gridded datasets found on the U.S. Geological Survey Geo Data Portal web application or elsewhere, using a web-enabled workflow that eliminates the need to download and store large datasets that are reliably hosted on the Internet. The package provides access to several data subset and summarization algorithms that are available on remote web processing servers. Outputs from geoknife include spatial and temporal data subsets, spatially-averaged time series values filtered by user-specified areas of interest, and categorical coverage fractions for various land-use types.

Dendritic cells and anergic type I NKT cells play a crucial role in sulfatide-mediated immune regulation in experimental autoimmune encephalomyelitis

PubMed Central

Maricic, Igor; Halder, Ramesh; Bischof, Felix; Kumar, Vipin

2014-01-01

CD1d-restricted NKT cells can be divided into two groups: type I NKT cells utilize a semi-invariant TCR whereas type II express a relatively diverse set of TCRs. A major subset of type II NKT cells recognizes myelin-derived sulfatides and is selectively enriched in the central nervous system tissue during experimental autoimmune encephalomyelitis (EAE). We have shown that activation of sulfatide-reactive type II NKT cells by sulfatide prevents induction of EAE. Here we have addressed the mechanism of regulation as well as whether a single immunodominant form of synthetic sulfatide can treat ongoing chronic and relapsing EAE in SJL/J mice. We have shown that the activation of sulfatide-reactive type II NKT cells leads to a significant reduction in the frequency and effector function of PLP139-151/I-As–tetramer+ cells in lymphoid and CNS tissues. In addition, type I NKT cells and dendritic cells in the periphery as well as CNS-resident microglia are inactivated following sulfatide administration, and mice deficient in type I NKT cells are not protected from disease. Moreover tolerized DCs from sulfatide-treated animals can adoptively transfer protection into naive mice. Treatment of SJL/J mice with a synthetic cis-tetracosenoyl sulfatide, but not αGalCer, reverses ongoing chronic and relapsing EAE. Our data highlight a novel immune regulatory pathway involving NKT subset interactions leading to inactivation of type I NKT cells, DCs, and microglial cells in suppression of autoimmunity. Since CD1 molecules are non-polymorphic, the sulfatide-mediated immune regulatory pathway can be targeted for development of non-HLA-dependent therapeutic approaches to T cell-mediated autoimmune diseases. PMID:24973441

Countably QC-Approximating Posets

PubMed Central

Mao, Xuxin; Xu, Luoshan

2014-01-01

As a generalization of countably C-approximating posets, the concept of countably QC-approximating posets is introduced. With the countably QC-approximating property, some characterizations of generalized completely distributive lattices and generalized countably approximating posets are given. The main results are as follows: (1) a complete lattice is generalized completely distributive if and only if it is countably QC-approximating and weakly generalized countably approximating; (2) a poset L having countably directed joins is generalized countably approximating if and only if the lattice σ c(L)op of all σ-Scott-closed subsets of L is weakly generalized countably approximating. PMID:25165730

Combined Effects of Gamma Radiation and High Dietary Iron on Peripheral Leukocyte Distribution and Function

NASA Technical Reports Server (NTRS)

Crucian, Brian E.; Morgan, Jennifer L. L.; Quiriarte, Heather A.; Sams, Clarence F.; Smith, Scott M.; Zwart, Sara R.

2012-01-01

Both radiation and increased iron stores can independently increase oxidative damage, resulting in protein, lipid and DNA oxidation. Oxidative stress increases the risk of many health problems including cancer, cataracts, and heart disease. This study, a subset of a larger interdisciplinary investigation of the combined effect of iron overload on sensitivity to radiation injury, monitored immune parameters in the peripheral blood of rats subjected to gamma radiation, high dietary iron or both. Specific immune measures consisted of: (1) peripheral leukocyte distribution, (2) plasma cytokine levels and (3) cytokine production profiles following whole blood mitogenic stimulation

CD8αβ+ γδ T Cells: A Novel T Cell Subset with a Potential Role in Inflammatory Bowel Disease.

PubMed

Kadivar, Mohammad; Petersson, Julia; Svensson, Lena; Marsal, Jan

2016-12-15

γδ T cells have been attributed a wide variety of functions, which in some cases may appear as contradictory. To better understand the enigmatic biology of γδ T cells it is crucial to define the constituting subpopulations. γδ T cells have previously been categorized into two subpopulations: CD8αα + and CD8 - cells. In this study we have defined and characterized a novel subset of human γδ T-cells expressing CD8αβ. These CD8αβ + γδ T cells differed from the previously described γδ T cell subsets in several aspects, including the degree of enrichment within the gut mucosa, the activation status in blood, the type of TCRδ variant used in blood, and small but significant differences in their response to IL-2 stimulation. Furthermore, the novel subset expressed cytotoxic mediators and CD69, and produced IFN-γ and TNF-α. In patients with active inflammatory bowel disease the mucosal frequencies of CD8αβ + γδ T cells were significantly lower as compared with healthy controls, correlated negatively with the degree of disease activity, and increased to normal levels as a result of anti-TNF-α therapy. In conclusion, our results demonstrate that CD8αβ + γδ T cells constitute a novel lymphocyte subset, which is strongly enriched within the gut and may play an important role in gut homeostasis and mucosal healing in inflammatory bowel disease. Copyright © 2016 by The American Association of Immunologists, Inc.

Encouraging top-down attention in visual search:A developmental perspective.

PubMed

Lookadoo, Regan; Yang, Yingying; Merrill, Edward C

2017-10-01

Four experiments are reported in which 60 younger children (7-8 years old), 60 older children (10-11 years old), and 60 young adults (18-25 years old) performed a conjunctive visual search task (15 per group in each experiment). The number of distractors of each feature type was unbalanced across displays to evaluate participants' ability to restrict search to the smaller subset of features. The use of top-down attention processes to restrict search was encouraged by providing external aids for identifying and maintaining attention on the smaller set. In Experiment 1, no external assistance was provided. In Experiment 2, precues and instructions were provided to focus attention on that subset. In Experiment 3, trials in which the smaller subset was represented by the same feature were presented in alternating blocks to eliminate the need to switch attention between features from trial to trial. In Experiment 4, consecutive blocks of the same subset features were presented in the first or second half of the experiment, providing additional consistency. All groups benefited from external support of top-down attention, although the pattern of improvement varied across experiments. The younger children benefited most from precues and instruction, using the subset search strategy when instructed. Furthermore, younger children benefited from blocking trials only when blocks of the same features did not alternate. Older participants benefited from the blocking of trials in both Experiments 3 and 4, but not from precues and instructions. Hence, our results revealed both malleability and limits of children's top-down control of attention.

Evaluation of reconstruction techniques in regional cerebral blood flow SPECT using trade-off plots: a Monte Carlo study.

PubMed

Olsson, Anna; Arlig, Asa; Carlsson, Gudrun Alm; Gustafsson, Agnetha

2007-09-01

The image quality of single photon emission computed tomography (SPECT) depends on the reconstruction algorithm used. The purpose of the present study was to evaluate parameters in ordered subset expectation maximization (OSEM) and to compare systematically with filtered back-projection (FBP) for reconstruction of regional cerebral blood flow (rCBF) SPECT, incorporating attenuation and scatter correction. The evaluation was based on the trade-off between contrast recovery and statistical noise using different sizes of subsets, number of iterations and filter parameters. Monte Carlo simulated SPECT studies of a digital human brain phantom were used. The contrast recovery was calculated as measured contrast divided by true contrast. Statistical noise in the reconstructed images was calculated as the coefficient of variation in pixel values. A constant contrast level was reached above 195 equivalent maximum likelihood expectation maximization iterations. The choice of subset size was not crucial as long as there were > or = 2 projections per subset. The OSEM reconstruction was found to give 5-14% higher contrast recovery than FBP for all clinically relevant noise levels in rCBF SPECT. The Butterworth filter, power 6, achieved the highest stable contrast recovery level at all clinically relevant noise levels. The cut-off frequency should be chosen according to the noise level accepted in the image. Trade-off plots are shown to be a practical way of deciding the number of iterations and subset size for the OSEM reconstruction and can be used for other examination types in nuclear medicine.

Lithologic Distribution and Geologic History of the Apollo 17 Site: The Record in Soils and Small Rock Particles from the Highland Massifs

NASA Technical Reports Server (NTRS)

Jolliff, Bradley L.; Rockow, Kaylynn M.; Korotev, Randy L.; Haskin, Larry A.

1996-01-01

Through analysis by instrumental neutron activation (INAA) of 789 individual lithic fragments from the 2 mm-4 mm grain-size fractions of five Apollo 17 soil samples (72443, 72503, 73243, 76283, and 76503) and petrographic examination of a subset, we have determined the diversity and proportions of rock types recorded within soils from the highland massifs. The distribution of rock types at the site, as recorded by lithic fragments in the soils, is an alternative to the distribution inferred from the limited number of large rock samples. The compositions and proportions of 2 mm-4 mm fragments provide a bridge between compositions of less than 1 mm fines and types and proportions of rocks observed in large collected breccias and their clasts. The 2 mm-4 mm fraction of soil from South Massif, represented by an unbiased set of lithic fragments from station-2 samples 72443 and 72503, consists of 71% noritic impact-melt breccia, 7% Incompatible-Trace-Element-(ITE)-poor highland rock types (mainly granulitic breccias), 19% agglutinates and regolith breccias, 1% high-Ti mare basalt, and 2% others (very-low-Ti (VLT) basalt, monzogabbro breccia, and metal). In contrast, the 2 mm - 4 mm fraction of a soil from the North Massif, represented by an unbiased set of lithic fragments from station-6 sample 76503, has a greater proportion of ITE-poor highland rock types and mare-basalt fragments: it consists of 29% ITE-poor highland rock types (mainly granulitic breccias and troctolitic anorthosite), 25% impact-melt breccia, 13% high-Ti mare basalt, 31 % agglutinates and regolith breccias, 1% orange glass and related breccia, and 1% others. Based on a comparison of mass- weighted mean compositions of the lithic fragments with compositions of soil fines from all Apollo 17 highland stations, differences between the station-2 and station-6 samples are representative of differences between available samples from the two massifs. From the distribution of different rock types and their compositions, we conclude the following: (1) North-Massif and South-Massif soil samples differ significantly in types and proportions of ITE-poor highland components and ITE-rich impact-melt-breccia components. These differences reflect crudely layered massifs and known local geology. The greater percentage of impact-melt breccia in the South- Massif light-mantle soil stems from derivation of the light mantle from the top of the massif, which apparently is richer in noritic impact-melt breccia than are lower parts of the massifs. (2) At station 2, the 2 mm-4 mm grain-size fraction is enriched in impact-melt breccias compared to the less than 1 mm fraction, suggesting that the <1 mm fraction within the light mantle has a greater proportion of lithologies such as granulitic breccias which are more prevalent lower in the massifs and which we infer to be older (pre-basin) highland components. (3) Soil from station 6, North Massif, contains magnesian troctolitic anorthosite, which is a component that is rare in station-2 South-Massif,contains magnesian troctolitic in impact-melt breccia interpreted by most investigators to be ejecta from the Serenitatis basin.

Floristic conservation value, nested understory floras, and the development of second-growth forest.

PubMed

Spyreas, Greg; Matthews, Jeffrey W

2006-08-01

Nestedness analysis can reveal patterns of plant composition and diversity among forest patches. For nested floral assemblages, the plants occupying any one patch are a nested subset of the plants present in successively more speciose patches. Elimination of sensitive understory plants with human disturbance is one of several mechanisms hypothesized to generate nonrandom, nested floral distributions. Hypotheses explaining distributions of understory plants remain unsubstantiated across broad landscapes of varying forest types and disturbance histories. We sampled the vegetation of 51 floodplain and 55 upland forests across Illinois (USA) to examine how the diversity, composition, and nestedness of understory floras related to their overstory growth and structure (basal area), and their overall floristic conservation value (mean C). We found that plant assemblages were nested with respect to site species richness, such that rare plants indicated diverse forests. Floras were also nested with respect to site mean C and basal area (BA). However, in an opposite pattern from what we had expected, floras of high-BA stands were nested subsets of those of low-BA stands. A set of early-successional plants restricted to low-BA stands, and more importantly, the absence of a set of true forest plants in high-BA stands, accounted for this pattern. Additionally, we observed a decrease in species richness with increasing BA. These results are consistent with the hypothesis that recovery of true forest plants does not occur concurrently with overstory regeneration following massive anthropogenic disturbance. Nestedness by site mean C indicates that high conservation value (conservative) plants co-occur in highly diverse stands; these forests are assumed to be less disturbed historically. Because site mean C was uncorrelated with BA, BA-neutral disturbances such as livestock usage are suggested as accounting for between-site differences in mean C. When considered individually, conservative plants were actually more likely to be found in low-BA stands (uplands only). This suggests that floras of historically more open-canopied oak-hickory uplands are being degraded by canopy closure from increasing density of "mesophytic, nonpyrogenic" trees. It also indirectly suggests that recent moderate logging is uncorrelated with floristic conservation values.

Analysis of uncertainties in GOSAT-inferred regional CO2 fluxes

NASA Astrophysics Data System (ADS)

Ishizawa, M.; Shirai, T.; Maksyutov, S. S.; Yoshida, Y.; Morino, I.; Inoue, M.; Nakatsuru, T.; Uchino, O.; Mabuchi, K.

2016-12-01

Satellite-based CO2 measurements have potential for improving our understanding global carbon cycle because of more spatiotemporal coverage than those from ground-based observations. Since the Greenhouse gases Observing Satellite (GOSAT) was launched in January 2009, it has been measuring the column-average dry air-mole function of CO2 (XCO2) from the space. To utilize the GOSAT XCO2 for better CO2 flux estimates, several challenges should be overcome. Systematic errors (biases) in XCO2 retrievals are a major factor which leads to large differences among inverted CO2 fluxes. Temporally variable data coverage and density are also taken into account when interpreting the estimated surface fluxes. In this study, we employ an atmospheric inverse model to investigate the impacts of retrievals biases and temporally varying global distribution of GOSAT XCO2 on surface CO2 flux estimates. Inversions are performed for 2009-2013, with several subsets of the 5-year record of GOSAT XCO2 (v2.21) and its bias-corrected XCO2. GOSAT XCO2 data consist of three types: H-gain for vegetated lands, M-gain for bright surfaces (desert areas), and sun-glint for ocean surface. The results show that the global spatial distributions of estimated CO2 fluxes depend on the subset of XCO2 used. M-gain XCO2 results in unrealistically high CO2 emissions in and around the Middle East, including the neighboring ocean regions. On the other hand, M-gain XCO2 causes compensating unrealistic uptakes far beyond M-gain regions in low latitudes, also partially contributing on the summer uptake in Europe. The joint inversions with both surface measurements and GOSAT XCO2 data obtain larger flux gradient between the northern extra-tropics and the tropics than the inversion with surface measurements only for the first 2 years. Recently, these North-South gradients seem to be gradually reducing as the tropics become a weaker source or turn into a sink, while the net emission strength in East Asia is increasing. The 5-year XCO2 data allows us detailed analysis of uncertainties in GOSAT-inferred fluxes and assessment of GOSAT XCO2 biases.

Novel Scalable 3-D MT Inverse Solver

NASA Astrophysics Data System (ADS)

Kuvshinov, A. V.; Kruglyakov, M.; Geraskin, A.

2016-12-01

We present a new, robust and fast, three-dimensional (3-D) magnetotelluric (MT) inverse solver. As a forward modelling engine a highly-scalable solver extrEMe [1] is used. The (regularized) inversion is based on an iterative gradient-type optimization (quasi-Newton method) and exploits adjoint sources approach for fast calculation of the gradient of the misfit. The inverse solver is able to deal with highly detailed and contrasting models, allows for working (separately or jointly) with any type of MT (single-site and/or inter-site) responses, and supports massive parallelization. Different parallelization strategies implemented in the code allow for optimal usage of available computational resources for a given problem set up. To parameterize an inverse domain a mask approach is implemented, which means that one can merge any subset of forward modelling cells in order to account for (usually) irregular distribution of observation sites. We report results of 3-D numerical experiments aimed at analysing the robustness, performance and scalability of the code. In particular, our computational experiments carried out at different platforms ranging from modern laptops to high-performance clusters demonstrate practically linear scalability of the code up to thousands of nodes. 1. Kruglyakov, M., A. Geraskin, A. Kuvshinov, 2016. Novel accurate and scalable 3-D MT forward solver based on a contracting integral equation method, Computers and Geosciences, in press.

Decisions with Uncertain Consequences—A Total Ordering on Loss-Distributions

PubMed Central

König, Sandra; Schauer, Stefan

2016-01-01

Decisions are often based on imprecise, uncertain or vague information. Likewise, the consequences of an action are often equally unpredictable, thus putting the decision maker into a twofold jeopardy. Assuming that the effects of an action can be modeled by a random variable, then the decision problem boils down to comparing different effects (random variables) by comparing their distribution functions. Although the full space of probability distributions cannot be ordered, a properly restricted subset of distributions can be totally ordered in a practically meaningful way. We call these loss-distributions, since they provide a substitute for the concept of loss-functions in decision theory. This article introduces the theory behind the necessary restrictions and the hereby constructible total ordering on random loss variables, which enables decisions under uncertainty of consequences. Using data obtained from simulations, we demonstrate the practical applicability of our approach. PMID:28030572

Validated and longitudinally stable asthma phenotypes based on cluster analysis of the ADEPT study.

PubMed

Loza, Matthew J; Djukanovic, Ratko; Chung, Kian Fan; Horowitz, Daniel; Ma, Keying; Branigan, Patrick; Barnathan, Elliot S; Susulic, Vedrana S; Silkoff, Philip E; Sterk, Peter J; Baribaud, Frédéric

2016-12-15

Asthma is a disease of varying severity and differing disease mechanisms. To date, studies aimed at stratifying asthma into clinically useful phenotypes have produced a number of phenotypes that have yet to be assessed for stability and to be validated in independent cohorts. The aim of this study was to define and validate, for the first time ever, clinically driven asthma phenotypes using two independent, severe asthma cohorts: ADEPT and U-BIOPRED. Fuzzy partition-around-medoid clustering was performed on pre-specified data from the ADEPT participants (n = 156) and independently on data from a subset of U-BIOPRED asthma participants (n = 82) for whom the same variables were available. Models for cluster classification probabilities were derived and applied to the 12-month longitudinal ADEPT data and to a larger subset of the U-BIOPRED asthma dataset (n = 397). High and low type-2 inflammation phenotypes were defined as high or low Th2 activity, indicated by endobronchial biopsies gene expression changes downstream of IL-4 or IL-13. Four phenotypes were identified in the ADEPT (training) cohort, with distinct clinical and biomarker profiles. Phenotype 1 was "mild, good lung function, early onset", with a low-inflammatory, predominantly Type-2, phenotype. Phenotype 2 had a "moderate, hyper-responsive, eosinophilic" phenotype, with moderate asthma control, mild airflow obstruction and predominant Type-2 inflammation. Phenotype 3 had a "mixed severity, predominantly fixed obstructive, non-eosinophilic and neutrophilic" phenotype, with moderate asthma control and low Type-2 inflammation. Phenotype 4 had a "severe uncontrolled, severe reversible obstruction, mixed granulocytic" phenotype, with moderate Type-2 inflammation. These phenotypes had good longitudinal stability in the ADEPT cohort. They were reproduced and demonstrated high classification probability in two subsets of the U-BIOPRED asthma cohort. Focusing on the biology of the four clinical independently-validated easy-to-assess ADEPT asthma phenotypes will help understanding the unmet need and will aid in developing tailored therapies. NCT01274507 (ADEPT), registered October 28, 2010 and NCT01982162 (U-BIOPRED), registered October 30, 2013.

Immune cell activation and cytokine release after stimulation of whole blood with pneumococcal C-polysaccharide and capsular polysaccharides.

PubMed

Sundberg-Kövamees, Marianne; Grunewald, Johan; Wahlström, Jan

2016-11-01

Streptococcus pneumonia is a major cause of morbidity and mortality in children and adults worldwide. Lack of fully effective pneumococcal vaccines is a problem. Streptococcus pneumoniae exposes on its surface C-polysaccharide (cell wall polysaccharide, CWPS) and serospecific capsular polysaccharides, used in pneumococcal vaccines. We investigated the effect of CWPS and individual capsular polysaccharides, with regard to activation of subsets of immune cells of healthy controls. Three different capsular polysaccharides, CWPS and LPS were used for in vitro stimulation of whole blood. Cell activation (CD69 expression) was assessed in CD4+ and CD4- T cells, NK-like T cells, NK cells and monocytes by flow cytometry. Cytokine levels in supernatants were quantified by Cytometric Bead Array (CBA). CWPS and the capsules activated immune cell subsets, but to different degrees. NK cells and NK-like T cells showed the strongest activation, followed by monocytes. Among the three capsules, capsule type 23 induced the strongest activation and cytokine release, followed by type 9 and type 3. This study increases the understanding of how the human immune system reacts to pneumococcal vaccine components. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

A pilot study showing associations between frequency of CD4(+) memory cell subsets at diagnosis and duration of partial remission in type 1 diabetes.

PubMed

Moya, Rosita; Robertson, Hannah Kathryn; Payne, Dawson; Narsale, Aditi; Koziol, Jim; Davies, Joanna Davida

2016-05-01

In some patients with type 1 diabetes the dose of insulin required to achieve euglycemia is substantially reduced soon after diagnosis. This partial remission is associated with β-cell function and good glucose control. The purpose of this study was to assess whether frequencies of CD4(+) T cell subsets in children newly diagnosed with type 1 diabetes are associated with length of partial remission. We found that the frequency of CD4(+) memory cells, activated Treg cells and CD25(+) cells that express a high density of the IL-7 receptor, CD127 (CD127(hi)) are strongly associated with length of partial remission. Prediction of length of remission via Cox regression is significantly enhanced when CD25(+) CD127(hi) cell frequency is combined with either Insulin Dependent Adjusted A1c (IDAA1c), or glycosylated hemoglobin (HbA1c), or C-peptide levels at diagnosis. CD25(+) CD127(hi) cells do not express Foxp3, LAG-3 and CD49b, indicating that they are neither Treg nor Tr1 cells. Copyright © 2016 Elsevier Inc. All rights reserved.

Three cases of pigmented cosmetic dermatitis-like eruptions associated with primary Sjögren's syndrome or anti-SSA antibody.

PubMed

Takeo, Naoko; Sakai, Takashi; Saito-Shono, Tomoko; Ishikawa, Kazushi; Hatano, Yutaka; Katagiri, Kazumoto; Takahashi, Yoshihiro; Kawano, Kenji; Kimoto, Kenichi; Kubota, Toshiaki; Eshima, Nobuoki; Kojima, Hiroto; Fujiwara, Sakuhei

2016-08-01

Pigmented cosmetic dermatitis-like (Riehl's melanosis-like) pigmentation was reported in three of 27 patients with primary Sjögren's syndrome. But case reports of such eruptions are rare. We describe three cases of such eruptions associated with primary Sjögren's syndrome or anti-SSA antibody and possible associations with specific types of human leukocyte antigen (HLA) and infiltrating lymphocytes. These middle-aged Japanese women had reticular facial pigmentation and histopathological examination revealed interface dermatitis, melanophages, and dense lymphocytic infiltration around hair follicles and sweat ducts. HLA typing revealed common antigenic equivalents or genetic typing of HLA-A2, DR52, DPA1(02:02) and DPB1(05:01). Immunohistochemical staining revealed major subsets of T cells to be CD8 and CD45RO. Some Foxp3- and few IL17-positive cells were found in strong contrast to the major CD4 subset of infiltrated T cells in annular erythema associated with Sjögren's syndrome. Apparently, our patients' pigmentation represented a specific etiology associated with primary Sjögren's syndrome or anti-SSA antibody. © 2016 Japanese Dermatological Association.

Celiac disease in type 1 diabetes mellitus in a North American community: prevalence, serologic screening, and clinical features.

PubMed

Mahmud, Farid H; Murray, Joseph A; Kudva, Yogish C; Zinsmeister, Alan R; Dierkhising, Ross A; Lahr, Brian D; Dyck, Peter J; Kyle, Robert A; El-Youssef, Mounif; Burgart, Lawrence J; Van Dyke, Carol T; Brogan, Deanna L; Melton, L Joseph

2005-11-01

To estimate the prevalence of cellac disease (CD) in pediatric and adult type 1 diabetes melitus in a defined population and to describe clinical features and HLA class II genotypes predictive of CD in screened patients with type 1 diabetes. All residents of Olmsted County, Minnesota, with type 1 diabetes mellitus on the prevalence date January 1, 2001, were identified with the use of an established medical records linkage system (Rochester Epidemiology Project) and defined clinical criteria. Consenting patients underwent serologic screening with endomyslal antibody and tissue transglutaminase antibody testing and Intestinal biopsies to confirm the diagnosis of CD. A subset of screened patients also underwent HLA class II genotyping. Quality-of-life screening (Medical Outcomes Study 36-Item Short-Form Health Survey) was completed in a subset of patients at the time of serologic screening. Overall, 392 Olmsted County residents with type 1 diabetes on January 1, 2001, were Identified. A total of 158 patients with type 1 diabetes were tested, representing 40% (158/392) of the enumerated diabetic population, and 11 had biopsy-proven CD for an estimated point prevalence of 7.0% (95% confidence Interval, 3.5%-12.1%). Most CD-positive diabetic patients were asymptomatic and expressed an at-risk CD haplotype with at least one of but not both HLA DQ2 or DQ8. Celiac disease Is not rare In North American patients with type 1 diabetes, and most CD-positive diabetic patients are asymptomatic Irrespective of age at screening.

Characterization of frequencies and distribution of single nucleotide insertions/deletions in the human genome.

PubMed

Tan, Ene-Choo; Li, Haixia

2006-07-19

Most of the studies on single nucleotide variations are on substitutions rather than insertions/deletions. In this study, we examined the distribution and characteristics of single nucleotide insertions/deletions (SNindels), using data available from dbSNP for all the human chromosomes. There are almost 300,000 SNindels in the database, of which only 0.8% are validated. They occur at the frequency of 0.887 per 10 kb on average for the whole genome, or approximately 1 for every 11,274 bp. More than half occur in regions with mononucleotide repeats the longest of which is 47 bases. Overall the mononucleotide repeats involving C and G are much shorter than those for A and T. About 12% are surrounded by palindromes. There is general correlation between chromosome size and total number for each chromosome. Inter-chromosomal variation in density ranges from 0.6 to 21.7 per kilobase. The overall spectrum shows very high proportion of SNindel of types -/A and -/T at over 81%. The proportion of -/A and -/T SNindels for each chromosome is correlated to its AT content. Less than half of the SNindels are within or near known genes and even fewer (<0.183%) in coding regions, and more than 1.4% of -/C and -/G are in coding compared to 0.2% for -/A and -/T types. SNindels of -/A and -/T types make up 80% of those found within untranslated regions but less than 40% of those within coding regions. A separate analysis using the subset of 2324 validated SNindels showed slightly less AT bias of 74%, SNindels not within mononucleotide repeats showed even less AT bias at 58%. Density of validated SNindels is 0.007/10 kb overall and 90% are found within or near genes. Among all chromosomes, Y has the lowest numbers and densities for all SNindels, validated SNindels, and SNindels not within repeats.

Immunolocalization of type X collagen in normal fetal and adult osteoarthritic cartilage with monoclonal antibodies.

PubMed

Girkontaite, I; Frischholz, S; Lammi, P; Wagner, K; Swoboda, B; Aigner, T; Von der Mark, K

1996-09-01

For studies on processing and tissue distribution of type X collagen, monoclonal antibodies were prepared against human recombinant collagen type X (hrCol X) and tested by ELISA, immunoblotting and immunohistology. Forty-two clones were obtained which were grouped into four different subsets based on their reactivity against native and denatured hrCol X, pepsin-treated hrCol X, and the C-terminal NC-1 domain. Here we present results obtained with four monoclonal antibodies: Clone X 53, a representative of group I, binds with high affinity to both native and pepsin-digested hrCol X but with low affinity to the NC-1 dimer; monoclonal antibodies of group II and III recognized native and denatured hrCol X but not NC-1; antibodies of group II, but not III, reacted to some extent with pepsin treated hrCol X; one antibody (X 34) was obtained that reacted strongly with the isolated NC-1 dimer and native hrCol X but not with the NC-1 monomer or pepsin-digested hrCol X (group IV). Antibodies of all groups stained specifically the hypertrophic zone of fetal human epiphyseal cartilage. Mab X 53 stained the peri- and extracellular matrix of hypertrophic chondrocytes in the lower hypertrophic zone and in the calcified cartilage core in endochondral bone trabecules, while clone X 34 stained intracellularly and the pericellular matrix. All other tissues or cells of the epiphysis were negative. Antibody X 53 reacted also with canine, murine and guinea pig hypertrophic cartilage in tissue sections, but not with bovine or porcine type X collagen. In sections of osteoarthritic cartilage, clusters of hypertrophic chondrocytes in the deep zone were stained, confirming previous observations on enhanced chondrocyte hypertrophy and type X collagen expression in osteoarthritic articular cartilage.

Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis

PubMed Central

Pourcel, C; André-Mazeaud, F; Neubauer, H; Ramisse, F; Vergnaud, G

2004-01-01

Background Yersinia pestis, the agent of plague, is a young and highly monomorphic species. Three biovars, each one thought to be associated with the last three Y. pestis pandemics, have been defined based on biochemical assays. More recently, DNA based assays, including DNA sequencing, IS typing, DNA arrays, have significantly improved current knowledge on the origin and phylogenetic evolution of Y. pestis. However, these methods suffer either from a lack of resolution or from the difficulty to compare data. Variable number of tandem repeats (VNTRs) provides valuable polymorphic markers for genotyping and performing phylogenetic analyses in a growing number of pathogens and have given promising results for Y. pestis as well. Results In this study we have genotyped 180 Y. pestis isolates by multiple locus VNTR analysis (MLVA) using 25 markers. Sixty-one different genotypes were observed. The three biovars were distributed into three main branches, with some exceptions. In particular, the Medievalis phenotype is clearly heterogeneous, resulting from different mutation events in the napA gene. Antiqua strains from Asia appear to hold a central position compared to Antiqua strains from Africa. A subset of 7 markers is proposed for the quick comparison of a new strain with the collection typed here. This can be easily achieved using a Web-based facility, specifically set-up for running such identifications. Conclusion Tandem-repeat typing may prove to be a powerful complement to the existing phylogenetic tools for Y. pestis. Typing can be achieved quickly at a low cost in terms of consumables, technical expertise and equipment. The resulting data can be easily compared between different laboratories. The number and selection of markers will eventually depend upon the type and aim of investigations. PMID:15186506

Biogeography of Puerto Rican ants: a non-equilibrium case?

Treesearch

J.A. Torres; R.R. Snelling

1997-01-01

Ants were studied on Puerto Rico and 44 islands surrounding Puerto Rico. Habitat diversity was the best predictor of the number of species per island and the distributions of species followed a nested subset pattern. The number of extinctions per island was low, approximately 1 to 2 extinctions per island in a period of 18 years, and the rates of colonization seem to...

Perceived Quality of Life in Mothers of Children with Fragile X Syndrome

ERIC Educational Resources Information Center

Wheeler, Anne C.; Skinner, Debra G.; Bailey, Donald B.

2008-01-01

A mixed method approach was used to explore quality of life of 101 mothers of children with fragile X syndrome. Mothers completed a self-report of personal quality of life and measures of mental health and well-being. A subset was interviewed about quality of life. The distribution of scores on the Quality of Life Inventory was similar to the…

Altered Distribution of Peripheral Blood Maturation-Associated B-Cell Subsets in Chronic Alcoholism.

PubMed

Almeida, Julia; Polvorosa, Maria Angeles; Gonzalez-Quintela, Arturo; Madruga, Ignacio; Marcos, Miguel; Pérez-Nieto, Maria Angeles; Hernandez-Cerceño, Maria Luisa; Orfao, Alberto; Laso, Francisco Javier

2015-08-01

Although decreased counts of peripheral blood (PB) B cells-associated with an apparently contradictory polyclonal hypergammaglobulinemia-have been reported in chronic alcoholism, no information exists about the specific subsets of circulating B cells altered and their relationship with antibody production. Here, we analyzed for the first time the distribution of multiple maturation-associated subpopulations of PB B cells in alcoholism and its potential relationship with the onset of liver disease. PB samples from 35 male patients-20 had alcoholic hepatitis (AH) and 15 chronic alcoholism without liver disease (AWLD)-were studied, in parallel to 19 male healthy donors (controls). The distribution of PB B-cell subsets (immature/regulatory, naïve, CD27(-) and CD27(+) memory B lymphocytes, and circulating plasmablasts of distinct immunoglobulin-Ig-isotypes) was analyzed by flow cytometry. Patients with AH showed significantly decreased numbers of total PB B lymphocytes (vs. controls and AWLD), at the expense of immature, memory, and, to a lesser extent, also naïve B cells. AWLD showed reduced numbers of immature and naïve B cells (vs. controls), but higher PB counts of plasmablasts (vs. the other 2 groups). Although PB memory B cells were reduced among the patients, the percentage of surface (s)IgA(+) cells (particularly CD27(-) /sIgA(+) cells) was increased in AH, whereas both sIgG(+) and sIgA(+) memory B cells were significantly overrepresented in AWLD versus healthy donors. Regarding circulating plasmablasts, patients with AH only showed significantly reduced counts of sIgG(+) cells versus controls. In contrast, the proportion of both sIgA(+) and sIgG(+) plasmablasts-from all plasmablasts-was reduced in AH and increased in AWLD (vs. the other 2 groups). AH and AWLD patients display a significantly reduced PB B-cell count, at the expense of decreased numbers of recently produced immature/regulatory B cells and naïve B cells, together with an increase in Ig-switched memory B lymphocytes and plasmablasts, particularly of IgA(+) cells. Copyright © 2015 by the Research Society on Alcoholism.

Elucidating tectonic events and processes from variably tectonized conglomerate clast detrital geochronology: examples from the Hongliuhe Formation in the southern Central Asian Orogenic Belt, NW China

NASA Astrophysics Data System (ADS)

Cleven, Nathan; Lin, Shoufa; Davis, Donald; Xiao, Wenjiao; Guilmette, Carl

2017-04-01

This work expands upon detrital zircon geochronology with a sampling and analysis strategy dating granitoid conglomerate clasts that exhibit differing degrees of internal ductile deformation. As deformation textures within clastic material reflect the variation and history of tectonization in the source region of a deposit, we outline a dating methodology that can provide details of the provenance's tectonomagmatic history from deformation-relative age distributions. The method involves bulk samples of solely granitoid clasts, as they are representative of the magmatic framework within the provenance. The clasts are classified and sorted into three subsets: undeformed, slightly deformed, and deformed. LA-ICPMS U-Pb geochronology is performed on zircon separates of each subset. Our case study, involving the Permian Hongliuhe Formation in the southern Central Asian Orogenic Belt, analyzes each of the three clast subsets, as well as sandstone detrital samples, at three stratigraphic levels to yield a profile of the unroofed provenance. The age spectra of the clast samples exhibit different, wider distributions than sandstone samples, considered an effect of proximity to the respective provenance. Comparisons of clast data to sandstone data, as well as comparisons between stratigraphic levels, yield indications of key tectonic processes, in addition to the typical characteristics provided by detrital geochronology. The clast data indicates a minimal lag time, implying rapid exhumation rates, whereas sandstone data alone would indicate a 90 m.y. lag time. Early Paleozoic arc building episodes appear as Ordovician peaks in sandstone data, and Silurian-Devonian peaks in clast data, indicating a younging of magmatism towards the proximal provenance. A magmatic hiatus starts in the Devonian, correlating with the latest age of deformed clasts, interpreted as timing of collisional tectonics. Provenance interpretation using the correlations seen between the clast and sandstone data proves to be more detailed and more robust than that determined from sandstone samples alone. The variably tectonized clast detrital geochronology method offers a regional reconnaissance tool that can address the practical limits of studying regional granitoid distributions.

Relationship Between Types of Exercise and Quality of Life in a Korean Metabolic Syndrome Population: A Cross-Sectional Study.

PubMed

Oh, Sang Ho; Son, Sun Han; Kang, Si Hyun; Kim, Don-Kyu; Seo, Kyung Mook; Lee, Sang Yoon

2017-05-01

Metabolic syndrome (MetS) significantly correlates with exercise. MetS also has an independent and inverse correlation to quality of life (QoL). However, few studies have examined the association between exercise and QoL in people with MetS. The aim of this study was to ascertain the relationship between exercise and QoL in a MetS population. This was a cross-sectional study using public data from the Sixth Korean National Health and Nutrition Examination Survey in 2014 (n = 7550). MetS was defined on the basis of the revised National Cholesterol Education Program criteria. Demographic factors, three types of exercise (resistance, flexibility, walking), five subsets of EuroQoL (mobility, self-care, usual activities, pain/discomfort, anxiety/depression), and QoL scores (EQ-VAS), were investigated. Independent associations of each exercise on five subsets of QoL were determined using odds ratios (OR) adjusted for four demographic factors (age group, sex, weight change, and area of residence) using multivariate logistic regression analysis. Prevalence of MetS was 26.4% and the ratio of subjects performing resistance, flexibility, or walking exercise was 17.7%, 45.8%, and 71.5% among this population, respectively. EQ-VAS of exercisers was significantly higher than that of non-exercisers in resistance, flexibility, and walking exercise. Although resistance and flexibility exercise did not correlate with any subsets of QoL, mobility and self-care were significantly associated with walking exercise (OR = 0.635, 95% CI = 0.439-0.919 and OR = 0.577, 95% CI = 0.348-0.958, respectively). All exercisers showed higher QoL scores than non-exercisers. Among QoL subsets, mobility and self-care were independently associated with walking exercise in the MetS population. Regular walking exercise was important to higher QoL in those with MetS. This is the first clinical report to indicate that QoL could be independently influenced by walking exercise.

Linear methods for reducing EMG contamination in peripheral nerve motor decodes.

PubMed

Kagan, Zachary B; Wendelken, Suzanne; Page, David M; Davis, Tyler; Hutchinson, Douglas T; Clark, Gregory A; Warren, David J

2016-08-01

Signals recorded from the peripheral nervous system (PNS) with high channel count penetrating microelectrode arrays, such as the Utah Slanted Electrode Array (USEA), often have electromyographic (EMG) signals contaminating the neural signal. This common-mode signal source may prevent single neural units from successfully being detected, thus hindering motor decode algorithms. Reducing this EMG contamination may lead to more accurate motor decode performance. A virtual reference (VR), created by a weighted linear combination of signals from a subset of all available channels, can be used to reduce this EMG contamination. Four methods of determining individual channel weights and six different methods of selecting subsets of channels were investigated (24 different VR types in total). The methods of determining individual channel weights were equal weighting, regression-based weighting, and two different proximity-based weightings. The subsets of channels were selected by a radius-based criteria, such that a channel was included if it was within a particular radius of inclusion from the target channel. These six radii of inclusion were 1.5, 2.9, 3.2, 5, 8.4, and 12.8 electrode-distances; the 12.8 electrode radius includes all USEA electrodes. We found that application of a VR improves the detectability of neural events via increasing the SNR, but we found no statistically meaningful difference amongst the VR types we examined. The computational complexity of implementation varies with respect to the method of determining channel weights and the number of channels in a subset, but does not correlate with VR performance. Hence, we examined the computational costs of calculating and applying the VR and based on these criteria, we recommend an equal weighting method of assigning weights with a 3.2 electrode-distance radius of inclusion. Further, we found empirically that application of the recommended VR will require less than 1 ms for 33.3 ms of data from one USEA.

CD4 T cells play important roles in maintaining IL-17-producing γδ T-cell subsets in naive animals.

PubMed

Do, Jeong-Su; Visperas, Anabelle; O'Brien, Rebecca L; Min, Booki

2012-04-01

A proportional balance between αβ and γδ T-cell subsets in the periphery is exceedingly well maintained by a homeostatic mechanism. However, a cellular mechanism underlying the regulation remains undefined. We recently reported that a subset of developing γδ T cells spontaneously acquires interleukin (IL)-17-producing capacity even within naive animals through a transforming growth factor (TGF)β1-dependent mechanism, thus considered 'innate' IL-17-producing cells. Here, we report that γδ T cells generated within αβ T cell (or CD4 T cell)-deficient environments displayed altered cytokine profiles; particularly, 'innate' IL-17 expression was significantly impaired compared with those in wild-type mice. Impaired IL-17 production in γδ T cells was directly related to CD4 T-cell deficiency, because depletion of CD4 T cells in wild-type mice diminished and adoptive CD4 T-cell transfer into T-cell receptor β-/- mice restored IL-17 expression in γδ T cells. CD4 T cell-mediated IL-17 expression required TGFβ1. Moreover, Th17 but not Th1 or Th2 effector CD4 T cells were highly efficient in enhancing γδ T-cell IL-17 expression. Taken together, our results highlight a novel CD4 T cell-dependent mechanism that shapes the generation of IL-17+ γδ T cells in naive settings.

Selection of reliable reference genes for quantitative real-time PCR gene expression analysis in Jute (Corchorus capsularis) under stress treatments

PubMed Central

Niu, Xiaoping; Qi, Jianmin; Zhang, Gaoyang; Xu, Jiantang; Tao, Aifen; Fang, Pingping; Su, Jianguang

2015-01-01

To accurately measure gene expression using quantitative reverse transcription PCR (qRT-PCR), reliable reference gene(s) are required for data normalization. Corchorus capsularis, an annual herbaceous fiber crop with predominant biodegradability and renewability, has not been investigated for the stability of reference genes with qRT-PCR. In this study, 11 candidate reference genes were selected and their expression levels were assessed using qRT-PCR. To account for the influence of experimental approach and tissue type, 22 different jute samples were selected from abiotic and biotic stress conditions as well as three different tissue types. The stability of the candidate reference genes was evaluated using geNorm, NormFinder, and BestKeeper programs, and the comprehensive rankings of gene stability were generated by aggregate analysis. For the biotic stress and NaCl stress subsets, ACT7 and RAN were suitable as stable reference genes for gene expression normalization. For the PEG stress subset, UBC, and DnaJ were sufficient for accurate normalization. For the tissues subset, four reference genes TUBβ, UBI, EF1α, and RAN were sufficient for accurate normalization. The selected genes were further validated by comparing expression profiles of WRKY15 in various samples, and two stable reference genes were recommended for accurate normalization of qRT-PCR data. Our results provide researchers with appropriate reference genes for qRT-PCR in C. capsularis, and will facilitate gene expression study under these conditions. PMID:26528312

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice[W

PubMed Central

Gingerich, Derek J.; Hanada, Kousuke; Shiu, Shin-Han; Vierstra, Richard D.

2007-01-01

Selective ubiquitination of proteins is directed by diverse families of ubiquitin-protein ligases (or E3s) in plants. One important type uses Cullin-3 as a scaffold to assemble multisubunit E3 complexes containing one of a multitude of bric-a-brac/tramtrack/broad complex (BTB) proteins that function as substrate recognition factors. We previously described the 80-member BTB gene superfamily in Arabidopsis thaliana. Here, we describe the complete BTB superfamily in rice (Oryza sativa spp japonica cv Nipponbare) that contains 149 BTB domain–encoding genes and 43 putative pseudogenes. Amino acid sequence comparisons of the rice and Arabidopsis superfamilies revealed a near equal repertoire of putative substrate recognition module types. However, phylogenetic comparisons detected numerous gene duplication and/or loss events since the rice and Arabidopsis BTB lineages split, suggesting possible functional specialization within individual BTB families. In particular, a major expansion and diversification of a subset of BTB proteins containing Meprin and TRAF homology (MATH) substrate recognition sites was evident in rice and other monocots that likely occurred following the monocot/dicot split. The MATH domain of a subset appears to have evolved significantly faster than those in a smaller core subset that predates flowering plants, suggesting that the substrate recognition module in many monocot MATH-BTB E3s are diversifying to ubiquitinate a set of substrates that are themselves rapidly changing. Intriguing possibilities include pathogen proteins attempting to avoid inactivation by the monocot host. PMID:17720868

Clonal group distribution of fluoroquinolone-resistant Escherichia coli among humans and companion animals in Australia.

PubMed

Platell, Joanne L; Cobbold, Rowland N; Johnson, James R; Trott, Darren J

2010-09-01

To determine the phylogenetic group distribution and prevalence of three major globally disseminated clonal groups [clonal group A (CGA) and O15:K52:H1, associated with phylogenetic group D, and sequence type ST131, associated with phylogenetic group B2] among fluoroquinolone-resistant extra-intestinal Escherichia coli isolates from humans and companion animals in Australia. Clinical extra-intestinal fluoroquinolone-resistant E. coli isolates were obtained from humans (n = 582) and companion animals (n = 125), on Australia's east coast (October 2007-October 2009). Isolates were tested for susceptibility to seven antimicrobial agents, and for phylogenetic group, O type and clonal-group-specific single nucleotide polymorphisms by PCR. The fluoroquinolone-resistant isolates were typically resistant to multiple agents (median of four). Analysis revealed that clonal group ST131 accounted for a large subset of the human isolates (202/585, 35%), but for a much smaller proportion of the companion animal isolates (9/125, 7.2%; P

A global analysis of bird plumage patterns reveals no association between habitat and camouflage

PubMed Central

Marshall, Kate L.A.; Gluckman, Thanh-Lan

2016-01-01

Evidence suggests that animal patterns (motifs) function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types—mottled (irregular), scales, bars and spots (regular)—and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species’ geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world’s birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world’s eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis. PMID:27867762

Two Trackers Are Better than One: Information about the Co-actor's Actions and Performance Scores Contribute to the Collective Benefit in a Joint Visuospatial Task.

PubMed

Wahn, Basil; Kingstone, Alan; König, Peter

2017-01-01

When humans collaborate, they often distribute task demands in order to reach a higher performance compared to performing the same task alone (i.e., a collective benefit). Here, we tested to what extent receiving information about the actions of a co-actor, performance scores, or receiving both types of information impacts the collective benefit in a collaborative multiple object tracking task. In a between-subject design, pairs of individuals jointly tracked a subset of target objects among several moving distractor objects on a computer screen for a 100 trials. At the end of a trial, pairs received performance scores (Experiment 1), information about their partner's target selections (Experiment 2), or both types of information (Experiment 3). In all experiments, the performance of the pair exceeded the individual performances and the simulated performance of two independent individuals combined. Initially, when receiving both types of information (Experiment 3), pairs achieved the highest performance and divided task demands most efficiently compared to the other two experiments. Over time, performances and the ability to divide task demands for pairs receiving a single type of information converged with those receiving both, suggesting that pairs' coordination strategies become equally effective over time across experiments. However, pairs' performances never reached a theoretical limit of performance in all experiments. For distributing task demands, members of a pair predominantly used a left-right division of labor strategy (i.e., the leftmost targets were tracked by one co-actor while the rightmost targets were tracked by the other co-actor). Overall, findings of the present study suggest that receiving information about actions of a co-actor, performance scores, or receiving both enables pairs to devise effective division of labor strategies in a collaborative visuospatial task. However, when pairs had both types of information available, the formation of division of labor strategies was facilitated, indicating that pairs benefited the most from having both types of information available (i.e., actions about the co-actor and performance scores). Findings are applicable to circumstances in which humans need to perform collaborative visuospatial tasks that are time-critical and/or only allow a very limited exchange of information between co-actors.

Who stops selling? A systematic analysis of ex-tobacco retailers.

PubMed

Feletto, Eleonora; Burton, Suzan; Williams, Kelly; Fry, Rae; Sutton, Clare; Bagus, Lachlan; Egger, Sam

2016-03-09

There is evidence that wide distribution of cigarettes contributes to smoking, and multiple commentators have called for a review of tobacco retailing. This study analyses retailers who stop selling cigarettes, why they do so, and discusses the implications for tobacco control. An audit of tobacco retailers in the Australian state of NSW was used to identify retailers who had stopped selling tobacco, and they were then compared with current retailers to determine how many, and what types of outlets stop selling tobacco. Attempts were made to contact and interview all former tobacco retailers identified in three audited regions. In-depth interviews were conducted with 13 ex-tobacco retailers, or 31% of the subset of ex-tobacco retailers. Low-volume outlet types were over-represented as a proportion of retailers exiting the market, and some had resumed selling within 18 months of the audit. Low profits were often cited as a contributor to stopping; however, in all but one case, the decision to stop selling was also influenced by a significant change in business circumstances-either legislative or other business changes. Few retailers stop selling tobacco while continuing in the same business, and those who stop disproportionately represent retailer types with low sales volume. The results suggest that legislative changes provide a window where retailers could be prompted to exit the market. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Genetic diversity, QoI fungicide resistance, and mating type distribution of Cercospora sojina—Implications for the disease dynamics of frogeye leaf spot on soybean

PubMed Central

Shrestha, Sandesh Kumar; Cochran, Alicia; Mengistu, Alemu; Castro-Rocha, Arturo; Young-Kelly, Heather

2017-01-01

Frogeye leaf spot (FLS), caused by Cercospora sojina, causes significant damage to soybean in the U.S. One control strategy is the use of quinone outside inhibitor (QoI) fungicides. QoI resistant isolates were first reported in Tennessee (TN) in 2010. To investigate the disease dynamics of C. sojina, we collected 437 C. sojina isolates in 2015 from Jackson and Milan, TN and used 40 historical isolates collected from 2006–2009 from TN and ten additional states for comparison. A subset of 186 isolates, including historical isolates, were genotyped for 49 single nucleotide polymorphism (SNP) markers and the QoI resistance locus, revealing 35 unique genotypes. The genotypes clustered into three groups with two groups containing only sensitive isolates and the remaining group containing all resistant isolates and a dominant clonal lineage of 130 isolates. All 477 C. sojina isolates were genotyped for the QoI locus revealing 344 resistant and 133 sensitive isolates. All isolates collected prior to 2015 were QoI sensitive. Both mating type alleles (MAT1-1-1 and MAT1-2) were found in Jackson and Milan, TN and recovered from single lesions suggesting sexual recombination may play a role in the epidemiology of field populations. Analysis of C. sojina isolates using SNP markers proved useful to investigate population diversity and to elaborate on diversity as it relates to QoI resistance and mating type. PMID:28486517

Nestedness across biological scales

PubMed Central

Marquitti, Flavia M. D.; Raimundo, Rafael L. G.; Sebastián-González, Esther; Coltri, Patricia P.; Perez, S. Ivan; Brandt, Débora Y. C.; Nunes, Kelly; Daura-Jorge, Fábio G.; Floeter, Sergio R.; Guimarães, Paulo R.

2017-01-01

Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness throughout biological scales can stimulate the debate on how pervasive nestedness may be in nature, while the theoretical emergent principles can aid further research on commonalities of biological networks. PMID:28166284

Integration of multispectral satellite and hyperspectral field data for aquatic macrophyte studies

NASA Astrophysics Data System (ADS)

John, C. M.; Kavya, N.

2014-11-01

Aquatic macrophytes (AM) can serve as useful indicators of water pollution along the littoral zones. The spectral signatures of various AM were investigated to determine whether species could be discriminated by remote sensing. In this study the spectral readings of different AM communities identified were done using the ASD Fieldspec® Hand Held spectro-radiometer in the wavelength range of 325-1075 nm. The collected specific reflectance spectra were applied to space borne multi-spectral remote sensing data from Worldview-2, acquired on 26th March 2011. The dimensionality reduction of the spectro-radiometric data was done using the technique principal components analysis (PCA). Out of the different PCA axes generated, 93.472 % variance of the spectra was explained by the first axis. The spectral derivative analysis was done to identify the wavelength where the greatest difference in reflectance is shown. The identified wavelengths are 510, 690, 720, 756, 806, 885, 907 and 923 nm. The output of PCA and derivative analysis were applied to Worldview-2 satellite data for spectral subsetting. The unsupervised classification was used to effectively classify the AM species using the different spectral subsets. The accuracy assessment of the results of the unsupervised classification and their comparison were done. The overall accuracy of the result of unsupervised classification using the band combinations Red-Edge, Green, Coastal blue & Red-edge, Yellow, Blue is 100%. The band combinations NIR-1, Green, Coastal blue & NIR-1, Yellow, Blue yielded an accuracy of 82.35 %. The existing vegetation indices and new hyper-spectral indices for the different type of AM communities were computed. Overall, results of this study suggest that high spectral and spatial resolution images provide useful information for natural resource managers especially with regard to the location identification and distribution mapping of macrophyte species and their communities.

RNAi pathways contribute to developmental history-dependent phenotypic plasticity in C. elegans

PubMed Central

Hall, Sarah E.; Chirn, Gung-Wei; Lau, Nelson C.; Sengupta, Piali

2013-01-01

Early environmental experiences profoundly influence adult phenotypes through complex mechanisms that are poorly understood. We previously showed that adult Caenorhabditis elegans that transiently passed through the stress-induced dauer larval stage (post-dauer adults) exhibit significant changes in gene expression profiles, chromatin states, and life history traits when compared with adults that bypassed the dauer stage (control adults). These wild-type, isogenic animals of equivalent developmental stages exhibit different signatures of molecular marks that reflect their distinct developmental trajectories. To gain insight into the mechanisms that contribute to these developmental history-dependent phenotypes, we profiled small RNAs from post-dauer and control adults by deep sequencing. RNA interference (RNAi) pathways are known to regulate genome-wide gene expression both at the chromatin and post-transcriptional level. By quantifying changes in endogenous small interfering RNA (endo-siRNA) levels in post-dauer as compared with control animals, our analyses identified a subset of genes that are likely targets of developmental history-dependent reprogramming through a complex RNAi-mediated mechanism. Mutations in specific endo-siRNA pathways affect expected gene expression and chromatin state changes for a subset of genes in post-dauer animals, as well as disrupt their increased brood size phenotype. We also find that both chromatin state and endo-siRNA distribution in dauers are unique, and suggest that remodeling in dauers provides a template for the subsequent establishment of adult post-dauer profiles. Our results indicate a role for endo-siRNA pathways as a contributing mechanism to early experience-dependent phenotypic plasticity in adults, and describe how developmental history can program adult physiology and behavior via epigenetic mechanisms. PMID:23329696

Effect of sialic acid loss on dendritic cell maturation

PubMed Central

Crespo, Hélio J; Guadalupe Cabral, M; Teixeira, Alexandra V; Lau, Joseph T Y; Trindade, Hélder; Videira, Paula A

2009-01-01

Sialic acids are key structural determinants and contribute to the functionality of a number of immune cell receptors. Previously, we demonstrated that differentiation of human dendritic cells (DCs) is accompanied by an increased expression of sialylated cell surface structures, putatively through the activity of the ST3Gal.I and ST6Gal.I sialyltransferases. Furthermore, DC endocytosis was reduced upon removal of the cell surface sialic acid residues by neuraminidase. In the present work, we evaluate the contribution of the sialic acid modifications in DC maturation. We demonstrate that neuraminidase-treated human DCs have increased expression of major histocompatibility complex (MHC) and costimulatory molecules, increased gene expression of specific cytokines and induce a higher proliferative response of T lymphocytes. Together, the data suggest that clearance of cell surface sialic acids contributes to the development of a T helper type 1 proinflammatory response. This postulate is supported by mouse models, where elevated MHC class II and increased maturation of specific DC subsets were observed in DCs harvested from ST3Gal.I−/− and ST6Gal.I−/− mice. Moreover, important qualitative differences, particularly in the extent of reduced endocytosis and in the peripheral distribution of DC subsets, existed between the ST3Gal.I−/− and ST6Gal.I−/− strains. Together, the data strongly suggest not only a role of cell surface sialic acid modifications in maturation and functionality of DCs, but also that the sialic acid linkages created by different sialyltransferases are functionally distinct. Consequently, with particular relevance to DC-based therapies, cell surface sialylation, mediated by individual sialyltransferases, can influence the immunogenicity of DCs upon antigen loading. PMID:19740323

Phenotypic and functional characterization of earthworm coelomocyte subsets: Linking light scatter-based cell typing and imaging of the sorted populations.

PubMed

Engelmann, Péter; Hayashi, Yuya; Bodó, Kornélia; Ernszt, Dávid; Somogyi, Ildikó; Steib, Anita; Orbán, József; Pollák, Edit; Nyitrai, Miklós; Németh, Péter; Molnár, László

2016-12-01

Flow cytometry is a common approach to study invertebrate immune cells including earthworm coelomocytes. However, the link between light-scatter- and microscopy-based phenotyping remains obscured. Here we show, by means of light scatter-based cell sorting, both subpopulations (amoebocytes and eleocytes) can be physically isolated with good sort efficiency and purity confirmed by downstream morphological and cytochemical applications. Immunocytochemical analysis using anti-EFCC monoclonal antibodies combined with phalloidin staining has revealed antigenically distinct, sorted subsets. Screening of lectin binding capacity indicated wheat germ agglutinin (WGA) as the strongest reactor to amoebocytes. This is further evidenced by WGA inhibition assays that suggest high abundance of N-acetyl-d-glucosamine in amoebocytes. Post-sort phagocytosis assays confirmed the functional differences between amoebocytes and eleocytes, with the former being in favor of bacterial engulfment. This study has proved successful in linking flow cytometry and microscopy analysis and provides further experimental evidence of phenotypic and functional heterogeneity in earthworm coelomocyte subsets. Copyright © 2016 Elsevier Ltd. All rights reserved.

Earthquake Nucleation on Faults With Heterogeneous Frictional Properties, Normal Stress

NASA Astrophysics Data System (ADS)

Ray, Sohom; Viesca, Robert C.

2017-10-01

We examine the development of an instability of fault slip rate. We consider a slip rate and state dependence of fault frictional strength, in which frictional properties and normal stress are functions of position. We pose the problem for a slip rate distribution that diverges quasi-statically within finite time in a self-similar fashion. Scenarios of property variations are considered and the corresponding self-similar solutions found. We focus on variations of coefficients, a and b, respectively, controlling the magnitude of a direct effect on strength due to instantaneous changes in slip rate and of strength evolution due to changes in a state variable. These results readily extend to variations in fault-normal stress, σ, or the characteristic slip distance for state evolution, Dc. We find that heterogeneous properties lead to a finite number of self-similar solutions, located about critical points of the distributions: maxima, minima, and between them. We examine the stability of these solutions and find that only a subset is asymptotically stable, occurring at just one of the critical point types. Such stability implies that during instability development, slip rate and state evolution can be attracted to develop in the manner of the self-similar solution, which is also confirmed by solutions to initial value problems for slip rate and state. A quasi-static slip rate divergence is ultimately limited by inertia, leading to the nucleation of an outward expanding dynamic rupture: asymptotic stability of self-similar solutions then implies preferential sites for earthquake nucleation, which are determined by distribution of frictional properties.

Evaluation of subset matching methods and forms of covariate balance.

PubMed

de Los Angeles Resa, María; Zubizarreta, José R

2016-11-30

This paper conducts a Monte Carlo simulation study to evaluate the performance of multivariate matching methods that select a subset of treatment and control observations. The matching methods studied are the widely used nearest neighbor matching with propensity score calipers and the more recently proposed methods, optimal matching of an optimally chosen subset and optimal cardinality matching. The main findings are: (i) covariate balance, as measured by differences in means, variance ratios, Kolmogorov-Smirnov distances, and cross-match test statistics, is better with cardinality matching because by construction it satisfies balance requirements; (ii) for given levels of covariate balance, the matched samples are larger with cardinality matching than with the other methods; (iii) in terms of covariate distances, optimal subset matching performs best; (iv) treatment effect estimates from cardinality matching have lower root-mean-square errors, provided strong requirements for balance, specifically, fine balance, or strength-k balance, plus close mean balance. In standard practice, a matched sample is considered to be balanced if the absolute differences in means of the covariates across treatment groups are smaller than 0.1 standard deviations. However, the simulation results suggest that stronger forms of balance should be pursued in order to remove systematic biases due to observed covariates when a difference in means treatment effect estimator is used. In particular, if the true outcome model is additive, then marginal distributions should be balanced, and if the true outcome model is additive with interactions, then low-dimensional joints should be balanced. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Pregnancy and malaria exposure are associated with changes in the B cell pool and in plasma eotaxin levels.

PubMed

Requena, Pilar; Campo, Joseph J; Umbers, Alexandra J; Ome, Maria; Wangnapi, Regina; Barrios, Diana; Robinson, Leanne J; Samol, Paula; Rosanas-Urgell, Anna; Ubillos, Itziar; Mayor, Alfredo; López, Marta; de Lazzari, Elisa; Arévalo-Herrera, Myriam; Fernández-Becerra, Carmen; del Portillo, Hernando; Chitnis, Chetan E; Siba, Peter M; Bardají, Azucena; Mueller, Ivo; Rogerson, Stephen; Menéndez, Clara; Dobaño, Carlota

2014-09-15

Pregnancy triggers immunological changes aimed to tolerate the fetus, but its impact on B lymphocytes is poorly understood. In addition, exposure to the Plasmodium parasite is associated with altered distribution of peripheral memory B cell (MBC) subsets. To study the combined impact of high malaria exposure and pregnancy in B cell subpopulations, we analyzed PBMCs from pregnant and nonpregnant individuals from a malaria-nonendemic country (Spain) and from a high malaria-endemic country (Papua New Guinea). In the malaria-naive cohorts, pregnancy was associated with a significant expansion of all switched (IgD(-)) MBC and a decrease of naive B cells. Malaria-exposed women had more atypical MBC and fewer marginal zone-like MBC, and their levels correlated with both Plasmodium vivax- and Plasmodium falciparum-specific plasma IgG levels. Classical but not atypical MBC were increased in P. falciparum infections. Moreover, active atypical MBC positively correlated with proinflammatory cytokine plasma concentrations and had lower surface IgG levels than the average. Decreased plasma eotaxin (CCL11) levels were associated with pregnancy and malaria exposure and also correlated with B cell subset frequencies. Additionally, active atypical and active classical MBC expressed higher levels of eotaxin receptor CCR3 than the other B cell subsets, suggesting a chemotactic effect of eotaxin on these B cell subsets. These findings are important to understand immunity to infections like malaria that result in negative outcomes for both the mother and the newborn and may have important implications on vaccine development. Copyright © 2014 by The American Association of Immunologists, Inc.

Use of diagnostic coronary angiography in women and men presenting with acute myocardial infarction: a matched cohort study.

PubMed

Bjerking, Louise Hougesen; Hansen, Kim Wadt; Madsen, Mette; Jensen, Jan Skov; Madsen, Jan Kyst; Sørensen, Rikke; Galatius, Søren

2016-06-01

Based on evident sex-related differences in the invasive management of patients presenting with acute myocardial infarction (AMI), we sought to identify predictors of diagnostic coronary angiography (DCA) and to investigate reasons for opting out an invasive strategy in women and men. The study was designed as a matched cohort study. We randomly selected 250 female cases from a source population of 4000 patients hospitalized with a first AMI in a geographically confined region of Denmark from January 2010 to November 2011. Each case was matched to a male control on age and availability of cardiac invasive facilities at the index hospital. We systematically reviewed medical records for risk factors, comorbid conditions, clinical presentation, and receipt of DCA. Clinical justifications, as stated by the treating physician, were noted for the subset of patients who did not receive a DCA. Overall, 187 women and 198 men received DCA within 60 days (75 % vs. 79 %, hazard ratio: 0.82 [0.67-1.00], p = 0.047).In the subset of patients who did not receive a DCA (n = 114), clinical justifications for opting out an invasive strategy was not documented for 21 patients (18.4 %). Type 2 myocardial infarction was noted in 11 patients (women versus men; 14.5 % vs. 3.8 %, p = 0.06) and identified as a potential confounder of the sex-DCA relationship. Receipt of DCA was predicted by traditional risk factors for ischaemic heart disease (family history of cardiovascular disease, hypercholesterolemia, and smoking) and clinical presentation (chest pain, ST-segment elevations). Although prevalent in both women and men, the presence of relative contraindications did not prohibit the use of DCA. In this matched cohort of patients with a first AMI, women and men had different clinical presentations despite similar age. However, no differences in the distribution of relative contraindications for DCA were found between the sexes. Type 2 MI posed a potentiel confounder for the sex-related differences in the use of DCA. Importantly,clinical justification for opting out an invasive strategy was not documented in almost one fifth of patients not receiving a DCA.

Type 1 diabetes risk for HLA-DR3 haplotypes depends on genotypic context: Association of DPB1 and HLA class I loci among DR3 and DR4 matched Italian patients and controls

PubMed Central

Noble, Janelle A.; Martin, Adelle; Valdes, Ana M.; Lane, Julie A.; Galgani, Andrea; Petrone, Antonio; Lorini, Renata; Pozzilli, Paolo; Buzzetti, Raffaella; Erlich, Henry A.

2008-01-01

Patients with high-risk HLA-DR-DQ genotypes for type 1 diabetes (T1D) were compared to HLA-matched controls to evaluate T1D risk for other HLA loci, including HLA-A, -B, -Cw, and DPB1. Patients (n=133) with high-risk genotypes (DR3/DR3, DR3/DR4, DR4/DR4) were selected from the Lazio (Rome) region of Italy. Screening of more than 9000 subjects from the Lazio region and northern Italy yielded 162 controls with high- T1D-risk haplotypes. Although the overall distributions were not significantly different, allele frequency differences were discovered between the controls from Lazio and those from Northern Italy for some alleles previously shown to affect T1D risk, such as A*3002, DPB1*0301, and DPB1*0402. Therefore, Lazio patient data were compared both to the Lazio subset of controls (n=53) and to the entire group of controls for association analyses. Significant allele frequency differences between patients and DR-DQ-matched controls were found for specific alleles at all loci. Data for the DR3/DR3 subset of patients and controls showed an increase of Cw*0702 in patients. Reduced patient, compared to control, frequencies were seen for several alleles, including A*0101, B*0801, and Cw*0701, all found on the highly-conserved, extended DR3 haplotype known as 8.1 in DR3/DR3, but not DR3/DR4, subgroup. DPB1*0101, often found on 8.1 haplotypes, was also less frequent in DR3/DR3 patients than controls. Analysis of family-based data from the HBDI repository was consistent with the observed results from the Italian subjects, suggesting the presence of a T1D-protective locus at or near A*0101 and a second T1D-protective locus at or near DPB1*0101. These data suggest that T1D risk conferred by the 8.1 haplotype is genotype dependent. PMID:18486765

On the reduced dynamics of a subset of interacting bosonic particles

NASA Astrophysics Data System (ADS)

Gessner, Manuel; Buchleitner, Andreas

2018-03-01

The quantum dynamics of a subset of interacting bosons in a subspace of fixed particle number is described in terms of symmetrized many-particle states. A suitable partial trace operation over the von Neumann equation of an N-particle system produces a hierarchical expansion for the subdynamics of M ≤ N particles. Truncating this hierarchy with a pure product state ansatz yields the general, nonlinear coherent mean-field equation of motion. In the special case of a contact interaction potential, this reproduces the Gross-Pitaevskii equation. To account for incoherent effects on top of the mean-field evolution, we discuss possible extensions towards a second-order perturbation theory that accounts for interaction-induced decoherence in form of a nonlinear Lindblad-type master equation.

Schizophrenia classification using functional network features

NASA Astrophysics Data System (ADS)

Rish, Irina; Cecchi, Guillermo A.; Heuton, Kyle

2012-03-01

This paper focuses on discovering statistical biomarkers (features) that are predictive of schizophrenia, with a particular focus on topological properties of fMRI functional networks. We consider several network properties, such as node (voxel) strength, clustering coefficients, local efficiency, as well as just a subset of pairwise correlations. While all types of features demonstrate highly significant statistical differences in several brain areas, and close to 80% classification accuracy, the most remarkable results of 93% accuracy are achieved by using a small subset of only a dozen of most-informative (lowest p-value) correlation features. Our results suggest that voxel-level correlations and functional network features derived from them are highly informative about schizophrenia and can be used as statistical biomarkers for the disease.

Heterogeneity in Neutrophil Microparticles Reveals Distinct Proteome and Functional Properties*

PubMed Central

Dalli, Jesmond; Montero-Melendez, Trinidad; Norling, Lucy V; Yin, Xiaoke; Hinds, Charles; Haskard, Dorian; Mayr, Manuel; Perretti, Mauro

2013-01-01

Altered plasma neutrophil microparticle levels have recently been implicated in a number of vascular and inflammatory diseases, yet our understanding of their actions is very limited. Herein, we investigate the proteome of neutrophil microparticles in order to shed light on their biological actions. Stimulation of human neutrophils, either in suspension or adherent to an endothelial monolayer, led to the production of microparticles containing >400 distinct proteins with only 223 being shared by the two subsets. For instance, postadherent microparticles were enriched in alpha-2 macroglobulin and ceruloplasmin, whereas microparticles produced by neutrophils in suspension were abundant in heat shock 70 kDa protein 1. Annexin A1 and lactotransferrin were expressed in both microparticle subsets. We next determined relative abundance of these proteins in three types of human microparticle samples: healthy volunteer plasma, plasma of septic patients and skin blister exudates finding that these proteins were differentially expressed on neutrophil microparticles from these samples reflecting in part the expression profiles we found in vitro. Functional assessment of the neutrophil microparticles subsets demonstrated that in response to direct stimulation neutrophil microparticles produced reactive oxygen species and leukotriene B4 as well as locomoted toward a chemotactic gradient. Finally, we investigated the actions of the two neutrophil microparticles subsets described herein on target cell responses. Microarray analysis with human primary endothelial cells incubated with either microparticle subset revealed a discrete modulation of endothelial cell gene expression profile. These findings demonstrate that neutrophil microparticles are heterogenous and can deliver packaged information propagating the activation status of the parent cell, potentially exerting novel and fundamental roles both under homeostatic and disease conditions. PMID:23660474

Bifidobacterium breve attenuates murine dextran sodium sulfate-induced colitis and increases regulatory T cell responses.

PubMed

Zheng, Bin; van Bergenhenegouwen, Jeroen; Overbeek, Saskia; van de Kant, Hendrik J G; Garssen, Johan; Folkerts, Gert; Vos, Paul; Morgan, Mary E; Kraneveld, Aletta D

2014-01-01

While some probiotics have shown beneficial effects on preventing or treating colitis development, others have shown no effects. In this study, we have assessed the immunomodulating effects of two probiotic strains, Lactobacillus rhamnosus (L. rhamnosus) and Bifidobacterium breve (B. breve) on T cell polarization in vitro, using human peripheral blood mononuclear cells (PBMC), and in vivo, using murine dextran sodium sulfate (DSS) colitis model. With respect to the latter, the mRNA expression of T cell subset-associated transcription factors and cytokines in the colon was measured and the T helper type (Th) 17 and regulatory T cell (Treg) subsets were determined in the Peyer's patches. Both L. rhamnosus and B. breve incubations in vitro reduced Th17 and increased Th2 cell subsets in human PBMCs. In addition, B. breve incubation was also able to reduce Th1 and increase Treg cell subsets in contrast to L. rhamnosus. In vivo intervention with B. breve, but not L. rhamnosus, significantly attenuated the severity of DSS-induced colitis. In DSS-treated C57BL/6 mice, intervention with B. breve increased the expression of mRNA encoding for Th2- and Treg-associated cytokines in the distal colon. In addition, intervention with B. breve led to increases of Treg and decreases of Th17 cell subsets in Peyer's patches of DSS-treated mice. B. breve modulates T cell polarization towards Th2 and Treg cell-associated responses in vitro and in vivo. In vivo B. breve intervention ameliorates DSS-induced colitis symptoms and this protective effect may mediated by its effects on the T-cell composition.

Metabolic Profile as a Potential Modifier of Long-Term Radiation Effects on Peripheral Lymphocyte Subsets in Atomic Bomb Survivors.

PubMed

Yoshida, Kengo; Nakashima, Eiji; Kyoizumi, Seishi; Hakoda, Masayuki; Hayashi, Tomonori; Hida, Ayumi; Ohishi, Waka; Kusunoki, Yoichiro

2016-09-01

Immune system impairments reflected by the composition and function of circulating lymphocytes are still observed in atomic bomb survivors, and metabolic abnormalities including altered blood triglyceride and cholesterol levels have also been detected in such survivors. Based on closely related features of immune and metabolic profiles of individuals, we investigated the hypothesis that long-term effects of radiation exposure on lymphocyte subsets might be modified by metabolic profiles in 3,113 atomic bomb survivors who participated in health examinations at the Radiation Effect Research Foundation, Hiroshima and Nagasaki, in 2000-2002. The lymphocyte subsets analyzed involved T-, B- and NK-cell subsets, and their percentages in the lymphocyte fraction were assessed using flow cytometry. Health examinations included metabolic indicators, body mass index, serum levels of total cholesterol, high-density lipoprotein cholesterol, C-reactive protein and hemoglobin A1c, as well as diabetes and fatty liver diagnoses. Standard regression analyses indicated that several metabolic indicators of obesity/related disease, particularly high-density lipoprotein cholesterol levels, were positively associated with type-1 helper T- and B-cell percentages but were inversely associated with naïve CD4 T and NK cells. A regression analysis adjusted for high-density lipoprotein cholesterol revealed a radiation dose relationship with increasing NK-cell percentage. Additionally, an interaction effect was suggested between radiation dose and C-reactive protein on B-cell percentage with a negative coefficient of the interaction term. Collectively, these findings suggest that radiation exposure and subsequent metabolic profile changes, potentially in relationship to obesity-related inflammation, lead to such long-term alterations in lymphocyte subset composition. Because this study is based on cross-sectional and exploratory analyses, the implications regarding radiation exposure, metabolic profiles and circulating lymphocytes warrant future longitudinal and molecular mechanistic studies.

Bifidobacterium breve Attenuates Murine Dextran Sodium Sulfate-Induced Colitis and Increases Regulatory T Cell Responses

PubMed Central

Zheng, Bin; van Bergenhenegouwen, Jeroen; Overbeek, Saskia; van de Kant, Hendrik J. G.; Garssen, Johan; Folkerts, Gert; Vos, Paul; Morgan, Mary E.; Kraneveld, Aletta D.

2014-01-01

While some probiotics have shown beneficial effects on preventing or treating colitis development, others have shown no effects. In this study, we have assessed the immunomodulating effects of two probiotic strains, Lactobacillus rhamnosus (L. rhamnosus) and Bifidobacterium breve (B. breve) on T cell polarization in vitro, using human peripheral blood mononuclear cells (PBMC), and in vivo, using murine dextran sodium sulfate (DSS) colitis model. With respect to the latter, the mRNA expression of T cell subset-associated transcription factors and cytokines in the colon was measured and the T helper type (Th) 17 and regulatory T cell (Treg) subsets were determined in the Peyer's patches. Both L. rhamnosus and B. breve incubations in vitro reduced Th17 and increased Th2 cell subsets in human PBMCs. In addition, B. breve incubation was also able to reduce Th1 and increase Treg cell subsets in contrast to L. rhamnosus. In vivo intervention with B. breve, but not L. rhamnosus, significantly attenuated the severity of DSS-induced colitis. In DSS-treated C57BL/6 mice, intervention with B. breve increased the expression of mRNA encoding for Th2- and Treg-associated cytokines in the distal colon. In addition, intervention with B. breve led to increases of Treg and decreases of Th17 cell subsets in Peyer's patches of DSS-treated mice. B. breve modulates T cell polarization towards Th2 and Treg cell-associated responses in vitro and in vivo. In vivo B. breve intervention ameliorates DSS-induced colitis symptoms and this protective effect may mediated by its effects on the T-cell composition. PMID:24787575

Invariant Theory for Dispersed Transverse Isotropy: An Efficient Means for Modeling Fiber Splay

NASA Technical Reports Server (NTRS)

Freed, alan D.; Einstein, Daniel R.; Vesely, Ivan

2004-01-01

Most soft tissues possess an oriented architecture of collagen fiber bundles, conferring both anisotropy and nonlinearity to their elastic behavior. Transverse isotropy has often been assumed for a subset of these tissues that have a single macroscopically-identifiable preferred fiber direction. Micro-structural studies, however, suggest that, in some tissues, collagen fibers are approximately normally distributed about a mean preferred fiber direction. Structural constitutive equations that account for this dispersion of fibers have been shown to capture the mechanical complexity of these tissues quite well. Such descriptions, however, are computationally cumbersome for two-dimensional (2D) fiber distributions, let alone for fully three-dimensional (3D) fiber populations. In this paper, we develop a new constitutive law for such tissues, based on a novel invariant theory for dispersed transverse isotropy. The invariant theory is based on a novel closed-form splay invariant that can easily handle 3D fiber populations, and that only requires a single parameter in the 2D case. The model is polyconvex and fits biaxial data for aortic valve tissue as accurately as the standard structural model. Modification of the fiber stress-strain law requires no re-formulation of the constitutive tangent matrix, making the model flexible for different types of soft tissues. Most importantly, the model is computationally expedient in a finite-element analysis.

Towards a Safer, More Randomized Lentiviral Vector Integration Profile Exploring Artificial LEDGF Chimeras

PubMed Central

Vranckx, Lenard S.; Demeulemeester, Jonas; Debyser, Zeger

2016-01-01

The capacity to integrate transgenes into the host cell genome makes retroviral vectors an interesting tool for gene therapy. Although stable insertion resulted in successful correction of several monogenic disorders, it also accounts for insertional mutagenesis, a major setback in otherwise successful clinical gene therapy trials due to leukemia development in a subset of treated patients. Despite improvements in vector design, their use is still not risk-free. Lentiviral vector (LV) integration is directed into active transcription units by LEDGF/p75, a host-cell protein co-opted by the viral integrase. We engineered LEDGF/p75-based hybrid tethers in an effort to elicit a more random integration pattern to increase biosafety, and potentially reduce proto-oncogene activation. We therefore truncated LEDGF/p75 by deleting the N-terminal chromatin-reading PWWP-domain, and replaced this domain with alternative pan-chromatin binding peptides. Expression of these LEDGF-hybrids in LEDGF-depleted cells efficiently rescued LV transduction and resulted in LV integrations that distributed more randomly throughout the host-cell genome. In addition, when considering safe harbor criteria, LV integration sites for these LEDGF-hybrids distributed more safely compared to LEDGF/p75-mediated integration in wild-type cells. This approach should be broadly applicable to introduce therapeutic or suicide genes for cell therapy, such as patient-specific iPS cells. PMID:27788138

SLX-1 Is Required for Maintaining Genomic Integrity and Promoting Meiotic Noncrossovers in the Caenorhabditis elegans Germline

PubMed Central

Meyer, Katherine; Harper, J. Wade; Colaiácovo, Monica P.

2012-01-01

Although the SLX4 complex, which includes structure-specific nucleases such as XPF, MUS81, and SLX1, plays important roles in the repair of several kinds of DNA damage, the function of SLX1 in the germline remains unknown. Here we characterized the endonuclease activities of the Caenorhabditis elegans SLX-1-HIM-18/SLX-4 complex co-purified from human 293T cells and determined SLX-1 germline function via analysis of slx-1(tm2644) mutants. SLX-1 shows a HIM-18/SLX-4–dependent endonuclease activity toward replication forks, 5′-flaps, and Holliday junctions. slx-1 mutants exhibit hypersensitivity to UV, nitrogen mustard, and camptothecin, but not gamma irradiation. Consistent with a role in DNA repair, recombination intermediates accumulate in both mitotic and meiotic germ cells in slx-1 mutants. Importantly, meiotic crossover distribution, but not crossover frequency, is altered on chromosomes in slx-1 mutants compared to wild type. This alteration is not due to changes in either the levels or distribution of double-strand breaks (DSBs) along chromosomes. We propose that SLX-1 is required for repair at stalled or collapsed replication forks, interstrand crosslink repair, and nucleotide excision repair during mitosis. Moreover, we hypothesize that SLX-1 regulates the crossover landscape during meiosis by acting as a noncrossover-promoting factor in a subset of DSBs. PMID:22927825

A cooperative approach among methods for photometric redshifts estimation: an application to KiDS data

NASA Astrophysics Data System (ADS)

Cavuoti, S.; Tortora, C.; Brescia, M.; Longo, G.; Radovich, M.; Napolitano, N. R.; Amaro, V.; Vellucci, C.; La Barbera, F.; Getman, F.; Grado, A.

2017-04-01

Photometric redshifts (photo-z) are fundamental in galaxy surveys to address different topics, from gravitational lensing and dark matter distribution to galaxy evolution. The Kilo Degree Survey (KiDS), I.e. the European Southern Observatory (ESO) public survey on the VLT Survey Telescope (VST), provides the unprecedented opportunity to exploit a large galaxy data set with an exceptional image quality and depth in the optical wavebands. Using a KiDS subset of about 25000 galaxies with measured spectroscopic redshifts, we have derived photo-z using (I) three different empirical methods based on supervised machine learning; (II) the Bayesian photometric redshift model (or BPZ); and (III) a classical spectral energy distribution (SED) template fitting procedure (LE PHARE). We confirm that, in the regions of the photometric parameter space properly sampled by the spectroscopic templates, machine learning methods provide better redshift estimates, with a lower scatter and a smaller fraction of outliers. SED fitting techniques, however, provide useful information on the galaxy spectral type, which can be effectively used to constrain systematic errors and to better characterize potential catastrophic outliers. Such classification is then used to specialize the training of regression machine learning models, by demonstrating that a hybrid approach, involving SED fitting and machine learning in a single collaborative framework, can be effectively used to improve the accuracy of photo-z estimates.

Sensor Network Localization by Eigenvector Synchronization Over the Euclidean Group

PubMed Central

CUCURINGU, MIHAI; LIPMAN, YARON; SINGER, AMIT

2013-01-01

We present a new approach to localization of sensors from noisy measurements of a subset of their Euclidean distances. Our algorithm starts by finding, embedding, and aligning uniquely realizable subsets of neighboring sensors called patches. In the noise-free case, each patch agrees with its global positioning up to an unknown rigid motion of translation, rotation, and possibly reflection. The reflections and rotations are estimated using the recently developed eigenvector synchronization algorithm, while the translations are estimated by solving an overdetermined linear system. The algorithm is scalable as the number of nodes increases and can be implemented in a distributed fashion. Extensive numerical experiments show that it compares favorably to other existing algorithms in terms of robustness to noise, sparse connectivity, and running time. While our approach is applicable to higher dimensions, in the current article, we focus on the two-dimensional case. PMID:23946700

Multiple descriptions based on multirate coding for JPEG 2000 and H.264/AVC.

PubMed

Tillo, Tammam; Baccaglini, Enrico; Olmo, Gabriella

2010-07-01

Multiple description coding (MDC) makes use of redundant representations of multimedia data to achieve resiliency. Descriptions should be generated so that the quality obtained when decoding a subset of them only depends on their number and not on the particular received subset. In this paper, we propose a method based on the principle of encoding the source at several rates, and properly blending the data encoded at different rates to generate the descriptions. The aim is to achieve efficient redundancy exploitation, and easy adaptation to different network scenarios by means of fine tuning of the encoder parameters. We apply this principle to both JPEG 2000 images and H.264/AVC video data. We consider as the reference scenario the distribution of contents on application-layer overlays with multiple-tree topology. The experimental results reveal that our method favorably compares with state-of-art MDC techniques.

Negotiating Multicollinearity with Spike-and-Slab Priors.

PubMed

Ročková, Veronika; George, Edward I

2014-08-01

In multiple regression under the normal linear model, the presence of multicollinearity is well known to lead to unreliable and unstable maximum likelihood estimates. This can be particularly troublesome for the problem of variable selection where it becomes more difficult to distinguish between subset models. Here we show how adding a spike-and-slab prior mitigates this difficulty by filtering the likelihood surface into a posterior distribution that allocates the relevant likelihood information to each of the subset model modes. For identification of promising high posterior models in this setting, we consider three EM algorithms, the fast closed form EMVS version of Rockova and George (2014) and two new versions designed for variants of the spike-and-slab formulation. For a multimodal posterior under multicollinearity, we compare the regions of convergence of these three algorithms. Deterministic annealing versions of the EMVS algorithm are seen to substantially mitigate this multimodality. A single simple running example is used for illustration throughout.

Anonymous quantum nonlocality.

PubMed

Liang, Yeong-Cherng; Curchod, Florian John; Bowles, Joseph; Gisin, Nicolas

2014-09-26

We investigate the phenomenon of anonymous quantum nonlocality, which refers to the existence of multipartite quantum correlations that are not local in the sense of being Bell-inequality-violating but where the nonlocality is--due to its biseparability with respect to all bipartitions--seemingly nowhere to be found. Such correlations can be produced by the nonlocal collaboration involving definite subset(s) of parties but to an outsider, the identity of these nonlocally correlated parties is completely anonymous. For all n≥3, we present an example of an n-partite quantum correlation exhibiting anonymous nonlocality derived from the n-partite Greenberger-Horne-Zeilinger state. An explicit biseparable decomposition of these correlations is provided for any partitioning of the n parties into two groups. Two applications of these anonymous Greenberger-Horne-Zeilinger correlations in the device-independent setting are discussed: multipartite secret sharing between any two groups of parties and bipartite quantum key distribution that is robust against nearly arbitrary leakage of information.

A Geographic Information Systems (GIS)-based analysis of modern South African rodent distributions, habitat use, and environmental tolerances.

PubMed

Campbell, Timothy L; Lewis, Patrick J; Thies, Monte L; Williams, Justin K

2012-11-01

GOALS OF THIS STUDY WERE TO: (1) develop distributional maps of modern rodent genera throughout the countries of South Africa, Lesotho, and Swaziland by georeferencing museum specimens; (2) assess habitat preferences for genera by cross-referencing locality position with South African vegetation; and (3) identify mean annual precipitation and temperature range where the genera are located. Conterminous South Africa including the countries of Lesotho and Swaziland Digital databases of rodent museum specimens housed in the Ditsong National Museum of Natural History, South Africa (DM), and the Division of Mammals, National Museum of Natural History, Smithsonian Institution, United States (NMNH), were acquired and then sorted into a subset of specimens with associated coordinate data. The coordinate data were then used to develop distributional maps for the rodent genera present within the study area. Percent habitat occupation and descriptive statistics for six climatic variables were then determined for each genus by cross-referencing locality positions with vegetation and climatic maps. This report presents a series of maps illustrating the distribution of 35 rodent genera based on 19,471 geo-referenced specimens obtained from two major collections. Inferred habitat use by taxon is provided for both locality and specimen percent occurrence at three hierarchical habitat levels: biome, bioregion, and vegetation unit. Descriptive statistics for six climatic variables are also provided for each genus based on locality and specimen percent incidence. As rodent faunas are commonly used in paleoenvironmental reconstructions, an accurate assessment of rodent environmental tolerance ranges is necessary before confidence can be placed in an actualistic model. While the data presented here represent only a subset of the modern geographic distributions for many of the taxa examined, a wide range of environmental regimes are observed, suggesting that more research is necessary in order to accurately reconstruct an environmental signature when these taxa are found in the fossil record.

Aftershock Analysis of the 2016 Mw7.8 Pedernales (Ecuador) Earthquake: Seismotectonics, Seismicity Distribution and Relationship with Coseismic Slip Distribution

NASA Astrophysics Data System (ADS)

Agurto-Detzel, H.; Font, Y.; Charvis, P.; Ambrois, D.; Cheze, J.; Courboulex, F.; De Barros, L.; Deschamps, A.; Galve, A.; Godano, M.; Laigle, M.; Maron, C.; Martin, X.; Monfret, T.; Oregioni, D.; Peix, F., Sr.; Regnier, M. M.; Yates, B.; Mercerat, D.; Leon Rios, S.; Rietbrock, A.; Acero, W.; Alvarado, A. P.; Gabriela, P.; Ramos, C.; Ruiz, M. C.; Singaucho, J. C.; Vasconez, F.; Viracucha, C.; Beck, S. L.; Lynner, C.; Hoskins, M.; Meltzer, A.; Soto-Cordero, L.; Stachnik, J.

2017-12-01

0n April 2016, a Mw 7.8 megathrust earthquake struck the coast of Ecuador causing vast human and material losses. The earthquake ruptured a 100 km-long segment of the subduction interface between Nazca and South America, spatially coinciding with the 1942 M 7.8 earthquake rupture area. Shortly after the mainshock, an international effort made by institutions from Ecuador, France, UK and USA, deployed a temporary network of +60 land and ocean-bottom seismometers to capture the aftershock sequence for the subsequent year. These stations came to join the local Ecuadorian national network already monitoring in place. Here we benefit from this dataset to produce a suite of automatic locations and a subset of regional moment tensors for high quality events. Over 2900 events were detected for the first month of postseismic activity alone, and a subset of 600 events were manually re-picked and located. Similarly, thousands of aftershocks were detected using the temporary deployment over the following months, with magnitudes ranging between 1 to 7. As expected, moment tensors show mostly thrust faulting at the interface, but we also observe sparse normal and strike-slip faulting at shallow depths in the forearc. The spatial distribution of seismicity delineates the coseismic rupture area, but extends well beyond it over a 300 km long segment. Main features include three seismicity alignments perpendicular to the trench, at the north, center and south of the mainshock rupture. Preliminary results comparing quantitatively the distribution of aftershocks to the distribution of the coseismic rupture show that the bulk of the aftershock seismicity occurs at intermediate levels of coseismic slip, while areas of maximum coseismic slip are mostly devoid of events M>3. Our results shed light on the interface processes occurring mainly during the early post-seismic period of large megathrust earthquakes, and implications on the earthquake cycle.

Case-control study of genus-beta human papillomaviruses in plucked eyebrow hairs and cutaneous squamous cell carcinoma.

PubMed

Iannacone, Michelle R; Gheit, Tarik; Pfister, Herbert; Giuliano, Anna R; Messina, Jane L; Fenske, Neil A; Cherpelis, Basil S; Sondak, Vernon K; Roetzheim, Richard G; Silling, Steffi; Pawlita, Michael; Tommasino, Massimo; Rollison, Dana E

2014-05-01

Cutaneous human papillomaviruses (HPV) have been reported in cutaneous squamous cell carcinoma (SCC). We conducted a clinic-based case-control study to investigate the association between genus-beta HPV DNA in eyebrow hairs (EBH) and SCC. EBH from 168 SCC cases and 290 controls were genotyped for genus-beta HPV DNA. SCC tumors from a subset of cases (n = 142) were also genotyped. Viral load was determined in a subset of specimens positive for a single HPV type. Associations with SCC were estimated by odds ratios (OR) and 95% confidence intervals (CI) adjusted for age and sex using logistic regression. Statistical tests were two-sided. EBH DNA prevalence was greater in cases (87%) than controls (73%) (p < 0.05), and the association with SCC increased with the number of HPV types present, (≥ 4 types vs. HPV-negative: OR = 2.02, 95% CI = 1.07-3.80; p(trend) = 0.02). Type-specific associations were observed between SCC and DNA in EBH for HPV23 (OR = 1.90, 95% CI = 1.10-3.30) and HPV38 (OR = 1.84, 95% CI = 1.04-3.24). Additionally, when compared with the controls, the DNA prevalence in EBH was significantly higher among cases for 11 of the 25 genus-beta types tested, when accounting for DNA for the same HPV type in the tumor (ORs = 3.44-76.50). Compared to controls, the mean viral DNA load in EBH among the selected cases was greater for HPV5, HPV8 and HPV24, but lower for HPV38. SCC cases were more likely than controls to have HPV DNA+ EBH for single and multiple HPV types, providing additional support for the potential role of genus-beta HPV infections in SCC development. © 2013 UICC.

The Quantification of Consistent Subjective Logic Tree Branch Weights for PSHA

NASA Astrophysics Data System (ADS)

Runge, A. K.; Scherbaum, F.

2012-04-01

The development of quantitative models for the rate of exceedance of seismically generated ground motion parameters is the target of probabilistic seismic hazard analysis (PSHA). In regions of low to moderate seismicity, the selection and evaluation of source- and/or ground-motion models is often a major challenge to hazard analysts and affected by large epistemic uncertainties. In PSHA this type of uncertainties is commonly treated within a logic tree framework in which the branch weights express the degree-of-belief values of an expert in the corresponding set of models. For the calculation of the distribution of hazard curves, these branch weights are subsequently used as subjective probabilities. However the quality of the results depends strongly on the "quality" of the expert knowledge. A major challenge for experts in this context is to provide weight estimates which are logically consistent (in the sense of Kolmogorov's axioms) and to be aware of and to deal with the multitude of heuristics and biases which affect human judgment under uncertainty. For example, people tend to give smaller weights to each branch of a logic tree the more branches it has, starting with equal weights for all branches and then adjusting this uniform distribution based on his/her beliefs about how the branches differ. This effect is known as pruning bias.¹ A similar unwanted effect, which may even wrongly suggest robustness of the corresponding hazard estimates, will appear in cases where all models are first judged according to some numerical quality measure approach and the resulting weights are subsequently normalized to sum up to one.2 To address these problems, we have developed interactive graphical tools for the determination of logic tree branch weights in form of logically consistent subjective probabilities, based on the concepts suggested in Curtis and Wood (2004).3 Instead of determining the set of weights for all the models in a single step, the computer driven elicitation process is performed as a sequence of evaluations of relative weights for small subsets of models which are presented to the analyst. From these, the distribution of logic tree weights for the whole model set is determined as solution of an optimization problem. The model subset presented to the analyst in each step is designed to maximize the expected information. The result of this process is a set of logically consistent weights together with a measure of confidence determined from the amount of conflicting information which is provided by the expert during the relative weighting process.

Predicting volume of distribution with decision tree-based regression methods using predicted tissue:plasma partition coefficients.

PubMed

Freitas, Alex A; Limbu, Kriti; Ghafourian, Taravat

2015-01-01

Volume of distribution is an important pharmacokinetic property that indicates the extent of a drug's distribution in the body tissues. This paper addresses the problem of how to estimate the apparent volume of distribution at steady state (Vss) of chemical compounds in the human body using decision tree-based regression methods from the area of data mining (or machine learning). Hence, the pros and cons of several different types of decision tree-based regression methods have been discussed. The regression methods predict Vss using, as predictive features, both the compounds' molecular descriptors and the compounds' tissue:plasma partition coefficients (Kt:p) - often used in physiologically-based pharmacokinetics. Therefore, this work has assessed whether the data mining-based prediction of Vss can be made more accurate by using as input not only the compounds' molecular descriptors but also (a subset of) their predicted Kt:p values. Comparison of the models that used only molecular descriptors, in particular, the Bagging decision tree (mean fold error of 2.33), with those employing predicted Kt:p values in addition to the molecular descriptors, such as the Bagging decision tree using adipose Kt:p (mean fold error of 2.29), indicated that the use of predicted Kt:p values as descriptors may be beneficial for accurate prediction of Vss using decision trees if prior feature selection is applied. Decision tree based models presented in this work have an accuracy that is reasonable and similar to the accuracy of reported Vss inter-species extrapolations in the literature. The estimation of Vss for new compounds in drug discovery will benefit from methods that are able to integrate large and varied sources of data and flexible non-linear data mining methods such as decision trees, which can produce interpretable models. Graphical AbstractDecision trees for the prediction of tissue partition coefficient and volume of distribution of drugs.

Fall 2014 SEI Research Review Probabilistic Analysis of Time Sensitive Systems

DTIC Science & Technology

2014-10-28

Osmosis SMC Tool Osmosis is a tool for Statistical Model Checking (SMC) with Semantic Importance Sampling. • Input model is written in subset of C...ASSERT() statements in model indicate conditions that must hold. • Input probability distributions defined by the user. • Osmosis returns the...on: – Target relative error, or – Set number of simulations Osmosis Main Algorithm 1 http://dreal.cs.cmu.edu/ (?⃑?): Indicator

Combining markers with and without the limit of detection

PubMed Central

Dong, Ting; Liu, Catherine Chunling; Petricoin, Emanuel F.; Tang, Liansheng Larry

2014-01-01

In this paper, we consider the combination of markers with and without the limit of detection (LOD). LOD is often encountered when measuring proteomic markers. Because of the limited detecting ability of an equipment or instrument, it is difficult to measure markers at a relatively low level. Suppose that after some monotonic transformation, the marker values approximately follow multivariate normal distributions. We propose to estimate distribution parameters while taking the LOD into account, and then combine markers using the results from the linear discriminant analysis. Our simulation results show that the ROC curve parameter estimates generated from the proposed method are much closer to the truth than simply using the linear discriminant analysis to combine markers without considering the LOD. In addition, we propose a procedure to select and combine a subset of markers when many candidate markers are available. The procedure based on the correlation among markers is different from a common understanding that a subset of the most accurate markers should be selected for the combination. The simulation studies show that the accuracy of a combined marker can be largely impacted by the correlation of marker measurements. Our methods are applied to a protein pathway dataset to combine proteomic biomarkers to distinguish cancer patients from non-cancer patients. PMID:24132938

Ontogeny and tissue distribution of the chicken Bu-1a antigen.

PubMed Central

Houssaint, E; Diez, E; Pink, J R

1987-01-01

By using a sensitive technique of immunofluorescence on polyethylene glycol-embedded tissue sections, we could better determine the distribution of L22+ cells in embryonic and adult chickens. L22 mAb was originally described as reacting with bursa and bursa-derived lymphocytes. We now present evidence to suggest that this mAb also reacts with a subset of macrophages found in bursa, thymus, spleen, liver, intestine and peritoneum. The L22+ cells appear early during embryonic life, simultaneously in yolk sac, bursa, thymus, spleen and bone marrow. At all steps of their ontogeny, thymocytes were L22-, while most, if not all, bursal lymphoid cells were L22+. Moreover, L22 antigen can be detected on haemopoietic cells probably precursors, before and during their entry into the bursal rudiment on Day 9 or 10 of embryonic life. We conclude from these data that L22 is not restricted to the B-cell lineage as it is shared with a subset of macrophages. Furthermore, our observations of L22+ cells during embryonic life favour the hypothesis of separate lineages for B-cell and T-cell precursors in chick embryo, which was previously put forward on the basis of different sets of experiments. Images Figure 1 Figure 3 Figure 4 PMID:3499381

Distributed Similarity based Clustering and Compressed Forwarding for wireless sensor networks.

PubMed

Arunraja, Muruganantham; Malathi, Veluchamy; Sakthivel, Erulappan

2015-11-01

Wireless sensor networks are engaged in various data gathering applications. The major bottleneck in wireless data gathering systems is the finite energy of sensor nodes. By conserving the on board energy, the life span of wireless sensor network can be well extended. Data communication being the dominant energy consuming activity of wireless sensor network, data reduction can serve better in conserving the nodal energy. Spatial and temporal correlation among the sensor data is exploited to reduce the data communications. Data similar cluster formation is an effective way to exploit spatial correlation among the neighboring sensors. By sending only a subset of data and estimate the rest using this subset is the contemporary way of exploiting temporal correlation. In Distributed Similarity based Clustering and Compressed Forwarding for wireless sensor networks, we construct data similar iso-clusters with minimal communication overhead. The intra-cluster communication is reduced using adaptive-normalized least mean squares based dual prediction framework. The cluster head reduces the inter-cluster data payload using a lossless compressive forwarding technique. The proposed work achieves significant data reduction in both the intra-cluster and the inter-cluster communications, with the optimal data accuracy of collected data. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Lapatinib distribution in HER2 overexpressing experimental brain metastases of breast cancer.

PubMed

Taskar, Kunal S; Rudraraju, Vinay; Mittapalli, Rajendar K; Samala, Ramakrishna; Thorsheim, Helen R; Lockman, Julie; Gril, Brunilde; Hua, Emily; Palmieri, Diane; Polli, Joseph W; Castellino, Stephen; Rubin, Stephen D; Lockman, Paul R; Steeg, Patricia S; Smith, Quentin R

2012-03-01

Lapatinib, a small molecule EGFR/HER2 inhibitor, partially inhibits the outgrowth of HER2+ brain metastases in preclinical models and in a subset of CNS lesions in clinical trials of HER2+ breast cancer. We investigated the ability of lapatinib to reach therapeutic concentrations in the CNS following (14)C-lapatinib administration (100 mg/kg p.o. or 10 mg/kg, i.v.) to mice with MDA-MD-231-BR-HER2 brain metastases of breast cancer. Drug concentrations were determined at differing times after administration by quantitative autoradiography and chromatography. (14)C-Lapatinib concentration varied among brain metastases and correlated with altered blood-tumor barrier permeability. On average, brain metastasis concentration was 7-9-fold greater than surrounding brain tissue at 2 and 12 h after oral administration. However, average lapatinib concentration in brain metastases was still only 10-20% of those in peripheral metastases. Only in a subset of brain lesions (17%) did lapatinib concentration approach that of systemic metastases. No evidence was found of lapatinib resistance in tumor cells cultured ex vivo from treated brains. Results show that lapatinib distribution to brain metastases of breast cancer is partially restricted and blood-tumor barrier permeability is a key component of lapatinib therapeutic efficacy which varies between tumors.

Altered Cytokine Production By Specific Human Peripheral Blood Cell Subsets Immediately Following Spaceflight

NASA Technical Reports Server (NTRS)

Crucian, Brian E.; Cubbage, Michael L.; Sams, Clarence F.

1999-01-01

In this study, we have attempted to combine standard immunological assays with the cellular resolving power of the flow cytometer to positively identify the specific cell types involved in spaceflight-induced immune alterations. We have obtained whole blood samples from 27 astronauts collected at three timepoints (L-10, R+0 and R+3) surrounding four recent space shuttle missions. The duration of these missions ranged from 10 to 18 days. Assays performed included serum/urine cortisol, comprehensive subset phenotyping, assessment of cellular activation markers and intracellular cytokine production following mitogenic stimulation. Absolute levels of peripheral granulocytes were significantly elevated following spaceflight, but the levels of circulating lymphocytes and monocytes were unchanged. Lymphocyte subset analysis demonstrated trends towards a decreased percentage of T cells and an increased percentage of B cells. Nearly all of the astronauts exhibited an increased CD4:CD8 ratio, which was dramatic in some individuals. Assessment of memory (CD45RA+) vs. naive (CD45RO+) CD4+ T cell subsets was more ambiguous, with subjects tending to group more as a flight crew. All subjects from one mission demonstrated an increased CD45RA:CD45RO ratio, while all subjects from another Mission demonstrated a decreased ratio. While no significant trend was seen in the monocyte population as defined by scatter, a decreased percentage of the CD14+ CD16+ monocyte subset was seen following spaceflight in all subjects tested. In general, most of the cellular changes described above which were assessed at R+O and compared to L-10 trended to pre-flight levels by R+3. Although no significant differences were seen in the expression of the cellular activation markers CD69 and CD25 following exposure to microgravity, significant alterations were seen in cytokine production in response to mitogenic activation for specific subsets. T cell (CD3+) production of IL-2 was significantly decreased after at R+O as was IL-2 production by both CD4+ and CD8+ T cell subsets for most subjects. Production of IFN(sub gamma) did not appear to be affected by microgravity exposure in either T cells in general or in the CD8+ T cell subset. There was a spaceflight-induced decrease in IFN(sub gamma) production in the CD4+ T cell subset, however it did not reach statistical significance. Serum and urine stress-hormone analysis indicated significant physiologic stresses in astronauts following spaceflight. In summary, these results demonstrate alterations in the peripheral immune system of astronauts immediately after spaceflight of 10 to 18 days duration and support continued research regarding microgravity and immunology (including in-flight sampling) prior to routine long-term spaceflight for astronauts.

Labelling and targeted ablation of specific bipolar cell types in the zebrafish retina

PubMed Central

2009-01-01

Background Development of a functional retina depends on regulated differentiation of several types of neurons and generation of a highly complex network between the different types of neurons. In addition, each type of retinal neuron includes several distinct morphological types. Very little is known about the mechanisms responsible for generating this diversity of retinal neurons, which may also display specific patterns of regional distribution. Results In a screen in zebrafish, using a trapping vector carrying an engineered yeast Gal4 transcription activator and a UAS:eGFP reporter cassette, we have identified two transgenic lines of zebrafish co-expressing eGFP and Gal4 in specific subsets of retinal bipolar cells. The eGFP-labelling facilitated analysis of axon terminals within the inner plexiform layer of the adult retina and showed that the fluorescent bipolar cells correspond to previously defined morphological types. Strong regional restriction of eGFP-positive bipolar cells to the central part of the retina surrounding the optic nerve was observed in adult zebrafish. Furthermore, we achieved specific ablation of the labelled bipolar cells in 5 days old larvae, using a bacterial nitroreductase gene under Gal4-UAS control in combination with the prodrug metronidazole. Following prodrug treatment, nitroreductase expressing bipolar cells were efficiently ablated without affecting surrounding retina architecture, and recovery occurred within a few days due to increased generation of new bipolar cells. Conclusion This report shows that enhancer trapping can be applied to label distinct morphological types of bipolar cells in the zebrafish retina. The genetic labelling of these cells yielded co-expression of a modified Gal4 transcription activator and the fluorescent marker eGFP. Our work also demonstrates the potential utility of the Gal4-UAS system for induction of other transgenes, including a bacterial nitroreductase fusion gene, which can facilitate analysis of bipolar cell differentiation and how the retina recovers from specific ablation of these cells. PMID:19712466

Density-Dependent Quantized Least Squares Support Vector Machine for Large Data Sets.

PubMed

Nan, Shengyu; Sun, Lei; Chen, Badong; Lin, Zhiping; Toh, Kar-Ann

2017-01-01

Based on the knowledge that input data distribution is important for learning, a data density-dependent quantization scheme (DQS) is proposed for sparse input data representation. The usefulness of the representation scheme is demonstrated by using it as a data preprocessing unit attached to the well-known least squares support vector machine (LS-SVM) for application on big data sets. Essentially, the proposed DQS adopts a single shrinkage threshold to obtain a simple quantization scheme, which adapts its outputs to input data density. With this quantization scheme, a large data set is quantized to a small subset where considerable sample size reduction is generally obtained. In particular, the sample size reduction can save significant computational cost when using the quantized subset for feature approximation via the Nyström method. Based on the quantized subset, the approximated features are incorporated into LS-SVM to develop a data density-dependent quantized LS-SVM (DQLS-SVM), where an analytic solution is obtained in the primal solution space. The developed DQLS-SVM is evaluated on synthetic and benchmark data with particular emphasis on large data sets. Extensive experimental results show that the learning machine incorporating DQS attains not only high computational efficiency but also good generalization performance.

Is it time for a new classification of mast cells? What do we know about mast cell heterogeneity?

PubMed

Frossi, Barbara; Mion, Francesca; Sibilano, Riccardo; Danelli, Luca; Pucillo, Carlo E M

2018-03-01

Mast cells (MCs) are derived from committed precursors that leave the hematopoietic tissue, migrate in the blood, and colonize peripheral tissues where they terminally differentiate under microenvironment stimuli. They are distributed in almost all vascularized tissues where they act both as immune effectors and housekeeping cells, contributing to tissue homeostasis. Historically, MCs were classified into 2 subtypes, according to tryptic enzymes expression. However, MCs display a striking heterogeneity that reflects a complex interplay between different microenvironmental signals delivered by various tissues, and a differentiation program that decides their identity. Moreover, tissue-specific MCs show a trained memory, which contributes to shape their function in a specific microenvironment. In this review, we summarize the current state of our understanding of MC heterogeneity that reflects their different tissue experiences. We describe the discovery of unique cell molecules that can be used to distinguish specific MC subsets in vivo, and discuss how the improved ability to recognize these subsets provided new insights into the biology of MCs. These recent advances will be helpful for the understanding of the specific role of individual MC subsets in the control of tissue homeostasis, and in the regulation of pathological conditions such as infection, autoimmunity, and cancer. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

ER-mitochondria contacts couple mtDNA synthesis with mitochondrial division in human cells.

PubMed

Lewis, Samantha C; Uchiyama, Lauren F; Nunnari, Jodi

2016-07-15

Mitochondrial DNA (mtDNA) encodes RNAs and proteins critical for cell function. In human cells, hundreds to thousands of mtDNA copies are replicated asynchronously, packaged into protein-DNA nucleoids, and distributed within a dynamic mitochondrial network. The mechanisms that govern how nucleoids are chosen for replication and distribution are not understood. Mitochondrial distribution depends on division, which occurs at endoplasmic reticulum (ER)-mitochondria contact sites. These sites were spatially linked to a subset of nucleoids selectively marked by mtDNA polymerase and engaged in mtDNA synthesis--events that occurred upstream of mitochondrial constriction and division machine assembly. Our data suggest that ER tubules proximal to nucleoids are necessary but not sufficient for mtDNA synthesis. Thus, ER-mitochondria contacts coordinate licensing of mtDNA synthesis with division to distribute newly replicated nucleoids to daughter mitochondria. Copyright © 2016, American Association for the Advancement of Science.

Maps on statistical manifolds exactly reduced from the Perron-Frobenius equations for solvable chaotic maps

NASA Astrophysics Data System (ADS)

Goto, Shin-itiro; Umeno, Ken

2018-03-01

Maps on a parameter space for expressing distribution functions are exactly derived from the Perron-Frobenius equations for a generalized Boole transform family. Here the generalized Boole transform family is a one-parameter family of maps, where it is defined on a subset of the real line and its probability distribution function is the Cauchy distribution with some parameters. With this reduction, some relations between the statistical picture and the orbital one are shown. From the viewpoint of information geometry, the parameter space can be identified with a statistical manifold, and then it is shown that the derived maps can be characterized. Also, with an induced symplectic structure from a statistical structure, symplectic and information geometric aspects of the derived maps are discussed.

Comparison of the Frontier Distributed Database Caching System to NoSQL Databases

NASA Astrophysics Data System (ADS)

Dykstra, Dave

2012-12-01

One of the main attractions of non-relational “NoSQL” databases is their ability to scale to large numbers of readers, including readers spread over a wide area. The Frontier distributed database caching system, used in production by the Large Hadron Collider CMS and ATLAS detector projects for Conditions data, is based on traditional SQL databases but also adds high scalability and the ability to be distributed over a wide-area for an important subset of applications. This paper compares the major characteristics of the two different approaches and identifies the criteria for choosing which approach to prefer over the other. It also compares in some detail the NoSQL databases used by CMS and ATLAS: MongoDB, CouchDB, HBase, and Cassandra.

Comparison of the Frontier Distributed Database Caching System to NoSQL Databases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dykstra, Dave

One of the main attractions of non-relational NoSQL databases is their ability to scale to large numbers of readers, including readers spread over a wide area. The Frontier distributed database caching system, used in production by the Large Hadron Collider CMS and ATLAS detector projects for Conditions data, is based on traditional SQL databases but also adds high scalability and the ability to be distributed over a wide-area for an important subset of applications. This paper compares the major characteristics of the two different approaches and identifies the criteria for choosing which approach to prefer over the other. It alsomore » compares in some detail the NoSQL databases used by CMS and ATLAS: MongoDB, CouchDB, HBase, and Cassandra.« less

Unsupervised Scalable Statistical Method for Identifying Influential Users in Online Social Networks.

PubMed

Azcorra, A; Chiroque, L F; Cuevas, R; Fernández Anta, A; Laniado, H; Lillo, R E; Romo, J; Sguera, C

2018-05-03

Billions of users interact intensively every day via Online Social Networks (OSNs) such as Facebook, Twitter, or Google+. This makes OSNs an invaluable source of information, and channel of actuation, for sectors like advertising, marketing, or politics. To get the most of OSNs, analysts need to identify influential users that can be leveraged for promoting products, distributing messages, or improving the image of companies. In this report we propose a new unsupervised method, Massive Unsupervised Outlier Detection (MUOD), based on outliers detection, for providing support in the identification of influential users. MUOD is scalable, and can hence be used in large OSNs. Moreover, it labels the outliers as of shape, magnitude, or amplitude, depending of their features. This allows classifying the outlier users in multiple different classes, which are likely to include different types of influential users. Applying MUOD to a subset of roughly 400 million Google+ users, it has allowed identifying and discriminating automatically sets of outlier users, which present features associated to different definitions of influential users, like capacity to attract engagement, capacity to attract a large number of followers, or high infection capacity.

Improving imbalanced scientific text classification using sampling strategies and dictionaries.

PubMed

Borrajo, L; Romero, R; Iglesias, E L; Redondo Marey, C M

2011-09-15

Many real applications have the imbalanced class distribution problem, where one of the classes is represented by a very small number of cases compared to the other classes. One of the systems affected are those related to the recovery and classification of scientific documentation. Sampling strategies such as Oversampling and Subsampling are popular in tackling the problem of class imbalance. In this work, we study their effects on three types of classifiers (Knn, SVM and Naive-Bayes) when they are applied to search on the PubMed scientific database. Another purpose of this paper is to study the use of dictionaries in the classification of biomedical texts. Experiments are conducted with three different dictionaries (BioCreative, NLPBA, and an ad-hoc subset of the UniProt database named Protein) using the mentioned classifiers and sampling strategies. Best results were obtained with NLPBA and Protein dictionaries and the SVM classifier using the Subsampling balancing technique. These results were compared with those obtained by other authors using the TREC Genomics 2005 public corpus. Copyright 2011 The Author(s). Published by Journal of Integrative Bioinformatics.

Detection of nicotine content impact in tobacco manufacturing using computational intelligence.

PubMed

Begic Fazlic, Lejla; Avdagic, Zikrija

2011-01-01

A study is presented for the detection of nicotine impact in different cigarette type, using recorded data and Computational Intelligence techniques. Recorded puffs are processed using Continuous Wavelet Transform and used to extract time-frequency features for normal and abnormal puffs conditions. The wavelet energy distributions are used as inputs to classifiers based on Adaptive Neuro-Fuzzy Inference Systems (ANFIS) and Genetic Algorithms (GAs). The number and the parameters of Membership Functions are used in ANFIS along with the features from wavelet energy distributionare selected using GAs, maximising the diagnosis success. GA with ANFIS (GANFIS) are trained with a subset of data with known nicotine conditions. The trained GANFIS are tested using the other set of data (testing data). A classical method by High-Performance Liquid Chromatography is also introduced to solve this problem, respectively. The results as well as the performances of these two approaches are compared. A combination of these two algorithms is also suggested to improve the efficiency of this solution procedure. Computational results show that this combined algorithm is promising.

A Leonard-Sanders-Budiansky-Koiter-Type Nonlinear Shell Theory with a Hierarchy of Transverse-Shearing Deformations

NASA Technical Reports Server (NTRS)

Nemeth, Michael P.

2013-01-01

A detailed exposition on a refined nonlinear shell theory suitable for nonlinear buckling analyses of laminated-composite shell structures is presented. This shell theory includes the classical nonlinear shell theory attributed to Leonard, Sanders, Koiter, and Budiansky as an explicit proper subset. This approach is used in order to leverage the exisiting experience base and to make the theory attractive to industry. In addition, the formalism of general tensors is avoided in order to expose the details needed to fully understand and use the theory. The shell theory is based on "small" strains and "moderate" rotations, and no shell-thinness approximations are used. As a result, the strain-displacement relations are exact within the presumptions of "small" strains and "moderate" rotations. The effects of transverse-shearing deformations are included in the theory by using analyst-defined functions to describe the through-the-thickness distributions of transverse-shearing strains. Constitutive equations for laminated-composite shells are derived without using any shell-thinness approximations, and simplified forms and special cases are presented.

MEN1, MEN4, and Carney Complex: Pathology and Molecular Genetics

PubMed Central

Schernthaner-Reiter, Marie Helene; Trivellin, Giampaolo; Stratakis, Constantine A.

2015-01-01

Pituitary adenomas are a common feature of a subset of endocrine neoplasia syndromes, which have otherwise highly variable disease manifestations. We provide here a review of the clinical features and human molecular genetics of multiple endocrine neoplasia type 1 and 4 (MEN1 and MEN4, respectively) and Carney complex (CNC). MEN1, MEN4 and CNC are hereditary autosomal dominant syndromes that can present with pituitary adenomas. MEN1 is caused by inactivating mutations in the MEN1 gene, whose product menin is involved in multiple intracellular pathways contributing to transcriptional control and cell proliferation. MEN1 clinical features include primary hyperparathyroidism, pancreatic neuroendocrine tumours and prolactinomas and other pituitary adenomas. A subset of patients with pituitary adenomas and other MEN1 features have mutations in the CDKN1B gene; their disease has been called MEN type 4 (MEN4). Inactivating mutations in the type 1α regulatory subunit of protein kinase A (PKA) (the PRKAR1A gene), that lead to dysregulation and activation of the PKA pathway, are the main genetic cause of CNC, which is clinically characterised by primary pigmented adrenocortical disease (PPNAD), spotty skin pigmentation (lentigines), cardiac and other myxomas and acromegaly due to somatotropinomas or somatotrope hyperplasia. PMID:25592387

Categorization and Reasoning among Tree Experts: Do All Roads Lead to Rome?

ERIC Educational Resources Information Center

Medin, Douglas L.; And Others

1997-01-01

Results of two experiments concerned with categorization among different types of tree experts (4 taxonomists, 10 landscape workers, and 10 park maintenance employees in the first experiment and a subset of these experts in the second) show a pattern of similarities and differences. Implications for theories of categorization are discussed. (SLD)

Multiple Victimization Experiences of Urban Elementary School Students: Associations with Psychosocial Functioning and Academic Performance

ERIC Educational Resources Information Center

Holt, Melissa K.; Finkelhor, David; Kantor, Glenda Kaufman

2007-01-01

Objective: This study explored the victimization experiences of urban elementary school students to determine whether subsets of youth emerged with similar victimization profiles (e.g., no victimization, multiple types of victimization). It also evaluated whether multiple victimization was associated with greater psychological distress and lower…

BOX-COUNTING DIMENSION COMPUTED BY α-DENSE CURVES

NASA Astrophysics Data System (ADS)

García, G.; Mora, G.; Redtwitz, D. A.

We introduce a method to reduce to the real case the calculus of the box-counting dimension of subsets of the unit cube In, n > 1. The procedure is based on the existence of special types of α-dense curves (a generalization of the space-filling curves) in In called δ-uniform curves.

Modelling Proportional Thinking with Threes and Twos

ERIC Educational Resources Information Center

Tabart, Paul; Skalicky, Jane; Watson, Jane

2005-01-01

The authors discuss proportional reasoning as a challenging yet central concept for students in the middle grades that lays a foundation for mathematics studied later in high school. Four types of proportional reasoning problems are discussed: (1) Part-part-whole (comparing a subset (part) of a whole with its complement (other part) or the whole…

Adherence capacity of methicillin resistant Staphylococcus aureus sequence type (ST) 5 isolates from health care and agricultural sources

USDA-ARS?s Scientific Manuscript database

Staphylococcus aureus is part of the nasal microbiome of many humans and has become significant public health burden due to infections with antibiotic resistant versions, including methicillin resistant S. aureus (MRSA). A subset of these isolates are found in livestock species and acquired by human...

A Comparison of Limb-Socket Kinematics of Bone-Bridging and Non-Bone-Bridging Wartime Transtibial Amputations

DTIC Science & Technology

2012-05-16

each successive loading interval. Subset analysis was performed on the basis of amputation type (bone bridging or non bone bridging) and suspension...fitting, patient care. Washington, DC: US Government Printing Office; 1969. 2. Ertl J. Uber amputationsstumpfe. Chirurg. 1949;20:218 24. 3. Pinto MA

Applying Statistical Process Quality Control Methodology to Educational Settings.

ERIC Educational Resources Information Center

Blumberg, Carol Joyce

A subset of Statistical Process Control (SPC) methodology known as Control Charting is introduced. SPC methodology is a collection of graphical and inferential statistics techniques used to study the progress of phenomena over time. The types of control charts covered are the null X (mean), R (Range), X (individual observations), MR (moving…

Arginine metabolism is altered in adults with A-B + ketosis-prone diabetes

USDA-ARS?s Scientific Manuscript database

A-B + ketosis-prone diabetes (KPD) is a subset of type 2 diabetes in which patients have severe but reversible B cell dysfunction of unknown etiology. Plasma metabolomic analysis indicates that abnormal arginine metabolism may be involved. The objective of this study was to determine the relation be...

An Introduction to the Extensible Markup Language (XML).

ERIC Educational Resources Information Center

Bryan, Martin

1998-01-01

Describes Extensible Markup Language (XML), a subset of the Standard Generalized Markup Language (SGML) that is designed to make it easy to interchange structured documents over the Internet. Topics include Document Type Definition (DTD), components of XML, the use of XML, text and non-text elements, and uses for XML-coded files. (LRW)

Documentation for the Machine-readable Version of the 0.2-A Resolution Far-ultraviolet Stellar Spectra Measured with COPERNICUS

NASA Technical Reports Server (NTRS)

Sheridan, W. T.; Warren, W. H., Jr.

1981-01-01

The spectra described represent a subset comprising data for 60 O- and B-type stars. The tape contains data in the spectral region lamda lamda 1000-1450 A with a resolution of 0.2 A. The magnetic tape version of the data is described.

ɣδ T cell receptor ligands and modes of antigen recognition

PubMed Central

Champagne, Eric

2011-01-01

T lymphocytes expressing the γδ-type of T cell receptors for antigens contribute to all aspects of immune responses, including defenses against viruses, bacteria, parasites and tumors, allergy and autoimmunity. Multiple subsets have been individualized in humans as well as in mice and they appear to recognize in a TCR-dependent manner antigens as diverse as small non-peptidic molecules, soluble or membrane-anchored polypeptides and molecules related to MHC antigens on cell surfaces, implying diverse modes of antigen recognition. We review here the γδ TCR ligands which have been identified along the years and their characteristics, with emphasis on a few systems which have been extensively studied such as human γδ T cells responding to phosphoantigens or murine γδ T cells activated by allogeneic MHC antigens. We discuss a speculative model of antigen recognition involving simultaneous TCR recognition of MHC-like and non-MHC ligands which could fit with most available data and shares many similarities with the classical model of MHC-restricted antigen recognition for peptides or lipids by T cells subsets with αβ-type TCRs. PMID:21298486

γδ T cell receptor ligands and modes of antigen recognition.

PubMed

Champagne, Eric

2011-04-01

T lymphocytes expressing the γδ-type of T cell receptors (TCRs) for antigens contribute to all aspects of immune responses, including defenses against viruses, bacteria, parasites and tumors, allergy and autoimmunity. Multiple subsets have been individualized in humans as well as in mice and they appear to recognize in a TCR-dependent manner antigens as diverse as small non-peptidic molecules, soluble or membrane-anchored polypeptides and molecules related to MHC antigens on cell surfaces, implying diverse modes of antigen recognition. We review here the γδ TCR ligands which have been identified along the years and their characteristics, with emphasis on a few systems which have been extensively studied such as human γδ T cells responding to phosphoantigens or murine γδ T cells activated by allogeneic MHC antigens. We discuss a speculative model of antigen recognition involving simultaneous TCR recognition of MHC-like and non-MHC ligands which could fit with most available data and shares many similarities with the classical model of MHC-restricted antigen recognition for peptides or lipids by T cells subsets with αβ-type TCRs.

Spatial and temporal study of nitrate concentration in groundwater by means of coregionalization

USGS Publications Warehouse

D'Agostino, V.; Greene, E.A.; Passarella, G.; Vurro, M.

1998-01-01

Spatial and temporal behavior of hydrochemical parameters in groundwater can be studied using tools provided by geostatistics. The cross-variogram can be used to measure the spatial increments between observations at two given times as a function of distance (spatial structure). Taking into account the existence of such a spatial structure, two different data sets (sampled at two different times), representing concentrations of the same hydrochemical parameter, can be analyzed by cokriging in order to reduce the uncertainty of the estimation. In particular, if one of the two data sets is a subset of the other (that is, an undersampled set), cokriging allows us to study the spatial distribution of the hydrochemical parameter at that time, while also considering the statistical characteristics of the full data set established at a different time. This paper presents an application of cokriging by using temporal subsets to study the spatial distribution of nitrate concentration in the aquifer of the Lucca Plain, central Italy. Three data sets of nitrate concentration in groundwater were collected during three different periods in 1991. The first set was from 47 wells, but the second and the third are undersampled and represent 28 and 27 wells, respectively. Comparing the result of cokriging with ordinary kriging showed an improvement of the uncertainty in terms of reducing the estimation variance. The application of cokriging to the undersampled data sets reduced the uncertainty in estimating nitrate concentration and at the same time decreased the cost of the field sampling and laboratory analysis.Spatial and temporal behavior of hydrochemical parameters in groundwater can be studied using tools provided by geostatistics. The cross-variogram can be used to measure the spatial increments between observations at two given times as a function of distance (spatial structure). Taking into account the existence of such a spatial structure, two different data sets (sampled at two different times), representing concentrations of the same hydrochemical parameter, can be analyzed by cokriging in order to reduce the uncertainty of the estimation. In particular, if one of the two data sets is a subset of the other (that is, an undersampled set), cokriging allows us to study the spatial distribution of the hydrochemical parameter at that time, while also considering the statistical characteristics of the full data set established at a different time. This paper presents an application of cokriging by using temporal subsets to study the spatial distribution of nitrate concentration in the aquifer of the Lucca Plain, central Italy. Three data sets of nitrate concentration in groundwater were collected during three different periods in 1991. The first set was from 47 wells, but the second and the third are undersampled and represent 28 and 27 wells, respectively. Comparing the result of cokriging with ordinary kriging showed an improvement of the uncertainty in terms of reducing the estimation variance. The application of cokriging to the undersampled data sets reduced the uncertainty in estimating nitrate concentration and at the same time decreased the cost of the field sampling and laboratory analysis.

Fractured-aquifer hydrogeology from geophysical logs; the passaic formation, New Jersey

USGS Publications Warehouse

Morin, R.H.; Carleton, G.B.; Poirier, S.

1997-01-01

The Passaic Formation consists of gradational sequences of mudstone, siltstone, and sandstone, and is a principal aquifer in central New Jersey. Ground-water flow is primarily controlled by fractures interspersed throughout these sedimentary rocks and characterizing these fractures in terms of type, orientation, spatial distribution, frequency, and transmissivity is fundamental towards understanding local fluid-transport processes. To obtain this information, a comprehensive suite of geophysical logs was collected in 10 wells roughly 46 m in depth and located within a .05 km2 area in Hopewell Township, New Jersey. A seemingly complex, heterogeneous network of fractures identified with an acoustic televiewer was statistically reduced to two principal subsets corresponding to two distinct fracture types: (1) bedding-plane partings and (2) high-angle fractures. Bedding-plane partings are the most numerous and have an average strike of N84??W and dip of 20??N. The high-angle fractures are oriented subparallel to these features, with an average strike of N79??E and dip of 71??S, making the two fracture types roughly orthogonal. Their intersections form linear features that also retain this approximately east-west strike. Inspection of fluid temperature and conductance logs in conjunction with flowmeter measurements obtained during pumping allows the transmissive fractures to be distinguished from the general fracture population. These results show that, within the resolution capabilities of the logging tools, approximately 51 (or 18 percent) of the 280 total fractures are water producing. The bedding-plane partings exhibit transmissivities that average roughly 5 m2/day and that generally diminish in magnitude and frequency with depth. The high-angle fractures have average transmissivities that are about half those of the bedding-plane partings and show no apparent dependence upon depth. The geophysical logging results allow us to infer a distinct hydrogeologic structure within this aquifer that is defined by fracture type and orientation. Fluid flow near the surface is controlled primarily by the highly transmissive, subhorizontal bedding-plane partings. As depth increases, the high-angle fractures apparently become more dominant hydrologically.The Passaic Formation consists of gradational sequences of mudstone, siltstone, and sandstone, and is a principal aquifer in central New Jersey. Ground-water flow is primarily controlled by fractures interspersed throughout these sedimentary rocks and characterizing these fractures in terms of type, orientation, spatial distribution, frequency, and transmissivity is fundamental towards understanding local fluid-transport processes. To obtain this information, a comprehensive suite of geophysical logs was collected in 10 wells roughly 46 m in depth and located within a .05 km2 area in Hopewell Township, New Jersey. A seemingly complex, heterogeneous network of fractures identified with an acoustic televiewer was statistically reduced to two principal subsets corresponding to two distinct fracture types: (1) bedding-plane partings and (2) high-angle fractures. Bedding-plane partings are the most numerous and have an average strike of N84?? W and dip of 20?? N. The high-angle fractures are oriented subparallel to these features, with an average strike of N79?? E and dip of 71?? S, making the two fracture types roughly orthogonal. Their intersections form linear features that also retain this approximately east-west strike. Inspection of fluid temperature and conductance logs in conjunction with flowmeter measurements obtained during pumping allows the transmissive fractures to be distinguished from the general fracture population. These results show that, within the resolution capabilities of the logging tools, approximately 51 (or 18 percent) of the 280 total fractures are water producing. The bedding-plane partings exhibit transmissivities that average roughly 5 m2/day and that generally dimi

The steady aerodynamics of aerofoils with porosity gradients.

PubMed

Hajian, Rozhin; Jaworski, Justin W

2017-09-01

This theoretical study determines the aerodynamic loads on an aerofoil with a prescribed porosity distribution in a steady incompressible flow. A Darcy porosity condition on the aerofoil surface furnishes a Fredholm integral equation for the pressure distribution, which is solved exactly and generally as a Riemann-Hilbert problem provided that the porosity distribution is Hölder-continuous. The Hölder condition includes as a subset any continuously differentiable porosity distributions that may be of practical interest. This formal restriction on the analysis is examined by a class of differentiable porosity distributions that approach a piecewise, discontinuous function in a certain parametric limit. The Hölder-continuous solution is verified in this limit against analytical results for partially porous aerofoils in the literature. Finally, a comparison made between the new theoretical predictions and experimental measurements of SD7003 aerofoils presented in the literature. Results from this analysis may be integrated into a theoretical framework to optimize turbulence noise suppression with minimal impact to aerodynamic performance.

The steady aerodynamics of aerofoils with porosity gradients

NASA Astrophysics Data System (ADS)

Hajian, Rozhin; Jaworski, Justin W.

2017-09-01

This theoretical study determines the aerodynamic loads on an aerofoil with a prescribed porosity distribution in a steady incompressible flow. A Darcy porosity condition on the aerofoil surface furnishes a Fredholm integral equation for the pressure distribution, which is solved exactly and generally as a Riemann-Hilbert problem provided that the porosity distribution is Hölder-continuous. The Hölder condition includes as a subset any continuously differentiable porosity distributions that may be of practical interest. This formal restriction on the analysis is examined by a class of differentiable porosity distributions that approach a piecewise, discontinuous function in a certain parametric limit. The Hölder-continuous solution is verified in this limit against analytical results for partially porous aerofoils in the literature. Finally, a comparison made between the new theoretical predictions and experimental measurements of SD7003 aerofoils presented in the literature. Results from this analysis may be integrated into a theoretical framework to optimize turbulence noise suppression with minimal impact to aerodynamic performance.

B cell modulation strategies in autoimmunity: the SLE example.

PubMed

Rosado, M Manuela; Diamanti, Andrea Picchianti; Capolunghi, Federica; Carsetti, Rita

2011-01-01

The paradigm that T cells are the prime effectors of autoimmune diseases has been recently challenged by growing evidence that B-lymphocytes play a role in the development, re-activation and persistence of autoimmune disorders. B-cells of different subsets may play different roles in autoimmune pathologies due to their ability to secrete antibodies, produce cytokines, present antigen and form ectopic germinal centers. Thus, a given therapeutic approach or drug may have distinct outcomes depending on which specific B cell subset is targeted. Immunosuppressive therapies such as azathioprine (AZA), cyclophosphamide (CyC) or methotrexate (MTX) are conventionally used in autoimmune diseases with the aim of reducing disease activity and improving the patient's general health conditions. These treatments do not target a specific cellular type or subset and have substantial side effects, such as impairment of liver function and fertility. Moreover, autoimmune patients may be refractory to immunosuppressive therapy. In these cases finding an effective treatment becomes a challenge. The fast evolution in antibody technology is leading to the production of a wide array of humanized monoclonal antibodies, targeting specific cell types or pathways, initiating a new era in the treatment of autoimmune disorders. In addition, the recent discovery that toll like receptors (TLRs) activation can fire up autoimmunity in humans and maintain disease gives the grounds for the development of new drugs targeting the TLR/MyD88 pathway. In contrast to conventional immune-suppression, the availability of drugs interfering with B-cell specific pathogenetic pathways gives the possibility to choose therapies tailored to each disease and, possibly, to each patient.

Rare cancers: a sea of opportunity.

PubMed

Boyd, Niki; Dancey, Janet E; Gilks, C Blake; Huntsman, David G

2016-02-01

Rare cancers, as a collective, account for around a quarter of all cancer diagnoses and deaths. Historically, they have been divided into two groups: cancers defined by their unusual histogenesis (cell of origin or differentiation state)--including chordomas or adult granulosa cell tumours--and histologically defined subtypes of common cancers. Most tumour types in the first group are still clinically and biologically relevant, and have been disproportionately important as sources of insight into cancer biology. By contrast, most of those in the second group have been shown to have neither defining molecular features nor clinical utility. Omics-based analyses have splintered common cancers into a myriad of molecularly, rather than histologically, defined subsets of common cancers, many of which have immediate clinical relevance. Now, almost all rare cancers are either histomolecular entities, which often have pathognomonic mutations, or molecularly defined subsets of more common cancers. The presence of specific genetic variants provides rationale for the testing of targeted drugs in rare cancers. However, in addition to molecular alterations, it is crucial to consider the contributions of both mutation and cell context in the development, biology, and behaviour of these cancers. Patients with rare cancers are disadvantaged because of the challenge of leading clinical trials in this setting due to poor accrual. However, the number of patients with rare cancers will only increase as more molecular subsets of common cancers are identified, necessitating a shift in the focus of clinical trials and research into these cancer types, which, by epidemiological definitions, will become rare tumours. Copyright © 2016 Elsevier Ltd. All rights reserved.

Habitability in Binary Systems: The Role of UV Reduction and Magnetic Protection

NASA Astrophysics Data System (ADS)

Clark, Joni; Mason, P. A.; Zuluaga, J. I.; Cuartas, P. A.; Bustamonte, S.

2013-06-01

The number of planets found in binary systems is growing rapidly and the discovery of many more planets in binary systems appears inevitable. We use the newly refined and more restrictive, single star habitable zone (HZ) models of Kopparapu et al. (2013) and include planetary magnetic protection calculations in order to investigate binary star habitability. Here we present results on circumstellar or S-type planets, which are planets orbiting a single star member of a binary. P-type planets, on the other hand, orbit the center of mass of the binary. Stable planetary orbits exist in HZs for both types of binaries as long as the semi-major axis of the planet is either greater than (P-type) or less than (S-type) a few times the semi-major axis of the binary. We define two types of S-type binaries for this investigation. The SA-type is a circumstellar planet orbiting the binary’s primary star. In this case, the limits of habitability are dominated by the primary being only slightly affected by the presence of the lower mass companion. Thus, the SA-type planets have habitability characteristics, including magnetic protection, similar to single stars of the same type. The SB-type is a circumstellar planet orbiting the secondary star in a wide binary. An SB-type planet needs to orbit slightly outside the secondary’s single star HZ and remain within the primary’s single star HZ at all times. We explore the parameter space for which this is possible. We have found that planets lying in the combined HZ of SB binaries can be magnetically protected against the effects of stellar winds from both primary and secondary stars in a limited number of cases. We conclude that habitable conditions exist for a subset of SA-type, and a smaller subset of SB-type binaries. However, circumbinary planets (P-types) provide the most intriguing possibilities for the existence of complex life due to the effect of synchronization of binaries with periods in the 20-30 day range which allows for planets with significant magnetic protection.

Conformational diversity analysis reveals three functional mechanisms in proteins

PubMed Central

Fornasari, María Silvina

2017-01-01

Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call “rigid” (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions. PMID:28192432

Activated T cell subsets in human type 1 diabetes: evidence for expansion of the DR+ CD30+ subpopulation in new-onset disease

PubMed Central

Baker, C; Chang, L; Elsegood, K A; Bishop, A J; Gannon, D H; Narendran, P; Leech, N J; Dayan, C M

2007-01-01

An important limitation in T cell studies of human autoimmune (type 1) diabetes is lack of direct access to cells infiltrating the pancreas. We hypothesized that cells recently released from the pancreas into the blood might express a characteristic combination of markers of activation. We therefore examined the recently activated circulating T cell population [CD3+, human leucocyte antigen D-related (HLA-DR+)] using cytokine production and 10 additional subset markers [CD69, CD25, CD122, CD30, CD44v6, CD57, CD71, CCR3 (CD193), CCR5 (CD195) or CXCR3 (CD183)], comparing newly diagnosed adult (ND) (age 18–40 years) patients (n = 19) to patients with diabetes for > 10 years [long-standing (LS), n = 19] and HLA-matched controls (C, n = 16). CD3+ DR+ cells were enriched by two-step immunomagnetic separation. No differences in basal or stimulated production of interleukin (IL)-4, IL-10, IL-13 or interferon (IFN)-γ by CD3+ DR+ enriched cells were observed between the different groups of subjects. However, among the CD3+ DR+ population, significant expansions appeared to be present in the very small CD30+, CD69+ and CD122+ subpopulations. A confirmatory study was then performed using new subjects (ND = 26, LS = 15), three-colour flow cytometry, unseparated cells and three additional subset markers (CD38, CD134, CD4/CD25). This confirmed the expansion of the CD3+ DR+ CD30+ subpopulation in ND subjects. We conclude that a relative expansion in the T cell subpopulation with the activated phenotype CD3+ DR+ CD30+ is seen in the peripheral blood of subjects with newly diagnosed type 1 diabetes. This subpopulation represents less than 0·7% of circulating T cells and may provide a rich source of disease-specific T cells that can be isolated from blood. PMID:17302896

A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells

PubMed Central

2012-01-01

Background CD4+ T cells have several subsets of functional phenotypes, which play critical yet diverse roles in the immune system. Pathogen-driven differentiation of these subsets of cells is often heterogeneous in terms of the induced phenotypic diversity. In vitro recapitulation of heterogeneous differentiation under homogeneous experimental conditions indicates some highly regulated mechanisms by which multiple phenotypes of CD4+ T cells can be generated from a single population of naïve CD4+ T cells. Therefore, conceptual understanding of induced heterogeneous differentiation will shed light on the mechanisms controlling the response of populations of CD4+ T cells under physiological conditions. Results We present a simple theoretical framework to show how heterogeneous differentiation in a two-master-regulator paradigm can be governed by a signaling network motif common to all subsets of CD4+ T cells. With this motif, a population of naïve CD4+ T cells can integrate the signals from their environment to generate a functionally diverse population with robust commitment of individual cells. Notably, two positive feedback loops in this network motif govern three bistable switches, which in turn, give rise to three types of heterogeneous differentiated states, depending upon particular combinations of input signals. We provide three prototype models illustrating how to use this framework to explain experimental observations and make specific testable predictions. Conclusions The process in which several types of T helper cells are generated simultaneously to mount complex immune responses upon pathogenic challenges can be highly regulated, and a simple signaling network motif can be responsible for generating all possible types of heterogeneous populations with respect to a pair of master regulators controlling CD4+ T cell differentiation. The framework provides a mathematical basis for understanding the decision-making mechanisms of CD4+ T cells, and it can be helpful for interpreting experimental results. Mathematical models based on the framework make specific testable predictions that may improve our understanding of this differentiation system. PMID:22697466

Acute progressive paravascular placoid neuroretinopathy with negative-type electroretinography in paraneoplastic retinopathy.

PubMed

Chen, Fred K; Chew, Avenell L; Zhang, Dan; Chen, Shang-Chih; Chelva, Enid; Chandrasekera, Erandi; Koay, Eleanor M H; Forrester, John; McLenachan, Samuel

2017-06-01

Paraneoplastic retinopathy can be the first manifestation of systemic malignancy. A subset of paraneoplastic retinopathy is characterized by negative-type electroretinography (ERG) without fundus abnormality. Here we describe the multimodal imaging and clinico-pathological correlation of a unique case of acute progressive paravascular placoid neuroretinopathy with suspected retinal depolarizing bipolar cell dysfunction preceding the diagnosis of metastatic small cell carcinoma of the prostate. ERG was performed according to the International Society for Clinical Electrophysiology of Vision standards. Imaging modalities included near-infrared reflectance, blue-light autofluorescence, fluorescein and indocyanine green angiographies, spectral domain optical coherence tomography, ultra-widefield colour and green-light autofluorescence imaging, microperimetry and adaptive optics imaging. Patient serum was screened for anti-retinal antibodies using western blotting. Immunostaining and histological analyses were performed on sections from human retinal tissues and a patient prostate biopsy. Serial multimodal retinal imaging, microperimetry and adaptive optics photography demonstrated a paravascular distribution of placoid lesions characterized by hyper-reflectivity within the outer nuclear layer resembling type 2 acute macular neuroretinopathy. There was no visible lesion within the inner nuclear layer despite electronegative-type ERG. Six months later, the patient presented with metastatic small cell carcinoma of the prostate. Tumour cells were immunopositive for glyceraldehyde-3-phosphate dehydrogenase, enolase and recoverin as well as neuroendocrine markers. The patient's serum reacted to cytoplasmic and nuclear antigens in the prostate biopsy and in human retina. Anti-retinal antibodies against several antigens were detected by both commercial and in-house western blots. A spectrum of autoreactive anti-retinal antibodies is associated with a unique phenotype of acute progressive paravascular placoid neuroretinopathy resulting in degeneration of photoreceptor cells, inner retinal dysfunction and classic electronegative ERG in paraneoplastic retinopathy. Detailed clinical, functional and immunological phenotyping of paraneoplastic retinopathy illustrated the complex mechanism of paraneoplastic syndrome.

Association between exercise type and quality of life in a community-dwelling older people: A cross-sectional study

PubMed Central

Oh, Sang-Ho; Kim, Don-Kyu; Lee, Shi-Uk; Jung, Se Hee

2017-01-01

Objectives This study aimed to investigate the effects of three major representative exercises (resistance, flexibility, and walking) on quality of life (QoL) in a population of community-dwelling older adults. Materials and methods This cross-sectional study used public data from the Sixth Korean National Health and Nutrition Examination Survey in 2014 (n = 1,586 older people). Demographic factors, three types of exercise, five EuroQoL subsets (mobility, self-care, usual activities, pain/discomfort, anxiety/depression), and QoL scores (EQ-VAS) were investigated. The independent associations between each exercise and the five QoL subsets were determined using odds ratios (OR) adjusted for three demographic factors (age group, sex, and area of residence), using multivariate logistic regression analysis. Results The EQ-VAS scores of the exercisers was significantly higher than those of the non-exercisers for all exercise types. Subjects with problems in mobility dimension performed less exercise of all types of than those with normal mobility (resistance: OR, 0.687; flexibility: OR, 0.733, and walking: OR, 0.489). The self-care dimension was independently correlated with flexibility (OR, 0.558) and walking (OR, 0.485). Conclusion All types of exercisers showed higher QoL scores than non-exercisers. Among the QoL dimensions, mobility and self-care were independently associated with flexibility and walking exercise in this older people, suggesting that engaging in regular flexibility and walking exercise is important for achieving higher QoL in the older people. PMID:29216283

PDGF-responsive progenitors persist in the subventricular zone across the lifespan

PubMed Central

Moore, Lisamarie; Bain, Jennifer M.; Loh, Ji Meng; Levison, Steven W.

2013-01-01

The SVZ (subventricular zone) contains neural stem cells and progenitors of various potentialities. Although initially parsed into A, B, and C cells, this germinal zone is comprised of a significantly more diverse population of cells. Here, we characterized a subset of postnatal PRPs (PDGF-AA-responsive precursors) that express functional PDGFα and β receptors from birth to adulthood. When grown in PDGF-AA, dissociated neonatal rat SVZ cells divided to produce non-adherent clusters of progeny. Unlike the self-renewing EGF/FGF-2-responsive precursors that produce neurospheres, these PRPs failed to self-renew after three passages; therefore, we refer to the colonies they produce as spheroids. Upon differentiation these spheroids could produce neurons, type 1 astrocytes and oligodendrocytes. When maintained in medium supplemented with BMP-4 they also produced type 2 astrocytes. Using lineage tracing methods, it became evident that there were multiple types of PRPs, including a subset that could produce neurons, oligodendrocytes, and type 1 and type 2 astrocytes; thus some of these PRPs represent a unique population of precursors that are quatropotential. Spheroids also could be generated from the newborn neocortex and they had the same potentiality as those from the SVZ. By contrast, the adult neocortex produced less than 20% of the numbers of spheroids than the adult SVZ and spheroids from the adult neocortex only differentiated into glial cells. Interestingly, SVZ spheroid producing capacity diminished only slightly from birth to adulthood. Altogether these data demonstrate that there are PRPs that persist in the SVZ that includes a unique population of quatropotential PRPs. PMID:24367913

Biases in comparative analyses of extinction risk: mind the gap.

PubMed

González-Suárez, Manuela; Lucas, Pablo M; Revilla, Eloy

2012-11-01

1. Comparative analyses are used to address the key question of what makes a species more prone to extinction by exploring the links between vulnerability and intrinsic species' traits and/or extrinsic factors. This approach requires comprehensive species data but information is rarely available for all species of interest. As a result comparative analyses often rely on subsets of relatively few species that are assumed to be representative samples of the overall studied group. 2. Our study challenges this assumption and quantifies the taxonomic, spatial, and data type biases associated with the quantity of data available for 5415 mammalian species using the freely available life-history database PanTHERIA. 3. Moreover, we explore how existing biases influence results of comparative analyses of extinction risk by using subsets of data that attempt to correct for detected biases. In particular, we focus on links between four species' traits commonly linked to vulnerability (distribution range area, adult body mass, population density and gestation length) and conduct univariate and multivariate analyses to understand how biases affect model predictions. 4. Our results show important biases in data availability with c.22% of mammals completely lacking data. Missing data, which appear to be not missing at random, occur frequently in all traits (14-99% of cases missing). Data availability is explained by intrinsic traits, with larger mammals occupying bigger range areas being the best studied. Importantly, we find that existing biases affect the results of comparative analyses by overestimating the risk of extinction and changing which traits are identified as important predictors. 5. Our results raise concerns over our ability to draw general conclusions regarding what makes a species more prone to extinction. Missing data represent a prevalent problem in comparative analyses, and unfortunately, because data are not missing at random, conventional approaches to fill data gaps, are not valid or present important challenges. These results show the importance of making appropriate inferences from comparative analyses by focusing on the subset of species for which data are available. Ultimately, addressing the data bias problem requires greater investment in data collection and dissemination, as well as the development of methodological approaches to effectively correct existing biases. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Enantioselectivity in Candida antarctica lipase B: A molecular dynamics study

PubMed Central

Raza, Sami; Fransson, Linda; Hult, Karl

2001-01-01

A major problem in predicting the enantioselectivity of an enzyme toward substrate molecules is that even high selectivity toward one substrate enantiomer over the other corresponds to a very small difference in free energy. However, total free energies in enzyme-substrate systems are very large and fluctuate significantly because of general protein motion. Candida antarctica lipase B (CALB), a serine hydrolase, displays enantioselectivity toward secondary alcohols. Here, we present a modeling study where the aim has been to develop a molecular dynamics-based methodology for the prediction of enantioselectivity in CALB. The substrates modeled (seven in total) were 3-methyl-2-butanol with various aliphatic carboxylic acids and also 2-butanol, as well as 3,3-dimethyl-2-butanol with octanoic acid. The tetrahedral reaction intermediate was used as a model of the transition state. Investigative analyses were performed on ensembles of nonminimized structures and focused on the potential energies of a number of subsets within the modeled systems to determine which specific regions are important for the prediction of enantioselectivity. One category of subset was based on atoms that make up the core structural elements of the transition state. We considered that a more favorable energetic conformation of such a subset should relate to a greater likelihood for catalysis to occur, thus reflecting higher selectivity. The results of this study conveyed that the use of this type of subset was viable for the analysis of structural ensembles and yielded good predictions of enantioselectivity. PMID:11266619

Human NK Cell Subset Functions Are Differentially Affected by Adipokines

PubMed Central

Huebner, Lena; Engeli, Stefan; Wrann, Christiane D.; Goudeva, Lilia; Laue, Tobias; Kielstein, Heike

2013-01-01

Background Obesity is a risk factor for various types of infectious diseases and cancer. The increase in adipose tissue causes alterations in both adipogenesis and the production of adipocyte-secreted proteins (adipokines). Since natural killer (NK) cells are the host’s primary defense against virus-infected and tumor cells, we investigated how adipocyte-conditioned medium (ACM) affects functions of two distinct human NK cell subsets. Methods Isolated human peripheral blood mononuclear cells (PBMCs) were cultured with various concentrations of human and murine ACM harvested on two different days during adipogenesis and analyzed by fluorescent-activated cell sorting (FACS). Results FACS analyses showed that the expression of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), granzyme A (GzmA) and interferon (IFN)-γ in NK cells was regulated in a subset-specific manner. ACM treatment altered IFN-γ expression in CD56dim NK cells. The production of GzmA in CD56bright NK cells was differentially affected by the distinct adipokine compositions harvested at different states of adipogenesis. Comparison of the treatment with either human or murine ACM revealed that adipokine-induced effects on NK cell expression of the leptin receptor (Ob-R), TRAIL and IFN-γ were species-specific. Conclusion Considering the growing prevalence of obesity and the various disorders related to it, the present study provides further insights into the roles human NK cell subsets play in the obesity-associated state of chronic low-grade inflammation. PMID:24098717

Directed Forgetting and Directed Remembering in Visual Working Memory

PubMed Central

Williams, Melonie; Woodman, Geoffrey F.

2013-01-01

A defining characteristic of visual working memory is its limited capacity. This means that it is crucial to maintain only the most relevant information in visual working memory. However, empirical research is mixed as to whether it is possible to selectively maintain a subset of the information previously encoded into visual working memory. Here we examined the ability of subjects to use cues to either forget or remember a subset of the information already stored in visual working memory. In Experiment 1, participants were cued to either forget or remember one of two groups of colored squares during a change-detection task. We found that both types of cues aided performance in the visual working memory task, but that observers benefited more from a cue to remember than a cue to forget a subset of the objects. In Experiment 2, we show that the previous findings, which indicated that directed-forgetting cues are ineffective, were likely due to the presence of invalid cues that appear to cause observers to disregard such cues as unreliable. In Experiment 3, we recorded event-related potentials (ERPs) and show that an electrophysiological index of focused maintenance is elicited by cues that indicate which subset of information in visual working memory needs to be remembered, ruling out alternative explanations of the behavioral effects of retention-interval cues. The present findings demonstrate that observers can focus maintenance mechanisms on specific objects in visual working memory based on cues indicating future task relevance. PMID:22409182

Altered Dynamics of Candida albicans Phagocytosis by Macrophages and PMNs When Both Phagocyte Subsets Are Present

PubMed Central

Rudkin, Fiona M.; Bain, Judith M.; Walls, Catriona; Lewis, Leanne E.; Gow, Neil A. R.; Erwig, Lars P.

2013-01-01

ABSTRACT An important first line of defense against Candida albicans infections is the killing of fungal cells by professional phagocytes of the innate immune system, such as polymorphonuclear cells (PMNs) and macrophages. In this study, we employed live-cell video microscopy coupled with dynamic image analysis tools to provide insights into the complexity of C. albicans phagocytosis when macrophages and PMNs were incubated with C. albicans alone and when both phagocyte subsets were present. When C. albicans cells were incubated with only one phagocyte subtype, PMNs had a lower overall phagocytic capacity than macrophages, despite engulfing fungal cells at a higher rate once fungal cells were bound to the phagocyte surface. PMNs were more susceptible to C. albicans-mediated killing than macrophages, irrespective of the number of C. albicans cells ingested. In contrast, when both phagocyte subsets were studied in coculture, the two cell types phagocytosed and cleared C. albicans at equal rates and were equally susceptible to killing by the fungus. The increase in macrophage susceptibility to C. albicans-mediated killing was a consequence of macrophages taking up a higher proportion of hyphal cells under these conditions. In the presence of both PMNs and macrophages, C. albicans yeast cells were predominantly cleared by PMNs, which migrated at a greater speed toward fungal cells and engulfed bound cells more rapidly. These observations demonstrate that the phagocytosis of fungal pathogens depends on, and is modified by, the specific phagocyte subsets present at the site of infection. PMID:24169578

An assessment of LANDSAT data acquisition history on identification and area estimation of corn and soybeans. [U.S. Corn Belti Indiana and Iowa

NASA Technical Reports Server (NTRS)

Hixson, M. M.; Bauer, M. E.; Scholz, D. K. (Principal Investigator)

1980-01-01

Multitemporally registered LANDSAT MSS data from four acquisitions during the 1978 growing season were used in classification of eight sample segments in Iowa and Indiana. The results illustrate that use of LANDSAT acquisition when corn has tasseled is critical, as this is the optimum time for separation of corn and soybeans. An early season acquisition when the summer crops appear as bare soil can be beneficial in reducing the confusion between these two crops and other cover types. A subset of one visible and one infrared band from each date was found to produce results not significantly different from the use of all bands. Selection of a subset of these bands may also be feasible for multitemporal analysis.

Understanding the Biology of Antigen Cross-Presentation for the Design of Vaccines Against Cancer

PubMed Central

Fehres, Cynthia M.; Unger, Wendy W. J.; Garcia-Vallejo, Juan J.; van Kooyk, Yvette

2014-01-01

Antigen cross-presentation, the process in which exogenous antigens are presented on MHC class I molecules, is crucial for the generation of effector CD8+ T cell responses. Although multiple cell types are being described to be able to cross-present antigens, in vivo this task is mainly carried out by certain subsets of dendritic cells (DCs). Aspects such as the internalization route, the pathway of endocytic trafficking, and the simultaneous activation through pattern-recognition receptors have a determining influence in how antigens are handled for cross-presentation by DCs. In this review, we will summarize new insights in factors that affect antigen cross-presentation of human DC subsets, and we will discuss the possibilities to exploit antigen cross-presentation for immunotherapy against cancer. PMID:24782858

Radiologic, pathologic and molecular attributes of two types of papillary renal adenocarcinomas.

PubMed

Mydlo, J H; Weinstein, R; Misseri, R; Axiotis, C; Thelmo, W

2001-09-01

Most papillary renal tumors are not as aggressive as clear cell carcinomas and thus carry a better prognosis. However, several reports in the literature have demonstrated a subset of patients with papillary tumors that have a more aggressive biology and advanced stage at presentation. We compared several parameters of these subsets of renal tumors in an effort to characterize these lesions. We reviewed 391 cases of nephrectomies that were performed for cancer over a 20-year period from four institutions. Of these, 41 were documented as papillary adenocarcinomas. We reviewed these cases with respect to stage at presentation, size, vascularity on (computerized tomography) CT scan, histology, and cytokeratin immunohistology. Thirty-two of the lesions presented in the fifth, sixth, seventh and eighth decades of life (Type I), while most of the remaining 9 tumors (Type II) presented in the fourth decade of life, and in more advanced stages. Tumor volumes ranged from 84 cm3 to 1660 cm3. Type I tumors had an average size of 515 cm3 and an enhancement on CT of 36 +/- 4 Hounsfield units, compared with Type II tumors which had an average size of 164 cm3 and an enhancement on CT of 92 +/- 8 Hounsfield units. Type II tumors also had a higher mean Fuhrman score of nuclear pleomorphism than Type I, and a greater expression of cytokeratin. We found that the more common Type I variant of papillary renal adenocarcinoma was less vascular on CT scan, larger in size, and had a lower amount of nuclear pleomorphism as well as decreased expression of cytokeratin 7. The more aggressive biological variant, Type II, presented in the earlier decades of life, with a smaller, but more vascular, cancer and had a greater nuclear pleomorphism. Nuclear pleomorphism still appears to have the best prognostic assessment. However, other molecular and genetic parameters of these tumors, as well as long-term survival data will be necessary to determine the significance of these findings.

The novel high-performance 3-D MT inverse solver

NASA Astrophysics Data System (ADS)

Kruglyakov, Mikhail; Geraskin, Alexey; Kuvshinov, Alexey

2016-04-01

We present novel, robust, scalable, and fast 3-D magnetotelluric (MT) inverse solver. The solver is written in multi-language paradigm to make it as efficient, readable and maintainable as possible. Separation of concerns and single responsibility concepts go through implementation of the solver. As a forward modelling engine a modern scalable solver extrEMe, based on contracting integral equation approach, is used. Iterative gradient-type (quasi-Newton) optimization scheme is invoked to search for (regularized) inverse problem solution, and adjoint source approach is used to calculate efficiently the gradient of the misfit. The inverse solver is able to deal with highly detailed and contrasting models, allows for working (separately or jointly) with any type of MT responses, and supports massive parallelization. Moreover, different parallelization strategies implemented in the code allow optimal usage of available computational resources for a given problem statement. To parameterize an inverse domain the so-called mask parameterization is implemented, which means that one can merge any subset of forward modelling cells in order to account for (usually) irregular distribution of observation sites. We report results of 3-D numerical experiments aimed at analysing the robustness, performance and scalability of the code. In particular, our computational experiments carried out at different platforms ranging from modern laptops to HPC Piz Daint (6th supercomputer in the world) demonstrate practically linear scalability of the code up to thousands of nodes.

Homeostatic migration and distribution of innate immune cells in primary and secondary lymphoid organs with ageing.

PubMed

Nikolich-Žugich, J; Davies, J S

2017-03-01

Ageing of the innate and adaptive immune system, collectively termed immune senescence, is a complex process. One method to understand the components of ageing involves dissociating the effects of ageing on the cells of the immune system, on the microenvironment in lymphoid organs and tissues where immune cells reside and on the circulating factors that interact with both immune cells and their microenvironment. Heterochronic parabiosis, a surgical union of two organisms of disparate ages, is ideal for this type of study, as it has the power to dissociate the age of the cell and the age of the microenvironment into which the cell resides or is migrating. So far, however, it has been used sparingly to study immune ageing. Here we review the limited literature on homeostatic innate immune cell trafficking in ageing in the absence of chronic inflammation. We also review our own recent data on trafficking of innate immune subsets between primary and secondary lymphoid organs in heterochronic parabiosis. We found no systemic bias in retention or acceptance of neutrophils, macrophages, dendritic cells or natural killer cells with ageing in primary and secondary lymphoid organs. We conclude that these four innate immune cell types migrate to and populate lymphoid organs (peripheral lymph nodes, spleen and bone marrow), regardless of their own age and of the age of lymphoid organs. © 2017 British Society for Immunology.

Vibratory regime classification of infant phonation.

PubMed

Buder, Eugene H; Chorna, Lesya B; Oller, D Kimbrough; Robinson, Rebecca B

2008-09-01

Infant phonation is highly variable in many respects, including the basic vibratory patterns by which the vocal tissues create acoustic signals. Previous studies have identified the regular occurrence of nonmodal phonation types in normal infant phonation. The glottis is like many oscillating systems that, because of nonlinear relationships among the elements, may vibrate in ways representing the deterministic patterns classified theoretically within the mathematical framework of nonlinear dynamics. The infant's preverbal vocal explorations present such a variety of phonations that it may be possible to find effectively all the classes of vibration predicted by nonlinear dynamic theory. The current report defines acoustic criteria for an important subset of such vibratory regimes, and demonstrates that analysts can be trained to reliably use these criteria for a classification that includes all instances of infant phonation in the recorded corpora. The method is thus internally comprehensive in the sense that all phonations are classified, but it is not exhaustive in the sense that all vocal qualities are thereby represented. Using the methods thus developed, this study also demonstrates that the distributions of these phonation types vary significantly across sessions of recording in the first year of life, suggesting developmental changes. The method of regime classification is thus capable of tracking changes that may be indicative of maturation of the mechanism, the learning of categories of phonatory control, and the possibly varying use of vocalizations across social contexts.

PyCCF: Python Cross Correlation Function for reverberation mapping studies

NASA Astrophysics Data System (ADS)

Sun, Mouyuan; Grier, C. J.; Peterson, B. M.

2018-05-01

PyCCF emulates a Fortran program written by B. Peterson for use with reverberation mapping. The code cross correlates two light curves that are unevenly sampled using linear interpolation and measures the peak and centroid of the cross-correlation function. In addition, it is possible to run Monto Carlo iterations using flux randomization and random subset selection (RSS) to produce cross-correlation centroid distributions to estimate the uncertainties in the cross correlation results.

Nonlinear Filtering in High Dimension

DTIC Science & Technology

2014-06-02

portion of this thesis deals with controlling the distance between conditional distributions in high dimension, we present a few elementary lemmas that...ergodicity. 14 Chapter 2 Preliminaries This chapter is devoted to introducing some elementary concepts and facts in prob- ability theory that will be...measurable space (E,E) to R̄ := [−∞,+∞], or a subset of it, is E-measurable it if is measurable relative to E and the Borel σ- algebra on R̄. We write

Heterogeneous clinicopathological features of intraductal carcinoma of the prostate: a comparison between "precursor-like" and "regular type" lesions.

PubMed

Miyai, Kosuke; Divatia, Mukul K; Shen, Steven S; Miles, Brian J; Ayala, Alberto G; Ro, Jae Y

2014-01-01

Intraductal carcinoma of the prostate (IDC-P) has been described as a lesion associated with intraductal spread of invasive carcinoma and consequently aggressive disease. However, there are a few reported cases of pure IDC-P without an associated invasive component, strongly suggesting that this subset of IDC-P may represent a precursor lesion. We compared the clinicopathological features between the morphologically "regular type" IDC-P and "precursor-like" IDC-P. IDC-P was defined as follows; 1) solid/dense cribriform lesions or 2) loose cribriform/micropapillary lesions with prominent nuclear pleomorphism and/or non-focal comedonecrosis. We defined precursor-like IDC-P as follows; 1) IDC-P without adjoining invasive adenocarcinoma but carcinoma present distant from the IDC-P or 2) IDC-P having adjoining invasive microcarcinoma (less than 0.05 ml) and showing a morphologic transition from high-grade prostatic intraepithelial neoplasia (HGPIN) to the IDC-P. IDC-P lacking the features of precursor-like IDC-P was categorized as regular type IDC-P. Of 901 radical prostatectomies performed at our hospital, 141 and 14 showed regular type IDC-P and precursor-like IDC-P in whole-mounted specimens, respectively. Regular type IDC-P cases had significantly higher Gleason score, more frequent extraprostatic extension and seminal vesicle invasion, more advanced pathological T stage, and lower 5-year biochemical recurrence-free rate than precursor-like IDC-P cases. Multivariate analysis revealed nodal metastasis and the presence of regular type IDC-P as independent predictors for biochemical recurrence. Our data suggest that IDC-P may be heterogeneous with variable clinicopathological features. We also suggest that not all IDC-P cases represent intraductal spread of pre-existing invasive cancer, and a subset of IDC-P may be a precursor lesion.

The immunoregulatory role of type I and type II NKT cells in cancer and other diseases

PubMed Central

Terabe, Masaki; Berzofsky, Jay A.

2014-01-01

NKT cells are CD1d-restricted T cells that recognize lipid antigens. They also have been shown to play critical roles in the regulation of immune responses. In the immune responses against tumors, two subsets of NKT cells, type I and type II, play opposing roles and cross-regulate each other. As members of both the innate and adaptive immune systems, which form a network of multiple components, they also interact with other immune components. Here we discuss the function of NKT cells in tumor immunity and their interaction with other regulatory cells, especially CD4+CD25+Foxp3+ regulatory T cells. PMID:24384834

Radiographic estimation in seropositive and seronegative rheumatoid arthritis

PubMed Central

Sahatçiu-Meka, Vjollca; Rexhepi, Sylejman; Manxhuka-Kërliu, Suzana; Rexhepi, Mjellma

2011-01-01

Long since it have been suggested that a subpopulation of patients with rheumatoid arthritis, diagnosed with negative rheumatoid factor tests, represents a clinical entity quite distinct from that of seropositive rheumatoid arthritis (RA). Our aim was to establish a scientific comparative analysis between seronegative and seropositive rheumatoid arthritis, regarding some radiological and clinical parameters, applied for the first time on patients from Kosovo. Two hundred fifty patients with rheumatoid arthritis according to the American College of Rheumatology criteria were retrospectively studied by analysis the radiographic damage and clinical parameters of the disease, using a data base. All examinees were between 25-60 years of age (Xb=49.96, SD=10.37) with disease duration between 1-27 years (Xb = 6.41, SD=6.47). All patients underwent a standardised evaluation radiographs. Baseline standardised poster anterior radiographs of hands and feet and radiographs of other joints, depending on indications, were assessed. Erythrocyte sedimentation rate values correlated with the radiological damages and statistical difference was found for seronegative subset (r=0.24, p<0.01). Longer duration of the disease resulted in the increase of radiological changes in both subsets (r=0.66, p<0.01) seronegative, (r=0.49, p<0.01) seropositive. Anatomic changes of IInd and IIIrd level were nearly equally distributed in both subsets, 76 (60.8%) seronegative, 75 (60%) seropositive. Radiological damages are nearly equal in both subsets, elevate in relation to the duration of the disease and correlate with ESR values. Regarding the sero-status, differences within sex, with some exceptions, are not relevant. Although there are some definite quantitative and qualitative differences regarding sero-status, obviously there is a great deal of overlap between the two groups. PMID:21875421

Radiographic estimation in seropositive and seronegative rheumatoid arthritis.

PubMed

Sahatçiu-Meka, Vjollca; Rexhepi, Sylejman; Manxhuka-Kërliu, Suzana; Rexhepi, Mjellma

2011-08-01

Long since it have been suggested that a subpopulation of patients with rheumatoid arthritis, diagnosed with negative rheumatoid factor tests, represents a clinical entity quite distinct from that of seropositive rheumatoid arthritis (RA). Our aim was to establish a scientific comparative analysis between seronegative and seropositive rheumatoid arthritis, regarding some radiological and clinical parameters, applied for the first time on patients from Kosovo. Two hundred fifty patients with rheumatoid arthritis according to the American College of Rheumatology criteria were retrospectively studied by analysis the radiographic damage and clinical parameters of the disease, using a data base. All examinees were between 25-60 years of age (Xb=49.96, SD=10.37) with disease duration between 1-27 years (Xb = 6.41, SD=6.47). All patients underwent a standardised evaluation radiographs. Baseline standardised poster anterior radiographs of hands and feet and radiographs of other joints, depending on indications, were assessed. Erythrocyte sedimentation rate values correlated with the radiological damages and statistical difference was found for seronegative subset (r=0.24, p<0.01). Longer duration of the disease resulted in the increase of radiological changes in both subsets (r=0.66, p<0.01) seronegative, (r=0.49, p<0.01) seropositive. Anatomic changes of IInd and IIIrd level were nearly equally distributed in both subsets, 76 (60.8%) seronegative, 75 (60%) seropositive. Radiological damages are nearly equal in both subsets, elevate in relation to the duration of the disease and correlate with ESR values. Regarding the sero-status, differences within sex, with some exceptions, are not relevant. Although there are some definite quantitative and qualitative differences regarding sero-status, obviously there is a great deal of overlap between the two groups.

Cerebellins are differentially expressed in selective subsets of neurons throughout the brain.

PubMed

Seigneur, Erica; Südhof, Thomas C

2017-10-15

Cerebellins are secreted hexameric proteins that form tripartite complexes with the presynaptic cell-adhesion molecules neurexins or 'deleted-in-colorectal-cancer', and the postsynaptic glutamate-receptor-related proteins GluD1 and GluD2. These tripartite complexes are thought to regulate synapses. However, cerebellins are expressed in multiple isoforms whose relative distributions and overall functions are not understood. Three of the four cerebellins, Cbln1, Cbln2, and Cbln4, autonomously assemble into homohexamers, whereas the Cbln3 requires Cbln1 for assembly and secretion. Here, we show that Cbln1, Cbln2, and Cbln4 are abundantly expressed in nearly all brain regions, but exhibit strikingly different expression patterns and developmental dynamics. Using newly generated knockin reporter mice for Cbln2 and Cbln4, we find that Cbln2 and Cbln4 are not universally expressed in all neurons, but only in specific subsets of neurons. For example, Cbln2 and Cbln4 are broadly expressed in largely non-overlapping subpopulations of excitatory cortical neurons, but only sparse expression was observed in excitatory hippocampal neurons of the CA1- or CA3-region. Similarly, Cbln2 and Cbln4 are selectively expressed, respectively, in inhibitory interneurons and excitatory mitral projection neurons of the main olfactory bulb; here, these two classes of neurons form dendrodendritic reciprocal synapses with each other. A few brain regions, such as the nucleus of the lateral olfactory tract, exhibit astoundingly high Cbln2 expression levels. Viewed together, our data show that cerebellins are abundantly expressed in relatively small subsets of neurons, suggesting specific roles restricted to subsets of synapses. © 2017 Wiley Periodicals, Inc.

Intestinal lymphocyte subsets and turnover are affected by chronic alcohol consumption: implications for SIV/HIV infection.

PubMed

Poonia, Bhawna; Nelson, Steve; Bagby, Greg J; Veazey, Ronald S

2006-04-15

We recently demonstrated that simian immunodeficiency virus (SIV) viral loads were significantly higher in the plasma of rhesus macaques consuming alcohol compared with controls following intrarectal SIV infection. To understand the possible reasons behind increased viral replication, here we assessed the effects of chronic alcohol consumption on distribution and cycling of various lymphocyte subsets in the intestine. Macaques were administered alcohol (n = 11) or sucrose (n = 12), and percentages of memory and naive and activated lymphocyte subsets were compared in the blood, lymph nodes, and intestines. Although minimal differences were detected in blood or lymph nodes, there were significantly higher percentages of central memory (CD95+CD28+) CD4+ lymphocytes in the intestines from alcohol-receiving animals before infection compared with controls. In addition, higher percentages of naive (CD45RA+CD95-) as well as CXCR4+CD4 cells were detected in intestines of alcohol-treated macaques. Moreover, alcohol consumption resulted in significantly lower percentages of effector memory (CD95+CD28-) CD8 lymphocytes as well as activated Ki67+CD8 cells in the intestines. A subset (7 receiving alcohol and 8 receiving sucrose) were then intrarectally inoculated with SIV(mac251). Viral RNA was compared in different tissues using real-time PCR and in situ hybridization. Higher levels of SIV replication were observed in tissues from alcohol-consuming macaques compared with controls. Central memory CD4 lymphocytes were significantly depleted in intestines and mesenteric lymph nodes from all alcohol animals at 8 weeks postinfection. Thus, changes in the mucosal immune compartment (intestines) in response to alcohol are likely the major reasons behind higher replication of SIV observed in these animals.

AIRS Data Subsetting Service at the Goddard Earth Sciences (GES) DISC/DAAC

NASA Technical Reports Server (NTRS)

Vicente, Gilberto A.; Qin, Jianchun; Li, Jason; Gerasimov, Irina; Savtchenko, Andrey

2004-01-01

The AIRS mission, as a combination of the Atmospheric Infrared Sounder (AIRS), the Advanced Microwave Sounding Unit (AMSU) and the Humidity Sounder for Brazil (HSB), brings climate research and weather prediction into 21st century. From NASA' Aqua spacecraft, the AIRS/AMSU/HSB instruments measure humidity, temperature, cloud properties and the amounts of greenhouse gases. The AIRS also reveals land and sea- surface temperatures. Measurements from these three instruments are analyzed . jointly to filter out the effects of clouds from the IR data in order to derive clear-column air-temperature profiles and surface temperatures with high vertical resolution and accuracy. Together, they constitute an advanced operational sounding data system that have contributed to improve global modeling efforts and numerical weather prediction; enhance studies of the global energy and water cycles, the effects of greenhouse gases, and atmosphere-surface interactions; and facilitate monitoring of climate variations and trends. The high data volume generated by the AIRS/AMSU/HSB instruments and the complexity of its data format (Hierarchical Data Format, HDF) are barriers to AIRS data use. Although many researchers are interested in only a fraction of the data they receive or request, they are forced to run their algorithms on a much larger data set to extract the information of interest. In order to better server its users, the GES DISC/DAAC, provider of long-term archives and distribution services as well science support for the AIRS/AMSU/HSB data products, has developed various tools for performing channels, variables, parameter, spatial and derived products subsetting, resampling and reformatting operations. This presentation mainly describes the web-enabled subsetting services currently available at the GES DISC/DAAC that provide subsetting functions for all the Level 1B and Level 2 data products from the AIRS/AMSU/HSB instruments.

Use of Anecdotal Occurrence Data in Species Distribution Models: An Example Based on the White-Nosed Coati (Nasua narica) in the American Southwest

PubMed Central

Frey, Jennifer K.; Lewis, Jeremy C.; Guy, Rachel K.; Stuart, James N.

2013-01-01

Simple Summary We evaluated the influence of occurrence records with different reliability on predicted distribution of a unique, rare mammal in the American Southwest, the white-nosed coati (Nasua narica). We concluded that occurrence datasets that include anecdotal records can be used to infer species distributions, providing such data are used only for easily-identifiable species and based on robust modeling methods such as maximum entropy. Use of a reliability rating system is critical for using anecdotal data. Abstract Species distributions are usually inferred from occurrence records. However, these records are prone to errors in spatial precision and reliability. Although influence of spatial errors has been fairly well studied, there is little information on impacts of poor reliability. Reliability of an occurrence record can be influenced by characteristics of the species, conditions during the observation, and observer’s knowledge. Some studies have advocated use of anecdotal data, while others have advocated more stringent evidentiary standards such as only accepting records verified by physical evidence, at least for rare or elusive species. Our goal was to evaluate the influence of occurrence records with different reliability on species distribution models (SDMs) of a unique mammal, the white-nosed coati (Nasua narica) in the American Southwest. We compared SDMs developed using maximum entropy analysis of combined bioclimatic and biophysical variables and based on seven subsets of occurrence records that varied in reliability and spatial precision. We found that the predicted distribution of the coati based on datasets that included anecdotal occurrence records were similar to those based on datasets that only included physical evidence. Coati distribution in the American Southwest was predicted to occur in southwestern New Mexico and southeastern Arizona and was defined primarily by evenness of climate and Madrean woodland and chaparral land-cover types. Coati distribution patterns in this region suggest a good model for understanding the biogeographic structure of range margins. We concluded that occurrence datasets that include anecdotal records can be used to infer species distributions, providing such data are used only for easily-identifiable species and based on robust modeling methods such as maximum entropy. Use of a reliability rating system is critical for using anecdotal data. PMID:26487405

Comparison of Antemortem and Environmental Samples for Zebrafish Health Monitoring and Quarantine.

PubMed

Crim, Marcus J; Lawrence, Christian; Livingston, Robert S; Rakitin, Andrei; Hurley, Shane J; Riley, Lela K

2017-07-01

Molecular diagnostic assays offer both exquisite sensitivity and the ability to test a wide variety of sample types. Various types of environmental sample, such as detritus and concentrated water, might provide a useful adjunct to sentinels in routine zebrafish health monitoring. Similarly, antemortem sampling would be advantageous for expediting zebrafish quarantine, without euthanasia of valuable fish. We evaluated the detection of Mycobacterium chelonae, M. fortuitum, M. peregrinum, Pseudocapillaria tomentosa, and Pseudoloma neurophilia in zebrafish, detritus, pooled feces, and filter membranes after filtration of 1000-, 500-, and 150-mL water samples by real-time PCR analysis. Sensitivity varied according to sample type and pathogen, and environmental sampling was significantly more sensitive than zebrafish sampling for detecting Mycobacterium spp. but not for Pseudocapillaria neurophilia or Pseudoloma tomentosa. The results of these experiments provide strong evidence of the utility of multiple sample types for detecting pathogens according to each pathogen's life cycle and ecological niche within zebrafish systems. In a separate experiment, zebrafish subclinically infected with M. chelonae, M. marinum, Pleistophora hyphessobryconis, Pseudocapillaria tomentosa, or Pseudoloma neurophilia were pair-spawned and individually tested with subsets of embryos from each clutch that received no rinse, a fluidizing rinse, or were surface-disinfected with sodium hypochlorite. Frequently, one or both parents were subclinically infected with pathogen(s) that were not detected in any embryo subset. Therefore, negative results from embryo samples may not reflect the health status of the parent zebrafish.

Comparison of Antemortem and Environmental Samples for Zebrafish Health Monitoring and Quarantine

PubMed Central

Crim, Marcus J; Lawrence, Christian; Livingston, Robert S; Rakitin, Andrei; Hurley, Shane J; Riley, Lela K

2017-01-01

Molecular diagnostic assays offer both exquisite sensitivity and the ability to test a wide variety of sample types. Various types of environmental sample, such as detritus and concentrated water, might provide a useful adjunct to sentinels in routine zebrafish health monitoring. Similarly, antemortem sampling would be advantageous for expediting zebrafish quarantine, without euthanasia of valuable fish. We evaluated the detection of Mycobacterium chelonae, M. fortuitum, M. peregrinum, Pseudocapillaria tomentosa, and Pseudoloma neurophilia in zebrafish, detritus, pooled feces, and filter membranes after filtration of 1000-, 500-, and 150-mL water samples by real-time PCR analysis. Sensitivity varied according to sample type and pathogen, and environmental sampling was significantly more sensitive than zebrafish sampling for detecting Mycobacterium spp. but not for Pseudocapillaria neurophilia or Pseudoloma tomentosa. The results of these experiments provide strong evidence of the utility of multiple sample types for detecting pathogens according to each pathogen's life cycle and ecological niche within zebrafish systems. In a separate experiment, zebrafish subclinically infected with M. chelonae, M. marinum, Pleistophora hyphessobryconis, Pseudocapillaria tomentosa, or Pseudoloma neurophilia were pair-spawned and individually tested with subsets of embryos from each clutch that received no rinse, a fluidizing rinse, or were surface-disinfected with sodium hypochlorite. Frequently, one or both parents were subclinically infected with pathogen(s) that were not detected in any embryo subset. Therefore, negative results from embryo samples may not reflect the health status of the parent zebrafish. PMID:28724491

The Extended Family of CD1d-Restricted NKT Cells: Sifting through a Mixed Bag of TCRs, Antigens, and Functions

PubMed Central

Macho-Fernandez, Elodie; Brigl, Manfred

2015-01-01

Natural killer T (NKT) cells comprise a family of specialized T cells that recognize lipid antigens presented by CD1d. Based on their T cell receptor (TCR) usage and antigen specificities, CD1d-restricted NKT cells have been divided into two main subsets: type I NKT cells that use a canonical invariant TCR α-chain and recognize α-galactosylceramide (α-GalCer), and type II NKT cells that use a more diverse αβ TCR repertoire and do not recognize α-GalCer. In addition, α-GalCer-reactive NKT cells that use non-canonical αβ TCRs and CD1d-restricted T cells that use γδ or δ/αβ TCRs have recently been identified, revealing further diversity among CD1d-restricted T cells. Importantly, in addition to their distinct antigen specificities, functional differences are beginning to emerge between the different members of the CD1d-restricted T cell family. In this review, while using type I NKT cells as comparison, we will focus on type II NKT cells and the other non-invariant CD1d-restricted T cell subsets, and discuss our current understanding of the antigens they recognize, the formation of stimulatory CD1d/antigen complexes, the modes of TCR-mediated antigen recognition, and the mechanisms and consequences of their activation that underlie their function in antimicrobial responses, anti-tumor immunity, and autoimmunity. PMID:26284062

Different responses to oxidized low-density lipoproteins in human polarized macrophages

PubMed Central

2011-01-01

Background Oxidized low-density lipoprotein (oxLDL) uptake by macrophages plays an important role in foam cell formation. It has been suggested the presence of heterogeneous subsets of macrophage, such as M1 and M2, in human atherosclerotic lesions. To evaluate which types of macrophages contribute to atherogenesis, we performed cDNA microarray analysis to determine oxLDL-induced transcriptional alterations of each subset of macrophages. Results Human monocyte-derived macrophages were polarized toward the M1 or M2 subset, followed by treatment with oxLDL. Then gene expression levels during oxLDL treatment in each subset of macrophages were evaluated by cDNA microarray analysis and quantitative real-time RT-PCR. In terms of high-ranking upregulated genes and functional ontologies, the alterations during oxLDL treatment in M2 macrophages were similar to those in nonpolarized macrophages (M0). Molecular network analysis showed that most of the molecules in the oxLDL-induced highest scoring molecular network of M1 macrophages were directly or indirectly related to transforming growth factor (TGF)-β1. Hierarchical cluster analysis revealed commonly upregulated genes in all subset of macrophages, some of which contained antioxidant response elements (ARE) in their promoter regions. A cluster of genes that were specifically upregulated in M1 macrophages included those encoding molecules related to nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-κB) signaling pathway. Quantitative real-time RT-PCR showed that the gene expression of interleukin (IL)-8 after oxLDL treatment in M2 macrophages was markedly lower than those in M0 and M1 cells. HMOX1 gene expression levels were almost the same in all 3 subsets of macrophages even after oxLDL treatment. Conclusions The present study demonstrated transcriptional alterations in polarized macrophages during oxLDL treatment. The data suggested that oxLDL uptake may affect TGF-β1- and NF-κB-mediated functions of M1 macrophages, but not those of M0 or M2 macrophages. It is likely that M1 macrophages characteristically respond to oxLDL. PMID:21199582

Standardization of milk infrared spectra for the retroactive application of calibration models.

PubMed

Bonfatti, V; Fleming, A; Koeck, A; Miglior, F

2017-03-01

The objective of this study was to standardize the infrared spectra obtained over time and across 2 milk laboratories of Canada to create a uniform historical database and allow (1) the retroactive application of calibration models for prediction of fine milk composition; and (2) the direct use of spectral information for the development of indicators of animal health and efficiency. Spectral variation across laboratories and over time was inspected by principal components analysis (PCA). Shifts in the PCA scores were detected over time, leading to the definition of different subsets of spectra having homogeneous infrared signal. To evaluate the possibility of using common equations on spectra collected by the 2 instruments and over time, we developed a standardization (STD) method. For each subset of data having homogeneous infrared signal, a total of 99 spectra corresponding to the percentiles of the distribution of the absorbance at each wavenumber were created and used to build the STD matrices. Equations predicting contents of saturated fatty acids, short-chain fatty acids, and C18:0 were created and applied on different subsets of spectra, before and after STD. After STD, bias and root mean squared error of prediction decreased by 66% and 32%, respectively. When calibration equations were applied to the historical nonstandardized database of spectra, shifts in the predictions could be observed over time for all investigated traits. Shifts in the distribution of the predictions over time corresponded to the shifts identified by the inspection of the PCA scores. After STD, shifts in the predicted fatty acid contents were greatly reduced. Standardization reduced spectral variability between instruments and over time, allowing the merging of milk spectra data from different instruments into a common database, the retroactive use of calibrations equations, or the direct use of the spectral data without restrictions. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Expression of programmed cell death1 in T follicular helper cells is regulated by prostaglandin E2 secreted by HBV-infected HepG2.2.1.5 cells.

PubMed

Sui, Zhefeng; Shi, Ying; Gao, Zhiling; Yang, Deguang; Wang, Zhihao

2017-06-01

The present study aimed to investigate the distribution of T follicular helper (Tfh)-cell subsets in patients with hepatitis B virus (HBV) and determine the underlying mechanism of HBV regulation of Tfh cells. The frequency of peripheral blood Tfh subsets was analyzed using flow cytometry. The expression level of programmed cell death‑1 (PD‑1) and prostaglandin E2 (PGE2) was quantified using reverse transcription‑quantitative polymerase chain reaction and western blotting. The PGE2 level in culture supernatant was detected using enzyme‑linked immunosorbent assay. A Transwell chamber was used to co‑culture Tfh cells with HepG2 and HepG2.2.1.5. The percentage of inducible T‑cell costimulator (ICOS)+ and total Tfh cells was high at the immune activation (IA) group; however, it was reduced in the immune tolerance (IT), responders with HBsAg seroconversion (RP) and healthy control (HC) groups. The percentage of PD‑1+ Tfh cells was significantly higher in IA and IT compared with RP and HC. The ratio of PD‑1+/total Tfh cells was positively correlated with the load of HBV DNA; therefore, this ratio may act as an indicator for HBV replication. The expression level of PD‑1 in Tfh cells was higher in the HepG2.2.1.5 co‑cultured group compared with the HepG2 group, this may be due to the high PGE2 expression level in HBV‑infected HepG2.2.1.5 cells. The findings of the present study revealed an imbalanced distribution of PD‑1+ Tfh cells in patients with HBV at different immune phases. Additionally, HBV may upregulate the expression of PD‑1 in Tfh cells by promoting HepG2.2.1.5 to secret PGE2. Identifying the effect of HBV on Tfh‑cell subsets is crucial for improving immuno-based therapy for HBV.

Hybrid reconstruction of field-reversed configurations

NASA Astrophysics Data System (ADS)

Steinhauer, Loren; TAE Team

2016-10-01

Field-reversed configurations (FRC) are poorly represented by fluid-based models and require instead an ion-distribution function. Two such populations are needed since ``core'' ions are roughly restricted to the region inside the separatrix, whereas ``periphery'' ions can escape along open field lines. The Vlasov equation governs the distribution, the general solution to which is an arbitrary function of the constants of motion (Hamiltonian, canonical angular momentum). Only a small subset of such distributions are realistic in view of collisions, which smooth the distribution, and instabilities, which reorganize the field structure. Collisions and end loss are included if the distribution is a solution to the Fokker-Planck (FP) equation. Vlasov and FP solutions are nearly identical in weakly-collisional plasmas. Numerical construction of such equilibria requires solving both Ampere's law for the magnetic flux variable and the ponderous task of a full velocity-space integration at each point. The latter can be done analytically by expressing the distribution as the superposition of simple basis elements. This procedure allows rapid reconstruction of evolving equilibria based on limited diagnostic observables in FRC experiments.