Prediction of an internal boundary layer on a flat plate after a step change in roughness using a near-wall RANS model

NASA Astrophysics Data System (ADS)

Chu, Minghan; Meng, Fanxiao; Bergstrom, Donald J.

2017-11-01

An in-house computational fluid dynamics code was used to simulate turbulent flow over a flat plate with a step change in roughness, exhibiting a smooth-rough-smooth configuration. An internal boundary layer (IBL) is formed at the transition from the smooth to rough (SR) and then the rough to smooth (RS) surfaces. For an IBL the flow far above the surface has experienced a wall shear stress that is different from the local value. Within a Reynolds-Averaged-Navier-Stokes (RANS) formulation, the two-layer k- ɛ model of Durbin et al. (2001) was implemented to analyze the response of the flow to the change in surface condition. The numerical results are compared to experimental data, including some in-house measurements and the seminal work of Antonia and Luxton (1971,72). This problem captures some aspects of roughness in industrial and environmental applications, such as corrosion and the earth's surface heterogeneity, where the roughness is often encountered as discrete distributions. It illustrates the challenge of incorporating roughness models in RANS that are capable of responding to complex surface roughness profiles.

On Fuzzy Sets and Rough Sets from the Perspective of Indiscernibility

NASA Astrophysics Data System (ADS)

Chakraborty, Mihir K.

The category theoretic approach of Obtułowicz to Pawlak's rough sets has been reintroduced in a somewhat modified form. A generalization is rendered to this approach that has been motivated by the notion of rough membership function. Thus, a link is established between rough sets and L-fuzzy sets for some special lattices. It is shown that a notion of indistinguishability lies at the root of vagueness. This observation in turn gives a common ground to the theories of rough sets and fuzzy sets.

Operational algorithm for ice-water classification on dual-polarized RADARSAT-2 images

NASA Astrophysics Data System (ADS)

Zakhvatkina, Natalia; Korosov, Anton; Muckenhuber, Stefan; Sandven, Stein; Babiker, Mohamed

2017-01-01

Synthetic Aperture Radar (SAR) data from RADARSAT-2 (RS2) in dual-polarization mode provide additional information for discriminating sea ice and open water compared to single-polarization data. We have developed an automatic algorithm based on dual-polarized RS2 SAR images to distinguish open water (rough and calm) and sea ice. Several technical issues inherent in RS2 data were solved in the pre-processing stage, including thermal noise reduction in HV polarization and correction of angular backscatter dependency in HH polarization. Texture features were explored and used in addition to supervised image classification based on the support vector machines (SVM) approach. The study was conducted in the ice-covered area between Greenland and Franz Josef Land. The algorithm has been trained using 24 RS2 scenes acquired in winter months in 2011 and 2012, and the results were validated against manually derived ice charts of the Norwegian Meteorological Institute. The algorithm was applied on a total of 2705 RS2 scenes obtained from 2013 to 2015, and the validation results showed that the average classification accuracy was 91 ± 4 %.

Characteristics of subgrid-resolved-scale dynamics in anisotropic turbulence, with application to rough-wall boundary layers

NASA Astrophysics Data System (ADS)

Juneja, Anurag; Brasseur, James G.

1999-10-01

Large-eddy simulation (LES) of the atmospheric boundary layer (ABL) using eddy viscosity subgrid-scale (SGS) models is known to poorly predict mean shear at the first few grid cells near the ground, a rough surface with no viscous sublayer. It has recently been shown that convective motions carry this localized error vertically to infect the entire ABL, and that the error is more a consequence of the SGS model than grid resolution in the near-surface inertial layer. Our goal was to determine what first-order errors in the predicted SGS terms lead to spurious expectation values, and what basic dynamics in the filtered equation for resolved scale (RS) velocity must be captured by SGS models to correct the deficiencies. Our analysis is of general relevance to LES of rough-wall high Reynolds number boundary layers, where the essential difficulty in the closure is the importance of the SGS acceleration terms, a consequence of necessary under-resolution of relevant energy-containing motions at the first few grid levels, leading to potentially strong couplings between the anisotropies in resolved velocity and predicted SGS dynamics. We analyze these two issues (under-resolution and anisotropy) in the absence of a wall using two direct numerical simulation datasets of homogeneous turbulence with very different anisotropic structure characteristic of the near-surface ABL: shear- and buoyancy-generated turbulence. We uncover three important issues which should be addressed in the design of SGS closures near rough walls and we provide a priori tests for the SGS model. First, we identify a strong spurious coupling between the anisotropic structure of the resolved velocity field and predicted SGS dynamics which can create a feedback loop to incorrectly enhance certain components of the predicted velocity field. Second, we find that eddy viscosity and "similarity" SGS models do not contain enough degrees of freedom to capture, at a sufficient level of accuracy, both RS-SGS energy flux and SGS-RS dynamics. Third, to correctly capture pressure transport near a wall, closures must be made more flexible to accommodate proper partitioning between SGS stress divergence and SGS pressure gradient.

Application of Rough Sets to Information Retrieval.

ERIC Educational Resources Information Center

Miyamoto, Sadaaki

1998-01-01

Develops a method of rough retrieval, an application of the rough set theory to information retrieval. The aim is to: (1) show that rough sets are naturally applied to information retrieval in which categorized information structure is used; and (2) show that a fuzzy retrieval scheme is induced from the rough retrieval. (AEF)

Independent Component Analysis-motivated Approach to Classificatory Decomposition of Cortical Evoked Potentials

PubMed Central

Smolinski, Tomasz G; Buchanan, Roger; Boratyn, Grzegorz M; Milanova, Mariofanna; Prinz, Astrid A

2006-01-01

Background Independent Component Analysis (ICA) proves to be useful in the analysis of neural activity, as it allows for identification of distinct sources of activity. Applied to measurements registered in a controlled setting and under exposure to an external stimulus, it can facilitate analysis of the impact of the stimulus on those sources. The link between the stimulus and a given source can be verified by a classifier that is able to "predict" the condition a given signal was registered under, solely based on the components. However, the ICA's assumption about statistical independence of sources is often unrealistic and turns out to be insufficient to build an accurate classifier. Therefore, we propose to utilize a novel method, based on hybridization of ICA, multi-objective evolutionary algorithms (MOEA), and rough sets (RS), that attempts to improve the effectiveness of signal decomposition techniques by providing them with "classification-awareness." Results The preliminary results described here are very promising and further investigation of other MOEAs and/or RS-based classification accuracy measures should be pursued. Even a quick visual analysis of those results can provide an interesting insight into the problem of neural activity analysis. Conclusion We present a methodology of classificatory decomposition of signals. One of the main advantages of our approach is the fact that rather than solely relying on often unrealistic assumptions about statistical independence of sources, components are generated in the light of a underlying classification problem itself. PMID:17118151

The Impact of Conceptualization Skills in Counseling Children.

ERIC Educational Resources Information Center

LaBauve, Bill J.; Rynearson, Kimberly

2001-01-01

Addresses the importance of client conceptualization skills in counseling as well as the limitations of child conceptualization skills in counseling. Provides a rough overview of the applicable points in Piaget's theory of cognitive development and a discussion of how these points relate to conceptualization skills in counseling. (RS)

Refurbishing of carbon contaminated pre-mirror of reflectivity beam line at Indus-1

NASA Astrophysics Data System (ADS)

Yadav, P. K.; Kumar, M.; Gupta, R. K.; Sinha, M.; Patel, H. S.; Modi, M. H.

2018-04-01

In recent days optics contamination and its refurbishing is a serious issue for synchrotron radiation beam line community. Here we refurbished a carbon contaminated mirror by Ar and O2 gas mixed (1:1) radio frequency plasma. For structural analysis pre and post characterization of the mirror was done by Soft X-ray reflectivity (SXRR), Raman Spectroscopy (RS) and Atomic force microscopy (AFM). Before refurbishing mirror, a low density graphitic carbon layer of thickness 400 Å with surface roughness about 55 Å and Au surface roughness 14Å was estimated by SXRR. After one hour RF plasma exposure it is observed by SXRR and Raman spectroscopy that carbon layer is completely removed. The AFM and SXRR results show that roughness of Au surface not increase after plasma exposure.

Clinical Resting-state fMRI in the Preoperative Setting

PubMed Central

Lee, Megan H.; Miller-Thomas, Michelle M.; Benzinger, Tammie L.; Marcus, Daniel S.; Hacker, Carl D.; Leuthardt, Eric C.; Shimony, Joshua S.

2017-01-01

The purpose of this manuscript is to provide an introduction to resting-state functional magnetic resonance imaging (RS-fMRI) and to review the current application of this new and powerful technique in the preoperative setting using our institute’s extensive experience. RS-fMRI has provided important insights into brain physiology and is an increasingly important tool in the clinical setting. As opposed to task-based functional MRI wherein the subject performs a task while being scanned, RS-fMRI evaluates low-frequency fluctuations in the blood oxygen level dependent (BOLD) signal while the subject is at rest. Multiple resting state networks (RSNs) have been identified, including the somatosensory, language, and visual networks, which are of primary importance for presurgical planning. Over the past 4 years, we have performed over 300 RS-fMRI examinations in the clinical setting and these have been used to localize eloquent somatosensory and language cortices before brain tumor resection. RS-fMRI is particularly useful in this setting for patients who are unable to cooperate with the task-based paradigm, such as young children or those who are sedated, paretic, or aphasic. Although RS-fMRI is still investigational, our experience indicates that this method is ready for clinical application in the presurgical setting. PMID:26848556

The Study of Imperfection in Rough Set on the Field of Engineering and Education

NASA Astrophysics Data System (ADS)

Sheu, Tian-Wei; Liang, Jung-Chin; You, Mei-Li; Wen, Kun-Li

Based on the characteristic of rough set, rough set theory overlaps with many other theories, especially with fuzzy set theory, evidence theory and Boolean reasoning methods. And the rough set methodology has found many real-life applications, such as medical data analysis, finance, banking, engineering, voice recognition, image processing and others. Till now, there is rare research associating to this issue in the imperfection of rough set. Hence, the main purpose of this paper is to study the imperfection of rough set in the field of engineering and education. First of all, we preview the mathematics model of rough set, and a given two examples to enhance our approach, which one is the weighting of influence factor in muzzle noise suppressor, and the other is the weighting of evaluation factor in English learning. Third, we also apply Matlab to develop a complete human-machine interface type of toolbox in order to support the complex calculation and verification the huge data. Finally, some further suggestions are indicated for the research in the future.

The Reed-Solomon encoders: Conventional versus Berlekamp's architecture

NASA Technical Reports Server (NTRS)

Perlman, M.; Lee, J. J.

1982-01-01

Concatenated coding was adopted for interplanetary space missions. Concatenated coding was employed with a convolutional inner code and a Reed-Solomon (RS) outer code for spacecraft telemetry. Conventional RS encoders are compared with those that incorporate two architectural features which approximately halve the number of multiplications of a set of fixed arguments by any RS codeword symbol. The fixed arguments and the RS symbols are taken from a nonbinary finite field. Each set of multiplications is bit-serially performed and completed during one (bit-serial) symbol shift. All firmware employed by conventional RS encoders is eliminated.

Airflow Dynamics and Sand Transport over a Coastal Foredune with Large Woody Debris.

NASA Astrophysics Data System (ADS)

Grilliot, M. J.; Walker, I. J.; Bauer, B. O.

2016-12-01

Airflow dynamics and sand transport patterns over beach-foredune systems are complex due to the effects of topographic forcing and varied surface roughness elements. The role of large woody debris (LWD) as a roughness element in foredune dynamics is understudied compared to the effects of plant cover. Unlike plants, non-porous objects like LWD impose bluff body effects and induce secondary flow circulation that varies with LWD size, density, and arrangement. It is hypothesized that modified flow patterns over LWD can influence beach-dune sediment budgets and dune geometry via changes to mean near-surface flow patterns, turbulence, sand transport pathways and sedimentation patterns. In turn, LWD may act as an accretion anchor and store appreciable amounts of aeolian sand that subsequently may provide an enhanced buffer against coastal and/or wind erosion. This study examines turbulent airflow dynamics and related sand transport patterns for oblique onshore flow conditions over a mesotidal beach and scarped dune on Calvert Island, British Columbia, Canada. Abundant exposed LWD fronting the foredune enhances turbulent Reynolds stress (RS) and turbulence intensity (TI) near the surface. During low, yet competent wind speeds (6.54 m s-1), RS and TI are not competent enough in the sheltered flow regions within the LWD matrix and sediment deposition occurs. However, small zones of localized acceleration were observed with sand transport. Higher wind speeds, well above the entrainment threshold, increase RS and TI over LWD relative to the beach, facilitating sediment transport through and over the LWD matrix, with localized pockets of deposition in sheltered areas. The majority of LWD deposits on beaches in the region are anthropogenic logging debris and are known to be decreasing since the 1950s, but likely earlier. Thus, it is important to understand how non-porous roughness elements, like LWD, affect beach-dune sediment budgets and evolution, particularly in light of increasing storminess and sea level rise.

Techniques for Liquid Rocket Combustion Spontaneous Stability and Rough Combustion Assessments

NASA Technical Reports Server (NTRS)

Kenny, R. J.; Giacomoni, C.; Casiano, M. J.; Fischbach, S. R.

2016-01-01

This work presents techniques for liquid rocket engine combustion stability assessments with respect to spontaneous stability and rough combustion. Techniques covering empirical parameter extraction, which were established in prior works, are applied for three additional programs: the F-1 Gas Generator (F1GG) component test program, the RS-84 preburner component test program, and the Marshall Integrated Test Rig (MITR) program. Stability assessment parameters from these programs are compared against prior established spontaneous stability metrics and updates are identified. Also, a procedure for comparing measured with predicted mode shapes is presented, based on an extension of the Modal Assurance Criterion (MAC).

Polymorphisms in Stromal Genes and Susceptibility to Serous Epithelial Ovarian Cancer: A Report from the Ovarian Cancer Association Consortium

PubMed Central

Amankwah, Ernest K.; Wang, Qinggang; Schildkraut, Joellen M.; Tsai, Ya-Yu; Ramus, Susan J.; Fridley, Brooke L.; Beesley, Jonathan; Johnatty, Sharon E.; Webb, Penelope M.; Chenevix-Trench, Georgia; Dale, Laura C.; Lambrechts, Diether; Amant, Frederic; Despierre, Evelyn; Vergote, Ignace; Gayther, Simon A.; Gentry-Maharaj, Aleksandra; Menon, Usha; Chang-Claude, Jenny; Wang-Gohrke, Shan; Anton-Culver, Hoda; Ziogas, Argyrios; Dörk, Thilo; Dürst, Matthias; Antonenkova, Natalia; Bogdanova, Natalia; Brown, Robert; Flanagan, James M.; Kaye, Stanley B.; Paul, James; Bützow, Ralf; Nevanlinna, Heli; Campbell, Ian; Eccles, Diana M.; Karlan, Beth Y.; Gross, Jenny; Walsh, Christine; Pharoah, Paul D. P.; Song, Honglin; Krüger Kjær, Susanne; Høgdall, Estrid; Høgdall, Claus; Lundvall, Lene; Nedergaard, Lotte; Kiemeney, Lambertus A. L. M.; Massuger, Leon F. A. G.; van Altena, Anne M.; Vermeulen, Sita H. H. M.; Le, Nhu D.; Brooks-Wilson, Angela; Cook, Linda S.; Phelan, Catherine M.; Cunningham, Julie M.; Vachon, Celine M.; Vierkant, Robert A.; Iversen, Edwin S.; Berchuck, Andrew; Goode, Ellen L.; Sellers, Thomas A.; Kelemen, Linda E.

2011-01-01

Alterations in stromal tissue components can inhibit or promote epithelial tumorigenesis. Decorin (DCN) and lumican (LUM) show reduced stromal expression in serous epithelial ovarian cancer (sEOC). We hypothesized that common variants in these genes associate with risk. Associations with sEOC among Caucasians were estimated with odds ratios (OR) among 397 cases and 920 controls in two U.S.-based studies (discovery set), 436 cases and 1,098 controls in Australia (replication set 1) and a consortium of 15 studies comprising 1,668 cases and 4,249 controls (replication set 2). The discovery set and replication set 1 (833 cases and 2,013 controls) showed statistically homogeneous (Pheterogeneity≥0.48) decreased risks of sEOC at four variants: DCN rs3138165, rs13312816 and rs516115, and LUM rs17018765 (OR = 0.6 to 0.9; Ptrend = 0.001 to 0.03). Results from replication set 2 were statistically homogeneous (Pheterogeneity≥0.13) and associated with increased risks at DCN rs3138165 and rs13312816, and LUM rs17018765: all ORs = 1.2; Ptrend≤0.02. The ORs at the four variants were statistically heterogeneous across all 18 studies (Pheterogeneity≤0.03), which precluded combining. In post-hoc analyses, interactions were observed between each variant and recruitment period (Pinteraction≤0.003), age at diagnosis (Pinteraction = 0.04), and year of diagnosis (Pinteraction = 0.05) in the five studies with available information (1,044 cases, 2,469 controls). We conclude that variants in DCN and LUM are not directly associated with sEOC, and that confirmation of possible effect modification of the variants by non-genetic factors is required. PMID:21637745

Intelligent System Development Using a Rough Sets Methodology

NASA Technical Reports Server (NTRS)

Anderson, Gray T.; Shelton, Robert O.

1997-01-01

The purpose of this research was to examine the potential of the rough sets technique for developing intelligent models of complex systems from limited information. Rough sets a simple but promising technology to extract easily understood rules from data. The rough set methodology has been shown to perform well when used with a large set of exemplars, but its performance with sparse data sets is less certain. The difficulty is that rules will be developed based on just a few examples, each of which might have a large amount of noise associated with them. The question then becomes, what is the probability of a useful rule being developed from such limited information? One nice feature of rough sets is that in unusual situations, the technique can give an answer of 'I don't know'. That is, if a case arises that is different from the cases the rough set rules were developed on, the methodology can recognize this and alert human operators of it. It can also be trained to do this when the desired action is unknown because conflicting examples apply to the same set of inputs. This summer's project was to look at combining rough set theory with statistical theory to develop confidence limits in rules developed by rough sets. Often it is important not to make a certain type of mistake (e.g., false positives or false negatives), so the rules must be biased toward preventing a catastrophic error, rather than giving the most likely course of action. A method to determine the best course of action in the light of such constraints was examined. The resulting technique was tested with files containing electrical power line 'signatures' from the space shuttle and with decompression sickness data.

Multimodal Learning and Intelligent Prediction of Symptom Development in Individual Parkinson’s Patients

PubMed Central

Przybyszewski, Andrzej W.; Kon, Mark; Szlufik, Stanislaw; Szymanski, Artur; Habela, Piotr; Koziorowski, Dariusz M.

2016-01-01

We still do not know how the brain and its computations are affected by nerve cell deaths and their compensatory learning processes, as these develop in neurodegenerative diseases (ND). Compensatory learning processes are ND symptoms usually observed at a point when the disease has already affected large parts of the brain. We can register symptoms of ND such as motor and/or mental disorders (dementias) and even provide symptomatic relief, though the structural effects of these are in most cases not yet understood. It is very important to obtain early diagnosis, which can provide several years in which we can monitor and partly compensate for the disease’s symptoms, with the help of various therapies. In the case of Parkinson’s disease (PD), in addition to classical neurological tests, measurements of eye movements are diagnostic. We have performed measurements of latency, amplitude, and duration in reflexive saccades (RS) of PD patients. We have compared the results of our measurement-based diagnoses with standard neurological ones. The purpose of our work was to classify how condition attributes predict the neurologist’s diagnosis. For n = 10 patients, the patient age and parameters based on RS gave a global accuracy in predictions of neurological symptoms in individual patients of about 80%. Further, by adding three attributes partly related to patient ‘well-being’ scores, our prediction accuracies increased to 90%. Our predictive algorithms use rough set theory, which we have compared with other classifiers such as Naïve Bayes, Decision Trees/Tables, and Random Forests (implemented in KNIME/WEKA). We have demonstrated that RS are powerful biomarkers for assessment of symptom progression in PD. PMID:27649187

Flu Diagnosis System Using Jaccard Index and Rough Set Approaches

NASA Astrophysics Data System (ADS)

Efendi, Riswan; Azah Samsudin, Noor; Mat Deris, Mustafa; Guan Ting, Yip

2018-04-01

Jaccard index and rough set approaches have been frequently implemented in decision support systems with various domain applications. Both approaches are appropriate to be considered for categorical data analysis. This paper presents the applications of sets operations for flu diagnosis systems based on two different approaches, such as, Jaccard index and rough set. These two different approaches are established using set operations concept, namely intersection and subset. The step-by-step procedure is demonstrated from each approach in diagnosing flu system. The similarity and dissimilarity indexes between conditional symptoms and decision are measured using Jaccard approach. Additionally, the rough set is used to build decision support rules. Moreover, the decision support rules are established using redundant data analysis and elimination of unclassified elements. A number data sets is considered to attempt the step-by-step procedure from each approach. The result has shown that rough set can be used to support Jaccard approaches in establishing decision support rules. Additionally, Jaccard index is better approach for investigating the worst condition of patients. While, the definitely and possibly patients with or without flu can be determined using rough set approach. The rules may improve the performance of medical diagnosis systems. Therefore, inexperienced doctors and patients are easier in preliminary flu diagnosis.

Improved eye- and skin-color prediction based on 8 SNPs.

PubMed

Hart, Katie L; Kimura, Shey L; Mushailov, Vladimir; Budimlija, Zoran M; Prinz, Mechthild; Wurmbach, Elisa

2013-06-01

To improve the 7-plex system to predict eye and skin color by increasing precision and detailed phenotypic descriptions. Analysis of an eighth single nucleotide polymorphism (SNP), rs12896399 (SLC24A4), showed a statistically significant association with human eye color (P=0.007) but a rather poor strength of agreement (κ=0.063). This SNP was added to the 7-plex system (rs12913832 at HERC2, rs1545397 at OCA2, rs16891982 at SLC45A2, rs1426654 at SLC24A5, rs885479 at MC1R, rs6119471 at ASIP, and rs12203592 at IRF4). Further, the instruction guidelines on the interpretation of genotypes were changed to create a new 8-plex system. This was based on the analysis of an 803-sample training set of various populations. The newly developed 8-plex system can predict the eye colors brown, green, and blue, and skin colors light, not dark, and not light. It is superior to the 7-plex system with its additional ability to predict blue eye and light skin color. The 8-plex system was tested on an additional 212 samples, the test set. Analysis showed that the number of positive descriptions for eye colors as being brown, green, or blue increased significantly (P=6.98e-15, z-score: -7.786). The error rate for eye-color prediction was low, at approximately 5%, while the skin color prediction showed no error in the test set (1% in training set). We can conclude that the new 8-plex system for the prediction of eye and skin color substantially enhances its former version.

Using Optimisation Techniques to Granulise Rough Set Partitions

NASA Astrophysics Data System (ADS)

Crossingham, Bodie; Marwala, Tshilidzi

2007-11-01

This paper presents an approach to optimise rough set partition sizes using various optimisation techniques. Three optimisation techniques are implemented to perform the granularisation process, namely, genetic algorithm (GA), hill climbing (HC) and simulated annealing (SA). These optimisation methods maximise the classification accuracy of the rough sets. The proposed rough set partition method is tested on a set of demographic properties of individuals obtained from the South African antenatal survey. The three techniques are compared in terms of their computational time, accuracy and number of rules produced when applied to the Human Immunodeficiency Virus (HIV) data set. The optimised methods results are compared to a well known non-optimised discretisation method, equal-width-bin partitioning (EWB). The accuracies achieved after optimising the partitions using GA, HC and SA are 66.89%, 65.84% and 65.48% respectively, compared to the accuracy of EWB of 59.86%. In addition to rough sets providing the plausabilities of the estimated HIV status, they also provide the linguistic rules describing how the demographic parameters drive the risk of HIV.

Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans

PubMed Central

Zhang, Mingfeng; Song, Fengju; Liang, Liming; Nan, Hongmei; Zhang, Jiangwen; Liu, Hongliang; Wang, Li-E.; Wei, Qingyi; Lee, Jeffrey E.; Amos, Christopher I.; Kraft, Peter; Qureshi, Abrar A.; Han, Jiali

2013-01-01

Aiming to identify novel genetic loci for pigmentation and skin cancer, we conducted a series of genome-wide association studies on hair color, eye color, number of sunburns, tanning ability and number of non-melanoma skin cancers (NMSCs) among 10 183 European Americans in the discovery stage and 4504 European Americans in the replication stage (for eye color, 3871 males in the discovery stage and 2496 males in the replication stage). We targeted novel chromosome regions besides the known ones for replication. As a result, we identified a new region downstream of the EDNRB gene on 13q22 associated with hair color and the strongest association was the single-nucleotide polymorphism (SNP) rs975739 (P = 2.4 × 10−14; P = 5.4 × 10−9 in the discovery set and P = 1.2 × 10−6 in the replication set). Using blue, intermediate (including green) and brown eye colors as co-dominant outcomes, we identified the SNP rs3002288 in VASH2 on 1q32.3 associated with brown eye (P = 7.0 × 10−8; P = 5.3 × 10−5 in the discovery set and P = 0.02 in the replication set). Additionally, we identified a significant interaction between the SNPs rs7173419 and rs12913832 in the OCA2 gene region on brown eye color (P-value for interaction = 3.8 × 10−3). As for the number of NMSCs, we identified two independent SNPs on chr6 and one SNP on chromosome 14: rs12203592 in IRF4 (P = 7.2 × 10−14; P = 1.8 × 10−8 in the discovery set and P = 6.7 × 10−7 in the replication set), rs12202284 between IRF4 and EXOC2 (P = 5.0 × 10−8; P = 6.6 × 10−7 in the discovery set and P = 3.0 × 10−3 in the replication set) and rs8015138 upstream of GNG2 (P = 6.6 × 10−8; P = 5.3 × 10−7 in the discovery set and P = 0.01 in the replication set). PMID:23548203

Role of the urate transporter SLC2A9 gene in susceptibility to gout in New Zealand Māori, Pacific Island, and Caucasian case-control sample sets.

PubMed

Hollis-Moffatt, Jade E; Xu, Xin; Dalbeth, Nicola; Merriman, Marilyn E; Topless, Ruth; Waddell, Chloe; Gow, Peter J; Harrison, Andrew A; Highton, John; Jones, Peter B B; Stamp, Lisa K; Merriman, Tony R

2009-11-01

To examine the role of genetic variation in the renal urate transporter SLC2A9 in gout in New Zealand sample sets of Māori, Pacific Island, and Caucasian ancestry and to determine if the Māori and Pacific Island samples could be useful for fine-mapping. Patients (n= 56 Māori, 69 Pacific Island, and 131 Caucasian) were recruited from rheumatology outpatient clinics and satisfied the American College of Rheumatology criteria for gout. The control samples comprised 125 Māori subjects, 41 Pacific Island subjects, and 568 Caucasian subjects without arthritis. SLC2A9 single-nucleotide polymorphisms rs16890979 (V253I), rs5028843, rs11942223, and rs12510549 were genotyped (possible etiologic variants in Caucasians). Association of the major allele of rs16890979, rs11942223, and rs5028843 with gout was observed in all sample sets (P = 3.7 x 10(-7), 1.6 x 10(-6), and 7.6 x 10(-5) for rs11942223 in the Māori, Pacific Island, and Caucasian samples, respectively). One 4-marker haplotype (1/1/2/1; more prevalent in the Māori and Pacific Island control samples) was not observed in a single gout case. Our data confirm a role of SLC2A9 in gout susceptibility in a New Zealand Caucasian sample set, with the effect on risk (odds ratio >2.0) greater than previous estimates. We also demonstrate association of SLC2A9 with gout in samples of Māori and Pacific Island ancestry and a consistent pattern of haplotype association. The presence of both alleles of rs16890979 on susceptibility and protective haplotypes in the Māori and Pacific Island sample is evidence against a role for this nonsynonymous variant as the sole etiologic agent. More extensive linkage disequilibrium in Māori and Pacific Island samples suggests that Caucasian samples may be more useful for fine-mapping.

In vivo imaging of the mouse model of X-linked juvenile retinoschisis with fourier domain optical coherence tomography.

PubMed

Xu, Jing; Molday, Laurie L; Molday, Robert S; Sarunic, Marinko V

2009-06-01

The purpose of this study was to investigate Fourier domain optical coherence tomography (FD OCT) as a noninvasive tool for retinal imaging in the Rs1h-knockout mouse (model for X-linked juvenile retinoschisis). A prototype spectrometer-based FD OCT system was used in combination with a custom optical beam-scanning platform. Images of the retinas from wild-type and Rs1h-knockout mice were acquired noninvasively with FD OCT with the specimen anesthetized. At the completion of the noninvasive FD OCT imaging, invasive retinal cross-sectional images (histology) were acquired from a nearby region for comparison to the FD OCT images. The retinal layers were identifiable in the FD OCT images, permitting delineation and thickness measurement of the outer nuclear layer (ONL). During FD OCT in vivo imaging of the Rs1h-knockout mouse, holes were observed in the inner nuclear layer (INL), and retinal cell disorganization was observed as a change in the backscattering intensity profile. Comparison of the ONL measurements acquired noninvasively with FD OCT to measurements taken using histology at nearby locations showed a degeneration of roughly 30% of the ONL by the age of 2 months in Rs1h-knockout mice relative to wild-type. FD OCT was demonstrated to be effective for noninvasive imaging of retinal degeneration and observation of retinal holes in Rs1h-knockout mice.

Characteristics of the Remote Sensing Data Used in the Proposed Unfccc REDD+ Forest Reference Emission Levels (frels)

NASA Astrophysics Data System (ADS)

Johnson, B. A.; Scheyvens, H.; Samejima, H.; Onoda, M.

2016-06-01

Developing countries must submit forest reference emission levels (FRELs) to the UNFCCC to receive incentives for REDD+ activities (e.g. reducing emissions from deforestation/forest degradation, sustainable management of forests, forest carbon stock conservation/enhancement). These FRELs are generated based on historical CO2 emissions in the land use, land use change, and forestry sector, and are derived using remote sensing (RS) data and in-situ forest carbon measurements. Since the quality of the historical emissions estimates is affected by the quality and quantity of the RS data used, in this study we calculated five metrics (i-v below) to assess the quality and quantity of the data that has been used thus far. Countries could focus on improving on one or more of these metrics for the submission of future FRELs. Some of our main findings were: (i) the median percentage of each country mapped was 100%, (ii) the median historical timeframe for which RS data was used was 11.5 years, (iii) the median interval of forest map updates was 4.5 years, (iv) the median spatial resolution of the RS data was 30m, and (v) the median number of REDD+ activities that RS data was used for operational monitoring of was 1 (typically deforestation). Many new sources of RS data have become available in recent years, so complementary or alternative RS data sets for generating future FRELs can potentially be identified based on our findings; e.g. alternative RS data sets could be considered if they have similar or higher quality/quantity than the currently-used data sets.

Application of preprocessing filtering on Decision Tree C4.5 and rough set theory

NASA Astrophysics Data System (ADS)

Chan, Joseph C. C.; Lin, Tsau Y.

2001-03-01

This paper compares two artificial intelligence methods: the Decision Tree C4.5 and Rough Set Theory on the stock market data. The Decision Tree C4.5 is reviewed with the Rough Set Theory. An enhanced window application is developed to facilitate the pre-processing filtering by introducing the feature (attribute) transformations, which allows users to input formulas and create new attributes. Also, the application produces three varieties of data set with delaying, averaging, and summation. The results prove the improvement of pre-processing by applying feature (attribute) transformations on Decision Tree C4.5. Moreover, the comparison between Decision Tree C4.5 and Rough Set Theory is based on the clarity, automation, accuracy, dimensionality, raw data, and speed, which is supported by the rules sets generated by both algorithms on three different sets of data.

No association between FTO or HHEX andendometrial cancer risk

PubMed Central

Gaudet, Mia M.; Yang, Hannah P.; Bosquet, Jesus Gonzalez; Healey, Catherine S.; Ahmed, Shahana; Dunning, Alison M.; Easton, Doug F.; Spurdle, Amanda B.; Ferguson, Kaltin; O’Mara, Tracy; Group, ANECS; Lambrechts, Diether; Despierre, Evelyn; Vergote, Ignace; Amant, Frederic; Lacey, James V.; Lissowska, Jola; Peplonska, Beata; Brinton, Louise A.; Chanock, Stephen; Garcia-Closas, Montserrat

2010-01-01

Introduction Obesity and diabetes are known risk factors for endometrial cancer; thus genetic risk factors of these phenotypes may also be associated with endometrial cancer risk. To evaluate this hypothesis, we genotyped tagSNPs and candidate SNPs in FTO and HHEX in a primary set of 417 endometrial cancer cases and 406 population-based controls, and validated significant findings in a replication set of approximately 2,347 cases and 3,140 controls from three additional studies. Methods We genotyped 189 tagSNPs in FTO (including rs8050136) and five tagSNPs in HHEX (including rs1111875) in the primary set and one SNP in each of FTO (rs12927155) and HHEX (rs1111875) in the validation set. Per allele odds ratios (OR) and 95% confidence intervals (CI) were calculated to estimate the association between the genotypes of each SNPs(as an ordinal variable)and endometrial cancer risk using unconditional logistic regression models, controlling for age and site. Results In the primary study, the most significant findings in FTO was rs12927155 (OR=1.56, 95% CI 1.21–2.01, p=5.8×10−4) and HHEX was rs1111875 (OR=0.80, 95% CI 0.66–0.97; p=0.026). In the validation studies, the pooled per allele ORs, adjusted for age and study, were for FTO rs12927155: OR=0.94, 95% CI 0.83–1.06, p=0.29 and for HHEX rs1111875: OR=1.00, 95%CI 0.92–1.10, p=0.96. Conclusion Our data indicate that common genetic variants in two genes previously related to obesity (FTO) and diabetes (HHEX) by genome-wide association scans are not associatedwith endometrial cancer risk. Impact Polymorphisms in FTO and HHEX are unlikely to have large effects on endometrial cancer risk but may have weaker effects. PMID:20647405

Granularity refined by knowledge: contingency tables and rough sets as tools of discovery

NASA Astrophysics Data System (ADS)

Zytkow, Jan M.

2000-04-01

Contingency tables represent data in a granular way and are a well-established tool for inductive generalization of knowledge from data. We show that the basic concepts of rough sets, such as concept approximation, indiscernibility, and reduct can be expressed in the language of contingency tables. We further demonstrate the relevance to rough sets theory of additional probabilistic information available in contingency tables and in particular of statistical tests of significance and predictive strength applied to contingency tables. Tests of both type can help the evaluation mechanisms used in inductive generalization based on rough sets. Granularity of attributes can be improved in feedback with knowledge discovered in data. We demonstrate how 49er's facilities for (1) contingency table refinement, for (2) column and row grouping based on correspondence analysis, and (3) the search for equivalence relations between attributes improve both granularization of attributes and the quality of knowledge. Finally we demonstrate the limitations of knowledge viewed as concept approximation, which is the focus of rough sets. Transcending that focus and reorienting towards the predictive knowledge and towards the related distinction between possible and impossible (or statistically improbable) situations will be very useful in expanding the rough sets approach to more expressive forms of knowledge.

Rough Evaluation Structure: Application of Rough Set Theory to Generate Simple Rules for Inconsistent Preference Relation

NASA Astrophysics Data System (ADS)

Gehrmann, Andreas; Nagai, Yoshimitsu; Yoshida, Osamu; Ishizu, Syohei

Since management decision-making becomes complex and preferences of the decision-maker frequently becomes inconsistent, multi-attribute decision-making problems were studied. To represent inconsistent preference relation, the concept of evaluation structure was introduced. We can generate simple rules to represent inconsistent preference relation by the evaluation structures. Further rough set theory for the preference relation was studied and the concept of approximation was introduced. One of our main aims of this paper is to introduce a concept of rough evaluation structure for representing inconsistent preference relation. We apply rough set theory to the evaluation structure, and develop a method for generating simple rules for inconsistent preference relations. In this paper, we introduce concepts of totally ordered information system, similarity class of preference relation, upper and lower approximation of preference relations. We also show the properties of rough evaluation structure and provide a simple example. As an application of rough evaluation structure, we analyze questionnaire survey of customer preferences about audio players.

The Shape of Near-Earth Asteroid 275677 (2000 RS11) From Inversion of Arecibo and Goldstone Radar Images

NASA Astrophysics Data System (ADS)

Brauer, Kaley; Busch, Michael W.; Benner, Lance A. M.; Brozovic, Marina; Howell, Ellen S.; Nolan, Michael C.; Springmann, Alessondra; Giorgini, Jon D.; Taylor, Patrick A.; Jao, Joseph S.

2015-11-01

We observed near-Earth asteroid 2000 RS11 with the Arecibo and Goldstone planetary radars during a 0.035 au approach in March 2014, obtaining delay-Doppler images between March 13 and March 17. The finest-resolution images have range resolution of 7.5 m/pixel and show that RS11 is a contact binary with complex topography. We used the SHAPE software package (Magri et al., Icarus 186, 156-160 2007) to create a physical model of RS11 and its spin state from these delay-Doppler images.The rotation period of RS11 is well constrained from optical lightcurves, P = 4.444 ± 0.001 h (Warner et al., Minor Planet Bulletin 41, 160; 2014 and Benishek, Minor Planet Bulletin 41, 257; 2014). We found two possible pole directions and corresponding shape models, mirror images of one another, which provide equally good fits to the radar data. RS11’s pole direction is either (λ , β) = (155°, 30°) ± 10° or (335°, -30°) ± 10° in J2000 ecliptic coordinates. The most likely pole directions of RS11 are not aligned with the heliocentric orbit normal and instead have an obliquity within 10° of 56° or 124°.Our best-fit shape models are 1400-vertex polyhedra comprising two lobes in contact. The lengths of RS11’s principal axes are 698 ± 71 m, 578 ± 59 m, and 758 ± 77 m. RS11 has a volume of 0.086 ± 0.026 km^3. The long axis of RS11’s larger lobe is 751 ± 77 m and the long axis of the smaller lobe is 398 ± 41 m; the volume ratio between these lobes is roughly 2.7 ± 10%. Spectral data informs us that RS11 is an S-class object (Lazzarin et al., Icarus 169, 379; 2004).RS11's shape is unusual compared with those of other contact binary NEAs imaged by radar. Its larger lobe is flattened. Additionally, while the neck between the smaller and larger lobes of most contact binaries is located near the larger lobe's longest principal axis (such as in the cases of 25143 Itokawa and 4179 Toutatis), RS11's neck is near its larger lobe's shortest principal axis. RS11 is the first asteroid of this type for which we have a shape model.

In vivo imaging of the Mouse Model of X-Linked Juvenile Retinoschisis Using Fourier Domain Optical Coherence Tomography

PubMed Central

Xu, Jing; Molday, Laurie L.; Molday, Robert S.; Sarunic, Marinko V.

2009-01-01

Purpose The purpose of this study is to investigate Fourier Domain Optical Coherence Tomography (FD OCT) as a non-invasive tool for retinal imaging in the Rs1h knockout mouse (model for X-linked Juvenile Retinoschisis). Methods A prototype spectrometer based FD OCT system was used in combination with a custom optical beam-scanning platform. Images of the retinas from wild type and Rs1h knockout mice were acquired non-invasively using FD OCT with the specimen anesthetized. At the completion of the non-invasive FD OCT imaging, invasive retinal cross sectional images (histology) were acquired from a nearby region for comparison to the FD OCT images. Results The retinal layers could be identified in the FD OCT images, permitting delineation and thickness measurement of the outer nuclear layer (ONL). During FD OCT in vivo imaging of the Rs1h knockout mouse, holes were observed in the inner nuclear layer (INL) and retinal cell disorganization was observed as a change in the backscattering intensity profile. Comparison of the ONL measurements acquired non-invasively using FD OCT to measurements taken using histology at nearby locations showed a degeneration of roughly thirty percent of the ONL by the age of two months in Rs1h knockout mice relative to wild type. Conclusions FD OCT has been demonstrated for non-invasive imaging of retinal degeneration and observation of retinal holes in Rs1h knockout mice. PMID:19182246

Assessment of physiological performance and perception of pushing different wheelchairs on indoor modular units simulating a surface roughness often encountered in under-resourced settings.

PubMed

Sasaki, Kotaro; Rispin, Karen

2017-01-01

In under-resourced settings where motorized wheelchairs are rarely available, manual wheelchair users with limited upper-body strength and functionalities need to rely on assisting pushers for their mobility. Because traveling surfaces in under-resourced settings are often unpaved and rough, wheelchair pushers could experience high physiological loading. In order to evaluate pushers' physiological loading and to improve wheelchair designs, we built indoor modular units that simulate rough surface conditions, and tested a hypothesis that pushing different wheelchairs would result in different physiological performances and pushers' perception of difficulty on the simulated rough surface. Eighteen healthy subjects pushed two different types of pediatric wheelchairs (Moti-Go manufactured by Motivation, and KidChair by Hope Haven) fitted with a 50-kg dummy on the rough and smooth surfaces at self-selected speeds. Oxygen uptake, traveling distance for 6 minutes, and the rating of difficulty were obtained. The results supported our hypothesis, showing that pushing Moti-Go on the rough surface was physiologically less loading than KidChair, but on the smooth surface, the two wheelchairs did not differ significantly. These results indicate wheelchair designs to improve pushers' performance in under-resourced settings should be evaluated on rough surfaces.

A Dual Hesitant Fuzzy Multigranulation Rough Set over Two-Universe Model for Medical Diagnoses

PubMed Central

Zhang, Chao; Li, Deyu; Yan, Yan

2015-01-01

In medical science, disease diagnosis is one of the difficult tasks for medical experts who are confronted with challenges in dealing with a lot of uncertain medical information. And different medical experts might express their own thought about the medical knowledge base which slightly differs from other medical experts. Thus, to solve the problems of uncertain data analysis and group decision making in disease diagnoses, we propose a new rough set model called dual hesitant fuzzy multigranulation rough set over two universes by combining the dual hesitant fuzzy set and multigranulation rough set theories. In the framework of our study, both the definition and some basic properties of the proposed model are presented. Finally, we give a general approach which is applied to a decision making problem in disease diagnoses, and the effectiveness of the approach is demonstrated by a numerical example. PMID:26858772

The First Attempt at Non-Linear in Silico Prediction of Sampling Rates for Polar Organic Chemical Integrative Samplers (POCIS)

PubMed Central

2016-01-01

Modeling and prediction of polar organic chemical integrative sampler (POCIS) sampling rates (Rs) for 73 compounds using artificial neural networks (ANNs) is presented for the first time. Two models were constructed: the first was developed ab initio using a genetic algorithm (GSD-model) to shortlist 24 descriptors covering constitutional, topological, geometrical and physicochemical properties and the second model was adapted for Rs prediction from a previous chromatographic retention model (RTD-model). Mechanistic evaluation of descriptors showed that models did not require comprehensive a priori information to predict Rs. Average predicted errors for the verification and blind test sets were 0.03 ± 0.02 L d–1 (RTD-model) and 0.03 ± 0.03 L d–1 (GSD-model) relative to experimentally determined Rs. Prediction variability in replicated models was the same or less than for measured Rs. Networks were externally validated using a measured Rs data set of six benzodiazepines. The RTD-model performed best in comparison to the GSD-model for these compounds (average absolute errors of 0.0145 ± 0.008 L d–1 and 0.0437 ± 0.02 L d–1, respectively). Improvements to generalizability of modeling approaches will be reliant on the need for standardized guidelines for Rs measurement. The use of in silico tools for Rs determination represents a more economical approach than laboratory calibrations. PMID:27363449

An Efficient Soft Set-Based Approach for Conflict Analysis

PubMed Central

Sutoyo, Edi; Mungad, Mungad; Hamid, Suraya; Herawan, Tutut

2016-01-01

Conflict analysis has been used as an important tool in economic, business, governmental and political dispute, games, management negotiations, military operations and etc. There are many mathematical formal models have been proposed to handle conflict situations and one of the most popular is rough set theory. With the ability to handle vagueness from the conflict data set, rough set theory has been successfully used. However, computational time is still an issue when determining the certainty, coverage, and strength of conflict situations. In this paper, we present an alternative approach to handle conflict situations, based on some ideas using soft set theory. The novelty of the proposed approach is that, unlike in rough set theory that uses decision rules, it is based on the concept of co-occurrence of parameters in soft set theory. We illustrate the proposed approach by means of a tutorial example of voting analysis in conflict situations. Furthermore, we elaborate the proposed approach on real world dataset of political conflict in Indonesian Parliament. We show that, the proposed approach achieves lower computational time as compared to rough set theory of up to 3.9%. PMID:26928627

An Efficient Soft Set-Based Approach for Conflict Analysis.

PubMed

Sutoyo, Edi; Mungad, Mungad; Hamid, Suraya; Herawan, Tutut

2016-01-01

Conflict analysis has been used as an important tool in economic, business, governmental and political dispute, games, management negotiations, military operations and etc. There are many mathematical formal models have been proposed to handle conflict situations and one of the most popular is rough set theory. With the ability to handle vagueness from the conflict data set, rough set theory has been successfully used. However, computational time is still an issue when determining the certainty, coverage, and strength of conflict situations. In this paper, we present an alternative approach to handle conflict situations, based on some ideas using soft set theory. The novelty of the proposed approach is that, unlike in rough set theory that uses decision rules, it is based on the concept of co-occurrence of parameters in soft set theory. We illustrate the proposed approach by means of a tutorial example of voting analysis in conflict situations. Furthermore, we elaborate the proposed approach on real world dataset of political conflict in Indonesian Parliament. We show that, the proposed approach achieves lower computational time as compared to rough set theory of up to 3.9%.

The renal urate transporter SLC17A1 locus: confirmation of association with gout.

PubMed

Hollis-Moffatt, Jade E; Phipps-Green, Amanda J; Chapman, Brett; Jones, Gregory T; van Rij, Andre; Gow, Peter J; Harrison, Andrew A; Highton, John; Jones, Peter B; Montgomery, Grant W; Stamp, Lisa K; Dalbeth, Nicola; Merriman, Tony R

2012-04-27

Two major gout-causing genes have been identified, the urate transport genes SLC2A9 and ABCG2. Variation within the SLC17A1 locus, which encodes sodium-dependent phosphate transporter 1, a renal transporter of uric acid, has also been associated with serum urate concentration. However, evidence for association with gout is equivocal. We investigated the association of the SLC17A1 locus with gout in New Zealand sample sets. Five variants (rs1165196, rs1183201, rs9358890, rs3799344, rs12664474) were genotyped across a New Zealand sample set totaling 971 cases and 1,742 controls. Cases were ascertained according to American Rheumatism Association criteria. Two population groups were studied: Caucasian and Polynesian. At rs1183201 (SLC17A1), evidence for association with gout was observed in both the Caucasian (odds ratio (OR) = 0.67, P = 3.0 × 10-6) and Polynesian (OR = 0.74, P = 3.0 × 10-3) groups. Meta-analysis confirmed association of rs1183201 with gout at a genome-wide level of significance (OR = 0.70, P = 3.0 × 10-8). Haplotype analysis suggested the presence of a common protective haplotype. We confirm the SLC17A1 locus as the third associated with gout at a genome-wide level of significance.

A Set of Functional Brain Networks for the Comprehensive Evaluation of Human Characteristics.

PubMed

Sung, Yul-Wan; Kawachi, Yousuke; Choi, Uk-Su; Kang, Daehun; Abe, Chihiro; Otomo, Yuki; Ogawa, Seiji

2018-01-01

Many human characteristics must be evaluated to comprehensively understand an individual, and measurements of the corresponding cognition/behavior are required. Brain imaging by functional MRI (fMRI) has been widely used to examine brain function related to human cognition/behavior. However, few aspects of cognition/behavior of individuals or experimental groups can be examined through task-based fMRI. Recently, resting state fMRI (rs-fMRI) signals have been shown to represent functional infrastructure in the brain that is highly involved in processing information related to cognition/behavior. Using rs-fMRI may allow diverse information about the brain through a single MRI scan to be obtained, as rs-fMRI does not require stimulus tasks. In this study, we attempted to identify a set of functional networks representing cognition/behavior that are related to a wide variety of human characteristics and to evaluate these characteristics using rs-fMRI data. If possible, these findings would support the potential of rs-fMRI to provide diverse information about the brain. We used resting-state fMRI and a set of 130 psychometric parameters that cover most human characteristics, including those related to intelligence and emotional quotients and social ability/skill. We identified 163 brain regions by VBM analysis using regression analysis with 130 psychometric parameters. Next, using a 163 × 163 correlation matrix, we identified functional networks related to 111 of the 130 psychometric parameters. Finally, we made an 8-class support vector machine classifiers corresponding to these 111 functional networks. Our results demonstrate that rs-fMRI signals contain intrinsic information about brain function related to cognition/behaviors and that this set of 111 networks/classifiers can be used to comprehensively evaluate human characteristics.

Utility of the Conconi's heart rate deflection to monitor the intensity of aerobic training.

PubMed

Passelergue, Philippe A; Cormery, Bruno; Lac, Gérard; Léger, Luc A

2006-02-01

The Conconi's heart-rate deflection point (HRd) in the heart rate (HR)/speed curve is often used to set aerobic training loads. Training could either be set in percentage running speed or HR at HRd. In order to establish the limits and usefulness of various aerobic-training modalities for intermediate athletic level (physical-education students), acute responses were analyzed while running for a typical 40-minute training session. Speed, HR, lactate, and cortisol were thus recorded during training at 90 and 100% of running speed (RS: n = 14) and HR (HR: n = 16) at HRd (90% running speed [RS90], 100% running speed [RS100], 90% HR [HR90], and 100% HR [HR100]). During constant HR training, RS decreases while HR drifts upward during constant RS training. Half of the subjects can not finish the 40-minute RS100 session. For HR90, RS90, HR100, and RS100, average intensities are 67, 69, 74.9, and 77% maximal aerobic speed (multistage test), respectively. This study indicates that (1) training at HR100 and RS100 is more appropriate to improve high-intensity metabolic capacities (increased cortisol and lactate) while RS100 is too difficult to be maintained for 40 minutes for subjects at that level at least, (2) training at HR90, however, is better to improve endurance and capacity to do a large amount of work considering cortisol and lactate homeostasis, and (3) training at a constant HR using a HR monitor is a good method to control the intensity of the training with subjects not used to pacing themselves with the split-time approach.

Association of Genetic Loci with Sleep Apnea in European Americans and African-Americans: The Candidate Gene Association Resource (CARe)

PubMed Central

Patel, Sanjay R.; Goodloe, Robert; De, Gourab; Kowgier, Matthew; Weng, Jia; Buxbaum, Sarah G.; Cade, Brian; Fulop, Tibor; Gharib, Sina A.; Gottlieb, Daniel J.; Hillman, David; Larkin, Emma K.; Lauderdale, Diane S.; Li, Li; Mukherjee, Sutapa; Palmer, Lyle; Zee, Phyllis; Zhu, Xiaofeng; Redline, Susan

2012-01-01

Although obstructive sleep apnea (OSA) is known to have a strong familial basis, no genetic polymorphisms influencing apnea risk have been identified in cross-cohort analyses. We utilized the National Heart, Lung, and Blood Institute (NHLBI) Candidate Gene Association Resource (CARe) to identify sleep apnea susceptibility loci. Using a panel of 46,449 polymorphisms from roughly 2,100 candidate genes on a customized Illumina iSelect chip, we tested for association with the apnea hypopnea index (AHI) as well as moderate to severe OSA (AHI≥15) in 3,551 participants of the Cleveland Family Study and two cohorts participating in the Sleep Heart Health Study. Among 647 African-Americans, rs11126184 in the pleckstrin (PLEK) gene was associated with OSA while rs7030789 in the lysophosphatidic acid receptor 1 (LPAR1) gene was associated with AHI using a chip-wide significance threshold of p-value<2×10−6. Among 2,904 individuals of European ancestry, rs1409986 in the prostaglandin E2 receptor (PTGER3) gene was significantly associated with OSA. Consistency of effects between rs7030789 and rs1409986 in LPAR1 and PTGER3 and apnea phenotypes were observed in independent clinic-based cohorts. Novel genetic loci for apnea phenotypes were identified through the use of customized gene chips and meta-analyses of cohort data with replication in clinic-based samples. The identified SNPs all lie in genes associated with inflammation suggesting inflammation may play a role in OSA pathogenesis. PMID:23155414

A resolvable subfilter-scale model specific to large-eddy simulation of under-resolved turbulence

NASA Astrophysics Data System (ADS)

Zhou, Yong; Brasseur, James G.; Juneja, Anurag

2001-09-01

Large-eddy simulation (LES) of boundary-layer flows has serious deficiencies near the surface when a viscous sublayer either does not exist (rough walls) or is not practical to resolve (high Reynolds numbers). In previous work, we have shown that the near-surface errors arise from the poor performance of algebraic subfilter-scale (SFS) models at the first several grid levels, where integral scales are necessarily under-resolved and the turbulence is highly anisotropic. In under-resolved turbulence, eddy viscosity and similarity SFS models create a spurious feedback loop between predicted resolved-scale (RS) velocity and modeled SFS acceleration, and are unable to simultaneously capture SFS acceleration and RS-SFS energy flux. To break the spurious coupling in a dynamically meaningful manner, we introduce a new modeling strategy in which the grid-resolved subfilter velocity is estimated from a separate dynamical equation containing the essential inertial interactions between SFS and RS velocity. This resolved SFS (RSFS) velocity is then used as a surrogate for the complete SFS velocity in the SFS stress tensor. We test the RSFS model by comparing LES of highly under-resolved anisotropic buoyancy-generated homogeneous turbulence with a corresponding direct numerical simulation (DNS). The new model successfully suppresses the spurious feedback loop between RS velocity and SFS acceleration, and greatly improves model predictions of the anisotropic structure of SFS acceleration and resolved velocity fields. Unlike algebraic models, the RSFS model accurately captures SFS acceleration intensity and RS-SFS energy flux, even during the nonequilibrium transient, and properly partitions SFS acceleration between SFS stress divergence and SFS pressure force.

Resistant Starch: Variation among High Amylose Rice Varieties and Its Relationship with Apparent Amylose Content, Pasting Properties and Cooking Methods

USDA-ARS?s Scientific Manuscript database

Resistant starch (RS), which is not hydrolyzed in the small intestines, has proposed health benefits. We evaluated a set of 40 high amylose rice varieties for RS levels in cooked rice and approximately a 1.9-fold difference was found. The highest ones had more than two-fold greater RS concentration ...

The effect of dietary resistant starch type 2 on the microbiota and markers of gut inflammation in rural Malawi children

USDA-ARS?s Scientific Manuscript database

Resistant starch (RS) decreases intestinal inflammation in some settings. We tested the hypothesis that gut inflammation will be reduced with dietary supplementation with RS in rural Malawian children. Eighteen stunted 3-5-year-old children were supplemented with 8.5 g/day of RS type 2 for 4 weeks. ...

Hailstone classifier based on Rough Set Theory

NASA Astrophysics Data System (ADS)

Wan, Huisong; Jiang, Shuming; Wei, Zhiqiang; Li, Jian; Li, Fengjiao

2017-09-01

The Rough Set Theory was used for the construction of the hailstone classifier. Firstly, the database of the radar image feature was constructed. It included transforming the base data reflected by the Doppler radar into the bitmap format which can be seen. Then through the image processing, the color, texture, shape and other dimensional features should be extracted and saved as the characteristic database to provide data support for the follow-up work. Secondly, Through the Rough Set Theory, a machine for hailstone classifications can be built to achieve the hailstone samples’ auto-classification.

Uncertainty Modeling for Database Design using Intuitionistic and Rough Set Theory

DTIC Science & Technology

2009-01-01

Definition. An intuitionistic rough relation R is a sub- set of the set cross product P(D1)× P(D2) × · · ·× P( Dm )× Dµ.× Dv. For a specific relation, R...that aj ∈ dij for all j. The interpretation space is the cross product D1× D2 × · · ·× Dm × Dµ× Dv but is limited for a given re- lation R to the set...systems, Journal of Information Science 11 (1985), 77–87. [7] T. Beaubouef and F. Petry, Rough Querying of Crisp Data in Relational Databases, Third

Patching C2n Time Series Data Holes using Principal Component Analysis

DTIC Science & Technology

2007-01-01

characteristic local scale exponent , regardless of dilation of the length examined. THE HURST PARAMETER There are a slew of methods13 available to...fractal dimension D0, which characterises the roughness of the data, and the Hurst parameter, H , which is a measure of the long range dependence (LRD...estimate H . For simplicity, we have opted to use the well known Hurst –Mandelbrot R/S technique, which is also the most elementary. The fitting curve

Association analysis of the beta-3 adrenergic receptor Trp64Arg (rs4994) polymorphism with urate and gout.

PubMed

Fatima, Tahzeeb; Altaf, Sara; Phipps-Green, Amanda; Topless, Ruth; Flynn, Tanya J; Stamp, Lisa K; Dalbeth, Nicola; Merriman, Tony R

2016-02-01

The Arg64 allele of variant rs4994 (Trp64Arg) in the β3-adrenergic receptor gene has been associated with increased serum urate and risk of gout. Our objective was to investigate the relationship of rs4994 with serum urate and gout in New Zealand European, Māori and Pacific subjects. A total of 1730 clinically ascertained gout cases and 2145 controls were genotyped for rs4994 by Taqman(®). Māori and Pacific subjects were subdivided into Eastern Polynesian (EP) and Western Polynesian (WP) sample sets. Publicly available genotype data from the Atherosclerosis Risk in Communities Study and the Framingham Heart Study were utilized for serum urate association analysis. Multivariate logistic and linear regression adjusted for potential confounders was carried out using R version 2.15.2. No significant association of the minor Arg64 (G) allele of rs4994 with gout was found in the combined Polynesian cohorts (OR = 0.98, P = 0.88), although there was evidence, after adjustment for renal disease, for association in both the WP (OR = 0.53, P = 0.03) and the lower Polynesian ancestry EP sample sets (OR = 1.86, P = 0.05). There was no evidence for association with gout in the European sample set (OR = 1.11, P = 0.57). However, the Arg64 allele was positively associated with urate in the WP data set (β = 0.036, P = 0.004, P Corrected = 0.032). Association of the Arg64 variant with increased urate in the WP sample set was consistent with the previous literature, although the protective effect of this variant with gout in WP was inconsistent. This association provides an etiological link between metabolic syndrome components and urate homeostasis.

Dementia revealed: novel chromosome 6 locus for late-onset Alzheimer disease provides genetic evidence for folate-pathway abnormalities.

PubMed

Naj, Adam C; Beecham, Gary W; Martin, Eden R; Gallins, Paul J; Powell, Eric H; Konidari, Ioanna; Whitehead, Patrice L; Cai, Guiqing; Haroutunian, Vahram; Scott, William K; Vance, Jeffery M; Slifer, Michael A; Gwirtsman, Harry E; Gilbert, John R; Haines, Jonathan L; Buxbaum, Joseph D; Pericak-Vance, Margaret A

2010-09-23

Genome-wide association studies (GWAS) of late-onset Alzheimer disease (LOAD) have consistently observed strong evidence of association with polymorphisms in APOE. However, until recently, variants at few other loci with statistically significant associations have replicated across studies. The present study combines data on 483,399 single nucleotide polymorphisms (SNPs) from a previously reported GWAS of 492 LOAD cases and 496 controls and from an independent set of 439 LOAD cases and 608 controls to strengthen power to identify novel genetic association signals. Associations exceeding the experiment-wide significance threshold (alpha=1.03x10(-7)) were replicated in an additional 1,338 cases and 2,003 controls. As expected, these analyses unequivocally confirmed APOE's risk effect (rs2075650, P=1.9x10(-36)). Additionally, the SNP rs11754661 at 151.2 Mb of chromosome 6q25.1 in the gene MTHFD1L (which encodes the methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like protein) was significantly associated with LOAD (P=4.70x10(-8); Bonferroni-corrected P=0.022). Subsequent genotyping of SNPs in high linkage disequilibrium (r2>0.8) with rs11754661 identified statistically significant associations in multiple SNPs (rs803424, P=0.016; rs2073067, P=0.03; rs2072064, P=0.035), reducing the likelihood of association due to genotyping error. In the replication case-control set, we observed an association of rs11754661 in the same direction as the previous association at P=0.002 (P=1.90x10(-10) in combined analysis of discovery and replication sets), with associations of similar statistical significance at several adjacent SNPs (rs17349743, P=0.005; rs803422, P=0.004). In summary, we observed and replicated a novel statistically significant association in MTHFD1L, a gene involved in the tetrahydrofolate synthesis pathway. This finding is noteworthy, as MTHFD1L may play a role in the generation of methionine from homocysteine and influence homocysteine-related pathways and as levels of homocysteine are a significant risk factor for LOAD development.

Impact of Surface Roughness and Soil Texture on Mineral Dust Emission Fluxes Modeling

NASA Technical Reports Server (NTRS)

Menut, Laurent; Perez, Carlos; Haustein, Karsten; Bessagnet, Bertrand; Prigent, Catherine; Alfaro, Stephane

2013-01-01

Dust production models (DPM) used to estimate vertical fluxes of mineral dust aerosols over arid regions need accurate data on soil and surface properties. The Laboratoire Inter-Universitaire des Systemes Atmospheriques (LISA) data set was developed for Northern Africa, the Middle East, and East Asia. This regional data set was built through dedicated field campaigns and include, among others, the aerodynamic roughness length, the smooth roughness length of the erodible fraction of the surface, and the dry (undisturbed) soil size distribution. Recently, satellite-derived roughness length and high-resolution soil texture data sets at the global scale have emerged and provide the opportunity for the use of advanced schemes in global models. This paper analyzes the behavior of the ERS satellite-derived global roughness length and the State Soil Geographic data base-Food and Agriculture Organization of the United Nations (STATSGO-FAO) soil texture data set (based on wet techniques) using an advanced DPM in comparison to the LISA data set over Northern Africa and the Middle East. We explore the sensitivity of the drag partition scheme (a critical component of the DPM) and of the dust vertical fluxes (intensity and spatial patterns) to the roughness length and soil texture data sets. We also compare the use of the drag partition scheme to a widely used preferential source approach in global models. Idealized experiments with prescribed wind speeds show that the ERS and STATSGO-FAO data sets provide realistic spatial patterns of dust emission and friction velocity thresholds in the region. Finally, we evaluate a dust transport model for the period of March to July 2011 with observed aerosol optical depths from Aerosol Robotic Network sites. Results show that ERS and STATSGO-FAO provide realistic simulations in the region.

The Research of Tax Text Categorization based on Rough Set

NASA Astrophysics Data System (ADS)

Liu, Bin; Xu, Guang; Xu, Qian; Zhang, Nan

To solve the problem of effective of categorization of text data in taxation system, the paper analyses the text data and the size calculation of key issues first, then designs text categorization based on rough set model.

Correlation of bond strength with surface roughness using a new roughness measurement technique.

PubMed

Winkler, M M; Moore, B K

1994-07-01

The correlation between shear bond strength and surface roughness was investigated using new surface measurement methods. Bonding agents and associated resin composites were applied to set amalgam after mechanically roughening its surface. Surface treatments were noe (as set against glass), 80 grit, and 600 grit abrasive paper. Surface roughness (R(a) as measured parallel and perpendicular (+) to the direction of the polishing scratches and true profile length were measured. A knife-edge was applied (rate = 2.54 mm/min) at the bonding agent/amalgam interface of each sample until failure. Coefficients of determination for mean bond strength vs either roughness (R(a), of profile length were significantly higher for measurements in parallel directions than for those measurements in (+) directions. The shear bond strength to set amalgam for a PENTA-containing adhesives system (L.D. Caulk Division) was not significantly different from that of a PENTA-free adhesive (3M Dental Products Division), even though PENTA has been reported to increase bond strength to nonprecious metals. The shear bond strength of resin composite to amalgam is correlated to surface roughness when it is measured parallel to the polishing scratches. This correlation is significantly lower when surface roughness is measured in the typical manner, perpendicular to the polishing scratches.

USE OF ROUGH SETS AND SPECTRAL DATA FOR BUILDING PREDICTIVE MODELS OF REACTION RATE CONSTANTS

EPA Science Inventory

A model for predicting the log of the rate constants for alkaline hydrolysis of organic esters has been developed with the use of gas-phase min-infrared library spectra and a rule-building software system based on the mathematical theory of rough sets. A diverse set of 41 esters ...

Recurrence of Early Stage Colon Cancer Predicted by Expression Pattern of Circulating microRNAs

PubMed Central

Shivapurkar, Narayan; Weiner, Louis M.; Marshall, John L.; Madhavan, Subha; Deslattes Mays, Anne; Juhl, Hartmut; Wellstein, Anton

2014-01-01

Systemic treatment of patients with early-stage cancers attempts to eradicate occult metastatic disease to prevent recurrence and increased morbidity. However, prediction of recurrence from an analysis of the primary tumor is limited because disseminated cancer cells only represent a small subset of the primary lesion. Here we analyze the expression of circulating microRNAs (miRs) in serum obtained pre-surgically from patients with early stage colorectal cancers. Groups of five patients with and without disease recurrence were used to identify an informative panel of circulating miRs using quantitative PCR of genome-wide miR expression as well as a set of published candidate miRs. A panel of six informative miRs (miR-15a, mir-103, miR-148a, miR-320a, miR-451, miR-596) was derived from this analysis and evaluated in a separate validation set of thirty patients. Hierarchical clustering of the expression levels of these six circulating miRs and Kaplan-Meier analysis showed that the risk of disease recurrence of early stage colon cancer can be predicted by this panel of miRs that are measurable in the circulation at the time of diagnosis (P = 0.0026; Hazard Ratio 5.4; 95% CI of 1.9 to 15). PMID:24400111

Role of genetic variation in insulin-like growth factor 1 receptor on insulin resistance and arterial hypertension.

PubMed

Sookoian, Silvia; Gianotti, Tomas Fernandez; Gemma, Carolina; Burgueño, Adriana L; Pirola, Carlos J

2010-06-01

To perform a two-stage study to explore the role of gene variants in the risk of insulin resistance and arterial hypertension. The selection of variants was performed by a first stage of in-silico analysis of the original genome-wide association data sets on genes involved in metabolic syndrome components, granted by the Diabetes Genetics Initiative and the Wellcome Trust Case-Control Consortium. We started by identifying single-nucleotide polymorphisms with a cutoff for association (P < 0.05) in both data sets after the application of a computational algorithm of gene prioritization. Among the more promising variants, six single-nucleotide polymorphisms in IGF1R (rs11247362, rs10902606, rs1317459, rs11854132, rs2684761, and rs2715416) were selected for further evaluation in our population. Altogether, 1094 men, aged 34.4 +/- 8.6 years, were included in a population-based study. Genotypes of rs2684761 showed significant association with insulin resistance (as a discrete trait, odds ratio per G allele 1.27, 95% confidence interval 1.03-1.56, P = 0.026; and homeostasis model assessment-insulin resistance as a continuous trait, P = 0.01). A significant association of rs2684761 with arterial hypertension was also observed (odds ratio per G allele 1.29, 95% confidence interval 1.02-1.64, P = 0.037) after adjusting for age and homeostasis model assessment-insulin resistance. Our study suggests for the first time a putative role of IGF1R variants in individual susceptibility to metabolic syndrome-related phenotypes, in particular on the risk of having insulin resistance and arterial hypertension.

A rough set approach for determining weights of decision makers in group decision making.

PubMed

Yang, Qiang; Du, Ping-An; Wang, Yong; Liang, Bin

2017-01-01

This study aims to present a novel approach for determining the weights of decision makers (DMs) based on rough group decision in multiple attribute group decision-making (MAGDM) problems. First, we construct a rough group decision matrix from all DMs' decision matrixes on the basis of rough set theory. After that, we derive a positive ideal solution (PIS) founded on the average matrix of rough group decision, and negative ideal solutions (NISs) founded on the lower and upper limit matrixes of rough group decision. Then, we obtain the weight of each group member and priority order of alternatives by using relative closeness method, which depends on the distances from each individual group member' decision to the PIS and NISs. Through comparisons with existing methods and an on-line business manager selection example, the proposed method show that it can provide more insights into the subjectivity and vagueness of DMs' evaluations and selections.

Measuring uncertainty by extracting fuzzy rules using rough sets and extracting fuzzy rules under uncertainty and measuring definability using rough sets

NASA Technical Reports Server (NTRS)

Worm, Jeffrey A.; Culas, Donald E.

1991-01-01

Computers are not designed to handle terms where uncertainty is present. To deal with uncertainty, techniques other than classical logic must be developed. This paper examines the concepts of statistical analysis, the Dempster-Shafer theory, rough set theory, and fuzzy set theory to solve this problem. The fundamentals of these theories are combined to provide the possible optimal solution. By incorporating principles from these theories, a decision-making process may be simulated by extracting two sets of fuzzy rules: certain rules and possible rules. From these rules a corresponding measure of how much we believe these rules is constructed. From this, the idea of how much a fuzzy diagnosis is definable in terms of its fuzzy attributes is studied.

Three-dimensional structure of clumpy outflow from supercritical accretion flow onto black holes

NASA Astrophysics Data System (ADS)

Kobayashi, Hiroshi; Ohsuga, Ken; Takahashi, Hiroyuki R.; Kawashima, Tomohisa; Asahina, Yuta; Takeuchi, Shun; Mineshige, Shin

2018-03-01

We perform global three-dimensional (3D) radiation-hydrodynamic (RHD) simulations of outflow from supercritical accretion flow around a 10 M⊙ black hole. We only solve the outflow part, starting from the axisymmetric 2D simulation data in a nearly steady state but with small perturbations in a sinusoidal form being added in the azimuthal direction. The mass accretion rate onto the black hole is ˜102LE/c2 in the underlying 2D simulation data, and the outflow rate is ˜10 LE/c2 (with LE and c being the Eddington luminosity and speed of light, respectively). We first confirm the emergence of clumpy outflow, which was discovered by the 2D RHD simulations, above the photosphere located at a few hundreds of Schwarzschild radii (rS) from the central black hole. As prominent 3D features we find that the clumps have the shape of a torn sheet, rather than a cut string, and that they are rotating around the central black hole with a sub-Keplerian velocity at a distance of ˜103 rS from the center. The typical clump size is ˜30 rS or less in the radial direction, and is more elongated in the angular directions, ˜ hundreds of rS at most. The sheet separation ranges from 50 to 150 rS. We expect stochastic time variations when clumps pass across the line of the sight of a distant observer. Variation timescales are estimated to be several seconds for a black hole with mass of ten to several tens of M⊙, in rough agreement with the observations of some ultra-luminous X-ray sources.

The influence of surface roughness of deserts on the July circulation - A numerical study

NASA Technical Reports Server (NTRS)

Sud, Y. C.; Smith, W. E.

1985-01-01

The effect of the low surface roughness characteristics of deserts on atmospheric circulation in July is examined using numerical simulations with the GCM of the Goddard Laboratory for Atmospheric Science (GLAS). Identical sets of simulations were carried out with the model starting from the initial state of the atmosphere on June 15, for the years 1979 and 1980. The first simulation included a surface roughness factor of 45 cm, and the second set had a surface roughness factor of 0.02 cm for desert regions, and 45 cm for all other land. A comparative analysis of the numerical data was carried out in order to study the variations for the desert regions. It is shown that rainfall in the Sahara desert was reduced significantly in the data set with the nonuniform surface roughness factor in comparison with the other data set. The inter-tropical convergence zone (ITCZ) moved southward to about 15 degrees, which was close to its observed location at about 10 degrees N. In other deserts, the North American Great Plains, Rajputana in India, and the Central Asian desert, no similar changes were observed. Detailed contour maps of the weather conditions in the different desert regions are provided.

Priority of road maintenance management based on halda reading range on NAASRA method

NASA Astrophysics Data System (ADS)

Surbakti, M.; Doan, A.

2018-02-01

The road pavement, constantly experiencing stress-strain due to traffic load through it, can cause damage to the pavement. Therefore, early detection and repair of the damage will be able to prevent more severe damage that can develop into pavement failure. A road condition survey is one of the earliest attempts to detect the initial damage of a pavement. In this case the driving comfort is the most important part for the driver in assessing road conditions that are affected by the level of road surface roughness. To determine the level of roughness of the road, one of the methods developed is the measurement using the NAASRA method. In this method the roughness of the road is an accumulation of the average unevenness of the road, with the general setting on halda of 100 m. However, with this 100-meter setting, in some places the final value of the roughness value is too large or too small so that it will result in the priority of the road maintenance. This is what underlies roughness research by comparing halda settings at 50 m and 200 m different from the general settings above.This study uses the International Roughness Index (IRI) method in determining the level of road stability concerning driving discomfort. IRI score obtained from direct survey in field by using Roughometer-NAASRA.The final result shows that there is a significant difference between the reading of halda which is set at 100 m reading with halda set with 50 and 200 meter readings. This may lead to differences in handling priorities, which may impact on the sustainability of road network maintenance management (Sustainaible Road Management)

Using Remote Sensing Platforms to Estimate Near-Surface Soil Properties

NASA Technical Reports Server (NTRS)

Sullivan, D. G.; Shaw, J. N.; Rickman, D.; Mask, P. L.; Wersinger, J. M.; Luvall, J.

2003-01-01

Evaluation of near-surface soil properties via remote sensing (RS) could facilitate soil survey mapping, erosion prediction, fertilization regimes, and allocation of agrochemicals. The objective of this study was to evaluate the relationship between soil spectral signature and near surface soil properties in conventionally managed row crop systems. High resolution RS data were acquired over bare fields in the Coastal Plain, Appalachian Plateau, and Ridge and Valley provinces of Alabama using the Airborne Terrestrial Applications Sensor (ATLAS) multispectral scanner. Soils ranged from sandy Kandiudults to fine textured Rhodudults. Surface soil samples (0-1 cm) were collected from 163 sampling points for soil water content, soil organic carbon (SOC), particle size distribution (PSD), and citrate dithionite extractable iron (Fed) content. Surface roughness, soil water content, and crusting were also measured at sampling. Results showed RS data acquired from lands with less than 4 % surface soil water content best approximated near-surface soil properties at the Coastal Plain site where loamy sand textured surfaces were predominant. Utilizing a combination of band ratios in stepwise regression, Fed (r2 = 0.61), SOC (r2 = 0.36), sand (r2 = 0.52), and clay (r2 = 0.76) were related to RS data at the Coastal Plain site. In contrast, the more clayey Ridge and Valley soils had r-squares of 0.50, 0.36, 0.17, and 0.57. for Fed, SOC, sand and clay, respectively. Use of estimated eEmissivity did not generally improve estimates of near-surface soil attributes.

Mapping a region within the 1RS.1BL translocation in common wheat affecting grain yield and canopy water status.

PubMed

Howell, Tyson; Hale, Iago; Jankuloski, Ljupcho; Bonafede, Marcos; Gilbert, Matthew; Dubcovsky, Jorge

2014-12-01

This study identifies a small distal region of the 1RS chromosome from rye that has a positive impact on wheat yield. The translocation of the short arm of rye (Secale cereale L.) chromosome one (1RS) onto wheat (Triticum aestivum L.) chromosome 1B (1RS.1BL) is used in wheat breeding programs worldwide due to its positive effect on yield, particularly under abiotic stress. Unfortunately, this translocation is associated with poor bread-making quality. To mitigate this problem, the 1RS arm was engineered by the removal and replacement of two interstitial rye segments with wheat chromatin: a distal segment to introduce the Glu-B3/Gli-B1 loci from wheat, and a proximal segment to remove the rye Sec-1 locus. We used this engineered 1RS chromosome (henceforth 1RS(WW)) to develop and evaluate two sets of 1RS/1RS(WW) near isogenic lines (NILs). Field trials showed that standard 1RS lines had significantly higher yield and better canopy water status than the 1RS(WW) NILs in both well-watered and water-stressed environments. We intercrossed the 1RS and 1RS(WW) lines and generated two additional NILs, one carrying the distal (1RS(RW)) and the other carrying the proximal (1RS(WR)) wheat segment. Lines not carrying the distal wheat region (1RS and 1RS(WR)) showed significant improvements in grain yield and canopy water status compared to NILs carrying the distal wheat segment (1RS(WW) and 1RS(RW)), indicating that the 1RS region replaced by the distal wheat segment carries the beneficial allele(s). NILs without the distal wheat segment also showed higher carbon isotope discrimination and increased stomatal conductance, suggesting that these plants had improved access to water. The 1RS(WW), 1RS(WR) and 1RS(RW) NILs have been deposited in the National Small Grains Collection.

Polygenic risk score, genome-wide association, and gene set analyses of cognitive domain deficits in schizophrenia.

PubMed

Nakahara, Soichiro; Medland, Sarah; Turner, Jessica A; Calhoun, Vince D; Lim, Kelvin O; Mueller, Bryon A; Bustillo, Juan R; O'Leary, Daniel S; Vaidya, Jatin G; McEwen, Sarah; Voyvodic, James; Belger, Aysenil; Mathalon, Daniel H; Ford, Judith M; Guffanti, Guia; Macciardi, Fabio; Potkin, Steven G; van Erp, Theo G M

2018-06-12

This study assessed genetic contributions to six cognitive domains, identified by the MATRICS Cognitive Consensus Battery as relevant for schizophrenia, cognition-enhancing, clinical trials. Psychiatric Genomics Consortium Schizophrenia polygenic risk scores showed significant negative correlations with each cognitive domain. Genome-wide association analyses identified loci associated with attention/vigilance (rs830786 within HNF4G), verbal memory (rs67017972 near NDUFS4), and reasoning/problem solving (rs76872642 within HDAC9). Gene set analysis identified unique and shared genes across cognitive domains. These findings suggest involvement of common and unique mechanisms across cognitive domains and may contribute to the discovery of new therapeutic targets to treat cognitive deficits in schizophrenia. Copyright © 2018 Elsevier B.V. All rights reserved.

Gene selection for tumor classification using neighborhood rough sets and entropy measures.

PubMed

Chen, Yumin; Zhang, Zunjun; Zheng, Jianzhong; Ma, Ying; Xue, Yu

2017-03-01

With the development of bioinformatics, tumor classification from gene expression data becomes an important useful technology for cancer diagnosis. Since a gene expression data often contains thousands of genes and a small number of samples, gene selection from gene expression data becomes a key step for tumor classification. Attribute reduction of rough sets has been successfully applied to gene selection field, as it has the characters of data driving and requiring no additional information. However, traditional rough set method deals with discrete data only. As for the gene expression data containing real-value or noisy data, they are usually employed by a discrete preprocessing, which may result in poor classification accuracy. In this paper, we propose a novel gene selection method based on the neighborhood rough set model, which has the ability of dealing with real-value data whilst maintaining the original gene classification information. Moreover, this paper addresses an entropy measure under the frame of neighborhood rough sets for tackling the uncertainty and noisy of gene expression data. The utilization of this measure can bring about a discovery of compact gene subsets. Finally, a gene selection algorithm is designed based on neighborhood granules and the entropy measure. Some experiments on two gene expression data show that the proposed gene selection is an effective method for improving the accuracy of tumor classification. Copyright © 2017 Elsevier Inc. All rights reserved.

Maternal and offspring genetic variants of AKR1C3 and the risk of childhood leukemia

PubMed Central

Liu, Chen-yu; Hsu, Yi-Hsiang; Pan, Pi-Chen; Wu, Ming-Tsang; Ho, Chi-Kung; Su, Li; Xu, Xin; Li, Yi; Christiani, David C.

2008-01-01

The aldo-keto reductase 1C3 (AKR1C3) gene located on chromosome 10p15-p14, a regulator of myeloid cell proliferation and differentiation, represents an important candidate gene for studying human carcinogenesis. In a prospectively enrolled population-based case–control study of Han Chinese conducted in Kaohsiung in southern Taiwan, a total of 114 leukemia cases and 221 controls <20 years old were recruited between November 1997 and December 2005. The present study set out to evaluate the association between childhood leukemia and both maternal and offspring's genotypes. To do so, we conducted a systematic assessment of common single-nucleotide polymorphisms (SNPs) at the 5′ flanking 10 kb to 3′ UTR of AKR1C3 gene. Gln5His and three tagSNPs (rs2245191, rs10508293 and rs3209896) and one multimarker (rs2245191, rs10508293 and rs3209896) were selected with average 90% coverage of untagged SNPs by using the HapMap II data set. Odds ratios and 95% confidence intervals were adjusted for age and gender. After correcting for multiple comparisons, we observed that risk of developing childhood leukemia is significantly associated with rs10508293 polymorphism on intron 4 of the AKR1C3 gene in both offspring alone and in the combined maternal and offspring genotypes (nominal P < 0.0001, permutation P < 0.005). The maternal methylenetetrahydrofolate reductase A1298C polymorphism was found to be an effect modifier of the maternal intron 4 polymorphism of the AKR1C3 gene (rs10508293) and the childhood leukemia risk. In conclusion, this study suggests that AKR1C3 polymorphisms may be important predictive markers for childhood leukemia susceptibility. PMID:18339682

GAB2 as an Alzheimer Disease Susceptibility Gene

PubMed Central

Schjeide, Brit-Maren M.; Hooli, Basavaraj; Parkinson, Michele; Hogan, Meghan F.; DiVito, Jason; Mullin, Kristina; Blacker, Deborah; Tanzi, Rudolph E.; Bertram, Lars

2009-01-01

Background Genomewide association (GWA) studies have recently implicated 4 novel Alzheimer disease (AD) susceptibility loci (GAB2, GOLM1, and 2 uncharacterized loci to date on chromosomes 9p and 15q). To our knowledge, these findings have not been independently replicated. Objective To assess these GWA findings in 4 large data sets of families affected by AD. Design Follow-up of genetic association findings in previous studies. Setting Academic research. Participants More than 4000 DNA samples from almost 1300 families affected with AD. Main Outcome Measures Genetic association analysis testing of 4 GWA signals (rs7101429 [GAB2], rs7019241 [GOLM1], rs10519262 [chromosome 15q], and rs9886784 [chromosome 9p]) using family-based methods. Results In the combined analyses, only rs7101429 in GAB2 yielded significant evidence of association with the same allele as in the original GWA study (P = .002). The results are in agreement with recent meta-analyses of this and other GAB2 polymorphisms suggesting approximately a 30% decrease in risk for AD among carriers of the minor alleles. None of the other 3 tested loci showed consistent evidence for association with AD across the investigated data sets. Conclusions GAB2 contains genetic variants that may lead to a modest change in the risk for AD. Despite these promising results, more data from independent samples are needed to better evaluate the potential contribution of GAB2 to AD risk in the general population. PMID:19204163

Standard Sizes for Rough-Dimension Exports to Europe and Japan

Treesearch

Philip A. Araman

1987-01-01

In this article, European and Japanese standard-sized rough dimension products are described, and their apparent sizes are listed. One set of proposed standard sizes of rough dimension that could be manufactured in the United States for these markets is presented. Also, the benefits of the production and sale of standard sizes of export rough dimension are highlighted...

RS-predictor: a new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4.

PubMed

Zaretzki, Jed; Bergeron, Charles; Rydberg, Patrik; Huang, Tao-wei; Bennett, Kristin P; Breneman, Curt M

2011-07-25

This article describes RegioSelectivity-Predictor (RS-Predictor), a new in silico method for generating predictive models of P450-mediated metabolism for drug-like compounds. Within this method, potential sites of metabolism (SOMs) are represented as "metabolophores": A concept that describes the hierarchical combination of topological and quantum chemical descriptors needed to represent the reactivity of potential metabolic reaction sites. RS-Predictor modeling involves the use of metabolophore descriptors together with multiple-instance ranking (MIRank) to generate an optimized descriptor weight vector that encodes regioselectivity trends across all cases in a training set. The resulting pathway-independent (O-dealkylation vs N-oxidation vs Csp(3) hydroxylation, etc.), isozyme-specific regioselectivity model may be used to predict potential metabolic liabilities. In the present work, cross-validated RS-Predictor models were generated for a set of 394 substrates of CYP 3A4 as a proof-of-principle for the method. Rank aggregation was then employed to merge independently generated predictions for each substrate into a single consensus prediction. The resulting consensus RS-Predictor models were shown to reliably identify at least one observed site of metabolism in the top two rank-positions on 78% of the substrates. Comparisons between RS-Predictor and previously described regioselectivity prediction methods reveal new insights into how in silico metabolite prediction methods should be compared.

Association of five SNPs with human hair colour in the Polish population.

PubMed

Siewierska-Górska, A; Sitek, A; Żądzińska, E; Bartosz, G; Strapagiel, D

2017-03-01

Twenty-two variants (single nucleotide polymorphisms - SNPs) of the genes involved in hair pigmentation (OCA2, HERC2, MC1R, SLC24A5, SLC45A2, TPCN2, TYR, TYRP1) were genotyped in a group of 186 Polish participants, representing a range of hair colours (45 red, 64 blond, 77 dark). A genotype-phenotype association analysis was performed. Using z-statistics we identified three variants highly associated with different hair colour categories (rs12913832:A>G in HERC2, rs1805007:T>C and rs1805008:C>T in MC1R). Two variants: rs1800401:C>T in OCA2 and rs16891982:C>G in SLC45A2 showed a high probability of a relation with hair colour, although that probability did not exceed the threshold of statistical significance after applying the Bonferroni correction. We created and validated mathematical logistic regression models in order to test the usefulness of the sets of polymorphisms for hair colour prediction in the Polish population. We subjected four models to stratified cross-validation. The first model consisted of three polymorphisms that proved to be important in the associative analysis. The second model included, apart from the mentioned polymorphisms, additionally rs16891982:C>G in SLC45A. The third model included, apart from the variants relevant in the associating analysis, rs1800401:C>T in OCA. The fourth model consisted of the set of polymorphisms from the first model supplemented with rs16891982:C>G in SLC45A and rs1800401:C>T in OCA. The validation of our models has shown that the inclusion of rs16891982:C>G in SLC45A and rs1800401:C>T in OCA increases the prediction of red hair in comparison with the algorithm including only rs12913832:A>G in HERC2, rs1805007:T>C and rs1805008:C>T in MC1R. The model consisting of all the five above-mentioned genetic variants has shown good prediction accuracies, expressed by the area under the curve (AUC) of the receiver operating characteristics: 0.84 for the red-haired, 0.82 for the dark-haired and 0.71 for the blond-haired. A genotype-phenotype association analysis brought results similar to those in other studies and confirmed the role of rs16891982:C>G, rs12913832:A>G, rs1805007:T>C and rs1805008:C>T in hair colour determination in the Polish population. Our study demonstrated for the first time the possibility of a share of the rs1800401:C>T SNP in the OCA2 gene in hair colour determination. Including this single nucleotide polymorphism in the actual hair colour predicting models would improve their predictive accuracy. Copyright © 2017 Elsevier GmbH. All rights reserved.

Capture-ELISA for serum IgM antibody to respiratory syncytial virus.

PubMed Central

Cevenini, R.; Donati, M.; Bertini, S.; Moroni, A.; Sambri, V.

1986-01-01

A four-component solid-phase capture enzyme immunoassay was set up to test for serum IgM antibody to respiratory syncytial (RS) virus and was compared with immunofluorescence assay (IFA). A total of 128 young children with acute respiratory infections were studied. Thirty-six were shown to be RS virus-positive by the detection of RS virus in nasopharyngeal secretions and 92 were RS virus-negative. A serum specimen was collected after admission to the hospital (days 0-4) and a further specimen was obtained during days 10-14. Out of 36 RS virus-positive patients, 28 (77.7%) were found to be positive for IgM by both capture-ELISA and IFA. Out of 92 RS virus-negative patients 5 (5.4%) were IgM-positive. Four false-positive results were obtained by IFA due to the presence of rheumatoid factor. The capture-ELISA was shown to be a reliable technique in detecting specific IgM antibody to RS virus. PMID:3540115

Spectral Analysis and Experimental Modeling of Ice Accretion Roughness

NASA Technical Reports Server (NTRS)

Orr, D. J.; Breuer, K. S.; Torres, B. E.; Hansman, R. J., Jr.

1996-01-01

A self-consistent scheme for relating wind tunnel ice accretion roughness to the resulting enhancement of heat transfer is described. First, a spectral technique of quantitative analysis of early ice roughness images is reviewed. The image processing scheme uses a spectral estimation technique (SET) which extracts physically descriptive parameters by comparing scan lines from the experimentally-obtained accretion images to a prescribed test function. Analysis using this technique for both streamwise and spanwise directions of data from the NASA Lewis Icing Research Tunnel (IRT) are presented. An experimental technique is then presented for constructing physical roughness models suitable for wind tunnel testing that match the SET parameters extracted from the IRT images. The icing castings and modeled roughness are tested for enhancement of boundary layer heat transfer using infrared techniques in a "dry" wind tunnel.

Parallel group independent component analysis for massive fMRI data sets.

PubMed

Chen, Shaojie; Huang, Lei; Qiu, Huitong; Nebel, Mary Beth; Mostofsky, Stewart H; Pekar, James J; Lindquist, Martin A; Eloyan, Ani; Caffo, Brian S

2017-01-01

Independent component analysis (ICA) is widely used in the field of functional neuroimaging to decompose data into spatio-temporal patterns of co-activation. In particular, ICA has found wide usage in the analysis of resting state fMRI (rs-fMRI) data. Recently, a number of large-scale data sets have become publicly available that consist of rs-fMRI scans from thousands of subjects. As a result, efficient ICA algorithms that scale well to the increased number of subjects are required. To address this problem, we propose a two-stage likelihood-based algorithm for performing group ICA, which we denote Parallel Group Independent Component Analysis (PGICA). By utilizing the sequential nature of the algorithm and parallel computing techniques, we are able to efficiently analyze data sets from large numbers of subjects. We illustrate the efficacy of PGICA, which has been implemented in R and is freely available through the Comprehensive R Archive Network, through simulation studies and application to rs-fMRI data from two large multi-subject data sets, consisting of 301 and 779 subjects respectively.

Initial performance of the radio occultation experiment in the Venus orbiter mission Akatsuki

NASA Astrophysics Data System (ADS)

Imamura, Takeshi; Ando, Hiroki; Tellmann, Silvia; Pätzold, Martin; Häusler, Bernd; Yamazaki, Atsushi; Sato, Takao M.; Noguchi, Katsuyuki; Futaana, Yoshifumi; Oschlisniok, Janusz; Limaye, Sanjay; Choudhary, R. K.; Murata, Yasuhiro; Takeuchi, Hiroshi; Hirose, Chikako; Ichikawa, Tsutomu; Toda, Tomoaki; Tomiki, Atsushi; Abe, Takumi; Yamamoto, Zen-ichi; Noda, Hirotomo; Iwata, Takahiro; Murakami, Shin-ya; Satoh, Takehiko; Fukuhara, Tetsuya; Ogohara, Kazunori; Sugiyama, Ko-ichiro; Kashimura, Hiroki; Ohtsuki, Shoko; Takagi, Seiko; Yamamoto, Yukio; Hirata, Naru; Hashimoto, George L.; Yamada, Manabu; Suzuki, Makoto; Ishii, Nobuaki; Hayashiyama, Tomoko; Lee, Yeon Joo; Nakamura, Masato

2017-10-01

After the arrival of Akatsuki spacecraft of Japan Aerospace Exploration Agency at Venus in December 2015, the radio occultation experiment, termed RS (Radio Science), obtained 19 vertical profiles of the Venusian atmosphere by April 2017. An onboard ultra-stable oscillator is used to generate stable X-band downlink signals needed for the experiment. The quantities to be retrieved are the atmospheric pressure, the temperature, the sulfuric acid vapor mixing ratio, and the electron density. Temperature profiles were successfully obtained down to 38 km altitude and show distinct atmospheric structures depending on the altitude. The overall structure is close to the previous observations, suggesting a remarkable stability of the thermal structure. Local time-dependent features are seen within and above the clouds, which is located around 48-70 km altitude. The H2SO4 vapor density roughly follows the saturation curve at cloud heights, suggesting equilibrium with cloud particles. The ionospheric electron density profiles are also successfully retrieved, showing distinct local time dependence. Akatsuki RS mainly probes the low and middle latitude regions thanks to the near-equatorial orbit in contrast to the previous radio occultation experiments using polar orbiters. Studies based on combined analyses of RS and optical imaging data are ongoing.[Figure not available: see fulltext.

A rough set approach for determining weights of decision makers in group decision making

PubMed Central

Yang, Qiang; Du, Ping-an; Wang, Yong; Liang, Bin

2017-01-01

This study aims to present a novel approach for determining the weights of decision makers (DMs) based on rough group decision in multiple attribute group decision-making (MAGDM) problems. First, we construct a rough group decision matrix from all DMs’ decision matrixes on the basis of rough set theory. After that, we derive a positive ideal solution (PIS) founded on the average matrix of rough group decision, and negative ideal solutions (NISs) founded on the lower and upper limit matrixes of rough group decision. Then, we obtain the weight of each group member and priority order of alternatives by using relative closeness method, which depends on the distances from each individual group member’ decision to the PIS and NISs. Through comparisons with existing methods and an on-line business manager selection example, the proposed method show that it can provide more insights into the subjectivity and vagueness of DMs’ evaluations and selections. PMID:28234974

Heat Transfer Measurements on Surfaces with Natural Ice Castings and Modeled Roughness

NASA Technical Reports Server (NTRS)

Breuer, Kenneth S.; Torres, Benjamin E.; Orr, D. J.; Hansman, R. John

1997-01-01

An experimental method is described to measure and compare the convective heat transfer coefficient of natural and simulated ice accretion roughness and to provide a rational means for determining accretion-related enhanced heat transfer coefficients. The natural ice accretion roughness was a sample casting made from accretions at the NASA Lewis Icing Research Tunnel (IRT). One of these castings was modeled using a Spectral Estimation Technique (SET) to produce three roughness elements patterns that simulate the actual accretion. All four samples were tested in a flat-plate boundary layer at angle of attack in a "dry" wind tunnel test. The convective heat transfer coefficient was measured using infrared thermography. It is shown that, dispite some problems in the current data set, the method does show considerable promise in determining roughness-induced heat transfer coefficients, and that, in addition to the roughness height and spacing in the flow direction, the concentration and spacing of elements in the spanwise direction are important parameters.

Do gene polymorphism in IL-1β, TNF-α and IL-6 influence therapeutic response in patients with drug refractory epilepsy?

PubMed

Tiwari, Prabhakar; Dwivedi, Rekha; Mansoori, Nasim; Alam, Rizwan; Chauhan, Ugam Kumari; Tripathi, Manjari; Mukhopadhyay, Asok Kumar

2012-09-01

Pro-inflammatory cytokines may play an important pathophysiological role in patients with epilepsy. To understand the role of genes encoding pro-inflammatory cytokines in epilepsy, this study aimed to evaluate the polymorphisms of the promoter regions of IL-1β-511C>T (rs16944), TNF-α-308G>A (rs1800629) and IL-6-174G>C (rs1800795) genes and to look into the interaction between these genes in influencing seizure susceptibility, seizure frequency and response to therapy. The comparative frequency of polymorphism was determined in rs16944, rs1800629 and rs1800795 using PCR-RFLP in a group of 120 persons with epilepsy (PWE) and 110 ethnically matched healthy subjects of comparable age and sex in the North Indian population. Alleles and genotypes of rs16944, rs1800629 and rs1800795 were not found to influence the odds ratio of having susceptibility to epilepsy. Also gene-gene interaction of possible nine combinations of these genes did not show any positive association with epilepsy. The genotype and allelic frequency of rs1800795 showed a significant association (p<0.05) in seizure frequency (number of seizures/6-months) and drug refractory epilepsy. However, the genotype and allelic frequency of rs16944 and rs1800629 were not found to have such effect. This study demonstrates that the rs16944, rs1800629 and rs1800795 polymorphism does not act as a strong susceptibility factor for epilepsy in North Indian population. The genotypic association of rs1800795 with seizure frequency and drug-refractory epilepsy raises the issue that a specific set of polymorphic genes can influence seizures and therapeutic response in epilepsy. Copyright © 2012 Elsevier B.V. All rights reserved.

CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility

PubMed Central

Raj, Towfique; Ryan, Katie J.; Replogle, Joseph M.; Chibnik, Lori B.; Rosenkrantz, Laura; Tang, Anna; Rothamel, Katie; Stranger, Barbara E.; Bennett, David A.; Evans, Denis A.; De Jager, Philip L.; Bradshaw, Elizabeth M.

2014-01-01

We previously demonstrated that the Alzheimer's disease (AD) associated risk allele, rs3865444C, results in a higher surface density of CD33 on monocytes. Here, we find alternative splicing of exon 2 to be the primary mechanism of the genetically driven differential expression of CD33 protein. We report that the risk allele, rs3865444C, is associated with greater cell surface expression of CD33 in both subjects of European and African–American ancestry and that there is a single haplotype influencing CD33 surface expression. A meta-analysis of the two populations narrowed the number of significant SNPs in high linkage disequilibrium (LD) (r2 > 0.8) with rs3865444 to just five putative causal variants associated with increased protein expression. Using gene expression data from flow-sorted CD14+CD16− monocytes from 398 healthy subjects of three populations, we show that the rs3865444C risk allele is strongly associated with greater expression of CD33 exon 2 (pMETA = 2.36 × 10−60). Western blotting confirms increased protein expression of the full-length CD33 isoform containing exon 2 relative to the rs3865444C allele (P < 0.0001). Of the variants in strong LD with rs3865444, rs12459419, which is located in a putative SRSF2 splice site of exon 2, is the most likely candidate to mediate the altered alternative splicing of CD33's Immunoglobulin V-set domain 2 and ultimately influence AD susceptibility. PMID:24381305

The SNP rs6500843 in 16p13.3 is associated with survival specifically among chemotherapy-treated breast cancer patients.

PubMed

Fagerholm, Rainer; Schmidt, Marjanka K; Khan, Sofia; Rafiq, Sajjad; Tapper, William; Aittomäki, Kristiina; Greco, Dario; Heikkinen, Tuomas; Muranen, Taru A; Fasching, Peter A; Janni, Wolfgang; Weinshilboum, Richard; Loehberg, Christian R; Hopper, John L; Southey, Melissa C; Keeman, Renske; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Chenevix-Trench, Georgia; Lambrechts, Diether; Wildiers, Hans; Chang-Claude, Jenny; Seibold, Petra; Couch, Fergus J; Olson, Janet E; Andrulis, Irene L; Knight, Julia A; García-Closas, Montserrat; Figueroa, Jonine; Hooning, Maartje J; Jager, Agnes; Shah, Mitul; Perkins, Barbara J; Luben, Robert; Hamann, Ute; Kabisch, Maria; Czene, Kamila; Hall, Per; Easton, Douglas F; Pharoah, Paul D P; Liu, Jianjun; Eccles, Diana; Blomqvist, Carl; Nevanlinna, Heli

2015-04-10

We have utilized a two-stage study design to search for SNPs associated with the survival of breast cancer patients treated with adjuvant chemotherapy. Our initial GWS data set consisted of 805 Finnish breast cancer cases (360 treated with adjuvant chemotherapy). The top 39 SNPs from this stage were analyzed in three independent data sets: iCOGS (n=6720 chemotherapy-treated cases), SUCCESS-A (n=3596), and POSH (n=518). Two SNPs were successfully validated: rs6500843 (any chemotherapy; per-allele HR 1.16, 95% C.I. 1.08-1.26, p=0.0001, p(adjusted)=0.0091), and rs11155012 (anthracycline therapy; per-allele HR 1.21, 95% C.I. 1.08-1.35, p=0.0010, p(adjusted)=0.0270). The SNP rs6500843 was found to specifically interact with adjuvant chemotherapy, independently of standard prognostic markers (p(interaction)=0.0009), with the rs6500843-GG genotype corresponding to the highest hazard among chemotherapy-treated cases (HR 1.47, 95% C.I. 1.20-1.80). Upon trans-eQTL analysis of public microarray data, the rs6500843 locus was found to associate with the expression of a group of genes involved in cell cycle control, notably AURKA, the expression of which also exhibited differential prognostic value between chemotherapy-treated and untreated cases in our analysis of microarray data. Based on previously published information, we propose that the eQTL genes may be connected to the rs6500843 locus via a RBFOX1-FOXM1 -mediated regulatory pathway.

Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts

PubMed Central

Kang, Wenjing; Bang-Berthelsen, Claus Heiner; Holm, Anja; Houben, Anna J.S.; Müller, Anne Holt; Thymann, Thomas; Pociot, Flemming; Estivill, Xavier; Friedländer, Marc R.

2017-01-01

miRNAs are small 22-nucleotide RNAs that can post-transcriptionally regulate gene expression. It has been proposed that dietary plant miRNAs can enter the human bloodstream and regulate host transcripts; however, these findings have been widely disputed. We here conduct the first comprehensive meta-study in the field, surveying the presence and abundances of cross-species miRNAs (xenomiRs) in 824 sequencing data sets from various human tissues and body fluids. We find that xenomiRs are commonly present in tissues (17%) and body fluids (69%); however, the abundances are low, comprising 0.001% of host human miRNA counts. Further, we do not detect a significant enrichment of xenomiRs in sequencing data originating from tissues and body fluids that are exposed to dietary intake (such as liver). Likewise, there is no significant depletion of xenomiRs in tissues and body fluids that are relatively separated from the main bloodstream (such as brain and cerebro-spinal fluids). Interestingly, the majority (81%) of body fluid xenomiRs stem from rodents, which are a rare human dietary contribution but common laboratory animals. Body fluid samples from the same studies tend to group together when clustered by xenomiR compositions, suggesting technical batch effects. Last, we performed carefully designed and controlled animal feeding studies, in which we detected no transfer of plant miRNAs into rat blood, or bovine milk sequences into piglet blood. In summary, our comprehensive computational and experimental results indicate that xenomiRs originate from technical artifacts rather than dietary intake. PMID:28062594

Role of redoximiRs in fibrogenesis.

PubMed

Fierro-Fernández, Marta; Miguel, Verónica; Lamas, Santiago

2016-04-01

Fibrosis can be defined as an excessive accumulation of extracellular matrix (ECM) components, ultimately leading to stiffness, scarring and devitalized tissue. MicroRNAs (miRNAs) are short, 19-25 nucleotides (nt), non-coding RNAs involved in the post-transcriptional regulation of gene expression. Recently, miRNAs have also emerged as powerful regulators of fibrotic processes and have been termed "fibromiRs". Oxidative stress represents a self-perpetuating mechanism in fibrogenesis. MiRNAs can also influence the expression of genes responsible for the generation of reactive oxygen species (ROS) and antioxidant defence and are termed "redoximiRs". Here, we review the current knowledge of mechanisms by which "redoximiRs" regulate fibrogenesis. This new set of miRNAs may be called "redoxifibromiRs". Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Performance review of the ROMI-RIP rough mill simulator

Treesearch

Edward Thomas; Urs Buehlmann

2003-01-01

The USDA Forest Service's ROMI-RIP version 2.0 (RR2) rough mill rip-first simulation program was validated in a recent study. The validation study found that when RR2 was set to search for optimum yield without considering actual rough mill strip solutions, it produced yields that were as much as 7 percent higher (71.1% versus 64.0%) than the actual rough mill....

Work in Progress: The Seven Rs of Team Building

ERIC Educational Resources Information Center

Brunelli, Jean; Schneider, Elaine Fogel

2004-01-01

This article argues that supportive teams--including professionals, paraprofessionals, and parents--can teach staff members how to identify and implement best practices in early intervention settings. The authors describe "the seven Rs of team building" distilled from their many years of team building and maintenance: 1) Reading cues; 2) Regular…

The peculiar architectural framework of tRNASec is fully recognized by yeast AspRS.

PubMed Central

Rudinger-Thirion, J; Giegé, R

1999-01-01

The wild-type transcript of Escherichia coli tRNASec, characterized by a peculiar core architecture and a large variable region, was shown to be aspartylatable by yeast AspRS. Similar activities were found for tRNASec mutants with methionine, leucine, and tryptophan anticodons. The charging efficiency of these molecules was found comparable to that of a minihelix derived from tRNAAsp and is accounted for by the presence of the discriminator residue G73, which is a major aspartate identity determinant. Introducing the aspartate identity elements from the anticodon loop (G34, U35, C36, C38) into tRNASec transforms this molecule into an aspartate acceptor with kinetic properties identical to tRNAAsp. Expression of the aspartate identity set in tRNASec is independent of the size of its variable region. The functional study was completed by footprinting experiments with four different nucleases as structural probes. Protection patterns by AspRS of transplanted tRNASec and tRNAAsp were found similar. They are modified, particularly in the anticodon loop, upon changing the aspartate anticodon into that of methionine. Altogether, it appears that recognition of a tRNA by AspRS is more governed by the presence of the aspartate identity set than by the structural framework that carries this set. PMID:10199566

The emerging role of the FKBP5 gene polymorphisms in vulnerability-stress model of schizophrenia: further evidence from a Serbian population.

PubMed

Mihaljevic, Marina; Zeljic, Katarina; Soldatovic, Ivan; Andric, Sanja; Mirjanic, Tijana; Richards, Alexander; Mantripragada, Kiran; Pekmezovic, Tatjana; Novakovic, Ivana; Maric, Nadja P

2017-09-01

Increased reactivity to stress is observed in patients with schizophrenia spectrum disorders and their healthy siblings in comparison with the general population. Additionally, higher levels of neuroticism, as a proposed psychological measure of stress sensitivity, increase the risk of schizophrenia. HPA axis dysregulation is one of the possible mechanisms related to the vulnerability-stress model of schizophrenia, and recent studies revealed a possible role of the functional genetic variants of FK506-binding protein 51 (FKBP5) gene which modulate activity of HPA axis. The purpose of the present study was to investigate impact of FKBP5 on schizophrenia in Serbian patients and to explore relationship between genetic variants and neuroticism by using the case-sibling-control design. In 158 subjects, we measured psychotic experiences, childhood trauma and neuroticism. Nine single-nucleotide polymorphisms (rs9295158, rs3800373, rs9740080, rs737054, rs6926133, rs9380529, rs9394314, rs2766533 and rs12200498) were genotyped. The genetic influence was modeled using logistic regression, and the relationship between genetic variants and neuroticism was assessed by linear mixed model. Our results revealed genetic main effect of FKBP5 risk alleles (A allele of rs9296158 and T allele of rs3800373) and AGTC "risk" haplotype combination (rs9296158, rs3800373, rs9470080 and rs737054, respectively) on schizophrenia, particularly when childhood trauma was set as a confounding factor. We confirmed strong relationship between neuroticism and psychotic experiences in patients and siblings and further showed relationship between higher levels of neuroticism and FKBP5 risk variants suggesting potential link between biological and psychosocial risk factors. Our data support previous findings that trauma exposure shapes FKBP5 impact on schizophrenia.

The role of gene polymorphisms in endometriosis

PubMed Central

Matalliotakis, Michail; Zervou, Maria I.; Matalliotaki, Charoula; Rahmioglu, Nilufer; Koumantakis, George; Kalogiannidis, Ioannis; Prapas, Ioannis; Zondervan, Krina; Spandidos, Demetrios A.; Matalliotakis, Ioannis; Goulielmos, George N.

2017-01-01

Endometriosis is a benign gynecologic disorder, affecting up to 10% of women, characterized by the presence of functional endometrial tissue at ectopic positions generally within the peritoneum. It is a heritable condition influenced by multiple genetic and environmental factors, with an overall heritability estimated at approximately 50%. In this study, we investigated whether single nucleotide polymorphisms (SNPs) rs7521902, rs10859871 and rs11031006, mapping to WNT4, VEZT and FSHB genetic loci, respectively, are associated with risk for endometriosis in a Greek population. This study included 166 women with histologically confirmed endometriosis diagnosed through surgery and 150 normal controls. Genotyping of the rs7521902, rs10859871 and rs11031006 SNPs was performed with Taqman primer/probe sets. A significant association was detected with the AC genotype of rs7521902 (WNT4) in patients with stage III and IV disease only. Evidence for association with endometriosis was also found for the AC genotype of the rs10859871 of VEZT. Notably, a significant difference in the distribution of the AG genotype and the minor allele A of FSHB rs11031006 SNP was found between the endometriosis patients and controls. We found a genetic association between rs11031006 (FSHB) SNP and endometriosis. WNT4 and VEZT genes constitute the most consistently associated genes with endometriosis. In the present study, an association of rs7521902 (WNT4) and rs10859871 (VEZT) was confirmed in women with endometriosis at the genotypic but not the allelic level. PMID:28901453

Association of CASP9, CASP10 gene polymorphisms and tea drinking with colorectal cancer risk in the Han Chinese population.

PubMed

Liu, He; Jiang, Xia; Zhang, Ming-wu; Pan, Yi-feng; Yu, Yun-xian; Zhang, Shan-chun; Ma, Xin-yuan; Li, Qi-long; Chen, Kun

2013-01-01

The initiators caspase-9 (CASP9) and caspase-10 (CASP10) are two key controllers of apoptosis and play important roles in carcinogenesis. This study aims to explore the association between CASPs gene polymorphisms and colorectal cancer (CRC) susceptibility in a population-based study. A two-stage designed population-based case-control study was carried out, including a testing set with 300 cases and 296 controls and a validation set with 206 cases and 845 controls. A total of eight tag selected single nucleotide polymorphisms (SNPs) in CASP9 and CASP10 were chosen based on HapMap and the National Center of Biotechnology Information (NCBI) datasets and genotyped by restriction fragment length polymorphism (RFLP) assay. Multivariate logistic regression models were applied to evaluate the association of SNPs with CRC risk. In the first stage, from eight tag SNPs, three polymorphisms rs4646077 (odds ratio (OR)(AA+AG): 0.654, 95% confidence interval (CI): 0.406-1.055; P=0.082), rs4233532 (OR(CC): 1.667, 95% CI: 0.967-2.876; OR(CT): 1.435, 95% CI: 0.998-2.063; P=0.077), and rs2881930 (OR(CC): 0.263, 95% CI: 0.095-0.728, P=0.036) showed possible association with CRC risk. However, none of the three SNPs, rs4646077 (OR(AA+AG): 1.233, 95% CI: 0.903-1.683), rs4233532 (OR(CC): 0.892, 95% CI: 0.640-1.243; OR(CT): 1.134, 95% CI: 0.897-1.433), and rs2881930 (OR(CC): 1.096, 95% CI: 0.620-1.938; OR(CT): 1.009, 95% CI: 0.801-1.271), remained significant with CRC risk in the validation set, even after stratification for different tumor locations (colon or rectum). In addition, never tea drinking was associated with a significantly increased risk of CRC in testing set together with validation set (OR: 1.755, 95% CI: 1.319-2.334). Our results found that polymorphisms of CASP9 and CASP10 genes may not contribute to CRC risk in Chinese population and thereby the large-scale case-control studies might be in consideration. In addition, tea drinking was a protective factor for CRC.

Association of CASP9, CASP10 gene polymorphisms and tea drinking with colorectal cancer risk in the Han Chinese population*

PubMed Central

Liu, He; Jiang, Xia; Zhang, Ming-wu; Pan, Yi-feng; Yu, Yun-xian; Zhang, Shan-chun; Ma, Xin-yuan; Li, Qi-long; Chen, Kun

2013-01-01

The initiators caspase-9 (CASP9) and caspase-10 (CASP10) are two key controllers of apoptosis and play important roles in carcinogenesis. This study aims to explore the association between CASPs gene polymorphisms and colorectal cancer (CRC) susceptibility in a population-based study. A two-stage designed population-based case-control study was carried out, including a testing set with 300 cases and 296 controls and a validation set with 206 cases and 845 controls. A total of eight tag selected single nucleotide polymorphisms (SNPs) in CASP9 and CASP10 were chosen based on HapMap and the National Center of Biotechnology Information (NCBI) datasets and genotyped by restriction fragment length polymorphism (RFLP) assay. Multivariate logistic regression models were applied to evaluate the association of SNPs with CRC risk. In the first stage, from eight tag SNPs, three polymorphisms rs4646077 (odds ratio (OR)AA+AG: 0.654, 95% confidence interval (CI): 0.406–1.055; P=0.082), rs4233532 (ORCC: 1.667, 95% CI: 0.967–2.876; ORCT: 1.435, 95% CI: 0.998–2.063; P=0.077), and rs2881930 (ORCC: 0.263, 95% CI: 0.095–0.728, P=0.036) showed possible association with CRC risk. However, none of the three SNPs, rs4646077 (ORAA+AG: 1.233, 95% CI: 0.903–1.683), rs4233532 (ORCC: 0.892, 95% CI: 0.640–1.243; ORCT: 1.134, 95% CI: 0.897–1.433), and rs2881930 (ORCC: 1.096, 95% CI: 0.620–1.938; ORCT: 1.009, 95% CI: 0.801–1.271), remained significant with CRC risk in the validation set, even after stratification for different tumor locations (colon or rectum). In addition, never tea drinking was associated with a significantly increased risk of CRC in testing set together with validation set (OR: 1.755, 95% CI: 1.319–2.334). Our results found that polymorphisms of CASP9 and CASP10 genes may not contribute to CRC risk in Chinese population and thereby the large-scale case-control studies might be in consideration. In addition, tea drinking was a protective factor for CRC. PMID:23303631

A common variant association study reveals novel susceptibility loci for low HDL-cholesterol levels in ethnic Arabs.

PubMed

Wakil, S M; Ram, R; Muiya, N P; Andres, E; Mazhar, N; Hagos, S; Alshahid, M; Meyer, B F; Morahan, G; Dzimiri, N

2016-12-01

The genetic susceptibility to acquiring low high density lipoprotein-cholesterol (LHDLC) levels is not completely elucidated yet. In this study, we performed a common variant association study for harboring this trait in ethnic Arabs. We employed the Affymetrix high-density Axiom Genome-Wide ASI Array (Asian population) providing a coverage of 598,000 single nucleotide variations (SNPs) to genotype 5495 individuals in a two-phase study involving discovery and validation sets of experiments. The rs1800775 [1.31 (1.22-1.42); p = 3.41E-12] in the CETP gene and rs359027 [1.26 (1.16-1.36); p = 2.55E-08] in the LMCD1 gene were significantly associated with LHDLC levels. Furthermore, rs3104435 [1.26 (1.15-1.38); p = 1.19E-06] at the MATN1 locus, rs9835344 [1.16 (1.08-1.26); p = 8.75E-06] in the CNTN6 gene, rs1559997 [1.3 (1.14-1.47); p = 9.48E-06] in the SDS gene and rs1670273 [1.2 (1.1-1.31); p = 4.81E-06] in the DMN/SYNM gene exhibited suggestive association with the disorder. Seven other variants including rs1147169 in the PLCL1 gene, rs10248618 in the DNAH11, rs476155 in the GLIS3, rs7024300 in the ABCA1, intergenic rs10836699, rs11603691 in P2RX3 and rs750134 in CORO1C gene exhibited borderline protective properties. Validation and joint meta-analysis resulted in rs1800775, rs3104435 and rs359027 retaining their predisposing properties, while rs10836699 and rs11603691 showed protective properties. Our data show several predisposing variants across the genome for LHDLC levels in ethnic Arabs. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Robotic Spectroscopy at the Dark Sky Observatory

NASA Astrophysics Data System (ADS)

Rosenberg, Daniel E.; Gray, Richard O.; Mashburn, Jonathan; Swenson, Aaron W.; McGahee, Courtney E.; Briley, Michael M.

2018-06-01

Spectroscopic observations using the classification-resolution Gray-Miller spectrograph attached to the Dark Sky Observatory 32 inch telescope (Appalachian State University, North Carolina) have been automated with a robotic script called the “Robotic Spectroscopist” (RS). RS runs autonomously during the night and controls all operations related to spectroscopic observing. At the heart of RS are a number of algorithms that first select and center the target star in the field of an imaging camera and then on the spectrograph slit. RS monitors the observatory weather station, and suspends operations and closes the dome when weather conditions warrant, and can reopen and resume observations when the weather improves. RS selects targets from a list using a queue-observing protocol based on observer-assigned priorities, but also uses target-selection criteria based on weather conditions, especially seeing. At the end of the night RS transfers the data files to the main campus, where they are reduced with an automatic pipeline. Our experience has shown that RS is more efficient and consistent than a human observer, and produces data sets that are ideal for automatic reduction. RS should be adaptable for use at other similar observatories, and so we are making the code freely available to the astronomical community.

Is remitting seronegative symmetrical synovitis with pitting edema (RS3PE) a subset of rheumatoid arthritis?

PubMed

Yao, Qingping; Su, Xiangqian; Altman, Roy D

2010-08-01

To contrast and compare the spectrum of remitting seronegative symmetrical synovitis with pitting edema (RS3PE) with rheumatoid arthritis (RA) using an illustrative case. The relevant English literature of RS3PE was searched using the keywords "RS3PE" alone and in combination with terms such as neoplasia and rheumatic disease. Original and review articles were reviewed and the clinical setting was exemplified with a case report. RS3PE initially was reported to represent a form of RA. However, RS3PE has clinical features that are different from both early- and late-onset RA, such as lack of bony erosions and rheumatoid factor. RS3PE is thought to involve vascular endothelial growth factor, suggesting an infectious etiology, generally has an excellent prognosis, and is associated with neoplasia not commonly seen in RA, and the RA associated human leukocyte antigen (HLA) DRB1 genotype is absent. Based on the clinical, laboratory, suspected infectious etiology, genetic differences, and types of associated malignancies, RS3PE appears to be a distinct entity rather than a subset of RA. Copyright 2010 Elsevier Inc. All rights reserved.

Analysis of energy fluxes and vegetation-atmosphere parameters in irrigated and natural ecosystems of semi-arid Brazil

NASA Astrophysics Data System (ADS)

Teixeira, A. H. de Castro; Bastiaanssen, W. G. M.; Ahmad, M. D.; Moura, M. S. B.; Bos, M. G.

2008-11-01

SummaryKnowledge on evapotranspiration is essential in quantifying water use depletion and to allocate scarce water resources to competing uses. Despite that an extensive literature describes the theoretical mechanisms of turbulent water vapour transport above and within crop canopies fewer studies have examined land surface parameters within composite landscapes of irrigated crops and semi-arid natural vegetation. Aiming to improve parameterizations of the radiation and energy balance in irrigated crops and natural vegetation, micro-climatic measurements were carried out on irrigated land (vineyards and mango orchard) and natural vegetation (caatinga) in the semi-arid zone of the São Francisco River basin (Brazil) from 2002 to 2005. The fractions of 24 h incident solar radiation available for net radiation were 46%, 55%, 51% and 53%, for wine grape, table grape, mango orchard and caatinga, respectively. Daily evaporative fractions of the net available energy used as latent heat flux ( λE) were 0.80, 0.88, 0.75 and 0.33 respectively. The daylight values of bulk surface resistances ( rs) averaged 128 s m -1, 73 s m -1, 133 s m -1 and 1940 s m -1 for wine grape, table grape, mango orchard and caatinga, respectively. Simplified parameterizations on roughness and evaporation resistances were performed. It could be concluded that net radiation can be estimated by means of a linear expression with incident global solar radiation depending on the type of vegetation. The variability of aerodynamic resistance ( ra) could be mainly explained by the friction velocity ( u ∗) which on turn depends on the surface roughness length for momentum transport ( z 0m). The experimental data showed that for sparse canopies z 0m being 9% of the mean vegetation height is a doable operational rule for the semi-arid region of São Francisco River basin. The seasonal values of rs for irrigated crops were highly correlated with water vapour pressure deficit. The availability of analytical methods to assess ra and rs makes the one-step Penman-Monteith equation suitable for the computation of actual evapotranspiration and water productivity analyses.

Religious/Spiritual Coping in Adolescents with Sickle Cell Disease

PubMed Central

Cotton, Sian; Grossoehme, Daniel; Rosenthal, Susan L.; McGrady, Meghan E.; Roberts, Yvonne Humenay; Hines, Janelle; Yi, Michael S.; Tsevat, Joel

2009-01-01

Religious/spiritual (R/S) coping has been associated with health outcomes in chronically ill adults; however, little is known about how adolescents use R/S to cope with a chronic illness such as sickle cell disease (SCD). Using a mixed method approach (quantitative surveys and qualitative interviews), we examined R/S coping, spirituality, and health-related quality of life in 48 adolescents with SCD and 42 parents of adolescents with SCD. Adolescents reported high rates of religious attendance and belief in God, prayed often, and had high levels of spirituality (e.g., finding meaning/peace in their lives and deriving comfort from faith). Thirty-five percent of adolescents reported praying once or more a day for symptom management. The most common positive R/S coping strategies used by adolescents were: “Asked forgiveness for my sins” (73% of surveys) and “Sought God’s love and care” (73% of surveys). Most parents used R/S coping strategies to cope with their child’s illness. R/S coping was not significantly associated with HRQOL (p = NS). R/S coping, particularly prayer, was relevant for adolescents with SCD and their parents. Future studies should assess adolescents’ preferences for discussing R/S in the medical setting and whether R/S coping is related to HRQOL in larger samples. PMID:19415008

In the Context of Multiple Intelligences Theory, Intelligent Data Analysis of Learning Styles Was Based on Rough Set Theory

ERIC Educational Resources Information Center

Narli, Serkan; Ozgen, Kemal; Alkan, Huseyin

2011-01-01

The present study aims to identify the relationship between individuals' multiple intelligence areas and their learning styles with mathematical clarity using the concept of rough sets which is used in areas such as artificial intelligence, data reduction, discovery of dependencies, prediction of data significance, and generating decision…

A Mathematical Approach in Evaluating Biotechnology Attitude Scale: Rough Set Data Analysis

ERIC Educational Resources Information Center

Narli, Serkan; Sinan, Olcay

2011-01-01

Individuals' thoughts and attitudes towards biotechnology have been investigated in many countries. A Likert-type scale is the most commonly used scale to measure attitude. However, the weak side of a likert-type scale is that different responses may produce the same score. The Rough set method has been regarded to address this shortcoming. A…

Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts.

PubMed

Kang, Wenjing; Bang-Berthelsen, Claus Heiner; Holm, Anja; Houben, Anna J S; Müller, Anne Holt; Thymann, Thomas; Pociot, Flemming; Estivill, Xavier; Friedländer, Marc R

2017-04-01

miRNAs are small 22-nucleotide RNAs that can post-transcriptionally regulate gene expression. It has been proposed that dietary plant miRNAs can enter the human bloodstream and regulate host transcripts; however, these findings have been widely disputed. We here conduct the first comprehensive meta-study in the field, surveying the presence and abundances of cross-species miRNAs (xenomiRs) in 824 sequencing data sets from various human tissues and body fluids. We find that xenomiRs are commonly present in tissues (17%) and body fluids (69%); however, the abundances are low, comprising 0.001% of host human miRNA counts. Further, we do not detect a significant enrichment of xenomiRs in sequencing data originating from tissues and body fluids that are exposed to dietary intake (such as liver). Likewise, there is no significant depletion of xenomiRs in tissues and body fluids that are relatively separated from the main bloodstream (such as brain and cerebro-spinal fluids). Interestingly, the majority (81%) of body fluid xenomiRs stem from rodents, which are a rare human dietary contribution but common laboratory animals. Body fluid samples from the same studies tend to group together when clustered by xenomiR compositions, suggesting technical batch effects. Last, we performed carefully designed and controlled animal feeding studies, in which we detected no transfer of plant miRNAs into rat blood, or bovine milk sequences into piglet blood. In summary, our comprehensive computational and experimental results indicate that xenomiRs originate from technical artifacts rather than dietary intake. © 2017 Kang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

High-intensity sprint fatigue does not alter constant-submaximal velocity running mechanics and spring-mass behavior.

PubMed

Morin, Jean-Benoit; Tomazin, Katja; Samozino, Pierre; Edouard, Pascal; Millet, Guillaume Y

2012-04-01

We investigated the changes in constant velocity spring-mass behavior after high intensity sprint fatigue in order to better interpret the results recently reported after ultra-long distance (ULD) exercises. Our hypothesis was that after repeated sprints (RS), subjects may likely experience losses of force such as after ULD, but the necessity to modify their running pattern to attenuate the overall impact at each step (such as after ULD) may not be present. Eleven male subjects performed four sets of five 6-s sprints with 24-s recovery between sprints and 3 min between sets, on a sprint treadmill and on a bicycle ergometer. For each session, their running mechanics and spring-mass characteristics were measured at 10 and 20 km h(-1) on an instrumented treadmill before and after RS. Two-way (period and velocity) ANOVAs showed that high-intensity fatigue did not induce any change in the constant velocity running pattern at low or high velocity, after both running and cycling RS, despite significant decreases (P < 0.001) in maximal power (-27.1 ± 8.2% after running RS and -15.4 ± 11.5 % after cycling RS) and knee extensors maximal voluntary force (-18.8 ± 6.7 % after running RS and -15.0 ± 7.6 % after cycling RS). These results bring indirect support to the hypothesis put forward in recent ULD studies that the changes in running mechanics observed after ULD are likely not related to the decrease in strength capabilities, but rather to the necessity for subjects to adopt a protective running pattern.

Simultaneous Genotyping of the rs4762 and rs699 Polymorphisms in Angiotensinogen Gene and Correlation with Iranian CAD Patients with Novel Hexa-primer ARMS-PCR

PubMed Central

KHATAMI, Mehri; HEIDARI, Mohammad Mehdi; HADADZADEH, Mehdi; SCHEIBER-MOJDEHKAR, Barbara; BITARAF SANI, Morteza; HOUSHMAND, Massoud

2017-01-01

Background: A significant role of Renin-angiotensin system (RAS) genetic variants in the pathogenesis of essential hypertension and cardiovascular diseases has been proved. This study aimed to develop a new, fast and cheap method for the simultaneous detection of two missense single nucleotide polymorphisms (T207M or rs4762 and M268T orrs699) of angiotensinogen (AGT) in single-step Multiplex Hexa-Primer Amplification Refractory Mutation System - polymerase chain reaction (H-ARMS-PCR). Methods: In this case-control study, 148 patients with coronary artery disease (CAD) and 135 controls were included. The patients were referred to cardiac centers in Afshar Hospital (Yazd, Iran) from 2012 to 2015. Two sets of inner primer (for each SNP) and one set outer primer pairs were designed for genotyping of rs4762 and rs699 in single tube H-ARMS-PCR. Direct sequencing of all samples was also performed to assess the accuracy of this method. DNA sequencing method validated the results of single tube H-ARMS-PCR. Results: We found full accordance for genotype adscription by sequencing method. The frequency of the AGT T521 and C702 alleles was significantly higher in CAD patients than in the control group (OR: 0.551, 95% CI: 0.359–0.846, P=0.008 and OR: 0.629, 95% CI: 0.422–0.936, P=0.028, respectively). Conclusion: This is the first work describing a rapid, low-cost, high-throughput simultaneous detection of rs4762 and rs699 polymorphisms in AGT gene, used in large clinical studies. PMID:28828324

Rough Play: One of the Most Challenging Behaviors

ERIC Educational Resources Information Center

Carlson, Frances M.

2011-01-01

Most children engage in rough play, and research demonstrates its physical, social, emotional, and cognitive value. Early childhood education settings have the responsibility to provide children with what best serves their developmental needs. One of the best ways teachers can support rough play is by modeling it for children. When adults model…

Defect inspection in hot slab surface: multi-source CCD imaging based fuzzy-rough sets method

NASA Astrophysics Data System (ADS)

Zhao, Liming; Zhang, Yi; Xu, Xiaodong; Xiao, Hong; Huang, Chao

2016-09-01

To provide an accurate surface defects inspection method and make the automation of robust image region of interests(ROI) delineation strategy a reality in production line, a multi-source CCD imaging based fuzzy-rough sets method is proposed for hot slab surface quality assessment. The applicability of the presented method and the devised system are mainly tied to the surface quality inspection for strip, billet and slab surface etcetera. In this work we take into account the complementary advantages in two common machine vision (MV) systems(line array CCD traditional scanning imaging (LS-imaging) and area array CCD laser three-dimensional (3D) scanning imaging (AL-imaging)), and through establishing the model of fuzzy-rough sets in the detection system the seeds for relative fuzzy connectedness(RFC) delineation for ROI can placed adaptively, which introduces the upper and lower approximation sets for RIO definition, and by which the boundary region can be delineated by RFC region competitive classification mechanism. For the first time, a Multi-source CCD imaging based fuzzy-rough sets strategy is attempted for CC-slab surface defects inspection that allows an automatic way of AI algorithms and powerful ROI delineation strategies to be applied to the MV inspection field.

Surface roughness measurement in the submicrometer range using laser scattering

NASA Astrophysics Data System (ADS)

Wang, S. H.; Quan, Chenggen; Tay, C. J.; Shang, H. M.

2000-06-01

A technique for measuring surface roughness in the submicrometer range is developed. The principle of the method is based on laser scattering from a rough surface. A telecentric optical setup that uses a laser diode as a light source is used to record the light field scattered from the surface of a rough object. The light intensity distribution of the scattered band, which is correlated to the surface roughness, is recorded by a linear photodiode array and analyzed using a single-chip microcomputer. Several sets of test surfaces prepared by different machining processes are measured and a method for the evaluation of surface roughness is proposed.

An intelligent knowledge mining model for kidney cancer using rough set theory.

PubMed

Durai, M A Saleem; Acharjya, D P; Kannan, A; Iyengar, N Ch Sriman Narayana

2012-01-01

Medical diagnosis processes vary in the degree to which they attempt to deal with different complicating aspects of diagnosis such as relative importance of symptoms, varied symptom pattern and the relation between diseases themselves. Rough set approach has two major advantages over the other methods. First, it can handle different types of data such as categorical, numerical etc. Secondly, it does not make any assumption like probability distribution function in stochastic modeling or membership grade function in fuzzy set theory. It involves pattern recognition through logical computational rules rather than approximating them through smooth mathematical functional forms. In this paper we use rough set theory as a data mining tool to derive useful patterns and rules for kidney cancer faulty diagnosis. In particular, the historical data of twenty five research hospitals and medical college is used for validation and the results show the practical viability of the proposed approach.

A bionic system with Fenton reaction and bacteria as a model for bioprocessing lignocellulosic biomass.

PubMed

Zhang, Kejing; Si, Mengying; Liu, Dan; Zhuo, Shengnan; Liu, Mingren; Liu, Hui; Yan, Xu; Shi, Yan

2018-01-01

The recalcitrance of lignocellulosic biomass offers a series of challenges for biochemical processing into biofuels and bio-products. For the first time, we address these challenges with a biomimetic system via a mild yet rapid Fenton reaction and lignocellulose-degrading bacterial strain Cupriavidus basilensis B-8 (here after B-8) to pretreat the rice straw (RS) by mimicking the natural fungal invasion process. Here, we also elaborated the mechanism through conducting a systematic study of physicochemical changes before and after pretreatment. After synergistic Fenton and B-8 pretreatment, the reducing sugar yield was increased by 15.6-56.6% over Fenton pretreatment alone and 2.7-5.2 times over untreated RS (98 mg g -1 ). Morphological analysis revealed that pretreatment changed the surface morphology of the RS, and the increase in roughness and hydrophilic sites enhanced lignocellulose bioavailability. Chemical components analyses showed that B-8 removed part of the lignin and hemicellulose which caused the cellulose content to increase. In addition, the important chemical modifications also occurred in lignin, 2D NMR analysis of the lignin in residues indicated that the Fenton pretreatment caused partial depolymerization of lignin mainly by cleaving the β- O -4 linkages and by demethoxylation to remove the syringyl (S) and guaiacyl (G) units. B-8 could depolymerize amount of the G units by cleaving the β-5 linkages that interconnect the lignin subunits. A biomimetic system with a biochemical Fenton reaction and lignocellulose-degrading bacteria was confirmed to be able for the pretreatment of RS to enhance enzymatic hydrolysis under mild conditions. The high digestibility was attributed to the destruction of the lignin structure, partial hydrolysis of the hemicellulose and partial surface oxidation of the cellulose. The mechanism of synergistic Fenton and B-8 pretreatment was also explored to understand the change in the RS and the bacterial effects on enzymatic hydrolysis. Furthermore, this biomimetic system offers new insights into the pretreatment of lignocellulosic biomass.

IRF4 rs12203592 functional variant and melanoma survival.

PubMed

Potrony, Miriam; Rebollo-Morell, Aida; Giménez-Xavier, Pol; Zimmer, Lisa; Puig-Butille, Joan Anton; Tell-Marti, Gemma; Sucker, Antje; Badenas, Celia; Carrera, Cristina; Malvehy, Josep; Schadendorf, Dirk; Puig, Susana

2017-04-15

Inherited genetic factors may modulate clinical outcome in melanoma. Some low-to-medium risk genes in melanoma susceptibility play a role in melanoma outcome. Our aim was to assess the role of the functional IRF4 SNP rs12203592 in melanoma prognosis in two independent sets (Barcelona, N = 493 and Essen, N = 438). Genotype association analyses showed that the IRF4 rs12203592 T allele increased the risk of dying from melanoma in both sets (Barcelona: odds ratio [OR] = 6.53, 95% CI 1.38-30.87, Adj p = 0.032; Essen: OR = 1.68, 95% CI 1.04-2.72, Adj p = 0.035). Survival analyses only showed significance for the Barcelona set (hazard ratio = 4.58, 95% CI 1.11-18.92, Adj p = 0.036). This SNP was also associated with tumour localization, increasing the risk of developing melanoma in head or neck (OR = 1.79, 95% CI 1.07-2.98, Adj p = 0.032) and protecting from developing melanoma in the trunk (OR = 0.59, 95% CI 0.41-0.85, Adj p = 0.004). These findings suggest for the first time that IRF4 rs12203592 plays a role in the modulation of melanoma outcome and confirms its contribution to the localization of the primary tumour. © 2017 UICC.

An evidence-based approach to globally assess the covariate-dependent effect of the MTHFR single nucleotide polymorphism rs1801133 on blood homocysteine: a systematic review and meta-analysis.

PubMed

Jin, Huifeng; Cheng, Haojie; Chen, Wei; Sheng, Xiaoming; Levy, Mark A; Brown, Mark J; Tian, Junqiang

2018-05-01

The single nucleotide polymorphism of the gene 5,10-methylenetetrahydrofolate reductase (MTHFR) C677T (or rs1801133) is the most established genetic factor that increases plasma total homocysteine (tHcy) and consequently results in hyperhomocysteinemia. Yet, given the limited penetrance of this genetic variant, it is necessary to individually predict the risk of hyperhomocysteinemia for an rs1801133 carrier. We hypothesized that variability in this genetic risk is largely due to the presence of factors (covariates) that serve as effect modifiers, confounders, or both, such as folic acid (FA) intake, and aimed to assess this risk in the complex context of these covariates. We systematically extracted from published studies the data on tHcy, rs1801133, and any previously reported rs1801133 covariates. The resulting metadata set was first used to analyze the covariates' modifying effect by meta-regression and other statistical means. Subsequently, we controlled for this modifying effect by genotype-stratifying tHcy data and analyzed the variability in the risk resulting from the confounding of covariates. The data set contains data on 36 rs1801133 covariates that were collected from 114,799 participants and 256 qualified studies, among which 6 covariates (sex, age, race, FA intake, smoking, and alcohol consumption) are the most frequently informed and therefore included for statistical analysis. The effect of rs1801133 on tHcy exhibits significant variability that can be attributed to effect modification as well as confounding by these covariates. Via statistical modeling, we predicted the covariate-dependent risk of tHcy elevation and hyperhomocysteinemia in a systematic manner. We showed an evidence-based approach that globally assesses the covariate-dependent effect of rs1801133 on tHcy. The results should assist clinicians in interpreting the rs1801133 data from genetic testing for their patients. Such information is also important for the public, who increasingly receive genetic data from commercial services without interpretation of its clinical relevance. This study was registered at Research Registry with the registration number reviewregistry328.

Indian Biotech Bazaar: a swot analysis.

PubMed

Kumar, Abhishek

2007-05-01

Biotechnology is a life science-based technique especially used in agriculture, medicine and food sciences. It is generally defined as the manipulation in organisms to generate products for the welfare of the world. Biotechnology combines disciplines such as genetics, biochemistry, microbiology, and cell biology along with information technology, chemical engineering, robotics etc. It includes basic industries such as food processing, tissue culture, plant development and other sophisticated ones such as recombinant therapeutics and diagnostics. Biotechnology, globally recognized as a rapidly emerging and far-reaching technology, is aptly described as the "technology of hope" for its promise of food, health and environmental sustainability. In India, biotechnology employs more than 10 000 people and generates roughly US$ 500 million in revenue annually. The biotechnology market has increased its sales from Rs. 50 billion in 1997 to Rs.70 billion in 2000, and is expected to cross Rs. 240 billion by the year 2010. In India, the human health biotech products account for 60% of the total market; agribiotech and veterinary 25%, medical devices, contract research and development (R&D), reagents and supplies constitute the remaining 15% Moreover, to facilitate foreign investment, capital and government policies are being revised. Other important industries include industrial enzyme manufacture, bioinformatics, and medical devices. Biotechnology has had limited appeal so far on our capital markets, and we have less then a dozen biotech companies listed on the public markets.

The combination of memantine and galantamine improves cognition in rats: The synergistic role of the α7 nicotinic acetylcholine and NMDA receptors.

PubMed

Nikiforuk, Agnieszka; Potasiewicz, Agnieszka; Kos, Tomasz; Popik, Piotr

2016-10-15

The combination of memantine and acetylcholinesterase inhibitors (AChEIs) is used as a therapeutic strategy to improve cognition in Alzheimer's disease. Among AChEIs, galantamine, which is also a positive allosteric modulator (PAM) of nicotinic acetylcholine receptors (nAChRs), including α7-nAChRs, may be particularly beneficial. The α7-nAChR is involved in interactions between the cholinergic and glutamatergic systems. In the present study, we investigated the potential role of α7-nAChRs in the pro-cognitive effects of this drug combination. To this aim, cognitive performance in rats was assessed using the attentional set shifting task (ASST) and novel object recognition task (NORT). Co-administration of inactive doses of memantine with galantamine facilitated the rats' set-shifting performance and reversed delay-induced deficits in object recognition. These effects were blocked by the α7-nAChR antagonist methyllycaconitine, suggesting that the observed cognitive enhancement is α7-nAChR dependent. Moreover, combined administration of memantine with inactive doses of selective α7-nAChRs PAMs, CCMI and PNU-120596, also improved ASST and NORT performance in a methyllycaconitine-dependent manner. Stimulation of α7-nAChRs may underlie the pro-cognitive effects of combining memantine and galantamine. Our results suggest that memantine, when given with enhancers of α7-nAChRs, may represent an effective strategy for cognitive improvement. Copyright © 2016 Elsevier B.V. All rights reserved.

GAB2 as an Alzheimer disease susceptibility gene: follow-up of genomewide association results.

PubMed

Schjeide, Brit-Maren M; Hooli, Basavaraj; Parkinson, Michele; Hogan, Meghan F; DiVito, Jason; Mullin, Kristina; Blacker, Deborah; Tanzi, Rudolph E; Bertram, Lars

2009-02-01

Genomewide association (GWA) studies have recently implicated 4 novel Alzheimer disease (AD) susceptibility loci (GAB2, GOLM1, and 2 uncharacterized loci to date on chromosomes 9p and 15q). To our knowledge, these findings have not been independently replicated. To assess these GWA findings in 4 large data sets of families affected by AD. Follow-up of genetic association findings in previous studies. Academic research. More than 4000 DNA samples from almost 1300 families affected with AD. Genetic association analysis testing of 4 GWA signals (rs7101429 [GAB2], rs7019241 [GOLM1], rs10519262 [chromosome 15q], and rs9886784 [chromosome 9p]) using family-based methods. In the combined analyses, only rs7101429 in GAB2 yielded significant evidence of association with the same allele as in the original GWA study (P =.002). The results are in agreement with recent meta-analyses of this and other GAB2 polymorphisms suggesting approximately a 30% decrease in risk for AD among carriers of the minor alleles. None of the other 3 tested loci showed consistent evidence for association with AD across the investigated data sets. GAB2 contains genetic variants that may lead to a modest change in the risk for AD. Despite these promising results, more data from independent samples are needed to better evaluate the potential contribution of GAB2 to AD risk in the general population.

Measuring Skew in Average Surface Roughness as a Function of Surface Preparation

NASA Technical Reports Server (NTRS)

Stahl, Mark

2015-01-01

Characterizing surface roughness is important for predicting optical performance. Better measurement of surface roughness reduces polishing time, saves money and allows the science requirements to be better defined. This study characterized statistics of average surface roughness as a function of polishing time. Average surface roughness was measured at 81 locations using a Zygo white light interferometer at regular intervals during the polishing process. Each data set was fit to a normal and Largest Extreme Value (LEV) distribution; then tested for goodness of fit. We show that the skew in the average data changes as a function of polishing time.

Association of SLC11A1 with tuberculosis interactions with NOS2A and TLR2 in African-Americans and Caucasians

PubMed Central

Velez, D.R.; Hulme, W.F.; Myers, J.L.; Stryjewski, M.E.; Abbate, E.; Estevan, R.; Patillo, S.G.; Gilbert, J.R.; Hamilton, C.D.; Scott, W.K.

2010-01-01

SETTING Host defense factors may influence the development of active tuberculosis (TB). OBJECTIVE To test variants in solute carrier family 11A, member 1 (SLC11A1), for an association with TB. METHODS A mixed case-control study of TB cases, relatives or close contact controls, consisting of 474 African-Americans (243 families) and 381 Caucasians (192 families), examined 13 SLC11A1 polymorphisms for association with pulmonary TB using generalized estimating equations adjusting for age and gender. RESULTS Two associations were observed in Caucasians (rs3731863, P = 0.03, and rs17221959, P = 0.04) and one in African-Americans (rs3731865, P = 0.05). Multilocus analyses between polymorphisms in SLC11A1 and 11 TB candidate genes detected interactions between SLC11A1 and inducible nitric oxide synthase (NOS2A) in Caucasians (rs3731863 [SLC11A1] × rs8073782 [NOS2A], P = 0.009; rs3731863 [SLC11A1] × rs17722851 [NOS2A], P = 0.007) and toll-like receptor 2 (TLR2) in African-Americans (rs3731865 [SLC11A1] x rs1816702, P = 0.005). CONCLUSIONS No association was detected with 5′(GT)n promoter polymorphism previously associated with lower SLC11A1 expression, rs17235409 (D543N), or rs17235416 (3′ TGTG insertion/deletion polymorphism). SLC11A1 polymorphism rs3731865 was associated with TB in African-Americans, consistent with previous findings in West Africans. These results suggest that variants in SLC11A1 increase susceptibility to pulmonary TB and interact with other variants that differ by race. PMID:19723394

Surface roughness of composite resin veneer after application of herbal and non-herbal toothpaste

NASA Astrophysics Data System (ADS)

Nuraini, S.; Herda, E.; Irawan, B.

2017-08-01

The aim of this study was to find out the surface roughness of composite resin veneer after brushing. In this study, 24 specimens of composite resin veneer are divided into three subgroups: brushed without toothpaste, brushed with non-herbal toothpaste, and brushed with herbal toothpaste. Brushing was performed for one set of 5,000 strokes and continued for a second set of 5,000 strokes. Roughness of composite resin veneer was determined using a Surface Roughness Tester. The results were statistically analyzed using Kruskal-Wallis nonparametric test and Post Hoc Mann-Whitney. The results indicate that the highest difference among the Ra values occurred within the subgroup that was brushed with the herbal toothpaste. In conclusion, the herbal toothpaste produced a rougher surface on composite resin veneer compared to non-herbal toothpaste.

Characterization of Ice Roughness From Simulated Icing Encounters

NASA Technical Reports Server (NTRS)

Anderson, David N.; Shin, Jaiwon

1997-01-01

Detailed measurements of the size of roughness elements on ice accreted on models in the NASA Lewis Icing Research Tunnel (IRT) were made in a previous study. Only limited data from that study have been published, but included were the roughness element height, diameter and spacing. In the present study, the height and spacing data were found to correlate with the element diameter, and the diameter was found to be a function primarily of the non-dimensional parameters freezing fraction and accumulation parameter. The width of the smooth zone which forms at the leading edge of the model was found to decrease with increasing accumulation parameter. Although preliminary, the success of these correlations suggests that it may be possible to develop simple relationships between ice roughness and icing conditions for use in ice-accretion-prediction codes. These codes now require an ice-roughness estimate to determine convective heat transfer. Studies using a 7.6-cm-diameter cylinder and a 53.3-cm-chord NACA 0012 airfoil were also performed in which a 1/2-min icing spray at an initial set of conditions was followed by a 9-1/2-min spray at a second set of conditions. The resulting ice shape was compared with that from a full 10-min spray at the second set of conditions. The initial ice accumulation appeared to have no effect on the final ice shape. From this result, it would appear the accreting ice is affected very little by the initial roughness or shape features.

Lack of replication of four candidate SNPs implicated in human male fertility traits: a large-scale population-based study.

PubMed

Sato, Youichi; Tajima, Atsushi; Tsunematsu, Kouki; Nozawa, Shiari; Yoshiike, Miki; Koh, Eitetsue; Kanaya, Jiro; Namiki, Mikio; Matsumiya, Kiyomi; Tsujimura, Akira; Komatsu, Kiyoshi; Itoh, Naoki; Eguchi, Jiro; Imoto, Issei; Yamauchi, Aiko; Iwamoto, Teruaki

2015-06-01

Are the four candidate loci (rs7867029, rs12870438, rs7174015 and rs724078) for human male fertility traits, identified in a genome-wide association study (GWAS) of a Hutterite population in the USA, associated with semen quality traits in a Japanese population? The four single nucleotide polymorphisms (SNPs) rs7867029, rs12870438, rs7174015 and rs724078 have no association with semen parameters in a meta-analysis of two Japanese male cohorts. Four (rs7867029, rs12870438, rs7174015 and rs724078) of the SNPs associated with family size or birth rate in the GWAS of a Hutterite population in the USA were associated with semen parameters in ethnically diverse men from Chicago, USA. This is a replication study in a total of 2015 Japanese subjects, including 791 fertile men and 1224 young men from the general population. We performed a replication study in two cohorts to assess whether the SNPs rs7867029, rs12870438, rs7174015 and rs724078 are associated with sperm concentration, semen volume, total sperm numbers, total motile sperm numbers or sperm motility. The rs12870438 SNP was detected by restriction fragment length polymorphism PCR while rs7174015, rs724078 and rs7867029 SNPs were genotyped using TaqMan probes. This study indicated that none of the four SNPs rs7867029, rs12870438, rs7174015 and rs724078 displayed a significant association with semen parameters in the meta-analysis of two Japanese male cohorts. Only four SNPs identified in the Hutterite GWAS were examined for associations with semen quality traits in a Japanese population. In addition, the linkage disequilibrium structures around the testing markers were different between ethnic groups. Locus mapping studies using a set of tagging SNPs across the loci will be necessary in populations with larger sample sizes in order to understand the contribution of specific genes to semen quality. This study was supported in part by the Ministry of Health and Welfare of Japan (1013201) (to T.I.), Grant-in-Aids for Scientific Research (C) (23510242) (to A.Ta.) from the Japan Society for the Promotion of Science, the European Union (BMH4-CT96-0314) (to T.I.), and the Takeda Science Foundation (to A.Ta.). None of the authors has any competing interests to declare. © The Author 2015. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Can We Make Definite Categorization of Student Attitudes? A Rough Set Approach to Investigate Students' Implicit Attitudinal Typologies toward Living Things

ERIC Educational Resources Information Center

Narli, Serkan; Yorek, Nurettin; Sahin, Mehmet; Usak, Muhammet

2010-01-01

This study investigates the possibility of analyzing educational data using the theory of rough sets which is mostly employed in the fields of data analysis and data mining. Data were collected using an open-ended conceptual understanding test of the living things administered to first-year high school students. The responses of randomly selected…

Pioneering better science through the 3Rs: an introduction to the national centre for the replacement, refinement, and reduction of animals in research (NC3Rs).

PubMed

Burden, Natalie; Chapman, Kathryn; Sewell, Fiona; Robinson, Vicky

2015-03-01

The National Centre for the Replacement, Refinement, and Reduction of Animals in Research (NC3Rs) is an independent scientific organization that is based in the United Kingdom, which was set up by the government to lead the discovery and application of new technologies and approaches that minimize the use of animals in research and improve animal welfare. The NC3Rs uses a range of strategies to improve and advance science through application of the 3Rs. These include funding basic research, open innovation (CRACK IT), and programs run by inhouse scientists. We present several case studies from the NC3Rs portfolio, featuring asthma research, the use of nonhuman primates in monoclonal antibody development, and CRACK IT. Finally, we anticipate the future, as we use our experience to move into new research fields and expand toward international collaboration. Here we highlight how equipping scientists with relevant and emerging 3Rs tools can help overcome the challenges and limitations of the use of animals in research to the benefit of the whole bioscience community.

Pioneering Better Science through the 3Rs: An Introduction to the National Centre for the Replacement, Refinement, and Reduction of Animals in Research (NC3Rs)

PubMed Central

Burden, Natalie; Chapman, Kathryn; Sewell, Fiona; Robinson, Vicky

2015-01-01

The National Centre for the Replacement, Refinement, and Reduction of Animals in Research (NC3Rs) is an independent scientific organization that is based in the United Kingdom, which was set up by the government to lead the discovery and application of new technologies and approaches that minimize the use of animals in research and improve animal welfare. The NC3Rs uses a range of strategies to improve and advance science through application of the 3Rs. These include funding basic research, open innovation (CRACK IT), and programs run by inhouse scientists. We present several case studies from the NC3Rs portfolio, featuring asthma research, the use of nonhuman primates in monoclonal antibody development, and CRACK IT. Finally, we anticipate the future, as we use our experience to move into new research fields and expand toward international collaboration. Here we highlight how equipping scientists with relevant and emerging 3Rs tools can help overcome the challenges and limitations of the use of animals in research to the benefit of the whole bioscience community. PMID:25836967

Extreme variability among mammalian V1R gene families.

PubMed

Young, Janet M; Massa, Hillary F; Hsu, Li; Trask, Barbara J

2010-01-01

We report an evolutionary analysis of the V1R gene family across 37 mammalian genomes. V1Rs comprise one of three chemosensory receptor families expressed in the vomeronasal organ, and contribute to pheromone detection. We first demonstrate that Trace Archive data can be used effectively to determine V1R family sizes and to obtain sequences of most V1R family members. Analyses of V1R sequences from trace data and genome assemblies show that species-specific expansions previously observed in only eight species were prevalent throughout mammalian evolution, resulting in "semi-private" V1R repertoires for most mammals. The largest families are found in mouse and platypus, whose V1R repertoires have been published previously, followed by mouse lemur and rabbit (approximately 215 and approximately 160 intact V1Rs, respectively). In contrast, two bat species and dolphin possess no functional V1Rs, only pseudogenes, and suffered inactivating mutations in the vomeronasal signal transduction gene Trpc2. We show that primate V1R decline happened prior to acquisition of trichromatic vision, earlier during evolution than was previously thought. We also show that it is extremely unlikely that decline of the dog V1R repertoire occurred in response to selective pressures imposed by humans during domestication. Functional repertoire sizes in each species correlate roughly with anatomical observations of vomeronasal organ size and quality; however, no single ecological correlate explains the very diverse fates of this gene family in different mammalian genomes. V1Rs provide one of the most extreme examples observed to date of massive gene duplication in some genomes, with loss of all functional genes in other species.

Setting up a proper power spectral density (PSD) and autocorrelation analysis for material and process characterization

NASA Astrophysics Data System (ADS)

Rutigliani, Vito; Lorusso, Gian Francesco; De Simone, Danilo; Lazzarino, Frederic; Rispens, Gijsbert; Papavieros, George; Gogolides, Evangelos; Constantoudis, Vassilios; Mack, Chris A.

2018-03-01

Power spectral density (PSD) analysis is playing more and more a critical role in the understanding of line-edge roughness (LER) and linewidth roughness (LWR) in a variety of applications across the industry. It is an essential step to get an unbiased LWR estimate, as well as an extremely useful tool for process and material characterization. However, PSD estimate can be affected by both random to systematic artifacts caused by image acquisition and measurement settings, which could irremediably alter its information content. In this paper, we report on the impact of various setting parameters (smoothing image processing filters, pixel size, and SEM noise levels) on the PSD estimate. We discuss also the use of PSD analysis tool in a variety of cases. Looking beyond the basic roughness estimate, we use PSD and autocorrelation analysis to characterize resist blur[1], as well as low and high frequency roughness contents and we apply this technique to guide the EUV material stack selection. Our results clearly indicate that, if properly used, PSD methodology is a very sensitive tool to investigate material and process variations

Implementation of RS-485 Communication between PLC and PC of Distributed Control System Based on VB

NASA Astrophysics Data System (ADS)

Lian Zhang, Chuan; Da Huang, Zhi; Qing Zhou, Gui; Chong, Kil To

2015-05-01

This paper focuses on achieving RS-485 communication between programmable logical controller (PLC) and PC based on visual basic 6.0 (VB6.0) on an experimental automatic production line. Mitsubishi FX2N PLCs and a PC are chosen as slave stations and main station, respectively. Monitoring software is developed using VB6.0 for data input/output, flow control and online parameters setting. As a result, all functions are fulfilled with robust performance. It is concluded from results that one PC can monitor several PLCs using RS-485 communication.

Error-Based Design Space Windowing

NASA Technical Reports Server (NTRS)

Papila, Melih; Papila, Nilay U.; Shyy, Wei; Haftka, Raphael T.; Fitz-Coy, Norman

2002-01-01

Windowing of design space is considered in order to reduce the bias errors due to low-order polynomial response surfaces (RS). Standard design space windowing (DSW) uses a region of interest by setting a requirement on response level and checks it by a global RS predictions over the design space. This approach, however, is vulnerable since RS modeling errors may lead to the wrong region to zoom on. The approach is modified by introducing an eigenvalue error measure based on point-to-point mean squared error criterion. Two examples are presented to demonstrate the benefit of the error-based DSW.

Predicting fatty acid profiles in blood based on food intake and the FADS1 rs174546 SNP.

PubMed

Hallmann, Jacqueline; Kolossa, Silvia; Gedrich, Kurt; Celis-Morales, Carlos; Forster, Hannah; O'Donovan, Clare B; Woolhead, Clara; Macready, Anna L; Fallaize, Rosalind; Marsaux, Cyril F M; Lambrinou, Christina-Paulina; Mavrogianni, Christina; Moschonis, George; Navas-Carretero, Santiago; San-Cristobal, Rodrigo; Godlewska, Magdalena; Surwiłło, Agnieszka; Mathers, John C; Gibney, Eileen R; Brennan, Lorraine; Walsh, Marianne C; Lovegrove, Julie A; Saris, Wim H M; Manios, Yannis; Martinez, Jose Alfredo; Traczyk, Iwona; Gibney, Michael J; Daniel, Hannelore

2015-12-01

A high intake of n-3 PUFA provides health benefits via changes in the n-6/n-3 ratio in blood. In addition to such dietary PUFAs, variants in the fatty acid desaturase 1 (FADS1) gene are also associated with altered PUFA profiles. We used mathematical modeling to predict levels of PUFA in whole blood, based on multiple hypothesis testing and bootstrapped LASSO selected food items, anthropometric and lifestyle factors, and the rs174546 genotypes in FADS1 from 1607 participants (Food4Me Study). The models were developed using data from the first reported time point (training set) and their predictive power was evaluated using data from the last reported time point (test set). Among other food items, fish, pizza, chicken, and cereals were identified as being associated with the PUFA profiles. Using these food items and the rs174546 genotypes as predictors, models explained 26-43% of the variability in PUFA concentrations in the training set and 22-33% in the test set. Selecting food items using multiple hypothesis testing is a valuable contribution to determine predictors, as our models' predictive power is higher compared to analogue studies. As unique feature, we additionally confirmed our models' power based on a test set. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Homoeologous cloning of omega-secalin gene family in a wheat 1BL/1RS translocation.

PubMed

Chai, Jian Fang; Liu, Xu; Jia, Ji Zeng

2005-08-01

Wheat 1BL/1RS translocations are widely planted in China as well as in most of the wheat producing area in the world for their good qualities of disease resistance and high yield. 1BL/1RS translocations are however poor in bread making, partially caused by a family of small monomeric proteins, omega-secalins, which are encoded by genes on 1RS. Based on published sequence of a rye omega-secalin gene we designed a pair of primers to cover the whole mature protein coding sequence. A major band could be amplified from 1BL/1RS translocations but not from euploid wheat. Using this primer set we conducted PCR amplification by using high fidelity Pfu polymerase on the genomic DNAs and cDNAs purified from a 1BL/1RS translocation Lankao 906. Sequencing analysis indicated that this gene family contains several members of 1150 bp, 1076 bp, 1075 bp, 1052 bp and 1004 bp genes, including two pseudogenes and three active genes. The gene transcripts were differentially expressed in developing seeds.

Data Quality in Remote Sensing

NASA Astrophysics Data System (ADS)

Batini, C.; Blaschke, T.; Lang, S.; Albrecht, F.; Abdulmutalib, H. M.; Barsi, Á.; Szabó, G.; Kugler, Zs.

2017-09-01

The issue of data quality (DQ) is of growing importance in Remote Sensing (RS), due to the widespread use of digital services (incl. apps) that exploit remote sensing data. In this position paper a body of experts from the ISPRS Intercommission working group III/IVb "DQ" identifies, categorises and reasons about issues that are considered as crucial for a RS research and application agenda. This ISPRS initiative ensures to build on earlier work by other organisations such as IEEE, CEOS or GEO, in particular on the meritorious work of the Quality Assurance Framework for Earth Observation (QA4EO) which was established and endorsed by the Committee on Earth Observation Satellites (CEOS) but aims to broaden the view by including experts from computer science and particularly database science. The main activities and outcomes include: providing a taxonomy of DQ dimensions in the RS domain, achieving a global approach to DQ for heterogeneous-format RS data sets, investigate DQ dimensions in use, conceive a methodology for managing cost effective solutions on DQ in RS initiatives, and to address future challenges on RS DQ dimensions arising in the new era of the big Earth data.

Rough set approach for accident chains exploration.

PubMed

Wong, Jinn-Tsai; Chung, Yi-Shih

2007-05-01

This paper presents a novel non-parametric methodology--rough set theory--for accident occurrence exploration. The rough set theory allows researchers to analyze accidents in multiple dimensions and to model accident occurrence as factor chains. Factor chains are composed of driver characteristics, trip characteristics, driver behavior and environment factors that imply typical accident occurrence. A real-world database (2003 Taiwan single auto-vehicle accidents) is used as an example to demonstrate the proposed approach. The results show that although most accident patterns are unique, some accident patterns are significant and worth noting. Student drivers who are young and less experienced exhibit a relatively high possibility of being involved in off-road accidents on roads with a speed limit between 51 and 79 km/h under normal driving circumstances. Notably, for bump-into-facility accidents, wet surface is a distinctive environmental factor.

Convection from Hemispherical and Conical Model Ice Roughness Elements in Stagnation Region Flows

NASA Technical Reports Server (NTRS)

Hughes, Michael T.; Shannon, Timothy A.; McClain, Stephen T.; Vargas, Mario; Broeren, Andy

2016-01-01

To improve ice accretion prediction codes, more data regarding ice roughness and its effects on convective heat transfer are required. The Vertical Icing Studies Tunnel (VIST) at NASA Glenn Research was used to model realistic ice roughness in the stagnation region of a NACA 0012 airfoil. In the VIST, a test plate representing the leading 2% chord of the airfoil was subjected to flows of 7.62 m/s (25 ft/s), 12.19 m/s (40 ft/s), and 16.76 m/s (55 ft/s). The test plate was fitted with multiple surfaces or sets of roughness panels, each with a different representation of ice roughness. The sets of roughness panels were constructed using two element distribution patterns that were created based on a laser scan of an iced airfoil acquired in the Icing Research Tunnel at NASA Glenn. For both roughness patterns, surfaces were constructed using plastic hemispherical elements, plastic conical elements, and aluminum conical elements. Infrared surface thermometry data from tests run in the VIST were used to calculate area averaged heat transfer coefficient values. The values from the roughness surfaces were compared to the smooth control surface, showing convective enhancement as high as 400% in some cases. The data gathered during this study will ultimately be used to improve the physical modeling in LEWICE or other ice accretion codes and produce predictions of in-flight ice accretion on aircraft surfaces with greater confidence.

a Rough Set Decision Tree Based Mlp-Cnn for Very High Resolution Remotely Sensed Image Classification

NASA Astrophysics Data System (ADS)

Zhang, C.; Pan, X.; Zhang, S. Q.; Li, H. P.; Atkinson, P. M.

2017-09-01

Recent advances in remote sensing have witnessed a great amount of very high resolution (VHR) images acquired at sub-metre spatial resolution. These VHR remotely sensed data has post enormous challenges in processing, analysing and classifying them effectively due to the high spatial complexity and heterogeneity. Although many computer-aid classification methods that based on machine learning approaches have been developed over the past decades, most of them are developed toward pixel level spectral differentiation, e.g. Multi-Layer Perceptron (MLP), which are unable to exploit abundant spatial details within VHR images. This paper introduced a rough set model as a general framework to objectively characterize the uncertainty in CNN classification results, and further partition them into correctness and incorrectness on the map. The correct classification regions of CNN were trusted and maintained, whereas the misclassification areas were reclassified using a decision tree with both CNN and MLP. The effectiveness of the proposed rough set decision tree based MLP-CNN was tested using an urban area at Bournemouth, United Kingdom. The MLP-CNN, well capturing the complementarity between CNN and MLP through the rough set based decision tree, achieved the best classification performance both visually and numerically. Therefore, this research paves the way to achieve fully automatic and effective VHR image classification.

Modeling Mode Choice Behavior Incorporating Household and Individual Sociodemographics and Travel Attributes Based on Rough Sets Theory

PubMed Central

Chen, Xuewu; Wei, Ming; Wu, Jingxian; Hou, Xianyao

2014-01-01

Most traditional mode choice models are based on the principle of random utility maximization derived from econometric theory. Alternatively, mode choice modeling can be regarded as a pattern recognition problem reflected from the explanatory variables of determining the choices between alternatives. The paper applies the knowledge discovery technique of rough sets theory to model travel mode choices incorporating household and individual sociodemographics and travel information, and to identify the significance of each attribute. The study uses the detailed travel diary survey data of Changxing county which contains information on both household and individual travel behaviors for model estimation and evaluation. The knowledge is presented in the form of easily understood IF-THEN statements or rules which reveal how each attribute influences mode choice behavior. These rules are then used to predict travel mode choices from information held about previously unseen individuals and the classification performance is assessed. The rough sets model shows high robustness and good predictive ability. The most significant condition attributes identified to determine travel mode choices are gender, distance, household annual income, and occupation. Comparative evaluation with the MNL model also proves that the rough sets model gives superior prediction accuracy and coverage on travel mode choice modeling. PMID:25431585

Study on parallel and distributed management of RS data based on spatial database

NASA Astrophysics Data System (ADS)

Chen, Yingbiao; Qian, Qinglan; Wu, Hongqiao; Liu, Shijin

2009-10-01

With the rapid development of current earth-observing technology, RS image data storage, management and information publication become a bottle-neck for its appliance and popularization. There are two prominent problems in RS image data storage and management system. First, background server hardly handle the heavy process of great capacity of RS data which stored at different nodes in a distributing environment. A tough burden has put on the background server. Second, there is no unique, standard and rational organization of Multi-sensor RS data for its storage and management. And lots of information is lost or not included at storage. Faced at the above two problems, the paper has put forward a framework for RS image data parallel and distributed management and storage system. This system aims at RS data information system based on parallel background server and a distributed data management system. Aiming at the above two goals, this paper has studied the following key techniques and elicited some revelatory conclusions. The paper has put forward a solid index of "Pyramid, Block, Layer, Epoch" according to the properties of RS image data. With the solid index mechanism, a rational organization for different resolution, different area, different band and different period of Multi-sensor RS image data is completed. In data storage, RS data is not divided into binary large objects to be stored at current relational database system, while it is reconstructed through the above solid index mechanism. A logical image database for the RS image data file is constructed. In system architecture, this paper has set up a framework based on a parallel server of several common computers. Under the framework, the background process is divided into two parts, the common WEB process and parallel process.

Study on parallel and distributed management of RS data based on spatial data base

NASA Astrophysics Data System (ADS)

Chen, Yingbiao; Qian, Qinglan; Liu, Shijin

2006-12-01

With the rapid development of current earth-observing technology, RS image data storage, management and information publication become a bottle-neck for its appliance and popularization. There are two prominent problems in RS image data storage and management system. First, background server hardly handle the heavy process of great capacity of RS data which stored at different nodes in a distributing environment. A tough burden has put on the background server. Second, there is no unique, standard and rational organization of Multi-sensor RS data for its storage and management. And lots of information is lost or not included at storage. Faced at the above two problems, the paper has put forward a framework for RS image data parallel and distributed management and storage system. This system aims at RS data information system based on parallel background server and a distributed data management system. Aiming at the above two goals, this paper has studied the following key techniques and elicited some revelatory conclusions. The paper has put forward a solid index of "Pyramid, Block, Layer, Epoch" according to the properties of RS image data. With the solid index mechanism, a rational organization for different resolution, different area, different band and different period of Multi-sensor RS image data is completed. In data storage, RS data is not divided into binary large objects to be stored at current relational database system, while it is reconstructed through the above solid index mechanism. A logical image database for the RS image data file is constructed. In system architecture, this paper has set up a framework based on a parallel server of several common computers. Under the framework, the background process is divided into two parts, the common WEB process and parallel process.

Polymorphisms in sodium-dependent vitamin C transporter genes and plasma, aqueous humor and lens nucleus ascorbate concentrations in an ascorbate depleted setting.

PubMed

Senthilkumari, Srinivasan; Talwar, Badri; Dharmalingam, Kuppamuthu; Ravindran, Ravilla D; Jayanthi, Ramamurthy; Sundaresan, Periasamy; Saravanan, Charu; Young, Ian S; Dangour, Alan D; Fletcher, Astrid E

2014-07-01

We have previously reported low concentrations of plasma ascorbate and low dietary vitamin C intake in the older Indian population and a strong inverse association of these with cataract. Little is known about ascorbate levels in aqueous humor and lens in populations habitually depleted of ascorbate and no studies in any setting have investigated whether genetic polymorphisms influence ascorbate levels in ocular tissues. Our objectives were to investigate relationships between ascorbate concentrations in plasma, aqueous humor and lens and whether these relationships are influenced by Single Nucleotide Polymorphisms (SNPs) in sodium-dependent vitamin C transporter genes (SLC23A1 and SLC23A2). We enrolled sixty patients (equal numbers of men and women, mean age 63 years) undergoing small incision cataract surgery in southern India. We measured ascorbate concentrations in plasma, aqueous humor and lens nucleus using high performance liquid chromatography. SLC23A1 SNPs (rs4257763, rs6596473) and SLC23A2 SNPs (rs1279683 and rs12479919) were genotyped using a TaqMan assay. Patients were interviewed for lifestyle factors which might influence ascorbate. Plasma vitamin C was normalized by a log10 transformation. Statistical analysis used linear regression with the slope of the within-subject associations estimated using beta (β) coefficients. The ascorbate concentrations (μmol/L) were: plasma ascorbate, median and inter-quartile range (IQR), 15.2 (7.8, 34.5), mean (SD) of aqueous humor ascorbate, 1074 (545) and lens nucleus ascorbate, 0.42 (0.16) (μmol/g lens nucleus wet weight). Minimum allele frequencies were: rs1279683 (0.28), rs12479919 (0.30), rs659647 (0.48). Decreasing concentrations of ocular ascorbate from the common to the rare genotype were observed for rs6596473 and rs12479919. The per allele difference in aqueous humor ascorbate for rs6596473 was -217 μmol/L, p < 0.04 and a per allele difference in lens nucleus ascorbate of -0.085 μmol/g, p < 0.02 for rs12479919. The β coefficients for the regression of log10 plasma ascorbate on aqueous humor ascorbate were higher for the GG genotype of rs6596473: GG, β = 1460 compared to carriage of the C allele, CG, β = 1059, CC, β = 1132, p interaction = 0.1. In conclusion we found that compared to studies in well-nourished populations, ascorbate concentrations in the plasma, aqueous humor and lens nucleus were low. We present novel findings that polymorphisms in SLC23A1/2 genes influenced ascorbate concentration in aqueous humor and lens nucleus. Copyright © 2014 Elsevier Ltd. All rights reserved.

A genome-wide association study of anorexia nervosa.

PubMed

Boraska, V; Franklin, C S; Floyd, J A B; Thornton, L M; Huckins, L M; Southam, L; Rayner, N W; Tachmazidou, I; Klump, K L; Treasure, J; Lewis, C M; Schmidt, U; Tozzi, F; Kiezebrink, K; Hebebrand, J; Gorwood, P; Adan, R A H; Kas, M J H; Favaro, A; Santonastaso, P; Fernández-Aranda, F; Gratacos, M; Rybakowski, F; Dmitrzak-Weglarz, M; Kaprio, J; Keski-Rahkonen, A; Raevuori, A; Van Furth, E F; Slof-Op 't Landt, M C T; Hudson, J I; Reichborn-Kjennerud, T; Knudsen, G P S; Monteleone, P; Kaplan, A S; Karwautz, A; Hakonarson, H; Berrettini, W H; Guo, Y; Li, D; Schork, N J; Komaki, G; Ando, T; Inoko, H; Esko, T; Fischer, K; Männik, K; Metspalu, A; Baker, J H; Cone, R D; Dackor, J; DeSocio, J E; Hilliard, C E; O'Toole, J K; Pantel, J; Szatkiewicz, J P; Taico, C; Zerwas, S; Trace, S E; Davis, O S P; Helder, S; Bühren, K; Burghardt, R; de Zwaan, M; Egberts, K; Ehrlich, S; Herpertz-Dahlmann, B; Herzog, W; Imgart, H; Scherag, A; Scherag, S; Zipfel, S; Boni, C; Ramoz, N; Versini, A; Brandys, M K; Danner, U N; de Kovel, C; Hendriks, J; Koeleman, B P C; Ophoff, R A; Strengman, E; van Elburg, A A; Bruson, A; Clementi, M; Degortes, D; Forzan, M; Tenconi, E; Docampo, E; Escaramís, G; Jiménez-Murcia, S; Lissowska, J; Rajewski, A; Szeszenia-Dabrowska, N; Slopien, A; Hauser, J; Karhunen, L; Meulenbelt, I; Slagboom, P E; Tortorella, A; Maj, M; Dedoussis, G; Dikeos, D; Gonidakis, F; Tziouvas, K; Tsitsika, A; Papezova, H; Slachtova, L; Martaskova, D; Kennedy, J L; Levitan, R D; Yilmaz, Z; Huemer, J; Koubek, D; Merl, E; Wagner, G; Lichtenstein, P; Breen, G; Cohen-Woods, S; Farmer, A; McGuffin, P; Cichon, S; Giegling, I; Herms, S; Rujescu, D; Schreiber, S; Wichmann, H-E; Dina, C; Sladek, R; Gambaro, G; Soranzo, N; Julia, A; Marsal, S; Rabionet, R; Gaborieau, V; Dick, D M; Palotie, A; Ripatti, S; Widén, E; Andreassen, O A; Espeseth, T; Lundervold, A; Reinvang, I; Steen, V M; Le Hellard, S; Mattingsdal, M; Ntalla, I; Bencko, V; Foretova, L; Janout, V; Navratilova, M; Gallinger, S; Pinto, D; Scherer, S W; Aschauer, H; Carlberg, L; Schosser, A; Alfredsson, L; Ding, B; Klareskog, L; Padyukov, L; Courtet, P; Guillaume, S; Jaussent, I; Finan, C; Kalsi, G; Roberts, M; Logan, D W; Peltonen, L; Ritchie, G R S; Barrett, J C; Estivill, X; Hinney, A; Sullivan, P F; Collier, D A; Zeggini, E; Bulik, C M

2014-10-01

Anorexia nervosa (AN) is a complex and heritable eating disorder characterized by dangerously low body weight. Neither candidate gene studies nor an initial genome-wide association study (GWAS) have yielded significant and replicated results. We performed a GWAS in 2907 cases with AN from 14 countries (15 sites) and 14 860 ancestrally matched controls as part of the Genetic Consortium for AN (GCAN) and the Wellcome Trust Case Control Consortium 3 (WTCCC3). Individual association analyses were conducted in each stratum and meta-analyzed across all 15 discovery data sets. Seventy-six (72 independent) single nucleotide polymorphisms were taken forward for in silico (two data sets) or de novo (13 data sets) replication genotyping in 2677 independent AN cases and 8629 European ancestry controls along with 458 AN cases and 421 controls from Japan. The final global meta-analysis across discovery and replication data sets comprised 5551 AN cases and 21 080 controls. AN subtype analyses (1606 AN restricting; 1445 AN binge-purge) were performed. No findings reached genome-wide significance. Two intronic variants were suggestively associated: rs9839776 (P=3.01 × 10(-7)) in SOX2OT and rs17030795 (P=5.84 × 10(-6)) in PPP3CA. Two additional signals were specific to Europeans: rs1523921 (P=5.76 × 10(-)(6)) between CUL3 and FAM124B and rs1886797 (P=8.05 × 10(-)(6)) near SPATA13. Comparing discovery with replication results, 76% of the effects were in the same direction, an observation highly unlikely to be due to chance (P=4 × 10(-6)), strongly suggesting that true findings exist but our sample, the largest yet reported, was underpowered for their detection. The accrual of large genotyped AN case-control samples should be an immediate priority for the field.

Measuring skew in average surface roughness as a function of surface preparation

NASA Astrophysics Data System (ADS)

Stahl, Mark T.

2015-08-01

Characterizing surface roughness is important for predicting optical performance. Better measurement of surface roughness reduces polishing time, saves money and allows the science requirements to be better defined. This study characterized statistics of average surface roughness as a function of polishing time. Average surface roughness was measured at 81 locations using a Zygo® white light interferometer at regular intervals during the polishing process. Each data set was fit to a normal and Largest Extreme Value (LEV) distribution; then tested for goodness of fit. We show that the skew in the average data changes as a function of polishing time.

Fuzzy-Rough Nearest Neighbour Classification

NASA Astrophysics Data System (ADS)

Jensen, Richard; Cornelis, Chris

A new fuzzy-rough nearest neighbour (FRNN) classification algorithm is presented in this paper, as an alternative to Sarkar's fuzzy-rough ownership function (FRNN-O) approach. By contrast to the latter, our method uses the nearest neighbours to construct lower and upper approximations of decision classes, and classifies test instances based on their membership to these approximations. In the experimental analysis, we evaluate our approach with both classical fuzzy-rough approximations (based on an implicator and a t-norm), as well as with the recently introduced vaguely quantified rough sets. Preliminary results are very good, and in general FRNN outperforms FRNN-O, as well as the traditional fuzzy nearest neighbour (FNN) algorithm.

Association between Eight Functional Polymorphisms and Haplotypes in the Cholesterol Ester Transfer Protein (CETP) Gene and Dyslipidemia in National Minority Adults in the Far West Region of China.

PubMed

Guo, Shuxia; Hu, Yunhua; Ding, Yusong; Liu, Jiaming; Zhang, Mei; Ma, Rulin; Guo, Heng; Wang, Kui; He, Jia; Yan, Yizhong; Rui, Dongsheng; Sun, Feng; Mu, Lati; Niu, Qiang; Zhang, Jingyu; Li, Shugang

2015-12-16

We have investigated the relationship between the polymorphisms and haplotypes in the CETP gene, and dyslipidemia among the Xinjiang Kazak and Uyghur populations in China. A total of 712 patients with dyslipidemia and 764 control subjects of CETP gene polymorphism at rs12149545, rs3764261, rs1800775, rs711752, rs708272, rs289714, rs5882, and rs1801706 loci were studied by the Snapshot method, linkage disequilibrium analysis and haplotype construction. The results are as follows: (1) the minor allele of eight loci of frequencies in the two groups were different from other results of similar studies in other countries; (2) In the linear regression analysis, the HDL-C levels of rs708272 TT, rs1800775 AA, rs289714 CC and rs711752 AA genotypes were significantly higher than those of other genotypes, however, the rs3764261 GG and rs12149545 GG genotypes were significantly lower than those of other genotypes in the two ethnic groups. The HDL-C levels of the rs12149545 GG genotype were lower than those of other genotypes; (3) in the control group, the rs708272 CT genotype of TG levels were lower than in the CC genotype, the T genotype of LDL-C levels were lower than in the CC genotype, and the HDL-C levels were higher than in the CT genotype; the rs1800775 AC genotype of TG levels were higher than in the AA genotype, the rs711752 AG genotype of TG levels were lower than in the GG genotype, the AA genotype LDL-C levels were lower than in the GG genotype, and the HDL-C levels were higher than in the AG genotype; the rs1800775 AC genotype of TG levels were higher than in the AA genotype. In the dyslipidemia group, the rs708272 TT genotype of TC and LDL-C levels were higher than in the CT genotype and the rs3764261 TT genotype of TC levels were higher than in the GG genotype. The rs711752 AA genotype of TC and LDL-C levels were higher than in the AG genotype, and the rs12149545 AA genotype of TC and LDL-C levels were higher than in the GG genotype; (4) perfect Linkage Disequilibrium was observed for two sets of two SNPs: rs3764261 and rs12149545; rs711752 and rs708272. (5) Using SHEsis software analysis, the five A/T/A/A/T/C/A/G, A/T/A/A/T/T/G/A, G/G/A/G/C/C/G/G, G/G/C/G/C/C/A/G and G/G/C/G/C/T/G/G haplotypes were between dyslipidemia group and control group statistically significantly different (p < 0.05 in each case). The polymorphism of CETP genes rs708272, rs3764261, rs1800775, rs711752, rs12149545 was closely related to the dyslipidemia in the Xinjiang Uyghur and Kazakh ethnic groups; and the rs708272 T, rs3764261 T, rs711752 A, and rs12149545 A alleles could reduce risk of dyslipidemia in the Uyghur and Kazakh populations, however, the rs1800775 C allele showed risk factors.

Association between Eight Functional Polymorphisms and Haplotypes in the Cholesterol Ester Transfer Protein (CETP) Gene and Dyslipidemia in National Minority Adults in the Far West Region of China

PubMed Central

Guo, Shuxia; Hu, Yunhua; Ding, Yusong; Liu, Jiaming; Zhang, Mei; Ma, Rulin; Guo, Heng; Wang, Kui; He, Jia; Yan, Yizhong; Rui, Dongsheng; Sun, Feng; Mu, Lati; Niu, Qiang; Zhang, Jingyu; Li, Shugang

2015-01-01

We have investigated the relationship between the polymorphisms and haplotypes in the CETP gene, and dyslipidemia among the Xinjiang Kazak and Uyghur populations in China. A total of 712 patients with dyslipidemia and 764 control subjects of CETP gene polymorphism at rs12149545, rs3764261, rs1800775, rs711752, rs708272, rs289714, rs5882, and rs1801706 loci were studied by the Snapshot method, linkage disequilibrium analysis and haplotype construction. The results are as follows: (1) the minor allele of eight loci of frequencies in the two groups were different from other results of similar studies in other countries; (2) In the linear regression analysis, the HDL-C levels of rs708272 TT, rs1800775 AA, rs289714 CC and rs711752 AA genotypes were significantly higher than those of other genotypes, however, the rs3764261 GG and rs12149545 GG genotypes were significantly lower than those of other genotypes in the two ethnic groups. The HDL-C levels of the rs12149545 GG genotype were lower than those of other genotypes; (3) in the control group, the rs708272 CT genotype of TG levels were lower than in the CC genotype, the T genotype of LDL-C levels were lower than in the CC genotype, and the HDL-C levels were higher than in the CT genotype; the rs1800775 AC genotype of TG levels were higher than in the AA genotype, the rs711752 AG genotype of TG levels were lower than in the GG genotype, the AA genotype LDL-C levels were lower than in the GG genotype, and the HDL-C levels were higher than in the AG genotype; the rs1800775 AC genotype of TG levels were higher than in the AA genotype. In the dyslipidemia group, the rs708272 TT genotype of TC and LDL-C levels were higher than in the CT genotype and the rs3764261 TT genotype of TC levels were higher than in the GG genotype. The rs711752 AA genotype of TC and LDL-C levels were higher than in the AG genotype, and the rs12149545 AA genotype of TC and LDL-C levels were higher than in the GG genotype; (4) perfect Linkage Disequilibrium was observed for two sets of two SNPs: rs3764261 and rs12149545; rs711752 and rs708272. (5) Using SHEsis software analysis, the five A/T/A/A/T/C/A/G, A/T/A/A/T/T/G/A, G/G/A/G/C/C/G/G, G/G/C/G/C/C/A/G and G/G/C/G/C/T/G/G haplotypes were between dyslipidemia group and control group statistically significantly different (p < 0.05 in each case). The polymorphism of CETP genes rs708272, rs3764261, rs1800775, rs711752, rs12149545 was closely related to the dyslipidemia in the Xinjiang Uyghur and Kazakh ethnic groups; and the rs708272 T, rs3764261 T, rs711752 A, and rs12149545 A alleles could reduce risk of dyslipidemia in the Uyghur and Kazakh populations, however, the rs1800775 C allele showed risk factors. PMID:26694435

The common occurrence of epistasis in the determination of human pigmentation and its impact on DNA-based pigmentation phenotype prediction.

PubMed

Pośpiech, Ewelina; Wojas-Pelc, Anna; Walsh, Susan; Liu, Fan; Maeda, Hitoshi; Ishikawa, Takaki; Skowron, Małgorzata; Kayser, Manfred; Branicki, Wojciech

2014-07-01

The role of epistatic effects in the determination of complex traits is often underlined but its significance in the prediction of pigmentation phenotypes has not been evaluated so far. The prediction of pigmentation from genetic data can be useful in forensic science to describe the physical appearance of an unknown offender, victim, or missing person who cannot be identified via conventional DNA profiling. Available forensic DNA prediction systems enable the reliable prediction of several eye and hair colour categories. However, there is still space for improvement. Here we verified the association of 38 candidate DNA polymorphisms from 13 genes and explored the extent to which interactions between them may be involved in human pigmentation and their impact on forensic DNA prediction in particular. The model-building set included 718 Polish samples and the model-verification set included 307 independent Polish samples and additional 72 samples from Japan. In total, 29 significant SNP-SNP interactions were found with 5 of them showing an effect on phenotype prediction. For predicting green eye colour, interactions between HERC2 rs12913832 and OCA2 rs1800407 as well as TYRP1 rs1408799 raised the prediction accuracy expressed by AUC from 0.667 to 0.697 and increased the prediction sensitivity by >3%. Interaction between MC1R 'R' variants and VDR rs731236 increased the sensitivity for light skin by >1% and by almost 3% for dark skin colour prediction. Interactions between VDR rs1544410 and TYR rs1042602 as well as between MC1R 'R' variants and HERC2 rs12913832 provided an increase in red/non-red hair prediction accuracy from an AUC of 0.902-0.930. Our results thus underline epistasis as a common phenomenon in human pigmentation genetics and demonstrate that considering SNP-SNP interactions in forensic DNA phenotyping has little impact on eye, hair and skin colour prediction. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver

PubMed Central

Sabidó, Eduard; Bosch, Elena

2016-01-01

Essential trace elements possess vital functions at molecular, cellular, and physiological levels in health and disease, and they are tightly regulated in the human body. In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 liver samples, together with the expression levels of 90 genes and abundances of 40 proteins involved in their homeostasis. Additionally, we genotyped 169 single nucleotide polymorphism (SNPs) in the same sample set. We detected significant associations for 8 protein quantitative trait loci (pQTL), 10 expression quantitative trait loci (eQTLs), and 15 micronutrient quantitative trait loci (nutriQTL). Six of these exceeded the false discovery rate cutoff and were related to essential trace elements: 1) one pQTL for GPX2 (rs10133290); 2) two previously described eQTLs for HFE (rs12346) and SELO (rs4838862) expression; and 3) three nutriQTLs: The pathogenic C282Y mutation at HFE affecting iron (rs1800562), and two SNPs within several clustered metallothionein genes determining selenium concentration (rs1811322 and rs904773). Within the complete set of significant QTLs (which involved 30 SNPs and 20 gene regions), we identified 12 SNPs with extreme patterns of population differentiation (FST values in the top 5% percentile in at least one HapMap population pair) and significant evidence for selective sweeps involving QTLs at GPX1, SELENBP1, GPX3, SLC30A9, and SLC39A8. Overall, this detailed study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive response to environmental pressures related to micronutrients. PMID:26582562

Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

PubMed Central

FitzGerald, Liesel M.; Kumar, Akash; Boyle, Evan A.; Zhang, Yuzheng; McIntosh, Laura M.; Kolb, Suzanne; Stott-Miller, Marni; Smith, Tiffany; Karyadi, Danielle M.; Ostrander, Elaine A.; Hsu, Li; Shendure, Jay; Stanford, Janet L.

2013-01-01

Background Rare, inherited mutations account for 5%–10% of all prostate cancer (PCa) cases. However, to date, few causative mutations have been identified. Methods To identify rare mutations for PCa, we performed whole-exome sequencing (WES) in multiple kindreds (n = 91) from 19 hereditary prostate cancer (HPC) families characterized by aggressive or early onset phenotypes. Candidate variants (n = 130) identified through family- and bioinformatics-based filtering of WES data were then genotyped in an independent set of 270 HPC families (n = 819 PCa cases; n = 496 unaffected relatives) for replication. Two variants with supportive evidence were subsequently genotyped in a population-based case-control study (n = 1,155 incident PCa cases; n = 1,060 age-matched controls) for further confirmation. All participants were men of European ancestry. Results The strongest evidence was for two germline missense variants in the butyrophilin-like 2 (BTNL2) gene (rs41441651, p.Asp336Asn and rs28362675, p.Gly454Cys) that segregated with affection status in two of the WES families. In the independent set of 270 HPC families, 1.5% (rs41441651; P = 0.0032) and 1.2% (rs28362675; P = 0.0070) of affected men, but no unaffected men, carried a variant. Both variants were associated with elevated PCa risk in the population-based study (rs41441651: OR = 2.7; 95% CI, 1.27–5.87; P = 0.010; rs28362675: OR = 2.5; 95% CI, 1.16–5.46; P = 0.019). Conclusions Results indicate that rare BTNL2 variants play a role in susceptibility to both familial and sporadic prostate cancer. Impact Results implicate BTNL2 as a novel PCa susceptibility gene. PMID:23833122

Genome-wide significant association between a sequence variant at 15q15.2 and lung cancer risk

PubMed Central

Rafnar, Thorunn; Sulem, Patrick; Besenbacher, Soren; Gudbjartsson, Daniel F.; Zanon, Carlo; Gudmundsson, Julius; Stacey, Simon N.; Kostic, Jelena P.; Thorgeirsson, Thorgeir E.; Thorleifsson, Gudmar; Bjarnason, Hjordis; Skuladottir, Halla; Gudbjartsson, Tomas; Isaksson, Helgi J.; Isla, Dolores; Murillo, Laura; García-Prats, Maria D.; Panadero, Angeles; Aben, Katja K.H.; Vermeulen, Sita H.; van der Heijden, Henricus F.M.; Feser, William; Miller, York E.; Bunn, Paul A.; Kong, Augustine; Wolf, Holly J.; Franklin, Wilbur A.; Mayordomo, Jose I; Kiemeney, Lambertus A.; Jonsson, Steinn; Thorsteinsdottir, Unnur; Stefansson, Kari

2010-01-01

Genome-wide association studies (GWAS) have identified three genomic regions, at 15q24-25.1, 5p15.33 and 6p21.33, which associate with risk of lung cancer. Large meta-analyses of GWA data have failed to find additional associations of genome-wide significance. In this study, we sought to confirm 7 variants with suggestive association to lung cancer (P<10−5) in a recently published meta-analysis. In a GWA dataset of 1,447 lung cancer cases and 36,256 controls in Iceland, three correlated variants on 15q15.2 (rs504417, rs11853991 and rs748404) showed a significant association with lung cancer whereas rs4254535 on 2p14, rs1530057 on 3p24.1, rs6438347 on 3q13.31 and rs1926203 on 10q23.31 did not. The most significant variant, rs748404, was genotyped in additional 1,299 lung cancer cases and 4,102 controls from the Netherlands, Spain and the USA and the results combined with published GWAS data. In this analysis, the T allele of rs748404 reached genome-wide significance (OR=1.15, P=1.1×10−9). Another variant at the same locus, rs12050604, showed association with lung cancer (OR=1.09, 3.6×10−6) and remained significant after adjustment for rs748404 and vice versa. rs748404 is located 140 kb centromeric of the TP53BP1 gene that has been implicated in lung cancer risk. Two fully correlated, non-synonymous coding variants in TP53BP1, rs2602141 (Q1136K) and rs560191 (E353D), showed association with lung cancer in our sample set; however, this association did not remain significant after adjustment for rs748404. Our data show that one or more lung cancer risk variants of genome-wide significance and distinct from the coding variants in TP53BP1 are located at 15q15.2. PMID:21303977

A distinction between summer rainy season and summer monsoon season over the Central Highlands of Vietnam

NASA Astrophysics Data System (ADS)

Ngo-Thanh, Huong; Ngo-Duc, Thanh; Nguyen-Hong, Hanh; Baker, Peter; Phan-Van, Tan

2018-05-01

The daily rainfall data at 13 stations over the Central Highlands (CH) Vietnam were collected for the period 1981-2014. Two different sets of criteria using daily observed rainfall and 850 hPa daily reanalysis wind data were applied to determine the onset (retreat) dates of the summer rainy season (RS) and summer monsoon (SM) season, respectively. Over the study period, the mean RS and SM onset dates were April 20 and May 13 with standard deviations of 17.4 and 17.8 days, respectively. The mean RS and SM retreat dates were November 1 and September 30 with standard deviations of 17.9 and 10.2 days, respectively . The year-to-year variations of the onset dates and the rainfall amount within the RS and SM season were closely linked with the preceding winter and spring sea surface temperature in the central-eastern and western Pacific. It was also found that the onset dates were significantly correlated with the RS and SM rainfall amount.

Parallel loss of nuclear-encoded mitochondrial aminoacyl-tRNA synthetases and mtDNA-encoded tRNAs in Cnidaria.

PubMed

Haen, Karri M; Pett, Walker; Lavrov, Dennis V

2010-10-01

Unlike most animal mitochondrial (mt) genomes, which encode a set of 22 transfer RNAs (tRNAs) sufficient for mt protein synthesis, those of cnidarians have only retained one or two tRNA genes. Whether the missing cnidarian mt-tRNA genes relocated outside the main mt chromosome or were lost remains unclear. It is also unknown what impact the loss of tRNA genes had on other components of the mt translational machinery. Here, we explored the nuclear genome of the cnidarian Nematostella vectensis for the presence of mt-tRNA genes and their corresponding mt aminoacyl-tRNA synthetases (mt-aaRS). We detected no candidates for mt-tRNA genes and only two mt-aaRS orthologs. At the same time, we found that all but one cytosolic aaRS appear to be targeted to mitochondria. These results indicate that the loss of mt-tRNAs in Cnidaria is genuine and occurred in parallel with the loss of nuclear-encoded mt-aaRS. Our phylogenetic analyses of individual aaRS revealed that although the nearly total loss of mt-aaRS is rare, aaRS gene deletion and replacement have occurred throughout the evolution of Metazoa.

On twelve types of covering-based rough sets.

PubMed

Safari, Samira; Hooshmandasl, Mohammad Reza

2016-01-01

Covering approximation spaces are a generalization of equivalence-based rough set theories. In this paper, we will consider twelve types of covering based approximation operators by combining four types of covering lower approximation operators and three types of covering upper approximation operators. Then, we will study the properties of these new pairs and show they have most of the common properties among existing covering approximation pairs. Finally, the relation between these new pairs is studied.

Hybrid machine learning technique for forecasting Dhaka stock market timing decisions.

PubMed

Banik, Shipra; Khodadad Khan, A F M; Anwer, Mohammad

2014-01-01

Forecasting stock market has been a difficult job for applied researchers owing to nature of facts which is very noisy and time varying. However, this hypothesis has been featured by several empirical experiential studies and a number of researchers have efficiently applied machine learning techniques to forecast stock market. This paper studied stock prediction for the use of investors. It is always true that investors typically obtain loss because of uncertain investment purposes and unsighted assets. This paper proposes a rough set model, a neural network model, and a hybrid neural network and rough set model to find optimal buy and sell of a share on Dhaka stock exchange. Investigational findings demonstrate that our proposed hybrid model has higher precision than the single rough set model and the neural network model. We believe this paper findings will help stock investors to decide about optimal buy and/or sell time on Dhaka stock exchange.

Hybrid Machine Learning Technique for Forecasting Dhaka Stock Market Timing Decisions

PubMed Central

Banik, Shipra; Khodadad Khan, A. F. M.; Anwer, Mohammad

2014-01-01

Forecasting stock market has been a difficult job for applied researchers owing to nature of facts which is very noisy and time varying. However, this hypothesis has been featured by several empirical experiential studies and a number of researchers have efficiently applied machine learning techniques to forecast stock market. This paper studied stock prediction for the use of investors. It is always true that investors typically obtain loss because of uncertain investment purposes and unsighted assets. This paper proposes a rough set model, a neural network model, and a hybrid neural network and rough set model to find optimal buy and sell of a share on Dhaka stock exchange. Investigational findings demonstrate that our proposed hybrid model has higher precision than the single rough set model and the neural network model. We believe this paper findings will help stock investors to decide about optimal buy and/or sell time on Dhaka stock exchange. PMID:24701205

MicroRNA-503 and the Extended MicroRNA-16 Family in Angiogenesis

PubMed Central

Caporali, Andrea; Emanueli, Costanza

2011-01-01

MicroRNAs (miRs) are post-transcriptional inhibitory regulators of gene expression acting by direct binding to complementary messenger RNA (mRNA) transcripts. Recent studies have demonstrated that miRs are crucial determinants of endothelial cell behavior and angiogenesis. We have provided evidence of the prominent role of miR-503 in impairment of postischemic reparative angiogenesis in the setting of diabetes. Because miR-503 belongs to the miR-16 extended family of miRs, in this review, we describe the cardiovascular functions of miR-503 and other members of the miR-16 family and their impact on angiogenesis. PMID:22814423

Common genetic variants associated with cognitive performance identified using the proxy-phenotype method

PubMed Central

Rietveld, Cornelius A.; Esko, Tõnu; Davies, Gail; Pers, Tune H.; Turley, Patrick; Benyamin, Beben; Chabris, Christopher F.; Emilsson, Valur; Johnson, Andrew D.; Lee, James J.; de Leeuw, Christiaan; Marioni, Riccardo E.; Medland, Sarah E.; Miller, Michael B.; Rostapshova, Olga; van der Lee, Sven J.; Vinkhuyzen, Anna A. E.; Amin, Najaf; Conley, Dalton; Derringer, Jaime; van Duijn, Cornelia M.; Fehrmann, Rudolf; Franke, Lude; Glaeser, Edward L.; Hansell, Narelle K.; Hayward, Caroline; Iacono, William G.; Ibrahim-Verbaas, Carla; Jaddoe, Vincent; Karjalainen, Juha; Laibson, David; Lichtenstein, Paul; Liewald, David C.; Magnusson, Patrik K. E.; Martin, Nicholas G.; McGue, Matt; McMahon, George; Pedersen, Nancy L.; Pinker, Steven; Porteous, David J.; Posthuma, Danielle; Rivadeneira, Fernando; Smith, Blair H.; Starr, John M.; Tiemeier, Henning; Timpson, Nicholas J.; Trzaskowski, Maciej; Uitterlinden, André G.; Verhulst, Frank C.; Ward, Mary E.; Wright, Margaret J.; Davey Smith, George; Deary, Ian J.; Johannesson, Magnus; Plomin, Robert; Visscher, Peter M.; Benjamin, Daniel J.; Koellinger, Philipp D.

2014-01-01

We identify common genetic variants associated with cognitive performance using a two-stage approach, which we call the proxy-phenotype method. First, we conduct a genome-wide association study of educational attainment in a large sample (n = 106,736), which produces a set of 69 education-associated SNPs. Second, using independent samples (n = 24,189), we measure the association of these education-associated SNPs with cognitive performance. Three SNPs (rs1487441, rs7923609, and rs2721173) are significantly associated with cognitive performance after correction for multiple hypothesis testing. In an independent sample of older Americans (n = 8,652), we also show that a polygenic score derived from the education-associated SNPs is associated with memory and absence of dementia. Convergent evidence from a set of bioinformatics analyses implicates four specific genes (KNCMA1, NRXN1, POU2F3, and SCRT). All of these genes are associated with a particular neurotransmitter pathway involved in synaptic plasticity, the main cellular mechanism for learning and memory. PMID:25201988

A Transport Equation Approach to Modeling the Influence of Surface Roughness on Boundary Layer Transition

NASA Astrophysics Data System (ADS)

Langel, Christopher Michael

A computational investigation has been performed to better understand the impact of surface roughness on the flow over a contaminated surface. This thesis highlights the implementation and development of the roughness amplification model in the flow solver OVERFLOW-2. The model, originally proposed by Dassler, Kozulovic, and Fiala, introduces an additional scalar field roughness amplification quantity. This value is explicitly set at rough wall boundaries using surface roughness parameters and local flow quantities. This additional transport equation allows non-local effects of surface roughness to be accounted for downstream of rough sections. This roughness amplification variable is coupled with the Langtry-Menter model and used to modify the criteria for transition. Results from flat plate test cases show good agreement with experimental transition behavior on the flow over varying sand grain roughness heights. Additional validation studies were performed on a NACA 0012 airfoil with leading edge roughness. The computationally predicted boundary layer development demonstrates good agreement with experimental results. New tests using varying roughness configurations are being carried out at the Texas A&M Oran W. Nicks Low Speed Wind Tunnel to provide further calibration of the roughness amplification method. An overview and preliminary results are provided of this concurrent experimental investigation.

The in vitro effects of retrograded starch (resistant starch type 3) from lotus seed starch on the proliferation of Bifidobacterium adolescentis.

PubMed

Zhang, Yi; Wang, Ying; Zheng, Baodong; Lu, Xu; Zhuang, Weijing

2013-11-01

Prebiotics such as oligosaccharides, fructans, and resistant starch (RS) stimulate the growth of beneficial bacteria in large bowel and modify the human gastrointestinal environment. In this study, compared with glucose (GLU) and high amylose maize starch (HAMS), the in vitro effects of LRS3 and P-LRS3 (RS3 and purified RS3 prepared from lotus seed starch) on the proliferation of bifidobacteria were assessed by assessing the changes in optical density (OD), pH values, short chain fatty acid (SCFA) production, and tolerance ability to gastrointestinal conditions. Significantly higher OD values were obtained from media containing LRS3 and P-LRS3, and especially in the medium containing P-LRS3, the OD value of which reached 1.36 when the concentration of the carbon source was 20 g L(-1). Additionally, the lag phase of bifidobacteria was 8 h in the medium with LRS3 or P-LRS3, whereas it was 16 h in the medium with GLU or HAMS. What is more, a higher content of butyric acid was obtained in the P-LRS3 medium. Compared with GLU and HAMS media, bifidobacteria had a higher tolerance to gastrointestinal conditions in LRS3 and P-LRS3 media. It shows that lotus seed resistant starch, especially P-LRS3, could stimulate the growth of bifidobacteria. The rough surface of resistant starch and the SCFAs produced during fermentation might influence the proliferation of bifidobacteria.

Microarray-based comparison of three amplification methods for nanogram amounts of total RNA

PubMed Central

Singh, Ruchira; Maganti, Rajanikanth J.; Jabba, Sairam V.; Wang, Martin; Deng, Glenn; Heath, Joe Don; Kurn, Nurith; Wangemann, Philine

2007-01-01

Gene expression profiling using microarrays requires microgram amounts of RNA, which limits its direct application for the study of nanogram RNA samples obtained using microdissection, laser capture microscopy, or needle biopsy. A novel system based on Ribo-SPIA technology (RS, Ovation-Biotin amplification and labeling system) was recently introduced. The utility of the RS system, an optimized prototype system for picogram RNA samples (pRS), and two T7-based systems involving one or two rounds of amplification (OneRA, Standard Protocol, or TwoRA, Small Sample Prototcol, version II) were evaluated in the present study. Mouse kidney (MK) and mouse universal reference (MUR) RNA samples, 0.3 ng to 10 μg, were analyzed using high-density Affymetrix Mouse Genome 430 2.0 GeneChip arrays. Call concordance between replicates, correlations of signal intensity, signal intensity ratios, and minimal fold increase necessary for significance were determined. All systems amplified partially overlapping sets of genes with similar signal intensity correlations. pRS amplified the highest number of genes from 10-ng RNA samples. We detected 24 of 26 genes verified by RT-PCR in samples prepared using pRS. TwoRA yielded somewhat higher call concordances than did RS and pRS (91.8% vs. 89.3% and 88.1%, respectively). Although all target preparation methods were suitable, pRS amplified the highest number of targets and was found to be suitable for amplification of as little as 0.3 ng of total RNA. In addition, RS and pRS were faster and simpler to use than the T7-based methods and resulted in the generation of cDNA, which is more stable than cRNA. PMID:15613496

Effect of truncated cone roughness element density on hydrodynamic drag

NASA Astrophysics Data System (ADS)

Womack, Kristofer; Schultz, Michael; Meneveau, Charles

2017-11-01

An experimental study was conducted on rough-wall, turbulent boundary layer flow with roughness elements whose idealized shape model barnacles that cause hydrodynamic drag in many applications. Varying planform densities of truncated cone roughness elements were investigated. Element densities studied ranged from 10% to 79%. Detailed turbulent boundary layer velocity statistics were recorded with a two-component LDV system on a three-axis traverse. Hydrodynamic roughness length (z0) and skin-friction coefficient (Cf) were determined and compared with the estimates from existing roughness element drag prediction models including Macdonald et al. (1998) and other recent models. The roughness elements used in this work model idealized barnacles, so implications of this data set for ship powering are considered. This research was supported by the Office of Naval Research and by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.

A new fiber optic sensor for inner surface roughness measurement

NASA Astrophysics Data System (ADS)

Xu, Xiaomei; Liu, Shoubin; Hu, Hong

2009-11-01

In order to measure inner surface roughness of small holes nondestructively, a new fiber optic sensor is researched and developed. Firstly, a new model for surface roughness measurement is proposed, which is based on intensity-modulated fiber optic sensors and scattering modeling of rough surfaces. Secondly, a fiber optical measurement system is designed and set up. Under the help of new techniques, the fiber optic sensor can be miniaturized. Furthermore, the use of micro prism makes the light turn 90 degree, so the inner side surface roughness of small holes can be measured. Thirdly, the fiber optic sensor is gauged by standard surface roughness specimens, and a series of measurement experiments have been done. The measurement results are compared with those obtained by TR220 Surface Roughness Instrument and Form Talysurf Laser 635, and validity of the developed fiber optic sensor is verified. Finally, precision and influence factors of the fiber optic sensor are analyzed.

Clinical and genetic factors associated with warfarin maintenance dose in northern Chinese patients with mechanical heart valve replacement

PubMed Central

Liu, Rui; Cao, Jian; Zhang, Qian; Shi, Xin-Miao; Pan, Xiao-Dong; Dong, Ran

2017-01-01

Abstract The effects of genetic variants on warfarin dosing vary among different ethnic groups, especially in the Chinese population. The objective of this study was to recruit patients through a rigorous experimental design and to perform a comprehensive screen to identify gene polymorphisms that may influence warfarin dosing in northern Han Chinese patients with mechanical heart valve replacement. Consenting patients (n = 183) with a stable warfarin dose were included in this study. Ninety-six single nucleotide polymorphisms (SNPs) in 30 genes involved in warfarin pharmacological pathways were genotyped using the Illumina SNP GoldenGate Assay, and their associations with warfarin dosing were assessed using univariate regression analysis with post hoc comparison using least significant difference analysis. Multiple linear regression was performed by incorporating patients’ clinical and genetic data to create a new algorithm for warfarin dosing. From the 96 SNPs analyzed, VKORC1 rs9923231, CYP1A2 rs2069514, CYP3A4 rs28371759, and APOE rs7412 were associated with higher average warfarin maintenance doses, whereas CYP2C9 rs1057910, EPHX1 rs2260863, and CYP4F2 rs2189784 were associated with lower warfarin doses (P < 0.05). Multiple linear regression analysis could estimate 44.4% of warfarin dose variability consisting of, in decreasing order, VKORC1 rs9923231 (14.2%), CYP2C9∗3 (9.6%), body surface area (6.7%), CYP1A2 rs2069514 (3.7%), age (2.7%), CYP3A4 rs28371759 (2.5%), CYP4F2 rs2108622 (1.9%), APOE rs7412 (1.7%), and VKORC1 rs2884737 (1.4%). In the dosing algorithm we developed, we confirmed the strongest effects of VKORC1, CYP2C9 on warfarin dosing. In the limited sample set, we also found that novel genetic predictors (CYP1A2, CYP3A4, APOE, EPHX1, CYP4F2, and VKORC1 rs2884737) may be associated with warfarin dosing. Further validation is needed to assess our results in larger independent northern Chinese samples. PMID:28079798

Mobile Phone-Based Questionnaire for Assessing 3 Months Modified Rankin Score After Acute Stroke: A Pilot Study.

PubMed

Cooray, Charith; Matusevicius, Marius; Wahlgren, Nils; Ahmed, Niaz

2015-10-01

In many countries, a majority of stroke patients are not assessed for long-term functional outcome owing to limited resources and time. We investigated whether automatic assessment of the modified Rankin Scale (mRS) based on a mobile phone questionnaire may serve as an alternative to mRS assessments at clinical visits after stroke. We enrolled 62 acute stroke patients admitted to our stroke unit during March to May 2014. Forty-eight patients completed the study. During the stay, patients and/or caregivers were equipped with a mobile phone application in their personal mobile phones. The mobile phone application contained a set of 20 questions, based on the Rankin Focused Assessment, which we previously tested in a pilot study. Three months after inclusion, the mobile phone application automatically prompted the study participants to answer the mRS questionnaire in the mobile phones. Each question or a group of questions in the questionnaire corresponded to a certain mRS score. Using a predefined protocol, the highest mRS score question where the study participant had answered yes was deemed the final mobile mRS score. A few days later, a study personnel performed a clinical visit mRS assessment. The 2 assessments were compared using quadratic weighing κ-statistics. Mean age was 67 years (38% females), and median baseline National Institutes of Health Stroke Scale (NIHSS) score was 5 (interquartile range 2-10.5, range 0-23). Median and mean clinical visit mRS at 3 months was 2 and 2.3, respectively. We found a 62.5% agreement between clinical visit and mobile mRS assessment, weighted kappa 0.89 (95% confidence interval 0.82-0.96), and unweighted kappa 0.53 (95% confidence interval 0.36-0.70). Dichotomized mRS outcome separating functionally independent (mRS score 0-2) from dependent (mRS score 3-5) showed 83% agreement and unweighted kappa of 0.66 (95% confidence interval 0.45-0.87). Mobile phone-based automatic assessments of mRS performed well in comparison with clinical visit mRS and could be used as an alternative in stroke follow-up. © 2015 American Heart Association, Inc.

Cumulative Small Effect Genetic Markers and the Risk of Colorectal Cancer in Poland, Estonia, Lithuania, and Latvia

PubMed Central

Serrano-Fernandez, Pablo; Dymerska, Dagmara; Kurzawski, Grzegorz; Derkacz, Róża; Sobieszczańska, Tatiana; Banaszkiewicz, Zbigniew; Roomere, Hanno; Oitmaa, Eneli; Metspalu, Andres; Janavičius, Ramūnas; Elsakov, Pavel; Razumas, Mindaugas; Petrulis, Kestutis; Irmejs, Arvīds; Miklaševičs, Edvīns; Scott, Rodney J.; Lubiński, Jan

2015-01-01

The continued identification of new low-penetrance genetic variants for colorectal cancer (CRC) raises the question of their potential cumulative effect among compound carriers. We focused on 6 SNPs (rs380284, rs4464148, rs4779584, rs4939827, rs6983267, and rs10795668), already described as risk markers, and tested their possible independent and combined contribution to CRC predisposition. Material and Methods. DNA was collected and genotyped from 2330 unselected consecutive CRC cases and controls from Estonia (166 cases and controls), Latvia (81 cases and controls), Lithuania (123 cases and controls), and Poland (795 cases and controls). Results. Beyond individual effects, the analysis revealed statistically significant linear cumulative effects for these 6 markers for all samples except of the Latvian one (corrected P value = 0.018 for the Estonian, corrected P value = 0.0034 for the Lithuanian, and corrected P value = 0.0076 for the Polish sample). Conclusions. The significant linear cumulative effects demonstrated here support the idea of using sets of low-risk markers for delimiting new groups with high-risk of CRC in clinical practice that are not carriers of the usual CRC high-risk markers. PMID:26101521

Cumulative Small Effect Genetic Markers and the Risk of Colorectal Cancer in Poland, Estonia, Lithuania, and Latvia.

PubMed

Serrano-Fernandez, Pablo; Dymerska, Dagmara; Kurzawski, Grzegorz; Derkacz, Róża; Sobieszczańska, Tatiana; Banaszkiewicz, Zbigniew; Roomere, Hanno; Oitmaa, Eneli; Metspalu, Andres; Janavičius, Ramūnas; Elsakov, Pavel; Razumas, Mindaugas; Petrulis, Kestutis; Irmejs, Arvīds; Miklaševičs, Edvīns; Scott, Rodney J; Lubiński, Jan

2015-01-01

The continued identification of new low-penetrance genetic variants for colorectal cancer (CRC) raises the question of their potential cumulative effect among compound carriers. We focused on 6 SNPs (rs380284, rs4464148, rs4779584, rs4939827, rs6983267, and rs10795668), already described as risk markers, and tested their possible independent and combined contribution to CRC predisposition. Material and Methods. DNA was collected and genotyped from 2330 unselected consecutive CRC cases and controls from Estonia (166 cases and controls), Latvia (81 cases and controls), Lithuania (123 cases and controls), and Poland (795 cases and controls). Results. Beyond individual effects, the analysis revealed statistically significant linear cumulative effects for these 6 markers for all samples except of the Latvian one (corrected P value = 0.018 for the Estonian, corrected P value = 0.0034 for the Lithuanian, and corrected P value = 0.0076 for the Polish sample). Conclusions. The significant linear cumulative effects demonstrated here support the idea of using sets of low-risk markers for delimiting new groups with high-risk of CRC in clinical practice that are not carriers of the usual CRC high-risk markers.

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

PubMed

Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

2017-07-01

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

Evaluating Reported Candidate Gene Associations with Polycystic Ovary Syndrome

PubMed Central

Pau, Cindy; Saxena, Richa; Welt, Corrine Kolka

2013-01-01

Objective To replicate variants in candidate genes associated with PCOS in a population of European PCOS and control subjects. Design Case-control association analysis and meta-analysis. Setting Major academic hospital Patients Women of European ancestry with PCOS (n=525) and controls (n=472), aged 18 to 45 years. Intervention Variants previously associated with PCOS in candidate gene studies were genotyped (n=39). Metabolic, reproductive and anthropomorphic parameters were examined as a function of the candidate variants. All genetic association analyses were adjusted for age, BMI and ancestry and were reported after correction for multiple testing. Main Outcome Measure Association of candidate gene variants with PCOS. Results Three variants, rs3797179 (SRD5A1), rs12473543 (POMC), and rs1501299 (ADIPOQ), were nominally associated with PCOS. However, they did not remain significant after correction for multiple testing and none of the variants replicated in a sufficiently powered meta-analysis. Variants in the FBN3 gene (rs17202517 and rs73503752) were associated with smaller waist circumferences and variant rs727428 in the SHBG gene was associated with lower SHBG levels. Conclusion Previously identified variants in candidate genes do not appear to be associated with PCOS risk. PMID:23375202

MicroRNAs Are Mediators of Androgen Action in Prostate and Muscle

PubMed Central

Narayanan, Ramesh; Jiang, Jinmai; Gusev, Yuriy; Jones, Amanda; Kearbey, Jeffrey D.; Miller, Duane D.; Schmittgen, Thomas D.; Dalton, James T.

2010-01-01

Androgen receptor (AR) function is critical for the development of male reproductive organs, muscle, bone and other tissues. Functionally impaired AR results in androgen insensitivity syndrome (AIS). The interaction between AR and microRNA (miR) signaling pathways was examined to understand the role of miRs in AR function. Reduction of androgen levels in Sprague-Dawley rats by castration inhibited the expression of a large set of miRs in prostate and muscle, which was reversed by treatment of castrated rats with 3 mg/day dihydrotestosterone (DHT) or selective androgen receptor modulators. Knockout of the miR processing enzyme, DICER, in LNCaP prostate cancer cells or tissue specifically in mice inhibited AR function leading to AIS. Since the only function of miRs is to bind to 3′ UTR and inhibit translation of target genes, androgens might induce miRs to inhibit repressors of AR function. In concordance, knock-down of DICER in LNCaP cells and in tissues in mice induced the expression of corepressors, NCoR and SMRT. These studies demonstrate a feedback loop between miRs, corepressors and AR and the imperative role of miRs in AR function in non-cancerous androgen-responsive tissues. PMID:21048966

Resistant starch can improve insulin sensitivity independently of the gut microbiota.

PubMed

Bindels, Laure B; Segura Munoz, Rafael R; Gomes-Neto, João Carlos; Mutemberezi, Valentin; Martínez, Inés; Salazar, Nuria; Cody, Elizabeth A; Quintero-Villegas, Maria I; Kittana, Hatem; de Los Reyes-Gavilán, Clara G; Schmaltz, Robert J; Muccioli, Giulio G; Walter, Jens; Ramer-Tait, Amanda E

2017-02-07

Obesity-related diseases, including type 2 diabetes and cardiovascular disease, have reached epidemic proportions in industrialized nations, and dietary interventions for their prevention are therefore important. Resistant starches (RS) improve insulin sensitivity in clinical trials, but the mechanisms underlying this health benefit remain poorly understood. Because RS fermentation by the gut microbiota results in the formation of physiologically active metabolites, we chose to specifically determine the role of the gut microbiota in mediating the metabolic benefits of RS. To achieve this goal, we determined the effects of RS when added to a Western diet on host metabolism in mice with and without a microbiota. RS feeding of conventionalized mice improved insulin sensitivity and redressed some of the Western diet-induced changes in microbiome composition. However, parallel experiments in germ-free littermates revealed that RS-mediated improvements in insulin levels also occurred in the absence of a microbiota. RS reduced gene expression of adipose tissue macrophage markers and altered cecal concentrations of several bile acids in both germ-free and conventionalized mice; these effects were strongly correlated with the metabolic benefits, providing a potential microbiota-independent mechanism to explain the physiological effects of RS. This study demonstrated that some metabolic benefits exerted by dietary RS, especially improvements in insulin levels, occur independently of the microbiota and could involve alterations in the bile acid cycle and adipose tissue immune modulation. This work also sets a precedent for future mechanistic studies aimed at establishing the causative role of the gut microbiota in mediating the benefits of bioactive compounds and functional foods.

A non-invasive assessment of skin carotenoid status through reflection spectroscopy is a feasible, reliable and potentially valid measure of fruit and vegetable consumption in a diverse community sample.

PubMed

Jilcott Pitts, Stephanie Bell; Jahns, Lisa; Wu, Qiang; Moran, Nancy E; Bell, Ronny A; Truesdale, Kimberly P; Laska, Melissa N

2018-06-01

To assess the feasibility, reliability and validity of reflection spectroscopy (RS) to assess skin carotenoids in a racially diverse sample. Study 1 was a cross-sectional study of corner store customers (n 479) who completed the National Cancer Institute Fruit and Vegetable Screener as well as RS measures. Feasibility was assessed by examining the time it took to complete three RS measures, reliability was assessed by examining the variation between three RS measures, and validity was examined by correlation with self-reported fruit and vegetable consumption. In Study 2, validity was assessed in a smaller sample (n 30) by examining associations between RS measures and dietary carotenoids, fruits and vegetables as calculated from a validated FFQ and plasma carotenoids. Eastern North Carolina, USA. It took on average 94·0 s to complete three RS readings per person. The average variation between three readings for each participant was 6·8 %. In Study 2, in models adjusted for age, race and sex, there were statistically significant associations between RS measures and (i) FFQ-estimated carotenoid intake (P<0·0001); (ii) FFQ-estimated fruit and vegetable consumption (P<0·010); and (iii) plasma carotenoids (P<0·0001). RS is a potentially improved method to approximate fruit and vegetable consumption among diverse participants. RS is portable and easy to use in field-based public health nutrition settings. More research is needed to investigate validity and sensitivity in diverse populations.

Genetic determinants for gestational diabetes mellitus and related metabolic traits in Mexican women.

PubMed

Huerta-Chagoya, Alicia; Vázquez-Cárdenas, Paola; Moreno-Macías, Hortensia; Tapia-Maruri, Leonardo; Rodríguez-Guillén, Rosario; López-Vite, Erika; García-Escalante, Guadalupe; Escobedo-Aguirre, Fernando; Parra-Covarrubias, Adalberto; Cordero-Brieño, Roberto; Manzo-Carrillo, Lizette; Zacarías-Castillo, Rogelio; Vargas-García, Carlos; Aguilar-Salinas, Carlos; Tusié-Luna, Teresa

2015-01-01

Epidemiological and physiological similarities among Gestational Diabetes Mellitus (GDM) and Type 2 Diabetes (T2D) suggest that both diseases, share a common genetic background. T2D risk variants have been associated to GDM susceptibility. However, the genetic architecture of GDM is not yet completely understood. We analyzed 176 SNPs for 115 loci previously associated to T2D, GDM and body mass index (BMI), as well as a set of 118 Ancestry Informative Markers (AIMs), in 750 pregnant Mexican women. Association with GDM was found for two of the most frequently replicated T2D loci: a TCF7L2 haplotype (CTTC: rs7901695, rs4506565, rs7903146, rs12243326; P=2.16 x 10(-06); OR=2.95) and a KCNQ1 haplotype (TTT: rs2237892, rs163184, rs2237897; P=1.98 x 10(-05); OR=0.55). In addition, we found two loci associated to glycemic traits: CENTD2 (60' OGTT glycemia: rs1552224, P=0.03727) and MTNR1B (HOMA B: rs1387153, P=0.05358). Remarkably, a major susceptibility SLC16A11 locus for T2D in Mexicans was not shown to play a role in GDM risk. The fact that two of the main T2D associated loci also contribute to the risk of developing GDM in Mexicans, confirm that both diseases share a common genetic background. However, lack of association with a Native American contribution T2D risk haplotype, SLC16A11, suggests that other genetic mechanisms may be in play for GDM.

Genetic Determinants for Gestational Diabetes Mellitus and Related Metabolic Traits in Mexican Women

PubMed Central

Huerta-Chagoya, Alicia; Vázquez-Cárdenas, Paola; Moreno-Macías, Hortensia; Tapia-Maruri, Leonardo; Rodríguez-Guillén, Rosario; López-Vite, Erika; García-Escalante, Guadalupe; Escobedo-Aguirre, Fernando; Parra-Covarrubias, Adalberto; Cordero-Brieño, Roberto; Manzo-Carrillo, Lizette; Zacarías-Castillo, Rogelio; Aguilar-Salinas, Carlos; Tusié-Luna, Teresa

2015-01-01

Epidemiological and physiological similarities among Gestational Diabetes Mellitus (GDM) and Type 2 Diabetes (T2D) suggest that both diseases, share a common genetic background. T2D risk variants have been associated to GDM susceptibility. However, the genetic architecture of GDM is not yet completely understood. We analyzed 176 SNPs for 115 loci previously associated to T2D, GDM and body mass index (BMI), as well as a set of 118 Ancestry Informative Markers (AIMs), in 750 pregnant Mexican women. Association with GDM was found for two of the most frequently replicated T2D loci: a TCF7L2 haplotype (CTTC: rs7901695, rs4506565, rs7903146, rs12243326; P=2.16x10-06; OR=2.95) and a KCNQ1 haplotype (TTT: rs2237892, rs163184, rs2237897; P=1.98x10-05; OR=0.55). In addition, we found two loci associated to glycemic traits: CENTD2 (60’ OGTT glycemia: rs1552224, P=0.03727) and MTNR1B (HOMA B: rs1387153, P=0.05358). Remarkably, a major susceptibility SLC16A11 locus for T2D in Mexicans was not shown to play a role in GDM risk. The fact that two of the main T2D associated loci also contribute to the risk of developing GDM in Mexicans, confirm that both diseases share a common genetic background. However, lack of association with a Native American contribution T2D risk haplotype, SLC16A11, suggests that other genetic mechanisms may be in play for GDM. PMID:25973943

Reduced risk of recurrent myocardial infarction in homozygous carriers of the chromosome 9p21 rs1333049 C risk allele in the contemporary percutaneous coronary intervention era: a prospective observational study

PubMed Central

Hara, Masahiko; Sakata, Yasuhiko; Nakatani, Daisaku; Suna, Shinichiro; Usami, Masaya; Matsumoto, Sen; Ozaki, Kouichi; Nishino, Masami; Sato, Hiroshi; Kitamura, Tetsuhisa; Nanto, Shinsuke; Hamasaki, Toshimitsu; Tanaka, Toshihiro; Hori, Masatsugu; Komuro, Issei

2014-01-01

Objectives Chromosome 9p21 single nucleotide polymorphism (SNP) is a susceptibility variant for acute myocardial infarction (AMI) in the primary prevention setting. However, it is controversial whether this SNP is also associated with recurrent myocardial infarction (ReMI) in the secondary prevention setting. The purpose of this study is to evaluate the impact of chromosome 9p21 SNP on ReMI in patients receiving secondary prevention programmes after AMI. Design A prospective observational study. Setting Osaka Acute Coronary Insufficiency Study (OACIS) in Japan. Participants 2022 patients from the OACIS database. Interventions Genotyping of the 9p21 rs1333049 variant. Primary outcome measures ReMI event after survival discharge for 1 year. Results A total of 43 ReMI occurred during the 1 year follow-up period. Although the rs1333049 C allele had an increased susceptibility to their first AMI in an additive model when compared with 1373 healthy controls (OR 1.20, 95% CI 1.09 to 1.33, p=2.3*10−4), patients with the CC genotype had a lower incidence of ReMI at 1 year after discharge of AMI (log-rank p=0.005). The adjusted HR of the CC genotype as compared with the CG/GG genotypes was 0.20 (0.06 to 0.65, p=0.007). Subgroup analysis demonstrated that the association between the rs1333049 CC genotype and a lower incidence of 1 year ReMI was common to all subgroups. Conclusions Homozygous carriers of the rs1333049 C allele on chromosome 9p21 showed a reduced risk of 1 year ReMI in the contemporary percutaneous coronary intervention era, although the C allele had conferred susceptibility to their first AMI. PMID:25232560

Role of PTPN22 and CSK gene polymorphisms as predictors of susceptibility and clinical heterogeneity in patients with Henoch-Schönlein purpura (IgA vasculitis).

PubMed

López-Mejías, Raquel; Genre, Fernanda; Remuzgo-Martínez, Sara; Pérez, Belén Sevilla; Castañeda, Santos; Llorca, Javier; Ortego-Centeno, Norberto; Ubilla, Begoña; Mijares, Verónica; Pina, Trinitario; Calvo-Río, Vanesa; Palmou, Natalia; Miranda-Filloy, José A; Parejo, Antonio Navas; Argila, Diego; Sánchez-Pérez, Javier; Rubio, Esteban; Luque, Manuel León; Blanco-Madrigal, Juan María; Galíndez-Aguirregoikoa, Eva; Ocejo-Vinyals, J Gonzalo; Martín, Javier; Blanco, Ricardo; González-Gay, Miguel A

2015-10-13

To determine whether the PTPN22 (protein tyrosine phosphatase nonreceptor 22)/CSK (c-src tyrosine kinase) pathway is implicated in the susceptibility and clinical heterogeneity of Henoch-Schönlein purpura (HSP) in the largest series of Caucasian HSP patients ever assessed for genetic studies. A set of 329 Spanish patients diagnosed with HSP fulfilling the American College of Rheumatology and the Michel et al. classification criteria and 515 sex and ethnically matched controls were recruited in this study. Two well-known CSK (CSK rs34933034 and CSK rs1378942) and two functional PTPN22 (PTPN22 rs2476601 (R620W) and PTPN22 rs33996649 (R263Q)) polymorphisms, previously associated with autoimmunity, were genotyped with TaqMan single nucleotide polymorphism (SNP) genotyping assays. No significant differences in the genotype and allele frequencies between HSP patients and controls were observed when the CSK rs34933034, CSK rs1378942, PTPN22 rs2476601 (R620W) and PTPN22 rs33996649 (R263Q) polymorphisms were analyzed independently. In keeping with this observation, no significant differences were found when we assessed these polymorphisms combined conforming haplotypes. In addition, there were no differences in the allele or genotype frequencies when HSP patients were stratified according the age at disease onset, sex, presence of arthralgia/arthritis, nephritis or gastrointestinal manifestations. Our results do not support association between PTPN22/CSK and HSP.

Rough Titanium Oxide Coating Prepared by Micro-Arc Oxidation Causes Down-Regulation of hTERT Expression, Molecular Presentation, and Cytokine Secretion in Tumor Jurkat T Cells

PubMed Central

Khlusov, Igor; Shupletsova, Valeria; Khaziakhmatova, Olga; Melashchenko, Elena; Yurova, Kristina; Khlusova, Marina; Pichugin, Vladimir; Sharkeev, Yurii

2018-01-01

The response of the human Jurkat T cell leukemia-derived cell line (Jurkat T cells) after 24 h of in vitro exposure to a titanium substrate (12 × 12 × 1 mm3) with a bilateral rough (Ra = 2.2–3.7 μm) titanium oxide coating (rTOC) applied using the micro-arc method in a 20% orthophosphoric acid solution was studied. A 1.5-fold down-regulation of hTERT mRNA expression and decreases in CD3, CD4, CD8, and CD95 presentation and IL-4 and TNFα secretion were observed. Jurkat T cell inactivation was not correlated with the generation of intracellular reactive oxygen species (ROS) and was not mediated by TiO2 nanoparticles with a diameter of 14 ± 8 nm at doses of 1 mg/L or 10 mg/L. The inhibitory effect of the rTOC (Ra = 2.2–3.7 μm) on the survival of Jurkat T cells (Spearman’s coefficient rs = −0.95; n = 9; p < 0.0001) was demonstrated by an increase in the necrotic cell count among the cell population. In turn, an elevation of the Ra index of the rTOC was accompanied by a linear increase (r = 0.6; p < 0.000001, n = 60) in the magnitude of the negative electrostatic potential of the titanium oxide surface. Thus, the roughness of the rTOC induces an electrostatic potential and decreases the viability of the immortalized Jurkat T cells through mechanisms unrelated to ROS generation. This may be useful for replacement surgery applications of rough TiO2 implants in cancer patients. PMID:29495627

Multimodal Optimization by Covariance Matrix Self-Adaptation Evolution Strategy with Repelling Subpopulations.

PubMed

Ahrari, Ali; Deb, Kalyanmoy; Preuss, Mike

2017-01-01

During the recent decades, many niching methods have been proposed and empirically verified on some available test problems. They often rely on some particular assumptions associated with the distribution, shape, and size of the basins, which can seldom be made in practical optimization problems. This study utilizes several existing concepts and techniques, such as taboo points, normalized Mahalanobis distance, and the Ursem's hill-valley function in order to develop a new tool for multimodal optimization, which does not make any of these assumptions. In the proposed method, several subpopulations explore the search space in parallel. Offspring of a subpopulation are forced to maintain a sufficient distance to the center of fitter subpopulations and the previously identified basins, which are marked as taboo points. The taboo points repel the subpopulation to prevent convergence to the same basin. A strategy to update the repelling power of the taboo points is proposed to address the challenge of basins of dissimilar size. The local shape of a basin is also approximated by the distribution of the subpopulation members converging to that basin. The proposed niching strategy is incorporated into the covariance matrix self-adaptation evolution strategy (CMSA-ES), a potent global optimization method. The resultant method, called the covariance matrix self-adaptation with repelling subpopulations (RS-CMSA), is assessed and compared to several state-of-the-art niching methods on a standard test suite for multimodal optimization. An organized procedure for parameter setting is followed which assumes a rough estimation of the desired/expected number of minima available. Performance sensitivity to the accuracy of this estimation is also studied by introducing the concept of robust mean peak ratio. Based on the numerical results using the available and the introduced performance measures, RS-CMSA emerges as the most successful method when robustness and efficiency are considered at the same time.

Nonvolatile resistive switching in metal/La-doped BiFeO3/Pt sandwiches.

PubMed

Li, Mi; Zhuge, Fei; Zhu, Xiaojian; Yin, Kuibo; Wang, Jinzhi; Liu, Yiwei; He, Congli; Chen, Bin; Li, Run-Wei

2010-10-22

The resistive switching (RS) characteristics of a Bi(0.95)La(0.05)FeO(3) (La-BFO) film sandwiched between a Pt bottom electrode and top electrodes (TEs) made of Al, Ag, Cu, and Au have been studied. Devices with TEs made of Ag and Cu showed stable bipolar RS behaviors, whereas those with TEs made of Al and Au exhibited unstable bipolar RS. The Ag/La-BFO/Pt structure showed an on/off ratio of 10(2), a retention time > 10(5) s, and programming voltages < 1 V. The RS effect can be attributed to the formation/rupture of nanoscale metal filaments due to the diffusion of the TEs under a bias voltage. The maximum current before the reset process (on-to-off switching) was found to increase linearly with the current compliance applied during the set process (off-to-on switching).

Distinguishing institutional identification from academic goal pursuit: interactive effects of ethnic identification and race-based rejection sensitivity.

PubMed

Mendoza-Denton, Rodolfo; Pietrzak, Janina; Downey, Geraldine

2008-08-01

We examined the interactive effects of ethnic identification (EI) and race-based rejection sensitivity (RS-race) on institutional outcomes among African American college students. We distinguished between effects on institutional identification on the one hand and academic goal pursuit (e.g., staying in school, grade point average [GPA]) on the other. Supporting the utility of this distinction, we found that EI and RS-race interacted to predict these outcomes differently. Higher EI in combination with higher RS-race predicted reduced identification with the institution (Studies 1, 2, and 3a). This combination, however, did not lead to decreases in GPA over time. Moreover, EI was positively related to intentions to stay in school as well as to GPA increases among those lower in RS-race (Studies 1 and 3b). Implications for understanding identity negotiation vis-à-vis performance in institutional settings are discussed. (c) 2008 APA, all rights reserved

Association between genetic variation within vitamin D receptor-DNA binding sites and risk of basal cell carcinoma.

PubMed

Lin, Yuan; Chahal, Harvind S; Wu, Wenting; Cho, Hyunje G; Ransohoff, Katherine J; Dai, Hongji; Tang, Jean Y; Sarin, Kavita Y; Han, Jiali

2017-05-01

An increasing number of studies have reported a protective association between vitamin D and cancer risk. The vitamin D endocrine system regulates transcriptional programs involved in inflammation, cell growth and differentiation through the binding of vitamin D receptor (VDR) to specific VDR elements. However, limited attention has been given to the role of variation within VDR binding sites in the development of basal cell carcinoma (BCC). Across 2,776 previously identified VDR binding sites, we identified 2,540 independent single-nucleotide polymorphisms (SNPs) and examined their associations with BCC risk in a genome-wide association meta-analysis totaling 17,187 BCC cases and 287,054 controls from two data sets. After multiple testing corrections, we identified two SNPs at new loci (rs16917546 at 10q21.1: odds ratio (OR) = 1.06, p = 3.16 × 10 -7 and rs79824801 at 12q13.3: OR = 1.10, p = 1.88 × 10 -5 ) for the first time as independently related to BCC risk in meta-analysis; and both SNPs were nominally significant in two data sets. In addition, the SNP rs3769823 within VDR binding site at a previously reported BCC susceptibility locus (2q33.1, rs13014235) also exhibited a significant association (OR = 1.12, p = 3.99 × 10 -18 ). A mutually adjusted model suggested that rs3769823 explained the signal in this region. Our findings support the hypothesis that inherited common variation in VDR binding sites affects the development of BCC. © 2017 UICC.

[Association of single nucleotide polymorphisms of susceptibility genes of type 2 diabetes mellitus with liability to gout among ethnic Han Chinese males from coastal region of Shandong].

PubMed

Han, Lin; Xin, Ruosai; Sun, Jian; Hou, Feng; Li, Changgui; Hu, Xinlin; Liu, Zhen; Wang, Yao; Li, Xinde; Ren, Wei; Wang, Xuefeng; Jia, Zhaotong

2015-10-01

OBJECTIVE To assess the association of single nucleotide polymorphisms (SNPs) of susceptibility genes of type 2 diabetes mellitus (T2DM) with liability to gout among ethnic Han Chinese males from coastal region of Shandong province. METHODS Seven SNPs within the susceptibility genes of T2DM, including rs10773971(G/C) and rs4766398(G/C) of WNT5B gene, rs10225163(G/C) of JAZF1 gene, rs2069590(T/A) of BDKRB2 gene, rs5745709(G/A) of HGF gene, rs1991914(C/A) of OTOP1 gene and rs2236479(G/A) of COL18A1 gene, were typed with a custom-made Illumina GoldenGate Genotyping assay in 480 male patients with gout and 480 male controls. Potential association was assessed with the chi-square test. RESULTS No significant difference was detected for the 7 selected SNPs in terms of genotypic and allelic frequencies (P > 0.05). When age and body mass index (BMI) were adjusted, the 7 genetic variants still showed no significant association with gout. CONCLUSION The genotypes of the 7 selected SNPs are not associated with gout in ethnic Han Chinese male patients from the coastal region of Shandong province. However, the results need to be replicated in larger sets of patients collected from other regions and populations.

A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation.

PubMed

Kılıç, Ayşe; Santolini, Marc; Nakano, Taiji; Schiller, Matthias; Teranishi, Mizue; Gellert, Pascal; Ponomareva, Yuliya; Braun, Thomas; Uchida, Shizuka; Weiss, Scott T; Sharma, Amitabh; Renz, Harald

2018-06-07

Allergic asthma is a chronic inflammatory disease dominated by a CD4+ T helper 2 (Th2) cell signature. The immune response amplifies in self-enforcing loops, promoting Th2-driven cellular immunity and leaving the host unable to terminate inflammation. Posttranscriptional mechanisms, including microRNAs (miRs), are pivotal in maintaining immune homeostasis. Since an altered expression of various miRs has been associated with T cell-driven diseases, including asthma, we hypothesized that miRs control mechanisms ensuring Th2 stability and maintenance in the lung. We isolated murine CD4+ Th2 cells from allergic inflamed lungs and profiled gene and miR expression. Instead of focusing on the magnitude of miR differential expression, here we addressed the secondary consequences for the set of molecular interactions in the cell, the interactome. We developed the Impact of Differential Expression Across Layers, a network-based algorithm to prioritize disease-relevant miRs based on the central role of their targets in the molecular interactome. This method identified 5 Th2-related miRs (mir27b, mir206, mir106b, mir203, and mir23b) whose antagonization led to a sharp reduction of the Th2 phenotype. Overall, a systems biology tool was developed and validated, highlighting the role of miRs in Th2-driven immune response. This result offers potentially novel approaches for therapeutic interventions.

Genome-wide Meta-analyses of Breast, Ovarian and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by At Least Two Cancer Types

PubMed Central

Kar, Siddhartha P.; Beesley, Jonathan; Al Olama, Ali Amin; Michailidou, Kyriaki; Tyrer, Jonathan; Kote-Jarai, ZSofia; Lawrenson, Kate; Lindstrom, Sara; Ramus, Susan J.; Thompson, Deborah J.; Kibel, Adam S.; Dansonka-Mieszkowska, Agnieszka; Michael, Agnieszka; Dieffenbach, Aida K.; Gentry-Maharaj, Aleksandra; Whittemore, Alice S.; Wolk, Alicja; Monteiro, Alvaro; Peixoto, Ana; Kierzek, Andrzej; Cox, Angela; Rudolph, Anja; Gonzalez-Neira, Anna; Wu, Anna H.; Lindblom, Annika; Swerdlow, Anthony; Ziogas, Argyrios; Ekici, Arif B.; Burwinkel, Barbara; Karlan, Beth Y.; Nordestgaard, Børge G.; Blomqvist, Carl; Phelan, Catherine; McLean, Catriona; Pearce, Celeste Leigh; Vachon, Celine; Cybulski, Cezary; Slavov, Chavdar; Stegmaier, Christa; Maier, Christiane; Ambrosone, Christine B.; Høgdall, Claus K.; Teerlink, Craig C.; Kang, Daehee; Tessier, Daniel C.; Schaid, Daniel J.; Stram, Daniel O.; Cramer, Daniel W.; Neal, David E.; Eccles, Diana; Flesch-Janys, Dieter; Velez Edwards, Digna R.; Wokozorczyk, Dominika; Levine, Douglas A.; Yannoukakos, Drakoulis; Sawyer, Elinor J.; Bandera, Elisa V.; Poole, Elizabeth M.; Goode, Ellen L.; Khusnutdinova, Elza; Høgdall, Estrid; Song, Fengju; Bruinsma, Fiona; Heitz, Florian; Modugno, Francesmary; Hamdy, Freddie C.; Wiklund, Fredrik; Giles, Graham G.; Olsson, Håkan; Wildiers, Hans; Ulmer, Hans-Ulrich; Pandha, Hardev; Risch, Harvey A.; Darabi, Hatef; Salvesen, Helga B.; Nevanlinna, Heli; Gronberg, Henrik; Brenner, Hermann; Brauch, Hiltrud; Anton-Culver, Hoda; Song, Honglin; Lim, Hui-Yi; McNeish, Iain; Campbell, Ian; Vergote, Ignace; Gronwald, Jacek; Lubiński, Jan; Stanford, Janet L.; Benítez, Javier; Doherty, Jennifer A.; Permuth, Jennifer B.; Chang-Claude, Jenny; Donovan, Jenny L.; Dennis, Joe; Schildkraut, Joellen M.; Schleutker, Johanna; Hopper, John L.; Kupryjanczyk, Jolanta; Park, Jong Y.; Figueroa, Jonine; Clements, Judith A.; Knight, Julia A.; Peto, Julian; Cunningham, Julie M.; Pow-Sang, Julio; Batra, Jyotsna; Czene, Kamila; Lu, Karen H.; Herkommer, Kathleen; Khaw, Kay-Tee; Matsuo, Keitaro; Muir, Kenneth; Offitt, Kenneth; Chen, Kexin; Moysich, Kirsten B.; Aittomäki, Kristiina; Odunsi, Kunle; Kiemeney, Lambertus A.; Massuger, Leon F.A.G.; Fitzgerald, Liesel M.; Cook, Linda S.; Cannon-Albright, Lisa; Hooning, Maartje J.; Pike, Malcolm C.; Bolla, Manjeet K.; Luedeke, Manuel; Teixeira, Manuel R.; Goodman, Marc T.; Schmidt, Marjanka K.; Riggan, Marjorie; Aly, Markus; Rossing, Mary Anne; Beckmann, Matthias W.; Moisse, Matthieu; Sanderson, Maureen; Southey, Melissa C.; Jones, Michael; Lush, Michael; Hildebrandt, Michelle A. T.; Hou, Ming-Feng; Schoemaker, Minouk J.; Garcia-Closas, Montserrat; Bogdanova, Natalia; Rahman, Nazneen; Le, Nhu D.; Orr, Nick; Wentzensen, Nicolas; Pashayan, Nora; Peterlongo, Paolo; Guénel, Pascal; Brennan, Paul; Paulo, Paula; Webb, Penelope M.; Broberg, Per; Fasching, Peter A.; Devilee, Peter; Wang, Qin; Cai, Qiuyin; Li, Qiyuan; Kaneva, Radka; Butzow, Ralf; Kopperud, Reidun Kristin; Schmutzler, Rita K.; Stephenson, Robert A.; MacInnis, Robert J.; Hoover, Robert N.; Winqvist, Robert; Ness, Roberta; Milne, Roger L.; Travis, Ruth C.; Benlloch, Sara; Olson, Sara H.; McDonnell, Shannon K.; Tworoger, Shelley S.; Maia, Sofia; Berndt, Sonja; Lee, Soo Chin; Teo, Soo-Hwang; Thibodeau, Stephen N.; Bojesen, Stig E.; Gapstur, Susan M.; Kjær, Susanne Krüger; Pejovic, Tanja; Tammela, Teuvo L.J.; Dörk, Thilo; Brüning, Thomas; Wahlfors, Tiina; Key, Tim J.; Edwards, Todd L.; Menon, Usha; Hamann, Ute; Mitev, Vanio; Kosma, Veli-Matti; Setiawan, Veronica Wendy; Kristensen, Vessela; Arndt, Volker; Vogel, Walther; Zheng, Wei; Sieh, Weiva; Blot, William J.; Kluzniak, Wojciech; Shu, Xiao-Ou; Gao, Yu-Tang; Schumacher, Fredrick; Freedman, Matthew L.; Berchuck, Andrew; Dunning, Alison M.; Simard, Jacques; Haiman, Christopher A.; Spurdle, Amanda; Sellers, Thomas A.; Hunter, David J.; Henderson, Brian E.; Kraft, Peter; Chanock, Stephen J.; Couch, Fergus J.; Hall, Per; Gayther, Simon A.; Easton, Douglas F.; Chenevix-Trench, Georgia; Eeles, Rosalind; Pharoah, Paul D.P.; Lambrechts, Diether

2016-01-01

Breast, ovarian, and prostate cancers are hormone-related and may have a shared genetic basis but this has not been investigated systematically by genome-wide association (GWA) studies. Meta-analyses combining the largest GWA meta-analysis data sets for these cancers totaling 112,349 cases and 116,421 controls of European ancestry, all together and in pairs, identified at P < 10−8 seven new cross-cancer loci: three associated with susceptibility to all three cancers (rs17041869/2q13/BCL2L11; rs7937840/11q12/INCENP; rs1469713/19p13/GATAD2A), two breast and ovarian cancer risk loci (rs200182588/9q31/SMC2; rs8037137/15q26/RCCD1), and two breast and prostate cancer risk loci (rs5013329/1p34/NSUN4; rs9375701/6q23/L3MBTL3). Index variants in five additional regions previously associated with only one cancer also showed clear association with a second cancer type. Cell-type specific expression quantitative trait locus and enhancer-gene interaction annotations suggested target genes with potential cross-cancer roles at the new loci. Pathway analysis revealed significant enrichment of death receptor signaling genes near loci with P < 10−5 in the three-cancer meta-analysis. PMID:27432226

A global regulatory system links virulence and antibiotic resistance to envelope homeostasis in Acinetobacter baumannii.

PubMed

Geisinger, Edward; Mortman, Nadav J; Vargas-Cuebas, Germán; Tai, Albert K; Isberg, Ralph R

2018-05-01

The nosocomial pathogen Acinetobacter baumannii is a significant threat due to its ability to cause infections refractory to a broad range of antibiotic treatments. We show here that a highly conserved sensory-transduction system, BfmRS, mediates the coordinate development of both enhanced virulence and resistance in this microorganism. Hyperactive alleles of BfmRS conferred increased protection from serum complement killing and allowed lethal systemic disease in mice. BfmRS also augmented resistance and tolerance against an expansive set of antibiotics, including dramatic protection from β-lactam toxicity. Through transcriptome profiling, we showed that BfmRS governs these phenotypes through global transcriptional regulation of a post-exponential-phase-like program of gene expression, a key feature of which is modulation of envelope biogenesis and defense pathways. BfmRS activity defended against cell-wall lesions through both β-lactamase-dependent and -independent mechanisms, with the latter being connected to control of lytic transglycosylase production and proper coordination of morphogenesis and division. In addition, hypersensitivity of bfmRS knockouts could be suppressed by unlinked mutations restoring a short, rod cell morphology, indicating that regulation of drug resistance, pathogenicity, and envelope morphogenesis are intimately linked by this central regulatory system in A. baumannii. This work demonstrates that BfmRS controls a global regulatory network coupling cellular physiology to the ability to cause invasive, drug-resistant infections.

Association between regulator of telomere elongation helicase1 (RTEL1) gene and HAPE risk: A case-control study.

PubMed

Rong, Hao; He, Xue; Zhu, Linhao; Zhu, Xikai; Kang, Longli; Wang, Li; He, Yongjun; Yuan, Dongya; Jin, Tianbo

2017-09-01

High altitude pulmonary edema (HAPE) is a paradigm of pulmonary edema. Mutations in regulator of telomere elongation helicase1 (RTEL1) represent an important contributor to risk for pulmonary fibrosis. However, little information is found about the association between RTEL1 and HAPE risk. The present study was undertaken to tentatively explore the potential relation between single-nucleotide polymorphisms (SNPs) in RTEL1 and HAPE risk in Chinese Han population. A total of 265 HAPE patients and 303 healthy controls were included in our case-control study. Four SNPs in RTEL1 were selected and genotyped using the Sequenom MassARRAY method. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated by unconditional logistic regression with adjustment for gender and age. All P values were Bonferroni corrected, and statistical significance was set at P < .0025 (.05/20). In allelic model analysis, we found that the allele "G" of rs6089953 and rs6010621 and the allele "A" of rs2297441 were associated with decreased risk of HAPE. In the genetic model analysis, we found that rs6010621, rs6089953, and rs2297441 were relevant to decreased HAPE risk under dominant model (rs6010621: OR = 0.55; 95% CI = 0.39-0.78; P = .001; rs6089953: OR = 0.68; 95% CI = 0.48-0.96; P = .027; rs2297441: OR = 0.63; 95% CI = 0.45-0.89; P = .008, respectively) and additive model (rs6010621: OR = 0.51; 95% CI = 0.46-0.81; P < .001; rs6089953: OR = 0.72; 95% CI = 0.55-0.95; P = .022; rs2297441: OR = 0.73; 95% CI = 0.57-0.95; P = .019, respectively). SNPs rs6010621 remained significant after Bonferroni correction (P < .0025). In addition, haplotype "GG, GT, AT" of rs6089953-rs6010621 were detected significantly associated with HAPE risk (P < .05), haplotype "GG" remained significant after Bonferroni correction (P < .0025). Our findings provide new evidence for the association between SNPs in RTEL1 and a decreased risk HAPE in the Chinese population. The results need further confirmation.

Association between regulator of telomere elongation helicase1 (RTEL1) gene and HAPE risk

PubMed Central

Rong, Hao; He, Xue; Zhu, Linhao; Zhu, Xikai; Kang, Longli; Wang, Li; He, Yongjun; Yuan, Dongya; Jin, Tianbo

2017-01-01

Abstract High altitude pulmonary edema (HAPE) is a paradigm of pulmonary edema. Mutations in regulator of telomere elongation helicase1 (RTEL1) represent an important contributor to risk for pulmonary fibrosis. However, little information is found about the association between RTEL1 and HAPE risk. The present study was undertaken to tentatively explore the potential relation between single-nucleotide polymorphisms (SNPs) in RTEL1 and HAPE risk in Chinese Han population. A total of 265 HAPE patients and 303 healthy controls were included in our case-control study. Four SNPs in RTEL1 were selected and genotyped using the Sequenom MassARRAY method. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated by unconditional logistic regression with adjustment for gender and age. All P values were Bonferroni corrected, and statistical significance was set at P < .0025 (.05/20). In allelic model analysis, we found that the allele “G” of rs6089953 and rs6010621 and the allele “A” of rs2297441 were associated with decreased risk of HAPE. In the genetic model analysis, we found that rs6010621, rs6089953, and rs2297441 were relevant to decreased HAPE risk under dominant model (rs6010621: OR = 0.55; 95% CI = 0.39–0.78; P = .001; rs6089953: OR = 0.68; 95% CI = 0.48–0.96; P = .027; rs2297441: OR = 0.63; 95% CI = 0.45–0.89; P = .008, respectively) and additive model (rs6010621: OR = 0.51; 95% CI = 0.46–0.81; P < .001; rs6089953: OR = 0.72; 95% CI = 0.55–0.95; P = .022; rs2297441: OR = 0.73; 95% CI = 0.57–0.95; P = .019, respectively). SNPs rs6010621 remained significant after Bonferroni correction (P < .0025). In addition, haplotype “GG, GT, AT” of rs6089953-rs6010621 were detected significantly associated with HAPE risk (P < .05), haplotype “GG” remained significant after Bonferroni correction (P < .0025). Our findings provide new evidence for the association between SNPs in RTEL1 and a decreased risk HAPE in the Chinese population. The results need further confirmation. PMID:28953687

Drexel at TREC 2014 Federated Web Search Track

DTIC Science & Technology

2014-11-01

of its input RS results. 1. INTRODUCTION Federated Web Search is the task of searching multiple search engines simultaneously and combining their...or distributed properly[5]. The goal of RS is then, for a given query, to select only the most promising search engines from all those available. Most...result pages of 149 search engines . 4000 queries are used in building the sample set. As a part of the Vertical Selection task, search engines are

Simulated annealing with restart strategy for the blood pickup routing problem

NASA Astrophysics Data System (ADS)

Yu, V. F.; Iswari, T.; Normasari, N. M. E.; Asih, A. M. S.; Ting, H.

2018-04-01

This study develops a simulated annealing heuristic with restart strategy (SA_RS) for solving the blood pickup routing problem (BPRP). BPRP minimizes the total length of the routes for blood bag collection between a blood bank and a set of donation sites, each associated with a time window constraint that must be observed. The proposed SA_RS is implemented in C++ and tested on benchmark instances of the vehicle routing problem with time windows to verify its performance. The algorithm is then tested on some newly generated BPRP instances and the results are compared with those obtained by CPLEX. Experimental results show that the proposed SA_RS heuristic effectively solves BPRP.

ROSAT x ray survey observations of active chromospheric binary systems and other selected sources

NASA Technical Reports Server (NTRS)

Ramsey, Lawrence W.

1993-01-01

The connection between processes that produce optical chromospheric activity indicators and those that produce x-rays in RS CVn binary systems by taking advantage of the ROSAT All-Sky Survey (RASS) results and our unique ground-based data set was investigated. In RS CVn systems, excess emission in the Ca 2 resonance (K & H) and infrared triplet (IRT) lines and in the Balmer lines of hydrogen is generally cited as evidence for chromospheric activity, which is usually modeled as scaled up solar-type activity. X-ray emission in RS CVn systems is believed to arise from coronal loop structures. Results from spectra data obtained from RASS observations are discussed and presented.

RS-Forest: A Rapid Density Estimator for Streaming Anomaly Detection.

PubMed

Wu, Ke; Zhang, Kun; Fan, Wei; Edwards, Andrea; Yu, Philip S

Anomaly detection in streaming data is of high interest in numerous application domains. In this paper, we propose a novel one-class semi-supervised algorithm to detect anomalies in streaming data. Underlying the algorithm is a fast and accurate density estimator implemented by multiple fully randomized space trees (RS-Trees), named RS-Forest. The piecewise constant density estimate of each RS-tree is defined on the tree node into which an instance falls. Each incoming instance in a data stream is scored by the density estimates averaged over all trees in the forest. Two strategies, statistical attribute range estimation of high probability guarantee and dual node profiles for rapid model update, are seamlessly integrated into RS-Forest to systematically address the ever-evolving nature of data streams. We derive the theoretical upper bound for the proposed algorithm and analyze its asymptotic properties via bias-variance decomposition. Empirical comparisons to the state-of-the-art methods on multiple benchmark datasets demonstrate that the proposed method features high detection rate, fast response, and insensitivity to most of the parameter settings. Algorithm implementations and datasets are available upon request.

The red-sequence of 72 WINGS local galaxy clusters

NASA Astrophysics Data System (ADS)

Valentinuzzi, T.; Poggianti, B. M.; Fasano, G.; D'Onofrio, M.; Moretti, A.; Ramella, M.; Biviano, A.; Fritz, J.; Varela, J.; Bettoni, D.; Vulcani, B.; Moles, M.; Couch, W. J.; Dressler, A.; Kjærgaard, P.; Omizzolo, A.; Cava, A.

2011-12-01

We study the color - magnitude red sequence and blue fraction of 72 X-ray selected galaxy clusters at z = 0.04-0.07 from the WINGS survey, searching for correlations between the characteristics of the red sequence (RS) and the environment. We consider the slope and scatter of the red sequence, the number ratio of red luminous-to-faint galaxies, the blue fraction, and the fractions of ellipticals, S0s, and spirals that compose the RS. None of these quantities correlate with the cluster velocity dispersion, X-ray luminosity, number of cluster substructures, BCG prevalence over next brightest galaxies, and the spatial concentration of ellipticals. The properties of the RS, instead, depend strongly on local galaxy density. Higher density regions have a smaller RS scatter, a higher luminous-to-faint ratio, a lower blue fraction, and a lower spiral fraction on the RS. Our results clearly illustrate the prominent effect of the local density in setting the epoch when galaxies become passive and join the red sequence, as opposed to the mass of the galaxy host structure.

RS-Forest: A Rapid Density Estimator for Streaming Anomaly Detection

PubMed Central

Wu, Ke; Zhang, Kun; Fan, Wei; Edwards, Andrea; Yu, Philip S.

2015-01-01

Anomaly detection in streaming data is of high interest in numerous application domains. In this paper, we propose a novel one-class semi-supervised algorithm to detect anomalies in streaming data. Underlying the algorithm is a fast and accurate density estimator implemented by multiple fully randomized space trees (RS-Trees), named RS-Forest. The piecewise constant density estimate of each RS-tree is defined on the tree node into which an instance falls. Each incoming instance in a data stream is scored by the density estimates averaged over all trees in the forest. Two strategies, statistical attribute range estimation of high probability guarantee and dual node profiles for rapid model update, are seamlessly integrated into RS-Forest to systematically address the ever-evolving nature of data streams. We derive the theoretical upper bound for the proposed algorithm and analyze its asymptotic properties via bias-variance decomposition. Empirical comparisons to the state-of-the-art methods on multiple benchmark datasets demonstrate that the proposed method features high detection rate, fast response, and insensitivity to most of the parameter settings. Algorithm implementations and datasets are available upon request. PMID:25685112

Effect of nitrogen-accommodation ability of electrodes in SiNx-based resistive switching devices

NASA Astrophysics Data System (ADS)

Yang, Mei; Wang, Hong; Ma, Xiaohua; Gao, Haixia; Wang, Bin

2017-12-01

Nitrides could create opportunities of tuning resistive-switching (RS) characteristics due to their different electrical properties and ionic chemistry with oxides. Here, we reported on the effect of nitrogen-accommodation ability of electrodes in SiNx-based RS devices. The Ti/SiNx/Pt devices show a self-compliance bipolar RS with excellent reliability. The W/SiNx/Pt devices provide an unstable RS and fall to an intermediate resistance state (IRS) after a set process. The low resistance states of the Ti/SiNx/Pt devices obey Ohmic conduction and Frenkel-Poole emission from a conductive channel. The IRS of the W/SiNx/Pt devices conforms to Schottky emission and Fowler-Nordheim tunneling from a conductive channel/insulator/electrode structure. A nitrogen-ion-based model is proposed to explain the experimental results. According to the model, the nitrogen-accommodation ability of the electrodes dominates the nitrogen-reservoir size and the nitrogen-ion migration at the metal/SiNx interface, modulating the RS characteristics of the SiNx memory devices.

Rough flows and homogenization in stochastic turbulence

NASA Astrophysics Data System (ADS)

Bailleul, I.; Catellier, R.

2017-10-01

We provide in this work a tool-kit for the study of homogenisation of random ordinary differential equations, under the form of a friendly-user black box based on the technology of rough flows. We illustrate the use of this setting on the example of stochastic turbulence.

In vitro evaluation of the influence of velocity on sliding resistance of stainless steel arch wires in a self-ligating orthodontic bracket.

PubMed

Savoldi, F; Visconti, L; Dalessandri, D; Bonetti, S; Tsoi, J K H; Matinlinna, J P; Paganelli, C

2017-05-01

Of the variables used by in vitro studies of resistance to sliding (RS) in orthodontics, sliding velocity (SV) of the wire is often the one farthest from its clinical counterpart. We investigated whether velocity influences the RS at values approximating the orthodontic movement. A SS self-ligating bracket with a NiTi clip was fixed onto a custom-made model. Different shaped orthodontic SS wires of four sizes and two types (round, 0.020″ and 0.022″; rectangular, 0.016″×0.022″ and 0.017″×0.025″) were tested using an Instron ® testing machine. Wires were pulled at four velocities (1×10 -2  mm/s, 1×10 -3  mm/s, 1×10 -4  mm/s, 1×10 -5  mm/s). Shapiro-Wilk test was used to evaluate the normal distribution of the data; two-way ANOVA was performed to compare means in the RS with wire characteristics and SV. Significance level was set at P<.05. RS was higher for rectangular wires, and for those with larger diameters. Lower SV was associated with lower RS, with wire type and size having an interaction effect. The RS relatively to SV can be represented as: RS ∝ α[ln(SV)]+β, where α and β are constants. At very low SV and low normal forces, SV influences the RS of SS archwires in orthodontic brackets, and the proportionality is logarithmic. Although respecting these parameters in vitro is challenging, quantitative evaluations of RS should be carried out at clinically relevant velocities if aiming at translational application in the clinical scenario. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Added Value of Patient-Reported Outcome Measures in Stroke Clinical Practice.

PubMed

Katzan, Irene L; Thompson, Nicolas R; Lapin, Brittany; Uchino, Ken

2017-07-21

There is uncertainty regarding the clinical utility of the data obtained from patient-reported outcome measures (PROMs) for patient care. We evaluated the incremental information obtained by PROMs compared to the clinician-reported modified Rankin Scale (mRS). This was an observational study of 3283 ischemic stroke patients seen in a cerebrovascular clinic from September 14, 2012 to June 16, 2015 who completed the routinely collected PROMs: Stroke Impact Scale-16 (SIS-16), EQ-5D, Patient Health Questionnaire-9, PROMIS Physical Function, and PROMIS fatigue. The amount of variation in the PROMs explained by mRS was determined using r 2 after adjustment for age and level of stroke impairment. The proportion with meaningful change was calculated for patients with ≥2 visits. Concordance with change in the other scales and the ability to discriminate changes in health state as measured by c-statistic was evaluated for mRS versus SIS-16. Correlation between PROMs and mRS was highest for SIS-16 ( r =-0.64, P <0.01). The r 2 ranged from 0.11 (PROMIS fatigue) to 0.56 (SIS-16). Change in scores occurred in 51% with mRS and 35% with SIS-16. There was lower agreement and less ability to discriminate change in mRS than in SIS-16 with change in the other measures. PROMs provide additional valuable information compared to the mRS alone in stroke patients seen in the ambulatory setting. SIS-16 may have a better ability to identify change than mRS in health status of relevance to the patient. PROMs may be a useful addition to mRS in the assessment of health status in clinical practice. © 2017 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

Confirmation of TNIP1 but not RHOB and PSORS1C1 as systemic sclerosis risk factors in a large independent replication study

PubMed Central

Bossini-Castillo, Lara; Martin, Jose Ezequiel; Broen, Jasper; Simeon, Carmen P; Beretta, Lorenzo; Gorlova, Olga Y; Vonk, Madelon C; Ortego-Centeno, Norberto; Espinosa, Gerard; Carreira, Patricia; García de la Peña, Paloma; Oreiro, Natividad; Román-Ivorra, José Andrés; Castillo, María Jesús; González-Gay, Miguel A; Sáez-Comet, Luis; Castellví, Ivan; Schuerwegh, Annemie J; Voskuyl, Alexandre E; Hoffmann-Vold, Anna-Maria; Hesselstrand, Roger; Nordin, Annika; Lunardi, Claudio; Scorza, Raffaella; van Laar, Jacob M; Shiels, Paul G; Herrick, Ariane; Worthington, Jane; Fonseca, Carmen; Denton, Christopher; Tan, Filemon K; Arnett, Frank C; Assassi, Shervin; Koeleman, Bobby P; Mayes, Maureen D; Radstake, Timothy R D J; Martin, Javier

2013-01-01

Introduction A recent genome-wide association study in European systemic sclerosis (SSc) patients identified three loci (PSORS1C1, TNIP1 and RHOB) as novel genetic risk factors for the disease. The aim of this study was to replicate the previously mentioned findings in a large multicentre independent SSc cohort of Caucasian ancestry. Methods 4389 SSc patients and 7611 healthy controls from different European countries and the USA were included in the study. Six single nucleotide polymorphisms (SNP): rs342070, rs13021401 (RHOB), rs2233287, rs4958881, rs3792783 (TNIP1) and rs3130573 (PSORS1C1) were analysed. Overall significance was calculated by pooled analysis of all the cohorts. Haplotype analyses and conditional logistic regression analyses were carried out to explore further the genetic structure of the tested loci. Results Pooled analyses of all the analysed SNPs in TNIP1 revealed significant association with the whole disease (rs2233287 pMH=1.94×10−4, OR 1.19; rs4958881 pMH=3.26×10−5, OR 1.19; rs3792783 pMH=2.16×10−4, OR 1.19). These associations were maintained in all the subgroups considered. PSORS1C1 comparison showed association with the complete set of patients and all the subsets except for the anti-centromere-positive patients. However, the association was dependent on different HLA class II alleles. The variants in the RHOB gene were not associated with SSc or any of its subsets. Conclusions These data confirmed the influence of TNIP1 on an increased susceptibility to SSc and reinforced this locus as a common autoimmunity risk factor. PMID:22896740

Surface roughness manifestations of deep-seated landslide processes

NASA Astrophysics Data System (ADS)

Booth, A. M.; Roering, J. J.; Lamb, M. P.

2012-12-01

In many mountainous drainage basins, deep-seated landslides evacuate large volumes of sediment from small surface areas, leaving behind a strong topographic signature that sets landscape roughness over a range of spatial scales. At long spatial wavelengths of hundreds to thousands of meters, landslides tend to inhibit channel incision and limit topographic relief, effectively smoothing the topography at this length scale. However, at short spatial wavelengths on the order of meters, deformation of deep-seated landslides generates surface roughness that allows expert mappers or automated algorithms to distinguish landslides from the surrounding terrain. Here, we directly connect the characteristic spatial wavelengths and amplitudes of this fine scale surface roughness to the underlying landslide deformation processes. We utilize the two-dimensional wavelet transform with high-resolution, airborne LiDAR-derived digital elevation models to systematically document the characteristic length scales and amplitudes of different kinematic units within slow moving earthflows, a common type of deep-seated landslide. In earthflow source areas, discrete slumped blocks generate high surface roughness, reflecting an extensional deformation regime. In earthflow transport zones, where material translates with minimal surface deformation, roughness decreases as other surface processes quickly smooth short wavelength features. In earthflow depositional toes, compression folds and thrust faults again increase short wavelength surface roughness. When an earthflow becomes inactive, roughness in all of these kinematic zones systematically decreases with time, allowing relative dating of earthflow deposits. We also document how each of these roughness expressions depends on earthflow velocity, using sub-pixel change detection software (COSI-Corr) and pairs of orthorectified aerial photographs to determine spatially extensive landslide surface displacements. In source areas, the wavelength of slumped blocks tends to correlate with velocity as predicted by a simple sliding block model, but the amplitude is insensitive to velocity, suggesting that landslide depth rather than velocity sets this characteristic block amplitude. In both transport zones and depositional toes, the amplitude of the surface roughness is higher where the longitudinal gradient in velocity is higher, confirming that differential movement generates and maintains this fine scale roughness.

Selection of representative embankments based on rough set - fuzzy clustering method

NASA Astrophysics Data System (ADS)

Bin, Ou; Lin, Zhi-xiang; Fu, Shu-yan; Gao, Sheng-song

2018-02-01

The premise condition of comprehensive evaluation of embankment safety is selection of representative unit embankment, on the basis of dividing the unit levee the influencing factors and classification of the unit embankment are drafted.Based on the rough set-fuzzy clustering, the influence factors of the unit embankment are measured by quantitative and qualitative indexes.Construct to fuzzy similarity matrix of standard embankment then calculate fuzzy equivalent matrix of fuzzy similarity matrix by square method. By setting the threshold of the fuzzy equivalence matrix, the unit embankment is clustered, and the representative unit embankment is selected from the classification of the embankment.

Study of self-compliance behaviors and internal filament characteristics in intrinsic SiO{sub x}-based resistive switching memory

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

Chang, Yao-Feng, E-mail: yfchang@utexas.edu; Zhou, Fei; Chen, Ying-Chen

2016-01-18

Self-compliance characteristics and reliability optimization are investigated in intrinsic unipolar silicon oxide (SiO{sub x})-based resistive switching (RS) memory using TiW/SiO{sub x}/TiW device structures. The program window (difference between SET voltage and RESET voltage) is dependent on external series resistance, demonstrating that the SET process is due to a voltage-triggered mechanism. The program window has been optimized for program/erase disturbance immunity and reliability for circuit-level applications. The SET and RESET transitions have also been characterized using a dynamic conductivity method, which distinguishes the self-compliance behavior due to an internal series resistance effect (filament) in SiO{sub x}-based RS memory. By using amore » conceptual “filament/resistive gap (GAP)” model of the conductive filament and a proton exchange model with appropriate assumptions, the internal filament resistance and GAP resistance can be estimated for high- and low-resistance states (HRS and LRS), and are found to be independent of external series resistance. Our experimental results not only provide insights into potential reliability issues but also help to clarify the switching mechanisms and device operating characteristics of SiO{sub x}-based RS memory.« less

An IDS Alerts Aggregation Algorithm Based on Rough Set Theory

NASA Astrophysics Data System (ADS)

Zhang, Ru; Guo, Tao; Liu, Jianyi

2018-03-01

Within a system in which has been deployed several IDS, a great number of alerts can be triggered by a single security event, making real alerts harder to be found. To deal with redundant alerts, we propose a scheme based on rough set theory. In combination with basic concepts in rough set theory, the importance of attributes in alerts was calculated firstly. With the result of attributes importance, we could compute the similarity of two alerts, which will be compared with a pre-defined threshold to determine whether these two alerts can be aggregated or not. Also, time interval should be taken into consideration. Allowed time interval for different types of alerts is computed individually, since different types of alerts may have different time gap between two alerts. In the end of this paper, we apply proposed scheme on DAPRA98 dataset and the results of experiment show that our scheme can efficiently reduce the redundancy of alerts so that administrators of security system could avoid wasting time on useless alerts.

The prefabricated building risk decision research of DM technology on the basis of Rough Set

NASA Astrophysics Data System (ADS)

Guo, Z. L.; Zhang, W. B.; Ma, L. H.

2017-08-01

With the resources crises and more serious pollution, the green building has been strongly advocated by most countries and become a new building style in the construction field. Compared with traditional building, the prefabricated building has its own irreplaceable advantages but is influenced by many uncertainties. So far, a majority of scholars have been studying based on qualitative researches from all of the word. This paper profoundly expounds its significance about the prefabricated building. On the premise of the existing research methods, combined with rough set theory, this paper redefines the factors which affect the prefabricated building risk. Moreover, it quantifies risk factors and establish an expert knowledge base through assessing. And then reduced risk factors about the redundant attributes and attribute values, finally form the simplest decision rule. This simplest decision rule, which is based on the DM technology of rough set theory, provides prefabricated building with a controllable new decision-making method.

CYP1A1, GCLC, AGT, AGTR1 gene-gene interactions in community-acquired pneumonia pulmonary complications.

PubMed

Salnikova, Lyubov E; Smelaya, Tamara V; Golubev, Arkadiy M; Rubanovich, Alexander V; Moroz, Viktor V

2013-11-01

This study was conducted to establish the possible contribution of functional gene polymorphisms in detoxification/oxidative stress and vascular remodeling pathways to community-acquired pneumonia (CAP) susceptibility in the case-control study (350 CAP patients, 432 control subjects) and to predisposition to the development of CAP complications in the prospective study. All subjects were genotyped for 16 polymorphic variants in the 14 genes of xenobiotics detoxification CYP1A1, AhR, GSTM1, GSTT1, ABCB1, redox-status SOD2, CAT, GCLC, and vascular homeostasis ACE, AGT, AGTR1, NOS3, MTHFR, VEGFα. Risk of pulmonary complications (PC) in the single locus analysis was associated with CYP1A1, GCLC and AGTR1 genes. Extra PC (toxic shock syndrome and myocarditis) were not associated with these genes. We evaluated gene-gene interactions using multi-factor dimensionality reduction, and cumulative gene risk score approaches. The final model which included >5 risk alleles in the CYP1A1 (rs2606345, rs4646903, rs1048943), GCLC, AGT, and AGTR1 genes was associated with pleuritis, empyema, acute respiratory distress syndrome, all PC and acute respiratory failure (ARF). We considered CYP1A1, GCLC, AGT, AGTR1 gene set using Set Distiller mode implemented in GeneDecks for discovering gene-set relations via the degree of sharing descriptors within a given gene set. N-acetylcysteine and oxygen were defined by Set Distiller as the best descriptors for the gene set associated in the present study with PC and ARF. Results of the study are in line with literature data and suggest that genetically determined oxidative stress exacerbation may contribute to the progression of lung inflammation.

A rough set-based measurement model study on high-speed railway safety operation.

PubMed

Hu, Qizhou; Tan, Minjia; Lu, Huapu; Zhu, Yun

2018-01-01

Aiming to solve the safety problems of high-speed railway operation and management, one new method is urgently needed to construct on the basis of the rough set theory and the uncertainty measurement theory. The method should carefully consider every factor of high-speed railway operation that realizes the measurement indexes of its safety operation. After analyzing the factors that influence high-speed railway safety operation in detail, a rough measurement model is finally constructed to describe the operation process. Based on the above considerations, this paper redistricts the safety influence factors of high-speed railway operation as 16 measurement indexes which include staff index, vehicle index, equipment index and environment. And the paper also provides another reasonable and effective theoretical method to solve the safety problems of multiple attribute measurement in high-speed railway operation. As while as analyzing the operation data of 10 pivotal railway lines in China, this paper respectively uses the rough set-based measurement model and value function model (one model for calculating the safety value) for calculating the operation safety value. The calculation result shows that the curve of safety value with the proposed method has smaller error and greater stability than the value function method's, which verifies the feasibility and effectiveness.

On the Effects of Surface Roughness on Boundary Layer Transition

NASA Technical Reports Server (NTRS)

Choudhari, Meelan M.; Li, Fei; Chang, Chau-Lyan; Edwards, Jack

2009-01-01

Surface roughness can influence laminar-turbulent transition in many different ways. This paper outlines selected analyses performed at the NASA Langley Research Center, ranging in speed from subsonic to hypersonic Mach numbers and highlighting the beneficial as well as adverse roles of the surface roughness in technological applications. The first theme pertains to boundary-layer tripping on the forebody of a hypersonic airbreathing configuration via a spanwise periodic array of trip elements, with the goal of understanding the physical mechanisms underlying roughness-induced transition in a high-speed boundary layer. The effect of an isolated, finite amplitude roughness element on a supersonic boundary layer is considered next. The other set of flow configurations examined herein corresponds to roughness based laminar flow control in subsonic and supersonic swept wing boundary layers. A common theme to all of the above configurations is the need to apply higher fidelity, physics based techniques to develop reliable predictions of roughness effects on laminar-turbulent transition.

Whole-exome Sequence Analysis Implicates Rare Il17REL Variants in Familial and Sporadic Inflammatory Bowel Disease.

PubMed

Sasaki, Mark M; Skol, Andrew D; Hungate, Eric A; Bao, Riyue; Huang, Lei; Kahn, Stacy A; Allan, James M; Brant, Steven R; McGovern, Dermot P B; Peter, Inga; Silverberg, Mark S; Cho, Judy H; Kirschner, Barbara S; Onel, Kenan

2016-01-01

Rare variants (<1%) likely contribute significantly to risk for common diseases such as inflammatory bowel disease (IBD) in specific patient subsets, such as those with high familiality. They are, however, extraordinarily challenging to identify. To discover candidate rare variants associated with IBD, we performed whole-exome sequencing on 6 members of a pediatric-onset IBD family with multiple affected individuals. To determine whether the variants discovered in this family are also associated with nonfamilial IBD, we investigated their influence on disease in 2 large case-control (CC) series. We identified 2 rare variants, rs142430606 and rs200958270, both in the established IBD-susceptibility gene IL17REL, carried by all 4 affected family members and their obligate carrier parents. We then demonstrated that both variants are associated with sporadic ulcerative colitis (UC) in 2 independent data sets. For UC in CC 1: rs142430606 (odds ratio [OR] = 2.99, Padj = 0.028; minor allele frequency [MAF]cases = 0.0063, MAFcontrols = 0.0021); rs200958270 (OR = 2.61, Padj = 0.082; MAFcases = 0.0045, MAFcontrols = 0.0017). For UC in CC 2: rs142430606 (OR = 1.94, P = 0.0056; MAFcases = 0.0071, MAFcontrols = 0.0045); rs200958270 (OR = 2.08, P = 0.0028; MAFcases = 0.0071, MAFcontrols = 0.0042). We discover in a family and replicate in 2 CC data sets 2 rare susceptibility variants for IBD, both in IL17REL. Our results illustrate that whole-exome sequencing performed on disease-enriched families to guide association testing can be an efficient strategy for the discovery of rare disease-associated variants. We speculate that rare variants identified in families and confirmed in the general population may be important modifiers of disease risk for patients with a family history, and that genetic testing of these variants may be warranted in this patient subset.

Genetic variants of JNK and p38α pathways and risk of non-small cell lung cancer in an Eastern Chinese population.

PubMed

Jia, Ming; Zhu, Meiling; Zhou, Fei; Wang, Mengyun; Sun, Menghong; Yang, Yajun; Wang, Xiaofeng; Wang, Jiucun; Jin, Li; Xiang, Jiaqing; Zhang, Yawei; Chang, Jianhua; Wei, Qingyi

2017-02-15

The JNK and p38α pathways play an important role in carcinogenesis. Therefore, we hypothesize that single nucleotide polymorphisms (SNPs) of genes involved in these pathways are associated with risk of lung cancer. We first selected and genotyped 11 independent SNPs of the JNK and p38α pathway-related genes in a discovery set of 1,002 non-small cell lung cancer (NSCLC) cases and 1,025 cancer-free controls of Eastern Chinese. Then, we validated those significant SNPs in a replication set of 1,333 NSCLC cases and 1,339 cancer-free controls of Eastern Chinese. Multifactor dimensionality reduction (MDR) and classification and regression tree (CART) analyses were used to identify interactions between significant SNPs and other covariates. In both discovery and replication as well as their pooled analysis, carriers of GADD45G rs8252T variant genotypes had a significantly lower risk of NSCLC (adjusted OR = 0.81 and 0.79, 95% CI = 0.72-0.92 and 0.64-0.99 and p = 0.001 and 0.040 for dominant and recessive genetic models, respectively) and carriers of MAP2K7 rs3679T variant genotypes had an increased risk of NSCLC (adjusted OR = 1.19 and 1.29, 95% CI = 1.05-1.34 and 1.09-1.54 and p = 0.005 and 0.004 for dominant and recessive genetic models, respectively). Furthermore, rs8252 variant CT/TT carriers showed significantly higher levels of GADD45G mRNA expression than CC carriers in the target tissues. We observed some evidence of interactions between rs8252 genotypes and sex in NSCLC risk. These results indicate that GADD45G rs8252 and MAP2K7 rs3679 SNPs may be susceptibility biomarkers for NSCLC in Eastern Chinese populations. © 2016 UICC.

Evaluation of intradermal vaccination at the anti rabies vaccination OPD.

PubMed

Mankeshwar, R; Silvanus, V; Akarte, S

2014-09-01

Rabies is a virtually 100% fatal acute viral encephalitis caused by an RNA virus belonging to family Rhabdoviridae and genus Lyssavirus. The virus can infect all warm blooded animals. The disease is transmitted to humans by the bite, lick or scratch of an infected animal. More than 99% of all human rabies deaths occur in the developing world. It is preventable with timely and proper usage of modern immunobiologicals (vaccines and immunoglobulins). Once exposure occurs, modern prophylaxis entails immediate wound care, local infiltration of rabies immune globulin and parenteral administration of modern cell culture vaccines in multiple doses. The annual medicinal (vaccines and other drugs) cost for animal bite treatment is Rs. 2 billion approximately (2004). The objective of the present study is to evaluate the performance of the Intradermal (i.d.) route visa vis the Intramuscular (i.m.) route in our clinical setting the Antirabies Vaccination (ARV) OPD, Sir J.J. Hospital, Mumbai. A total of 1460 patients were administered the Antirabies vaccine by the Intradermal route over the 1 year period as compared to 1075 patients who were administered the Antirabies vaccine by the Intramuscular route in the previous year. 1230 (84.2) of the patients who were administered the vaccine by the i.d. route completed the schedule and 230 (15.8%) partially completed the schedule. Four hundred thirty two (40%) of the patients who were administered the vaccine by the Intramuscular route completed the schedule and 643 (59.8%) partially completed the schedule. The vaccine cost for i.d. was Rs. 2,80,600. The vaccine cost for the intramuscular (i.m.) assuming 84% compliance was estimated as Rs. 15, 64, 000. Assuming 40% compliance the cost was estimated as Rs. 7, 82, 230. Thus a saving of Rs. 5, 01, 630 to Rs. 12, 83, 400 was effected. In our setting, the Intradermal regime was cost effective and increased patient adherence and enrolment. It has now been routinely adopted at the clinic.

Measuring Skew in Average Surface Roughness as a Function of Surface Preparation

NASA Technical Reports Server (NTRS)

Stahl, Mark T.

2015-01-01

Characterizing surface roughness is important for predicting optical performance. Better measurement of surface roughness reduces grinding saving both time and money and allows the science requirements to be better defined. In this study various materials are polished from a fine grind to a fine polish. Each sample's RMS surface roughness is measured at 81 locations in a 9x9 square grid using a Zygo white light interferometer at regular intervals during the polishing process. Each data set is fit with various standard distributions and tested for goodness of fit. We show that the skew in the RMS data changes as a function of polishing time.

Religion, Spirituality, and Health: The Research and Clinical Implications

PubMed Central

Koenig, Harold G.

2012-01-01

This paper provides a concise but comprehensive review of research on religion/spirituality (R/S) and both mental health and physical health. It is based on a systematic review of original data-based quantitative research published in peer-reviewed journals between 1872 and 2010, including a few seminal articles published since 2010. First, I provide a brief historical background to set the stage. Then I review research on R/S and mental health, examining relationships with both positive and negative mental health outcomes, where positive outcomes include well-being, happiness, hope, optimism, and gratefulness, and negative outcomes involve depression, suicide, anxiety, psychosis, substance abuse, delinquency/crime, marital instability, and personality traits (positive and negative). I then explain how and why R/S might influence mental health. Next, I review research on R/S and health behaviors such as physical activity, cigarette smoking, diet, and sexual practices, followed by a review of relationships between R/S and heart disease, hypertension, cerebrovascular disease, Alzheimer's disease and dementia, immune functions, endocrine functions, cancer, overall mortality, physical disability, pain, and somatic symptoms. I then present a theoretical model explaining how R/S might influence physical health. Finally, I discuss what health professionals should do in light of these research findings and make recommendations in this regard. PMID:23762764

Comprehensive survey of deep learning in remote sensing: theories, tools, and challenges for the community

NASA Astrophysics Data System (ADS)

Ball, John E.; Anderson, Derek T.; Chan, Chee Seng

2017-10-01

In recent years, deep learning (DL), a rebranding of neural networks (NNs), has risen to the top in numerous areas, namely computer vision (CV), speech recognition, and natural language processing. Whereas remote sensing (RS) possesses a number of unique challenges, primarily related to sensors and applications, inevitably RS draws from many of the same theories as CV, e.g., statistics, fusion, and machine learning, to name a few. This means that the RS community should not only be aware of advancements such as DL, but also be leading researchers in this area. Herein, we provide the most comprehensive survey of state-of-the-art RS DL research. We also review recent new developments in the DL field that can be used in DL for RS. Namely, we focus on theories, tools, and challenges for the RS community. Specifically, we focus on unsolved challenges and opportunities as they relate to (i) inadequate data sets, (ii) human-understandable solutions for modeling physical phenomena, (iii) big data, (iv) nontraditional heterogeneous data sources, (v) DL architectures and learning algorithms for spectral, spatial, and temporal data, (vi) transfer learning, (vii) an improved theoretical understanding of DL systems, (viii) high barriers to entry, and (ix) training and optimizing the DL.

How restful is it with all that noise? Comparison of Interleaved silent steady state (ISSS) and conventional imaging in resting-state fMRI.

PubMed

Andoh, J; Ferreira, M; Leppert, I R; Matsushita, R; Pike, B; Zatorre, R J

2017-02-15

Resting-state fMRI studies have become very important in cognitive neuroscience because they are able to identify BOLD fluctuations in brain circuits involved in motor, cognitive, or perceptual processes without the use of an explicit task. Such approaches have been fruitful when applied to various disordered populations, or to children or the elderly. However, insufficient attention has been paid to the consequences of the loud acoustic scanner noise associated with conventional fMRI acquisition, which could be an important confounding factor affecting auditory and/or cognitive networks in resting-state fMRI. Several approaches have been developed to mitigate the effects of acoustic noise on fMRI signals, including sparse sampling protocols and interleaved silent steady state (ISSS) acquisition methods, the latter being used only for task-based fMRI. Here, we developed an ISSS protocol for resting-state fMRI (rs-ISSS) consisting of rapid acquisition of a set of echo planar imaging volumes following each silent period, during which the steady state longitudinal magnetization was maintained with a train of relatively silent slice-selective excitation pulses. We evaluated the test-retest reliability of intensity and spatial extent of connectivity networks of fMRI BOLD signal across three different days for rs-ISSS and compared it with a standard resting-state fMRI (rs-STD). We also compared the strength and distribution of connectivity networks between rs-ISSS and rs-STD. We found that both rs-ISSS and rs-STD showed high reproducibility of fMRI signal across days. In addition, rs-ISSS showed a more robust pattern of functional connectivity within the somatosensory and motor networks, as well as an auditory network compared with rs-STD. An increased connectivity between the default mode network and the language network and with the anterior cingulate cortex (ACC) network was also found for rs-ISSS compared with rs-STD. Finally, region of interest analysis showed higher interhemispheric connectivity in Heschl's gyri in rs-ISSS compared with rs-STD, with lower variability across days. The present findings suggest that rs-ISSS may be advantageous for detecting network connectivity in a less noisy environment, and that resting-state studies carried out with standard scanning protocols should consider the potential effects of loud noise on the measured networks. Copyright © 2017 Elsevier Inc. All rights reserved.

A facile approach for reducing the working voltage of Au/TiO2/Au nanostructured memristors by enhancing the local electric field

NASA Astrophysics Data System (ADS)

Arab Bafrani, Hamidreza; Ebrahimi, Mahdi; Bagheri Shouraki, Saeed; Moshfegh, Alireza Z.

2018-01-01

Memristor devices have attracted tremendous interest due to different applications ranging from nonvolatile data storage to neuromorphic computing units. Exploring the role of surface roughness of the bottom electrode (BE)/active layer interface provides useful guidelines for the optimization of the memristor switching performance. This study focuses on the effect of surface roughness of the BE electrode on the switching characteristics of Au/TiO2/Au three-layer memristor devices. An optimized wet-etching treatment condition was found to modify the surface roughness of the Au BE where the measurement results indicate that the roughness of the Au BE is affected by both duration time and solution concentrations of the wet-etching process. Then we fabricated arrays of TiO2-based nanostructured memristors sandwiched between two sets of cross-bar Au electrode lines (junction area 900 μm2). The results revealed a reduction in the working voltages in current-voltage characteristic of the device performance when increasing the surface roughness at the Au(BE)/TiO2 active layer interface. The set voltage of the device (Vset) significantly decreased from 2.26-1.93 V when we increased the interface roughness from 4.2-13.1 nm. The present work provides information for better understanding the switching mechanism of titanium-dioxide-based devices, and it can be inferred that enhancing the roughness of the Au BE/TiO2 active layer interface leads to a localized non-uniform electric field distribution that plays a vital role in reducing the energy consumption of the device.

Association of a four-locus gene model including IL13, IL4, FCER1B, and ADRB2 with the Asthma Predictive Index and atopy in Chinese Han children.

PubMed

Bai, S; Hua, L; Wang, X; Liu, Q; Bao, Y

2018-05-11

Asthma is a complex and heterogeneous disease. We found that gene-gene interactions among IL13 rs20541, IL4 rs2243250, ADRB2 rs1042713, and FCER1B rs569108 in asthmatic children of Chinese Han nationality. This four-locus set constituted an optimal statistical interaction model. Objective: This study examined associations of the four-gene model consisting of IL13, IL4, FCER1B, and ADRB2 with the Asthma Predictive Index (API) and atopy in Chinese Han children. Four single-nucleotide polymorphisms (SNPs) in the four genes were genotyped in 385 preschool children with wheezing symptoms using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Student's t test and x2 tests were used for this analysis. : Significant correlations were found between the four-locus gene model and the stringent and loose API (both P<0.0001). Additionally, a high-risk asthma genotype was a risk factor for the positive API (stringent API: OR= 4.08, loose API: OR=2.36). We also found a statistically significant association of the four-locus gene model with atopy (P<0.01, OR= 2.09). Our results indicated that the four-locus gene model consisting of L13 rs20541, IL4 rs2243250, ADRB2 rs1042713 and FCER1B rs569108 was associated with the API and atopy. These findings provide an evidence of the gene model for determining a high risk of developing asthma and atopy in Chinese Han children.

Genome-Wide Analysis in Brazilians Reveals Highly Differentiated Native American Genome Regions

PubMed Central

Havt, Alexandre; Nayak, Uma; Pinkerton, Relana; Farber, Emily; Concannon, Patrick; Lima, Aldo A.; Guerrant, Richard L.

2017-01-01

Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental admixture in 1,538 North-Eastern Brazilians to estimate individual ancestry and ancestral allele frequencies, we computed 400,000 genome-wide locus-specific branch length (LSBL) Fst statistics of Brazilian Amerindian ancestry compared to European and African; and a similar set of differentiation statistics for their Amerindian component compared with the closest Asian 1000 Genomes population (surprisingly, Bengalis in Bangladesh). After ranking SNPs by these statistics, we identified the top 10 highly differentiated SNPs in five genome regions in the LSBL tests of Brazilian Amerindian ancestry compared to European and African; and the top 10 SNPs in eight regions comparing their Amerindian component to the closest Asian 1000 Genomes population. We found SNPs within or proximal to the genes CIITA (rs6498115), SMC6 (rs1834619), and KLHL29 (rs2288697) were most differentiated in the Amerindian-specific branch, while SNPs in the genes ADAMTS9 (rs7631391), DOCK2 (rs77594147), SLC28A1 (rs28649017), ARHGAP5 (rs7151991), and CIITA (rs45601437) were most highly differentiated in the Asian comparison. These genes are known to influence immune function, metabolic and anthropometry traits, and embryonic development. These analyses have identified candidate genes for selection within Amerindian ancestry, and by comparison of the two analyses, those for which the differentiation may have arisen during the migration from Asia to the Americas. PMID:28100790

Water Quality Assessment in the Harbin Reach of the Songhuajiang River (China) Based on a Fuzzy Rough Set and an Attribute Recognition Theoretical Model

PubMed Central

An, Yan; Zou, Zhihong; Li, Ranran

2014-01-01

A large number of parameters are acquired during practical water quality monitoring. If all the parameters are used in water quality assessment, the computational complexity will definitely increase. In order to reduce the input space dimensions, a fuzzy rough set was introduced to perform attribute reduction. Then, an attribute recognition theoretical model and entropy method were combined to assess water quality in the Harbin reach of the Songhuajiang River in China. A dataset consisting of ten parameters was collected from January to October in 2012. Fuzzy rough set was applied to reduce the ten parameters to four parameters: BOD5, NH3-N, TP, and F. coli (Reduct A). Considering that DO is a usual parameter in water quality assessment, another reduct, including DO, BOD5, NH3-N, TP, TN, F, and F. coli (Reduct B), was obtained. The assessment results of Reduct B show a good consistency with those of Reduct A, and this means that DO is not always necessary to assess water quality. The results with attribute reduction are not exactly the same as those without attribute reduction, which can be attributed to the α value decided by subjective experience. The assessment results gained by the fuzzy rough set obviously reduce computational complexity, and are acceptable and reliable. The model proposed in this paper enhances the water quality assessment system. PMID:24675643

A three-way approach for protein function classification

PubMed Central

2017-01-01

The knowledge of protein functions plays an essential role in understanding biological cells and has a significant impact on human life in areas such as personalized medicine, better crops and improved therapeutic interventions. Due to expense and inherent difficulty of biological experiments, intelligent methods are generally relied upon for automatic assignment of functions to proteins. The technological advancements in the field of biology are improving our understanding of biological processes and are regularly resulting in new features and characteristics that better describe the role of proteins. It is inevitable to neglect and overlook these anticipated features in designing more effective classification techniques. A key issue in this context, that is not being sufficiently addressed, is how to build effective classification models and approaches for protein function prediction by incorporating and taking advantage from the ever evolving biological information. In this article, we propose a three-way decision making approach which provides provisions for seeking and incorporating future information. We considered probabilistic rough sets based models such as Game-Theoretic Rough Sets (GTRS) and Information-Theoretic Rough Sets (ITRS) for inducing three-way decisions. An architecture of protein functions classification with probabilistic rough sets based three-way decisions is proposed and explained. Experiments are carried out on Saccharomyces cerevisiae species dataset obtained from Uniprot database with the corresponding functional classes extracted from the Gene Ontology (GO) database. The results indicate that as the level of biological information increases, the number of deferred cases are reduced while maintaining similar level of accuracy. PMID:28234929

A three-way approach for protein function classification.

PubMed

Ur Rehman, Hafeez; Azam, Nouman; Yao, JingTao; Benso, Alfredo

2017-01-01

The knowledge of protein functions plays an essential role in understanding biological cells and has a significant impact on human life in areas such as personalized medicine, better crops and improved therapeutic interventions. Due to expense and inherent difficulty of biological experiments, intelligent methods are generally relied upon for automatic assignment of functions to proteins. The technological advancements in the field of biology are improving our understanding of biological processes and are regularly resulting in new features and characteristics that better describe the role of proteins. It is inevitable to neglect and overlook these anticipated features in designing more effective classification techniques. A key issue in this context, that is not being sufficiently addressed, is how to build effective classification models and approaches for protein function prediction by incorporating and taking advantage from the ever evolving biological information. In this article, we propose a three-way decision making approach which provides provisions for seeking and incorporating future information. We considered probabilistic rough sets based models such as Game-Theoretic Rough Sets (GTRS) and Information-Theoretic Rough Sets (ITRS) for inducing three-way decisions. An architecture of protein functions classification with probabilistic rough sets based three-way decisions is proposed and explained. Experiments are carried out on Saccharomyces cerevisiae species dataset obtained from Uniprot database with the corresponding functional classes extracted from the Gene Ontology (GO) database. The results indicate that as the level of biological information increases, the number of deferred cases are reduced while maintaining similar level of accuracy.

Vitamin D receptor and megalin gene polymorphisms are associated with central adiposity status and changes among US adults.

PubMed

Beydoun, May A; Tanaka, Toshiko; Beydoun, Hind A; Ding, Eric L; Ferrucci, Luigi; Zonderman, Alan B

2013-01-01

We examined longitudinal associations of vitamin D receptor (VDR) and megalin (LRP2; LDL receptor-related protein-2) gene polymorphisms with central adiposity. We used data from the Baltimore Longitudinal Study of Aging (BLSA), an ongoing prospective open cohort study. Study participants consisted of non-Hispanic white adults residing in Baltimore city, with one or more visits at age ≥50 years, and complete data (n 609-617). Repeated assessments on waist circumference (WC) and waist:hip ratio (WHR) were available. Multiple linear mixed models were used to estimate mid-follow-up age central adiposity level and annual rate of change with cut-points set at the sex-specific 80th percentile. The four binary outcomes were: 'elevated central adiposity' (ECA-WC and ECA-WHR) and 'significant increase in central adiposity' (SICA-WC and SICA-WHR). SNP for VDR (four SNP: (1) rs11568820 (CdX-2:T/C); (2) rs1544410 (BsmI:G/A); (3) rs7975232 (ApaI:A/C); (4) rs731236 (TaqI:G/A)) and Megalin (three SNP: (1) rs3755166:G/A; (2) rs2075252:C/T; (3) rs4668123:C/T) genes were selected. SNP latent classes (SNPLC) and SNP haplotypes (SNPHAP) were created. Multiple logistic regression analyses indicated that, in men, higher ECA-WHR odds were associated with SNPLC Megalin2:rs3755166[-]/rs2075252[TT]/rs4668123[T-] (v. Megalin1:rs3755166[-]/rs2075252[CC]/rs4668123[-]) (OR 2·87; 95 % CI 1·15, 7·12; P = 0·023) and that SNPLC Megalin3:rs3755166[-]/rs2075252[CT]/rs4668123[-] (v. Megalin1) was linked to lower SICA-WC odds (OR 0·48; 95 % CI 0·26, 0·88; P = 0·019) (P > 0·05 for sex × SNPLC). In women, VDR3 SNPHAP (GAA:bAT) was related to lower odds of ECA-WC (OR 0·37; 95 % CI 0·16, 0·87; P = 0·023) (P < 0·05 for sex × SNPHAP), VDR1 SNPHAP (GCA:baT) was associated with greater odds and VDR3 SNPHAP (GAA:bAT) with lower odds of SICA-WC (P > 0·05 for sex × SNPHAP). Vitamin D-related gene polymorphisms were associated with central adiposity status and change. Future mechanistic studies are needed to confirm those polymorphisms' biological significance to central adiposity.

Hypoxia/oxidative stress alters the pharmacokinetics of CPU86017-RS through mitochondrial dysfunction and NADPH oxidase activation.

PubMed

Gao, Jie; Ding, Xuan-sheng; Zhang, Yu-mao; Dai, De-zai; Liu, Mei; Zhang, Can; Dai, Yin

2013-12-01

Hypoxia/oxidative stress can alter the pharmacokinetics (PK) of CPU86017-RS, a novel antiarrhythmic agent. The aim of this study was to investigate the mechanisms underlying the alteration of PK of CPU86017-RS by hypoxia/oxidative stress. Male SD rats exposed to normal or intermittent hypoxia (10% O2) were administered CPU86017-RS (20, 40 or 80 mg/kg, ig) for 8 consecutive days. The PK parameters of CPU86017-RS were examined on d 8. In a separate set of experiments, female SD rats were injected with isoproterenol (ISO) for 5 consecutive days to induce a stress-related status, then CPU86017-RS (80 mg/kg, ig) was administered, and the tissue distributions were examined. The levels of Mn-SOD (manganese containing superoxide dismutase), endoplasmic reticulum (ER) stress sensor proteins (ATF-6, activating transcription factor 6 and PERK, PRK-like ER kinase) and activation of NADPH oxidase (NOX) were detected with Western blotting. Rat liver microsomes were incubated under N2 for in vitro study. The Cmax, t1/2, MRT (mean residence time) and AUC (area under the curve) of CPU86017-RS were significantly increased in the hypoxic rats receiving the 3 different doses of CPU86017-RS. The hypoxia-induced alteration of PK was associated with significantly reduced Mn-SOD level, and increased ATF-6, PERK and NOX levels. In ISO-treated rats, the distributions of CPU86017-RS in plasma, heart, kidney, and liver were markedly increased, and NOX levels in heart, kidney, and liver were significantly upregulated. Co-administration of the NOX blocker apocynin eliminated the abnormalities in the PK and tissue distributions of CPU86017-RS induced by hypoxia/oxidative stress. The metabolism of CPU86017-RS in the N2-treated liver microsomes was significantly reduced, addition of N-acetylcysteine (NAC), but not vitamin C, effectively reversed this change. The altered PK and metabolism of CPU86017-RS induced by hypoxia/oxidative stress are produced by mitochondrial abnormalities, NOX activation and ER stress; these abnormalities are significantly alleviated by apocynin or NAC.

Case management in primary care among frequent users of healthcare services with chronic conditions: protocol of a realist synthesis.

PubMed

Hudon, Catherine; Chouinard, Maud-Christine; Aubrey-Bassler, Kris; Muhajarine, Nazeem; Burge, Fred; Pluye, Pierre; Bush, Paula L; Ramsden, Vivian R; Legare, France; Guenette, Line; Morin, Paul; Lambert, Mireille; Groulx, Antoine; Couture, Martine; Campbell, Cameron; Baker, Margaret; Edwards, Lynn; Sabourin, Véronique; Spence, Claude; Gauthier, Gilles; Warren, Mike; Godbout, Julie; Davis, Breanna; Rabbitskin, Norma

2017-09-03

A common reason for frequent use of healthcare services is the complex healthcare needs of individuals suffering from multiple chronic conditions, especially in combination with mental health comorbidities and/or social vulnerability. Frequent users (FUs) of healthcare services are more at risk for disability, loss of quality of life and mortality. Case management (CM) is a promising intervention to improve care integration for FU and to reduce healthcare costs. This review aims to develop a middle-range theory explaining how CM in primary care improves outcomes among FU with chronic conditions, for what types of FU and in what circumstances. A realist synthesis (RS) will be conducted between March 2017 and March 2018 to explore the causal mechanisms that underlie CM and how contextual factors influence the link between these causal mechanisms and outcomes. According to RS methodology, five steps will be followed: (1) focusing the scope of the RS; (2) searching for the evidence; (3) appraising the quality of evidence; (4) extracting the data; and (5) synthesising the evidence. Patterns in context-mechanism-outcomes (CMOs) configurations will be identified, within and across identified studies. Analysis of CMO configurations will help confirm, refute, modify or add to the components of our initial rough theory and ultimately produce a refined theory explaining how and why CM interventions in primary care works, in which contexts and for which FU with chronic conditions. Research ethics is not required for this review, but publication guidelines on RS will be followed. Based on the review findings, we will develop and disseminate messages tailored to various relevant stakeholder groups. These messages will allow the development of material that provides guidance on the design and the implementation of CM in health organisations. Prospero CRD42017057753. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Mendelian randomization shows sex-specific associations between long-chain PUFA-related genotypes and cognitive performance in Danish schoolchildren.

PubMed

Lauritzen, Lotte; Sørensen, Louise B; Harsløf, Laurine B; Ritz, Christian; Stark, Ken D; Astrup, Arne; Dyssegaard, Camilla B; Egelund, Niels; Michaelsen, Kim F; Damsgaard, Camilla T

2017-07-01

Background: Dietary and endogenously formed long-chain polyunsaturated fatty acids (LCPUFAs) are hypothesized to improve cognitive development, but results are inconclusive, with suggestions of sex specificity. One study suggested that single-nucleotide polymorphisms (SNPs) rs1535 and rs174448 in the fatty acid desaturase ( FADS ) gene cluster have opposite effects on erythrocyte LCPUFAs at 9 mo. Objective: To explore whether SNPs in FADS and elongase ( ELOVL ) genes were associated with school performance in a sex-specific manner, we performed a Mendelian randomization study using data from the Optimal well-being, development and health for Danish children through a healthy New Nordic Diet (OPUS) School Meal Study with 765 Danish schoolchildren 8-11 y old. Design: Associations between selected FADS1/2 SNPs (rs1535, rs174448, and rs174468) and ELOVL5 rs2397142, whole-blood fatty acid composition, and performance in the d2 Test of Attention and a reading test were analyzed in multiple regression models including all SNPs, SNP-sex interactions, and covariates related to testing conditions. Results: FADS , rs1535 minor allele carriage associated with lower whole-blood arachidonic acid ( P ≤ 0.002), and minor alleles of rs174448 tended to associate with lower docosahexaenoic acid (DHA) ( P = 0.052). We identified sex interactions in 50% of the SNP performance sets. Sex-dependent associations were observed for rs174448 and rs1535 on the d2 Test of Attention outcomes ( P < 0.03) and for the associations between reading scores and rs174448 and rs2397142 ( P < 0.01). All of the sex-specific analyses showed associations in opposite directions in girls and boys. The minor allele carriage of rs174448 was associated with lower d2 Test of Attention performance ( P < 0.02) and reading scores ( P < 0.001) in boys but with better reading scores in girls ( P ≤ 0.002). The associations were consistently the opposite for rs1535 minor allele carriage ( P < 0.05). Associations with rs2397142 also appeared to be opposite of those of rs174448, but only for reading and not significant after adjustment for parental educational level and whole-blood DHA. Conclusions: This study showed associations between rs1535 minor allele homozygosity and rs174448 major allele carriage and improved performance in 8- to 11-y-old boys but not in girls, thereby counteracting existing sex differences. This may be a consequence of increased endogenous DHA synthesis in infancy but not at school-age. This trial was registered at clinicaltrials.gov as NCT01457794. © 2017 American Society for Nutrition.

Performance study and influence of radiation emission energy and soil contamination level on γ-radiation shielding of stabilised/solidified radionuclide-polluted soils.

PubMed

Falciglia, Pietro P; Puccio, Valentina; Romano, Stefano; Vagliasindi, Federico G A

2015-05-01

This work focuses on the stabilisation/solidification (S/S) of radionuclide-polluted soils at different (232)Th levels using Portland cement alone and with barite aggregates. The potential of S/S was assessed applying a full testing protocol and calculating γ-radiation shielding (γRS) index, that included the measurement of soil radioactivity before and after the S/S as a function of the emission energy and soil contamination level. The results indicate that setting processes are strongly dependent on the contaminant concentration, and for contamination level higher than 5%, setting time values longer than 72 h. The addition of barite aggregates to the cement gout leads to a slight improvement of the S/S performance in terms of durability and contaminant leaching but reduces the mechanical resistance of the treated soils samples. Barite addition also causes an increase in the γ-rays shielding properties of the S/S treatment up to about 20%. Gamma-ray measurements show that γRS strongly depends on the energy, and that the radioactivity with the contamination level was governed by a linear trend, while, γRS index does not depend on the radionuclide concentration. Results allow the calculated γRS values and those available from other experiments to be applied to hazard radioactive soil contaminations. Copyright © 2015 Elsevier Ltd. All rights reserved.

A polymorphism in CCR1/CCR3 is associated with narcolepsy.

PubMed

Toyoda, Hiromi; Miyagawa, Taku; Koike, Asako; Kanbayashi, Takashi; Imanishi, Aya; Sagawa, Yohei; Kotorii, Nozomu; Kotorii, Tatayu; Hashizume, Yuji; Ogi, Kimihiro; Hiejima, Hiroshi; Kamei, Yuichi; Hida, Akiko; Miyamoto, Masayuki; Imai, Makoto; Fujimura, Yota; Tamura, Yoshiyuki; Ikegami, Azusa; Wada, Yamato; Moriya, Shunpei; Furuya, Hirokazu; Takeuchi, Masaki; Kirino, Yohei; Meguro, Akira; Remmers, Elaine F; Kawamura, Yoshiya; Otowa, Takeshi; Miyashita, Akinori; Kashiwase, Koichi; Khor, Seik-Soon; Yamasaki, Maria; Kuwano, Ryozo; Sasaki, Tsukasa; Ishigooka, Jun; Kuroda, Kenji; Kume, Kazuhiko; Chiba, Shigeru; Yamada, Naoto; Okawa, Masako; Hirata, Koichi; Mizuki, Nobuhisa; Uchimura, Naohisa; Shimizu, Tetsuo; Inoue, Yuichi; Honda, Yutaka; Mishima, Kazuo; Honda, Makoto; Tokunaga, Katsushi

2015-10-01

Etiology of narcolepsy-cataplexy involves multiple genetic and environmental factors. While the human leukocyte antigen (HLA)-DRB1*15:01-DQB1*06:02 haplotype is strongly associated with narcolepsy, it is not sufficient for disease development. To identify additional, non-HLA susceptibility genes, we conducted a genome-wide association study (GWAS) using Japanese samples. An initial sample set comprising 409 cases and 1562 controls was used for the GWAS of 525,196 single nucleotide polymorphisms (SNPs) located outside the HLA region. An independent sample set comprising 240 cases and 869 controls was then genotyped at 37 SNPs identified in the GWAS. We found that narcolepsy was associated with a SNP in the promoter region of chemokine (C-C motif) receptor 1 (CCR1) (rs3181077, P=1.6×10(-5), odds ratio [OR]=1.86). This rs3181077 association was replicated with the independent sample set (P=0.032, OR=1.36). We measured mRNA levels of candidate genes in peripheral blood samples of 38 cases and 37 controls. CCR1 and CCR3 mRNA levels were significantly lower in patients than in healthy controls, and CCR1 mRNA levels were associated with rs3181077 genotypes. In vitro chemotaxis assays were also performed to measure monocyte migration. We observed that monocytes from carriers of the rs3181077 risk allele had lower migration indices with a CCR1 ligand. CCR1 and CCR3 are newly discovered susceptibility genes for narcolepsy. These results highlight the potential role of CCR genes in narcolepsy and support the hypothesis that patients with narcolepsy have impaired immune function. Copyright © 2015 Elsevier Inc. All rights reserved.

Insertion of a pentacene layer into the gold/poly(methyl methacrylate)/heavily doped p-type Si/indium device leading to the modulation of resistive switching characteristics

NASA Astrophysics Data System (ADS)

Hung, Cheng-Chun; Lin, Yow-Jon

2018-01-01

In order to get a physical insight into the pentacene interlayer-modulated resistive switching (RS) characteristics, the Au/pentacene/poly(methyl methacrylate) (PMMA)/heavily doped p-type Si (p+-Si)/In and Au/PMMA/p+-Si/In devices are fabricated and the device performance is provided. The Au/pentacene/PMMA/p+-Si/In device shows RS behavior, whereas the Au/PMMA/p+-Si/In device exhibits the set/reset-free hysteresis current-voltage characteristics. The insertion of a pentacene layer is a noticeable contribution to the RS characteristic. This is because of the occurrence of carrier accumulation/depletion in the pentacene interlayer. The transition from carrier depletion to carrier accumulation (carrier accumulation to carrier depletion) in pentacene occurring under negative (positive) voltage induces the process of set (reset). The switching conduction mechanism is primarily described as space charge limited conduction according to the electrical transport properties measurement. The concept of a pentacene/PMMA heterostructure opens a promising direction for organic memory devices.

Comparison between performances of three types of manual wheelchairs often distributed in low-resource settings.

PubMed

Rispin, Karen; Wee, Joy

2015-07-01

This study was conducted to compare the performance of three types of chairs in a low-resource setting. The larger goal was to provide information which will enable more effective use of limited funds by wheelchair manufacturers and suppliers in low-resource settings. The Motivation Rough Terrain and Whirlwind Rough Rider were compared in six skills tests which participants completed in one wheelchair type and then a day later in the other. A hospital-style folding transport wheelchair was also included in one test. For all skills, participants rated the ease or difficulty on a visual analogue scale. For all tracks, distance traveled and the physiological cost index were recorded. Data were analyzed using repeated measures analysis of variance. The Motivation wheelchair outperformed Whirlwind wheelchair on rough and smooth tracks, and in some metrics on the tight spaces track. Motivation and Whirlwind wheelchairs significantly outperformed the hospital transport wheelchair in all metrics on the rough track skills test. This comparative study provides data that are valuable for manufacturers and for those who provide wheelchairs to users. The comparison with the hospital-style transport chair confirms the cost to users of inappropriate wheelchair provision. Implications for Rehabilitation For those with compromised lower limb function, wheelchairs are essential to enable full participation and improved quality of life. Therefore, provision of wheelchairs which effectively enable mobility in the cultures and environments in which people with disabilities live is crucial. This includes low-resource settings where the need for appropriate seating is especially urgent. A repeated measures study to measure wheelchair performances in everyday skills in the setting where wheelchairs are used gives information on the quality of mobility provided by those wheelchairs. This study highlights differences in the performance of three types of wheelchairs often distributed in low-resource settings. This information can improve mobility for wheelchair users in those settings by enabling wheelchair manufacturers to optimize wheelchair design and providers to optimize the use of limited funds.

Interaction between Social/Psychosocial Factors and Genetic Variants on Body Mass Index: A Gene-Environment Interaction Analysis in a Longitudinal Setting.

PubMed

Zhao, Wei; Ware, Erin B; He, Zihuai; Kardia, Sharon L R; Faul, Jessica D; Smith, Jennifer A

2017-09-29

Obesity, which develops over time, is one of the leading causes of chronic diseases such as cardiovascular disease. However, hundreds of BMI (body mass index)-associated genetic loci identified through large-scale genome-wide association studies (GWAS) only explain about 2.7% of BMI variation. Most common human traits are believed to be influenced by both genetic and environmental factors. Past studies suggest a variety of environmental features that are associated with obesity, including socioeconomic status and psychosocial factors. This study combines both gene/regions and environmental factors to explore whether social/psychosocial factors (childhood and adult socioeconomic status, social support, anger, chronic burden, stressful life events, and depressive symptoms) modify the effect of sets of genetic variants on BMI in European American and African American participants in the Health and Retirement Study (HRS). In order to incorporate longitudinal phenotype data collected in the HRS and investigate entire sets of single nucleotide polymorphisms (SNPs) within gene/region simultaneously, we applied a novel set-based test for gene-environment interaction in longitudinal studies (LGEWIS). Childhood socioeconomic status (parental education) was found to modify the genetic effect in the gene/region around SNP rs9540493 on BMI in European Americans in the HRS. The most significant SNP (rs9540488) by childhood socioeconomic status interaction within the rs9540493 gene/region was suggestively replicated in the Multi-Ethnic Study of Atherosclerosis (MESA) ( p = 0.07).

Interaction between Social/Psychosocial Factors and Genetic Variants on Body Mass Index: A Gene-Environment Interaction Analysis in a Longitudinal Setting

PubMed Central

Zhao, Wei; He, Zihuai; Kardia, Sharon L. R.; Faul, Jessica D.

2017-01-01

Obesity, which develops over time, is one of the leading causes of chronic diseases such as cardiovascular disease. However, hundreds of BMI (body mass index)-associated genetic loci identified through large-scale genome-wide association studies (GWAS) only explain about 2.7% of BMI variation. Most common human traits are believed to be influenced by both genetic and environmental factors. Past studies suggest a variety of environmental features that are associated with obesity, including socioeconomic status and psychosocial factors. This study combines both gene/regions and environmental factors to explore whether social/psychosocial factors (childhood and adult socioeconomic status, social support, anger, chronic burden, stressful life events, and depressive symptoms) modify the effect of sets of genetic variants on BMI in European American and African American participants in the Health and Retirement Study (HRS). In order to incorporate longitudinal phenotype data collected in the HRS and investigate entire sets of single nucleotide polymorphisms (SNPs) within gene/region simultaneously, we applied a novel set-based test for gene-environment interaction in longitudinal studies (LGEWIS). Childhood socioeconomic status (parental education) was found to modify the genetic effect in the gene/region around SNP rs9540493 on BMI in European Americans in the HRS. The most significant SNP (rs9540488) by childhood socioeconomic status interaction within the rs9540493 gene/region was suggestively replicated in the Multi-Ethnic Study of Atherosclerosis (MESA) (p = 0.07). PMID:28961216

Mixed convection heat transfer enhancement in a cubic lid-driven cavity containing a rotating cylinder through the introduction of artificial roughness on the heated wall

NASA Astrophysics Data System (ADS)

Kareem, Ali Khaleel; Gao, Shian

2018-02-01

The aim of the present numerical investigation is to comprehensively analyse and understand the heat transfer enhancement process using a roughened, heated bottom wall with two artificial rib types (R-s and R-c) due to unsteady mixed convection heat transfer in a 3D moving top wall enclosure that has a central rotating cylinder, and to compare these cases with the smooth bottom wall case. These different cases (roughened and smooth bottom walls) are considered at various clockwise and anticlockwise rotational speeds, -5 ≤ Ω ≤ 5, and Reynolds numbers of 5000 and 10 000. The top and bottom walls of the lid-driven cavity are differentially heated, whilst the remaining cavity walls are assumed to be stationary and adiabatic. A standard k-ɛ model for the Unsteady Reynolds-Averaged Navier-Stokes equations is used to deal with the turbulent flow. The heat transfer improvement is carefully considered and analysed through the detailed examinations of the flow and thermal fields, the turbulent kinetic energy, the mean velocity profiles, the wall shear stresses, and the local and average Nusselt numbers. It has been concluded that artificial roughness can strongly affect the thermal fields and fluid flow patterns. Ultimately, the heat transfer rate has been dramatically increased by involving the introduced artificial rips. Increasing the cylinder rotational speed or Reynolds number can enhance the heat transfer process, especially when the wall roughness exists.

ALPK1 genetic regulation and risk in relation to gout.

PubMed

Ko, Albert Min-Shan; Tu, Hung-Pin; Liu, Tze-Tze; Chang, Jan-Gowth; Yuo, Chung-Yee; Chiang, Shang-Lun; Chang, Shun-Jen; Liu, Yu-Fan; Ko, Allen Min-Jen; Lee, Chien-Hung; Lee, Chi-Pin; Chang, Chung-Ming; Tsai, Shih-Feng; Ko, Ying-Chin

2013-04-01

The present study investigated whether single nucleotide polymorphisms (SNPs) in the alpha-protein kinase 1 (ALPK1) gene are associated with gout in aboriginal and Han Chinese Taiwanese. A total of 1351 aborigines from the community (511 cases and 840 controls) and 511 Han people from hospital (104 cases and 407 controls) were recruited. SNPs in potentially functional regions of the 38 genes within 4q25 were identified and genotypes determined by direct sequencing. Quantitation of blood ALPK1 mRNA expression levels and luciferase assay of gout-associated rs231253 pGL3-SNP constructs cotransfected with hsa-miR-519e were examined. We found that ALPK1 gene was the most determinant of gout. Three SNPs of rs11726117 M861T [C], rs231247 [G] and rs231253 [G] were most associated with gout risk [odd ratios (OR) ≥1.44, P ≤ 3.78 × 10(-6)) in aborigines. A replication set using Han people had risk at rs11726117 and rs231247 (OR ≥1.72, P ≤ 4.08 × 10(-3)). From pooled analysis (Breslow-Day test, P > 0.33) assuming an additive model, each increasing copy of the risk allele of rs11726117 [C], rs231247 [G] and rs231253 [G] showed significantly elevated OR for gout ≥1.42 (P ≥ 1.53 × 10(-6)). Consistently, the composite homozygous of linked 3 SNPs (versus wild-type, OR = 1.83, P = 8.21 × 10(-4)) had strong associations with ALPK1 mRNA expression. Luciferase showed reduced hybridization between hsa-miR-519e and construct carrying gout-associated rs231253 [G] than the wild-type [C] (P = 6.19 × 10(-4)). Our study found that a newly identified ALPK1 gene can effectively interfere with microRNA target recognition and modulates the mRNA expression; and the varying distribution of the implicated SNPs among cases and controls in the two studied populations suggests a significant role in gout susceptibility.

Differential effects of donor and recipient IL28B and DDX58 SNPs on severity of HCV after liver transplantation.

PubMed

Biggins, Scott W; Trotter, James; Gralla, Jane; Burton, James R; Bambha, Kiran M; Dodge, Jennifer; Brocato, Megan; Cheng, Linling; McQueen, Matt; Forman, Lisa; Chang, Michael; Kam, Igal; Everson, Gregory; Spritz, Richard A; Klintmalm, Goran; Rosen, Hugo R

2013-05-01

IL28B single nucleotide polymorphisms are strongly associated with spontaneous HCV clearance and treatment response in non-transplant populations. A DDX58 single nucleotide polymorphism is associated with the antiviral response of innate lymphocytes. We aimed at evaluating the associations of donor and recipient IL28B (rs12979860 and rs8099917) and DDX58 (rs10813831) genotypes with severity of HCV recurrence after liver transplantation. In a case-control study of 523 liver transplantation recipients with HCV, we matched severe with mild recurrent HCV based on 2-year clinical and histologic follow-up. A total of 440 liver transplantation recipients (severe, n=235; mild, n=205) with recipient DNA and 225 (severe, n=123; mild, n=102) with both recipient and donor DNA were analyzed. IL28B [rs12979860, non-CC (vs. CC) and rs8099917, non-TT (vs. TT)] in the recipient-only analysis had higher risk of severe recurrent HCV [OR 1.57 and 1.58, p<0.05]. However, for the 225 with donor and recipient DNA, IL28B rs12979860 CC (vs. non-CC) and rs8099917 TT (vs. non-TT) and DDX58 rs10813831 non-GG (vs. GG) were associated with more (not less) severe recurrent HCV. The greatest risk of severe recurrent HCV was for rs12979860 CC donors in non-CC recipients (OR 7.02, p <0.001, vs. non-CC donor/recipient) and for rs8099917 TT donors in non-TT recipients (OR 5.78, p=0.001, vs. non-TT donor/recipient). These associations persisted after controlling for donor age, donor race, and donor risk index. IL28B and DDX58 single nucleotide polymorphisms that are favorable when present in the non-transplant setting or in the recipient are unfavorable when present in a donor liver graft. Copyright © 2013 European Association for the Study of the Liver. All rights reserved.

Measuring uncertainty by extracting fuzzy rules using rough sets

NASA Technical Reports Server (NTRS)

Worm, Jeffrey A.

1991-01-01

Despite the advancements in the computer industry in the past 30 years, there is still one major deficiency. Computers are not designed to handle terms where uncertainty is present. To deal with uncertainty, techniques other than classical logic must be developed. The methods are examined of statistical analysis, the Dempster-Shafer theory, rough set theory, and fuzzy set theory to solve this problem. The fundamentals of these theories are combined to possibly provide the optimal solution. By incorporating principles from these theories, a decision making process may be simulated by extracting two sets of fuzzy rules: certain rules and possible rules. From these rules a corresponding measure of how much these rules is believed is constructed. From this, the idea of how much a fuzzy diagnosis is definable in terms of a set of fuzzy attributes is studied.

Genetic association between NRG1 and schizophrenia, major depressive disorder, bipolar disorder in Han Chinese population.

PubMed

Wen, Zujia; Chen, Jianhua; Khan, Raja Amjad Waheed; Song, Zhijian; Wang, Meng; Li, Zhiqiang; Shen, Jiawei; Li, Wenjin; Shi, Yongyong

2016-04-01

Schizophrenia, major depressive disorder, and bipolar disorder are three major psychiatric disorders affecting around 0.66%, 3.3%, and 1.5% of the Han Chinese population respectively. Several genetic linkage analyses and genome wide association studies identified NRG1 as a susceptibility gene of schizophrenia, which was validated by its role in neurodevelopment, glutamate, and other neurotransmitter receptor expression regulation. To further investigate whether NRG1 is a shared risk gene for major depressive disorder, bipolar disorder as well as schizophrenia, we performed an association study among 1,248 schizophrenia cases, 1,056 major depression cases, 1,344 bipolar disorder cases, and 1,248 controls. Totally 15 tag SNPs were genotyped and analyzed, and no population stratification was found in our sample set. Among the sites, rs4236710 (corrected Pgenotye  = 0.015) and rs4512342 (Pallele  = 0.03, Pgenotye  = 0.045 after correction) were associated with schizophrenia, and rs2919375 (corrected Pgenotye  = 0.004) was associated with major depressive disorder. The haplotype rs4512342-rs6982890 showed association with schizophrenia (P = 0.03 for haplotype "TC" after correction), and haplotype rs4531002-rs11989919 proved to be a shared risk factor for both major depressive disorder ("CC": corrected P = 0.009) and bipolar disorder ("CT": corrected P = 0.003). Our results confirmed that NRG1 was a shared common susceptibility gene for major mental disorders in Han Chinese population. © 2016 Wiley Periodicals, Inc.

Effect of saliva and blood contamination after etching upon the shear bond strength between composite resin and enamel

NASA Astrophysics Data System (ADS)

Armadi, A. S.; Usman, M.; Suprastiwi, E.

2017-08-01

The aim of this study was to find out the surface roughness of composite resin veneer after brushing. In this study, 24 specimens of composite resin veneer are divided into three subgroups: brushed without toothpaste, brushed with non-herbal toothpaste, and brushed with herbal toothpaste. Brushing was performed for one set of 5,000 strokes and continued for a second set of 5,000 strokes. Roughness of composite resin veneer was determined using a Surface Roughness Tester. The results were statistically analyzed using Kruskal-Wallis nonparametric test and Post Hoc Mann-Whitney. The results indicate that the highest difference among the Ra values occurred within the subgroup that was brushed with the herbal toothpaste. In conclusion, the herbal toothpaste produced a rougher surface on composite resin veneer compared to non-herbal toothpaste.

Simulation for Rough Mill Options

Treesearch

Janice K. Wiedenbeck

1992-01-01

How is rough mill production affected by lumber length? Lumber grade? Cutting quality? Cutting sizes? How would equipment purchase plans be prioritized? How do personnel shifts affect system productivity? What effect would a reduction in machine set-up time have on material flow? Simulation modeling is being widely used in many industries to provide valuable insight...

Benchmarking performance measurement and lean manufacturing in the rough mill

Treesearch

Dan Cumbo; D. Earl Kline; Matthew S. Bumgardner

2006-01-01

Lean manufacturing represents a set of tools and a stepwise strategy for achieving smooth, predictable product flow, maximum product flexibility, and minimum system waste. While lean manufacturing principles have been successfully applied to some components of the secondary wood products value stream (e.g., moulding, turning, assembly, and finishing), the rough mill is...

Cross-Modal Perception of Noise-in-Music: Audiences Generate Spiky Shapes in Response to Auditory Roughness in a Novel Electroacoustic Concert Setting

PubMed Central

Liew, Kongmeng; Lindborg, PerMagnus; Rodrigues, Ruth; Styles, Suzy J.

2018-01-01

Noise has become integral to electroacoustic music aesthetics. In this paper, we define noise as sound that is high in auditory roughness, and examine its effect on cross-modal mapping between sound and visual shape in participants. In order to preserve the ecological validity of contemporary music aesthetics, we developed Rama, a novel interface, for presenting experimentally controlled blocks of electronically generated sounds that varied systematically in roughness, and actively collected data from audience interaction. These sounds were then embedded as musical drones within the overall sound design of a multimedia performance with live musicians, Audience members listened to these sounds, and collectively voted to create the shape of a visual graphic, presented as part of the audio–visual performance. The results of the concert setting were replicated in a controlled laboratory environment to corroborate the findings. Results show a consistent effect of auditory roughness on shape design, with rougher sounds corresponding to spikier shapes. We discuss the implications, as well as evaluate the audience interface. PMID:29515494

A Granular Self-Organizing Map for Clustering and Gene Selection in Microarray Data.

PubMed

Ray, Shubhra Sankar; Ganivada, Avatharam; Pal, Sankar K

2016-09-01

A new granular self-organizing map (GSOM) is developed by integrating the concept of a fuzzy rough set with the SOM. While training the GSOM, the weights of a winning neuron and the neighborhood neurons are updated through a modified learning procedure. The neighborhood is newly defined using the fuzzy rough sets. The clusters (granules) evolved by the GSOM are presented to a decision table as its decision classes. Based on the decision table, a method of gene selection is developed. The effectiveness of the GSOM is shown in both clustering samples and developing an unsupervised fuzzy rough feature selection (UFRFS) method for gene selection in microarray data. While the superior results of the GSOM, as compared with the related clustering methods, are provided in terms of β -index, DB-index, Dunn-index, and fuzzy rough entropy, the genes selected by the UFRFS are not only better in terms of classification accuracy and a feature evaluation index, but also statistically more significant than the related unsupervised methods. The C-codes of the GSOM and UFRFS are available online at http://avatharamg.webs.com/software-code.

Cross-Modal Perception of Noise-in-Music: Audiences Generate Spiky Shapes in Response to Auditory Roughness in a Novel Electroacoustic Concert Setting.

PubMed

Liew, Kongmeng; Lindborg, PerMagnus; Rodrigues, Ruth; Styles, Suzy J

2018-01-01

Noise has become integral to electroacoustic music aesthetics. In this paper, we define noise as sound that is high in auditory roughness, and examine its effect on cross-modal mapping between sound and visual shape in participants. In order to preserve the ecological validity of contemporary music aesthetics, we developed Rama , a novel interface, for presenting experimentally controlled blocks of electronically generated sounds that varied systematically in roughness, and actively collected data from audience interaction. These sounds were then embedded as musical drones within the overall sound design of a multimedia performance with live musicians, Audience members listened to these sounds, and collectively voted to create the shape of a visual graphic, presented as part of the audio-visual performance. The results of the concert setting were replicated in a controlled laboratory environment to corroborate the findings. Results show a consistent effect of auditory roughness on shape design, with rougher sounds corresponding to spikier shapes. We discuss the implications, as well as evaluate the audience interface.

Realization of PLC to the Variable Frequency Speed Regulation System of Mine Local Ventilator based on RS-485 Communication

NASA Astrophysics Data System (ADS)

Ma, Kai; Li, Jian; Yun, Yichong

2018-03-01

The article first introduces the merits of serial communication in the PLC to the variable frequency speed regulation system of mine local ventilator, and then sets up a hardware application development platform of PLC and inverter based on RS-485 communication technology, next presents communication initialization of the PLC and Inverter. Finally according to the control requirements, PLC send run operation & monitoring instruction to Inverter, realizes the serial communication control between the PLC and Inverter.

Development of the 3-SET 4P questionnaire for evaluating former ICU patients' physical and psychosocial problems over time: a pilot study.

PubMed

Akerman, Eva; Fridlund, Bengt; Ersson, Anders; Granberg-Axéll, Anetth

2009-04-01

Current studies reveal a lack of consensus for the evaluation of physical and psychosocial problems after ICU stay and their changes over time. The aim was to develop and evaluate the validity and reliability of a questionnaire for assessing physical and psychosocial problems over time for patients following ICU recovery. Thirty-nine patients completed the questionnaire, 17 were retested. The questionnaire was constructed in three sets: physical problems, psychosocial problems and follow-up care. Face and content validity were tested by nurses, researchers and patients. The questionnaire showed good construct validity in all three sets and had strong factor loadings (explained variance >70%, factor loadings >0.5) for all three sets. There was good concurrent validity compared with the SF 12 (r(s)>0.5). Internal consistency was shown to be reliable (Cronbach's alpha 0.70-0.85). Stability reliability on retesting was good for the physical and psychosocial sets (r(s)>0.5). The 3-set 4P questionnaire was a first step in developing an instrument for assessment of former ICU patients' problems over time. The sample size was small and thus, further studies are needed to confirm these findings.

Interferon-related genetic markers of necroinflammatory activity in chronic hepatitis C.

PubMed

López-Rodríguez, Rosario; Hernández-Bartolomé, Ángel; Borque, María Jesús; Rodríguez-Muñoz, Yolanda; Martín-Vílchez, Samuel; García-Buey, Luisa; González-Moreno, Leticia; Real-Martínez, Yolanda; Muñoz de Rueda, Paloma; Salmerón, Javier; Vidal-Castiñeira, José Ramón; López-Larrea, Carlos; Rodrigo, Luis; Moreno-Otero, Ricardo; Sanz-Cameno, Paloma

2017-01-01

Chronic hepatitis C (CHC) is a major cause of liver disease worldwide which often leads to progressive liver inflammation, fibrosis, cirrhosis and hepatocellular carcinoma (HCC). CHC displays heterogeneous progression depending on a broad set of factors, some of them intrinsic to each individual such as the patient's genetic profile. This study aims to evaluate the contribution of certain genetic variants of crucial interferon alpha and lambda signaling pathways to the hepatic necroinflammatory activity (NIA) grade of CHC patients. NIA was evaluated in 119 CHC patients by METAVIR scale and classified as low (NIA = 0-2, n = 80) or high grade (NIA = 3, n = 39). In a candidate gene approach, 64 SNPs located in 30 different genes related to interferon pathways (IL-28B, IFNAR1-2, JAK-STAT and OAS1-3, among others) were genotyped using the Illumina GoldenGate® Genotyping Assay. Statistical association was determined by logistic regression and expressed as OR and 95% CI. Those SNPs significantly associated were further adjusted by other covariates. Seven SNPs located in IL-28B (rs12979860), JAK1 (rs11576173 and rs1497056), TYK2 (rs280519), OAS1 (rs2057778), SOCS1 (rs33932899) and RNASEL (rs3738579) genes were significantly related to severe NIA grade (p<0.05). Regarding to clinical variables, elevated NIA was notably associated with aspartate aminotransferase (AST) serum levels >40 IU/L (p<0.05) but not with other clinical factors. Multivariate logistic regression analysis of these factors reflected that AST (>40 IU/L), TYK2 rs280519 (G allele) and RNASEL rs3738579 (G allele) were factors independently associated with elevated NIA (p<0.05). AST concentration showed a moderate AUC value (AUC = 0.63), similar to TYK2 (rs280519) and RNASEL (rs3738579) SNPs (AUC = 0.61, both) in the ROC_AUC analysis. Interestingly, the model including all significant variables reached a considerable predictive value (AUC = 0.74). The identified genetic variants in interferon signaling pathways may constitute useful prognostic markers of CHC progression. Further validation in larger cohorts of patients is needed.

Psychometric properties of the Chinese version of resilience scale specific to cancer: an item response theory analysis.

PubMed

Ye, Zeng Jie; Liang, Mu Zi; Zhang, Hao Wei; Li, Peng Fei; Ouyang, Xue Ren; Yu, Yuan Liang; Liu, Mei Ling; Qiu, Hong Zhong

2018-06-01

Classic theory test has been used to develop and validate the 25-item Resilience Scale Specific to Cancer (RS-SC) in Chinese patients with cancer. This study was designed to provide additional information about the discriminative value of the individual items tested with an item response theory analysis. A two-parameter graded response model was performed to examine whether any of the items of the RS-SC exhibited problems with the ordering and steps of thresholds, as well as the ability of items to discriminate patients with different resilience levels using item characteristic curves. A sample of 214 Chinese patients with cancer diagnosis was analyzed. The established three-dimension structure of the RS-SC was confirmed. Several items showed problematic thresholds or discrimination ability and require further revision. Some problematic items should be refined and a short-form of RS-SC maybe feasible in clinical settings in order to reduce burden on patients. However, the generalizability of these findings warrants further investigations.

In vitro evaluation of resistance to sliding in self-ligating and conventional bracket systems during dental alignment.

PubMed

Cordasco, Giancarlo; Lo Giudice, Antonino; Militi, Angela; Nucera, Riccardo; Triolo, Giuseppe; Matarese, Giovanni

2012-08-01

To investigate the resistance to sliding (RS) in self-ligating and conventional ligation bracket systems at 5 different second-order bracket angulations by using low-stiffness alignment wires in a 3-bracket experimental model and to verify the performance of the main RS components in both systems when these wires are used. Interactive self-ligating brackets with closed and open slides were used for the self-ligating (SL) and conventional ligation (CL) groups, respectively; elastomeric ligatures (1 mm inner diameter) were used in the latter system. The alignment wire used was 0.014 inch heat-activated NiTi (austenitic finish temperature set at 36℃ by the manufacturer). A custom-made testing machine was used to measure frictional resistance. Tests were repeated 5 times at every angulation simulated. All data were analyzed statistically. The RS increased significantly with increasing angulation in both SL and CL groups (p < 0.0001). However, the RS values were significantly higher at every angulation (p < 0.0001) in the CL group. Despite the relevance of the binding phenomenon, ligation forces predominantly affect the RS when low-stiffness alignment wires are used.

In vitro evaluation of resistance to sliding in self-ligating and conventional bracket systems during dental alignment

PubMed Central

Cordasco, Giancarlo; Lo Giudice, Antonino; Militi, Angela; Nucera, Riccardo; Triolo, Giuseppe

2012-01-01

Objective To investigate the resistance to sliding (RS) in self-ligating and conventional ligation bracket systems at 5 different second-order bracket angulations by using low-stiffness alignment wires in a 3-bracket experimental model and to verify the performance of the main RS components in both systems when these wires are used. Methods Interactive self-ligating brackets with closed and open slides were used for the self-ligating (SL) and conventional ligation (CL) groups, respectively; elastomeric ligatures (1 mm inner diameter) were used in the latter system. The alignment wire used was 0.014 inch heat-activated NiTi (austenitic finish temperature set at 36℃ by the manufacturer). A custom-made testing machine was used to measure frictional resistance. Tests were repeated 5 times at every angulation simulated. All data were analyzed statistically. Results The RS increased significantly with increasing angulation in both SL and CL groups (p < 0.0001). However, the RS values were significantly higher at every angulation (p < 0.0001) in the CL group. Conclusions Despite the relevance of the binding phenomenon, ligation forces predominantly affect the RS when low-stiffness alignment wires are used. PMID:23112953

Levels of human platelet-derived soluble CD40 ligand depend on haplotypes of CD40LG-CD40-ITGA2

PubMed Central

Aloui, Chaker; Prigent, Antoine; Tariket, Sofiane; Sut, Caroline; Fagan, Jocelyne; Cognasse, Fabrice; Chakroun, Tahar; Garraud, Olivier; Laradi, Sandrine

2016-01-01

Increased circulating soluble CD40 ligand (sCD40L) is commonly associated with inflammatory disorders. We aimed to investigate whether gene polymorphisms in CD40LG, CD40 and ITGA2 are associated with a propensity to secrete sCD40L; thus, we examined this issue at the level of human platelets, the principal source of sCD40L. We performed single polymorphism and haplotype analyses to test for the effect of twelve polymorphisms across the CD40LG, CD40 and ITGA2 genes in blood donors. ITGA2 presented a positive association with rs1126643, with a significant modification in sCD40L secretion (carriers of C allele, P = 0.02), unlike the investigated CD40LG and CD40 polymorphisms. One CD40LG haplotype (TGGC) showing rs975379 (C/T), rs3092952 (A/G), rs3092933 (A/G) and rs3092929 (A/C) was associated with increased sCD40L levels (1.906 μg/L (95% CI: 1.060 to 2.751); P = 0.000009). The sCD40L level was associated with the inter-chromosomal CD40LG/CD40/ITGA2 haplotype (ATC), displaying rs3092952 (A/G), rs1883832 (C/T) and rs1126643 (C/T), with increased sCD40L levels (P = 0.0135). Our results help to decipher the genetic role of CD40LG, CD40 and ITGA2 with regard to sCD40L levels found in platelet components. Given the crucial role of sCD40L, this haplotype study in a transfusion model may be helpful to further determine the role of haplotypes in inflammatory clinical settings. PMID:27094978

Common NOTCH3 Variants and Cerebral Small-Vessel Disease.

PubMed

Rutten-Jacobs, Loes C A; Traylor, Matthew; Adib-Samii, Poneh; Thijs, Vincent; Sudlow, Cathie; Rothwell, Peter M; Boncoraglio, Giorgio; Dichgans, Martin; Bevan, Steve; Meschia, James; Levi, Christopher; Rost, Natalia S; Rosand, Jonathan; Hassan, Ahamad; Markus, Hugh S

2015-06-01

The most common monogenic cause of cerebral small-vessel disease is cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, caused by NOTCH3 gene mutations. It has been hypothesized that more common variants in NOTCH3 may also contribute to the risk of sporadic small-vessel disease. Previously, 4 common variants (rs10404382, rs1043994, rs10423702, and rs1043997) were found to be associated with the presence of white matter hyperintensity in hypertensive community-dwelling elderly. We investigated the association of common single nucleotide polymorphisms (SNPs) in NOTCH3 in 1350 patients with MRI-confirmed lacunar stroke and 7397 controls, by meta-analysis of genome-wide association study data sets. In addition, we investigated the association of common SNPs in NOTCH3 with MRI white matter hyperintensity volumes in 3670 white patients with ischemic stroke. In each analysis, we considered all SNPs within the NOTCH3 gene, and within 50-kb upstream and downstream of the coding region. A total of 381 SNPs from the 1000 genome population with a mean allele frequency>0.01 were included in the analysis. A significance level of P<0.0015 was used, adjusted for the effective number of independent SNPs in the region using the Galwey method. We found no association of any common variants in NOTCH3 (including rs10404382, rs1043994, rs10423702, and rs1043997) with lacunar stroke or white matter hyperintensity volume. We repeated our analysis stratified for hypertension but again found no association. Our study does not support a role for common NOTCH3 variation in the risk of sporadic small-vessel disease. © 2015 The Authors.

Resistance switching behavior of atomic layer deposited SrTiO3 film through possible formation of Sr2Ti6O13 or Sr1Ti11O20 phases

PubMed Central

Lee, Woongkyu; Yoo, Sijung; Yoon, Kyung Jean; Yeu, In Won; Chang, Hye Jung; Choi, Jung-Hae; Hoffmann-Eifert, Susanne; Waser, Rainer; Hwang, Cheol Seong

2016-01-01

Identification of microstructural evolution of nanoscale conducting phase, such as conducting filament (CF), in many resistance switching (RS) devices is a crucial factor to unambiguously understand the electrical behaviours of the RS-based electronic devices. Among the diverse RS material systems, oxide-based redox system comprises the major category of these intriguing electronic devices, where the local, along both lateral and vertical directions of thin films, changes in oxygen chemistry has been suggested to be the main RS mechanism. However, there are systems which involve distinctive crystallographic phases as CF; the Magnéli phase in TiO2 is one of the very well-known examples. The current research reports the possible presence of distinctive local conducting phase in atomic layer deposited SrTiO3 RS thin film. The conducting phase was identified through extensive transmission electron microscopy studies, which indicated that oxygen-deficient Sr2Ti6O13 or Sr1Ti11O20 phase was presumably present mainly along the grain boundaries of SrTiO3 after the unipolar set switching in Pt/TiN/SrTiO3/Pt structure. A detailed electrical characterization revealed that the samples showed typical bipolar and complementary RS after the memory cell was unipolar reset. PMID:26830978

Survey of thermal plasma ions in Saturn's magnetosphere utilizing a forward model

NASA Astrophysics Data System (ADS)

Wilson, R. J.; Bagenal, F.; Persoon, A. M.

2017-07-01

The Cassini Plasma Spectrometer instrument gathered thermal ion data at Saturn from 2004 to 2012, predominantly observing water group ions and protons. Plasma parameters, with uncertainties, for those two ion species are derived using a forward model of anisotropic convected Maxwellians moving at a shared velocity. The resulting data set is filtered by various selection criteria to produce a survey of plasma parameters derived within 10° of the equator at radial distances of 5.5 to 30 RS (1 RS = Saturn's radius). The previous 2008 work used a simpler method and had just 150 records over 5 orbits; this comprehensive survey has 9736 records over all 9 years. We present the results of this survey and compare them with a previous survey derived from numerical moments, highlighting the differences between the reported densities and temperatures from the two methods. Radial profiles of the plasma parameters in the inner and middle magnetospheres out to ≈22RS are stable year by year, but variable at distances larger than 23 RS near the magnetopause. New results include proton densities increasing in the near magnetopause region, suggestive of plasma mixing; evidence for the global electric field in Saturn's inner magnetosphere extends out to ≈15RS; no evidence for supercorotating plasma nor the middle magnetosphere "plasma cam" feature is present; the thermal plasma β is found to exceed unity at equatorial distances greater than 15 RS.

Readout-Segmented Echo-Planar Imaging in Diffusion-Weighted MR Imaging in Breast Cancer: Comparison with Single-Shot Echo-Planar Imaging in Image Quality

PubMed Central

Kim, Yun Ju; Kang, Bong Joo; Park, Chang Suk; Kim, Hyeon Sook; Son, Yo Han; Porter, David Andrew; Song, Byung Joo

2014-01-01

Objective The purpose of this study was to compare the image quality of standard single-shot echo-planar imaging (ss-EPI) and that of readout-segmented EPI (rs-EPI) in patients with breast cancer. Materials and Methods Seventy-one patients with 74 breast cancers underwent both ss-EPI and rs-EPI. For qualitative comparison of image quality, three readers independently assessed the two sets of diffusion-weighted (DW) images. To evaluate geometric distortion, a comparison was made between lesion lengths derived from contrast enhanced MR (CE-MR) images and those obtained from the corresponding DW images. For assessment of image parameters, signal-to-noise ratio (SNR), lesion contrast, and contrast-to-noise ratio (CNR) were calculated. Results The rs-EPI was superior to ss-EPI in most criteria regarding the qualitative image quality. Anatomical structure distinction, delineation of the lesion, ghosting artifact, and overall image quality were significantly better in rs-EPI. Regarding the geometric distortion, lesion length on ss-EPI was significantly different from that of CE-MR, whereas there were no significant differences between CE-MR and rs-EPI. The rs-EPI was superior to ss-EPI in SNR and CNR. Conclusion Readout-segmented EPI is superior to ss-EPI in the aspect of image quality in DW MR imaging of the breast. PMID:25053898

Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer.

PubMed

Klein, Alison P; Wolpin, Brian M; Risch, Harvey A; Stolzenberg-Solomon, Rachael Z; Mocci, Evelina; Zhang, Mingfeng; Canzian, Federico; Childs, Erica J; Hoskins, Jason W; Jermusyk, Ashley; Zhong, Jun; Chen, Fei; Albanes, Demetrius; Andreotti, Gabriella; Arslan, Alan A; Babic, Ana; Bamlet, William R; Beane-Freeman, Laura; Berndt, Sonja I; Blackford, Amanda; Borges, Michael; Borgida, Ayelet; Bracci, Paige M; Brais, Lauren; Brennan, Paul; Brenner, Hermann; Bueno-de-Mesquita, Bas; Buring, Julie; Campa, Daniele; Capurso, Gabriele; Cavestro, Giulia Martina; Chaffee, Kari G; Chung, Charles C; Cleary, Sean; Cotterchio, Michelle; Dijk, Frederike; Duell, Eric J; Foretova, Lenka; Fuchs, Charles; Funel, Niccola; Gallinger, Steven; M Gaziano, J Michael; Gazouli, Maria; Giles, Graham G; Giovannucci, Edward; Goggins, Michael; Goodman, Gary E; Goodman, Phyllis J; Hackert, Thilo; Haiman, Christopher; Hartge, Patricia; Hasan, Manal; Hegyi, Peter; Helzlsouer, Kathy J; Herman, Joseph; Holcatova, Ivana; Holly, Elizabeth A; Hoover, Robert; Hung, Rayjean J; Jacobs, Eric J; Jamroziak, Krzysztof; Janout, Vladimir; Kaaks, Rudolf; Khaw, Kay-Tee; Klein, Eric A; Kogevinas, Manolis; Kooperberg, Charles; Kulke, Matthew H; Kupcinskas, Juozas; Kurtz, Robert J; Laheru, Daniel; Landi, Stefano; Lawlor, Rita T; Lee, I-Min; LeMarchand, Loic; Lu, Lingeng; Malats, Núria; Mambrini, Andrea; Mannisto, Satu; Milne, Roger L; Mohelníková-Duchoňová, Beatrice; Neale, Rachel E; Neoptolemos, John P; Oberg, Ann L; Olson, Sara H; Orlow, Irene; Pasquali, Claudio; Patel, Alpa V; Peters, Ulrike; Pezzilli, Raffaele; Porta, Miquel; Real, Francisco X; Rothman, Nathaniel; Scelo, Ghislaine; Sesso, Howard D; Severi, Gianluca; Shu, Xiao-Ou; Silverman, Debra; Smith, Jill P; Soucek, Pavel; Sund, Malin; Talar-Wojnarowska, Renata; Tavano, Francesca; Thornquist, Mark D; Tobias, Geoffrey S; Van Den Eeden, Stephen K; Vashist, Yogesh; Visvanathan, Kala; Vodicka, Pavel; Wactawski-Wende, Jean; Wang, Zhaoming; Wentzensen, Nicolas; White, Emily; Yu, Herbert; Yu, Kai; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Kraft, Peter; Li, Donghui; Chanock, Stephen; Obazee, Ofure; Petersen, Gloria M; Amundadottir, Laufey T

2018-02-08

In 2020, 146,063 deaths due to pancreatic cancer are estimated to occur in Europe and the United States combined. To identify common susceptibility alleles, we performed the largest pancreatic cancer GWAS to date, including 9040 patients and 12,496 controls of European ancestry from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4). Here, we find significant evidence of a novel association at rs78417682 (7p12/TNS3, P = 4.35 × 10 -8 ). Replication of 10 promising signals in up to 2737 patients and 4752 controls from the PANcreatic Disease ReseArch (PANDoRA) consortium yields new genome-wide significant loci: rs13303010 at 1p36.33 (NOC2L, P = 8.36 × 10 -14 ), rs2941471 at 8q21.11 (HNF4G, P = 6.60 × 10 -10 ), rs4795218 at 17q12 (HNF1B, P = 1.32 × 10 -8 ), and rs1517037 at 18q21.32 (GRP, P = 3.28 × 10 -8 ). rs78417682 is not statistically significantly associated with pancreatic cancer in PANDoRA. Expression quantitative trait locus analysis in three independent pancreatic data sets provides molecular support of NOC2L as a pancreatic cancer susceptibility gene.

Methods for Kinetic and Thermodynamic Analysis of Aminoacyl-tRNA Synthetases

PubMed Central

Francklyn, Christopher S.; First, Eric A.; Perona, John J.; Hou, Ya-Ming

2008-01-01

The accuracy of protein synthesis relies on the ability of aminoacyl-tRNA synthetases (aaRSs) to discriminate among true and near cognate substrates. To date, analysis of aaRSs function, including identification of residues of aaRS participating in amino acid and tRNA discrimination, has largely relied on the steady state kinetic pyrophosphate exchange and aminoacylation assays. Pre-steady state kinetic studies investigating a more limited set of aaRS systems have also been undertaken to assess the energetic contributions of individual enzyme-substrate interactions, particularly in the adenylation half reaction. More recently, a renewed interest in the use of rapid kinetics approaches for aaRSs has led to their application to several new aaRS systems, resulting in the identification of mechanistic differences that distinguish the two structurally distinct aaRS classes. Here, we review the techniques for thermodynamic and kinetic analysis of aaRS function. Following a brief survey of methods for the preparation of materials and for steady state kinetic analysis, this review will describe pre-steady state kinetic methods employing rapid quench and stopped-flow fluorescence for analysis of the activation and aminoacyl transfer reactions. Application of these methods to any aaRS system allows the investigator to derive detailed kinetic mechanisms for the activation and aminoacyl transfer reactions, permitting issues of substrate specificity, stereochemical mechanism, and inhibitor interaction to be addressed in a rigorous and quantitative fashion. PMID:18241792

The Backscattering Phase Function for a Sphere with a Two-Scale Relief of Rough Surface

NASA Astrophysics Data System (ADS)

Klass, E. V.

2017-12-01

The backscattering of light from spherical surfaces characterized by one and two-scale roughness reliefs has been investigated. The analysis is performed using the three-dimensional Monte-Carlo program POKS-RG (geometrical-optics approximation), which makes it possible to take into account the roughness of objects under study by introducing local geometries of different levels. The geometric module of the program is aimed at describing objects by equations of second-order surfaces. One-scale roughness is set as an ensemble of geometric figures (convex or concave halves of ellipsoids or cones). The two-scale roughness is modeled by convex halves of ellipsoids, with surface containing ellipsoidal pores. It is shown that a spherical surface with one-scale convex inhomogeneities has a flatter backscattering phase function than a surface with concave inhomogeneities (pores). For a sphere with two-scale roughness, the dependence of the backscattering intensity is found to be determined mostly by the lower-level inhomogeneities. The influence of roughness on the dependence of the backscattering from different spatial regions of spherical surface is analyzed.

Non-Mydriatic Fundus Retinography in Screening for Diabetic Retinopathy: Agreement Between Family Physicians, General Ophthalmologists, and a Retinal Specialist.

PubMed

Cunha, Leonardo Provetti; Figueiredo, Evelyn Alvernaz; Araújo, Henrique Pereira; Costa-Cunha, Luciana Virgínia Ferreira; Costa, Carolina Ferreira; Neto, José de Melo Costa; Matos, Aline Mota Freitas; de Oliveira, Marise Machado; Bastos, Marcus Gomes; Monteiro, Mário Luiz Ribeiro

2018-01-01

To determine the level of agreement between trained family physicians (FPs), general ophthalmologists (GOs), and a retinal specialist (RS) in the assessment of non-mydriatic fundus retinography in screening for diabetic retinopathy (DR) in the primary health-care setting. 200 Diabetic patients were submitted to two-field non-mydriatic digital fundus camera. The images were examined by four trained FPs, two GOs, and one RS with regard to the diagnosis and severity of DR and the diagnosis of macular edema. The RS served as gold standard. Reliability and accuracy were determined with the kappa test and diagnostic measures. A total of 397 eyes of 200 patients were included. The mean age was 55.1 (±11.7) years, and 182 (91%) had type 2 diabetes. The mean levels of serum glucose and glycosylated hemoglobin A1c were 195.6 (±87.3) mg/dL and 8.9% (±2.1), respectively. DR was diagnosed in 166 eyes by the RS and in 114 and 182 eyes by GO 1 and GO 2 , respectively. For severity, DR was graded as proliferative in 8 eyes by the RS vs. 15 and 9 eyes by GO 1 and GO 2 , respectively. The agreement between the RS and the GOs was substantial for both DR diagnosis (GO 1 k  = 0.65; GO 2 k  = 0.74) and severity (GO 1 k  = 0.60; GO 2 k  = 0.71), and fair or moderate for macular edema (GO 1 k  = 0.27; GO 2 k  = 0.43). FP 1 , FP 2 , FP 3 , and FP 4 diagnosed DR in 108, 119, 163, and 117 eyes, respectively. The agreement between the RS and the FPs with regard to DR diagnosis was substantial (FP 2 k  = 0.69; FP 3 k  = 0.73; FP 4 k  = 0.71) or moderate (FP 1 k  = 0.56). As for DR severity, the agreement between the FPs and the RS was substantial (FP 2 k  = 0.66; FP 3 k  = 069; FP 4 k  = 0.64) or moderate (FP 1 k  = 0.51). Agreement between the FPs and the RS with regard to macular edema was fair (FP 1 k  = 0.33; FP 2 k  = 0.39; FP 3 k  = 0.37) or moderate (FP 4 k  = 0.51). Non-mydriatic fundus retinography was shown to be useful in DR screening in the primary health-care setting. FPs made assessments with good levels of agreement with an RS. Non-mydriatic fundus retinography associated with appropriate general physicians training is essential for the DR screening.

Modeling and evaluating of surface roughness prediction in micro-grinding on soda-lime glass considering tool characterization

NASA Astrophysics Data System (ADS)

Cheng, Jun; Gong, Yadong; Wang, Jinsheng

2013-11-01

The current research of micro-grinding mainly focuses on the optimal processing technology for different materials. However, the material removal mechanism in micro-grinding is the base of achieving high quality processing surface. Therefore, a novel method for predicting surface roughness in micro-grinding of hard brittle materials considering micro-grinding tool grains protrusion topography is proposed in this paper. The differences of material removal mechanism between convention grinding process and micro-grinding process are analyzed. Topography characterization has been done on micro-grinding tools which are fabricated by electroplating. Models of grain density generation and grain interval are built, and new predicting model of micro-grinding surface roughness is developed. In order to verify the precision and application effect of the surface roughness prediction model proposed, a micro-grinding orthogonally experiment on soda-lime glass is designed and conducted. A series of micro-machining surfaces which are 78 nm to 0.98 μm roughness of brittle material is achieved. It is found that experimental roughness results and the predicting roughness data have an evident coincidence, and the component variable of describing the size effects in predicting model is calculated to be 1.5×107 by reverse method based on the experimental results. The proposed model builds a set of distribution to consider grains distribution densities in different protrusion heights. Finally, the characterization of micro-grinding tools which are used in the experiment has been done based on the distribution set. It is concluded that there is a significant coincidence between surface prediction data from the proposed model and measurements from experiment results. Therefore, the effectiveness of the model is demonstrated. This paper proposes a novel method for predicting surface roughness in micro-grinding of hard brittle materials considering micro-grinding tool grains protrusion topography, which would provide significant research theory and experimental reference of material removal mechanism in micro-grinding of soda-lime glass.

In search of a Self-Consistent Explanation of Saturn's Magnetospheric Periodicities

NASA Astrophysics Data System (ADS)

Brandt, P. C.; Mitchell, D. G.; Carbary, J. F.; Tsyganenko, N. A.; Ebihara, Y.

2011-12-01

A global picture of Saturn's magnetospheric periodicities is emerging from several observations and modeling efforts. In this presentation we demonstrate that these observations likely contain sufficient information to explain the mysterious periodicities at Saturn, without the need of any prescribed (and often, unobservable) longitudinal anomalies. In this picture plasmoids are released quasi-periodically down the tail, leading to fast planet-ward flows and particle energization ("injections") that enhance the plasma pressure in the night side magnetosphere in the 8-20 Rs region as clearly observed in energetic neutral atom (ENA) observations by the Ion Neutral Camera (INCA) on board Cassini. Both the fast flows and the enhanced pressure drive a 3D current system that closes through the ionosphere, whose upward field-aligned component can be linked to bursts of Saturn Kilometric Radition (SKR). The current system driven by the energetic particle pressure - the partial ring current (PRC) - also distorts the magnetic field significantly leading to its periodic oscillations as the enhanced particle pressure island drifts around Saturn with a period between 10-11 h. The missing link is how the plasmoid release can be periodic. We present global INCA observations showing that pre-existing energetic particle pressure distributions from a previous injection seem to trigger the next injection. This is likely to happen due to the inflation of the magnetic field and modification of the properties of the night side current sheet, leading to an unstable current sheet. The presence of a PRC rotating around Saturn also modifies the electric field in the magnetosphere due to its closure through the ionosphere. Such a modification is called a shielding electric field, and is commonly observed at Earth associated with a radially outward density enhancement of the cold, dense plasmasphere below the PRC. This can further contribute to triggering the plasmoid release. In regards to the "dual" SKR and field periodicities that appear to be different in the northern and southern hemispheres, we investigate the possibilities that this could be a combined effect of injections in to two different radial ranges and inter-hemispheric field-aligned currents (FAC) set up by the seasonal conductance differences of the two hemispheres. Injections have been observed in the two radial ranges of roughly 9-12 Rs and >15Rs where the drift periods differ. We will attempt to quantify if this holds statistically and visualize what the combination of a rotating PRC and inter hemispheric currents look like.

Comparison of two metrological approaches for the prediction of human haptic perception

NASA Astrophysics Data System (ADS)

Neumann, Annika; Frank, Daniel; Vondenhoff, Thomas; Schmitt, Robert

2016-06-01

Haptic perception is regarded as a key component of customer appreciation and acceptance for various products. The prediction of customers’ haptic perception is of interest both during product development and production phases. This paper presents the results of a multivariate analysis between perceived roughness and texture related surface measurements, to examine whether perceived roughness can be accurately predicted using technical measurements. Studies have shown that standardized measurement parameters, such as the roughness coefficients (e.g. Rz or Ra), do not show a one-dimensional linear correlation with the human perception (of roughness). Thus, an alternative measurement method was compared to standard measurements of roughness, in regard to its capability of predicting perceived roughness through technical measurements. To estimate perceived roughness, an experimental study was conducted in which 102 subjects evaluated four sets of 12 different geometrical surface structures regarding their relative perceived roughness. The two different metrological procedures were examined in relation to their capability to predict the perceived roughness of the subjects stated within the study. The standardized measurements of the surface roughness were made using a structured light 3D-scanner. As an alternative method, surface induced vibrations were measured by a finger-like sensor during robot-controlled traverse over a surface. The presented findings provide a better understanding of the predictability of human haptic perception using technical measurements.

The role of connectedness in haptic object perception.

PubMed

Plaisier, Myrthe A; van Polanen, Vonne; Kappers, Astrid M L

2017-03-02

We can efficiently detect whether there is a rough object among a set of smooth objects using our sense of touch. We can also quickly determine the number of rough objects in our hand. In this study, we investigated whether the perceptual processing of rough and smooth objects is influenced if these objects are connected. In Experiment 1, participants were asked to identify whether there were exactly two rough target spheres among smooth distractor spheres, while we recorded their response times. The spheres were connected to form pairs: rough spheres were paired together and smooth spheres were paired together ('within pairs arrangement'), or a rough and a smooth sphere were connected ('between pairs arrangement'). Participants responded faster when the spheres in a pair were identical. In Experiment 2, we found that the advantage for within pairs arrangements was not driven by feature saliency. Overall our results show that haptic information is processed faster when targets were connected together compared to when targets were connected to distractors.

ROMI-RIP: Rough Mill RIP-first simulator user's guide

Treesearch

R. Edward Thomas

1995-01-01

The ROugh Mill RIP-first simulator (ROMI-RIP) is a computer software package for IBM compatible personal computers that simulates current industrial practices for gang-ripping lumber. This guide shows the user how to set and examine the results of simulations regarding current or proposed mill practices. ROMI-RIP accepts cutting bills with up to 300 different part...

Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk.

PubMed

Dunlop, Malcolm G; Dobbins, Sara E; Farrington, Susan Mary; Jones, Angela M; Palles, Claire; Whiffin, Nicola; Tenesa, Albert; Spain, Sarah; Broderick, Peter; Ooi, Li-Yin; Domingo, Enric; Smillie, Claire; Henrion, Marc; Frampton, Matthew; Martin, Lynn; Grimes, Graeme; Gorman, Maggie; Semple, Colin; Ma, Yusanne P; Barclay, Ella; Prendergast, James; Cazier, Jean-Baptiste; Olver, Bianca; Penegar, Steven; Lubbe, Steven; Chander, Ian; Carvajal-Carmona, Luis G; Ballereau, Stephane; Lloyd, Amy; Vijayakrishnan, Jayaram; Zgaga, Lina; Rudan, Igor; Theodoratou, Evropi; Starr, John M; Deary, Ian; Kirac, Iva; Kovacević, Dujo; Aaltonen, Lauri A; Renkonen-Sinisalo, Laura; Mecklin, Jukka-Pekka; Matsuda, Koichi; Nakamura, Yusuke; Okada, Yukinori; Gallinger, Steven; Duggan, David J; Conti, David; Newcomb, Polly; Hopper, John; Jenkins, Mark A; Schumacher, Fredrick; Casey, Graham; Easton, Douglas; Shah, Mitul; Pharoah, Paul; Lindblom, Annika; Liu, Tao; Smith, Christopher G; West, Hannah; Cheadle, Jeremy P; Midgley, Rachel; Kerr, David J; Campbell, Harry; Tomlinson, Ian P; Houlston, Richard S

2012-05-27

We performed a meta-analysis of five genome-wide association studies to identify common variants influencing colorectal cancer (CRC) risk comprising 8,682 cases and 9,649 controls. Replication analysis was performed in case-control sets totaling 21,096 cases and 19,555 controls. We identified three new CRC risk loci at 6p21 (rs1321311, near CDKN1A; P = 1.14 × 10(-10)), 11q13.4 (rs3824999, intronic to POLD3; P = 3.65 × 10(-10)) and Xp22.2 (rs5934683, near SHROOM2; P = 7.30 × 10(-10)) This brings the number of independent loci associated with CRC risk to 20 and provides further insight into the genetic architecture of inherited susceptibility to CRC.

Advanced Connectivity Analysis (ACA): a Large Scale Functional Connectivity Data Mining Environment.

PubMed

Chen, Rong; Nixon, Erika; Herskovits, Edward

2016-04-01

Using resting-state functional magnetic resonance imaging (rs-fMRI) to study functional connectivity is of great importance to understand normal development and function as well as a host of neurological and psychiatric disorders. Seed-based analysis is one of the most widely used rs-fMRI analysis methods. Here we describe a freely available large scale functional connectivity data mining software package called Advanced Connectivity Analysis (ACA). ACA enables large-scale seed-based analysis and brain-behavior analysis. It can seamlessly examine a large number of seed regions with minimal user input. ACA has a brain-behavior analysis component to delineate associations among imaging biomarkers and one or more behavioral variables. We demonstrate applications of ACA to rs-fMRI data sets from a study of autism.

Reconstruction of hyperspectral reflectance for optically complex turbid inland lakes: test of a new scheme and implications for inversion algorithms.

PubMed

Sun, Deyong; Hu, Chuanmin; Qiu, Zhongfeng; Wang, Shengqiang

2015-06-01

A new scheme has been proposed by Lee et al. (2014) to reconstruct hyperspectral (400 - 700 nm, 5 nm resolution) remote sensing reflectance (R_rs(λ), sr^-1) of representative global waters using measurements at 15 spectral bands. This study tested its applicability to optically complex turbid inland waters in China, where R_rs(λ) are typically much higher than those used in Lee et al. (2014). Strong interdependence of R_rs(λ) between neighboring bands (≤ 10 nm interval) was confirmed, with Pearson correlation coefficient (PCC) mostly above 0.98. The scheme of Lee et al. (2014) for R_rs(λ) re-construction with its original global parameterization worked well with this data set, while new parameterization showed improvement in reducing uncertainties in the reconstructed R_rs(λ). Mean absolute error (MAE_Rrs(λ_i)) in the reconstructed R_rs(λ) was mostly < 0.0002 sr^-1 between 400 and 700nm, and mean relative error (MRE_Rrs(λ_i)) was < 1% when the comparison was made between reconstructed and measured R_rs(λ) spectra. When R_rs(λ) at the MODIS bands were used to reconstruct the hyperspectral R_rs(λ), MAE_Rrs(λ_i) was < 0.001 sr^-1 and MRE_Rrs(λ_i) was < 3%. When R_rs(λ) at the MERIS bands were used, MAE_Rrs(λ_i) in the reconstructed hyperspectral R_rs(λ) was < 0.0004 sr^-1 and MRE_Rrs(λ_i) was < 1%. These results have significant implications for inversion algorithms to retrieve concentrations of phytoplankton pigments (e.g., chlorophyll-a or Chla, and phycocyanin or PC) and total suspended materials (TSM) as well as absorption coefficient of colored dissolved organic matter (CDOM), as some of the algorithms were developed from in situ R_rs(λ) data using spectral bands that may not exist on satellite sensors.

Why rate when you could compare? Using the "EloChoice" package to assess pairwise comparisons of perceived physical strength.

PubMed

Clark, Andrew P; Howard, Kate L; Woods, Andy T; Penton-Voak, Ian S; Neumann, Christof

2018-01-01

We introduce "EloChoice", a package for R which uses Elo rating to assess pairwise comparisons between stimuli in order to measure perceived stimulus characteristics. To demonstrate the package and compare results from forced choice pairwise comparisons to those from more standard single stimulus rating tasks using Likert (or Likert-type) items, we investigated perceptions of physical strength from images of male bodies. The stimulus set comprised images of 82 men standing on a raised platform with minimal clothing. Strength-related anthropometrics and grip strength measurements were available for each man in the set. UK laboratory participants (Study 1) and US online participants (Study 2) viewed all images in both a Likert rating task, to collect mean Likert scores, and a pairwise comparison task, to calculate Elo, mean Elo (mElo), and Bradley-Terry scores. Within both studies, Likert, Elo and Bradley-Terry scores were closely correlated to mElo scores (all rs > 0.95), and all measures were correlated with stimulus grip strength (all rs > 0.38) and body size (all rs > 0.59). However, mElo scores were less variable than Elo scores and were hundreds of times quicker to compute than Bradley-Terry scores. Responses in pairwise comparison trials were 2/3 quicker than in Likert tasks, indicating that participants found pairwise comparisons to be easier. In addition, mElo scores generated from a data set with half the participants randomly excluded produced very comparable results to those produced with Likert scores from the full participant set, indicating that researchers require fewer participants when using pairwise comparisons.

Evolution of Space Shuttle Range Safety Ascent Flight Envelope Design

NASA Technical Reports Server (NTRS)

Brewer, Joan; Davis, Jerel; Glenn, Christopher

2011-01-01

For every space vehicle launch from the Eastern Range in Florida, the range user must provide specific Range Safety (RS) data products to the Air Force's 45th Space Wing in order to obtain flight plan approval. One of these data products is a set of RS ascent flight envelope trajectories that define the normal operating region of the vehicle during powered flight. With the Shuttle Program launching 135 manned missions over a 30-year period, 135 envelope sets were delivered to the range. During this time, the envelope methodology and design process evolved to support mission changes, maintain high data quality, and reduce costs. The purpose of this document is to outline the shuttle envelope design evolution and capture the lessons learned that could apply to future spaceflight endeavors.

Rough set soft computing cancer classification and network: one stone, two birds.

PubMed

Zhang, Yue

2010-07-15

Gene expression profiling provides tremendous information to help unravel the complexity of cancer. The selection of the most informative genes from huge noise for cancer classification has taken centre stage, along with predicting the function of such identified genes and the construction of direct gene regulatory networks at different system levels with a tuneable parameter. A new study by Wang and Gotoh described a novel Variable Precision Rough Sets-rooted robust soft computing method to successfully address these problems and has yielded some new insights. The significance of this progress and its perspectives will be discussed in this article.

Rough Set Approach to Incomplete Multiscale Information System

PubMed Central

Yang, Xibei; Qi, Yong; Yu, Dongjun; Yu, Hualong; Song, Xiaoning; Yang, Jingyu

2014-01-01

Multiscale information system is a new knowledge representation system for expressing the knowledge with different levels of granulations. In this paper, by considering the unknown values, which can be seen everywhere in real world applications, the incomplete multiscale information system is firstly investigated. The descriptor technique is employed to construct rough sets at different scales for analyzing the hierarchically structured data. The problem of unravelling decision rules at different scales is also addressed. Finally, the reduct descriptors are formulated to simplify decision rules, which can be derived from different scales. Some numerical examples are employed to substantiate the conceptual arguments. PMID:25276852

Determination of the minimal clinically important difference for seven fatigue measures in rheumatoid arthritis

PubMed Central

Pouchot, Jacques; Kherani, Raheem B.; Brant, Rollin; Lacaille, Diane; Lehman, Allen J.; Ensworth, Stephanie; Kopec, Jacek; Esdaile, John M.; Liang, Matthew H.

2008-01-01

Objective To estimate the minimal clinically important difference (MCID) of seven measures of fatigue in rheumatoid arthritis. Study Design and Setting A cross-sectional study design based on inter-individual comparisons was used. Six to eight subjects participated in a single meeting and completed seven fatigue questionnaires (nine sessions were organized and 61 subjects participated). After completion of the questionnaires, the subjects had five one-on-one 10-minute conversations with different people in the group to discuss their fatigue. After each conversation, each patient compared their fatigue to their conversational partner’s on a global rating. Ratings were compared to the scores of the fatigue measures to estimate the MCID. Both non-parametric and linear regression analyses were used. Results Non-parametric estimates for the MCID relative to “little more fatigue” tended to be smaller than those for “little less fatigue”. The global MCIDs estimated by linear regression were: FSS 20.2, VT 14.8, MAF 18.7, MFI 16.6, FACIT–F 15.9, CFS 9.9, RS 19.7, for normalized scores (0 to 100). The standardized MCIDs for the seven measures were roughly similar (0.67 to 0.76). Conclusion These estimates of MCID will help to interpret changes observed in a fatigue score and will be critical in estimating sample size requirements. PMID:18359189

ALPK1 genetic regulation and risk in relation to gout

PubMed Central

Min-Shan Ko, Albert; Tu, Hung-Pin; Liu, Tze-Tze; Chang, Jan-Gowth; Yuo, Chung-Yee; Chiang, Shang-Lun; Chang, Shun-Jen; Liu, Yu-Fan; Min-Jen Ko, Allen; Lee, Chien-Hung; Lee, Chi-Pin; Chang, Chung-Ming; Tsai, Shih-Feng; Ko, Ying-Chin

2013-01-01

Background The present study investigated whether single nucleotide polymorphisms (SNPs) in the alpha-protein kinase 1 (ALPK1) gene are associated with gout in aboriginal and Han Chinese Taiwanese. Methods A total of 1351 aborigines from the community (511 cases and 840 controls) and 511 Han people from hospital (104 cases and 407 controls) were recruited. SNPs in potentially functional regions of the 38 genes within 4q25 were identified and genotypes determined by direct sequencing. Quantitation of blood ALPK1 mRNA expression levels and luciferase assay of gout-associated rs231253 pGL3-SNP constructs cotransfected with hsa-miR-519e were examined. Results We found that ALPK1 gene was the most determinant of gout. Three SNPs of rs11726117 M861T [C], rs231247 [G] and rs231253 [G] were most associated with gout risk [odd ratios (OR) ≥1.44, P ≤ 3.78 × 10−6) in aborigines. A replication set using Han people had risk at rs11726117 and rs231247 (OR ≥1.72, P ≤ 4.08 × 10−3). From pooled analysis (Breslow-Day test, P > 0.33) assuming an additive model, each increasing copy of the risk allele of rs11726117 [C], rs231247 [G] and rs231253 [G] showed significantly elevated OR for gout ≥1.42 (P ≥ 1.53 × 10−6). Consistently, the composite homozygous of linked 3 SNPs (versus wild-type, OR = 1.83, P = 8.21 × 10−4) had strong associations with ALPK1 mRNA expression. Luciferase showed reduced hybridization between hsa-miR-519e and construct carrying gout-associated rs231253 [G] than the wild-type [C] (P = 6.19 × 10−4). Conclusions Our study found that a newly identified ALPK1 gene can effectively interfere with microRNA target recognition and modulates the mRNA expression; and the varying distribution of the implicated SNPs among cases and controls in the two studied populations suggests a significant role in gout susceptibility. PMID:23569188

Variants in DENND1A Are Associated with Polycystic Ovary Syndrome in Women of European Ancestry

PubMed Central

Styrkarsdottir, Unnur; Ehrmann, David A.; Thorleifsson, Gudmar; Arason, Gudmundur; Gudmundsson, Jens A.; Ober, Carole; Rosenfield, Robert L.; Saxena, Richa; Thorsteinsdottir, Unnur; Crowley, William F.

2012-01-01

Context: A genome-wide association study has identified three loci (five independent signals) that confer risk for polycystic ovary syndrome (PCOS) in Han Chinese women. Replication is necessary to determine whether the same variants confer risk for PCOS in women of European ancestry. Objective: The objective of the study was to test whether these PCOS risk variants in Han Chinese women confer risk for PCOS in women of European ancestry. Design: This was a case-control study. Setting: The study was conducted at deCODE Genetics in Iceland and two academic medical centers in the United States. Patients: Cases were 376 Icelandic women and 565 and 203 women from Boston, MA, and Chicago, IL, respectively, all diagnosed with PCOS by the National Institutes of Health criteria. Controls were 16,947, 483, and 189 women not known to have PCOS from Iceland, Boston, and Chicago, respectively. Intervention: There were no interventions. Main Outcomes: Main outcomes were allele frequencies for seven variants in PCOS cases and controls. Results: Two strongly correlated Han Chinese PCOS risk variants on chromosome 9q33.3, rs10986105[C], and rs10818854[A], were replicated in samples of European ancestry with odds ratio of 1.68 (P = 0.00033) and odds ratio of 1.53 (P = 0.0019), respectively. Other risk variants at 2p16.3 (rs13405728), 2p21 (rs12468394, rs12478601, and rs13429458), and 9q33.3 (rs2479106), or variants correlated with them, did not associate with PCOS. The same allele of rs10986105 that increased the risk of PCOS also increased the risk of hyperandrogenism in women without PCOS from Iceland and demonstrated a stronger risk for PCOS defined by the National Institutes of Health criteria than the Rotterdam criteria. Conclusions: We replicated one of the five Chinese PCOS association signals, represented by rs10986105 and rs10818854 on 9q33, in individuals of European ancestry. Examination of the subjects meeting at least one of the Rotterdam criteria for PCOS suggests that the variant may be involved in the hyperandrogenism and possibly the irregular menses of PCOS. PMID:22547425

Genetic variants in loci 1p13 and 9p21 and fatal coronary heart disease in a Norwegian case-cohort study.

PubMed

Jansen, Mona Dverdal; Knudsen, Gun Peggy; Myhre, Ronny; Høiseth, Gudrun; Mørland, Jørg; Næss, Øyvind; Tambs, Kristian; Magnus, Per

2014-05-01

Single nucleotide polymorphisms (SNPs) in loci 1p13 and 9p21 have previously been found to be associated with incident coronary heart disease (CHD). This study aimed to investigate whether these SNPs show associations with fatal CHD in a population-based cohort study after adjustment for socioeconomic- and lifestyle-related CHD risk factors not commonly included in genetic association studies. Using the population-based Cohort of Norway (CONOR), a nested case-cohort study was set up and DNA from 2,953 subjects (829 cases and 2,124 non-cases) were genotyped. The association with fatal CHD was estimated for four SNPs, three from locus 1p13 and one from locus 9p21. Multivariable Cox regression was used to estimate unstratified and gender-stratified hazard ratios while adjusting for major CHD risk factors. The associations between three SNPs from locus 1p13 and non-HDL cholesterol levels were also estimated. Men homozygous for the risk alleles on rs1333049 (9p21) and rs14000 (1p13) were found to have significantly increased hazard ratios in crude and adjusted models, and the hazard ratios remained statistically significant when both genders were analyzed together. Adjustment for additional socioeconomic- and lifestyle-related CHD risk factors influenced the association estimates only slightly. No significant associations were observed between the other two SNPs in loci 1p13 (rs599839 and rs646776) and CHD mortality in either gender. Both rs599839 and rs646776 showed significant, gradual increases in non-HDL cholesterol levels with increasing number of risk alleles. This study confirms the association between 9p21 (rs1333049) and fatal CHD in a Norwegian population-based cohort. The effect was not influenced by several socioeconomic- and lifestyle-related risk factors. Our results show that 1p13 (rs14000) may also be associated with fatal CHD. SNPs at 1p13 (rs599839 and rs646776) were associated with non-HDL cholesterol levels.

Turn around to have a look? Spatial referencing in dorsal vs. frontal settings in cross-linguistic comparison

PubMed Central

Beller, Sieghard; Singmann, Henrik; Hüther, Lisa; Bender, Andrea

2015-01-01

When referring to an object in relation to another, speakers of many languages can adopt a relative frame of reference (FoR). Following Levinson (2003), this kind of FoR can be established by projecting an observer's perspective onto the ground object either by translation, reflection, or rotation. So far, research on spatial FoRs has largely ignored the extent of variation in which of these projections are preferred generally, and specifically what kind of FoR is established for spatial arrays in one's back. This may seem justified by assumptions on “natural” preferences: for reflection in frontal settings (Canonical Encounter Hypothesis), and for converting dorsal into frontal situations by a turn of the observer before a reference is made (Turn Hypothesis). We scrutinize these assumptions by comparing the FoRs adopted for small-scale, static spatial arrays by speakers of four languages (German, US-English, Mandarin Chinese, and Tongan). Addressing the problem of inherent ambiguities on the item level when assessing FoRs from spatial prepositions, we use a multinomial processing tree (MPT) model for estimating probabilities of referencing strategies across sets of items. Substantial differences in frontal settings, both between and within languages, disprove the Canonical Encounter Hypothesis—translation occurs as frequently as reflection across samples. In dorsal settings, in contrast, the same type of response dominates in all samples. We suggest that this response is produced by a backward projection of the observer's coordinate system in correspondence with the two main FoR preferences for frontal settings. However, none of these strategies involves a turn of the observer, thus also disproving the Turn Hypothesis. In conclusion, we discuss possible causes of the observed variability, explore links between the domains of space and time, and reflect the relation between language, communication, and culture. PMID:26388802

ROMI 4.0: Rough mill simulator 4.0 users manual

Treesearch

R. Edward Thomas; Timo Grueneberg; Urs Buehlmann

2015-01-01

The Rough MIll simulator (ROMI Version 4.0) is a computer software package for personal computers (PCs) that simulates current industrial practices for rip-first, chop-first, and rip and chop-first lumber processing. This guide shows how to set up the software; design, implement, and execute simulations; and examine the results. ROMI 4.0 accepts cutting bills with as...

The fission yeast cytokinetic contractile ring regulates septum shape and closure

PubMed Central

Thiyagarajan, Sathish; Munteanu, Emilia Laura; Arasada, Rajesh; Pollard, Thomas D.; O'Shaughnessy, Ben

2015-01-01

ABSTRACT During cytokinesis, fission yeast and other fungi and bacteria grow a septum that divides the cell in two. In fission yeast closure of the circular septum hole by the β-glucan synthases (Bgs) and other glucan synthases in the plasma membrane is tightly coupled to constriction of an actomyosin contractile ring attached to the membrane. It is unknown how septum growth is coordinated over scales of several microns to maintain septum circularity. Here, we documented the shapes of ingrowing septum edges by measuring the roughness of the edges, a measure of the deviation from circularity. The roughness was small, with spatial correlations indicative of spatially coordinated growth. We hypothesized that Bgs-mediated septum growth is mechanosensitive and coupled to contractile ring tension. A mathematical model showed that ring tension then generates almost circular septum edges by adjusting growth rates in a curvature-dependent fashion. The model reproduced experimental roughness statistics and showed that septum synthesis sets the mean closure rate. Our results suggest that the fission yeast cytokinetic ring tension does not set the constriction rate but regulates septum closure by suppressing roughness produced by inherently stochastic molecular growth processes. PMID:26240178

The fission yeast cytokinetic contractile ring regulates septum shape and closure.

PubMed

Thiyagarajan, Sathish; Munteanu, Emilia Laura; Arasada, Rajesh; Pollard, Thomas D; O'Shaughnessy, Ben

2015-10-01

During cytokinesis, fission yeast and other fungi and bacteria grow a septum that divides the cell in two. In fission yeast closure of the circular septum hole by the β-glucan synthases (Bgs) and other glucan synthases in the plasma membrane is tightly coupled to constriction of an actomyosin contractile ring attached to the membrane. It is unknown how septum growth is coordinated over scales of several microns to maintain septum circularity. Here, we documented the shapes of ingrowing septum edges by measuring the roughness of the edges, a measure of the deviation from circularity. The roughness was small, with spatial correlations indicative of spatially coordinated growth. We hypothesized that Bgs-mediated septum growth is mechanosensitive and coupled to contractile ring tension. A mathematical model showed that ring tension then generates almost circular septum edges by adjusting growth rates in a curvature-dependent fashion. The model reproduced experimental roughness statistics and showed that septum synthesis sets the mean closure rate. Our results suggest that the fission yeast cytokinetic ring tension does not set the constriction rate but regulates septum closure by suppressing roughness produced by inherently stochastic molecular growth processes. © 2015. Published by The Company of Biologists Ltd.

Optical spectroscopy of the recurrent nova RS Ophiuchi - from the outburst of 2006 to quiescence

NASA Astrophysics Data System (ADS)

Mondal, Anindita; Anupama, G. C.; Kamath, U. S.; Das, Ramkrishna; Selvakumar, G.; Mondal, Soumen

2018-03-01

Optical spectra of the 2006 outburst of RS Ophiuchi beginning one day after discovery to over a year after the outburst are presented here. The spectral evolution is found to be similar to that in previous outbursts. The early-phase spectra are dominated by hydrogen and helium (I and II) lines. Coronal and nebular lines appear in the later phases. Emission line widths are found to narrow with time, which is interpreted as a shock expanding into the red giant wind. Using the photoionization code CLOUDY, spectra at nine epochs spanning 14 months after the outburst peak, thus covering a broad range of ionization and excitation levels in the ejecta, are modelled. The best-fitting model parameters indicate the presence of a hot white dwarf source with a roughly constant luminosity of 1.26 × 1037 erg s-1. During the first three months, the abundances (by number) of He, N, O, Ne, Ar, Fe, Ca, S and Ni are found to be above solar abundances; the abundances of these elements decreased in the later phase. Also presented are spectra obtained during quiescence. A photoionization model of the quiescent spectrum indicates the presence of a low-luminosity accretion disc. The helium abundance is found to be subsolar at quiescence.

[Association between genetic polymorphisms in pre-miR-146a and pre-miR-196a2 and genetic damage levels among coke oven workers].

PubMed

Wang, Tian; Deng, Qi-fei; Zhang, Xiao; Li, Xiao-liang; Deng, Si-yun; Dai, Xia-yun; Huang, Su-li; Feng, Jing; Li, Jun; Wu, Tang-chun; Guo, Huan

2013-08-01

To investigate the association of rs2910164 G > C polymorphism and rs11614913 T > C polymorphism in pre-miR-146a and pre-miR-196a2 with genetic damage levels in coke oven workers. A total of 575 nonsmoking workers who have worked for more than one year in a coke-oven plant at Wuhan, Hubei Province were enrolled in this study in September to October, 2010. The general characteristics as well as blood and urine samples were collected. The genetic damage levels were detected by cytokinesis-block micronucleus cytom assay and represented as micronucleus (MN) frequencies of binucleate cells in peripheral blood lymphocytes. The rs2910164 G > C polymorphisms in pre-miR-146a and rs11614913 T > C polymorphisms in pre-miR-196a2 were genotyped by using TaqMan assay. The plasma concentrations of benzo[a]pyrene-diolepoxide (BPDE)-albumin adducts were determined by using ELISA. All data were analyzed, the frequency ratio (FR) and 95%CI were calculated. Totally, 575 workers were taken into consideration. The rs2910164 C allele was associated with increased MN frequencies in the coke oven workers (P trend = 0.025), and the MN frequencies were higher in rs2910164 CC genotype carriers (4.38 ± 3.46) than in wild-type rs2910164 GG genotype carriers (4.02 ± 3.09) (FR = 1.18, 95%CI:1.04-1.34). The further stratified analyses by working years, gender, alcohol consumption, and the levels of BPDE-albumin adducts showed that the effects of rs2910164 C allele in increasing MN frequencies were robust in subjects who were males (FR = 1.11, 95%CI:1.02-1.20), nondrinkers (FR = 1.07, 95%CI:1.00-1.14), working years less than 20 (FR = 1.12, 95%CI:1.03-1.22), and workers with lower BPDE-albumin adducts levels (FR = 1.11, 95%CI:1.02-1.21) (P trend = 0.011, 0.044, 0.006 and 0.020, respectively). In addition, the MN frequencies were higher in workers with rs11614913 TC genotype (4.27 ± 2.91) than workers with rs11614913 TT genotype (3.90 ± 3.32) (FR = 1.12, 95%CI:1.02-1.23).Workers carried both rs2910164 GG and rs11614913 TT genotypes were set as a control, and the MN frequencies of workers with both rs2910164 CC and rs11614913 CC genotypes (5.32 ± 4.94) were 1.51 (1.21-1.89) times higher than the control (3.75 ± 3.01). The rs2910164 C allele in pre-miR-146a and rs11614913 C allele in pre-miR-196a2 were associated with increased genetic damage levels in coke oven workers.

Active-passive synergy for interpreting ocean L-band emissivity: Results from the CAROLS airborne campaigns

NASA Astrophysics Data System (ADS)

Martin, A. C. H.; Boutin, J.; Hauser, D.; Dinnat, E. P.

2014-08-01

The impact of the ocean surface roughness on the ocean L-band emissivity is investigated using simultaneous airborne measurements from an L-band radiometer (CAROLS) and from a C-band scatterometer (STORM) acquired in the Gulf of Biscay (off-the French Atlantic coasts) in November 2010. Two synergetic approaches are used to investigate the impact of surface roughness on the L-band brightness temperature (Tb). First, wind derived from the scatterometer measurements is used to analyze the roughness contribution to Tb as a function of wind and compare it with the one simulated by SMOS and Aquarius roughness models. Then residuals from this mean relationship are analyzed in terms of mean square slope derived from the STORM instrument. We show improvement of new radiometric roughness models derived from SMOS and Aquarius satellite measurements in comparison with prelaunch models. Influence of wind azimuth on Tb could not be evidenced from our data set. However, we point out the importance of taking into account large roughness scales (>20 cm) in addition to small roughness scale (5 cm) rapidly affected by wind to interpret radiometric measurements far from nadir. This was made possible thanks to simultaneous estimates of large and small roughness scales using STORM at small (7-16°) and large (30°) incidence angles.

Mechanisms of starch digestion by α-amylase-Structural basis for kinetic properties.

PubMed

Dhital, Sushil; Warren, Frederick J; Butterworth, Peter J; Ellis, Peter R; Gidley, Michael J

2017-03-24

Recent studies of the mechanisms determining the rate and extent of starch digestion by α-amylase are reviewed in the light of current widely-used classifications for (a) the proportions of rapidly-digestible (RDS), slowly-digestible (SDS), and resistant starch (RS) based on in vitro digestibility, and (b) the types of resistant starch (RS 1,2,3,4…) based on physical and/or chemical form. Based on methodological advances and new mechanistic insights, it is proposed that both classification systems should be modified. Kinetic analysis of digestion profiles provides a robust set of parameters that should replace the classification of starch as a combination of RDS, SDS, and RS from a single enzyme digestion experiment. This should involve determination of the minimum number of kinetic processes needed to describe the full digestion profile, together with the proportion of starch involved in each process, and the kinetic properties of each process. The current classification of resistant starch types as RS1,2,3,4 should be replaced by one which recognizes the essential kinetic nature of RS (enzyme digestion rate vs. small intestinal passage rate), and that there are two fundamental origins for resistance based on (i) rate-determining access/binding of enzyme to substrate and (ii) rate-determining conversion of substrate to product once bound.

Approach to the determination of the contact angle in hydrophobic samples with simultaneous correction of the effect of the roughness

NASA Astrophysics Data System (ADS)

Domínguez, Noemí; Castilla, Pau; Linzoain, María Eugenia; Durand, Géraldine; García, Cristina; Arasa, Josep

2018-04-01

This work presents the validation study of a method developed to measure contact angles with a confocal device in a set of hydrophobic samples. The use of this device allows the evaluation of the roughness of the surface and the determination of the contact angle in the same area of the sample. Furthermore, a theoretical evaluation of the impact of the roughness of a nonsmooth surface in the calculation of the contact angle when it is not taken into account according to Wenzel's model is also presented.

Seasonal spread and control of Bluetongue in cattle.

PubMed

Charron, Maud V P; Seegers, Henri; Langlais, Michel; Ezanno, Pauline

2011-12-21

Bluetongue is a seasonal midge-borne disease of ruminants with economic consequences on herd productivity and animal trade. Recently, two new modes of transmission have been demonstrated in cattle for Bluetongue virus serotype 8 (BTV8): vertical and pseudo-vertical transmission. Our objective was to model the seasonal spread of BTV8 over several years in a homogeneous population of cattle, and to evaluate the effectiveness of vaccination strategies. We built a deterministic mathematical model accounting for the seasonality in vector abundance and all the modes of transmission. We proposed a counterpart of the basic reproduction number (R(0)) in a seasonal context (R(S)). Set A(t) is the number of secondary cases produced by a primary case introduced at time t. R(S) is the average of A(t). It is a function of midge abundance and vaccination strategy. We also used A*, the maximum of A(t), as an indicator of the risk of an epidemic. Without vaccination, the model predicted a large first epidemic peak followed by smaller annual peaks if R(S)>1. When R(S)<1, small epidemics could occur if A* >1. Vaccination reduced R(S) and A* to less than one, but almost perfect vaccine efficacy and coverage were required to ensure no epidemics occurred. However, a lower coverage resulting in R(S)>1 could decrease infection prevalence. A further step would be to optimize vaccination strategies by targeting an appropriate period of the year to implement the vaccination. Copyright © 2011 Elsevier Ltd. All rights reserved.

FABP4 plasma concentrations are determined by acquired metabolic derangements rather than genetic determinants.

PubMed

Ibarretxe, D; Girona, J; Plana, N; Cabré, A; Heras, M; Ferré, R; Merino, J; Vallvé, J C; Masana, L

2015-09-01

Circulating FABP4 is strongly associated with metabolic and cardiovascular risk (CVR) and has been proposed as a new risk biomarker. Several FABP4 gene polymorphisms have been associated with protein expression in vitro and metabolic and vascular alterations in vivo. The aim of this study is to evaluate the impact of FABP4 polymorphisms on FABP4 plasma levels and subclinical arteriosclerosis in patients with obesity, metabolic syndrome (MS) or type 2 diabetes (T2DM). We studied 440 individuals with obesity, MS, T2DM or other cardiovascular risk conditions who attended the vascular medicine and metabolism unit of our hospital. Anamnesis, physical examination and anthropometry data were recorded. Standard biochemical parameters were determined. Plasma FABP4 concentrations were measured. Carotid intima-media thickness (cIMT) was assessed using ultrasonography. The following FABP4 gene single-nucleotide polymorphisms (SNPs) were analyzed: rs3834363, rs16909233, rs1054135, rs77878271, rs10808846 and rs8192688. None of the studied gene allele variants were hyper-represented in patients grouped according the presence of metabolic alterations nor were they associated with the FABP4 concentration. The FABP4 gene variants did not determine cIMT differences between the groups. In a multivariate analysis, gender and BMI, but not gene variants, significantly determined plasma FABP4 concentrations. In clinical settings, the circulating FABP4 levels are determined by the acquired metabolic derangements and not genetic variation. Copyright © 2015 Elsevier B.V. All rights reserved.

CD28 and PTPN22 are associated with susceptibility to rheumatoid arthritis in Egyptians.

PubMed

Hegab, Mohsen M; Abdelwahab, Aml Fawzy; El-Sayed Yousef, Ali M; Salem, Mohamed Nabil; El-Baz, Walaa; Abdelrhman, Sherry; Elshabacy, Fatemah; Alhefny, Abdelazim; Abouraya, Wagida; Ibrahim, Saleh Mohamed; Ragab, Gaafar

2016-06-01

Limited data are available on the genetics of rheumatoid arthritis (RA) in Egyptians. Therefore, we investigated whether the confirmed genetic risk factors for RA in Europeans and/or Asians contribute to RA susceptibility in Egyptians. A set of seven single-nucleotide polymorphisms (SNPs) in the vicinity of CD28, TNFAIP3, PTPN22, PADI4 and HLA-DRA were tested in a large multi-centric RA cohort in Egypt, consisting of 394 cases and 398 matched controls. Patients were stratified based on the positivity of either anti-citrullinated protein antibodies (ACPAs) or rheumatoid factor (RF). Significant association was evident for three SNPs in this cohort: the CD28 (rs1980422) variant showed a strong association in the whole cohort (P=0.000119) and in seropositive subsets of the disease (PACPA+=0.004; PRF+=0.0005). Upon stratification, the PTPN22 (rs2476601) and TNFAIP3(rs5029939) variants showed association only with ACPA positive (PACPA+=0.00573) and negative (PACPA-=0.00999) phenotypes, respectively. Our results suggest that CD28(rs1980422) and PTPN22(rs2476601) contribute to RA-susceptibility in Egyptians. Failure to replicate the association of PADI4(rs2240340)/(PADI4_94) in Egyptian RA patients provides further support for the notion that genetic architecture of RA is different in multiple populations of European, Asian, African, and Middle Eastern ancestries. Further investigation using large-scale studies is thus needed to maximize the power of genetic association. Copyright © 2016. Published by Elsevier Inc.

Evolvable rough-block-based neural network and its biomedical application to hypoglycemia detection system.

PubMed

San, Phyo Phyo; Ling, Sai Ho; Nuryani; Nguyen, Hung

2014-08-01

This paper focuses on the hybridization technology using rough sets concepts and neural computing for decision and classification purposes. Based on the rough set properties, the lower region and boundary region are defined to partition the input signal to a consistent (predictable) part and an inconsistent (random) part. In this way, the neural network is designed to deal only with the boundary region, which mainly consists of an inconsistent part of applied input signal causing inaccurate modeling of the data set. Owing to different characteristics of neural network (NN) applications, the same structure of conventional NN might not give the optimal solution. Based on the knowledge of application in this paper, a block-based neural network (BBNN) is selected as a suitable classifier due to its ability to evolve internal structures and adaptability in dynamic environments. This architecture will systematically incorporate the characteristics of application to the structure of hybrid rough-block-based neural network (R-BBNN). A global training algorithm, hybrid particle swarm optimization with wavelet mutation is introduced for parameter optimization of proposed R-BBNN. The performance of the proposed R-BBNN algorithm was evaluated by an application to the field of medical diagnosis using real hypoglycemia episodes in patients with Type 1 diabetes mellitus. The performance of the proposed hybrid system has been compared with some of the existing neural networks. The comparison results indicated that the proposed method has improved classification performance and results in early convergence of the network.

Fingerprinting the type of line edge roughness

NASA Astrophysics Data System (ADS)

Fernández Herrero, A.; Pflüger, M.; Scholze, F.; Soltwisch, V.

2017-06-01

Lamellar gratings are widely used diffractive optical elements and are prototypes of structural elements in integrated electronic circuits. EUV scatterometry is very sensitive to structure details and imperfections, which makes it suitable for the characterization of nanostructured surfaces. As compared to X-ray methods, EUV scattering allows for steeper angles of incidence, which is highly preferable for the investigation of small measurement fields on semiconductor wafers. For the control of the lithographic manufacturing process, a rapid in-line characterization of nanostructures is indispensable. Numerous studies on the determination of regular geometry parameters of lamellar gratings from optical and Extreme Ultraviolet (EUV) scattering also investigated the impact of roughness on the respective results. The challenge is to appropriately model the influence of structure roughness on the diffraction intensities used for the reconstruction of the surface profile. The impact of roughness was already studied analytically but for gratings with a periodic pseudoroughness, because of practical restrictions of the computational domain. Our investigation aims at a better understanding of the scattering caused by line roughness. We designed a set of nine lamellar Si-gratings to be studied by EUV scatterometry. It includes one reference grating with no artificial roughness added, four gratings with a periodic roughness distribution, two with a prevailing line edge roughness (LER) and another two with line width roughness (LWR), and four gratings with a stochastic roughness distribution (two with LER and two with LWR). We show that the type of line roughness has a strong impact on the diffuse scatter angular distribution. Our experimental results are not described well by the present modelling approach based on small, periodically repeated domains.

Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk

PubMed Central

Dunlop, Malcolm G; Dobbins, Sara E; Farrington, Susan Mary; Jones, Angela M; Palles, Claire; Whiffin, Nicola; Tenesa, Albert; Spain, Sarah; Broderick, Peter; Ooi, Li-Yin; Domingo, Enric; Smillie, Claire; Henrion, Marc; Frampton, Matthew; Martin, Lynn; Grimes, Graeme; Gorman, Maggie; Semple, Colin; Ma, Yussanne; Barclay, Ella; Prendergast, James; Cazier, Jean-Baptiste; Olver, Bianca; Carvajal-Carmona, Luis G; Ballereau, Stephane; Lloyd, Amy; Vijayakrishnan, Jayaram; Zgaga, Lina; Rudan, Igor; Theodoratou, Evropi; Starr, John M; Deary, Ian; Kirac, Iva; Kovačević, Dujo; Aaltonen, Lauri A; Renkonen-Sinisalo, Laura; Mecklin, Jukka-Pekka; Matsuda, Koichi; Nakamura, Yusuke; Okada, Yukinori; Gallinger, Steven; Duggan, David J; Conti, David; Newcomb, Polly; Hopper, John; Jenkins, Mark A.; Schumacher, Fredrick; Casey, Graham; Easton, Douglas; Shah, Mitul; Pharoah, Paul; Lindblom, Annika; Liu, Tao; Smith, Christopher G; West, Hannah; Cheadle, Jeremy P.; Midgley, Rachel; Kerr, David J; Campbell, Harry; Tomlinson, Ian P; Houlston, Richard S

2015-01-01

We performed a meta-analysis of five genome-wide association studies to identify common variants influencing colorectal cancer (CRC) risk comprising 8,682 cases and 9,649 controls. Replication analysis was performed in case-control sets totalling 21,096 cases and 19,555 controls. We identified three novel CRC risk loci at 6p21 (rs1321311, near CDKN1A; P=1.14×10−10), 11q13.4 (rs3824999, intronic to POLD3; P=3.65×10−10) and Xp22.2 (rs5934683, near SHROOM2; P=7.30×10−10) This brings to 20 the number of independent loci associated with CRC risk, and provides further insight into the genetic architecture of inherited susceptibility to CRC. PMID:22634755

Influence of COX-2 and OXTR polymorphisms on treatment outcome in treatment resistant depression.

PubMed

Mendlewicz, Julien; Crisafulli, Concetta; Calati, Raffaella; Kocabas, Neslihan Aygun; Massat, Isabelle; Linotte, Sylvie; Kasper, Siegfried; Fink, Martin; Sidoti, Antonina; Scantamburlo, Gabrielle; Ansseau, Marc; Antonijevic, Irina; Forray, Carlos; Snyder, Lenore; Bollen, Joseph; Montgomery, Stuart; Zohar, Joseph; Souery, Daniel; Serretti, Alessandro

2012-05-10

Inflammatory pathways play a crucial role in the pathomechanisms of antidepressant efficacy. The aim of this study was to investigate whether a set of single nucleotide polymorphisms (SNPs) within cyclooxygenase-2 (COX-2, rs5275 and rs20417) and oxytocin receptor (OXTR, rs53576 and rs2254298) genes was associated with antidepressant treatment resistance, response or remission. Three hundred seventy-two patients were recruited in the context of a multicenter resistant depression study. They were genotyped for COX-2 and OXTR SNPs. Treatment resistance (according to two different definitions), response and remission were recorded. We did not observe any association between the genotypes or alleles of the selected SNPs within COX-2 and OXTR genes and treatment resistance, response and remission in the whole sample. Our results are consistent with those of some studies but not with those of other ones. Indeed, several factors could be involved in the discrepancy observed across studies. They include sample size, environmental factors, differences in ethnicity, different study designs, and different definitions of treatment resistance. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Depression Status Is Associated with Functional Decline Over 1-Year Following Acute Stroke.

PubMed

El Husseini, Nada; Goldstein, Larry B; Peterson, Eric D; Zhao, Xin; Olson, DaiWai M; Williams, John W; Bushnell, Cheryl; Laskowitz, Daniel T

2017-07-01

We investigated the independent association of depression status at 3 and 12 months after stroke and functional decline. Data were obtained as part of the multicenter Adherence eValuation After Ischemic stroke Longitudinal (AVAIL) registry. Depression was assessed with the Patient Health Questionnaire-8 (depression, PHQ-8 ≥ 10), and functional status was assessed with the modified Rankin score (mRS) at 3 and 12 months following hospitalization for ischemic stroke. We used logistic regression analyses to evaluate the independent association between the change in depression rating and the change in mRS. Among 1444 patients, 75% did not have depression at either time point, 9.2% had persistent depression, 8.7% had resolving depression, and 7% had incident depression at 12 months. After covariate adjustment, depression status at 3 and 12 months remained associated with worsening mRS (P = .01). Compared with patients without depression, those with resolving depression were less likely to have a worsening mRS (odds ratio [OR] = .49, 95% confidence interval [CI]: .29-0.83). There was no difference in functional decline between those with no depression and those with persistent depression; however, those with persistent depression had worse mRS at both time points (median mRS: 2.5 [Q1-Q3: 2-3] at 3 months; 2 [2-3] at 12 months) than those with no depression (mRS: 1 [0-2] at both 3 and 12 months), P < .0001. Patients with resolving depression in the first year after stroke were less likely to have functional deterioration than those without depression. Greater functional impairment was present in the setting of depression. Copyright © 2017 National Stroke Association. Published by Elsevier Inc. All rights reserved.

The rate of polymyalgia rheumatica (PMR) and remitting seronegative symmetrical synovitis with pitting edema (RS3PE) syndrome in a clinic where primary care physicians are working in Japan.

PubMed

Okumura, Toshikatsu; Tanno, Satoshi; Ohhira, Masumi; Nozu, Tsukasa

2012-06-01

We analyzed the rate of polymyalgia rheumatica (PMR) and remitting seronegative symmetrical synovitis with pitting edema (RS3PE) syndrome, both characterized as seronegative inflammatory arthritis in elderly, in an outpatient unit where primary care physicians are working in Japan to better understand the epidemiological characteristics of the diseases in Japan. Consecutive outpatients who newly visited at Department of General Medicine, Asahikawa Medical University Hospital, Japan, between April 2004 and March 2010 were analyzed. Each parameter such as age, sex, diagnosis, and biochemical examination was investigated. During the 6 years, 10 or 3 patients were diagnosed as PMR or RS3PE syndrome, respectively. The patients with PMR were 7 women and 3 men, and the average age at diagnosis was 69. Out of all patients aged over 50 (n = 3,347), the rate of PMR was 0.22% in men or 0.36% in women, respectively. On the other hand, RS3PE syndrome was diagnosed in 3 men (76, 76, and 81 years old). The rate of patients with RS3PE syndrome was 0.09% among outpatients aged over 50 indicating that the rate of PMR in an outpatient clinic in Japan is not far from previous findings reported from western countries. When compared with PMR, the rate of RS3PE syndrome was approximately one-third, providing for the first time the rate of RS3PE syndrome when compared with PMR. These epidemilogical data might help us pick up the diseases in primary care setting in Japan.

Resistance to pentamidine is mediated by AdeAB, regulated by AdeRS, and influenced by growth conditions in Acinetobacter baumannii ATCC 17978.

PubMed

Adams, Felise G; Stroeher, Uwe H; Hassan, Karl A; Marri, Shashikanth; Brown, Melissa H

2018-01-01

In recent years, effective treatment of infections caused by Acinetobacter baumannii has become challenging due to the ability of the bacterium to acquire or up-regulate antimicrobial resistance determinants. Two component signal transduction systems are known to regulate expression of virulence factors including multidrug efflux pumps. Here, we investigated the role of the AdeRS two component signal transduction system in regulating the AdeAB efflux system, determined whether AdeA and/or AdeB can individually confer antimicrobial resistance, and explored the interplay between pentamidine resistance and growth conditions in A. baumannii ATCC 17978. Results identified that deletion of adeRS affected resistance towards chlorhexidine and 4',6-diamidino-2-phenylindole dihydrochloride, two previously defined AdeABC substrates, and also identified an 8-fold decrease in resistance to pentamidine. Examination of ΔadeA, ΔadeB and ΔadeAB cells augmented results seen for ΔadeRS and identified a set of dicationic AdeAB substrates. RNA-sequencing of ΔadeRS revealed transcription of 290 genes were ≥2-fold altered compared to the wildtype. Pentamidine shock significantly increased adeA expression in the wildtype, but decreased it in ΔadeRS, implying that AdeRS activates adeAB transcription in ATCC 17978. Investigation under multiple growth conditions, including the use of Biolog phenotypic microarrays, revealed resistance to pentamidine in ATCC 17978 and mutants could be altered by bioavailability of iron or utilization of different carbon sources. In conclusion, the results of this study provide evidence that AdeAB in ATCC 17978 can confer intrinsic resistance to a subset of dicationic compounds and in particular, resistance to pentamidine can be significantly altered depending on the growth conditions.

Retrieving air humidity, global solar radiation, and reference evapotranspiration from daily temperatures: development and validation of new methods for Mexico. Part III: reference evapotranspiration

NASA Astrophysics Data System (ADS)

Lobit, P.; Gómez Tagle, A.; Bautista, F.; Lhomme, J. P.

2017-07-01

We evaluated two methods to estimate evapotranspiration (ETo) from minimal weather records (daily maximum and minimum temperatures) in Mexico: a modified reduced set FAO-Penman-Monteith method (Allen et al. 1998, Rome, Italy) and the Hargreaves and Samani (Appl Eng Agric 1(2): 96-99, 1985) method. In the reduced set method, the FAO-Penman-Monteith equation was applied with vapor pressure and radiation estimated from temperature data using two new models (see first and second articles in this series): mean temperature as the average of maximum and minimum temperature corrected for a constant bias and constant wind speed. The Hargreaves-Samani method combines two empirical relationships: one between diurnal temperature range ΔT and shortwave radiation Rs, and another one between average temperature and the ratio ETo/Rs: both relationships were evaluated and calibrated for Mexico. After performing a sensitivity analysis to evaluate the impact of different approximations on the estimation of Rs and ETo, several model combinations were tested to predict ETo from daily maximum and minimum temperature alone. The quality of fit of these models was evaluated on 786 weather stations covering most of the territory of Mexico. The best method was found to be a combination of the FAO-Penman-Monteith reduced set equation with the new radiation estimation and vapor pressure model. As an alternative, a recalibration of the Hargreaves-Samani equation is proposed.

Optimizing the Determination of Roughness Parameters for Model Urban Canopies

NASA Astrophysics Data System (ADS)

Huq, Pablo; Rahman, Auvi

2018-05-01

We present an objective optimization procedure to determine the roughness parameters for very rough boundary-layer flow over model urban canopies. For neutral stratification the mean velocity profile above a model urban canopy is described by the logarithmic law together with the set of roughness parameters of displacement height d, roughness length z_0 , and friction velocity u_* . Traditionally, values of these roughness parameters are obtained by fitting the logarithmic law through (all) the data points comprising the velocity profile. The new procedure generates unique velocity profiles from subsets or combinations of the data points of the original velocity profile, after which all possible profiles are examined. Each of the generated profiles is fitted to the logarithmic law for a sequence of values of d, with the representative value of d obtained from the minima of the summed least-squares errors for all the generated profiles. The representative values of z_0 and u_* are identified by the peak in the bivariate histogram of z_0 and u_* . The methodology has been verified against laboratory datasets of flow above model urban canopies.

Non-Contact Surface Roughness Measurement by Implementation of a Spatial Light Modulator

PubMed Central

Aulbach, Laura; Salazar Bloise, Félix; Lu, Min; Koch, Alexander W.

2017-01-01

The surface structure, especially the roughness, has a significant influence on numerous parameters, such as friction and wear, and therefore estimates the quality of technical systems. In the last decades, a broad variety of surface roughness measurement methods were developed. A destructive measurement procedure or the lack of feasibility of online monitoring are the crucial drawbacks of most of these methods. This article proposes a new non-contact method for measuring the surface roughness that is straightforward to implement and easy to extend to online monitoring processes. The key element is a liquid-crystal-based spatial light modulator, integrated in an interferometric setup. By varying the imprinted phase of the modulator, a correlation between the imprinted phase and the fringe visibility of an interferogram is measured, and the surface roughness can be derived. This paper presents the theoretical approach of the method and first simulation and experimental results for a set of surface roughnesses. The experimental results are compared with values obtained by an atomic force microscope and a stylus profiler. PMID:28294990

A rough set-based association rule approach implemented on a brand trust evaluation model

NASA Astrophysics Data System (ADS)

Liao, Shu-Hsien; Chen, Yin-Ju

2017-09-01

In commerce, businesses use branding to differentiate their product and service offerings from those of their competitors. The brand incorporates a set of product or service features that are associated with that particular brand name and identifies the product/service segmentation in the market. This study proposes a new data mining approach, a rough set-based association rule induction, implemented on a brand trust evaluation model. In addition, it presents as one way to deal with data uncertainty to analyse ratio scale data, while creating predictive if-then rules that generalise data values to the retail region. As such, this study uses the analysis of algorithms to find alcoholic beverages brand trust recall. Finally, discussions and conclusion are presented for further managerial implications.

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

Stulberg, Michael J.; Huang, Qi

Ralstonia solanacearum race 3 biovar 2 strains belonging to phylotype IIB, sequevars 1 and 2 (IIB-1&2) cause brown rot of potato in temperate climates, and are quarantined pathogens in Canada and Europe. Since these strains are not established in the U.S. and because of their potential risk to the potato industry, the U.S. government has listed them as select agents. Cultivated geraniums are also a host and have the potential to spread the pathogen through trade, and its extracts strongly inhibits DNA-based detection methods. We designed four primer and probe sets for an improved qPCR method that targets stable regionsmore » of DNA. RsSA1 and RsSA2 recognize IIB-1&2 strains, RsII recognizes the current phylotype II (the newly proposed R. solanacearum species) strains (and a non-plant associated R. mannitolilytica), and Cox1 recognizes eight plant species including major hosts of R. solanacearum such as potato, tomato and cultivated geranium as an internal plant control. We multiplexed the RsSA2 with the RsII and Cox1 sets to provide two layers of detection of a positive IIB-1&2 sample, and to validate plant extracts and qPCR reactions. The TaqMan-based uniplex and multiplex qPCR assays correctly identified 34 IIB-1&2 and 52 phylotype II strains out of 90 R. solanacearum species complex strains. Additionally, the multiplex qPCR assay was validated successfully using 169 artificially inoculated symptomatic and asymptomatic plant samples from multiple plant hosts including geranium. Moreover, we developed an extraction buffer that allowed for a quick and easy DNA extraction from infected plants including geranium for detection of R. solanacearum by qPCR. Our multiplex qPCR assay, especially when coupled with the quick extraction buffer method, allows for quick, easy and reliable detection and differentiation of the IIB-1&2 strains of R. solanacearum.« less

Possible combinations of electronic data capture and randomization systems. principles and the realization with RANDI2 and OpenClinica.

PubMed

Schrimpf, D; Haag, M; Pilz, L R

2014-01-01

Clinical trials (CT) are in a wider sense experiments to prove and establish clinical benefit of treatments. Nowadays electronic data capture systems (EDCS) are used more often bringing a better data management and higher data quality into clinical practice. Also electronic systems for the randomization are used to assign the patients to the treatments. If the mentioned randomization system (RS) and EDCS are used, possibly identical data are collected in both, especially by stratified randomization. This separated data storage may lead to data inconsistency and in general data samples have to be aligned. The article discusses solutions to combine RS and EDCS. In detail one approach is realized and introduced. Different possible settings of combination of EDCS and RS are determined and the pros and cons for each solution are worked out. For the combination of two independent applications the necessary interfaces for the communication are defined. Thereby, existing standards are considered. An example realization is implemented with the help of open-source applications and state-of-the-art software development procedures. Three possibilities of separate usage or combination of EDCS and RS are presented and assessed: i) the complete independent usage of both systems; ii) realization of one system with both functions; and iii) two separate systems, which communicate via defined interfaces. In addition a realization of our preferred approach, the combination of both systems, is introduced using the open source tools RANDI2 and OpenClinica. The advantage of a flexible independent development of EDCS and RS is shown based on the fact that these tool are very different featured. In our opinion the combination of both systems via defined interfaces fulfills the requirements of randomization and electronic data capture and is feasible in practice. In addition, the use of such a setting can reduce the training costs and the error-prone duplicated data entry.

A TaqMan-Based Multiplex qPCR Assay and DNA Extraction Method for Phylotype IIB Sequevars 1&2 (Select Agent) Strains of Ralstonia solanacearum

PubMed Central

Stulberg, Michael J.; Huang, Qi

2015-01-01

Ralstonia solanacearum race 3 biovar 2 strains belonging to phylotype IIB, sequevars 1 and 2 (IIB-1&2) cause brown rot of potato in temperate climates, and are quarantined pathogens in Canada and Europe. Since these strains are not established in the U.S. and because of their potential risk to the potato industry, the U.S. government has listed them as select agents. Cultivated geraniums are also a host and have the potential to spread the pathogen through trade, and its extracts strongly inhibits DNA-based detection methods. We designed four primer and probe sets for an improved qPCR method that targets stable regions of DNA. RsSA1 and RsSA2 recognize IIB-1&2 strains, RsII recognizes the current phylotype II (the newly proposed R. solanacearum species) strains (and a non-plant associated R. mannitolilytica), and Cox1 recognizes eight plant species including major hosts of R. solanacearum such as potato, tomato and cultivated geranium as an internal plant control. We multiplexed the RsSA2 with the RsII and Cox1 sets to provide two layers of detection of a positive IIB-1&2 sample, and to validate plant extracts and qPCR reactions. The TaqMan-based uniplex and multiplex qPCR assays correctly identified 34 IIB-1&2 and 52 phylotype II strains out of 90 R. solanacearum species complex strains. Additionally, the multiplex qPCR assay was validated successfully using 169 artificially inoculated symptomatic and asymptomatic plant samples from multiple plant hosts including geranium. Furthermore, we developed an extraction buffer that allowed for a quick and easy DNA extraction from infected plants including geranium for detection of R. solanacearum by qPCR. Our multiplex qPCR assay, especially when coupled with the quick extraction buffer method, allows for quick, easy and reliable detection and differentiation of the IIB-1&2 strains of R. solanacearum. PMID:26426354

Surgeons' physical discomfort and symptoms during robotic surgery: a comprehensive ergonomic survey study.

PubMed

Lee, G I; Lee, M R; Green, I; Allaf, M; Marohn, M R

2017-04-01

It is commonly believed that robotic surgery systems provide surgeons with an ergonomically sound work environment; however, the actual experience of surgeons practicing robotic surgery (RS) has not been thoroughly researched. In this ergonomics survey study, we investigated surgeons' physical symptom reports and their association with factors including demographics, specialties, and robotic systems. Four hundred and thirty-two surgeons regularly practicing RS completed this comprehensive survey comprising 20 questions in four categories: demographics, systems, ergonomics, and physical symptoms. Chi-square and multinomial logistic regression analyses were used for statistical analysis. Two hundred and thirty-six surgeons (56.1 %) reported physical symptoms or discomfort. Among those symptoms, neck stiffness, finger, and eye fatigues were the most common. With the newest robot, eye symptom rate was considerably reduced, while neck and finger symptoms did not improve significantly. A high rate of lower back stiffness was correlated with higher annual robotic case volume, and eye symptoms were more common with longer years practicing robotic surgery (p < 0.05). The symptom report rate from urology surgeons was significantly higher than other specialties (p < 0.05). Noticeably, surgeons with higher confidence and helpfulness levels with their ergonomic settings reported lower symptom report rates. Symptoms were not correlated with age and gender. Although RS provides relatively better ergonomics, this study demonstrates that 56.1 % of regularly practicing robotic surgeons still experience related physical symptoms or discomfort. In addition to system improvement, surgeon education in optimizing the ergonomic settings may be necessary to maximize the ergonomic benefits in RS.

Rough Set Soft Computing Cancer Classification and Network: One Stone, Two Birds

PubMed Central

Zhang, Yue

2010-01-01

Gene expression profiling provides tremendous information to help unravel the complexity of cancer. The selection of the most informative genes from huge noise for cancer classification has taken centre stage, along with predicting the function of such identified genes and the construction of direct gene regulatory networks at different system levels with a tuneable parameter. A new study by Wang and Gotoh described a novel Variable Precision Rough Sets-rooted robust soft computing method to successfully address these problems and has yielded some new insights. The significance of this progress and its perspectives will be discussed in this article. PMID:20706619

Rough sets and Laplacian score based cost-sensitive feature selection

PubMed Central

Yu, Shenglong

2018-01-01

Cost-sensitive feature selection learning is an important preprocessing step in machine learning and data mining. Recently, most existing cost-sensitive feature selection algorithms are heuristic algorithms, which evaluate the importance of each feature individually and select features one by one. Obviously, these algorithms do not consider the relationship among features. In this paper, we propose a new algorithm for minimal cost feature selection called the rough sets and Laplacian score based cost-sensitive feature selection. The importance of each feature is evaluated by both rough sets and Laplacian score. Compared with heuristic algorithms, the proposed algorithm takes into consideration the relationship among features with locality preservation of Laplacian score. We select a feature subset with maximal feature importance and minimal cost when cost is undertaken in parallel, where the cost is given by three different distributions to simulate different applications. Different from existing cost-sensitive feature selection algorithms, our algorithm simultaneously selects out a predetermined number of “good” features. Extensive experimental results show that the approach is efficient and able to effectively obtain the minimum cost subset. In addition, the results of our method are more promising than the results of other cost-sensitive feature selection algorithms. PMID:29912884

City traffic flow breakdown prediction based on fuzzy rough set

NASA Astrophysics Data System (ADS)

Yang, Xu; Da-wei, Hu; Bing, Su; Duo-jia, Zhang

2017-05-01

In city traffic management, traffic breakdown is a very important issue, which is defined as a speed drop of a certain amount within a dense traffic situation. In order to predict city traffic flow breakdown accurately, in this paper, we propose a novel city traffic flow breakdown prediction algorithm based on fuzzy rough set. Firstly, we illustrate the city traffic flow breakdown problem, in which three definitions are given, that is, 1) Pre-breakdown flow rate, 2) Rate, density, and speed of the traffic flow breakdown, and 3) Duration of the traffic flow breakdown. Moreover, we define a hazard function to represent the probability of the breakdown ending at a given time point. Secondly, as there are many redundant and irrelevant attributes in city flow breakdown prediction, we propose an attribute reduction algorithm using the fuzzy rough set. Thirdly, we discuss how to predict the city traffic flow breakdown based on attribute reduction and SVM classifier. Finally, experiments are conducted by collecting data from I-405 Freeway, which is located at Irvine, California. Experimental results demonstrate that the proposed algorithm is able to achieve lower average error rate of city traffic flow breakdown prediction.

Rough sets and Laplacian score based cost-sensitive feature selection.

PubMed

Yu, Shenglong; Zhao, Hong

2018-01-01

Cost-sensitive feature selection learning is an important preprocessing step in machine learning and data mining. Recently, most existing cost-sensitive feature selection algorithms are heuristic algorithms, which evaluate the importance of each feature individually and select features one by one. Obviously, these algorithms do not consider the relationship among features. In this paper, we propose a new algorithm for minimal cost feature selection called the rough sets and Laplacian score based cost-sensitive feature selection. The importance of each feature is evaluated by both rough sets and Laplacian score. Compared with heuristic algorithms, the proposed algorithm takes into consideration the relationship among features with locality preservation of Laplacian score. We select a feature subset with maximal feature importance and minimal cost when cost is undertaken in parallel, where the cost is given by three different distributions to simulate different applications. Different from existing cost-sensitive feature selection algorithms, our algorithm simultaneously selects out a predetermined number of "good" features. Extensive experimental results show that the approach is efficient and able to effectively obtain the minimum cost subset. In addition, the results of our method are more promising than the results of other cost-sensitive feature selection algorithms.

A word by any other intonation: fMRI evidence for implicit memory traces for pitch contours of spoken words in adult brains.

PubMed

Inspector, Michael; Manor, David; Amir, Noam; Kushnir, Tamar; Karni, Avi

2013-01-01

Intonation may serve as a cue for facilitated recognition and processing of spoken words and it has been suggested that the pitch contour of spoken words is implicitly remembered. Thus, using the repetition suppression (RS) effect of BOLD-fMRI signals, we tested whether the same spoken words are differentially processed in language and auditory brain areas depending on whether or not they retain an arbitrary intonation pattern. Words were presented repeatedly in three blocks for passive and active listening tasks. There were three prosodic conditions in each of which a different set of words was used and specific task-irrelevant intonation changes were applied: (i) All words presented in a set flat monotonous pitch contour (ii) Each word had an arbitrary pitch contour that was set throughout the three repetitions. (iii) Each word had a different arbitrary pitch contour in each of its repetition. The repeated presentations of words with a set pitch contour, resulted in robust behavioral priming effects as well as in significant RS of the BOLD signals in primary auditory cortex (BA 41), temporal areas (BA 21 22) bilaterally and in Broca's area. However, changing the intonation of the same words on each successive repetition resulted in reduced behavioral priming and the abolition of RS effects. Intonation patterns are retained in memory even when the intonation is task-irrelevant. Implicit memory traces for the pitch contour of spoken words were reflected in facilitated neuronal processing in auditory and language associated areas. Thus, the results lend support for the notion that prosody and specifically pitch contour is strongly associated with the memory representation of spoken words.

Why rate when you could compare? Using the “EloChoice” package to assess pairwise comparisons of perceived physical strength

PubMed Central

Howard, Kate L.; Woods, Andy T.; Penton-Voak, Ian S.; Neumann, Christof

2018-01-01

We introduce “EloChoice”, a package for R which uses Elo rating to assess pairwise comparisons between stimuli in order to measure perceived stimulus characteristics. To demonstrate the package and compare results from forced choice pairwise comparisons to those from more standard single stimulus rating tasks using Likert (or Likert-type) items, we investigated perceptions of physical strength from images of male bodies. The stimulus set comprised images of 82 men standing on a raised platform with minimal clothing. Strength-related anthropometrics and grip strength measurements were available for each man in the set. UK laboratory participants (Study 1) and US online participants (Study 2) viewed all images in both a Likert rating task, to collect mean Likert scores, and a pairwise comparison task, to calculate Elo, mean Elo (mElo), and Bradley-Terry scores. Within both studies, Likert, Elo and Bradley-Terry scores were closely correlated to mElo scores (all rs > 0.95), and all measures were correlated with stimulus grip strength (all rs > 0.38) and body size (all rs > 0.59). However, mElo scores were less variable than Elo scores and were hundreds of times quicker to compute than Bradley-Terry scores. Responses in pairwise comparison trials were 2/3 quicker than in Likert tasks, indicating that participants found pairwise comparisons to be easier. In addition, mElo scores generated from a data set with half the participants randomly excluded produced very comparable results to those produced with Likert scores from the full participant set, indicating that researchers require fewer participants when using pairwise comparisons. PMID:29293615

A Word by Any Other Intonation: FMRI Evidence for Implicit Memory Traces for Pitch Contours of Spoken Words in Adult Brains

PubMed Central

Inspector, Michael; Manor, David; Amir, Noam; Kushnir, Tamar; Karni, Avi

2013-01-01

Objectives Intonation may serve as a cue for facilitated recognition and processing of spoken words and it has been suggested that the pitch contour of spoken words is implicitly remembered. Thus, using the repetition suppression (RS) effect of BOLD-fMRI signals, we tested whether the same spoken words are differentially processed in language and auditory brain areas depending on whether or not they retain an arbitrary intonation pattern. Experimental design Words were presented repeatedly in three blocks for passive and active listening tasks. There were three prosodic conditions in each of which a different set of words was used and specific task-irrelevant intonation changes were applied: (i) All words presented in a set flat monotonous pitch contour (ii) Each word had an arbitrary pitch contour that was set throughout the three repetitions. (iii) Each word had a different arbitrary pitch contour in each of its repetition. Principal findings The repeated presentations of words with a set pitch contour, resulted in robust behavioral priming effects as well as in significant RS of the BOLD signals in primary auditory cortex (BA 41), temporal areas (BA 21 22) bilaterally and in Broca's area. However, changing the intonation of the same words on each successive repetition resulted in reduced behavioral priming and the abolition of RS effects. Conclusions Intonation patterns are retained in memory even when the intonation is task-irrelevant. Implicit memory traces for the pitch contour of spoken words were reflected in facilitated neuronal processing in auditory and language associated areas. Thus, the results lend support for the notion that prosody and specifically pitch contour is strongly associated with the memory representation of spoken words. PMID:24391713

ROMI-3: Rough-Mill Simulator Version 3.0: User's Guide

Treesearch

Joel M. Weiss; R. Edward Thomas; R. Edward Thomas

2005-01-01

ROMI-3 Rough-Mill Simulator is a software package that simulates current industrial practices for rip-first and chop-first lumber processing. This guide shows the user how to set up and examine the results of simulations of current or proposed mill practices. ROMI-3 accepts cutting bills with as many as 600 combined solid and/or panel part sizes. Plots of processed...

Role of roughness parameters on the tribology of randomly nano-textured silicon surface.

PubMed

Gualtieri, E; Pugno, N; Rota, A; Spagni, A; Lepore, E; Valeri, S

2011-10-01

This experimental work is oriented to give a contribution to the knowledge of the relationship among surface roughness parameters and tribological properties of lubricated surfaces; it is well known that these surface properties are strictly related, but a complete comprehension of such correlations is still far to be reached. For this purpose, a mechanical polishing procedure was optimized in order to induce different, but well controlled, morphologies on Si(100) surfaces. The use of different abrasive papers and slurries enabled the formation of a wide spectrum of topographical irregularities (from the submicro- to the nano-scale) and a broad range of surface profiles. An AFM-based morphological and topographical campaign was carried out to characterize each silicon rough surface through a set of parameters. Samples were subsequently water lubricated and tribologically characterized through ball-on-disk tribometer measurements. Indeed, the wettability of each surface was investigated by measuring the water droplet contact angle, that revealed a hydrophilic character for all the surfaces, even if no clear correlation with roughness emerged. Nevertheless, this observation brings input to the purpose, as it allows to exclude that the differences in surface profile affect lubrication. So it is possible to link the dynamic friction coefficient of rough Si samples exclusively to the opportune set of surface roughness parameters that can exhaustively describe both height amplitude variations (Ra, Rdq) and profile periodicity (Rsk, Rku, Ic) that influence asperity-asperity interactions and hydrodynamic lift in different ways. For this main reason they cannot be treated separately, but with dependent approach through which it was possible to explain even counter intuitive results: the unexpected decreasing of friction coefficient with increasing Ra is justifiable by a more consistent increasing of kurtosis Rku.

Comparative evaluation of topographical data of dental implant surfaces applying optical interferometry and scanning electron microscopy.

PubMed

Kournetas, N; Spintzyk, S; Schweizer, E; Sawada, T; Said, F; Schmid, P; Geis-Gerstorfer, J; Eliades, G; Rupp, F

2017-08-01

Comparability of topographical data of implant surfaces in literature is low and their clinical relevance often equivocal. The aim of this study was to investigate the ability of scanning electron microscopy and optical interferometry to assess statistically similar 3-dimensional roughness parameter results and to evaluate these data based on predefined criteria regarded relevant for a favorable biological response. Four different commercial dental screw-type implants (NanoTite Certain Prevail, TiUnite Brånemark Mk III, XiVE S Plus and SLA Standard Plus) were analyzed by stereo scanning electron microscopy and white light interferometry. Surface height, spatial and hybrid roughness parameters (Sa, Sz, Ssk, Sku, Sal, Str, Sdr) were assessed from raw and filtered data (Gaussian 50μm and 5μm cut-off-filters), respectively. Data were statistically compared by one-way ANOVA and Tukey-Kramer post-hoc test. For a clinically relevant interpretation, a categorizing evaluation approach was used based on predefined threshold criteria for each roughness parameter. The two methods exhibited predominantly statistical differences. Dependent on roughness parameters and filter settings, both methods showed variations in rankings of the implant surfaces and differed in their ability to discriminate the different topographies. Overall, the analyses revealed scale-dependent roughness data. Compared to the pure statistical approach, the categorizing evaluation resulted in much more similarities between the two methods. This study suggests to reconsider current approaches for the topographical evaluation of implant surfaces and to further seek after proper experimental settings. Furthermore, the specific role of different roughness parameters for the bioresponse has to be studied in detail in order to better define clinically relevant, scale-dependent and parameter-specific thresholds and ranges. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

The PNPLA3 rs738409 G-allele associates with reduced fasting serum triglyceride and serum cholesterol in Danes with impaired glucose regulation.

PubMed

Krarup, Nikolaj Thure; Grarup, Niels; Banasik, Karina; Friedrichsen, Martin; Færch, Kristine; Sandholt, Camilla Helene; Jørgensen, Torben; Poulsen, Pernille; Witte, Daniel Rinse; Vaag, Allan; Sørensen, Thorkild; Pedersen, Oluf; Hansen, Torben

2012-01-01

Non-alcoholic fatty liver disease (NAFLD) is a common condition, associated with hepatic insulin resistance and the metabolic syndrome including hyperglycaemia and dyslipidemia. We aimed at studying the potential impact of the NAFLD-associated PNPLA3 rs738409 G-allele on NAFLD-related metabolic traits in hyperglycaemic individuals. The rs738409 variant was genotyped in the population-based Inter99 cohort examined by an oral glucose-tolerance test, and a combined study-sample consisting of 192 twins (96 twin pairs) and a sub-set of the Inter99 population (n = 63) examined by a hyperinsulinemic euglycemic clamp (n(total) = 255). In Inter99, we analyzed associations of rs738409 with components of the WHO-defined metabolic syndrome (n = 5,847) and traits related to metabolic disease (n = 5,663). In the combined study sample we elucidated whether the rs738409 G-allele altered hepatic or peripheral insulin sensitivity. Study populations were divided into individuals with normal glucose-tolerance (NGT) and with impaired glucose regulation (IGR). The case-control study showed no associations with components of the metabolic syndrome or the metabolic syndrome. Among 1,357 IGR individuals, the rs738409 G-allele associated with decreased fasting serum triglyceride levels (per allele effect(β) = -9.9% [-14.4%;-4.0% (95% CI)], p = 5.1×10(-5)) and fasting total cholesterol (β = -0.2 mmol/l [-0.3;-0.01 mmol/l(95% CI)], p = 1.5×10(-4)). Meta-analyses showed no impact on hepatic or peripheral insulin resistance in carriers of the rs738409 G-allele. Our findings suggest that the G-allele of PNPLA3 rs738409 associates with reduced fasting levels of cholesterol and triglyceride in individuals with IGR.

The role of established East Asian obesity-related loci on pediatric leptin levels highlights a neuronal influence on body weight regulation in Chinese children and adolescents: the BCAMS study

PubMed Central

Fu, Junling; Li, Ge; Li, Lujiao; Yin, Jinhua; Cheng, Hong; Han, Lanwen; Zhang, Qian; Li, Naishi; Xiao, Xinhua; Grant, Struan F.A.; Li, Mingyao; Gao, Shan; Mi, Jie; Li, Ming

2017-01-01

Genome-wide association studies have identified multiple variants associated with adult obesity, mostly in European-ancestry populations. We aimed to systematically assess the contribution of key loci, which had been previously shown to be associated in East Asian adults, to childhood obesity, related adipokine profiles and metabolic traits in a Chinese pediatric population. Twelve single-nucleotide polymorphisms (SNPs) plus metabolic profiles and levels of five adipokines (leptin, adiponectin, resistin, fibroblast growth factor 21 and retinol binding protein 4) were evaluated in 3,506 Chinese children and adolescents aged 6-18. After correction for multiple comparisons, six of these SNPs were robustly associated with childhood obesity: FTO-rs1558902 (P=5.6×10−5), MC4R-rs2331841 (P=4.4×10−4), GNPDA2-rs16858082 (P = 3.4×10−4), PCSK1-rs261967 (P = 0.001), SEC16B-rs516636 (P = 0.004) and MAP2K5-rs4776970 (P = 0.004), with odds ratios ranging from 1.211 to 1.421; while ITIH4-rs2535633 and BDNF-rs2030323 yielded nominal association with the same trait (P < 0.05). Moreover, the risk alleles of six SNPs displayed significant (P < 0.004) or nominal (P < 0.05) association with leptin levels, namely at in/near PCSK1, MC4R, FTO, MAP2K5, GNPDA2 and BDNF plus their cumulative genetic score yielded stronger association with increased leptin levels (P = 6.2×10−11). Our results reveal that key obesity-associated loci previously reported in Europeans, but also associated with East Asian adults, are also associated with obesity and/or metabolic quantitative traits in Chinese children. These associations coincide with six brain-expressed loci that correlate with leptin levels, thus may point to an important neuronal influence on body weight regulation in the pediatric setting. PMID:29212175

The role of established East Asian obesity-related loci on pediatric leptin levels highlights a neuronal influence on body weight regulation in Chinese children and adolescents: the BCAMS study.

PubMed

Fu, Junling; Li, Ge; Li, Lujiao; Yin, Jinhua; Cheng, Hong; Han, Lanwen; Zhang, Qian; Li, Naishi; Xiao, Xinhua; Grant, Struan F A; Li, Mingyao; Gao, Shan; Mi, Jie; Li, Ming

2017-11-07

Genome-wide association studies have identified multiple variants associated with adult obesity, mostly in European-ancestry populations. We aimed to systematically assess the contribution of key loci, which had been previously shown to be associated in East Asian adults, to childhood obesity, related adipokine profiles and metabolic traits in a Chinese pediatric population. Twelve single-nucleotide polymorphisms (SNPs) plus metabolic profiles and levels of five adipokines (leptin, adiponectin, resistin, fibroblast growth factor 21 and retinol binding protein 4) were evaluated in 3,506 Chinese children and adolescents aged 6-18. After correction for multiple comparisons, six of these SNPs were robustly associated with childhood obesity: FTO -rs1558902 ( P =5.6×10 -5 ), MC4R -rs2331841 ( P =4.4×10 -4 ), GNPDA2 -rs16858082 ( P = 3.4×10 -4 ), PCSK1 -rs261967 ( P = 0.001), SEC16B -rs516636 ( P = 0.004) and MAP2K5 -rs4776970 ( P = 0.004), with odds ratios ranging from 1.211 to 1.421; while ITIH4 -rs2535633 and BDNF -rs2030323 yielded nominal association with the same trait ( P < 0.05). Moreover, the risk alleles of six SNPs displayed significant ( P < 0.004) or nominal ( P < 0.05) association with leptin levels, namely at in/near PCSK1, MC4R, FTO, MAP2K5, GNPDA2 and BDNF plus their cumulative genetic score yielded stronger association with increased leptin levels ( P = 6.2×10 -11 ). Our results reveal that key obesity-associated loci previously reported in Europeans, but also associated with East Asian adults, are also associated with obesity and/or metabolic quantitative traits in Chinese children. These associations coincide with six brain-expressed loci that correlate with leptin levels, thus may point to an important neuronal influence on body weight regulation in the pediatric setting.

Age-Dependent Association between Pulmonary Tuberculosis and Common TOX Variants in the 8q12–13 Linkage Region

PubMed Central

Grant, Audrey V.; El Baghdadi, Jamila; Sabri, Ayoub; El Azbaoui, Safa; Alaoui-Tahiri, Kebir; Abderrahmani Rhorfi, Ismail; Gharbaoui, Yasser; Abid, Ahmed; Benkirane, Majid; Raharimanga, Vaomalala; Richard, Vincent; Orlova, Marianna; Boland, Anne; Migaud, Mélanie; Okada, Satoshi; Nolan, Daniel K.; Bustamante, Jacinta; Barreiro, Luis B.; Schurr, Erwin; Boisson-Dupuis, Stephanie; Rasolofo, Voahangy; Casanova, Jean-Laurent; Abel, Laurent

2013-01-01

Only a small fraction of individuals infected with Mycobacterium tuberculosis develop clinical tuberculosis (TB) in their lifetime. Genetic epidemiological evidence suggests a genetic determinism of pulmonary TB (PTB), but the molecular basis of genetic predisposition to PTB remains largely unknown. We used a positional-cloning approach to carry out ultrafine linkage-disequilibrium mapping of a previously identified susceptibility locus in chromosomal region 8q12–13 by genotyping 3,216 SNPs in a family-based Moroccan sample including 286 offspring with PTB. We observed 44 PTB-associated SNPs (p < 0.01), which were genotyped in an independent set of 317 cases and 650 controls from Morocco. A single signal, consisting of two correlated SNPs close to TOX, rs1568952 and rs2726600 (combined p = 1.1 × 10−5 and 9.2 × 10−5, respectively), was replicated. Stronger evidence of association was found in individuals who developed PTB before the age of 25 years (combined p for rs1568952 = 4.4 × 10−8; odds ratio of PTB for AA versus AG/GG = 3.09 [1.99–4.78]). The association with rs2726600 (p = 0.04) was subsequently replicated in PTB-affected subjects under 25 years in a study of 243 nuclear families from Madagascar. Stronger evidence of replication in Madagascar was obtained for additional SNPs in strong linkage disequilibrium with the two initial SNPs (p = 0.003 for rs2726597), further confirming the signal. We thus identified around rs1568952 and rs2726600 a cluster of SNPs strongly associated with early-onset PTB in Morocco and Madagascar. SNP rs2726600 is located in a transcription-factor binding site in the 3′ region of TOX, and further functional explorations will focus on CD4 T lymphocytes. PMID:23415668

The supportive roles of religion and spirituality in end-of-life and palliative care of patients with cancer in a culturally diverse context: a literature review.

PubMed

López-Sierra, Héctor E; Rodríguez-Sánchez, Jesús

2015-03-01

This is a literature review of the supportive roles of religion and spirituality (R/S) in end-of-life (EoL) and palliative care of patients with cancer in a culturally diverse context. This review examines 26 noteworthy articles published between August 2013 and August 2014 from five well supported databases. Current evidence shows that R/S evokes in patients the sources to find the necessary inner strengths, which includes perspective thinking, rituals for transcending immediate physical condition and modalities of coping with their oncological illnesses. R/S are not a monolithically experience for they always manifest themselves in diverse cultural settings. As such, R/S provide the individual and their families with a practical context and social memory, which includes traditions and social family practices for maintaining meaning and well-being. Nonetheless, although various dimensions of R/S show a link between cancer risk factors and well being in cancer patients, more specific dimensions of R/S need to be studied taking into account the individuals' particular religious and cultural contexts, so that R/S variables within that context can provide a greater integrative structure for understanding and to move the field forward. Behavioral, cognitive and psychosocial scientists have taken a more in-depth look at the claims made in the past, suggesting that a relationship between R/S, cultural diversity and health exists. Case in point are the studies on EoL care, which have progressively considered the role of cultural, religion and spiritual diversity in the care of patients with oncological terminal illnesses. Beyond these facts, this review also shows that EoL supportive and palliative care providers could further enhance their practical interventions by being sensitive and supportive of cultural diversity. http://links.lww.com/COSPC/A10

Genome-wide search followed by replication reveals genetic interaction of CD80 and ALOX5AP associated with systemic lupus erythematosus in Asian populations.

PubMed

Zhang, Yan; Yang, Jing; Zhang, Jing; Sun, Liangdan; Hirankarn, Nattiya; Pan, Hai-Feng; Lau, Chak Sing; Chan, Tak Mao; Lee, Tsz Leung; Leung, Alexander Moon Ho; Mok, Chi Chiu; Zhang, Lu; Wang, Yongfei; Shen, Jiangshan Jane; Wong, Sik Nin; Lee, Ka Wing; Ho, Marco Hok Kung; Lee, Pamela Pui Wah; Chung, Brian Hon-Yin; Chong, Chun Yin; Wong, Raymond Woon Sing; Mok, Mo Yin; Wong, Wilfred Hing Sang; Tong, Kwok Lung; Tse, Niko Kei Chiu; Li, Xiang-Pei; Avihingsanon, Yingyos; Rianthavorn, Pornpimol; Deekajorndej, Thavatchai; Suphapeetiporn, Kanya; Shotelersuk, Vorasuk; Ying, Shirley King Yee; Fung, Samuel Ka Shun; Lai, Wai Ming; Wong, Chun-Ming; Ng, Irene Oi Lin; Garcia-Barcelo, Maria-Merce; Cherny, Stacey S; Cui, Yong; Sham, Pak Chung; Yang, Sen; Ye, Dong-Qing; Zhang, Xue-Jun; Lau, Yu Lung; Yang, Wanling

2016-05-01

Genetic interaction has been considered as a hallmark of the genetic architecture of systemic lupus erythematosus (SLE). Based on two independent genome-wide association studies (GWAS) on Chinese populations, we performed a genome-wide search for genetic interactions contributing to SLE susceptibility. The study involved a total of 1 659 cases and 3 398 controls in the discovery stage and 2 612 cases and 3 441 controls in three cohorts for replication. Logistic regression and multifactor dimensionality reduction were used to search for genetic interaction. Interaction of CD80 (rs2222631) and ALOX5AP (rs12876893) was found to be significantly associated with SLE (OR_int=1.16, P_int_all=7.7E-04 at false discovery rate<0.05). Single nuclear polymorphism rs2222631 was found associated with SLE with genome-wide significance (P_all=4.5E-08, OR=0.86) and is independent of rs6804441 in CD80, whose association was reported previously. Significant correlation was observed between expression of these two genes in healthy controls and SLE cases, together with differential expression of these genes between cases and controls, observed from individuals from the Hong Kong cohort. Genetic interactions between BLK (rs13277113) and DDX6 (rs4639966), and between TNFSF4 (rs844648) and PXK (rs6445975) were also observed in both GWAS data sets. Our study represents the first genome-wide evaluation of epistasis interactions on SLE and the findings suggest interactions and independent variants may help partially explain missing heritability for complex diseases. 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 Modifiers of Neurofibromatosis Type 1-Associated Café-au-Lait Macule Count Identified Using Multi-platform Analysis

PubMed Central

Pemov, Alexander; Sung, Heejong; Hyland, Paula L.; Sloan, Jennifer L.; Ruppert, Sarah L.; Baldwin, Andrea M.; Boland, Joseph F.; Bass, Sara E.; Lee, Hyo Jung; Jones, Kristine M.; Zhang, Xijun; Mullikin, James C.; Widemann, Brigitte C.; Wilson, Alexander F.; Stewart, Douglas R.

2014-01-01

Neurofibromatosis type 1 (NF1) is an autosomal dominant, monogenic disorder of dysregulated neurocutaneous tissue growth. Pleiotropy, variable expressivity and few NF1 genotype-phenotype correlates limit clinical prognostication in NF1. Phenotype complexity in NF1 is hypothesized to derive in part from genetic modifiers unlinked to the NF1 locus. In this study, we hypothesized that normal variation in germline gene expression confers risk for certain phenotypes in NF1. In a set of 79 individuals with NF1, we examined the association between gene expression in lymphoblastoid cell lines with NF1-associated phenotypes and sequenced select genes with significant phenotype/expression correlations. In a discovery cohort of 89 self-reported European-Americans with NF1 we examined the association between germline sequence variants of these genes with café-au-lait macule (CALM) count, a tractable, tumor-like phenotype in NF1. Two correlated, common SNPs (rs4660761 and rs7161) between DPH2 and ATP6V0B were significantly associated with the CALM count. Analysis with tiled regression also identified SNP rs4660761 as significantly associated with CALM count. SNP rs1800934 and 12 rare variants in the mismatch repair gene MSH6 were also associated with CALM count. Both SNPs rs7161 and rs4660761 (DPH2 and ATP6V0B) were highly significant in a mega-analysis in a combined cohort of 180 self-reported European-Americans; SNP rs1800934 (MSH6) was near-significant in a meta-analysis assuming dominant effect of the minor allele. SNP rs4660761 is predicted to regulate ATP6V0B, a gene associated with melanosome biology. Individuals with homozygous mutations in MSH6 can develop an NF1-like phenotype, including multiple CALMs. Through a multi-platform approach, we identified variants that influence NF1 CALM count. PMID:25329635

Gene Selection and Cancer Classification: A Rough Sets Based Approach

NASA Astrophysics Data System (ADS)

Sun, Lijun; Miao, Duoqian; Zhang, Hongyun

Indentification of informative gene subsets responsible for discerning between available samples of gene expression data is an important task in bioinformatics. Reducts, from rough sets theory, corresponding to a minimal set of essential genes for discerning samples, is an efficient tool for gene selection. Due to the compuational complexty of the existing reduct algoritms, feature ranking is usually used to narrow down gene space as the first step and top ranked genes are selected . In this paper,we define a novel certierion based on the expression level difference btween classes and contribution to classification of the gene for scoring genes and present a algorithm for generating all possible reduct from informative genes.The algorithm takes the whole attribute sets into account and find short reduct with a significant reduction in computational complexity. An exploration of this approach on benchmark gene expression data sets demonstrates that this approach is successful for selecting high discriminative genes and the classification accuracy is impressive.

Entropy Based Feature Selection for Fuzzy Set-Valued Information Systems

NASA Astrophysics Data System (ADS)

Ahmed, Waseem; Sufyan Beg, M. M.; Ahmad, Tanvir

2018-06-01

In Set-valued Information Systems (SIS), several objects contain more than one value for some attributes. Tolerance relation used for handling SIS sometimes leads to loss of certain information. To surmount this problem, fuzzy rough model was introduced. However, in some cases, SIS may contain some real or continuous set-values. Therefore, the existing fuzzy rough model for handling Information system with fuzzy set-values needs some changes. In this paper, Fuzzy Set-valued Information System (FSIS) is proposed and fuzzy similarity relation for FSIS is defined. Yager's relative conditional entropy was studied to find the significance measure of a candidate attribute of FSIS. Later, using these significance values, three greedy forward algorithms are discussed for finding the reduct and relative reduct for the proposed FSIS. An experiment was conducted on a sample population of the real dataset and a comparison of classification accuracies of the proposed FSIS with the existing SIS and single-valued Fuzzy Information Systems was made, which demonstrated the effectiveness of proposed FSIS.

The Last of the Gem Elixir (Research).

ERIC Educational Resources Information Center

Otto, Wayne

1988-01-01

Draws a humorous analogy between the Harmonic Convergence ushering in the dawn of the New Age and the convergence of a whole set of different views of reading instruction with established views and practices. (RS)

Response to Antenatal Cholecalciferol Supplementation Is Associated With Common Vitamin D–Related Genetic Variants

PubMed Central

Moon, Rebecca J.; Harvey, Nicholas C.; D’Angelo, Stefania; Curtis, Elizabeth M.; Crozier, Sarah R.; Barton, Sheila J.; Robinson, Sian M.; Godfrey, Keith M.; Graham, Nikki J.; Holloway, John W.; Bishop, Nicholas J.; Kennedy, Stephen; Papageorghiou, Aris T.; Schoenmakers, Inez; Fraser, Robert; Gandhi, Saurabh V.; Prentice, Ann; Inskip, Hazel M.; Javaid, M. Kassim

2017-01-01

Context: Single-nucleotide polymorphisms (SNPs) in genes related to vitamin D metabolism have been associated with serum 25-hydroxyvitamin D [25(OH)D] concentration, but these relationships have not been examined following antenatal cholecalciferol supplementation. Objective: To determine whether SNPs in DHCR7, CYP2R1, CYP24A1, and GC are associated with the response to gestational cholecalciferol supplementation. Design: Within-randomization group analysis of the Maternal Vitamin D Osteoporosis Study trial of antenatal cholecalciferol supplementation. Setting: Hospital antenatal clinics. Participants: In total, 682 women of white ethnicity (351 placebo, 331 cholecalciferol) were included. SNPs at rs12785878 (DHCR7), rs10741657 (CYP2R1), rs6013897 (CYP24A1), and rs2282679 (GC) were genotyped. Interventions: 1000 IU/d cholecalciferol from 14 weeks of gestation until delivery. Main Outcome Measure: 25(OH)D at randomization and 34 weeks of gestation were measured in a single batch (Liaison; Diasorin, Dartford, UK). Associations between 25(OH)D and the SNPs were assessed by linear regression using an additive model [β represents the change in 25(OH)D per additional common allele]. Results: Only rs12785878 (DHCR7) was associated with baseline 25(OH)D [β = 3.1 nmol/L; 95% confidence interval (CI), 1.0 to 5.2 nmol/L; P < 0.004]. In contrast, rs10741657 (CYP2R1) (β = −5.2 nmol/L; 95% CI, −8.2 to −2.2 nmol/L; P = 0.001) and rs2282679 (GC) (β = 4.2 nmol/L; 95% CI, 0.9 to 7.5 nmol/L; P = 0.01) were associated with achieved 25(OH)D status following supplementation, whereas rs12785878 and rs6013897 (CYP24A1) were not. Conclusions: Genetic variation in DHCR7, which encodes 7-dehyrocholesterol reductase in the epidermal vitamin D biosynthesis pathway, appears to modify baseline 25(OH)D. In contrast, the response to antenatal cholecalciferol supplementation was associated with SNPs in CYP2R1, which may alter 25-hydroxylase activity, and GC, which may affect vitamin D binding protein synthesis or metabolite affinity. PMID:28575224

Relation Between Type II Bursts and CMEs Inferred from STEREO Observations

NASA Technical Reports Server (NTRS)

Gopalswamy, N.; Thompson, W.; Davila, J.; Kaiser, M. L.; Yashiro, S.; Maekelae, P.; Michalek, G.; Bougeret, J.-L.; Hoawrd, R. A.

2010-01-01

The inner coronagraph (COR1) of the Solar Terrestrial Relations Observatory (STEREO) mission has made it possible to observe coronal mass ejections (CMEs) a in the spatial domain overlapping with that of the metric type II radio bursts. The type II bursts were associated with generally weak flares (mostly B and C class soft X-ray flares), but the CMEs were quite energetic. Using CME data for a set of type II bursts during the declining phase of solar cycle 23, we determine the CME height when the type II bursts start, thus giving an estimate of the heliocentric distance at which CME-driven shocks form. This distance has been determined to be approximately 1.5Rs (solar radii), which coincides with the distance at which the Alfv?n speed profile has a minimum value. We also use type II radio observations from STEREO/WAVES and Wind/WAVES observations to show that CMEs with moderate speed drive either weak shocks or no shock at all when they attain a height where the Alfv?n speed peaks (?3Rs ? 4Rs). Thus the shocks seem to be most efficient in accelerating electrons in the heliocentric distance range of 1.5Rs to 4Rs. By combining the radial variation of the CME speed in the inner corona (CME speed increase) and interplanetary medium (speed decrease) we were able to correctly account for the deviations from the universal drift-rate spectrum of type II bursts, thus confirming the close physical connection between type II bursts and CMEs. The average height (approximately 1.5 Rs) of STEREO CMEs at the time of type II bursts is smaller than that (2.2 Rs) obtained for SOHO (Solar and Heliospheric Observatory) CMEs. We suggest that this may indicate, at least partly, the density reduction in the corona between the maximum and declining phases, so a given plasma level occurs closer to the Sun in the latter phase. In two cases, there was a diffuse shock-like feature ahead of the main body of the CME, indicating a standoff distance of 1Rs - 2Rs by the time the CME left the LASCO field of view.

Relation Between Type II Bursts and CMEs Inferred from STEREO Observations

NASA Technical Reports Server (NTRS)

Gopalswamy, N.; Thompson, W.; Davila, J.; Kaiser, M.; Yashiro, S.; Maelekae, P.; Michalek, G.; Bougret, J.-L.; Howard, R. A.

2009-01-01

The inner coronagraph (COR1) of the Solar Terrestrial Relations Observatory (STEREO) mission has made it possible to observe CMEs in the spatial domain overlapping with that of the metric type II radio bursts. The type II bursts were associated with generally weak flares (mostly B and C class soft X-ray flares), but the CMEs were quite energetic. Using CME data for a set of type II bursts during the declining phase of solar cycle 23, we determine the CME height when the type II bursts start, thus giving an estimate of the heliocentric distance at which CME-driven shocks form. This distance has been determined to be approx. 1.5Rs (solar radii), which coincides with the distance at which the Alfven speed profile has a minimum value.We also use type II radio observations from STEREO/WAVES and Wind/WAVES observations to show that CMEs with moderate speed drive either weak shocks or no shock at all when they attain a height where the Alfven speed peaks (approx. 3Rs - 4Rs). Thus the shocks seem to be most efficient in accelerating electrons in the heliocentric distance range of 1.5Rs to 4Rs. By combining the radial variation of the CME speed in the inner corona (CME speed increase) and interplanetary medium (speed decrease) we were able to correctly account for the deviations from the universal drift-rate spectrum of type II bursts, thus confirming the close physical connection between type II bursts and CMEs. The average height (approx 1.5Rs) of STEREO CMEs at the time of type II bursts is smaller than that (2.2Rs) obtained for SOHO (Solar and Heliospheric Observatory) CMEs. We suggest that this may indicate, at least partly, the density reduction in the corona between the maximum and declining phases, so a given plasma level occurs closer to the Sun in the latter phase. In two cases, there was a diffuse shock-like feature ahead of the main body of the CME, indicating a standoff distance of 1Rs - 2Rs by the time the CME left the LASCO field of view.

Shear Model Development of Limestone Joints with Incorporating Variations of Basic Friction Coefficient and Roughness Components During Shearing

NASA Astrophysics Data System (ADS)

Mehrishal, Seyedahmad; Sharifzadeh, Mostafa; Shahriar, Korosh; Song, Jae-Jon

2017-04-01

In relation to the shearing of rock joints, the precise and continuous evaluation of asperity interlocking, dilation, and basic friction properties has been the most important task in the modeling of shear strength. In this paper, in order to investigate these controlling factors, two types of limestone joint samples were prepared and CNL direct shear tests were performed on these joints under various shear conditions. One set of samples were travertine and another were onyx marble with slickensided surfaces, surfaces ground to #80, and rough surfaces were tested. Direct shear experiments conducted on slickensided and ground surfaces of limestone indicated that by increasing the applied normal stress, under different shearing rates, the basic friction coefficient decreased. Moreover, in the shear tests under constant normal stress and shearing rate, the basic friction coefficient remained constant for the different contact sizes. The second series of direct shear experiments in this research was conducted on tension joint samples to evaluate the effect of surface roughness on the shear behavior of the rough joints. This paper deals with the dilation and roughness interlocking using a method that characterizes the surface roughness of the joint based on a fundamental combined surface roughness concept. The application of stress-dependent basic friction and quantitative roughness parameters in the continuous modeling of the shear behavior of rock joints is an important aspect of this research.

Set-up and calibration of an indoor nozzle-type rainfall simulator for soil erosion studies

NASA Astrophysics Data System (ADS)

Lassu, T.; Seeger, M.

2012-04-01

Rainfall simulation is one of the most prevalent methods used in soil erosion studies on agricultural land. In-situ simulators have been used to relate soil surface characteristics and management to runoff generation, infiltration and erosion, eg. the influence of different cultivation systems, and to parameterise erosion models. Laboratory rainfall simulators have been used to determine the impact of the soil surface characteristics such as micro-topography, surface roughness, and soil chemistry on infiltration and erosion rates, and to elucidate the processes involved. The purpose of the following study is to demonstrate the set-up and the calibration of a large indoor, nozzle-type rainfall simulator (RS) for soil erosion, surface runoff and rill development studies. This RS is part of the Kraijenhoff van de Leur Laboratory for Water and Sediment Dynamics in Wageningen University. The rainfall simulator consists from a 6 m long and 2,5 m wide plot, with metal lateral frame and one open side. Infiltration can be collected in different segments. The plot can be inclined up to 15.5° slope. From 3,85 m height above the plot 2 Lechler nozzles 460.788 are sprinkling the water onto the surface with constant intensity. A Zehnder HMP 450 pump provides the constant water supply. An automatic pressure switch on the pump keeps the pressure constant during the experiments. The flow rate is controlled for each nozzle by independent valves. Additionally, solenoid valves are mounted at each nozzle to interrupt water flow. The flow is monitored for each nozzle with flow meters and can be recorded within the computer network. For calibration of the RS we measured the rainfall distribution with 60 gauges equally distributed over the plot during 15 minutes for each nozzle independently and for a combination of 2 identical nozzles. The rainfall energy was recorded on the same grid by measuring drop size distribution and fall velocity with a laser disdrometer. We applied 2 different flow rates (4,5 l/min and 5,5 l/min), resulting in different rainfall intensities and made 2 repetitions each. The average rainfall intensity was 36,8 mm/h at the first and 37,6 mm/h at the second repetition with the lower flow rate (4,5 l/min). With the higher flow rate (5,5 l/min) at the first repetition it was 44,4 mm/h and 46 mm/h at the second one. The maximum and minimum values were 22 mm and 2 mm at the lower (4,5 l/min) flow rate, respectively 26 mm and 4 mm at the higher one (5,5 l/min). In this latter case, the resulting average kinetic energy reached 7 J m-2 mm-1, with a maximum 31,3 J m-2 mm-1 of and a minimum of 2,9 J m-2 mm-1. The Christiansen Uniformity coefficient (CU) for the lower intensities was 66% and 69%, respectively, with the higher intensities slightly better (70% and 72%). The data of the rainfall simulator in Wageningen make it a promising tool for research in soil erosion processes.

Temporal Stability of Surface Roughness Effects on Radar Based Soil Moisture Retrieval During the Corn Growth Cycle

NASA Technical Reports Server (NTRS)

Joseph, A.T.; Lang, R.; O'Neill, P.E.; van der Velde, R.; Gish, T.

2008-01-01

A representative soil surface roughness parameterization needed for the retrieval of soil moisture from active microwave satellite observation is difficult to obtain through either in-situ measurements or remote sensing-based inversion techniques. Typically, for the retrieval of soil moisture, temporal variations in surface roughness are assumed to be negligible. Although previous investigations have suggested that this assumption might be reasonable for natural vegetation covers (Moran et al. 2002, Thoma et al. 2006), insitu measurements over plowed agricultural fields (Callens et al. 2006) have shown that the soil surface roughness can change considerably over time. This paper reports on the temporal stability of surface roughness effects on radar observations and soil moisture retrieved from these radar observations collected once a week during a corn growth cycle (May 10th - October 2002). The data set employed was collected during the Optimizing Production Inputs for Economic and Environmental Enhancement (OPE3) field campaign covering this 2002 corn growth cycle and consists of dual-polarized (HH and VV) L-band (1.6 GHz) acquired at view angles of 15, 35, and 55 degrees. Cross-polarized L baud radar data were also collected as part of this experiment, but are not used in the analysis reported on here. After accounting for vegetation effects on radar observations, time-invariant optimum roughness parameters were determined using the Integral Equation Method (IEM) and radar observations acquired over bare soil and cropped conditions (the complete radar data set includes entire corn growth cycle). The optimum roughness parameters, soil moisture retrieval uncertainty, temporal distribution of retrieval errors and its relationship with the weather conditions (e.g. rainfall and wind speed) have been analyzed. It is shown that over the corn growth cycle, temporal roughness variations due to weathering by rain are responsible for almost 50% of soil moisture retrieval uncertainty depending on the sensing configuration. The effects of surface roughness variations are found to be smallest for observations acquired at a view angle of 55 degrees and HH polarization. A possible explanation for this result is that at 55 degrees and HH polarization the effect of vertical surface height changes on the observed radar response are limited because the microwaves travel parallel to the incident plane and as a result will not interact directly with vertically oriented soil structures.

Effect of Blade-surface Finish on Performance of a Single-stage Axial-flow Compressor

NASA Technical Reports Server (NTRS)

Moses, Jason J; Serovy, George, K

1951-01-01

A set of modified NACA 5509-34 rotor and stator blades was investigated with rough-machine, hand-filed, and highly polished surface finishes over a range of weight flows at six equivalent tip speeds from 672 to 1092 feet per second to determine the effect of blade-surface finish on the performance of a single-stage axial-flow compressor. Surface-finish effects decreased with increasing compressor speed and with decreasing flow at a given speed. In general, finishing blade surfaces below the roughness that may be considered aerodynamically smooth on the basis of an admissible-roughness formula will have no effect on compressor performance.

Signal Processing Methods for Liquid Rocket Engine Combustion Spontaneous Stability and Rough Combustion Assessments

NASA Technical Reports Server (NTRS)

Kenny, R. Jeremy; Casiano, Matthew; Fischbach, Sean; Hulka, James R.

2012-01-01

Liquid rocket engine combustion stability assessments are traditionally broken into three categories: dynamic stability, spontaneous stability, and rough combustion. This work focuses on comparing the spontaneous stability and rough combustion assessments for several liquid engine programs. The techniques used are those developed at Marshall Space Flight Center (MSFC) for the J-2X Workhorse Gas Generator program. Stability assessment data from the Integrated Powerhead Demonstrator (IPD), FASTRAC, and Common Extensible Cryogenic Engine (CECE) programs are compared against previously processed J-2X Gas Generator data. Prior metrics for spontaneous stability assessments are updated based on the compilation of all data sets.

Float polishing of optical materials.

PubMed

Bennett, J M; Shaffer, J J; Shibano, Y; Namba, Y

1987-02-15

The float-polishing technique has been studied to determine its suitability for producing supersmooth surfaces on optical materials, yielding a roughness of <2 A rms. An attempt was made to polish six different materials including fused quartz, Zerodur, and sapphire. The low surface roughness was achieved on fused quartz, Zerodur, and Corning experimental glass-ceramic materials, and a surface roughness of <1 A rms was obtained on O-cut single-crystal sapphire. Presumably, similar surface finishes can also be obtained on CerVit and ULE quartz, which could not be polished satisfactorily in this set of experiments because of a mismatch between sample mounting and machine configuration.

Interim Service ISDN Satellite (ISIS) hardware experiment development for advanced ISDN satellite designs and experiments

NASA Technical Reports Server (NTRS)

Pepin, Gerard R.

1992-01-01

The Interim Service Integrated Service Digital Network (ISDN) Satellite (ISIS) Hardware Experiment Development for Advanced Satellite Designs describes the development of the ISDN Satellite Terminal Adapter (ISTA) capable of translating ISDN protocol traffic into Time Division Multiple Access (TDMA) signals for use by a communications satellite. The ISTA connects the Type 1 Network Termination (NT1) via the U-interface on the line termination side of the CPE to the RS-499 interface for satellite uplink. The same ISTA converts in the opposite direction the RS-499 to U-interface data with a simple switch setting.

[RS3PE syndrome: report of 11 cases].

PubMed

Bruscas Izu, C; Medrano San Ildefonso, M; Simon, L

2000-09-01

The RS3P syndrome or remitting seronegative symmetrical synovitis with pitting oedema, was described in 1985 by McCarty. The description refers to a rheumatologic set of symptoms with an acute commence, with no erosive lesions, with seronegativity, affecting more frequently to elderly males and showing an excellent prognosis. These characteristics make it possible to difference from the rheumatoid arthritis and from the rheumatic polymyalgia. We present eleven cases which confirm the good prognosis already described, but we suggest the possibility of this syndrome could be a manifestation or the beginning of other possible diseases.

Two new loci and gene sets related to sex determination and cancer progression are associated with susceptibility to testicular germ cell tumor.

PubMed

Kristiansen, Wenche; Karlsson, Robert; Rounge, Trine B; Whitington, Thomas; Andreassen, Bettina K; Magnusson, Patrik K; Fosså, Sophie D; Adami, Hans-Olov; Turnbull, Clare; Haugen, Trine B; Grotmol, Tom; Wiklund, Fredrik

2015-07-15

Genome-wide association (GWA) studies have reported 19 distinct susceptibility loci for testicular germ cell tumor (TGCT). A GWA study for TGCT was performed by genotyping 610 240 single-nucleotide polymorphisms (SNPs) in 1326 cases and 6687 controls from Sweden and Norway. No novel genome-wide significant associations were observed in this discovery stage. We put forward 27 SNPs from 15 novel regions and 12 SNPs previously reported, for replication in 710 case-parent triads and 289 cases and 290 controls. Predefined biological pathways and processes, in addition to a custom-built sex-determination gene set, were subject to enrichment analyses using Meta-Analysis Gene Set Enrichment of Variant Associations (M) and Improved Gene Set Enrichment Analysis for Genome-wide Association Study (I). In the combined meta-analysis, we observed genome-wide significant association for rs7501939 on chromosome 17q12 (OR = 0.78, 95% CI = 0.72-0.84, P = 1.1 × 10(-9)) and rs2195987 on chromosome 19p12 (OR = 0.76, 95% CI: 0.69-0.84, P = 3.2 × 10(-8)). The marker rs7501939 on chromosome 17q12 is located in an intron of the HNF1B gene, encoding a member of the homeodomain-containing superfamily of transcription factors. The sex-determination gene set (false discovery rate, FDRM < 0.001, FDRI < 0.001) and pathways related to NF-κB, glycerophospholipid and ether lipid metabolism, as well as cancer and apoptosis, was associated with TGCT (FDR < 0.1). In addition to revealing two new TGCT susceptibility loci, our results continue to support the notion that genes governing normal germ cell development in utero are implicated in the development of TGCT. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Performance and Value of IFN-Lambda3 and IFN-Lambda4 Genotyping in Patients with Chronic Hepatitis C (CHC) Genotype 2/3 in a Real World Setting

PubMed Central

Susser, Simone; Rogalska-Taranta, Magdalena; Petersen, Jörg; Böker, Klaus H. W.; Grigorian, Natalia; Link, Ralph; Naumann, Uwe; John, Christine; Lueth, Stefan; Malfertheiner, Peter; Manns, Michael P.; Wedemeyer, Heiner; Sarrazin, Christoph; Cornberg, Markus

2015-01-01

Background SNPs near the interferon lambda (IFNL) 3 gene are predictors for sustained virological response (SVR) in patients with chronic hepatitis C genotype (GT) 1. In addition, a dinucleotide frame shift in ss469415590 was described, which generates IFNL4. In this study, we compared the role of IFNL4 variants with IFNL3-(rs12979860) and IFNL3-(rs8099917) on response to pegylated (PEG)-IFN and Ribavirin (RBV) in patients with chronic hepatitis C GT2/3. Methods We recruited 1006 patients with chronic hepatitis C and GT2/3 in a large German registry. A treatment with PEG-IFN and Ribavirin was started by 959 patients. We performed genotyping of IFNL3 (rs12979860, n = 726; rs8099917, n = 687) and of IFNL4 (ss469415590; n = 631). Results Both preferable IFNL3 genotypes were associated with RVR (both p<0.0001) rather than with SVR (rs12979860: p = 0.251; rs8099917: p = 0.447). Only RVR was linked to SVR in univariate and multivariate analyzes (both p<0.001). Concordance of genotyping in patients with available serum samples and EDTA blood samples (n = 259) was more than 96% for both IFNL3 SNPs. IFNL3-(rs12979860) correlated with IFNL4: 99.2% of patients with IFNL3-(rs12979860)-CC were IFNL4-(ss469415590)-TT/TT. IFNL3-(rs12979860)-CT was linked with IFNL4-(ss469415590)-TT/ΔG (98.0%) and IFNL3-(rs12979860)-TT was associated with IFNL4-(ss469415590)-ΔG/ΔG (97.6%). Conclusion IFNL3 genotyping from serum was highly efficient and can be used as an alternative if EDTA whole blood is not available. In Caucasian GT2/3 patients genotyping for INFL4-(ss469415590) does not lead to additional information for the decision-making process. Importantly, IFNL3 SNPs were not associated with SVR but with RVR. Even in the era of new direct acting antiviral (DAA) therapies, IFNL3 testing may therefore still be considered for naïve GT2/3 patients to decide if dual Peg-IFN/RBV therapy is an option in resource limited regions. PMID:26699619

Performance and Value of IFN-Lambda3 and IFN-Lambda4 Genotyping in Patients with Chronic Hepatitis C (CHC) Genotype 2/3 in a Real World Setting.

PubMed

Wiegand, Steffen B; Heidrich, Benjamin; Susser, Simone; Rogalska-Taranta, Magdalena; Petersen, Jörg; Böker, Klaus H W; Grigorian, Natalia; Link, Ralph; Naumann, Uwe; John, Christine; Lueth, Stefan; Malfertheiner, Peter; Manns, Michael P; Wedemeyer, Heiner; Sarrazin, Christoph; Cornberg, Markus

2015-01-01

SNPs near the interferon lambda (IFNL) 3 gene are predictors for sustained virological response (SVR) in patients with chronic hepatitis C genotype (GT) 1. In addition, a dinucleotide frame shift in ss469415590 was described, which generates IFNL4. In this study, we compared the role of IFNL4 variants with IFNL3-(rs12979860) and IFNL3-(rs8099917) on response to pegylated (PEG)-IFN and Ribavirin (RBV) in patients with chronic hepatitis C GT2/3. We recruited 1006 patients with chronic hepatitis C and GT2/3 in a large German registry. A treatment with PEG-IFN and Ribavirin was started by 959 patients. We performed genotyping of IFNL3 (rs12979860, n = 726; rs8099917, n = 687) and of IFNL4 (ss469415590; n = 631). Both preferable IFNL3 genotypes were associated with RVR (both p<0.0001) rather than with SVR (rs12979860: p = 0.251; rs8099917: p = 0.447). Only RVR was linked to SVR in univariate and multivariate analyzes (both p<0.001). Concordance of genotyping in patients with available serum samples and EDTA blood samples (n = 259) was more than 96% for both IFNL3 SNPs. IFNL3-(rs12979860) correlated with IFNL4: 99.2% of patients with IFNL3-(rs12979860)-CC were IFNL4-(ss469415590)-TT/TT. IFNL3-(rs12979860)-CT was linked with IFNL4-(ss469415590)-TT/ΔG (98.0%) and IFNL3-(rs12979860)-TT was associated with IFNL4-(ss469415590)-ΔG/ΔG (97.6%). IFNL3 genotyping from serum was highly efficient and can be used as an alternative if EDTA whole blood is not available. In Caucasian GT2/3 patients genotyping for INFL4-(ss469415590) does not lead to additional information for the decision-making process. Importantly, IFNL3 SNPs were not associated with SVR but with RVR. Even in the era of new direct acting antiviral (DAA) therapies, IFNL3 testing may therefore still be considered for naïve GT2/3 patients to decide if dual Peg-IFN/RBV therapy is an option in resource limited regions.

Is love of nature in the US becoming love of electronic media? 16-year downtrend in national park visits explained by watching movies, playing video games, internet use, and oil prices.

PubMed

Pergams, Oliver R W; Zaradic, Patricia A

2006-09-01

After 50 years of steady increase, per capita visits to US national parks have declined since 1988. This decline, coincident with the rise in electronic entertainment media, may represent a shift in recreation choices with broader implications for the value placed on biodiversity conservation and environmentally responsible behavior. We compared the decline in per capita visits with a set of indicators representing alternate recreation choices and constraints. The Spearman correlation analyses found this decline in NPV to be significantly negatively correlated with several electronic entertainment indicators: hours of television, (rs=-0.743, P<0.001), video games (rs=-0.773, P<0.001), home movies (rs=-0.788, P<0.001), theatre attendance (rs=-0.587, P<0.025) and internet use (rs=-0.783, P<0.001). There were also significant negative correlations with oil prices (rs=-0.547, P<0.025), foreign travel (rs=-0.452, P<0.05), and Appalachian Trail hikers (rs=-0.785, P<0.001). Income was significantly positively correlated with foreign travel (rs=0.621, P<0.005) but negatively correlated with national park visits (rs=-0.697, P<0.005). There was no significant correlation of mean number of vacation days, indicating available vacation time is probably not a factor. Federal funding actually increased during this period, and so was rejected as a probable factor. Park capacity was rejected as limiting since both total overnight stays and visits at the seven most popular parks rose well into the mid-1990s. Aging of baby boomers was also rejected as they are only now reaching retirement age, and thus during the period of visitation decline were still of prime family vacation age. Multiple linear regression of four of the entertainment media variables as well as oil prices explains 97.5% of this recent decline (r=0.975, multiple r2=0.950, adjusted multiple r2=0.925, SE=0.015, F=37.800, P<0.0001). We may be seeing evidence of a fundamental shift away from people's appreciation of nature (biophilia, Wilson 1984) to 'videophilia,' which we here define as "the new human tendency to focus on sedentary activities involving electronic media." Such a shift would not bode well for the future of biodiversity conservation.

A Mössbauer study of some new trinuclear Fe-S cluster compounds

NASA Astrophysics Data System (ADS)

Zhang, Jing-Kun; Song, Li-Cheng; Zhang, Ze-Min; Liu, Rong-Gon; Cheng, Zheng-Zhung; Wang, Ji-Tao

1988-02-01

The reaction of (u-RS)2 (XMgS) Fe2 (CO)2 with CpFe (CO)2I gave thirteen new compounds (u-RS) [CpFe (CO)2S] Fe2 (CO)4. Mossbauer spectra were obtained at 80K. Two quadrupote doubles (A set and B set) were present. The ratio of areas between A set and B set was close to 2∶1. The molecule of every compound contained two Fe (2+) which were in the same chemical environment of low spin state with a coordination number of six, and the Mossbauer parameters of the two Fe (2+), IS=0.2 0.3 mm/s, QS=0.7 0.8 mm/s. In addition, the molecule contained a Fe (3+) in low spin state which was proved by ESR. Its Mossbauer parameters, IS=0.4 0.5 mm/s. QS=1.5±1.6 mm/s, The molecular structure of (u-MeS) [u-CpFe (CO)2S] Fe2 (CO)4 was determined by X-ray diffraction, monoclinic form, space group P21/n z=4, unit cell parameters, a=7.90A, b=10.77A, c=22.53A.

Identification of novel loci for Alzheimer disease and replication of CLU, PICALM, and BIN1 in Caribbean Hispanic individuals.

PubMed

Lee, Joseph H; Cheng, Rong; Barral, Sandra; Reitz, Christiane; Medrano, Martin; Lantigua, Rafael; Jiménez-Velazquez, Ivonne Z; Rogaeva, Ekaterina; St George-Hyslop, Peter H; Mayeux, Richard

2011-03-01

To identify novel loci for late-onset Alzheimer disease (LOAD) in Caribbean Hispanic individuals and to replicate the findings in a publicly available data set from the National Institute on Aging Late-Onset Alzheimer's Disease Family Study. Nested case-control genome-wide association study. The Washington Heights-Inwood Columbia Aging Project and the Estudio Familiar de Influencia Genetica de Alzheimer study. Five hundred forty-nine affected and 544 unaffected individuals of Caribbean Hispanic ancestry. The Illumina HumanHap 650Y chip for genotyping. Clinical diagnosis or pathologically confirmed diagnosis of LOAD. The strongest support for allelic association was for rs9945493 on 18q23 (P=1.7×10(-7)), but 22 additional single-nucleotide polymorphisms (SNPs) had a P value less than 9×10(-6) under 3 different analyses: unadjusted and stratified by the presence or absence of the APOE ε4 allele. Of these SNPs, 5 SNPs (rs4669573 and rs10197851 on 2p25.1; rs11711889 on 3q25.2; rs1117750 on 7p21.1; and rs7908652 on 10q23.1) were associated with LOAD in an independent cohort from the National Institute on Aging Late-Onset Alzheimer's Disease Family Study. We also replicated genetic associations for CLU, PICALM, and BIN1. Our genome-wide search of Caribbean Hispanic individuals identified several novel genetic variants associated with LOAD and replicated these associations in a white cohort. We also replicated associations in CLU, PICALM, and BIN1 in the Caribbean Hispanic cohort.

The biomarker-based validity of a brief-type diet history questionnaire for estimating eicosapentaenoic acid and docosahexaenoic acid intakes in pregnant Japanese women.

PubMed

Shiraishi, Mie; Haruna, Megumi; Matsuzaki, Masayo; Murayama, Ryoko; Sasaki, Satoshi

2015-01-01

Maternal docosahexaenoic acid (DHA) intakes is important for brain development in fetuses. Accurate assessment of EPA and DHA intakes is required in clinical settings to identify women with deficiency of these nutrients and provide an appropriate intervention for them. We examined the validity and reproducibility of a brief-type self-administered diet history questionnaire (BDHQ) for evaluating EPA and DHA intakes of pregnant Japanese women, to establish an easily administered dietary assessment tool. A total of 105 women in the second trimester and 102 women in the third trimester were studied at a university hospital in Tokyo, between November 2010 and February 2012. The reference values for the validation study were plasma concentrations of EPA and DHA. For the reproducibility study, 54 women completed the BDHQ twice, within a 4-week period in the second trimester. Energy-adjusted intakes of EPA, DHA, and EPA+DHA were significantly associated with the corresponding plasma concentrations (rs=0.354, rs=0.305, and rs=0.327 in the second trimester; rs=0.391, rs=0.316, and rs=0.358 in the third trimester, respectively). Intraclass correlation coefficients for the two-time BDHQ were 0.543 (EPA), 0.611 (DHA), and 0.581 (EPA+DHA). In the Bland-Altman plots, the intakes of EPA, DHA, and EPA+DHA in the two-time BDHQ showed that the values for most participants were in the accepted range of agreement. BDHQ has an acceptable validity level for assessing EPA and DHA intakes among Japanese women in the second and third trimesters.

Effect of laser parameters on surface roughness of laser modified tool steel after thermal cyclic loading

NASA Astrophysics Data System (ADS)

Lau Sheng, Annie; Ismail, Izwan; Nur Aqida, Syarifah

2018-03-01

This study presents the effects of laser parameters on the surface roughness of laser modified tool steel after thermal cyclic loading. Pulse mode Nd:YAG laser was used to perform the laser surface modification process on AISI H13 tool steel samples. Samples were then treated with thermal cyclic loading experiments which involved alternate immersion in molten aluminium (800°C) and water (27°C) for 553 cycles. A full factorial design of experiment (DOE) was developed to perform the investigation. Factors for the DOE are the laser parameter namely overlap rate (η), pulse repetition frequency (f PRF) and peak power (Ppeak ) while the response is the surface roughness after thermal cyclic loading. Results indicate the surface roughness of the laser modified surface after thermal cyclic loading is significantly affected by laser parameter settings.

Adventitious sounds identification and extraction using temporal-spectral dominance-based features.

PubMed

Jin, Feng; Krishnan, Sridhar Sri; Sattar, Farook

2011-11-01

Respiratory sound (RS) signals carry significant information about the underlying functioning of the pulmonary system by the presence of adventitious sounds (ASs). Although many studies have addressed the problem of pathological RS classification, only a limited number of scientific works have focused on the analysis of the evolution of symptom-related signal components in joint time-frequency (TF) plane. This paper proposes a new signal identification and extraction method for various ASs based on instantaneous frequency (IF) analysis. The presented TF decomposition method produces a noise-resistant high definition TF representation of RS signals as compared to the conventional linear TF analysis methods, yet preserving the low computational complexity as compared to those quadratic TF analysis methods. The discarded phase information in conventional spectrogram has been adopted for the estimation of IF and group delay, and a temporal-spectral dominance spectrogram has subsequently been constructed by investigating the TF spreads of the computed time-corrected IF components. The proposed dominance measure enables the extraction of signal components correspond to ASs from noisy RS signal at high noise level. A new set of TF features has also been proposed to quantify the shapes of the obtained TF contours, and therefore strongly, enhances the identification of multicomponents signals such as polyphonic wheezes. An overall accuracy of 92.4±2.9% for the classification of real RS recordings shows the promising performance of the presented method.

Global analysis of population stratification using a smart panel of 27 continental ancestry-informative SNPs.

PubMed

Jiang, Li; Wei, Yi-Liang; Zhao, Lei; Li, Na; Liu, Tao; Liu, Hai-Bo; Ren, Li-Jie; Li, Jiu-Ling; Hao, Hui-Fang; Li, Qing; Li, Cai-Xia

2018-07-01

Over the last decade, several panels of ancestry-informative markers have been proposed for the analysis of population genetic structure. The differentiation efficiency depends on the discriminatory ability of the included markers and the reference population coverage. We previously developed a small set of 27 autosomal single nucleotide polymorphisms (SNPs) for analyzing African, European, and East Asian ancestries. In the current study, we gathered a high-coverage reference database of 110 populations (10,350 individuals) from across the globe. The discrimination power of the panel was re-evaluated using four continental ancestry groups (as well as Indigenous Americans). We observed that all the 27 SNPs demonstrated stratified population specificity leading to a striking ancestral discrimination. Five markers (rs728404, rs7170869, rs2470102, rs1448485, and rs4789193) showed differences (δ > 0.3) in the frequency profiles between East Asian and Indigenous American populations. Ancestry components of all involved populations were accurately accessed compared with those from previous genome-wide analyses, thereafter achieved broadly population separation. Thus, our ancestral inference panel of a small number of highly informative SNPs in combination with a large-scale reference database provides a high-resolution in estimating ancestry compositions and distinguishing individual origins. We propose extensive usage in biomedical studies and forensics. Copyright © 2018 Elsevier B.V. All rights reserved.

Common Genetic Variants in ARNTL and NPAS2 and at Chromosome 12p13 are Associated with Objectively Measured Sleep Traits in the Elderly

PubMed Central

Evans, Daniel S.; Parimi, Neeta; Nievergelt, Caroline M.; Blackwell, Terri; Redline, Susan; Ancoli-Israel, Sonia; Orwoll, Eric S.; Cummings, Steven R.; Stone, Katie L.; Tranah, Gregory J.

2013-01-01

Study Objectives: To determine the association between common genetic variation in the clock gene pathway and objectively measured acti-graphic sleep and activity rhythm traits. Design: Genetic association study in two population-based cohorts of elderly participants: the Study of Osteoporotic Fractures (SOF) and the Osteoporotic Fractures in Men (MrOS) study. Setting: Population-based. Participants: SOF participants (n = 1,407, 100% female, mean age 84 years) and MrOS participants (n = 2,527, 100% male, mean age 77 years) with actigraphy and genotype data. Interventions: N/A. Measurements and Results: Common genetic variation in 30 candidate genes was captured using 529 single nucleotide polymorphisms (SNPs). Sleep and activity rhythm traits were objectively measured using wrist actigraphy. In a region of high linkage disequilibrium on chromosome 12p13 containing the candidate gene GNB3, the rs1047776 A allele and the rs2238114 C allele were significantly associated with higher wake after sleep onset (meta-analysis: rs1047776 PADD = 2 × 10-5, rs2238114 PADD = 5 × 10-5) and lower LRRC23 gene expression (rs1047776: ρ = -0.22, P = 0.02; rs2238114: ρ = -0.50, P = 5 × 10-8). In MrOS participants, SNPs in ARNTL and NPAS2, genes coding for binding partners, were associated with later sleep and wake onset time (sleep onset time: ARNTL rs3816358 P2DF = 1 × 10-4, NPAS2 rs3768984 P2DF = 5 × 10-5; wake onset time: rs3816358 P2DF = 3 × 10-3, rs3768984 P2DF = 2 × 10-4) and the SNP interaction was significant (sleep onset time PINT = 0.003, wake onset time PINT = 0.001). A SNP association in the CLOCK gene replicated in the MrOS cohort, and rs3768984 was associated with sleep duration in a previously reported study. Cluster analysis identified four clusters of genetic associations. Conclusions: These findings support a role for common genetic variation in clock genes in the regulation of inter-related sleep traits in the elderly. Citation: Evans DS; Parimi N; Nievergelt CM; Blackwell T; Redline S; Ancoli-Israel S; Orwoll ES; Cummings SR; Stone KL; Tranah GJ. Common genetic variants in ARNTL and NPAS2 and at chromosome 12p13 are associated with objectively measured sleep traits in the elderly. SLEEP 2013;36(3):431-446. PMID:23449886

Local Table Condensation in Rough Set Approach for Jumping Emerging Pattern Induction

NASA Astrophysics Data System (ADS)

Terlecki, Pawel; Walczak, Krzysztof

This paper extends the rough set approach for JEP induction based on the notion of a condensed decision table. The original transaction database is transformed to a relational form and patterns are induced by means of local reducts. The transformation employs an item aggregation obtained by coloring a graph that re0ects con0icts among items. For e±ciency reasons we propose to perform this preprocessing locally, i.e. at the transaction level, to achieve a higher dimensionality gain. Special maintenance strategy is also used to avoid graph rebuilds. Both global and local approach have been tested and discussed for dense and synthetically generated sparse datasets.

Modification of surface morphology of Ti6Al4V alloy manufactured by Laser Sintering

NASA Astrophysics Data System (ADS)

Draganovská, Dagmar; Ižariková, Gabriela; Guzanová, Anna; Brezinová, Janette; Koncz, Juraj

2016-06-01

The paper deals with the evaluation of relation between roughness parameters of Ti6Al4V alloy produced by DMLS and modified by abrasive blasting. There were two types of blasting abrasives that were used - white corundum and Zirblast at three levels of air pressure. The effect of pressure on the value of individual roughness parameters and an influence of blasting media on the parameters for samples blasted by white corundum and Zirblast were evaluated by ANOVA. Based on the measured values, the correlation matrix was set and the standard of correlation statistic importance between the monitored parameters was determined from it. The correlation coefficient was also set.

Exploring KM Features of High-Performance Companies

NASA Astrophysics Data System (ADS)

Wu, Wei-Wen

2007-12-01

For reacting to an increasingly rival business environment, many companies emphasize the importance of knowledge management (KM). It is a favorable way to explore and learn KM features of high-performance companies. However, finding out the critical KM features of high-performance companies is a qualitative analysis problem. To handle this kind of problem, the rough set approach is suitable because it is based on data-mining techniques to discover knowledge without rigorous statistical assumptions. Thus, this paper explored KM features of high-performance companies by using the rough set approach. The results show that high-performance companies stress the importance on both tacit and explicit knowledge, and consider that incentives and evaluations are the essentials to implementing KM.

Mass Spectrometry and Fourier Transform Infrared Spectroscopy for Analysis of Biological Materials

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

Anderson, Timothy J.

Time-of-flight mass spectrometry along with statistical analysis was utilized to study metabolic profiles among rats fed resistant starch (RS) diets. Fischer 344 rats were fed four starch diets consisting of 55% (w/w, dbs) starch. A control starch diet consisting of corn starch was compared against three RS diets. The RS diets were high-amylose corn starch (HA7), HA7 chemically modified with octenyl succinic anhydride, and stearic-acid-complexed HA7 starch. A subgroup received antibiotic treatment to determine if perturbations in the gut microbiome were long lasting. A second subgroup was treated with azoxymethane (AOM), a carcinogen. At the end of the eight weekmore » study, cecal and distal-colon contents samples were collected from the sacrificed rats. Metabolites were extracted from cecal and distal colon samples into acetonitrile. The extracts were then analyzed on an accurate-mass time-of-flight mass spectrometer to obtain their metabolic profile. The data were analyzed using partial least-squares discriminant analysis (PLS-DA). The PLS-DA analysis utilized a training set and verification set to classify samples within diet and treatment groups. PLS-DA could reliably differentiate the diet treatments for both cecal and distal colon samples. The PLS-DA analyses of the antibiotic and no antibiotic treated subgroups were well classified for cecal samples and modestly separated for distal-colon samples. PLS-DA analysis had limited success separating distal colon samples for rats given AOM from those not treated; the cecal samples from AOM had very poor classification. Mass spectrometry profiling coupled with PLS-DA can readily classify metabolite differences among rats given RS diets.« less

High-resolution time-of-flight mass spectrometry fingerprinting of metabolites from cecum and distal colon contents of rats fed resistant starch

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

Anderson, Timothy J.; Jones, Roger W.; Ai, Yongfeng

Time-of-flight mass spectrometry along with statistical analysis was utilized to study metabolic profiles among rats fed resistant starch (RS) diets. Fischer 344 rats were fed four starch diets consisting of 55 % (w/w, dbs) starch. A control starch diet consisting of corn starch was compared against three RS diets. The RS diets were high-amylose corn starch (HA7), HA7 chemically modified with octenyl succinic anhydride, and stearic-acid-complexed HA7 starch. A subgroup received antibiotic treatment to determine if perturbations in the gut microbiome were long lasting. A second subgroup was treated with azoxymethane (AOM), a carcinogen. At the end of the 8-weekmore » study, cecal and distal colon content samples were collected from the sacrificed rats. Metabolites were extracted from cecal and distal colon samples into acetonitrile. The extracts were then analyzed on an accurate-mass time-of-flight mass spectrometer to obtain their metabolic profile. The data were analyzed using partial least-squares discriminant analysis (PLS-DA). The PLS-DA analysis utilized a training set and verification set to classify samples within diet and treatment groups. PLS-DA could reliably differentiate the diet treatments for both cecal and distal colon samples. The PLS-DA analyses of the antibiotic and no antibiotic-treated subgroups were well classified for cecal samples and modestly separated for distal colon samples. PLS-DA analysis had limited success separating distal colon samples for rats given AOM from those not treated; the cecal samples from AOM had very poor classification. Mass spectrometry profiling coupled with PLS-DA can readily classify metabolite differences among rats given RS diets.« less

Increasing expenditure on health care incurred by diabetic subjects in a developing country: a study from India.

PubMed

Ramachandran, Ambady; Ramachandran, Shobhana; Snehalatha, Chamukuttan; Augustine, Christina; Murugesan, Narayanasamy; Viswanathan, Vijay; Kapur, Anil; Williams, Rhys

2007-02-01

This study aimed to assess the direct cost incurred by diabetic subjects who were in different income groups in urban and rural India, as well as to examine the changing trends of costs in the urban setting from 1998 to 2005. A total of 556 diabetic subjects from various urban and rural regions of seven Indian states were enrolled. A brief uniform coded questionnaire (24 items) on direct cost was used. Annual family income was higher in urban subjects (rupees [Rs] 100,000 or $2,273) than in the rural subjects (Rs 36,000 or $818) (P < 0.001). Total median expenditure on health care was Rs 10,000 ($227) in urban and Rs 6,260 ($142) in rural (P < 0.001) subjects. Treatment costs increased with duration of diabetes, presence of complications, hospitalization, surgery, insulin therapy, and urban setting. Lower-income groups spent a higher proportion of their income on diabetes care (urban poor 34% and rural poor 27%). After accounting for inflation, a secular increase of 113% was observed in the total expenses between 1998 and 2005 in the urban population. The highest increase in percentage of household income devoted to diabetes care was in the lowest economic group (34% of income in 1998 vs. 24.5% in 2005) (P < 0.01). There was a significant improvement in urban subjects in medical reimbursement from 2% (1998) to 21.3% (2005). Urban and rural diabetic subjects spend a large percentage of income on diabetes management. The economic burden on urban families in developing countries is rising, and the total direct cost has doubled from 1998 to 2005.

Changes in Behaviour Symptoms of Patients with Attention Deficit/Hyperactivity Disorder during Treatment: Observation from Different Informants.

PubMed

Wang, Liang-Jen; Chen, Chih-Ken; Huang, Yu-Shu

2013-03-01

The aim of this study was to determine changes in behaviour among patients with attention deficit/hyperactivity disorder (ADHD) by different informants during treatment in the clinical setting. Seventy-nine patients with ADHD were recruited. They completed 12-months of treatment with oral short-acting methylphenidate, two-to-three times per day, at a dose of 0.3-1.0 mg/kg. Among the 79 patients (mean age, 9.1±1.9 years), 39 were classified as the ADHD-C/H type (hyperactive-impulsive type and combined type) and 40 as the ADHD-I type (inattentive type). At baseline, and after 12 months, their behaviour was assessed using the Child Behaviour Checklist (CBCL), Teacher's Report Form (TRF), ADHD Rating Scale (ADHD-RS), and Clinical Global Impression-Severity (CGI-S). Patients classified as the ADHD-C/H type had higher scores on three CBCL subscales, on the ADHD-RS and CGI-S compared to the ADHD-I type patients. After 12-months of treatment, for all patients, there were significant improvements in the four subscales of the TRF as well as the ADHD-RS and CGI-S scores, but not on the CBCL. In addition, the patients with the ADHD-C/H type had greater improvements on the four subscales of the TRF after treatment. However, there were no differences noted on the CBCL, ADHD-RS and CGI-S. The results of this study showed that during treatment, in the clinical setting, there are different assessments of behaviour symptoms, associated with ADHD, reported by different informants. Assessments of behaviour profiles from multiple informants are crucial for establishing a fuller picture of patients with ADHD.

Informed genome-wide association analysis with family history as a secondary phenotype identifies novel loci of lung cancer.

PubMed

Poirier, Julia G; Brennan, Paul; McKay, James D; Spitz, Margaret R; Bickeböller, Heike; Risch, Angela; Liu, Geoffrey; Le Marchand, Loic; Tworoger, Shelley; McLaughlin, John; Rosenberger, Albert; Heinrich, Joachim; Brüske, Irene; Muley, Thomas; Henderson, Brian E; Wilkens, Lynne R; Zong, Xuchen; Li, Yafang; Hao, Ke; Timens, Wim; Bossé, Yohan; Sin, Don D; Obeidat, Ma'en; Amos, Christopher I; Hung, Rayjean J

2015-03-01

Lung cancer is the leading cause of cancer death worldwide. Although several genetic variants associated with lung cancer have been identified in the past, stringent selection criteria of genome-wide association studies (GWAS) can lead to missed variants. The objective of this study was to uncover missed variants by using the known association between lung cancer and first-degree family history of lung cancer to enrich the variant prioritization for lung cancer susceptibility regions. In this two-stage GWAS study, we first selected a list of variants associated with both lung cancer and family history of lung cancer in four GWAS (3,953 cases, 4,730 controls), then replicated our findings for 30 variants in a meta-analysis of four additional studies (7,510 cases, 7,476 controls). The top ranked genetic variant rs12415204 in chr10q23.33 encoding FFAR4 in the Discovery set was validated in the Replication set with an overall OR of 1.09 (95% CI=1.04, 1.14, P=1.63×10(-4)). When combining the two stages of the study, the strongest association was found in rs1158970 at Ch4p15.2 encoding KCNIP4 with an OR of 0.89 (95% CI=0.85, 0.94, P=9.64×10(-6)). We performed a stratified analysis of rs12415204 and rs1158970 across all eight studies by age, gender, smoking status, and histology, and found consistent results across strata. Four of the 30 replicated variants act as expression quantitative trait loci (eQTL) sites in 1,111 nontumor lung tissues and meet the genome-wide 10% FDR threshold. © 2015 Wiley Periodicals, Inc.

Effect of sputtering atmosphere on the characteristics of ZrOx resistive switching memory

NASA Astrophysics Data System (ADS)

He, Pin; Ye, Cong; Wu, Jiaji; Wei, Wei; Wei, Xiaodi; Wang, Hao; Zhang, Rulin; Zhang, Li; Xia, Qing; Wang, Hanbin

2017-05-01

A ZrOx switching layer with different oxygen content for TiN/ZrOx/Pt resistive switching (RS) memory was prepared by magnetron sputtering in different atmospheres such as N2/Ar mixture, O2/Ar mixture as well as pure Ar. The morphology, structure and RS characteristics were systemically investigated and it was found that the RS performance is highly dependent on the sputtering atmosphere. For the memory device sputtered in N2/Ar mixture, with 8.06% nitrogen content in the ZrOx switching layer, the highest uniformity with smallest distribution of V set and high resistance states (HRS)/low resistance states (LRS) values were achieved. By analyzing the current conduction mechanisms combined with possible RS mechanisms for three devices, we deduce that for the device with a ZrOx layer sputtered in N2/Ar mixture, oxygen ions (O2-), which are decisive to the disruption/formation of the conductive filament, will gather around the tip of the filament due to the existence of doping nitrogen, and lead to the reduction of O2- migration randomness in the operation process, so that the uniformity of the N-doped ZrOx device can be improved.

Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main driver of the association signal.

PubMed

Parra, Esteban J; Mazurek, Andrew; Gignoux, Christopher R; Sockell, Alexandra; Agostino, Michael; Morris, Andrew P; Petty, Lauren E; Hanis, Craig L; Cox, Nancy J; Valladares-Salgado, Adan; Below, Jennifer E; Cruz, Miguel

2017-01-01

We carried out an admixture mapping study of lipid traits in two samples from Mexico City. Native American locus ancestry was significantly associated with triglyceride levels in a broad region of chromosome 11 overlapping the BUD13, ZNF259 and APOA5 genes. In our fine-mapping analysis of this region using dense genome-wide data, rs964184 is the only marker included in the 99% credible set of SNPs, providing strong support for rs964184 as the causal variant within this region. The frequency of the allele associated with increased triglyceride concentrations (rs964184-G) is between 30-40% higher in Native American populations from Mexico than in European populations. The evidence currently available for this variant indicates that it may be exerting its effect through three potential mechanisms: 1) modification of enhancer activity, 2) regulation of the expression of several genes in cis and/or trans, or 3) modification of the methylation patterns of the promoter of the APOA5 gene.

Candidate genes for COPD in two large data sets.

PubMed

Bakke, P S; Zhu, G; Gulsvik, A; Kong, X; Agusti, A G N; Calverley, P M A; Donner, C F; Levy, R D; Make, B J; Paré, P D; Rennard, S I; Vestbo, J; Wouters, E F M; Anderson, W; Lomas, D A; Silverman, E K; Pillai, S G

2011-02-01

Lack of reproducibility of findings has been a criticism of genetic association studies on complex diseases, such as chronic obstructive pulmonary disease (COPD). We selected 257 polymorphisms of 16 genes with reported or potential relationships to COPD and genotyped these variants in a case-control study that included 953 COPD cases and 956 control subjects. We explored the association of these polymorphisms to three COPD phenotypes: a COPD binary phenotype and two quantitative traits (post-bronchodilator forced expiratory volume in 1 s (FEV₁) % predicted and FEV₁/forced vital capacity (FVC)). The polymorphisms significantly associated to these phenotypes in this first study were tested in a second, family-based study that included 635 pedigrees with 1,910 individuals. Significant associations to the binary COPD phenotype in both populations were seen for STAT1 (rs13010343) and NFKBIB/SIRT2 (rs2241704) (p<0.05). Single-nucleotide polymorphisms rs17467825 and rs1155563 of the GC gene were significantly associated with FEV₁ % predicted and FEV₁/FVC, respectively, in both populations (p<0.05). This study has replicated associations to COPD phenotypes in the STAT1, NFKBIB/SIRT2 and GC genes in two independent populations, the associations of the former two genes representing novel findings.

Cerebellar Functional Parcellation Using Sparse Dictionary Learning Clustering.

PubMed

Wang, Changqing; Kipping, Judy; Bao, Chenglong; Ji, Hui; Qiu, Anqi

2016-01-01

The human cerebellum has recently been discovered to contribute to cognition and emotion beyond the planning and execution of movement, suggesting its functional heterogeneity. We aimed to identify the functional parcellation of the cerebellum using information from resting-state functional magnetic resonance imaging (rs-fMRI). For this, we introduced a new data-driven decomposition-based functional parcellation algorithm, called Sparse Dictionary Learning Clustering (SDLC). SDLC integrates dictionary learning, sparse representation of rs-fMRI, and k-means clustering into one optimization problem. The dictionary is comprised of an over-complete set of time course signals, with which a sparse representation of rs-fMRI signals can be constructed. Cerebellar functional regions were then identified using k-means clustering based on the sparse representation of rs-fMRI signals. We solved SDLC using a multi-block hybrid proximal alternating method that guarantees strong convergence. We evaluated the reliability of SDLC and benchmarked its classification accuracy against other clustering techniques using simulated data. We then demonstrated that SDLC can identify biologically reasonable functional regions of the cerebellum as estimated by their cerebello-cortical functional connectivity. We further provided new insights into the cerebello-cortical functional organization in children.

Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main driver of the association signal

PubMed Central

Mazurek, Andrew; Sockell, Alexandra; Morris, Andrew P.; Petty, Lauren E.; Hanis, Craig L.; Cox, Nancy J.; Cruz, Miguel

2017-01-01

We carried out an admixture mapping study of lipid traits in two samples from Mexico City. Native American locus ancestry was significantly associated with triglyceride levels in a broad region of chromosome 11 overlapping the BUD13, ZNF259 and APOA5 genes. In our fine-mapping analysis of this region using dense genome-wide data, rs964184 is the only marker included in the 99% credible set of SNPs, providing strong support for rs964184 as the causal variant within this region. The frequency of the allele associated with increased triglyceride concentrations (rs964184-G) is between 30–40% higher in Native American populations from Mexico than in European populations. The evidence currently available for this variant indicates that it may be exerting its effect through three potential mechanisms: 1) modification of enhancer activity, 2) regulation of the expression of several genes in cis and/or trans, or 3) modification of the methylation patterns of the promoter of the APOA5 gene. PMID:28245265

Association study of IL10 and IL23R-IL12RB2 in Iranian patients with Behçet's disease.

PubMed

Xavier, Joana M; Shahram, Farhad; Davatchi, Fereydoun; Rosa, Alexandra; Crespo, Jorge; Abdollahi, Bahar Sadeghi; Nadji, Abdolhadi; Jesus, Gorete; Barcelos, Filipe; Patto, José Vaz; Shafiee, Niloofar Mojarad; Ghaderibarim, Fahmida; Oliveira, Sofia A

2012-08-01

Independent replication of the findings from genome-wide association studies (GWAS) remains the gold standard for results validation. Our aim was to test the association of Behçet's disease (BD) with the interleukin-10 gene (IL10) and the IL-23 receptor-IL-12 receptor β2 (IL23R-IL12RB2) locus, each of which has been previously identified as a risk factor for BD in 2 different GWAS. Six haplotype-tagging single-nucleotide polymorphisms (SNPs) in IL10 and 42 in IL23R-IL12RB2 were genotyped in 973 Iranian patients with BD and 637 non-BD controls. Population stratification was assessed using a panel of 86 ancestry-informative markers. Subtle evidence of population stratification was found in our data set. In IL10, rs1518111 was nominally associated with BD before and after adjustment for population stratification (odds ratio [OR] for T allele 1.20, 95% confidence interval [95% CI] 1.02-1.40, unadjusted P [P(unadj) ] = 2.53 × 10(-2) ; adjusted P [P(adj) ] = 1.43 × 10(-2) ), and rs1554286 demonstrated a trend toward association (P(unadj) = 6.14 × 10(-2) ; P(adj) = 3.21 × 10(-2) ). Six SNPs in IL23R-IL12RB2 were found to be associated with BD after Bonferroni correction for multiple testing, the most significant of which were rs17375018 (OR for G allele 1.51, 95% CI 1.27-1.78, P(unadj) = 1.93 × 10(-6) ), rs7517847 (OR for T allele 1.48, 95% CI 1.26-1.74, P(unadj) = 1.23 × 10(-6) ), and rs924080 (OR for T allele 1.29, 95% CI 1.20-1.39, P = 1.78 × 10(-5) ). SNPs rs10489629, rs1343151, and rs1495965 were also significantly associated with BD in all tests performed. Results of meta-analyses of our data combined with data from other populations further confirmed the role of rs1518111, rs17375018, rs7517847, and rs924080 in the risk of BD, but no epistatic interactions between IL10 and IL23R-IL12RB2 were detected. Results of imputation analysis highlighted the importance of IL23R regulatory regions in the susceptibility to BD. These findings independently confirm, extend, and refine the association of BD with IL10 and IL23R-IL12RB2. These associations warrant further validation and investigation in patients with BD, as they may have implications for the development of novel therapies (e.g., immunosuppressive therapy targeted at IL-23p19). Copyright © 2012 by the American College of Rheumatology.

Comparative histomorphometry and resonance frequency analysis of implants with moderately rough surfaces in a loaded animal model.

PubMed

Al-Nawas, B; Groetz, K A; Goetz, H; Duschner, H; Wagner, W

2008-01-01

Test of favourable conditions for osseointegration with respect to optimum bone-implant contact (BIC) in a loaded animal model. The varied parameters were surface roughness and surface topography of commercially available dental implants. Thirty-two implants of six types of macro and microstructure were included in the study (total 196). The different types were: minimally rough control: Branemark machined Mk III; oxidized surface: TiUnite MkIII and MkIV; ZL Ticer; blasted and etched surface: Straumann SLA; rough control: titanium plasma sprayed (TPS). Sixteen beagle dogs were implanted with the whole set of the above implants. After a healing period of 8 weeks, implants were loaded for 3 months. For the evaluation of the BIC areas, adequately sectioned biopsies were visualized by subsurface scans with confocal laser scanning microscopy (CLSM). The primary statistical analysis testing BIC of the moderately rough implants (mean 56.1+/-13.0%) vs. the minimally rough and the rough controls (mean 53.9+/-11.2%) does not reveal a significant difference (P=0.57). Mean values of 50-70% BIC were found for all implant types. Moderately rough oxidized implants show a median BIC, which is 8% higher than their minimally rough turned counterpart. The intraindividual difference between the TPS and the blasted and etched counterparts revealed no significant difference. The turned and the oxidized implants show median values of the resonance frequency [implant stability quotients (ISQ)] over 60; the nonself-tapping blasted and etched and TPS implants show median values below 60. In conclusion, the benefit of rough surfaces relative to minimally rough ones in this loaded animal model was confirmed histologically. The comparison of different surface treatment modalities revealed no significant differences between the modern moderately rough surfaces. Resonance frequency analysis seems to be influenced in a major part by the transducer used, thus prohibiting the comparison of different implant systems.

Use of Satellite Technology in Local Television News.

ERIC Educational Resources Information Center

Lacy, Stephen; And Others

1988-01-01

Assesses the state of satellite news gathering (SNG) among commercial broadcast, nonsatellite stations in the United States. Finds that 75 percent of the stations set SNG feeds but that only 50 percent have their own SNG equipment. (RS)

Analysis of accuracy in photogrammetric roughness measurements

NASA Astrophysics Data System (ADS)

Olkowicz, Marcin; Dąbrowski, Marcin; Pluymakers, Anne

2017-04-01

Regarding permeability, one of the most important features of shale gas reservoirs is the effective aperture of cracks opened during hydraulic fracturing, both propped and unpropped. In a propped fracture, the aperture is controlled mostly by proppant size and its embedment, and fracture surface roughness only has a minor influence. In contrast, in an unpropped fracture aperture is controlled by the fracture roughness and the wall displacement. To measure fracture surface roughness, we have used the photogrammetric method since it is time- and cost-efficient. To estimate the accuracy of this method we compare the photogrammetric measurements with reference measurements taken with a White Light Interferometer (WLI). Our photogrammetric setup is based on high resolution 50 Mpx camera combined with a focus stacking technique. The first step for photogrammetric measurements is to determine the optimal camera positions and lighting. We compare multiple scans of one sample, taken with different settings of lighting and camera positions, with the reference WLI measurement. The second step is to perform measurements of all studied fractures with the parameters that produced the best results in the first step. To compare photogrammetric and WLI measurements we regrid both data sets onto a regular 10 μm grid and determined the best fit, followed by a calculation of the difference between the measurements. The first results of the comparison show that for 90 % of measured points the absolute vertical distance between WLI and photogrammetry is less than 10 μm, while the mean absolute vertical distance is 5 μm. This proves that our setup can be used for fracture roughness measurements in shales.

Counterintuitive effects of substrate roughness on PDCs

NASA Astrophysics Data System (ADS)

Andrews, B. J.; Manga, M.

2012-12-01

We model dilute pyroclastic density currents (PDCs) using scaled, warm, particle-laden density currents in a 6 m long, 0.6 m wide, 1.8 m tall air-filled tank. In this set of experiments, we run currents over substrates with characteristic roughness scales, hr, ranging over ~3 orders of magnitude from smooth, through 250 μm sandpaper, 0.1-, 1-, 2-, 5-, and 10 cm hemispheres. As substrate roughness increases, runout distance increases until a critical roughness height, hrc, is reached; further increases in roughness height decrease runout. The critical roughness height appears to be 0.25-0.5 htb, the thickness of the turbulent lower layer of the density currents. The dependence of runout on hr is most likely the result of increases in substrate roughness decreasing the average current velocity and converting that energy into increased turbulence intensity. Small values of hr thus result in increased runout as sedimentation is inhibited by the increased turbulence intensity. At larger values of hr current behavior is controlled by much larger decreases in average current velocity, even though sedimentation decreases. Scaling our experiments up to the size of real volcanic eruptions suggests that landscapes must have characteristic roughness hr>10 m to reduce the runout of natural PDCs, smaller roughness scales can increase runout. Comparison of relevant bulk (Reynolds number, densimetric and thermal Richardson numbers, excess buoyant thermal energy density) and turbulent (Stokes and settling numbers) between our experiments and natural dilute PDCs indicates that we are accurately modeling at least the large scale behaviors and dynamics of dilute PDCs.

Identifying Degenerative Brain Disease Using Rough Set Classifier Based on Wavelet Packet Method.

PubMed

Cheng, Ching-Hsue; Liu, Wei-Xiang

2018-05-28

Population aging has become a worldwide phenomenon, which causes many serious problems. The medical issues related to degenerative brain disease have gradually become a concern. Magnetic Resonance Imaging is one of the most advanced methods for medical imaging and is especially suitable for brain scans. From the literature, although the automatic segmentation method is less laborious and time-consuming, it is restricted in several specific types of images. In addition, hybrid techniques segmentation improves the shortcomings of the single segmentation method. Therefore, this study proposed a hybrid segmentation combined with rough set classifier and wavelet packet method to identify degenerative brain disease. The proposed method is a three-stage image process method to enhance accuracy of brain disease classification. In the first stage, this study used the proposed hybrid segmentation algorithms to segment the brain ROI (region of interest). In the second stage, wavelet packet was used to conduct the image decomposition and calculate the feature values. In the final stage, the rough set classifier was utilized to identify the degenerative brain disease. In verification and comparison, two experiments were employed to verify the effectiveness of the proposed method and compare with the TV-seg (total variation segmentation) algorithm, Discrete Cosine Transform, and the listing classifiers. Overall, the results indicated that the proposed method outperforms the listing methods.

On the use of published radiobiological parameters and the evaluation of NTCP models regarding lung pneumonitis in clinical breast radiotherapy.

PubMed

Svolos, Patricia; Tsougos, Ioannis; Kyrgias, Georgios; Kappas, Constantine; Theodorou, Kiki

2011-04-01

In this study we sought to evaluate and accent the importance of radiobiological parameter selection and implementation to the normal tissue complication probability (NTCP) models. The relative seriality (RS) and the Lyman-Kutcher-Burman (LKB) models were studied. For each model, a minimum and maximum set of radiobiological parameter sets was selected from the overall published sets applied in literature and a theoretical mean parameter set was computed. In order to investigate the potential model weaknesses in NTCP estimation and to point out the correct use of model parameters, these sets were used as input to the RS and the LKB model, estimating radiation induced complications for a group of 36 breast cancer patients treated with radiotherapy. The clinical endpoint examined was Radiation Pneumonitis. Each model was represented by a certain dose-response range when the selected parameter sets were applied. Comparing the models with their ranges, a large area of coincidence was revealed. If the parameter uncertainties (standard deviation) are included in the models, their area of coincidence might be enlarged, constraining even greater their predictive ability. The selection of the proper radiobiological parameter set for a given clinical endpoint is crucial. Published parameter values are not definite but should be accompanied by uncertainties, and one should be very careful when applying them to the NTCP models. Correct selection and proper implementation of published parameters provides a quite accurate fit of the NTCP models to the considered endpoint.

Effects of setting under air pressure on the number of surface pores and irregularities of dental investment materials.

PubMed

Tourah, Anita; Moshaverinia, Alireza; Chee, Winston W

2014-02-01

Surface roughness and irregularities are important properties of dental investment materials that can affect the fit of a restoration. Whether setting under air pressure affects the surface irregularities of gypsum-bonded and phosphate-bonded investment materials is unknown. The purpose of this study was to investigate the effect of air pressure on the pore size and surface irregularities of investment materials immediately after pouring. Three dental investments, 1 gypsum-bonded investment and 2 phosphate-bonded investments, were investigated. They were vacuum mixed according to the manufacturers' recommendations, then poured into a ringless casting system. The prepared specimens were divided into 2 groups: 1 bench setting and the other placed in a pressure pot at 172 kPa. After 45 minutes of setting, the rings were removed and the investments were cut at a right angle to the long axis with a diamond disk. The surfaces of the investments were steam cleaned, dried with an air spray, and observed with a stereomicroscope. A profilometer was used to evaluate the surface roughness (μm) of the castings. The number of surface pores was counted for 8 specimens from each group and the means and standard deviations were reported. Two-way ANOVA was used to compare the data. Specimens that set under atmospheric air pressure had a significantly higher number of pores than specimens that set under increased pressure (P<.05). No statistically significant differences for surface roughness were found (P=.078). Also, no significant difference was observed among the 3 different types of materials tested (P>.05). Specimens set under positive pressure in a pressure chamber presented fewer surface bubbles than specimens set under atmospheric pressure. Positive pressure is effective and, therefore, is recommended for both gypsum-bonded and phosphate-bonded investment materials. Copyright © 2014 Editorial Council for the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

Concatenated Coding Using Trellis-Coded Modulation

NASA Technical Reports Server (NTRS)

Thompson, Michael W.

1997-01-01

In the late seventies and early eighties a technique known as Trellis Coded Modulation (TCM) was developed for providing spectrally efficient error correction coding. Instead of adding redundant information in the form of parity bits, redundancy is added at the modulation stage thereby increasing bandwidth efficiency. A digital communications system can be designed to use bandwidth-efficient multilevel/phase modulation such as Amplitude Shift Keying (ASK), Phase Shift Keying (PSK), Differential Phase Shift Keying (DPSK) or Quadrature Amplitude Modulation (QAM). Performance gain can be achieved by increasing the number of signals over the corresponding uncoded system to compensate for the redundancy introduced by the code. A considerable amount of research and development has been devoted toward developing good TCM codes for severely bandlimited applications. More recently, the use of TCM for satellite and deep space communications applications has received increased attention. This report describes the general approach of using a concatenated coding scheme that features TCM and RS coding. Results have indicated that substantial (6-10 dB) performance gains can be achieved with this approach with comparatively little bandwidth expansion. Since all of the bandwidth expansion is due to the RS code we see that TCM based concatenated coding results in roughly 10-50% bandwidth expansion compared to 70-150% expansion for similar concatenated scheme which use convolution code. We stress that combined coding and modulation optimization is important for achieving performance gains while maintaining spectral efficiency.

Cloud Detection Using Measured and Modeled State Parameters

NASA Technical Reports Server (NTRS)

Yi, Y.; Minnis, P.; Huang, J.; Ayers, J. K.; Doelling, D. R.; Khaiyer, M. M.; Nordeen, M. L.

2004-01-01

In this study, hourly RUC analyses were used to examine the differences between RH and temperature values from RUC reanalysis data and from radiosonde atmospheric profiles obtained at the ARM SCF. The results show that the temperature observations from the SONDE and RUC are highly correlated. The RHs are also well-correlated, but the SONDE values generally exceed those from RUC. Inside cloud layers, the RH from RUC is 2-14% lower than the RH from SONDE for all RUC layers. Although the layer mean RH within clouds is much greater than the layer mean RH outside cloud or in the clear-sky, RH thresholds chosen as a function of temperature can more accurately diagnose cloud occurrence for either dataset. For overcast clouds, it was found that the 50% probability RH threshold for diagnosing a cloud, within a given upper tropospheric layer is roughly 90% for the Vaisala RS80-15LH radisonde and 80% for RUC data. While for the partial cloud (cloud amount is less than 90%), the RH thresholds of SONDE are close to RUC for a given probability in upper tropospheric layers. The probabilities of detecting clouds at a given RH and temperature should be useful for a variety of application such as the development of new cloud parameterizations or for estimating the vertical profile of cloudiness underneath a given cloud observed from the satellite to construct a 3-D cloud data set for computing atmospheric radiative heating profiles or determining potential aircraft icing conditions.

Radiative transfer simulations of the two-dimensional ocean glint reflectance and determination of the sea surface roughness.

PubMed

Lin, Zhenyi; Li, Wei; Gatebe, Charles; Poudyal, Rajesh; Stamnes, Knut

2016-02-20

An optimized discrete-ordinate radiative transfer model (DISORT3) with a pseudo-two-dimensional bidirectional reflectance distribution function (BRDF) is used to simulate and validate ocean glint reflectances at an infrared wavelength (1036 nm) by matching model results with a complete set of BRDF measurements obtained from the NASA cloud absorption radiometer (CAR) deployed on an aircraft. The surface roughness is then obtained through a retrieval algorithm and is used to extend the simulation into the visible spectral range where diffuse reflectance becomes important. In general, the simulated reflectances and surface roughness information are in good agreement with the measurements, and the diffuse reflectance in the visible, ignored in current glint algorithms, is shown to be important. The successful implementation of this new treatment of ocean glint reflectance and surface roughness in DISORT3 will help improve glint correction algorithms in current and future ocean color remote sensing applications.

Radiative Transfer Simulations of the Two-Dimensional Ocean Glint Reflectance and Determination of the Sea Surface Roughness

NASA Technical Reports Server (NTRS)

Lin, Zhenyi; Li, Wei; Gatebe, Charles; Poudyal, Rajesh; Stamnes, Knut

2016-01-01

An optimized discrete-ordinate radiative transfer model (DISORT3) with a pseudo-two-dimensional bidirectional reflectance distribution function (BRDF) is used to simulate and validate ocean glint reflectances at an infrared wavelength (1036 nm) by matching model results with a complete set of BRDF measurements obtained from the NASA cloud absorption radiometer (CAR) deployed on an aircraft. The surface roughness is then obtained through a retrieval algorithm and is used to extend the simulation into the visible spectral range where diffuse reflectance becomes important. In general, the simulated reflectances and surface roughness information are in good agreement with the measurements, and the diffuse reflectance in the visible, ignored in current glint algorithms, is shown to be important. The successful implementation of this new treatment of ocean glint reflectance and surface roughness in DISORT3 will help improve glint correction algorithms in current and future ocean color remote sensing applications.

Quantitative three-dimensional ice roughness from scanning electron microscopy

NASA Astrophysics Data System (ADS)

Butterfield, Nicholas; Rowe, Penny M.; Stewart, Emily; Roesel, David; Neshyba, Steven

2017-03-01

We present a method for inferring surface morphology of ice from scanning electron microscope images. We first develop a novel functional form for the backscattered electron intensity as a function of ice facet orientation; this form is parameterized using smooth ice facets of known orientation. Three-dimensional representations of rough surfaces are retrieved at approximately micrometer resolution using Gauss-Newton inversion within a Bayesian framework. Statistical analysis of the resulting data sets permits characterization of ice surface roughness with a much higher statistical confidence than previously possible. A survey of results in the range -39°C to -29°C shows that characteristics of the roughness (e.g., Weibull parameters) are sensitive not only to the degree of roughening but also to the symmetry of the roughening. These results suggest that roughening characteristics obtained by remote sensing and in situ measurements of atmospheric ice clouds can potentially provide more facet-specific information than has previously been appreciated.

Cleaning of optical surfaces by capacitively coupled RF discharge plasma

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

Yadav, P. K., E-mail: praveenyadav@rrcat.gov.in; Rai, S. K.; Nayak, M.

2014-04-24

In this paper, we report cleaning of carbon capped molybdenum (Mo) thin film by in-house developed radio frequency (RF) plasma reactor, at different powers and exposure time. Carbon capped Mo films were exposed to oxygen plasma for different durations at three different power settings, at a constant pressure. After each exposure, the thickness of the carbon layer and the roughness of the film were determined by hard x-ray reflectivity measurements. It was observed that most of the carbon film got removed in first 15 minutes exposure. A high density layer formed on top of the Mo film was also observedmore » and it was noted that this layer cannot be removed by successive exposures at different powers. A significant improvement in interface roughness with a slight improvement in top film roughness was observed. The surface roughness of the exposed and unexposed samples was also confirmed by atomic force microscopy measurements.« less

Genetic variations in the CLNK gene and ZNF518B gene are associated with gout in case-control sample sets.

PubMed

Jin, Tian-Bo; Ren, Yongchao; Shi, Xugang; Jiri, Mutu; He, Na; Feng, Tian; Yuan, Dongya; Kang, Longli

2015-07-01

A genome-wide association study of gout in European populations identified 12 genetic variants strongly associated with risk of gout, but it is unknown whether these variants are also associated with gout risk in Chinese populations. A total of 145 patients with gout and 310 healthy control patients were recruited for a case-control association study. Twelve SNPs of CLNK and ZNF518B gene were genotyped, and association analysis was performed. Odds ratios (ORs) with 95 % confidence intervals (CIs) were used to assess the association. Overall, we found four risk alleles for gout in patients: the allele "G" of rs2041215 and rs1686947 in the CLNK gene by dominant model (OR 1.66; 95 % CI 1.04-2.63; p = 0.031) (OR 2.19; 95 % CI 1.38-3.46; p = 0.001) and additive model (OR 1.39; 95 % CI 1.00-1.93; p = 0.049) (OR 1.67; 95 % CI 1.19-2.32; p = 0.003), respectively, and the allele "A" of rs10938799 and rs10016022 in ZNF518B gene by recessive model (OR 4.66; 95 % CI 1.44-15.09; p = 0.008) (OR 4.54; 95 % CI 1.23-16.76; p = 0.020). Further haplotype analysis showed that the TCATTCTGA haplotype of CLNK was more frequent among patients with gout (adjusted OR 0.48; 95 % CI 0.24-0.95; p = 0.036). Additionally, polymorphisms of rs2041215, rs10938799, and rs17467273 were also correlated with clinical pathological parameters. This study provides evidence for gout susceptibility genes, CLNK and ZNF518B, in a Chinese population, which may have potential as diagnostic and prognostic marker for gout patients.

Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types.

PubMed

Kar, Siddhartha P; Beesley, Jonathan; Amin Al Olama, Ali; Michailidou, Kyriaki; Tyrer, Jonathan; Kote-Jarai, ZSofia; Lawrenson, Kate; Lindstrom, Sara; Ramus, Susan J; Thompson, Deborah J; Kibel, Adam S; Dansonka-Mieszkowska, Agnieszka; Michael, Agnieszka; Dieffenbach, Aida K; Gentry-Maharaj, Aleksandra; Whittemore, Alice S; Wolk, Alicja; Monteiro, Alvaro; Peixoto, Ana; Kierzek, Andrzej; Cox, Angela; Rudolph, Anja; Gonzalez-Neira, Anna; Wu, Anna H; Lindblom, Annika; Swerdlow, Anthony; Ziogas, Argyrios; Ekici, Arif B; Burwinkel, Barbara; Karlan, Beth Y; Nordestgaard, Børge G; Blomqvist, Carl; Phelan, Catherine; McLean, Catriona; Pearce, Celeste Leigh; Vachon, Celine; Cybulski, Cezary; Slavov, Chavdar; Stegmaier, Christa; Maier, Christiane; Ambrosone, Christine B; Høgdall, Claus K; Teerlink, Craig C; Kang, Daehee; Tessier, Daniel C; Schaid, Daniel J; Stram, Daniel O; Cramer, Daniel W; Neal, David E; Eccles, Diana; Flesch-Janys, Dieter; Edwards, Digna R Velez; Wokozorczyk, Dominika; Levine, Douglas A; Yannoukakos, Drakoulis; Sawyer, Elinor J; Bandera, Elisa V; Poole, Elizabeth M; Goode, Ellen L; Khusnutdinova, Elza; Høgdall, Estrid; Song, Fengju; Bruinsma, Fiona; Heitz, Florian; Modugno, Francesmary; Hamdy, Freddie C; Wiklund, Fredrik; Giles, Graham G; Olsson, Håkan; Wildiers, Hans; Ulmer, Hans-Ulrich; Pandha, Hardev; Risch, Harvey A; Darabi, Hatef; Salvesen, Helga B; Nevanlinna, Heli; Gronberg, Henrik; Brenner, Hermann; Brauch, Hiltrud; Anton-Culver, Hoda; Song, Honglin; Lim, Hui-Yi; McNeish, Iain; Campbell, Ian; Vergote, Ignace; Gronwald, Jacek; Lubiński, Jan; Stanford, Janet L; Benítez, Javier; Doherty, Jennifer A; Permuth, Jennifer B; Chang-Claude, Jenny; Donovan, Jenny L; Dennis, Joe; Schildkraut, Joellen M; Schleutker, Johanna; Hopper, John L; Kupryjanczyk, Jolanta; Park, Jong Y; Figueroa, Jonine; Clements, Judith A; Knight, Julia A; Peto, Julian; Cunningham, Julie M; Pow-Sang, Julio; Batra, Jyotsna; Czene, Kamila; Lu, Karen H; Herkommer, Kathleen; Khaw, Kay-Tee; Matsuo, Keitaro; Muir, Kenneth; Offitt, Kenneth; Chen, Kexin; Moysich, Kirsten B; Aittomäki, Kristiina; Odunsi, Kunle; Kiemeney, Lambertus A; Massuger, Leon F A G; Fitzgerald, Liesel M; Cook, Linda S; Cannon-Albright, Lisa; Hooning, Maartje J; Pike, Malcolm C; Bolla, Manjeet K; Luedeke, Manuel; Teixeira, Manuel R; Goodman, Marc T; Schmidt, Marjanka K; Riggan, Marjorie; Aly, Markus; Rossing, Mary Anne; Beckmann, Matthias W; Moisse, Matthieu; Sanderson, Maureen; Southey, Melissa C; Jones, Michael; Lush, Michael; Hildebrandt, Michelle A T; Hou, Ming-Feng; Schoemaker, Minouk J; Garcia-Closas, Montserrat; Bogdanova, Natalia; Rahman, Nazneen; Le, Nhu D; Orr, Nick; Wentzensen, Nicolas; Pashayan, Nora; Peterlongo, Paolo; Guénel, Pascal; Brennan, Paul; Paulo, Paula; Webb, Penelope M; Broberg, Per; Fasching, Peter A; Devilee, Peter; Wang, Qin; Cai, Qiuyin; Li, Qiyuan; Kaneva, Radka; Butzow, Ralf; Kopperud, Reidun Kristin; Schmutzler, Rita K; Stephenson, Robert A; MacInnis, Robert J; Hoover, Robert N; Winqvist, Robert; Ness, Roberta; Milne, Roger L; Travis, Ruth C; Benlloch, Sara; Olson, Sara H; McDonnell, Shannon K; Tworoger, Shelley S; Maia, Sofia; Berndt, Sonja; Lee, Soo Chin; Teo, Soo-Hwang; Thibodeau, Stephen N; Bojesen, Stig E; Gapstur, Susan M; Kjær, Susanne Krüger; Pejovic, Tanja; Tammela, Teuvo L J; Dörk, Thilo; Brüning, Thomas; Wahlfors, Tiina; Key, Tim J; Edwards, Todd L; Menon, Usha; Hamann, Ute; Mitev, Vanio; Kosma, Veli-Matti; Setiawan, Veronica Wendy; Kristensen, Vessela; Arndt, Volker; Vogel, Walther; Zheng, Wei; Sieh, Weiva; Blot, William J; Kluzniak, Wojciech; Shu, Xiao-Ou; Gao, Yu-Tang; Schumacher, Fredrick; Freedman, Matthew L; Berchuck, Andrew; Dunning, Alison M; Simard, Jacques; Haiman, Christopher A; Spurdle, Amanda; Sellers, Thomas A; Hunter, David J; Henderson, Brian E; Kraft, Peter; Chanock, Stephen J; Couch, Fergus J; Hall, Per; Gayther, Simon A; Easton, Douglas F; Chenevix-Trench, Georgia; Eeles, Rosalind; Pharoah, Paul D P; Lambrechts, Diether

2016-09-01

Breast, ovarian, and prostate cancers are hormone-related and may have a shared genetic basis, but this has not been investigated systematically by genome-wide association (GWA) studies. Meta-analyses combining the largest GWA meta-analysis data sets for these cancers totaling 112,349 cases and 116,421 controls of European ancestry, all together and in pairs, identified at P < 10(-8) seven new cross-cancer loci: three associated with susceptibility to all three cancers (rs17041869/2q13/BCL2L11; rs7937840/11q12/INCENP; rs1469713/19p13/GATAD2A), two breast and ovarian cancer risk loci (rs200182588/9q31/SMC2; rs8037137/15q26/RCCD1), and two breast and prostate cancer risk loci (rs5013329/1p34/NSUN4; rs9375701/6q23/L3MBTL3). Index variants in five additional regions previously associated with only one cancer also showed clear association with a second cancer type. Cell-type-specific expression quantitative trait locus and enhancer-gene interaction annotations suggested target genes with potential cross-cancer roles at the new loci. Pathway analysis revealed significant enrichment of death receptor signaling genes near loci with P < 10(-5) in the three-cancer meta-analysis. We demonstrate that combining large-scale GWA meta-analysis findings across cancer types can identify completely new risk loci common to breast, ovarian, and prostate cancers. We show that the identification of such cross-cancer risk loci has the potential to shed new light on the shared biology underlying these hormone-related cancers. Cancer Discov; 6(9); 1052-67. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 932. ©2016 American Association for Cancer Research.

Serum microRNAs explain discordance of non-alcoholic fatty liver disease in monozygotic and dizygotic twins: a prospective study.

PubMed

Zarrinpar, Amir; Gupta, Shakti; Maurya, Mano R; Subramaniam, Shankar; Loomba, Rohit

2016-09-01

In the setting where two individuals are genetically similar, epigenetic mechanisms could account for discordance in the presence or absence of non-alcoholic fatty liver disease (NAFLD). This study investigated if serum microRNAs (miRs) could explain discordance in NAFLD. This is a cross-sectional analysis of a prospective cohort study of 40 (n=80) twin-pairs residing in Southern California. All participants underwent a standardised research visit, liver MRI using proton-density fat fraction to quantify fat content and miR profiling of their serum. Among the 40 twin-pairs, there were 6 concordant for NAFLD, 28 were concordant for non-NAFLD and 6 were discordant for NAFLD. The prevalence of NAFLD was 22.5% (18/80). Within the six discordant twins, a panel of 10 miRs differentiated the twin with NAFLD from the one without. Two of these miRs, miR-331-3p and miR-30c, were also among the 21 miRs that were different between NAFLD and non-NAFLD groups (for miR-331-3p: 7.644±0.091 vs 8.057±0.071, respectively, p=0.004; for miR-30c: 10.013±0.126 vs 10.418±0.086, respectively, p=0.008). Both miRs were highly heritable (35.9% and 10.7%, respectively) and highly correlated with each other (R=0.90, p=2.2×10(-16)) suggesting involvement in a common mechanistic pathway. An interactome analysis of these two miRs showed seven common target genes. Using a novel human twin-study design, we demonstrate that discordancy in liver fat content between the twins can be explained by miRs, and that they are heritable. 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/

Personality, behavior and environmental features associated with OXTR genetic variants in British mothers.

PubMed

Connelly, Jessica J; Golding, Jean; Gregory, Steven P; Ring, Susan M; Davis, John M; Davey Smith, George; Harris, James C; Carter, C Sue; Pembrey, Marcus

2014-01-01

It is assumed that the oxytocin receptor gene (OXTR) is associated with factors that are related to features of reproduction as well as the currently emerging fields of mood and emotional response. We analysed data from over 8000 mothers who participated in the Avon Longitudinal Study of Parents and Children (ALSPAC). We determined reproductive, emotional and personality differences related to the two SNPs rs53576 and rs2254298 of the oxytocin receptor gene to determine whether there was evidence in this population for: (i) associations with emotional and personality differences, and (ii) behavioural or environmental links with these SNPs using a hypothesis free approach with over 1000 types of exposure. Our analyses of 7723 women showed that there were no differences in 11 mood, social or relationship characteristics associated with the rs2254298, and just one with rs53576 (with emotional loneliness)--one statistically significant out of 22 tests is no more than would be expected by chance. There were no interactions with childhood abuse. Using a hypothesis-free approach we found few indicators of environmental or behavioural differences associated with rs2254298, but there was an excess of associations with eating habits with rs53576. The findings included an association with dieting to lose weight, and habits typical of bulimia for the women with GG. The nutrition of the women also showed negative associations of the GG genotype with 13 nutrients, including vitamins D, B12 and retinol, and intake of calcium, potassium and iodine. We conclude that this large database of pregnant women was unable to provide confirmation of the types of personality associated with these two OXTR SNPs, but we have shown some evidence of eating differences in those with GG on rs53576. Confirmation of our hypothesis free associations using other data sets is important.

Genetic polymorphisms of SCN9A are associated with oxaliplatin-induced neuropathy.

PubMed

Sereno, María; Gutiérrez-Gutiérrez, Gerardo; Rubio, Juan Moreno; Apellániz-Ruiz, María; Sánchez-Barroso, Lara; Casado, Enrique; Falagan, Sandra; López-Gómez, Miriam; Merino, María; Gómez-Raposo, César; Rodriguez-Salas, Nuria; Tébar, Francisco Zambrana; Rodríguez-Antona, Cristina

2017-01-19

Oxaliplatin is a chemotherapy agent active against digestive tumors. Peripheral neuropathy is one of the most important dose-limiting toxicity of this drug. It occurs in around 60-80% of the patients, and 15% of them develop severe neuropathy. The pathophysiology of oxaliplatin neurotoxicity remains unclear. SCN9A is a gene codifying for a subtype sodium channel (type IX, subunit α) and mutations in this gene are involved in neuropathic perception. In this study we investigated whether SCN9A genetic variants were associated with risk of neurotoxicity in patients diagnosed of cancer on treatment with oxaliplatin. Blood samples from 94 patients diagnosed of digestive cancer that had received oxaliplatin in adjuvant or metastatic setting were obtained from three hospitals in Madrid. These patients were classified into two groups: "cases" developed oxaliplatin-induced grade 3-4 neuropathy (n = 48), and "controls" (n = 46) had no neuropathy or grade 1. The neuropathy was evaluated by an expert neurologist and included a clinical examination and classification according to validated neurological scales: National Cancer Institute Common Toxicity Criteria (NCI-CTC), Oxaliplatin-Specific Neurotoxicity Scale (OSNS) and Total Neuropathy score (TNS). Genotyping was performed for 3 SCN9A missense polymorphisms: rs6746030 (R1150W), rs74401238 (R1110Q) and rs41268673 (P610T), and associations between genotypes and neuropathy were evaluated. We found that SCN9A rs6746030 was associated with protection for severe neuropathy (OR = 0.39, 95% CI = 0.16-0.96; p = 0.041). Multivariate analysis adjusting for diabetes provided similar results (p = 0.036). No significant differences in neuropathy risk were detected for rs74401238 and rs41268673. SCN9A rs6746030 was associated with protection for severe oxaliplatin-induced peripheral neuropathy. The validation of this exploratory study is ongoing in an independent series.

Transverse momentum and rapidity dependence of Hanbury-Brown Twiss correlations in Au+Au collisions at sNN= 62.4 and 200 GeV

NASA Astrophysics Data System (ADS)

Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Budzanowski, A.; Busza, W.; Carroll, A.; Chai, Z.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Hauer, M.; Heintzelman, G. A.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Katzy, J.; Khan, N.; Kucewicz, W.; Kulinich, P.; Kuo, C. M.; Lin, W. T.; Manly, S.; McLeod, D.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Remsberg, L. P.; Reuter, M.; Roland, C.; Roland, G.; Rosenberg, L.; Sagerer, J.; Sarin, P.; Sawicki, P.; Seals, H.; Sedykh, I.; Skulski, W.; Smith, C. E.; Stankiewicz, M. A.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tang, J.-L.; Tonjes, M. B.; Trzupek, A.; Vale, C.; Nieuwenhuizen, G. J. Van; Vaurynovich, S. S.; Verdier, R.; Veres, G. I.; Wenger, E.; Wolfs, F. L. H.; Wosiek, B.; Woźniak, K.; Wuosmaa, A. H.; Wysłouch, B.

2006-03-01

Two-particle correlations of identical charged pion pairs from Au+Au collisions at sNN=62.4 and 200 GeV were measured by the PHOBOS experiment at BNL Relativistic Heavy Ion Collider (RHIC). Data for the 15% most central events were analyzed with Bertsch-Pratt and Yano-Koonin-Podgoretskii parametrizations using pairs with rapidities of 0.4

Planned versus actual outcomes as a result of animal feeding operation decisions for managing phosphorus.

PubMed

Cabot, Perry E; Nowak, Pete

2005-01-01

The paper explores how decisions made on animal feeding operations (AFOs) influence the management of manure and phosphorus. Variability among these decisions from operation to operation and from field to field can influence the validity of nutrient loss risk assessments. These assessments are based on assumptions that the decision outcomes regarding manure distribution will occur as they are planned. The discrepancy between planned versus actual outcomes in phosphorus management was explored on nine AFOs managing a contiguous set of 210 fields in south-central Wisconsin. A total of 2611 soil samples were collected and multiple interviews conducted to assign phosphorus index (PI) ratings to the fields. Spearman's rank correlation coefficients (r(S)) indicated that PI ratings were less sensitive to soil test phosphorus (STP) levels (r(S) = 0.378), universal soil loss equation (USLE) (r(S) = 0.261), ratings for chemical fertilizer application (r(S) = 0.185), and runoff class (r(S) = -0.089), and more sensitive to ratings for manure application (r(S) = 0.854). One-way ANOVA indicated that mean field STP levels were more homogenous than field PI ratings between AFOs. Kolmogorov-Smirnov (K-S) tests displayed several nonsignificant comparisons for cumulative distribution functions, S(x), of mean STP levels on AFO fields. On the other hand, the K-S tests of S(x) for PI ratings indicated that the majority of these S(x) functions were significantly different between AFOs at or greater than the 0.05 significance level. Interviews suggested multiple reasons for divergence between planned and actual outcomes in managing phosphorus, and that this divergence arises at the strategic, tactical, and operational levels of decision-making.

Interaction between childhood adversity and functional polymorphisms in the dopamine pathway on first-episode psychosis.

PubMed

Trotta, Antonella; Iyegbe, Conrad; Yiend, Jenny; Dazzan, Paola; David, Anthony S; Pariante, Carmine; Mondelli, Valeria; Colizzi, Marco; Murray, Robin M; Di Forti, Marta; Fisher, Helen L

2018-04-10

There is consistent evidence of a cumulative relationship between childhood adversity and psychosis, with number of adversities experienced increasing the probability of psychosis onset. It is possible that genetic factors moderate the association between childhood adversity and psychosis, potentially by influencing how an individual reacts biologically and/or psychologically following exposure to adversity, in such a way as to set them off on the path to psychosis. However, identifying the specific genetic variants involved and how they interact with childhood adversity remains challenging. We examined whether the association between cumulative exposure to childhood adversity and development of psychotic disorder was moderated by the COMT Val 158 Met, AKT1 rs2494732 or DRD2 rs1076560 polymorphisms, known to affect dopamine levels. Participants were 285 first-presentation psychosis cases and 256 geographically-matched controls drawn from the Genetics and Psychosis (GAP) study. Childhood adversity was assessed using the Childhood Experience of Care and Abuse Questionnaire (CECA.Q) and blood- and cheek-derived genotype data were collected. Our findings revealed no main effect of COMT Val 158 Met, AKT1 rs2494732 and DRD2 rs1076560 polymorphisms on psychosis case status or reports of childhood adversity. Individuals reporting a history of multiple adversities were more likely to be psychosis patients than controls, regardless of their genetic risk. There was no evidence of candidate genotype by childhood adversity interactions in relation to psychosis onset. These findings did not provide evidence of a possible role of COMT Val 158 Met, AKT1 rs2494732 or DRD2 rs1076560 genotypes in modifying the association between childhood adversity and onset of psychosis. Copyright © 2018 Elsevier B.V. All rights reserved.

Interspecies synteny mapping identifies a quantitative trait locus for bone mineral density on human chromosome Xp22.

PubMed

Parsons, Claire A; Mroczkowski, H Joel; McGuigan, Fiona E A; Albagha, Omar M E; Manolagas, Stavros; Reid, David M; Ralston, Stuart H; Shmookler Reis, Robert J

2005-11-01

Bone mineral density (BMD) is a complex trait with a strong genetic component and an important predictor of osteoporotic fracture risk. Here we report the use of a cross-species strategy to identify genes that regulate BMD, proceeding from quantitative trait mapping in mice to association mapping of the syntenic region in the human genome. We identified a quantitative trait locus (QTL) on the mouse X-chromosome for post-maturity change in spine BMD in a cross of SAMP6 and AKR/J mice and conducted association mapping of the syntenic region on human chromosome Xp22. We studied 76 single nucleotide polymorphisms (SNP) from the human region in two sets of DNA pools prepared from individuals with lumbar spine-BMD (LS-BMD) values falling into the top and bottom 13th percentiles of a population-based study of 3100 post-menopausal women. This procedure identified a region of significant association for two adjacent SNP (rs234494 and rs234495) within the Xp22 locus (P<0.001). Individual genotyping for rs234494 in the BMD pools confirmed the presence of an association for alleles (P=0.018) and genotypes (P=0.008). Analysis of rs234494 and rs234495 in 1053 women derived from the same population who were not selected for BMD values showed an association with LS-BMD for rs234495 (P=0.01) and for haplotypes defined by both SNP (P=0.002). Our study illustrates that interspecies synteny can be used to identify and refine QTL for complex traits and represents the first example where a human QTL for BMD regulation has been mapped using this approach.

Factors associated with quality of life in elderly hospitalised patients undergoing post-acute rehabilitation: a cross-sectional analytical study in Switzerland

PubMed Central

Rubli Truchard, Eve; Rochat, Etienne; Pasquier, Jérôme; Monod, Stéfanie

2017-01-01

Objectives We investigated whether biopsychosocial and spiritual factors and satisfaction with care were associated with patients’ perceived quality of life. Design This was a cross-sectional analytical study. Setting Data were collected from inpatients at a postacute geriatric rehabilitation centre in a university hospital in Switzerland. Participants Participants aged 65 years and over were consecutively recruited from October 2014 to January 2016. Exclusion criteria included significant cognitive disorder and terminal illness. Of 227 eligible participants, complete data were collected from 167. Main outcome measures Perceived quality of life was measured using WHO Quality of Life Questionnaire—version for older people. Predictive factors were age, sex, functional status at admission, comorbidities, cognitive status, depressive symptoms, living conditions and satisfaction with care. A secondary focus was the association between spiritual needs and quality of life. Results Patients undergoing geriatric rehabilitation experienced a good quality of life. Greater quality of life was significantly associated with higher functional status (rs=0.204, p=0.011), better cognitive status (rs=0.175, p=0.029) and greater satisfaction with care (rs=0.264, p=0.003). Poorer quality of life was significantly associated with comorbidities (rs=−.226, p=0.033), greater depressive symptoms (rs=−.379, p<0.001) and unmet spiritual needs (rs=−.211, p=0.049). Multivariate linear regression indicated that depressive symptoms (β=−0.961; 95% CIs −1.449 to 0.472; p<0.001) significantly predicted quality of life. Conclusions Patient perceptions of quality of life were significantly associated with depression. More research is needed to assess whether considering quality of life could improve care plan creation. PMID:29061633

Hydrologic and hydraulic flood forecasting constrained by remote sensing data

NASA Astrophysics Data System (ADS)

Li, Y.; Grimaldi, S.; Pauwels, V. R. N.; Walker, J. P.; Wright, A. J.

2017-12-01

Flooding is one of the most destructive natural disasters, resulting in many deaths and billions of dollars of damages each year. An indispensable tool to mitigate the effect of floods is to provide accurate and timely forecasts. An operational flood forecasting system typically consists of a hydrologic model, converting rainfall data into flood volumes entering the river system, and a hydraulic model, converting these flood volumes into water levels and flood extents. Such a system is prone to various sources of uncertainties from the initial conditions, meteorological forcing, topographic data, model parameters and model structure. To reduce those uncertainties, current forecasting systems are typically calibrated and/or updated using ground-based streamflow measurements, and such applications are limited to well-gauged areas. The recent increasing availability of spatially distributed remote sensing (RS) data offers new opportunities to improve flood forecasting skill. Based on an Australian case study, this presentation will discuss the use of 1) RS soil moisture to constrain a hydrologic model, and 2) RS flood extent and level to constrain a hydraulic model.The GRKAL hydrological model is calibrated through a joint calibration scheme using both ground-based streamflow and RS soil moisture observations. A lag-aware data assimilation approach is tested through a set of synthetic experiments to integrate RS soil moisture to constrain the streamflow forecasting in real-time.The hydraulic model is LISFLOOD-FP which solves the 2-dimensional inertial approximation of the Shallow Water Equations. Gauged water level time series and RS-derived flood extent and levels are used to apply a multi-objective calibration protocol. The effectiveness with which each data source or combination of data sources constrained the parameter space will be discussed.

Comparison of visible and near infrared reflectance spectroscopy on fat to authenticate dietary history of lambs.

PubMed

Huang, Y; Andueza, D; de Oliveira, L; Zawadzki, F; Prache, S

2015-11-01

Since consumers are showing increased interest in the origin and method of production of their food, it is important to be able to authenticate dietary history of animals by rapid and robust methods used in the ruminant products. Promising breakthroughs have been made in the use of spectroscopic methods on fat to discriminate pasture-fed and concentrate-fed lambs. However, questions remained on their discriminatory ability in more complex feeding conditions, such as concentrate-finishing after pasture-feeding. We compared the ability of visible reflectance spectroscopy (Vis RS, wavelength range: 400 to 700 nm) with that of visible-near-infrared reflectance spectroscopy (Vis-NIR RS, wavelength range: 400 to 2500 nm) to differentiate between carcasses of lambs reared with three feeding regimes, using partial least square discriminant analysis (PLS-DA) as a classification method. The sample set comprised perirenal fat of Romane male lambs fattened at pasture (P, n = 69), stall-fattened indoors on commercial concentrate and straw (S, n = 55) and finished indoors with concentrate and straw for 28 days after pasture-feeding (PS, n = 65). The overall correct classification rate was better for Vis-NIR RS than for Vis RS (99.0% v. 95.1%, P < 0.05). Vis-NIR RS allowed a correct classification rate of 98.6%, 100.0% and 98.5% for P, S and PS lambs, respectively, whereas Vis RS allowed a correct classification rate of 98.6%, 94.5% and 92.3% for P, S and PS lambs, respectively. This study suggests the likely implication of molecules absorbing light in the non-visible part of the Vis-NIR spectra (possibly fatty acids), together with carotenoid and haem pigments, in the discrimination of the three feeding regimes.

Statistical Evaluation of the Rodin–Ohno Hypothesis: Sense/Antisense Coding of Ancestral Class I and II Aminoacyl-tRNA Synthetases

PubMed Central

Chandrasekaran, Srinivas Niranj; Yardimci, Galip Gürkan; Erdogan, Ozgün; Roach, Jeffrey; Carter, Charles W.

2013-01-01

We tested the idea that ancestral class I and II aminoacyl-tRNA synthetases arose on opposite strands of the same gene. We assembled excerpted 94-residue Urgenes for class I tryptophanyl-tRNA synthetase (TrpRS) and class II Histidyl-tRNA synthetase (HisRS) from a diverse group of species, by identifying and catenating three blocks coding for secondary structures that position the most highly conserved, active-site residues. The codon middle-base pairing frequency was 0.35 ± 0.0002 in all-by-all sense/antisense alignments for 211 TrpRS and 207 HisRS sequences, compared with frequencies between 0.22 ± 0.0009 and 0.27 ± 0.0005 for eight different representations of the null hypothesis. Clustering algorithms demonstrate further that profiles of middle-base pairing in the synthetase antisense alignments are correlated along the sequences from one species-pair to another, whereas this is not the case for similar operations on sets representing the null hypothesis. Most probable reconstructed sequences for ancestral nodes of maximum likelihood trees show that middle-base pairing frequency increases to approximately 0.42 ± 0.002 as bacterial trees approach their roots; ancestral nodes from trees including archaeal sequences show a less pronounced increase. Thus, contemporary and reconstructed sequences all validate important bioinformatic predictions based on descent from opposite strands of the same ancestral gene. They further provide novel evidence for the hypothesis that bacteria lie closer than archaea to the origin of translation. Moreover, the inverse polarity of genetic coding, together with a priori α-helix propensities suggest that in-frame coding on opposite strands leads to similar secondary structures with opposite polarity, as observed in TrpRS and HisRS crystal structures. PMID:23576570

Hodgkin/Reed-Sternberg cells and Hodgkin's disease in patients with B-cell chronic lymphocytic leukaemia: an immunohistological, molecular and clinical study of four cases suggesting a heterogeneous pathogenetic background.

PubMed

Pescarmona, E; Pignoloni, P; Mauro, F R; Cerretti, R; Anselmo, A P; Mandelli, F; Baroni, C D

2000-08-01

We report the immunohistological, molecular and clinical findings in four patients affected by B-cell chronic lymphocytic leukaemia (CLL) who developed "Richter's syndrome with Hodgkin's disease (HD) features" or "CLL with Hodgkin's transformation", all characterised by the presence of typical Hodgkin/Reed-Sternberg (H/RS) cells in lymph node biopsies. In three cases the nodal involvement by CLL was demonstrated both by the presence of a predominant background of CD5/CD19/CD23+ small lymphocytes and an IgH monoclonal rearrangement revealed by PCR analysis. Conversely, in the remaining case there was neither immunohistological nor molecular evidence of lymph node involvement by CLL. In all four cases H/RS cells were Epstein-Barr virus (EBV) latent membrane protein (LMP-1) positive. These findings suggest that the presence of H/RS cells in the first three patients, who had CLL/HD nodal involvement, might be related to transformation or clonal evolution of CLL cells in H/RS cells, which is in keeping with use of the term "CLL with Hodgkin's transformation". In the fourth case a de novo HD may be postulated, representing a second malignancy presumably not clonally related to CLL. In all cases a key pathogenetic role of EBV is suggested by the expression of LMP-1 in H/RS cells. Our findings indicate that the presence of typical H/RS cells in lymph node biopsies in CLL patients may reflect a heterogeneous pathogenetic background. The different clinico-pathologic settings should be taken into consideration because of their possible implications for patients' treatment and prognosis.

Systematic review: genetic biomarkers associated with anti-TNF treatment response in inflammatory bowel diseases.

PubMed

Bek, S; Nielsen, J V; Bojesen, A B; Franke, A; Bank, S; Vogel, U; Andersen, V

2016-09-01

Personalised medicine, including biomarkers for treatment selection, may provide new algorithms for more effective treatment of patients. Genetic variation may impact drug response and genetic markers could help selecting the best treatment strategy for the individual patient. To identify polymorphisms and candidate genes from the literature that are associated with anti-tumour necrosis factor (TNF) treatment response in patients with inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis. We performed a PubMed literature search and retrieved studies reporting original data on association between polymorphisms and anti-TNF treatment response and conducted a meta-analysis. A functional polymorphism in FCGR3A was significantly associated with anti-TNF treatment response among CD patients using biological response criterion (decrease in C-reactive protein, levels). Meta-analyses showed that polymorphisms in TLR2 (rs3804099, OR (95% CI) = 2.17 (1.35-3.47)], rs11938228 [OR = 0.64 (0.43-0.96)], TLR4 (rs5030728) [OR = 3.18 (1.63-6.21)], TLR9 (rs352139) [OR = 0.43 (0.21-0.88)], TNFRSF1A (rs4149570) [OR = 2.06 (1.02-4.17)], IFNG (rs2430561) [OR = 1.66 (1.05-2.63)], IL6 (rs10499563) [OR = 1.65 (1.04-2.63)] and IL1B (rs4848306) [OR = 1.88 (1.05-3.35)] were significantly associated with response among IBD patients using clinical response criteria. A positive predictive value of 0.96 was achieved by combining five genetic markers in an explorative analysis. There are no genetic markers currently available which are adequately predictive of anti-TNF response for use in the clinic. Genetic markers bear the advantage that they do not change over time. Therefore, hypothesis-free approaches, testing a large number of polymorphisms in large, well-characterised cohorts, are required in order to identify genetic profiles with larger effect sizes, which could be employed as biomarkers for treatment selection in clinical settings. © 2016 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd.

Operant learning (R-S) principles applied to nail-biting.

PubMed

McClanahan, T M

1995-10-01

The principles of R-S learning were applied to a 32-yr.-old Caucasian woman to reduce the frequency and duration of fingernail-biting activity in a reversal-replication (ABAB) research design. The undesirable behavior, fingernail-biting which included frequency and duration, antecedents, and setting events, was recorded during a 28-day study. Self-monitoring recordings indicated that anxiety was the most prevalent antecedent. Through the use of a preliminary questionnaire and interview, increase in self-awareness was judged to be most effective in the extinction of the undesired behavior. The systematic desensitization techniques of deep muscle relaxation and Transcendental Meditation were used during the treatment phase.

Setting Standards: Confronting Paradox.

ERIC Educational Resources Information Center

Doecke, Brenton; Gill, Margaret

2001-01-01

Discusses implications of the issues of continuity and discontinuity, commonality and difference, congruity and paradox as they engage the research team, the industry partners, and the teachers around Australia who constitute the STELLA (Standards for Teachers of English Language and Literacy in Australia) project. (RS)

Determining the Effect of Material Hardness During the Hard Turning of AISI4340 Steel

NASA Astrophysics Data System (ADS)

Kambagowni, Venkatasubbaiah; Chitla, Raju; Challa, Suresh

2018-05-01

In the present manufacturing industries hardened steels are most widely used in the applications like tool design and mould design. It enhances the application range of hard turning of hardened steels in manufacturing industries. This study discusses the impact of workpiece hardness, feed and depth of cut on Arithmetic mean roughness (Ra), root mean square roughness (Rq), mean depth of roughness (Rz) and total roughness (Rt) during the hard turning. Experiments have been planned according to the Box-Behnken design and conducted on hardened AISI4340 steel at 45, 50 and 55 HRC with wiper ceramic cutting inserts. Cutting speed is kept constant during this study. The analysis of variance was used to determine the effects of the machining parameters. 3-D response surface plots drawn based on RSM were utilized to set up the input-output relationships. The results indicated that the feed rate has the most significant parameter for Ra, Rq and Rz and hardness has the most critical parameter for the Rt. Further, hardness shows its influence over all the surface roughness characteristics.

Variation in bed level shear stress on surfaces sheltered by nonerodible roughness elements

NASA Astrophysics Data System (ADS)

Sutton, Stephen L. F.; McKenna-Neuman, Cheryl

2008-09-01

Direct bed level observations of surface shear stress, pressure gradient variability, turbulence intensity, and fluid flow patterns were carried out in the vicinity of cylindrical roughness elements mounted in a boundary layer wind tunnel. Paired corkscrew vortices shed from each of the elements result in elevated shear stress and increased potential for the initiation of particle transport within the far wake. While the size and shape of these trailing vortices change with the element spacing, they persist even for large roughness densities. Wake interference coincides with the impingement of the upwind horseshoe vortices upon one another at a point when their diameter approaches half the distance between the roughness elements. While the erosive capability of the horseshoe vortex has been suggested for a variety of settings, the present study shows that the fluid stress immediately beneath this coherent structure is actually small in comparison to that caused by compression of the incident flow as it is deflected around the element and attached vortex. Observations such as these are required for further refinement of models of stress partitioning on rough surfaces.

Association analysis of nine candidate gene polymorphisms in Indian patients with type 2 diabetic retinopathy.

PubMed

Balasubbu, Suganthalakshmi; Sundaresan, Periasamy; Rajendran, Anand; Ramasamy, Kim; Govindarajan, Gowthaman; Perumalsamy, Namperumalsamy; Hejtmancik, J Fielding

2010-11-10

Diabetic retinopathy (DR) is classically defined as a microvasculopathy that primarily affects the small blood vessels of the inner retina as a complication of diabetes mellitus (DM).It is a multifactorial disease with a strong genetic component. The aim of this study is to investigate the association of a set of nine candidate genes with the development of diabetic retinopathy in a South Indian cohort who have type 2 diabetes mellitus (T2DM). Seven candidate genes (RAGE, PEDF, AKR1B1, EPO, HTRA1, ICAM and HFE) were chosen based on reported association with DR in the literature. Two more, CFH and ARMS2, were chosen based on their roles in biological pathways previously implicated in DR. Fourteen single nucleotide polymorphisms (SNPs) and one dinucleotide repeat polymorphism, previously reported to show association with DR or other related diseases, were genotyped in 345 DR and 356 diabetic patients without retinopathy (DNR). The genes which showed positive association in this screening set were tested further in additional sets of 100 DR and 90 DNR additional patients from the Aravind Eye Hospital. Those which showed association in the secondary screen were subjected to a combined analysis with the 100 DR and 100 DNR subjects previously recruited and genotyped through the Sankara Nethralaya Hospital, India. Genotypes were evaluated using a combination of direct sequencing, TaqMan SNP genotyping, RFLP analysis, and SNaPshot PCR assays. Chi-square and Fisher exact tests were used to analyze the genotype and allele frequencies. Among the nine loci (15 polymorphisms) screened, SNP rs2070600 (G82S) in the RAGE gene, showed significant association with DR (allelic P = 0.016, dominant model P = 0.012), compared to DNR. SNP rs2070600 further showed significant association with DR in the confirmation cohort (P = 0.035, dominant model P = 0.032). Combining the two cohorts gave an allelic P < 0.003 and dominant P = 0.0013). Combined analysis with the Sankara Nethralaya cohort gave an allelic P = 0.0003 and dominant P = 0.00011 with an OR = 0.49 (0.34 - 0.70) for the minor allele. In HTRA1, rs11200638 (G>A), showed marginal significance with DR (P = 0.055) while rs10490924 in LOC387715 gave a P = 0.07. No statistical significance was observed for SNPs in the other 7 genes studied. This study confirms significant association of one polymorphism only (rs2070600 in RAGE) with DR in an Indian population which had T2DM.

Specific physical trainability in elite young soccer players: efficiency over 6 weeks’ in-season training

PubMed Central

Rouissi, M; Haddad, M; Chtara, H; Chaalali, A; Owen, A; Chamari, K

2017-01-01

The aim of the present study was to compare the effects of 3 training protocols (plyometric [PLYO], agility [AG], or repeated shuttle sprints [RS]) on physical performance in the same population of young soccer players. Forty-two youth-level male players (13.6±0.3-years; 1.65±0.07 m; 54.1±6.5 kg; body fat: 12.8±2.6%) participated in a short-term (6-week) randomized parallel fully controlled training study (pre-to-post measurements): PLYO group, n=10; AG group, n=10; RS group, n=12; and control group [CON] n=10. PLYO training = 9 lower limb exercises (2-3 sets of 8-12 repetitions). The AG group performed planned AG drills and direction changes. RS training consisted of 2-4 sets of 5-6x 20 to 30 m shuttle sprints (20 seconds recovery in between). Progressive overload principles were incorporated into the programme by increasing the number of foot contacts and varying the complexity of the exercises. Pre/post-training tests were: bilateral standing horizontal jump, and unilateral horizontal jumps, sprint (30 m with 10 m lap time), agility (20 m zigzag), and repeated sprint ability (RSA) (i.e. 6x30 m shuttle sprints: 2x15 m with 180° turns). Significant main effects for time (i.e. training application) and group (training type) were detected. Improvements in horizontal jumping were higher (p<0.01: ES=large) in PLYO. The RS group improved significantly more (p<0.01; ES=large) than other groups: 30 m sprint, RSAbest and RSAmean performances. Significantly greater increases in 20 m zigzag performance were observed following AG and RS training (4.0 and 3.8%, respectively) compared with PLYO (2.0%) and CON training (0.8%). No significant differences were reported in the RSAdec between groups. Elite young male soccer players’ physical performances can be significantly and specifically improved either using PLYO or AG or RSA training over short-term in-season training. PMID:28566807

Specific physical trainability in elite young soccer players: efficiency over 6 weeks' in-season training.

PubMed

Chtara, M; Rouissi, M; Haddad, M; Chtara, H; Chaalali, A; Owen, A; Chamari, K

2017-06-01

The aim of the present study was to compare the effects of 3 training protocols (plyometric [PLYO], agility [AG], or repeated shuttle sprints [RS]) on physical performance in the same population of young soccer players. Forty-two youth-level male players (13.6±0.3-years; 1.65±0.07 m; 54.1±6.5 kg; body fat: 12.8±2.6%) participated in a short-term (6-week) randomized parallel fully controlled training study (pre-to-post measurements): PLYO group, n=10; AG group, n=10; RS group, n=12; and control group [CON] n=10. PLYO training = 9 lower limb exercises (2-3 sets of 8-12 repetitions). The AG group performed planned AG drills and direction changes. RS training consisted of 2-4 sets of 5-6x 20 to 30 m shuttle sprints (20 seconds recovery in between). Progressive overload principles were incorporated into the programme by increasing the number of foot contacts and varying the complexity of the exercises. Pre/post-training tests were: bilateral standing horizontal jump, and unilateral horizontal jumps, sprint (30 m with 10 m lap time), agility (20 m zigzag), and repeated sprint ability (RSA) (i.e. 6x30 m shuttle sprints: 2x15 m with 180° turns). Significant main effects for time (i.e. training application) and group (training type) were detected. Improvements in horizontal jumping were higher (p<0.01: ES=large) in PLYO. The RS group improved significantly more (p<0.01; ES=large) than other groups: 30 m sprint, RSA best and RSA mean performances. Significantly greater increases in 20 m zigzag performance were observed following AG and RS training (4.0 and 3.8%, respectively) compared with PLYO (2.0%) and CON training (0.8%). No significant differences were reported in the RSA dec between groups. Elite young male soccer players' physical performances can be significantly and specifically improved either using PLYO or AG or RSA training over short-term in-season training.

A TaqMan-based multiplex qPCR assay and DNA extraction method for phylotype IIB sequevars 1&2 (select agent) strains of Ralstonia solanacearum

DOE PAGES

Stulberg, Michael J.; Huang, Qi

2015-10-01

Ralstonia solanacearum race 3 biovar 2 strains belonging to phylotype IIB, sequevars 1 and 2 (IIB-1&2) cause brown rot of potato in temperate climates, and are quarantined pathogens in Canada and Europe. Since these strains are not established in the U.S. and because of their potential risk to the potato industry, the U.S. government has listed them as select agents. Cultivated geraniums are also a host and have the potential to spread the pathogen through trade, and its extracts strongly inhibits DNA-based detection methods. We designed four primer and probe sets for an improved qPCR method that targets stable regionsmore » of DNA. RsSA1 and RsSA2 recognize IIB-1&2 strains, RsII recognizes the current phylotype II (the newly proposed R. solanacearum species) strains (and a non-plant associated R. mannitolilytica), and Cox1 recognizes eight plant species including major hosts of R. solanacearum such as potato, tomato and cultivated geranium as an internal plant control. We multiplexed the RsSA2 with the RsII and Cox1 sets to provide two layers of detection of a positive IIB-1&2 sample, and to validate plant extracts and qPCR reactions. The TaqMan-based uniplex and multiplex qPCR assays correctly identified 34 IIB-1&2 and 52 phylotype II strains out of 90 R. solanacearum species complex strains. Additionally, the multiplex qPCR assay was validated successfully using 169 artificially inoculated symptomatic and asymptomatic plant samples from multiple plant hosts including geranium. Moreover, we developed an extraction buffer that allowed for a quick and easy DNA extraction from infected plants including geranium for detection of R. solanacearum by qPCR. Our multiplex qPCR assay, especially when coupled with the quick extraction buffer method, allows for quick, easy and reliable detection and differentiation of the IIB-1&2 strains of R. solanacearum.« less

Validity of the Timed Up and Go Test as a Measure of Functional Mobility in Persons With Multiple Sclerosis.

PubMed

Sebastião, Emerson; Sandroff, Brian M; Learmonth, Yvonne C; Motl, Robert W

2016-07-01

To examine the validity of the timed Up and Go (TUG) test as a measure of functional mobility in persons with multiple sclerosis (MS) by using a comprehensive framework based on construct validity (ie, convergent and divergent validity). Cross-sectional study. Hospital setting. Community-residing persons with MS (N=47). Not applicable. Main outcome measures included the TUG test, timed 25-foot walk test, 6-minute walk test, Multiple Sclerosis Walking Scale-12, Late-Life Function and Disability Instrument, posturography evaluation, Activities-specific Balance Confidence scale, Symbol Digits Modalities Test, Expanded Disability Status Scale, and the number of steps taken per day. The TUG test was strongly associated with other valid outcome measures of ambulatory mobility (Spearman rank correlation, rs=.71-.90) and disability status (rs=.80), moderately to strongly associated with balance confidence (rs=.66), and weakly associated with postural control (ie, balance) (rs=.31). The TUG test was moderately associated with cognitive processing speed (rs=.59), but not associated with other nonambulatory measures (ie, Late-Life Function and Disability Instrument-upper extremity function). Our findings support the validity of the TUG test as a measure of functional mobility. This warrants its inclusion in patients' assessment alongside other valid measures of functional mobility in both clinical and research practice in persons with MS. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Association between single nucleotide polymorphisms of the transforming growth factor β1 gene and the risk of severe radiation esophagitis in patients with lung cancer.

PubMed

Guerra, Jose Luis Lopez; Gomez, Daniel; Wei, Qingyi; Liu, Zhengshen; Wang, Li-E; Yuan, Xianglin; Zhuang, Yan; Komaki, Ritusko; Liao, Zhongxing

2012-12-01

We investigated the association between single nucleotide polymorphisms (SNPs) in the transforming growth factor β1 (TGFβ1) gene and the risk of radiation-induced esophageal toxicity (RE) in patients with non-small-cell lung cancer (NSCLC). Ninety-seven NSCLC patients with available genomic DNA samples and mostly treated with intensity modulated radio(chemo)therapy from 2003 to 2006 were used as a test dataset and 101 NSCLC patients treated with 3-dimensional conformal radio(chemo)therapy from 1998 to 2002 were used as a validation set. We genotyped three SNPs of the TGFβ1 gene (rs1800469:C-509T, rs1800471:G915C, and rs1982073:T869C) by the polymerase chain reaction restriction fragment length polymorphism method. In the test dataset, the CT/TT genotypes of TGFβ1 rs1800469:C-509T were associated with a statistically significant higher risk of RE grade⩾3 in univariate (P=0.026) and multivariate analysis (P=0.045) when compared with the CC genotype. These results were again observed in both univariate (P=0.045) and multivariate (P=0.023) analysis in the validation dataset. We found and validated that the TGFβ1 rs1800469:C-509T genotype is associated with severe RE. This response marker may be used for guiding therapy intensity in an individual patient, which would further the goal of individualized therapy. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Mars radar clutter and surface roughness characteristics from MARSIS data

NASA Astrophysics Data System (ADS)

Campbell, Bruce A.; Schroeder, Dustin M.; Whitten, Jennifer L.

2018-01-01

Radar sounder studies of icy, sedimentary, and volcanic settings can be affected by reflections from surface topography surrounding the sensor nadir location. These off-nadir ;clutter; returns appear at similar time delays to subsurface echoes and complicate geologic interpretation. Additionally, broadening of the radar echo in delay by surface returns sets a limit on the detectability of subsurface interfaces. We use MARSIS 4 MHz data to study variations in the nadir and off-nadir clutter echoes, from about 300 km to 1000 km altitude, R, for a wide range of surface roughness. This analysis uses a new method of characterizing ionospheric attenuation to merge observations over a range of solar zenith angle and date. Mirror-like reflections should scale as R-2, but the observed 4 MHz nadir echoes often decline by a somewhat smaller power-law factor because MARSIS on-board processing increases the number of summed pulses with altitude. Prior predictions of the contributions from clutter suggest a steeper decline with R than the nadir echoes, but in very rough areas the ratio of off-nadir returns to nadir echoes shows instead an increase of about R1/2 with altitude. This is likely due in part to an increase in backscatter from the surface as the radar incidence angle at some round-trip time delay declines with increasing R. It is possible that nadir and clutter echo properties in other planetary sounding observations, including RIME and REASON flyby data for Europa, will vary in the same way with altitude, but there may be differences in the nature and scale of target roughness (e.g., icy versus rocky surfaces). We present global maps of the ionosphere- and altitude-corrected nadir echo strength, and of a ;clutter; parameter based on the ratio of off-nadir to nadir echoes. The clutter map offers a view of surface roughness at ∼75 m length scale, bridging the spatial-scale gap between SHARAD roughness estimates and MOLA-derived parameters.

Examination of Routine Practice Patterns in the Hospital Information Data Warehouse: Use of OLAP and Rough Set Analysis with Clinician Feedback

PubMed Central

Grant, Andrew; Grant, Gwyneth; Gagné, Jean; Blanchette, Carl; Comeau, Émilie; Brodeur, Guillaume; Dionne, Jonathon; Ayite, Alphonse; Synak, Piotr; Wroblewski, Jakub; Apanowitz, Cas

2001-01-01

The patient centred electronic patient record enables retrospective analysis of practice patterns as one means to assist clinicians adjust and improve their practice. An interrogation of the data-warehouse linking test use to Diagnostic Related Group (DRG) of one years data of the Sherbrooke University Hospital showed that one-third of patients used two-thirds of these diagnostic tests. Using RoughSets analysis, zones of repeated tests were demonstrated where results remained within stable limits. It was concluded that 30% of fluid and electrolyte testing was probably unnecessary. These findings led to an endorsement of changing the test request formats in the hospital information system from profiles to individual tests requiring justification.

Quantitative trait loci at the 11q23.3 chromosomal region related to dyslipidemia in the population of Andhra Pradesh, India.

PubMed

Pranavchand, Rayabarapu; Reddy, Battini Mohan

2017-06-13

Given the characteristic atherogenic dyslipidemia of south Indian population and crucial role of APOA1, APOC3, APOA4 and APOA5 genes clustered in 11q23.3 chromosomal region in regulating lipoprotein metabolism and cholesterol homeostasis, a large number of recently identified variants are to be explored for their role in regulating the serum lipid parameters among south Indians. Using fluidigm SNP genotyping platform, a prioritized set of 96 SNPs of the 11q23.3 chromosomal region were genotyped on 516 individuals from Hyderabad, India, and its vicinity and aged >45 years. The linear regression analysis of the individual lipid traits viz., TC, LDLC, HDLC, VLDL and TG with each of the 78 SNPs that confirm to HWE and with minor allele frequency > 1%, suggests 23 of those to be significantly associated (p ≤ 0.05) with at least one of these quantitative traits. Most importantly, the variant rs632153 is involved in elevating TC, LDLC, TG and VLDLs and probably playing a crucial role in the manifestation of dyslipidemia. Additionally, another three SNPs rs633389, rs2187126 and rs1263163 are found risk conferring to dyslipidemia by elevating LDLC and TC levels in the present population. Further, the ROC (receiver operating curve) analysis for the risk scores and dyslipidemia status yielded a significant area under curve (AUC) = 0.675, suggesting high discriminative power of the risk variants towards the condition. The interaction analysis suggests rs10488699-rs2187126 pair of the BUD13 gene to confer significant risk (Interaction odds ratio = 14.38, P = 7.17 × 10 5 ) towards dyslipidemia by elevating the TC levels (β = 37.13, p = 6.614 × 10 5 ). On the other hand, the interaction between variants of APOA1 gene and BUD13 and/or ZPR1 regulatory genes at this region are associated with elevated TG and VLDL. The variants at 11q23.3 chromosomal region seem to determine the quantitative lipid traits and in turn dyslipidemia in the population of Hyderabad. Particularly, the variants rs632153, rs633389, rs2187126 and rs1263163 might be risk conferring to dyslipidemia by elevating LDLC and TC levels, while the variants of APOC3 and APOA1 genes might be the genetic determinants of elevated triglycerides in the present population.

Statins: cost analysis in Indian scenario from eight major clinical trials.

PubMed

Sanmukhani, J; Shah, V

2010-01-01

Coronary heart disease (CHD) is the leading cause of death in India resulting in loss of young Indians. Statins have proved to reduce the CHD mortality in various clinical trials. The aim of the study is to find the cost-effectiveness ratio (CER) for each major coronary event averted and a coronary death avoided by use of statins in different clinical settings based on the data from the major clinical trials on statins. Using electronic database and as per our inclusion and exclusion criteria we selected the West of Scotland Coronary Prevention Study (WOSCOPS), the Air Force Coronary Atherosclerosis Prevention Study (AFCAPS) and the Anglo-Scandinavian Cardiac Outcomes Trial--Lipid Lowering Arm (ASCOT-LLA) study for primary prevention; the Cholesterol and Recurrent Events Trial (CARE), the Long-term Intervention with Pravastatin in Ischemic Disease (LIPID) Study and the Scandinavian Simvastatin Survival Study (4S) for secondary prevention and two studies, the Heart Protection Study (HPS) and the Pravastatin in elderly individuals at risk of vascular disease (PROSPER) study for high-risk patients. The results of these studies were used for cost-effectiveness analysis of statins in different patient groups. Absolute risk reduction, Number Needed to Benefit (NNTB), NNTB/year for total sample and in subgroups of males, females and age >65 was derived. CER for branded and generic versions was calculated by using the prices of statins listed in Indian Drug Review Triple i. Cost-effectiveness ratio (CER) in primary prevention studies i.e., the WOSCOPS, the AFCAPS and the ASCOT-LLA was Rs. 25.8 lacs, Rs. 23.8 lacs and Rs. 7.9 lacs per major coronary event averted respectively. CER in secondary prevention studies i.e., the CARE and the LIPID was approximately Rs. 20 lacs per major coronary event averted while it was Rs. 52.4 lacs and Rs. 37 lacs per coronary heart disease (CHD) death avoided. CER from the 4S was Rs. 6.9 lacs per major coronary event and Rs. 16.9 lacs per CHD death averted. CER in the HPS and the PROSPER study was Rs. 17.9 lacs and Rs. 27.1 lacs per major coronary event avoided in high-risk patients. Cost associated with the use of statins is higher in primary prevention as compared to secondary prevention. More studies are needed to confirm the cost-effectiveness of statins to make any decision for health policy.

Association of Liver Injury From Specific Drugs, or Groups of Drugs, With Polymorphisms in HLA and Other Genes in a Genome-wide Association Study

PubMed Central

Nicoletti, Paola; Aithal, Guruprasad P.; Bjornsson, Einar S.; Andrade, Raul J.; Sawle, Ashley; Arrese, Marco; Barnhart, Huiman X.; Bondon-Guitton, Emmanuelle; Hayashi, Paul H.; Bessone, Fernando; Carvajal, Alfonso; Cascorbi, Ingolf; Cirulli, Elizabeth T.; Chalasani, Naga; Conforti, Anita; Coulthard, Sally A.; Daly, Mark J.; Day, Christopher P.; Dillon, John F.; Fontana, Robert J.; Grove, Jane I.; Hallberg, Pär; Hernández, Nelia; Ibáñez, Luisa; Kullak-Ublick, Gerd A.; Laitinen, Tarja; Larrey, Dominique; Lucena, M. Isabel; Maitland-van der Zee, Anke H.; Martin, Jennifer H.; Molokhia, Mariam; Pirmohamed, Munir; Powell, Elizabeth E.; Qin, Shengying; Serrano, Jose; Stephens, Camilla; Stolz, Andrew; Wadelius, Mia; Watkins, Paul B.; Floratos, Aris; Shen, Yufeng; Nelson, Matthew R.; Urban, Thomas J.; Daly, Ann K.

2017-01-01

BACKGROUND & AIMS We performed a genome-wide association study (GWAS) to identify genetic risk factors for drug-induced liver injury (DILI) from licensed drugs without previously reported genetic risk factors. METHODS We performed a GWAS of 862 persons with DILI and 10588 population-matched controls. The first set of cases was recruited prior to May 2009 in Europe (n=137) or the USA (n=274). The second set of cases were identified from May 2009 through May 2013 from international collaborative studies performed in Europe, the USA and South America. For the GWAS, we included only cases of European ancestry associated with a particular drug (but not flucloxacillin or amoxicillin-clavulanate). We used DNA samples from all subjects to analyze human leukocyte antigen (HLA) genes and single nucleotide polymorphisms (SNPs). After the discovery analysis was concluded, we validated our findings using data from 283 European patients with diagnosis of DILI associated with various drugs. RESULTS We associated DILI with rs114577328 (a proxy for A*33:01 a HLA class I allele; odds ratio [OR], 2.7; 95% CI, 1.9–3.8; P=2.4×10−8) and with rs72631567 on chromosome 2 (OR, 2.0; 95% CI, 1.6–2.5; P=9.7×10−9). The association with A*33:01 was mediated by large effects for terbinafine-, fenofibrate-, and ticlopidine-related DILI. The variant on chromosome 2 was associated with DILI from a variety of drugs. Further phenotypic analysis indicated that the association between DILI and A*33:01 was significant, genome wide, for cholestatic and mixed DILI, but not for hepatocellular DILI; the polymorphism on chromosome 2 associated with cholestatic and mixed DILI as well as hepatocellular DILI. We identified an association between rs28521457 (within the LRBA gene) and only hepatocellular DILI (OR, 2.1; 95% CI, 1.6–2.7; P=4.8×10−9). We did not associate any specific drug classes with genetic polymorphisms, except for statin-associated DILI, which was associated with rs116561224 on chromosome 18 (OR=5.4; 95% CI, 3.0–9.5; P=7.1×10−9). We validated the association between A*33:01 terbinafine- and sertraline-induced DILI. We could not validate the association between DILI and rs72631567, rs28521457, or rs116561224. CONCLUSIONS In a GWAS of persons of European descent with DILI, we associated HLA-A*33:01 with DILI due to terbinafine and possibly fenofibrate and ticlopidine. We identified polymorphisms that appear to be associated with DILI from statins, as well as 2 non–drug-specific risk factors. PMID:28043905

A method to estimate the neutral atmospheric density near the ionospheric main peak of Mars

NASA Astrophysics Data System (ADS)

Zou, Hong; Ye, Yu Guang; Wang, Jin Song; Nielsen, Erling; Cui, Jun; Wang, Xiao Dong

2016-04-01

A method to estimate the neutral atmospheric density near the ionospheric main peak of Mars is introduced in this study. The neutral densities at 130 km can be derived from the ionospheric and atmospheric measurements of the Radio Science experiment on board Mars Global Surveyor (MGS). The derived neutral densities cover a large longitude range in northern high latitudes from summer to late autumn during 3 Martian years, which fills the gap of the previous observations for the upper atmosphere of Mars. The simulations of the Laboratoire de Météorologie Dynamique Mars global circulation model can be corrected with a simple linear equation to fit the neutral densities derived from the first MGS/RS (Radio Science) data sets (EDS1). The corrected simulations with the same correction parameters as for EDS1 match the derived neutral densities from two other MGS/RS data sets (EDS2 and EDS3) very well. The derived neutral density from EDS3 shows a dust storm effect, which is in accord with the Mars Express (MEX) Spectroscopy for Investigation of Characteristics of the Atmosphere of Mars measurement. The neutral density derived from the MGS/RS measurements can be used to validate the Martian atmospheric models. The method presented in this study can be applied to other radio occultation measurements, such as the result of the Radio Science experiment on board MEX.

Stress-Induced Resistive Switching in Pt/HfO2/Ti Devices

NASA Astrophysics Data System (ADS)

Zeevi, Gilad; Katsman, Alexander; Yaish, Yuval E.

2018-02-01

In the present work, we study the initial SET mechanism of resistive switching (RS) in Pt/HfO2/Ti devices under a static electrical stress and the RS mechanism under a bias sweeping mode with rates of 100 mV/s-300 mV/s. We characterize the thin HfO2 dielectric layer by x-ray photoelectron spectroscopy and x-ray diffraction. These findings show that the layer structure is stoichiometric and nanocrystalline with a crystal diameter of ˜ 14 Å. We measure the temporal dependence of the conductive filament growth at different temperatures and for various biases. Furthermore, these devices present stable bipolar resistive switching with a high-to-low resistive state (HRS/LRS) ratio of more than three orders of magnitude. Activation energy E RS ≈ 0.56 eV and drift current parameter V 0 ≈ 0.07 V were determined from the temporal dependence of the initial `SET' process, first HRS to LRS transition [for static electrical stress of V DS = (4.7-5.0 V)]. We analyze the results according to our model suggesting generation of double-charge oxygen vacancies at the anode and their diffusion across the dielectric layer. The double-charge vacancies transform to a single charge and then to neutral vacancies by capturing hot electrons, and form a conductive filament as soon as a critical neutral-vacancy cluster is formed across the dielectric layer.

A Genome-wide Association Study of Myasthenia Gravis

PubMed Central

Renton, Alan E.; Pliner, Hannah A.; Provenzano, Carlo; Evoli, Amelia; Ricciardi, Roberta; Nalls, Michael A.; Marangi, Giuseppe; Abramzon, Yevgeniya; Arepalli, Sampath; Chong, Sean; Hernandez, Dena G.; Johnson, Janel O.; Bartoccioni, Emanuela; Scuderi, Flavia; Maestri, Michelangelo; Raphael Gibbs, J.; Errichiello, Edoardo; Chiò, Adriano; Restagno, Gabriella; Sabatelli, Mario; Macek, Mark; Scholz, Sonja W.; Corse, Andrea; Chaudhry, Vinay; Benatar, Michael; Barohn, Richard J.; McVey, April; Pasnoor, Mamatha; Dimachkie, Mazen M.; Rowin, Julie; Kissel, John; Freimer, Miriam; Kaminski, Henry J.; Sanders, Donald B.; Lipscomb, Bernadette; Massey, Janice M.; Chopra, Manisha; Howard, James F.; Koopman, Wilma J.; Nicolle, Michael W.; Pascuzzi, Robert M.; Pestronk, Alan; Wulf, Charlie; Florence, Julaine; Blackmore, Derrick; Soloway, Aimee; Siddiqi, Zaeem; Muppidi, Srikanth; Wolfe, Gil; Richman, David; Mezei, Michelle M.; Jiwa, Theresa; Oger, Joel; Drachman, Daniel B.; Traynor, Bryan J.

2016-01-01

IMPORTANCE Myasthenia gravis is a chronic, autoimmune, neuromuscular disease characterized by fluctuating weakness of voluntary muscle groups. Although genetic factors are known to play a role in this neuroimmunological condition, the genetic etiology underlying myasthenia gravis is not well understood. OBJECTIVE To identify genetic variants that alter susceptibility to myasthenia gravis, we performed a genome-wide association study. DESIGN, SETTING, AND PARTICIPANTS DNA was obtained from 1032 white individuals from North America diagnosed as having acetylcholine receptor antibody–positive myasthenia gravis and 1998 race/ethnicity-matched control individuals from January 2010 to January 2011. These samples were genotyped on Illumina OmniExpress single-nucleotide polymorphism arrays. An independent cohort of 423 Italian cases and 467 Italian control individuals were used for replication. MAIN OUTCOMES AND MEASURES We calculated P values for association between 8114394 genotyped and imputed variants across the genome and risk for developing myasthenia gravis using logistic regression modeling. A threshold P value of 5.0 × 10−8 was set for genome-wide significance after Bonferroni correction for multiple testing. RESULTS In the over all case-control cohort, we identified association signals at CTLA4 (rs231770; P = 3.98 × 10−8; odds ratio, 1.37; 95% CI, 1.25–1.49), HLA-DQA1 (rs9271871; P = 1.08 × 10−8; odds ratio, 2.31; 95% CI, 2.02 – 2.60), and TNFRSF11A (rs4263037; P = 1.60 × 10−9; odds ratio, 1.41; 95% CI, 1.29–1.53). These findings replicated for CTLA4 and HLA-DQA1 in an independent cohort of Italian cases and control individuals. Further analysis revealed distinct, but overlapping, disease-associated loci for early- and late-onset forms of myasthenia gravis. In the late-onset cases, we identified 2 association peaks: one was located in TNFRSF11A (rs4263037; P = 1.32 × 10−12; odds ratio, 1.56; 95% CI, 1.44–1.68) and the other was detected in the major histocompatibility complex on chromosome 6p21 (HLA-DQA1; rs9271871; P = 7.02 × 10−18; odds ratio, 4.27; 95% CI, 3.92–4.62). Association within the major histocompatibility complex region was also observed in early-onset cases (HLA-DQA1; rs601006; P = 2.52 × 10−11; odds ratio, 4.0; 95% CI, 3.57–4.43), although the set of single-nucleotide polymorphisms was different from that implicated among late-onset cases. CONCLUSIONS AND RELEVANCE Our genetic data provide insights into aberrant cellular mechanisms responsible for this prototypical autoimmune disorder. They also suggest that clinical trials of immunomodulatory drugs related to CTLA4 and that are already Food and Drug Administration approved as therapies for other autoimmune diseases could be considered for patients with refractory disease. PMID:25643325

Fast Spatial Resolution Analysis of Quadratic Penalized Least-Squares Image Reconstruction With Separate Real and Imaginary Roughness Penalty: Application to fMRI.

PubMed

Olafsson, Valur T; Noll, Douglas C; Fessler, Jeffrey A

2018-02-01

Penalized least-squares iterative image reconstruction algorithms used for spatial resolution-limited imaging, such as functional magnetic resonance imaging (fMRI), commonly use a quadratic roughness penalty to regularize the reconstructed images. When used for complex-valued images, the conventional roughness penalty regularizes the real and imaginary parts equally. However, these imaging methods sometimes benefit from separate penalties for each part. The spatial smoothness from the roughness penalty on the reconstructed image is dictated by the regularization parameter(s). One method to set the parameter to a desired smoothness level is to evaluate the full width at half maximum of the reconstruction method's local impulse response. Previous work has shown that when using the conventional quadratic roughness penalty, one can approximate the local impulse response using an FFT-based calculation. However, that acceleration method cannot be applied directly for separate real and imaginary regularization. This paper proposes a fast and stable calculation for this case that also uses FFT-based calculations to approximate the local impulse responses of the real and imaginary parts. This approach is demonstrated with a quadratic image reconstruction of fMRI data that uses separate roughness penalties for the real and imaginary parts.

Investigation of roughing machining simulation by using visual basic programming in NX CAM system

NASA Astrophysics Data System (ADS)

Hafiz Mohamad, Mohamad; Nafis Osman Zahid, Muhammed

2018-03-01

This paper outlines a simulation study to investigate the characteristic of roughing machining simulation in 4th axis milling processes by utilizing visual basic programming in NX CAM systems. The selection and optimization of cutting orientation in rough milling operation is critical in 4th axis machining. The main purpose of roughing operation is to approximately shape the machined parts into finished form by removing the bulk of material from workpieces. In this paper, the simulations are executed by manipulating a set of different cutting orientation to generate estimated volume removed from the machine parts. The cutting orientation with high volume removal is denoted as an optimum value and chosen to execute a roughing operation. In order to run the simulation, customized software is developed to assist the routines. Operations build-up instructions in NX CAM interface are translated into programming codes via advanced tool available in the Visual Basic Studio. The codes is customized and equipped with decision making tools to run and control the simulations. It permits the integration with any independent program files to execute specific operations. This paper aims to discuss about the simulation program and identifies optimum cutting orientations for roughing processes. The output of this study will broaden up the simulation routines performed in NX CAM systems.

Common variants at the promoter region of the APOM confer a risk of rheumatoid arthritis

PubMed Central

Hu, Hae-Jin; Jin, Eun-Heui; Yim, Seon-Hee; Yang, So-Young; Jung, Seung-Hyun; Shin, Seung-Hun; Kim, Wan-Uk; Shim, Seung-Cheol; Kim, Tai-Gyu

2011-01-01

Although the genetic component in the etiology of rheumatoid arthritis (RA) has been consistently suggested, many novel genetic loci remain to uncover. To identify RA risk loci, we performed a genome-wide association study (GWAS) with 100 RA cases and 600 controls using Affymetrix SNP array 5.0. The candidate risk locus (APOM gene) was re-sequenced to discover novel promoter and coding variants in a group of the subjects. Replication was performed with the independent case-control set comprising of 578 RAs and 711 controls. Through GWAS, we identified a novel SNP associated with RA at the APOM gene in the MHC class III region on 6p21.33 (rs805297, odds ratio (OR) = 2.28, P = 5.20 × 10-7). Three more polymorphisms were identified at the promoter region of the APOM by the re-sequencing. For the replication, we genotyped the four SNP loci in the independent case-control set. The association of rs805297 identified by GWAS was successfully replicated (OR = 1.40, P = 6.65 × 10-5). The association became more significant in the combined analysis of discovery and replication sets (OR = 1.56, P = 2.73 ± 10-10). The individuals with the rs805297 risk allele (A) at the promoter region showed a significantly lower level of APOM expression compared with those with the protective allele (C) homozygote. In the logistic regressions by the phenotype status, the homozygote risk genotype (A/A) consistently showed higher ORs than the heterozygote one (A/C) for the phenotype-positive RAs. These results indicate that APOM promoter polymorphisms are significantly associated with the susceptibility to RA. PMID:21844665

Bed roughness of palaeo-ice streams: insights and implications for contemporary ice sheet dynamics

NASA Astrophysics Data System (ADS)

Falcini, Francesca; Rippin, David; Selby, Katherine; Krabbendam, Maarten

2017-04-01

Bed roughness is the vertical variation of elevation along a horizontal transect. It is an important control on ice stream location and dynamics, with a correspondingly important role in determining the behaviour of ice sheets. Previous studies of bed roughness have been limited to insights derived from Radio Echo Sounding (RES) profiles across parts of Antarctica and Greenland. Such an approach has been necessary due to the inaccessibility of the underlying bed. This approach has led to important insights, such as identifying a general link between smooth beds and fast ice flow, as well as rough beds and slow ice flow. However, these insights are mainly derived from relatively coarse datasets, so that links between roughness and flow are generalised and rather simplistic. Here, we explore the use of DTMs from the well-preserved footprints of palaeo-ice streams, coupled with high resolution models of palaeo-ice flow, as a tool for investigating basal controls on the behaviour of contemporary, active ice streams in much greater detail. Initially, artificial transects were set up across the Minch palaeo-ice stream (NW Scotland) to mimic RES flight lines from past studies in Antarctica. We then explored how increasing data-resolution impacted upon the roughness measurements that were derived. Our work on the Minch palaeo-ice stream indicates that different roughness signatures are associated with different glacial landforms, and we discuss the potential for using these insights to infer, from RES-based roughness measurements, the occurrence of particular landform assemblages that may exist beneath contemporary ice sheets.

“Not Being Able to Talk was Horrid”: A Descriptive, Correlational Study of Communication During Mechanical Ventilation

PubMed Central

Guttormson, Jill L.; Bremer, Karin Lindstrom; Jones, Rachel M.

2015-01-01

Objectives The purpose of this study was to describe the patient experience of communication during mechanical ventilation Research Methodology This descriptive study is a secondary analysis of data collected to study the relationship between sedation and the MV patients' recall of the ICU. Interviews, conducted after extubation, included the Intensive Care Experience Questionnaire. Data were analyzed with Spearman correlation coefficients (rs) and content analysis. Setting Participants were recruited from a medical-surgical intensive care unit in the Midwest United States. Results Participants (n=31) with a mean age of 65 ± 11.9 were on the ventilator a median of 5 days. Inability to communicate needs was associated with helplessness (rs = .43). While perceived lack of information received was associated with not feeling in control (rs =.41) and helplessness (rs =.41). Ineffective communication negatively impacted satisfaction with care. Participants expressed frustration with failed communication and a lack of information received. They believed receipt of information helped them cope and desired a better system of communication during mechanical ventilation. Conclusion Communication effectiveness impacts patients' sense of safety and well-being during mechanical ventilation. Greater emphasis needs to be placed on the development and integration of communication strategies into critical care nursing practice. PMID:25579081

Genome-wide association study identifies multiple loci associated with bladder cancer risk

PubMed Central

Figueroa, Jonine D.; Ye, Yuanqing; Siddiq, Afshan; Garcia-Closas, Montserrat; Chatterjee, Nilanjan; Prokunina-Olsson, Ludmila; Cortessis, Victoria K.; Kooperberg, Charles; Cussenot, Olivier; Benhamou, Simone; Prescott, Jennifer; Porru, Stefano; Dinney, Colin P.; Malats, Núria; Baris, Dalsu; Purdue, Mark; Jacobs, Eric J.; Albanes, Demetrius; Wang, Zhaoming; Deng, Xiang; Chung, Charles C.; Tang, Wei; Bas Bueno-de-Mesquita, H.; Trichopoulos, Dimitrios; Ljungberg, Börje; Clavel-Chapelon, Françoise; Weiderpass, Elisabete; Krogh, Vittorio; Dorronsoro, Miren; Travis, Ruth; Tjønneland, Anne; Brenan, Paul; Chang-Claude, Jenny; Riboli, Elio; Conti, David; Gago-Dominguez, Manuela; Stern, Mariana C.; Pike, Malcolm C.; Van Den Berg, David; Yuan, Jian-Min; Hohensee, Chancellor; Rodabough, Rebecca; Cancel-Tassin, Geraldine; Roupret, Morgan; Comperat, Eva; Chen, Constance; De Vivo, Immaculata; Giovannucci, Edward; Hunter, David J.; Kraft, Peter; Lindstrom, Sara; Carta, Angela; Pavanello, Sofia; Arici, Cecilia; Mastrangelo, Giuseppe; Kamat, Ashish M.; Lerner, Seth P.; Barton Grossman, H.; Lin, Jie; Gu, Jian; Pu, Xia; Hutchinson, Amy; Burdette, Laurie; Wheeler, William; Kogevinas, Manolis; Tardón, Adonina; Serra, Consol; Carrato, Alfredo; García-Closas, Reina; Lloreta, Josep; Schwenn, Molly; Karagas, Margaret R.; Johnson, Alison; Schned, Alan; Armenti, Karla R.; Hosain, G.M.; Andriole, Gerald; Grubb, Robert; Black, Amanda; Ryan Diver, W.; Gapstur, Susan M.; Weinstein, Stephanie J.; Virtamo, Jarmo; Haiman, Chris A.; Landi, Maria T.; Caporaso, Neil; Fraumeni, Joseph F.; Vineis, Paolo; Wu, Xifeng; Silverman, Debra T.; Chanock, Stephen; Rothman, Nathaniel

2014-01-01

Candidate gene and genome-wide association studies (GWAS) have identified 11 independent susceptibility loci associated with bladder cancer risk. To discover additional risk variants, we conducted a new GWAS of 2422 bladder cancer cases and 5751 controls, followed by a meta-analysis with two independently published bladder cancer GWAS, resulting in a combined analysis of 6911 cases and 11 814 controls of European descent. TaqMan genotyping of 13 promising single nucleotide polymorphisms with P < 1 × 10−5 was pursued in a follow-up set of 801 cases and 1307 controls. Two new loci achieved genome-wide statistical significance: rs10936599 on 3q26.2 (P = 4.53 × 10−9) and rs907611 on 11p15.5 (P = 4.11 × 10−8). Two notable loci were also identified that approached genome-wide statistical significance: rs6104690 on 20p12.2 (P = 7.13 × 10−7) and rs4510656 on 6p22.3 (P = 6.98 × 10−7); these require further studies for confirmation. In conclusion, our study has identified new susceptibility alleles for bladder cancer risk that require fine-mapping and laboratory investigation, which could further understanding into the biological underpinnings of bladder carcinogenesis. PMID:24163127

Ecological association between scarlet fever and asthma.

PubMed

Vargas, Mario H

2006-02-01

One plausible explanation for the worldwide epidemic increase of asthma prevalence is the hygiene hypothesis, which suggests that better control of infections shifts the immune response toward an allergic phenotype. However, studies demonstrating an inverse association between asthma and infectious diseases are scarce and possess conflicting results. To explore the relationship between asthma and scarlet fever, an ecological analysis of their national trends was carried out. Association of both diseases in their annual (1996-2003), seasonal (by month) and geographic (by state) trends was evaluated using the Spearman's correlation coefficient (r(S)). Results showed a strong inverse association between asthma and scarlet fever in all settings. Thus, annual incidence rates of both diseases showed an r(S)=-0.93 (P=0.0009). Seasonal patterns showed a higher proportion of new asthma cases from September to January, while the number of scarlet fever cases increased from March to June (r(S)=-0.84, P=0.0006, 1-month lag). Among the 32 Mexican states, the higher the incidence of scarlet fever the lower the incidence of asthma (r(S)=-0.47, P=0.007). These results suggest that Streptococcus pyogenes, the causative agent of scarlet fever, might be one of the major protagonists of the hygiene hypothesis, a possibility deserving of further investigation.

Identification of Lethal Mutations in Yeast Threonyl-tRNA Synthetase Revealing Critical Residues in Its Human Homolog*

PubMed Central

Ruan, Zhi-Rong; Fang, Zhi-Peng; Ye, Qing; Lei, Hui-Yan; Eriani, Gilbert; Zhou, Xiao-Long; Wang, En-Duo

2015-01-01

Aminoacyl-tRNA synthetases (aaRSs) are a group of ancient enzymes catalyzing aminoacylation and editing reactions for protein biosynthesis. Increasing evidence suggests that these critical enzymes are often associated with mammalian disorders. Therefore, complete determination of the enzymes functions is essential for informed diagnosis and treatment. Here, we show that a yeast knock-out strain for the threonyl-tRNA synthetase (ThrRS) gene is an excellent platform for such an investigation. Saccharomyces cerevisiae ThrRS has a unique modular structure containing four structural domains and a eukaryote-specific N-terminal extension. Using randomly mutated libraries of the ThrRS gene (thrS) and a genetic screen, a set of loss-of-function mutants were identified. The mutations affected the synthetic and editing activities and influenced the dimer interface. The results also highlighted the role of the N-terminal extension for enzymatic activity and protein stability. To gain insights into the pathological mechanisms induced by mutated aaRSs, we systematically introduced the loss-of-function mutations into the human cytoplasmic ThrRS gene. All mutations induced similar detrimental effects, showing that the yeast model could be used to study pathology-associated point mutations in mammalian aaRSs. PMID:25416776

GWAS of cerebrospinal fluid tau levels identifies risk variants for Alzheimer's disease.

PubMed

Cruchaga, Carlos; Kauwe, John S K; Harari, Oscar; Jin, Sheng Chih; Cai, Yefei; Karch, Celeste M; Benitez, Bruno A; Jeng, Amanda T; Skorupa, Tara; Carrell, David; Bertelsen, Sarah; Bailey, Matthew; McKean, David; Shulman, Joshua M; De Jager, Philip L; Chibnik, Lori; Bennett, David A; Arnold, Steve E; Harold, Denise; Sims, Rebecca; Gerrish, Amy; Williams, Julie; Van Deerlin, Vivianna M; Lee, Virginia M-Y; Shaw, Leslie M; Trojanowski, John Q; Haines, Jonathan L; Mayeux, Richard; Pericak-Vance, Margaret A; Farrer, Lindsay A; Schellenberg, Gerard D; Peskind, Elaine R; Galasko, Douglas; Fagan, Anne M; Holtzman, David M; Morris, John C; Goate, Alison M

2013-04-24

Cerebrospinal fluid (CSF) tau, tau phosphorylated at threonine 181 (ptau), and Aβ₄₂ are established biomarkers for Alzheimer's disease (AD) and have been used as quantitative traits for genetic analyses. We performed the largest genome-wide association study for cerebrospinal fluid (CSF) tau/ptau levels published to date (n = 1,269), identifying three genome-wide significant loci for CSF tau and ptau: rs9877502 (p = 4.89 × 10⁻⁹ for tau) located at 3q28 between GEMC1 and OSTN, rs514716 (p = 1.07 × 10⁻⁸ and p = 3.22 × 10⁻⁹ for tau and ptau, respectively), located at 9p24.2 within GLIS3 and rs6922617 (p = 3.58 × 10⁻⁸ for CSF ptau) at 6p21.1 within the TREM gene cluster, a region recently reported to harbor rare variants that increase AD risk. In independent data sets, rs9877502 showed a strong association with risk for AD, tangle pathology, and global cognitive decline (p = 2.67 × 10⁻⁴, 0.039, 4.86 × 10⁻⁵, respectively) illustrating how this endophenotype-based approach can be used to identify new AD risk loci. Copyright © 2013 Elsevier Inc. All rights reserved.

Selection of an evaluation index for water ecological civilizations of water-shortage cities based on the grey rough set

NASA Astrophysics Data System (ADS)

Zhang, X. Y.; Zhu, J. W.; Xie, J. C.; Liu, J. L.; Jiang, R. G.

2017-08-01

According to the characteristics and existing problems of water ecological civilization of water-shortage cities, the evaluation index system of water ecological civilization was established using a grey rough set. From six aspects of water resources, water security, water environment, water ecology, water culture and water management, this study established the prime frame of the evaluation system, including 28 items, and used rough set theory to undertake optimal selection of the index system. Grey correlation theory then was used for weightings in order that the integrated evaluation index system for water ecology civilization of water-shortage cities could be constituted. Xi’an City was taken as an example, for which the results showed that 20 evaluation indexes could be obtained after optimal selection of the preliminary framework of evaluation index. The most influential indices were the water-resource category index and water environment category index. The leakage rate of the public water supply pipe network, as well as the disposal, treatment and usage rate of polluted water, urban water surface area ratio, the water quality of the main rivers, and so on also are important. It was demonstrated that the evaluation index could provide an objectively reflection of regional features and key points for the development of water ecology civilization for cities with scarce water resources. It is considered that the application example has universal applicability.

Definitions and Omissions of Heroism

ERIC Educational Resources Information Center

Martens, Jeffrey W.

2005-01-01

This article presents comments on "The Heroism of Women and Men" by Selwyn W. Becker and Alice H. Eagly. Their article specifically addressed the "cultural association of heroism with men and masculinity . . . in natural settings." Becker and Eagly evidenced roughly equivalent rates of heroism by women and men in a variety of settings. However,…

Intrusion detection using rough set classification.

PubMed

Zhang, Lian-hua; Zhang, Guan-hua; Zhang, Jie; Bai, Ying-cai

2004-09-01

Recently machine learning-based intrusion detection approaches have been subjected to extensive researches because they can detect both misuse and anomaly. In this paper, rough set classification (RSC), a modern learning algorithm, is used to rank the features extracted for detecting intrusions and generate intrusion detection models. Feature ranking is a very critical step when building the model. RSC performs feature ranking before generating rules, and converts the feature ranking to minimal hitting set problem addressed by using genetic algorithm (GA). This is done in classical approaches using Support Vector Machine (SVM) by executing many iterations, each of which removes one useless feature. Compared with those methods, our method can avoid many iterations. In addition, a hybrid genetic algorithm is proposed to increase the convergence speed and decrease the training time of RSC. The models generated by RSC take the form of "IF-THEN" rules, which have the advantage of explication. Tests and comparison of RSC with SVM on DARPA benchmark data showed that for Probe and DoS attacks both RSC and SVM yielded highly accurate results (greater than 99% accuracy on testing set).

An Association Between Functional Polymorphisms of the Interleukin 1 Gene Complex and Schizophrenia Using Transmission Disequilibrium Test.

PubMed

Kapelski, Pawel; Skibinska, Maria; Maciukiewicz, Malgorzata; Pawlak, Joanna; Dmitrzak-Weglarz, Monika; Szczepankiewicz, Aleksandra; Zaremba, Dorota; Twarowska-Hauser, Joanna

2016-12-01

IL1 gene complex has been implicated in the etiology of schizophrenia. To assess whether IL1 gene complex is associated with susceptibility to schizophrenia in Polish population we conducted family-based study. Functional polymorphisms from IL1A (rs1800587, rs17561, rs11677416), IL1B (rs1143634, rs1143643, rs16944, rs4848306, rs1143623, rs1143633, rs1143627) and IL1RN (rs419598, rs315952, rs9005, rs4251961) genes were genotyped in 143 trio with schizophrenia. Statistical analysis was performed using transmission disequilibrium test. We have found a trend toward an association of rs1143627, rs16944, rs1143623 in IL1B gene with the risk of schizophrenia. Our results show a protective effect of allele T of rs4251961 in IL1RN against schizophrenia. We also performed haplotype analysis of IL1 gene complex and found a trend toward an association with schizophrenia of GAGG haplotype (rs1143627, rs16944, rs1143623, rs4848306) in IL1B gene, haplotypes: TG (rs315952, rs9005) and TT (rs4251961, rs419598) in IL1RN. Haplotype CT (rs4251961, rs419598) in IL1RN was found to be associated with schizophrenia. After correction for multiple testing associations did not reach significance level. Our results might support theory that polymorphisms of interleukin 1 complex genes (rs1143627, rs16944, rs1143623, rs4848306 in IL1B gene and rs4251961, rs419598, rs315952, rs9005 in IL1RN gene) are involved in the pathogenesis of schizophrenia, however, none of the results reach significance level after correction for multiple testing.

Rough Set Theory based prognostication of life expectancy for terminally ill patients.

PubMed

Gil-Herrera, Eleazar; Yalcin, Ali; Tsalatsanis, Athanasios; Barnes, Laura E; Djulbegovic, Benjamin

2011-01-01

We present a novel knowledge discovery methodology that relies on Rough Set Theory to predict the life expectancy of terminally ill patients in an effort to improve the hospice referral process. Life expectancy prognostication is particularly valuable for terminally ill patients since it enables them and their families to initiate end-of-life discussions and choose the most desired management strategy for the remainder of their lives. We utilize retrospective data from 9105 patients to demonstrate the design and implementation details of a series of classifiers developed to identify potential hospice candidates. Preliminary results confirm the efficacy of the proposed methodology. We envision our work as a part of a comprehensive decision support system designed to assist terminally ill patients in making end-of-life care decisions.

Access Selection Algorithm of Heterogeneous Wireless Networks for Smart Distribution Grid Based on Entropy-Weight and Rough Set

NASA Astrophysics Data System (ADS)

Xiang, Min; Qu, Qinqin; Chen, Cheng; Tian, Li; Zeng, Lingkang

2017-11-01

To improve the reliability of communication service in smart distribution grid (SDG), an access selection algorithm based on dynamic network status and different service types for heterogeneous wireless networks was proposed. The network performance index values were obtained in real time by multimode terminal and the variation trend of index values was analyzed by the growth matrix. The index weights were calculated by entropy-weight and then modified by rough set to get the final weights. Combining the grey relational analysis to sort the candidate networks, and the optimum communication network is selected. Simulation results show that the proposed algorithm can implement dynamically access selection in heterogeneous wireless networks of SDG effectively and reduce the network blocking probability.

Allowable SEM noise for unbiased LER measurement

NASA Astrophysics Data System (ADS)

Papavieros, George; Constantoudis, Vassilios; Gogolides, Evangelos

2018-03-01

Recently, a novel method for the calculation of unbiased Line Edge Roughness based on Power Spectral Density analysis has been proposed. In this paper first an alternative method is discussed and investigated, utilizing the Height-Height Correlation Function (HHCF) of edges. The HHCF-based method enables the unbiased determination of the whole triplet of LER parameters including besides rms the correlation length and roughness exponent. The key of both methods is the sensitivity of PSD and HHCF on noise at high frequencies and short distance respectively. Secondly, we elaborate a testbed of synthesized SEM images with controlled LER and noise to justify the effectiveness of the proposed unbiased methods. Our main objective is to find out the boundaries of the method in respect to noise levels and roughness characteristics, for which the method remains reliable, i.e the maximum amount of noise allowed, for which the output results cope with the controllable known inputs. At the same time, we will also set the extremes of roughness parameters for which the methods hold their accuracy.

Association of FTO rs9939609 with Obesity.

PubMed

Yasri, Sora; Wiwanitkit, Viroj

2018-05-30

Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity

Materials (Subjects) and Methods

Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity

Results:

Association of FTO rs9939609 with Obesity

Conclusion:

Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity Association of FTO rs9939609 with Obesity. ©2018The Author(s). Published by S. Karger AG, Basel.

Effects of cutting parameters and machining environments on surface roughness in hard turning using design of experiment

NASA Astrophysics Data System (ADS)

Mia, Mozammel; Bashir, Mahmood Al; Dhar, Nikhil Ranjan

2016-07-01

Hard turning is gradually replacing the time consuming conventional turning process, which is typically followed by grinding, by producing surface quality compatible to grinding. The hard turned surface roughness depends on the cutting parameters, machining environments and tool insert configurations. In this article the variation of the surface roughness of the produced surfaces with the changes in tool insert configuration, use of coolant and different cutting parameters (cutting speed, feed rate) has been investigated. This investigation was performed in machining AISI 1060 steel, hardened to 56 HRC by heat treatment, using coated carbide inserts under two different machining environments. The depth of cut, fluid pressure and material hardness were kept constant. The Design of Experiment (DOE) was performed to determine the number and combination sets of different cutting parameters. A full factorial analysis has been performed to examine the effect of main factors as well as interaction effect of factors on surface roughness. A statistical analysis of variance (ANOVA) was employed to determine the combined effect of cutting parameters, environment and tool configuration. The result of this analysis reveals that environment has the most significant impact on surface roughness followed by feed rate and tool configuration respectively.

Effects of bio-inspired microscale roughness on macroscale flow structures

NASA Astrophysics Data System (ADS)

Bocanegra Evans, Humberto; Hamed, Ali M.; Gorumlu, Serdar; Doosttalab, Ali; Aksak, Burak; Chamorro, Leonardo P.; Castillo, Luciano

2016-11-01

The interaction between rough surfaces and flows is a complex physical situation that produces rich flow phenomena. While random roughness typically increases drag, properly engineered roughness patterns may produce positive results, e.g. dimples in a golf ball. Here we present a set of PIV measurements in an index matched facility of the effect of a bio-inspired surface that consists of an array of mushroom-shaped micro-pillars. The experiments are carried out-under fully wetted conditions-in a flow with adverse pressure gradient, triggering flow separation. The introduction of the micro-pillars dramatically decreases the size of the recirculation bubble; the area with backflow is reduced by approximately 60%. This suggests a positive impact on the form drag generated by the fluid. Furthermore, a negligible effect is seen on the turbulence production terms. The micro-pillars affect the flow by generating low and high pressure perturbations at the interface between the bulk and roughness layer, in a fashion comparable to that of synthetic jets. The passive approach, however, facilitates the implementation of this coating. As the mechanism does not rely on surface hydrophobicity, it is well suited for underwater applications and its functionality should not degrade over time.

MCP1 SNPs and Pulmonary Tuberculosis in Cohorts from West Africa, the USA and Argentina: Lack of Association or Epistasis with IL12B Polymorphisms

PubMed Central

Velez Edwards, Digna R.; Tacconelli, Alessandra; Wejse, Christian; Hill, Philip C.; Morris, Gerard A. J.; Edwards, Todd L.; Gilbert, John R.; Myers, Jamie L.; Park, Yo Son; Stryjewski, Martin E.; Abbate, Eduardo; Estevan, Rosa; Rabna, Paulo; Novelli, Giuseppe; Hamilton, Carol D.; Adegbola, Richard; Østergaard, Lars; Williams, Scott M.; Scott, William K.; Sirugo, Giorgio

2012-01-01

The monocyte chemotactic protein-1 (MCP-1) is a chemokine that plays an important role in the recruitment of monocytes to M. tuberculosis infection sites, and previous studies have reported that genetic variants in MCP1 are associated with differential susceptibility to pulmonary tuberculosis (PTB). We examined eight MCP1 single nucleotide polymorphisms (SNPs) in a multi-ethnic, case-control design that included: 321 cases and 346 controls from Guinea-Bissau, 258 cases and 271 controls from The Gambia, 295 cases and 179 controls from the U.S. (African-Americans), and an additional set of 237 cases and 144 controls of European ancestry from the U.S. and Argentina. Two locus interactions were also examined for polymorphisms in MCP1 and interleukin 12B (IL12B), another gene implicated in PTB risk. Examination of previously associated MCP1 SNPs rs1024611 (−2581A/G), rs2857656 (−362G/C) and rs4586 (+900C/T) did not show evidence for association. One interaction between rs2857656 and IL12B SNP rs2288831 was observed among Africans but the effect was in the opposite direction in Guineans (OR = 1.90, p = 0.001) and Gambians (OR = 0.64, p = 0.024). Our data indicate that the effect of genetic variation within MCP1 is not clear cut and additional studies will be needed to elucidate its role in TB susceptibility. PMID:22384203

Tumor margin assessment in Mohs surgery using reflectance, fluorescence and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Nguyen, Hieu T. M.; Moy, Austin J.; Zhang, Yao; Feng, Xu; Reichenberg, Jason S.; Fox, Matthew; Tunnell, James W.

2017-02-01

Mohs surgery is the current gold standard to treat large, aggressive or high-risk non-melanoma skin cancer (NMSC) cases. While Mohs surgery is an effective treatment, the procedure is time-consuming and expensive for physicians as well as burdensome for patients as they wait for frozen section histology. Our group has recently demonstrated high diagnostic accuracy using a noninvasive "spectral biopsy" (combination of diffuse reflectance (DRS), fluorescence (FS) and Raman spectroscopy (RS)) to classify NMSC vs. normal lesion in a screening setting of intact tissue. Here, we examine the sensitivity of spectral biopsy to pathology in excised Mohs sections. The system is designed with three modalities integrated into one fiber probe, which is utilized to measure DRS, FS, and RS of freshly excised skin from patients with various NMSC pathologies including basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), where each measurement location is correlated to histopathology. The spectral biopsy provides complimentary physiological information including the reduced scattering coefficient, hemoglobin content and oxygen saturation from DRS, NADH and collagen contribution from FS and information regarding multiple proteins and lipids from RS. We then apply logistic regression model to the extracted physiological parameters to classify NMSC vs. normal tissue. The results on the excised tissue are generally consistent with in vivo measurements showing decreased scattering within the tumor and reduced fluorescence. Due to the high sensitivity of RS to lipids, subcutaneous fat often dominates the RS signal. This pilot study demonstrates the potential for a spectral biopsy to classify NMSC vs. normal tissue, indicating the opportunity to guide Mohs excisions.

Resting-state functional connectivity predicts the strength of hemispheric lateralization for language processing in temporal lobe epilepsy and normals

PubMed Central

Doucet, Gaëlle E.; Pustina, Dorian; Skidmore, Christopher; Sharan, Ashwini; Sperling, Michael R.; Tracy, Joseph I.

2015-01-01

In temporal lobe epilepsy (TLE), determining the hemispheric specialization for language before surgery is critical to preserving a patient's cognitive abilities post-surgery. To date, the major techniques utilized are limited by the capacity of patients to efficiently realize the task. We determined whether resting-state functional connectivity (rsFC) is a reliable predictor of language hemispheric dominance in right and left TLE patients, relative to controls. We chose three subregions of the inferior frontal cortex (pars orbitalis, pars triangularis and pars opercularis) as the seed regions. All participants performed both a verb generation task and a resting-state fMRI procedure. Based on the language task, we computed a laterality index (LI) for the resulting network. This revealed that 96% of the participants were left-hemisphere dominant, although there remained a large degree of variability in the strength of left lateralization. We tested whether LI correlated with rsFC values emerging from each seed. We revealed a set of regions that was specific to each group. Unique correlations involving the epileptic mesial temporal lobe were revealed for the right and left TLE patients, but not for the controls. Importantly, for both TLE groups, the rsFC emerging from a contralateral seed was the most predictive of LI. Overall, our data depict the broad patterns of rsFC that support strong versus weak left hemisphere language laterality. This project provides the first evidence that rsFC data may potentially be used on its own to verify the strength of hemispheric dominance for language in impaired or pathologic populations. PMID:25187327

Common rs5918 (PlA1/A2) polymorphism in the ITGB3 gene and risk of coronary artery disease

PubMed Central

Heidari, Mohammad Mehdi; Soheilyfar, Sorour

2016-01-01

Introduction The T to C transition at nucleotide 1565 of the human glycoprotein IIIa (ITGB3) gene represents a genetic polymorphism (PlA1/A2) that can influence both platelet activation and aggregation and that has been associated with many types of disease. Here, we present a newly designed multiplex tetra-primer amplification refractory mutation system – polymerase chain reaction (T-ARMS-PCR) for genotyping a single nucleotide polymorphism (SNP) (dbSNP ID: rs5918) in the human ITGB3 gene. Material and methods We set up T-ARMS-PCR for the rs5918 SNP in a single-step PCR and the results were validated by the PCR-RFLP method in 132 coronary artery disease (CAD) patients and 122 unrelated healthy individuals. Results Full accordance was found for genotype determination by the PCR-RFLP method. The multiple logistic regression analysis showed a significant association of the rs5918 polymorphism and CAD according to dominant and recessive models (dominant model OR: 2.40, 95% CI: 1.33–4.35; p = 0.003, recessive model OR: 4.71, 95% CI: 1.32–16.80; p = 0.0067). Conclusions Our T-ARMS-PCR in comparison with RFLP and allele-specific PCR is more advantageous because this PCR method allows the evaluation of both the wild type and the mutant allele in the same tube. Our results suggest that the rs5918 (PlA1/A2) polymorphism in the ITGB3 gene may contribute to the susceptibility of sporadic Iranian coronary artery disease (CAD) patients. PMID:28905013

[Genes for Fibrogenesis in the Determination of Susceptibility to Myocardial Infarction].

PubMed

Goncharova, I A; Makeeva, O A; Golubenko, M V; Markov, A V; Tarasenko, N V; Sleptsov, A A; Puzyrev, V P

2016-01-01

A group of patients with ischemic heart disease and myocardial infarction (N = 156) and a reference population sample (N = 300) were genotyped for 58 single nucleotide polymorphisms (SNPs) in the genes involved in extracellular matrix function and collagen metabolism or associated with cardiovascular diseases and atherosclerotic plaque stability. Genotyping was performed by mass-spectrometry with two multiplex sets of 27 and 31 SNPs. The study revealed different genetic composition of predisposition to cardiovascular disease continuum (CVDC) syntropy (patients with concomitant conditions: hypercholesterolemia, hypertension, and type-II diabetes mellitus, N = 96) and to isolated myocardial infarction (without these conditions, N = 60). Only the KIAA1462 gene (rs3739998) showed associations with both CVDC syntropy (OR = 1.71; 95% CI 1.19-2.45; р = 0.003) and isolated infarction (OR = 1.58; 95% CI 1.05-2.40; р = 0.028). Isolated myocardial infarction was also associated with LIG1 (rs20579) (OR = 2.08; 95% CI 1.06-4.17; р = 0.028) and ADAMDEC1 (rs3765124) (OR = 1.63; 95% CI 1.07-2.50; р = 0.020). CVDC syntropy was associated with CDKN2BAS1 (rs1333049) (OR = 1.48; 95% CI 1.03-2.12; р = 0.029) and APOA2 (rs5082) (OR = 1.47; 95% CI 1.02-2.11; р = 0.035). So, genes involved in fibrogenesis contribute to predisposition to the myocardial infarction as well. Isolated myocardial infarction and CVDC syntropy can be considered as pathogenetically different cardiovascular conditions, with different genes that contribute to the susceptibility.

Focus Groups in Elderly Ophthalmologic Patients: Setting the Stage for Quantitative Preference Elicitation.

PubMed

Danner, Marion; Vennedey, Vera; Hiligsmann, Mickaël; Fauser, Sascha; Stock, Stephanie

2016-02-01

Patients suffering from age-related macular degeneration (AMD) are rarely actively involved in decision-making, despite facing preference-sensitive treatment decisions. This paper presents a qualitative study to prepare quantitative preference elicitation in AMD patients. The aims of this study were (1) to gain familiarity with and learn about the special requirements of the AMD patient population for quantitative data collection; and (2) to select/refine patient-relevant treatment attributes and levels, and gain insights into preference structures. Semi-structured focus group interviews were performed. An interview guide including preselected categories in the form of seven potentially patient-relevant treatment attributes was followed. To identify the most patient-relevant treatment attributes, a ranking exercise was performed. Deductive content analyses were done by two independent reviewers for each attribute to derive subcategories (potential levels of attributes) and depict preference trends. The focus group interviews included 21 patients. The interviews revealed that quantitative preference surveys in this population will have to be interviewer assisted to make the survey feasible for patients. The five most patient-relevant attributes were the effect on visual function [ranking score (RS): 139], injection frequency (RS: 101), approval status (RS: 83), side effects (RS: 79), and monitoring frequency (RS: 76). Attribute and level refinement was based on patients' statements. Preference trends and dependencies between attributes informed the quantitative instrument design. This study suggests that qualitative research is a very helpful step to prepare the design and administration of quantitative preference elicitation instruments. It especially facilitated familiarization with the target population and its preferences, and it supported attribute/level refinement.

Multicapillary gel electrophoresis based analysis of genetic variants in the WFS1 gene.

PubMed

Elek, Zsuzsanna; Dénes, Réka; Prokop, Susanne; Somogyi, Anikó; Yowanto, Handy; Luo, Jane; Souquet, Manfred; Guttman, András; Rónai, Zsolt

2016-09-01

The WFS1 gene is one of the thoroughly investigated targets in diabetes research, variants of the gene were suggested to be the genetic components of the common forms (type 1 and type 2) of diabetes. Our project focused on the analysis of polymorphisms (rs4689388, rs148797429, rs4273545) localized in the WFS1 promoter region. Although submarine gel electrophoresis based approaches were also employed in the genetic tests, it was demonstrated that multicapillary electrophoresis offers a state of the art approach for reliable high-throughput SNP and VNTR analysis. Association studies were carried out in a case-control setup. Luciferase reporter assay was employed to test the effect of the investigated loci on the activity of gene expression in vitro. Significant association could be demonstrated between all three polymorphisms and type 2 diabetes in both allele- and genotype-wise settings even using Bonferroni correction. It is notable; however, that the three loci were in strong linkage disequilibrium, thus the observed associations cannot be considered as separate effects. Molecular analyses showed that the rs4273545 GT SNP played a role in the regulation of transcription in vitro. However, this effect took place only in the presence of the region including the rs148797429 site, although this latter locus did not have its own impact on the regulation of gene expression. The paper provides genotyping protocols readily applicable in any multiplex SNP and VNTR analyses, moreover confirms and extends previous results about the role of WFS1 polymorphisms in the genetic risk of diabetes mellitus. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assessment of Ice Shape Roughness Using a Self-Orgainizing Map Approach

NASA Technical Reports Server (NTRS)

Mcclain, Stephen T.; Kreeger, Richard E.

2013-01-01

Self-organizing maps are neural-network techniques for representing noisy, multidimensional data aligned along a lower-dimensional and nonlinear manifold. For a large set of noisy data, each element of a finite set of codebook vectors is iteratively moved in the direction of the data closest to the winner codebook vector. Through successive iterations, the codebook vectors begin to align with the trends of the higher-dimensional data. Prior investigations of ice shapes have focused on using self-organizing maps to characterize mean ice forms. The Icing Research Branch has recently acquired a high resolution three dimensional scanner system capable of resolving ice shape surface roughness. A method is presented for the evaluation of surface roughness variations using high-resolution surface scans based on a self-organizing map representation of the mean ice shape. The new method is demonstrated for 1) an 18-in. NACA 23012 airfoil 2 AOA just after the initial ice coverage of the leading 5 of the suction surface of the airfoil, 2) a 21-in. NACA 0012 at 0AOA following coverage of the leading 10 of the airfoil surface, and 3) a cold-soaked 21-in.NACA 0012 airfoil without ice. The SOM method resulted in descriptions of the statistical coverage limits and a quantitative representation of early stages of ice roughness formation on the airfoils. Limitations of the SOM method are explored, and the uncertainty limits of the method are investigated using the non-iced NACA 0012 airfoil measurements.

Biochemical signatures of in vitro radiation response in human lung, breast and prostate tumour cells observed with Raman spectroscopy

NASA Astrophysics Data System (ADS)

Matthews, Q.; Jirasek, A.; Lum, J. J.; Brolo, A. G.

2011-11-01

This work applies noninvasive single-cell Raman spectroscopy (RS) and principal component analysis (PCA) to analyze and correlate radiation-induced biochemical changes in a panel of human tumour cell lines that vary by tissue of origin, p53 status and intrinsic radiosensitivity. Six human tumour cell lines, derived from prostate (DU145, PC3 and LNCaP), breast (MDA-MB-231 and MCF7) and lung (H460), were irradiated in vitro with single fractions (15, 30 or 50 Gy) of 6 MV photons. Remaining live cells were harvested for RS analysis at 0, 24, 48 and 72 h post-irradiation, along with unirradiated controls. Single-cell Raman spectra were acquired from 20 cells per sample utilizing a 785 nm excitation laser. All spectra (200 per cell line) were individually post-processed using established methods and the total data set for each cell line was analyzed with PCA using standard algorithms. One radiation-induced PCA component was detected for each cell line by identification of statistically significant changes in the PCA score distributions for irradiated samples, as compared to unirradiated samples, in the first 24-72 h post-irradiation. These RS response signatures arise from radiation-induced changes in cellular concentrations of aromatic amino acids, conformational protein structures and certain nucleic acid and lipid functional groups. Correlation analysis between the radiation-induced PCA components separates the cell lines into three distinct RS response categories: R1 (H460 and MCF7), R2 (MDA-MB-231 and PC3) and R3 (DU145 and LNCaP). These RS categories partially segregate according to radiosensitivity, as the R1 and R2 cell lines are radioresistant (SF2 > 0.6) and the R3 cell lines are radiosensitive (SF2 < 0.5). The R1 and R2 cell lines further segregate according to p53 gene status, corroborated by cell cycle analysis post-irradiation. Potential radiation-induced biochemical response mechanisms underlying our RS observations are proposed, such as (1) the regulated synthesis and degradation of structured proteins and (2) the expression of anti-apoptosis factors or other survival signals. This study demonstrates the utility of RS for noninvasive radiobiological analysis of tumour cell radiation response, and indicates the potential for future RS studies designed to investigate, monitor or predict radiation response.

Parameterized Spectral Bathymetric Roughness Using the Nonequispaced Fast Fourier Transform

NASA Astrophysics Data System (ADS)

Fabre, David Hanks

The ocean and acoustic modeling community has specifically asked for roughness from bathymetry. An effort has been undertaken to provide what can be thought of as the high frequency content of bathymetry. By contrast, the low frequency content of bathymetry is the set of contours. The two-dimensional amplitude spectrum calculated with the nonequispaced fast Fourier transform (Kunis, 2006) is exploited as the statistic to provide several parameters of roughness following the method of Fox (1996). When an area is uniformly rough, it is termed isotropically rough. When an area exhibits lineation effects (like in a trough or a ridge line in the bathymetry), the term anisotropically rough is used. A predominant spatial azimuth of lineation summarizes anisotropic roughness. The power law model fit produces a roll-off parameter that also provides insight into the roughness of the area. These four parameters give rise to several derived parameters. Algorithmic accomplishments include reviving Fox's method (1985, 1996) and improving the method with the possibly geophysically more appropriate nonequispaced fast Fourier transform. A new composite parameter, simply the overall integral length of the nonlinear parameterizing function, is used to make within-dataset comparisons. A synthetic dataset and six multibeam datasets covering practically all depth regimes have been analyzed with the tools that have been developed. Data specific contributions include possibly discovering an aspect ratio isotropic cutoff level (less than 1.2), showing a range of spectral fall-off values between about -0.5 for a sandybottomed Gulf of Mexico area, to about -1.8 for a coral reef area just outside of the Saipan harbor. We also rank the targeted type of dataset, the best resolution gridded datasets, from smoothest to roughest using a factor based on the kernel dimensions, a percentage from the windowing operation, all multiplied by the overall integration length.

Remote sensing-based estimation of annual soil respiration at two contrasting forest sites

NASA Astrophysics Data System (ADS)

Huang, Ni; Gu, Lianhong; Black, T. Andrew; Wang, Li; Niu, Zheng

2015-11-01

Soil respiration (Rs), an important component of the global carbon cycle, can be estimated using remotely sensed data, but the accuracy of this technique has not been thoroughly investigated. In this study, we proposed a methodology for the remote estimation of annual Rs at two contrasting FLUXNET forest sites (a deciduous broadleaf forest and an evergreen needleleaf forest). A version of the Akaike's information criterion was used to select the best model from a range of models for annual Rs estimation based on the remotely sensed data products from the Moderate Resolution Imaging Spectroradiometer and root-zone soil moisture product derived from assimilation of the NASA Advanced Microwave Scanning Radiometer soil moisture products and a two-layer Palmer water balance model. We found that the Arrhenius-type function based on nighttime land surface temperature (LST-night) was the best model by comprehensively considering the model explanatory power and model complexity at the Missouri Ozark and BC-Campbell River 1949 Douglas-fir sites. In addition, a multicollinearity problem among LST-night, root-zone soil moisture, and plant photosynthesis factor was effectively avoided by selecting the LST-night-driven model. Cross validation showed that temporal variation in Rs was captured by the LST-night-driven model with a mean absolute error below 1 µmol CO2 m-2 s-1 at both forest sites. An obvious overestimation that occurred in 2005 and 2007 at the Missouri Ozark site reduced the evaluation accuracy of cross validation because of summer drought. However, no significant difference was found between the Arrhenius-type function driven by LST-night and the function considering LST-night and root-zone soil moisture. This finding indicated that the contribution of soil moisture to Rs was relatively small at our multiyear data set. To predict intersite Rs, maximum leaf area index (LAImax) was used as an upscaling factor to calibrate the site-specific reference respiration rates. Independent validation demonstrated that the model incorporating LST-night and LAImax efficiently predicted the spatial and temporal variabilities of Rs. Based on the Arrhenius-type function using LST-night as an input parameter, the rates of annual C release from Rs were 894-1027 g C m-2 yr-1 at the BC-Campbell River 1949 Douglas-fir site and 818-943 g C m-2 yr-1 at the Missouri Ozark site. The ratio between annual Rs estimates based on remotely sensed data and the total annual ecosystem respiration from eddy covariance measurements fell within the range reported in previous studies. Our results demonstrated that estimating annual Rs based on remote sensing data products was possible at deciduous and evergreen forest sites.

Six Novel Loci Associated with Circulating VEGF Levels Identified by a Meta-analysis of Genome-Wide Association Studies

PubMed Central

Song, Ci; Nutile, Teresa; Vernon Smith, Albert; Concas, Maria Pina; Traglia, Michela; Barbieri, Caterina; Ndiaye, Ndeye Coumba; Stathopoulou, Maria G.; Lagou, Vasiliki; Maestrale, Giovanni Battista; Sala, Cinzia; Debette, Stephanie; Kovacs, Peter; Lind, Lars; Lamont, John; Fitzgerald, Peter; Tönjes, Anke; Gudnason, Vilmundur; Toniolo, Daniela; Pirastu, Mario; Bellenguez, Celine; Vasan, Ramachandran S.; Ingelsson, Erik; Leutenegger, Anne-Louise; Johnson, Andrew D.; DeStefano, Anita L.; Visvikis-Siest, Sophie; Seshadri, Sudha; Ciullo, Marina

2016-01-01

Vascular endothelial growth factor (VEGF) is an angiogenic and neurotrophic factor, secreted by endothelial cells, known to impact various physiological and disease processes from cancer to cardiovascular disease and to be pharmacologically modifiable. We sought to identify novel loci associated with circulating VEGF levels through a genome-wide association meta-analysis combining data from European-ancestry individuals and using a dense variant map from 1000 genomes imputation panel. Six discovery cohorts including 13,312 samples were analyzed, followed by in-silico and de-novo replication studies including an additional 2,800 individuals. A total of 10 genome-wide significant variants were identified at 7 loci. Four were novel loci (5q14.3, 10q21.3, 16q24.2 and 18q22.3) and the leading variants at these loci were rs114694170 (MEF2C, P = 6.79x10-13), rs74506613 (JMJD1C, P = 1.17x10-19), rs4782371 (ZFPM1, P = 1.59x10-9) and rs2639990 (ZADH2, P = 1.72x10-8), respectively. We also identified two new independent variants (rs34528081, VEGFA, P = 1.52x10-18; rs7043199, VLDLR-AS1, P = 5.12x10-14) at the 3 previously identified loci and strengthened the evidence for the four previously identified SNPs (rs6921438, LOC100132354, P = 7.39x10-1467; rs1740073, C6orf223, P = 2.34x10-17; rs6993770, ZFPM2, P = 2.44x10-60; rs2375981, KCNV2, P = 1.48x10-100). These variants collectively explained up to 52% of the VEGF phenotypic variance. We explored biological links between genes in the associated loci using Ingenuity Pathway Analysis that emphasized their roles in embryonic development and function. Gene set enrichment analysis identified the ERK5 pathway as enriched in genes containing VEGF associated variants. eQTL analysis showed, in three of the identified regions, variants acting as both cis and trans eQTLs for multiple genes. Most of these genes, as well as some of those in the associated loci, were involved in platelet biogenesis and functionality, suggesting the importance of this process in regulation of VEGF levels. This work also provided new insights into the involvement of genes implicated in various angiogenesis related pathologies in determining circulating VEGF levels. The understanding of the molecular mechanisms by which the identified genes affect circulating VEGF levels could be important in the development of novel VEGF-related therapies for such diseases. PMID:26910538

Probabilistic flood inundation mapping at ungauged streams due to roughness coefficient uncertainty in hydraulic modelling

NASA Astrophysics Data System (ADS)

Papaioannou, George; Vasiliades, Lampros; Loukas, Athanasios; Aronica, Giuseppe T.

2017-04-01

Probabilistic flood inundation mapping is performed and analysed at the ungauged Xerias stream reach, Volos, Greece. The study evaluates the uncertainty introduced by the roughness coefficient values on hydraulic models in flood inundation modelling and mapping. The well-established one-dimensional (1-D) hydraulic model, HEC-RAS is selected and linked to Monte-Carlo simulations of hydraulic roughness. Terrestrial Laser Scanner data have been used to produce a high quality DEM for input data uncertainty minimisation and to improve determination accuracy on stream channel topography required by the hydraulic model. Initial Manning's n roughness coefficient values are based on pebble count field surveys and empirical formulas. Various theoretical probability distributions are fitted and evaluated on their accuracy to represent the estimated roughness values. Finally, Latin Hypercube Sampling has been used for generation of different sets of Manning roughness values and flood inundation probability maps have been created with the use of Monte Carlo simulations. Historical flood extent data, from an extreme historical flash flood event, are used for validation of the method. The calibration process is based on a binary wet-dry reasoning with the use of Median Absolute Percentage Error evaluation metric. The results show that the proposed procedure supports probabilistic flood hazard mapping at ungauged rivers and provides water resources managers with valuable information for planning and implementing flood risk mitigation strategies.

Accelerated aging effects on surface hardness and roughness of lingual retainer adhesives.

PubMed

Ramoglu, Sabri Ilhan; Usumez, Serdar; Buyukyilmaz, Tamer

2008-01-01

To test the null hypothesis that accelerated aging has no effect on the surface microhardness and roughness of two light-cured lingual retainer adhesives. Ten samples of light-cured materials, Transbond Lingual Retainer (3M Unitek) and Light Cure Retainer (Reliance) were cured with a halogen light for 40 seconds. Vickers hardness and surface roughness were measured before and after accelerated aging of 300 hours in a weathering tester. Differences between mean values were analyzed for statistical significance using a t-test. The level of statistical significance was set at P < .05. The mean Vickers hardness of Transbond Lingual Retainer was 62.8 +/- 3.5 and 79.6 +/- 4.9 before and after aging, respectively. The mean Vickers hardness of Light Cure Retainer was 40.3 +/- 2.6 and 58.3 +/- 4.3 before and after aging, respectively. Differences in both groups were statistically significant (P < .001). Following aging, mean surface roughness was changed from 0.039 microm to 0.121 microm and from 0.021 microm to 0.031 microm for Transbond Lingual Retainer and Light Cure Retainer, respectively. The roughening of Transbond Lingual Retainer with aging was statistically significant (P < .05), while the change in the surface roughness of Light Cure Retainer was not (P > .05). Accelerated aging significantly increased the surface microhardness of both light-cured retainer adhesives tested. It also significantly increased the surface roughness of the Transbond Lingual Retainer.

Rough case-based reasoning system for continues casting

NASA Astrophysics Data System (ADS)

Su, Wenbin; Lei, Zhufeng

2018-04-01

The continuous casting occupies a pivotal position in the iron and steel industry. The rough set theory and the CBR (case based reasoning, CBR) were combined in the research and implementation for the quality assurance of continuous casting billet to improve the efficiency and accuracy in determining the processing parameters. According to the continuous casting case, the object-oriented method was applied to express the continuous casting cases. The weights of the attributes were calculated by the algorithm which was based on the rough set theory and the retrieval mechanism for the continuous casting cases was designed. Some cases were adopted to test the retrieval mechanism, by analyzing the results, the law of the influence of the retrieval attributes on determining the processing parameters was revealed. A comprehensive evaluation model was established by using the attribute recognition theory. According to the features of the defects, different methods were adopted to describe the quality condition of the continuous casting billet. By using the system, the knowledge was not only inherited but also applied to adjust the processing parameters through the case based reasoning method as to assure the quality of the continuous casting and improve the intelligent level of the continuous casting.

Berlyne Revisited: Evidence for the Multifaceted Nature of Hedonic Tone in the Appreciation of Paintings and Music

PubMed Central

Marin, Manuela M.; Lampatz, Allegra; Wandl, Michaela; Leder, Helmut

2016-01-01

In his seminal book on esthetics, Berlyne (1971) posited an inverted-U relationship between complexity and hedonic tone in arts appreciation, however, converging evidence for his theory is still missing. The disregard of the multidimensionality of complexity may explain some of the divergent results. Here, we argue that definitions of hedonic tone are manifold and systematically examined whether the nature of the relationship between complexity and hedonic tone is determined by the specific measure of hedonic tone. In Experiment 1, we studied three picture categories with similar affective and semantic contents: 96 affective environmental scenes, which were also converted into 96 cartoons, and 96 representational paintings. Complexity varied along the dimension of elements. In a between-subjects design, each stimulus was presented for 5 s to 206 female participants. Subjective ratings of hedonic tone (either beauty, pleasantness or liking), arousal, complexity and familiarity were collected in three conditions per stimulus set. Complexity and arousal were positively associated in all conditions, with the strongest association observed for paintings. For environmental scenes and cartoons, there was no significant association between complexity and hedonic tone, and the three measures of hedonic tone were highly correlated (all rs > 0.85). As predicted, in paintings the measures of hedonic tone were less strongly correlated (all rs > 0.73), and when controlling for familiarity, the association with complexity was significantly positive for beauty (rs = 0.26), weakly negative for pleasantness (rs = -0.16) and not present for liking. Experiment 2 followed a similar approach and 77 female participants, all non-musicians, rated 92 musical excerpts (15 s) in three conditions of hedonic tone (either beauty, pleasantness or liking). Results indicated a strong relationship between complexity and arousal (all rs > 0.85). When controlling for familiarity effects, the relationship between complexity and beauty followed an inverted-U curve, whereas the relationship between complexity and pleasantness was negative (rs = -0.26) and the one between complexity and liking positive (rs = 0.29). We relate our results to Berlyne’s theory and the latest findings in neuroaesthetics, proposing that future studies need to acknowledge the multifaceted nature of hedonic tone in esthetic experiences of artforms. PMID:27867350

Gas/solid particulate phthalic esters (PAEs) in Masson pine (Pinus massoniana L.) needles and rhizosphere surface soils.

PubMed

Wang, Wen-xin; Fan, Chinbay Q

2014-07-15

Phthalic acid esters (PAEs) are used in many branches of industry and are produced in huge amounts throughout the world. An investigation on particulate- and gas-phase distribution of PAEs has been conducted between January 2011 and December 2012 in Nanjing (China). Masson pine (Pinus massoniana L.) needles and rhizosphere surface soils were sampled from urban to suburban/remote sites, to investigate the pine needle/soil distribution of PAEs. The results showed that the average total PAE concentration (gas+particle) was 97.0ngm(-3). The six PAE congeners considered predominantly existed in the gas phase and the average contribution of gas phase to total PAEs ranged from 75.0% to 89.1%. The PAE concentrations in rhizosphere soils and pine needles were positively correlated with their particulate- and gas-phase concentrations, respectively, which suggested that surface soils accumulated PAEs mainly through gravity deposition of particles and pine needle stomata absorbed PAEs mainly from the gas phase. The gas/particle partitioning (KP) and soil-pine needle ratio (Rs/n) were determined. Experimentally determined KP values correlated well with the subcooled liquid vapor pressures (PL). A set of interesting relationships of logRs/n-logKP-logPL was employed to explain the experimental findings of PAEs deposition to surface soils and to needles. This data set offered a unique perspective into the influence that Rs/n played in KP and correlated with PL. Copyright © 2014 Elsevier B.V. All rights reserved.

Positive modulation of α5 GABAA receptors in preadolescence prevents reduced locomotor response to amphetamine in adult female but not male rats prenatally exposed to lipopolysaccharide.

PubMed

Batinić, Bojan; Santrač, Anja; Jančić, Ivan; Li, Guanguan; Vidojević, Aleksandra; Marković, Bojan; Cook, James M; Savić, Miroslav M

2017-10-01

We previously demonstrated that lipopolysaccharide (LPS) administered intraperitoneally (i.p.) to pregnant Wistar rat dams, at embryonic days 15 and 16 (E15/16), induced a decrease of baseline locomotor activity and diminished reactivity to amphetamine in adult female offspring. In the present study we aimed to assess the duration of LPS-induced maternal immune activation (MIA) and investigate possible changes in levels of main neurotransmitters in fetal brain during MIA. We hypothesized that the observed behavioral changes may be linked with MIA-induced disturbance of prenatal GABAergic system development, especially with α5 GABA A receptors (α5GABA A Rs), expression of which takes place between E14 and E17. Thereafter, we set to investigate if later potentiation of α5GABA A Rs in offspring's preadolescence (from postnatal day 22-28) could prevent the deficit in locomotor reactivity to amphetamine observed in adulthood, at postnatal day P60. The elevation of IL-6 in amniotic fluid 6h after LPS treatment (100μg/kg, i.p.) at E15 was concurrent with a significant increase of GABA and decrease of glutamate concentration in fetal brain. Moreover, repeated administration of MP-III-022, a selective positive allosteric modulator of α5GABA A Rs, at a dose (2mg/kg daily, i.p.) derived from a separate pharmacokinetic study, prevented the LPS-induced decrease in locomotor reactivity to amphetamine (0.5mg/kg, i.p.) in adult females. These results were not mirrored in the parallel set of experiments with male offspring from LPS-treated rats. The results suggest that pharmacological potentiation of α5GABA A Rs activity in preadolescence may ameliorate at least some of adverse consequences of exposure to MIA in utero. Copyright © 2017 ISDN. Published by Elsevier Ltd. All rights reserved.

Retrieval of Soil Moisture and Roughness from the Polarimetric Radar Response

NASA Technical Reports Server (NTRS)

Sarabandi, Kamal; Ulaby, Fawwaz T.

1997-01-01

The main objective of this investigation was the characterization of soil moisture using imaging radars. In order to accomplish this task, a number of intermediate steps had to be undertaken. In this proposal, the theoretical, numerical, and experimental aspects of electromagnetic scattering from natural surfaces was considered with emphasis on remote sensing of soil moisture. In the general case, the microwave backscatter from natural surfaces is mainly influenced by three major factors: (1) the roughness statistics of the soil surface, (2) soil moisture content, and (3) soil surface cover. First the scattering problem from bare-soil surfaces was considered and a hybrid model that relates the radar backscattering coefficient to soil moisture and surface roughness was developed. This model is based on extensive experimental measurements of the radar polarimetric backscatter response of bare soil surfaces at microwave frequencies over a wide range of moisture conditions and roughness scales in conjunction with existing theoretical surface scattering models in limiting cases (small perturbation, physical optics, and geometrical optics models). Also a simple inversion algorithm capable of providing accurate estimates of soil moisture content and surface rms height from single-frequency multi-polarization radar observations was developed. The accuracy of the model and its inversion algorithm is demonstrated using independent data sets. Next the hybrid model for bare-soil surfaces is made fully polarimetric by incorporating the parameters of the co- and cross-polarized phase difference into the model. Experimental data in conjunction with numerical simulations are used to relate the soil moisture content and surface roughness to the phase difference statistics. For this purpose, a novel numerical scattering simulation for inhomogeneous dielectric random surfaces was developed. Finally the scattering problem of short vegetation cover above a rough soil surface was considered. A general scattering model for grass-blades of arbitrary cross section was developed and incorporated in a first order random media model. The vegetation model and the bare-soil model are combined and the accuracy of the combined model is evaluated against experimental observations from a wheat field over the entire growing season. A complete set of ground-truth data and polarimetric backscatter data were collected. Also an inversion algorithm for estimating soil moisture and surface roughness from multi-polarized multi-frequency observations of vegetation-covered ground is developed.

Response to Ridgeway, Dunston, and Qian: On Methodological Rigor: Has Rigor Mortis Set In?

ERIC Educational Resources Information Center

Baldwin, R. Scott; Vaughn, Sharon

1993-01-01

Responds to an article in the same issue of the journal presenting a meta-analysis of reading research. Expresses concern that the authors' conclusions will promote a slavish adherence to a methodology and a rigidity of thought that reading researchers can ill afford. (RS)

Choosing the Standard of Care in Private Individual Defamation Cases.

ERIC Educational Resources Information Center

Caudill, Susan

1989-01-01

Examines private individual defamation cases that include discussion of whether the reasonably prudent publisher/editor or the reasonably prudent person should set the standard of care when negligence is at issue. Considers the implication of judicial reasoning in adopting one standard of care rather than the other. (RS)

Genome-wide association study of acute kidney injury after coronary bypass graft surgery identifies susceptibility loci.

PubMed

Stafford-Smith, Mark; Li, Yi-Ju; Mathew, Joseph P; Li, Yen-Wei; Ji, Yunqi; Phillips-Bute, Barbara G; Milano, Carmelo A; Newman, Mark F; Kraus, William E; Kertai, Miklos D; Shah, Svati H; Podgoreanu, Mihai V

2015-10-01

Acute kidney injury (AKI) is a common, serious complication of cardiac surgery. Since prior studies have supported a genetic basis for postoperative AKI, we conducted a genome-wide association study (GWAS) for AKI following coronary bypass graft (CABG) surgery. The discovery data set consisted of 873 nonemergent CABG surgery patients with cardiopulmonary bypass (PEGASUS), while a replication data set had 380 cardiac surgical patients (CATHGEN). Single-nucleotide polymorphism (SNP) data were based on Illumina Human610-Quad (PEGASUS) and OMNI1-Quad (CATHGEN) BeadChips. We used linear regression with adjustment for a clinical AKI risk score to test SNP associations with the postoperative peak rise relative to preoperative serum creatinine concentration as a quantitative AKI trait. Nine SNPs meeting significance in the discovery set were detected. The rs13317787 in GRM7|LMCD1-AS1 intergenic region (3p21.6) and rs10262995 in BBS9 (7p14.3) were replicated with significance in the CATHGEN data set and exhibited significantly strong overall association following meta-analysis. Additional fine mapping using imputed SNPs across these two regions and meta-analysis found genome-wide significance at the GRM7|LMCD1-AS1 locus and a significantly strong association at BBS9. Thus, through an unbiased GWAS approach, we found two new loci associated with post-CABG AKI providing new insights into the pathogenesis of perioperative AKI.

Synthesis of Selective Agonists for the α7 Nicotinic Acetylcholine Receptor with In Situ Click-Chemistry on Acetylcholine-Binding Protein Templates

PubMed Central

Yamauchi, John G.; Gomez, Kimberly; Grimster, Neil; Dufouil, Mikael; Nemecz, Ákos; Fotsing, Joseph R.; Ho, Kwok-Yiu; Talley, Todd T.; Sharpless, K. Barry; Fokin, Valery V.

2012-01-01

The acetylcholine-binding proteins (AChBPs), which serve as structural surrogates for the extracellular domain of nicotinic acetylcholine receptors (nAChRs), were used as reaction templates for in situ click-chemistry reactions to generate a congeneric series of triazoles from azide and alkyne building blocks. The catalysis of in situ azide-alkyne cycloaddition reactions at a dynamic subunit interface facilitated the synthesis of potentially selective compounds for nAChRs. We investigated compound sets generated in situ with soluble AChBP templates through pharmacological characterization with α7 and α4β2 nAChRs and 5-hydroxytryptamine type 3A receptors. Analysis of activity differences between the triazole 1,5-syn- and 1,4-anti-isomers showed a preference for the 1,4-anti-triazole regioisomers among nAChRs. To improve nAChR subtype selectivity, the highest-potency building block for α7 nAChRs, i.e., 3α-azido-N-methylammonium tropane, was used for additional in situ reactions with a mutated Aplysia californica AChBP that was made to resemble the ligand-binding domain of the α7 nAChR. Fourteen of 50 possible triazole products were identified, and their corresponding tertiary analogs were synthesized. Pharmacological assays revealed that the mutated binding protein template provided enhanced selectivity of ligands through in situ reactions. Discrete trends in pharmacological profiles were evident, with most compounds emerging as α7 nAChR agonists and α4β2 nAChR antagonists. Triazoles bearing quaternary tropanes and aromatic groups were most potent for α7 nAChRs. Pharmacological characterization of the in situ reaction products established that click-chemistry synthesis with surrogate receptor templates offered novel extensions of fragment-based drug design that were applicable to multisubunit ion channels. PMID:22784805

Association of Parkinson Disease Risk Loci With Mild Parkinsonian Signs in Older Persons

PubMed Central

Shulman, Joshua M.; Yu, Lei; Buchman, Aron S.; Evans, Denis A.; Schneider, Julie A.; Bennett, David A.; De Jager, Philip L.

2014-01-01

IMPORTANCE Parkinsonian motor signs are common in the aging population and are associated with adverse health outcomes. Compared with Parkinson disease (PD), potential genetic risk factors for mild parkinsonian signs have been largely unexplored. OBJECTIVE To determine whether PD susceptibility loci are associated with parkinsonism or substantia nigra pathology in a large community-based cohort of older persons. DESIGN, SETTING, AND PARTICIPANTS Eighteen candidate single-nucleotide polymorphisms from PD genome-wide association studies were evaluated in a joint clinicopathologic cohort. Participants included 1698 individuals and a nested autopsy collection of 821 brains from the Religious Orders Study and the Rush Memory and Aging Project, 2 prospective community-based studies. MAIN OUTCOMES AND MEASURES The primary outcomes were a quantitative measure of global parkinsonism or component measures of bradykinesia, rigidity, tremor, and gait impairment that were based on the motor Unified Parkinson’s Disease Rating Scale. In secondary analyses, we examined associations with additional quantitative motor traits and postmortem indices, including substantia nigra Lewy bodies and neuronal loss. RESULTS Parkinson disease risk alleles in the MAPT (rs2942168; P = .0006) and CCDC62 (rs12817488; P = .004) loci were associated with global parkinsonism, and these associations remained after exclusion of patients with a PD diagnosis. Based on motor Unified Parkinson’s Disease Rating Scale subscores, MAPT (P = .0002) and CCDC62 (P = .003) were predominantly associated with bradykinesia, and we further discovered associations between SREBF1 (rs11868035; P = .005) and gait impairment, SNCA (rs356220; P = .04) and rigidity, and GAK (rs1564282; P = .03) and tremor. In the autopsy cohort, only NMD3 (rs34016896; P = .03) was related to nigral neuronal loss, and no associations were detected with Lewy bodies. CONCLUSIONS AND RELEVANCE In addition to the established link to PD susceptibility, our results support a broader role for several loci in the development of parkinsonian motor signs and nigral pathology in older persons. PMID:24514572

Balance deficiencies in women with fibromyalgia assessed using computerised dynamic posturography: a cross-sectional study in Spain

PubMed Central

Pérez-de-Heredia-Torres, Marta; Huertas-Hoyas, Elisabet; Martínez-Piédrola, Rosa; Palacios-Ceña, Domingo; Alegre-Ayala, Jorge; Santamaría-Vázquez, Montserrat; Fernández-de-las-Peñas, César

2017-01-01

Objectives Our aims were (1) to compare the sensory organisation of balance control and balance strategies between women with fibromyalgia (FM) and healthy women; (2) to investigate which sensory component, that is, vestibular, visual or somato-sensory, is the most affected in FM and (3) to determine the associations between the functional independence measure (FIM) and balance responses in FM. Design Cross-sectional observational study. Setting Urban regional hospital and university (Universidad Rey Juan Carlos, Madrid, Spain). Participants Twenty women with FM and 20 matched healthy women. Primary/secondary outcome measures The sensory organisation test (SOT) was used to determine postural sway and balance during six different conditions with subjects in a standing position. The FIM was used to determine the level of functional independence in daily life activities (ADL). Between-group differences were analysed with analysis of covariance, and the Spearman's test was used for correlations. Results Significant differences between-groups and between-conditions were found for all SOT conditions (all, p<0.001): women with FM showed lower scores being the vestibular score the most affected. Different correlations between SOT conditions and some specific ADL were observed in the FM group: bathing activity and balance condition 6 (rs=0.541; p<0.001), bed transfers activity and conditions 2 (rs=0.491; p<0.001) and 3 (rs=0.510; p<0.001), positioning strategy six and dressing the upper (rs=0.530; p<0.001) or lower (rs=0.562; p<0.001) body, and toileting (rs=0.521; p<0.001): the greater the loss of balance, the greater the interference on some daily life activities. Conclusions Women with FM exhibited balance deficiencies and used different strategies for maintaining their balance in standing, which was associated with a negative impact on functional independence. PMID:28765133

Do genetic modifiers of high-density lipoprotein cholesterol and triglyceride levels also modify their response to a lifestyle intervention in the setting of obesity and type-2 diabetes mellitus?: The Action for Health in Diabetes (Look AHEAD) study.

PubMed

Huggins, Gordon S; Papandonatos, George D; Erar, Bahar; Belalcazar, L Maria; Brautbar, Ariel; Ballantyne, Christie; Kitabchi, Abbas E; Wagenknecht, Lynne E; Knowler, William C; Pownall, Henry J; Wing, Rena R; Peter, Inga; McCaffery, Jeanne M

2013-08-01

High-density lipoprotein cholesterol (HDL-C) and triglycerides are cardiovascular risk factors susceptible to lifestyle behavior modification and genetics. We hypothesized that genetic variants identified by genome-wide association studies as associated with HDL-C or triglyceride levels modify 1-year treatment response to an intensive lifestyle intervention, relative to a usual care of diabetes mellitus support and education. We evaluated 82 single-nucleotide polymorphisms, which represent 31 loci demonstrated by genome-wide association studies to be associated with HDL-C and triglycerides, in 3561 participants who consented for genetic studies and met eligibility criteria. Variants associated with higher baseline HDL-C levels, cholesterol ester transfer protein (CETP) rs3764261 and hepatic lipase (LIPC) rs8034802, were found to be associated with HDL-C increases with intensive lifestyle intervention (P=0.0038 and 0.013, respectively) and had nominally significant treatment interactions (P=0.047 and 0.046, respectively). The fatty acid desaturase-2 rs1535 variant, associated with low baseline HDL-C (P=0.017), was associated with HDL-C increases with intensive lifestyle intervention (0.0037) and had a nominal treatment interaction (P=0.035). Apolipoprotein B (rs693) and LIPC (rs8034802) single-nucleotide polymorphisms showed nominally significant associations with HDL-C and triglyceride changes with intensive lifestyle intervention and a treatment interaction (P<0.05). Phosphatidylglycerophosphate synthase-1 single-nucleotide polymorphisms (rs4082919) showed the most significant triglyceride treatment interaction in the full cohort (P=0.0009). This is the first study to identify genetic variants modifying lipid responses to a randomized lifestyle behavior intervention in overweight or obese individuals with diabetes mellitus. The effects of genetic factors on lipid changes may differ from the effects on baseline lipids and are modifiable by behavioral intervention.

Do Genetic Modifiers of HDL-C and Triglyceride Levels also Modify Their Response to a Lifestyle Intervention in the Setting of Obesity and Type-2 Diabetes Mellitus? The Look AHEAD Study

PubMed Central

Huggins, Gordon S.; Papandonatos, George D.; Erar, Bahar; Belalcazar, L. Maria; Brautbar, Ariel; Ballantyne, Christie; Kitabchi, Abbas E.; Wagenknecht, Lynne E.; Knowler, William C.; Pownall, Henry J.; Wing, Rena R.; Peter, Inga; McCaffery, Jeanne M.

2014-01-01

Background High-density lipoprotein cholesterol (HDL-C) and triglycerides are cardiovascular risk factors susceptible to lifestyle behavior modification and genetics. We hypothesized that genetic variants identified by genome-wide association studies (GWASs) as associated with HDL-C or triglyceride levels will modify 1-year treatment response to an intensive lifestyle intervention (ILI), relative to a usual care of diabetes support and education (DSE). Methods and Results We evaluated 82 SNPs, representing 31 loci demonstrated by GWAS to be associated with HDL-C and/or triglycerides, in 3,561 participants who consented for genetic studies and met eligibility criteria. Variants associated with higher baseline HDL-C levels, cholesterol ester transfer protein (CETP) rs3764261 and hepatic lipase (LIPC) rs8034802, were found to be associated with HDL-C increases with ILI (p=0.0038 and 0.013, respectively) and had nominally significant treatment interactions (p=0.047 and 0.046, respectively). The fatty acid desaturase-2 (FADS-2) rs1535 variant, associated with low baseline HDL-C (p=0.017), was associated with HDL-C increases with ILI (0.0037) and had a nominal treatment interaction (p= 0.035). ApoB (rs693) and LIPC (rs8034802) SNPs showed nominally significant associations with HDL-C and triglyceride changes with ILI and a treatment interaction (p<0.05). A PGS1 SNP (rs4082919) showed the most significant triglyceride treatment interaction in the full cohort (p=0.0009). Conclusions This is the first study to identify genetic variants modifying lipid responses to a randomized lifestyle behavior intervention in overweight/obese diabetic individuals. The effect of genetic factors on lipid changes may differ from the effects on baseline lipids and are modifiable by behavioral intervention. PMID:23861364

Impact of forced displacement during World War II on the present-day mental health of the elderly: a population-based study.

PubMed

Kuwert, Philipp; Brähler, Elmar; Glaesmer, Heide; Freyberger, Harald Jürgen; Decker, Oliver

2009-08-01

The effects of traumatization among the elderly is a neglected topic in research and clinical settings. Forced displacement of civilians is one of the main traumatic features of modern armed conflict. Roughly 12 million German people were displaced in World War II (WWII) and to our knowledge there has been no representative study investigating the mental health outcomes of such trauma in the elderly population. The survey assessed whether current depression, anxiety, resilience and life satisfaction were significantly associated with forced displacement in WWII. A nationwide representative face-to-face household survey was conducted in Germany. A representative sample of the German population aged 61 years or older (N = 1513 participants, N = 239 displaced in WWII) was approached using 258 sample points. Measurements included depressive symptoms (PHQ-2), anxiety (GAD-7), resilience (RS-11), general and domain-specific life satisfaction (FLZ(M)) and sociodemographic variables. Forced displacement in WWII is significantly associated with higher levels of anxiety and lower levels of resilience and life satisfaction 60 years later. In regression analyses, forced displacement in WWII significantly predicted current anxiety (beta 0.07; p < 0.01), life satisfaction (beta -0.06; p < 0.05) and resilience (beta -0.07; p < 0.01). To our knowledge this is the first nationwide representative survey to examine the late-life effects of forced displacement, particularly of persons displaced during WWII in Germany. Further research is needed to identify mediating variables and to evaluate psychotherapeutic interventions in elderly trauma survivors.

Association study of functional polymorphisms in interleukins and interleukin receptors genes: IL1A, IL1B, IL1RN, IL6, IL6R, IL10, IL10RA and TGFB1 in schizophrenia in Polish population.

PubMed

Kapelski, Pawel; Skibinska, Maria; Maciukiewicz, Malgorzata; Wilkosc, Monika; Frydecka, Dorota; Groszewska, Agata; Narozna, Beata; Dmitrzak-Weglarz, Monika; Czerski, Piotr; Pawlak, Joanna; Rajewska-Rager, Aleksandra; Leszczynska-Rodziewicz, Anna; Slopien, Agnieszka; Zaremba, Dorota; Twarowska-Hauser, Joanna

2015-12-01

Schizophrenia has been associated with a large range of autoimmune diseases, with a history of any autoimmune disease being associated with a 45% increase in risk for the illness. The inflammatory system may trigger or modulate the course of schizophrenia through complex mechanisms influencing neurodevelopment, neuroplasticity and neurotransmission. In particular, increases or imbalance in cytokine before birth or during the early stages of life may affect neurodevelopment and produce vulnerability to the disease. A total of 27 polymorphisms of IL1N gene: rs1800587, rs17561; IL1B gene: rs1143634, rs1143643, rs16944, rs4848306, rs1143623, rs1143633, rs1143627; IL1RN gene: rs419598, rs315952, rs9005, rs4251961; IL6 gene: rs1800795, rs1800797; IL6R gene: rs4537545, rs4845617, rs2228145, IL10 gene: rs1800896, rs1800871, rs1800872, rs1800890, rs6676671; IL10RA gene: rs2229113, rs3135932; TGF1B gene: rs1800469, rs1800470; each selected on the basis of molecular evidence for functionality, were investigated in this study. Analysis was performed on a group of 621 patients with diagnosis of schizophrenia and 531 healthy controls in Polish population. An association of rs4848306 in IL1B gene, rs4251961 in IL1RN gene, rs2228145 and rs4537545 in IL6R with schizophrenia have been observed. rs6676671 in IL10 was associated with early age of onset. Strong linkage disequilibrium was observed between analyzed polymorphisms in each gene, except of IL10RA. We observed that haplotypes composed of rs4537545 and rs2228145 in IL6R gene were associated with schizophrenia. Analyses with family history of schizophrenia, other psychiatric disorders and alcohol abuse/dependence did not show any positive findings. Further studies on larger groups along with correlation with circulating protein levels are needed. Copyright © 2015 Elsevier B.V. All rights reserved.

From smooth to rough, from water to air: the intertidal habitat of Northern clingfish ( Gobiesox maeandricus)

NASA Astrophysics Data System (ADS)

Ditsche, Petra; Hicks, Madeline; Truong, Lisa; Linkem, Christina; Summers, Adam

2017-04-01

The Northern clingfish is a small, Eastern North Pacific fish that can attach to rough, fouled rocks in the intertidal. Their ability to attach to surfaces has been measured previously in the laboratory, and in this study, we show the roughness and fouling of the natural habitat of these fish. We introduce a new method for measuring surface roughness of natural substrates with time-limited accessibility. We expect this method to be broadly applicable in studies of animal/substrate surface interactions in habitats difficult to characterize. Our roughness measurements demonstrate that the fish's ability to attach to very coarse roughness is required in its natural environment. Some of the rocks showed even coarser roughness than the fish could attach to in the lab setting. We also characterized the clingfish's preference for other habitat descriptors such as the size of the rocks, biofilm, and Aufwuchs (macroalgae, encrusting invertebrates) cover, as well as grain size of underlying substrate. Northern clingfish seek shelter under rocks of 15-45 cm in size. These rocks have variable Aufwuchs cover, and gravel is the main underlying substrate type. In the intertidal, environmental conditions change with the tides, and for clingfish, the daily time under water (DTUW%) was a key parameter explaining distribution. Rather than location being determined by intertidal zonation, an 80% DTUW, a finer scale concept of tidal inundation, was required by the fish. We expect that this is likely because the mobility of the fish allows them to more closely track the ideal inundation in the marine intertidal.

Surface roughness evaluation on mandrels and mirror shells for future X-ray telescopes

NASA Astrophysics Data System (ADS)

Sironi, Giorgia; Spiga, D.

2008-07-01

More X-ray missions that will be operating in near future, like particular SIMBOL-X, e-Rosita, Con-X/HXT, SVOM/XIAO and Polar-X, will be based on focusing optics manufactured by means of the Ni electroforming replication technique. This production method has already been successfully exploited for SAX, XMM and Swift-XRT. Optical surfaces for X-ray reflection have to be as smooth as possible also at high spatial frequencies. Hence it will be crucial to take under control microroughness in order to reduce the scattering effects. A high rms microroughness would cause the degradation of the angular resolution and loss of effective area. Stringent requirements have therefore to be fixed for mirror shells surface roughness depending on the specific energy range investigated, and roughness evolution has to be carefully monitored during the subsequent steps of the mirror-shells realization. This means to study the roughness evolution in the chain mandrel, mirror shells, multilayer deposition and also the degradation of mandrel roughness following iterated replicas. Such a study allows inferring which phases of production are the major responsible of the roughness growth and could help to find solutions optimizing the involved processes. The exposed study is carried out in the context of the technological consolidation related to SIMBOL-X, along with a systematic metrological study of mandrels and mirror shells. To monitor the roughness increase following each replica, a multiinstrumental approach was adopted: microprofiles were analysed by means of their Power Spectral Density (PSD) in the spatial frequency range 1000-0.01 μm. This enables the direct comparison of roughness data taken with instruments characterized by different operative ranges of frequencies, and in particular optical interferometers and Atomic Force Microscopes. The performed analysis allowed us to set realistic specifications on the mandrel roughness to be achieved, and to suggest a limit for the maximum number of a replica a mandrel can undergo before being refurbished.

Evaluation of Prediction of Polymorphisms of DNA Repair Genes on the Efficacy of Platinum-Based Chemotherapy in Patients With Non-Small Cell Lung Cancer: A Network Meta-Analysis.

PubMed

Yu, Shao-Nan; Liu, Gui-Feng; Li, Xue-Feng; Fu, Bao-Hong; Dong, Li-Xin; Zhang, Shu-Hua

2017-12-01

This network meta-analysis (NMA) was conducted to compare the predictive value of 14 SNPs in eight DNA repair genes on the efficacy of platinum-based chemotherapy in patients with non-small cell lung cancer (NSCLC). These included ERCC1 (rs11615, rs3212986, rs3212948), XRCC1 (rs25487, rs25489, rs1799782), XPD (rs13181, rs1799793), XPG (rs1047768, rs17655), XPA (rs1800975), XRCC3 (rs861539), APE1 (rs3136820), and RRM1 (rs1042858). The PubMed and Cochrane library databases were reviewed from their inception to February 2017 and studies which met our inclusion criteria were included in our investigation. This network meta-analysis combines direct and indirect evidence to assess the predictive value of 14 SNPs in eight DNA repair genes on the efficacy of platinum-based chemotherapy in NSCLC. We evaluated the predictive value through the use of the odd ratios (OR) and drawing surface under the cumulative ranking curves (SUCRA). A total of 26 eligible cohort studies were enrolled in this NMA. The pairwise meta-analysis indicated that in terms of overall response ratio (ORR), ERCC1 (rs11615), XRCC1 (rs25487, rs1799782), and XPD (rs13181) polymorphisms are associated with the efficacy of platinum-based chemotherapy in NSCLC. The result of this NMA suggests that there is no significant difference in predictive value of 8 DNA repair genes on the efficacy of platinum-based chemotherapy in NSCLC patients. The rank of SUCRA values of the 14 SNPs in the eight DNA repair genes were: XPD (rs1799793)→ERCC1 (rs3212986)→XPA(rs1800975)→ERCC1(rs3212948)→XRCC1(rs25487)→XRCC3(rs861539)→APE1(rs3136820)→ERCC1(rs11615)→XRCC1(rs1799782)→RRM1(rs1042858)→XPD(rs13181)→XPG (rs1047768)→XPG(rs17655)→XRCC1(rs25489). ERCC1(rs11615), XRCC1(rs25487, rs1799782) and XPD(rs13181) polymorphisms were better predictors in evaluating the efficacy of platinum-based chemotherapy in NSCLC patients. J. Cell. Biochem. 118: 4782-4791, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Association of ARID5B gene variants with acute lymphoblastic leukemia in Yemeni children.

PubMed

Al-Absi, Boshra; Noor, Suzita M; Saif-Ali, Riyadh; Salem, Sameer D; Ahmed, Radwan H; Razif, Muhammad Fm; Muniandy, Sekaran

2017-04-01

Studies have shown an association between ARID5B gene polymorphisms and childhood acute lymphoblastic leukemia. However, the association between ARID5B variants and acute lymphoblastic leukemia among the Arab population still needs to be studied. The aim of this study was to investigate the association between ARID5B variants with acute lymphoblastic leukemia in Yemeni children. A total of 14 ARID5B gene single nucleotide polymorphisms (SNPs) were genotyped in 289 Yemeni children, of whom 136 had acute lymphoblastic leukemia and 153 were controls, using the nanofluidic Dynamic Array (Fluidigm 192.24 Dynamic Array). Using logistic regression adjusted for age and gender, the risks of acute lymphoblastic leukemia were presented as odds ratios and 95% confidence intervals. We found that nine SNPs were associated with acute lymphoblastic leukemia under additive genetic models: rs7073837, rs10740055, rs7089424, rs10821936, rs4506592, rs10994982, rs7896246, rs10821938, and rs7923074. Furthermore, the recessive models revealed that six SNPs were risk factors for acute lymphoblastic leukemia: rs10740055, rs7089424, rs10994982, rs7896246, rs10821938, and rs7923074. The gender-specific impact of these SNPs under the recessive genetic model revealed that SNPs rs10740055, rs10994982, and rs6479779 in females, and rs10821938 and rs7923074 in males were significantly associated with acute lymphoblastic leukemia risk. Under the dominant model, SNPs rs7073837, rs10821936, rs7896246, and rs6479778 in males only showed striking association with acute lymphoblastic leukemia. The additive model revealed that SNPs with significant association with acute lymphoblastic leukemia were rs10821936 (both males and females); rs7073837, rs10740055, rs10994982, and rs4948487 (females only); and rs7089424, rs7896246, rs10821938, and rs7923074 (males only). In addition, the ARID5B haplotype block (CGAACACAA) showed a higher risk for acute lymphoblastic leukemia. The haplotype (CCCGACTGC) was associated with protection against acute lymphoblastic leukemia. In conclusion, our study has shown that ARID5B variants are associated with acute lymphoblastic leukemia in Yemeni children with several gender biases of ARID5B single nucleotide polymorphisms reported.

Automated extraction of decision rules for leptin dynamics--a rough sets approach.

PubMed

Brtka, Vladimir; Stokić, Edith; Srdić, Biljana

2008-08-01

A significant area in the field of medical informatics is concerned with the learning of medical models from low-level data. The goals of inducing models from data are twofold: analysis of the structure of the models so as to gain new insight into the unknown phenomena, and development of classifiers or outcome predictors for unseen cases. In this paper, we will employ approach based on the relation of indiscernibility and rough sets theory to study certain questions concerning the design of model based on if-then rules, from low-level data including 36 parameters, one of them leptin. To generate easy to read, interpret, and inspect model, we have used ROSETTA software system. The main goal of this work is to get new insight into phenomena of leptin levels while interplaying with other risk factors in obesity.

Impact of the ongoing Amazonian deforestation on local precipitation: A GCM simulation study

NASA Technical Reports Server (NTRS)

Walker, G. K.; Sud, Y. C.; Atlas, R.

1995-01-01

Numerical simulation experiments were conducted to delineate the influence of in situ deforestation data on episodic rainfall by comparing two ensembles of five 5-day integrations performed with a recent version of the Goddard Laboratory for Atmospheres General Circulation Model (GCM) that has a simple biosphere model (SiB). The first set, called control cases, used the standard SiB vegetation cover (comprising 12 biomes) and assumed a fully forested Amazonia, while the second set, called deforestation cases, distinguished the partially deforested regions of Amazonia as savanna. Except for this difference, all other initial and prescribed boundary conditions were kept identical in both sets of integrations. The differential analyses of these five cases show the following local effects of deforestation. (1) A discernible decrease in evapotranspiration of about 0.80 mm/d (roughly 18%) that is quite robust in the averages for 1-, 2-, and 5-day forecasts. (2) A decrease in precipitation of about 1.18 mm/d (roughly 8%) that begins to emerge even in 1-2 day averages and exhibits complex evolution that extends downstream with the winds. (3) A significant decrease in the surface drag force (as a consequence of reduced surface roughness of deforested regions) that, in turn, affects the dynamical structure of moisture convergence and circulation. The surface winds increase significantly during the first day, and thereafter the increase is well maintained even in the 2- and 5-day averages.

Transcriptional regulation of PNPLA3 and its impact on susceptibility to nonalcoholic fatty liver Disease (NAFLD) in humans

PubMed Central

Wang, Xiaoliang; Gawrieh, Samer; Gamazon, Eric R.; Athinarayanan, Shaminie; Liu, Yang-Lin; Darlay, Rebecca; Cordell, Heather J; Daly, Ann K

2017-01-01

The increased expression of PNPLA3148M leads to hepatosteatosis in mice. This study aims to investigate the genetic control of hepatic PNPLA3 transcription and to explore its impact on NAFLD risk in humans. Through a locus-wide expression quantitative trait loci (eQTL) mapping in two human liver sample sets, a PNPLA3 intronic SNP, rs139051 A>G was identified as a significant eQTL (p = 6.6×10−8) influencing PNPLA3 transcription, with the A allele significantly associated with increased PNPLA3 mRNA. An electrophoresis mobility shift assay further demonstrated that the A allele has enhanced affinity to nuclear proteins than the G allele. The impact of this eQTL on NAFLD risk was further tested in three independent populations. We found that rs139051 did not independently affect the NAFLD risk, whilst rs738409 did not significantly modulate PNPLA3 transcription but was associated with NAFLD risk. The A-G haplotype associated with higher transcription of the disease-risk rs738409 G allele conferred similar risk for NAFLD compared to the G-G haplotype that possesses a lower transcription level. Our study suggests that the pathogenic role of PNPLA3148M in NAFLD is independent of the gene transcription in humans, which may be attributed to the high endogenous transcription level of PNPLA3 gene in human livers. PMID:27744419

Transcriptional regulation of PNPLA3 and its impact on susceptibility to nonalcoholic fatty liver Disease (NAFLD) in humans.

PubMed

Liu, Wanqing; Anstee, Quentin M; Wang, Xiaoliang; Gawrieh, Samer; Gamazon, Eric R; Athinarayanan, Shaminie; Liu, Yang-Lin; Darlay, Rebecca; Cordell, Heather J; Daly, Ann K; Day, Chris P; Chalasani, Naga

2016-10-13

The increased expression of PNPLA3 148M leads to hepatosteatosis in mice. This study aims to investigate the genetic control of hepatic PNPLA3 transcription and to explore its impact on NAFLD risk in humans. Through a locus-wide expression quantitative trait loci (eQTL) mapping in two human liver sample sets, a PNPLA3 intronic SNP, rs139051 A>G was identified as a significant eQTL ( p = 6.6×10 -8 ) influencing PNPLA3 transcription, with the A allele significantly associated with increased PNPLA3 mRNA. An electrophoresis mobility shift assay further demonstrated that the A allele has enhanced affinity to nuclear proteins than the G allele. The impact of this eQTL on NAFLD risk was further tested in three independent populations. We found that rs139051 did not independently affect the NAFLD risk, whilst rs738409 did not significantly modulate PNPLA3 transcription but was associated with NAFLD risk. The A-G haplotype associated with higher transcription of the disease-risk rs738409 G allele conferred similar risk for NAFLD compared to the G-G haplotype that possesses a lower transcription level. Our study suggests that the pathogenic role of PNPLA3 148M in NAFLD is independent of the gene transcription in humans, which may be attributed to the high endogenous transcription level of PNPLA3 gene in human livers.

The interaction of combined effects of the BDNF and PRKCG genes and negative life events in major depressive disorder.

PubMed

Yang, Chunxia; Sun, Ning; Liu, Zhifen; Li, Xinrong; Xu, Yong; Zhang, Kerang

2016-03-30

Major depressive disorder (MDD) is a mental disorder that results from complex interplay between multiple and partially overlapping sets of susceptibility genes and environmental factors. The brain derived neurotrophic factor (BDNF) and Protein kinase C gamma type (PRKCG) are logical candidate genes in MDD. Among diverse environmental factors, negative life events have been suggested to exert a crucial impact on brain development. In the present study, we hypothesized that interactions between genetic variants in BDNF and PRKCG and negative life events may play an important role in the development of MDD. We recruited a total of 406 patients with MDD and 391 age- and gender-matched control subjects. Gene-environment interactions were analyzed using generalized multifactor dimensionality reduction (GMDR). Under a dominant model, we observed a significant three-way interaction among BDNF rs6265, PRKCG rs3745406, and negative life events. The gene-environment combination of PRKCG rs3745406 C allele, BDNF rs6265 G allele and high level of negative life events (C-G-HN) was significantly associated with MDD (OR, 5.97; 95% CI, 2.71-13.15). To our knowledge, this is the first report of evidence that the BDNF-PRKCG interaction may modify the relationship between negative life events and MDD in the Chinese population. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Resolution enhancement of tri-stereo remote sensing images by super resolution methods

NASA Astrophysics Data System (ADS)

Tuna, Caglayan; Akoguz, Alper; Unal, Gozde; Sertel, Elif

2016-10-01

Super resolution (SR) refers to generation of a High Resolution (HR) image from a decimated, blurred, low-resolution (LR) image set, which can be either a single frame or multi-frame that contains a collection of several images acquired from slightly different views of the same observation area. In this study, we propose a novel application of tri-stereo Remote Sensing (RS) satellite images to the super resolution problem. Since the tri-stereo RS images of the same observation area are acquired from three different viewing angles along the flight path of the satellite, these RS images are properly suited to a SR application. We first estimate registration between the chosen reference LR image and other LR images to calculate the sub pixel shifts among the LR images. Then, the warping, blurring and down sampling matrix operators are created as sparse matrices to avoid high memory and computational requirements, which would otherwise make the RS-SR solution impractical. Finally, the overall system matrix, which is constructed based on the obtained operator matrices is used to obtain the estimate HR image in one step in each iteration of the SR algorithm. Both the Laplacian and total variation regularizers are incorporated separately into our algorithm and the results are presented to demonstrate an improved quantitative performance against the standard interpolation method as well as improved qualitative results due expert evaluations.

Effect of tillage system and cumulative rainfall on multifractal parameters of soil surface microrelief

NASA Astrophysics Data System (ADS)

Vidal Vázquez, E.; Miranda, J. G. V.; Mirás-Avalos, J. M.; Díaz, M. C.; Paz-Ferreiro, J.

2009-04-01

Mathematical description of the spatial characteristics of soil surface microrelief still remains a challenge. Soil surface roughness parameters are required for modelling overland flow and erosion. The objective of this work was to evaluate the potential of multifractal for analyzing the decay of initial surface roughness induced by natural rainfall under different soil tillage systems. Field experiments were performed on an Oxisol at Campinas, São Paulo State (Brazil). Six tillage treatments, namely, disc harrow, disc plow, chisel plow, disc harrow + disc level, disc plow + disc level and chisel plow + disc level were tested. In each plot soil surface microrelief was measured for times, with increasing amounts of natural rainfall using a pinmeter. The sampling scheme was a square grid with 25 x 25 mm point spacing and the plot size was 1350 x 1350 mm, so that each data set consisted of 3025 individual elevation points. Duplicated measurements were taken per treatment and date, yielding a total of 48 experimental data sets. All the investigated microrelief data sets exhibited, in general, scale properties, and the degree of multifractality showed wide differences between them. Multifractal analysis distinguishes two different patterns of soil surface microrelief, the first one has features close to monofractal spectra and the second clearly indicates multifractal behavior. Both, singularity spectra and generalized dimension spectra allow differentiating between soil tillage systems. In general, changes in values of multifractal parameters under simulated rainfall showed no or little correspondence with the evolution of the vertical microrelief component described by indices such as the standard deviation of the point height measurements. Multifractal parameters provided valuable information for chararacterizing the spatial features of soil surface microrelief as they were able to discriminate data sets with similar values for the vertical component of roughness.

Artery Tertiary Lymphoid Organs Control Aorta Immunity and Protect against Atherosclerosis via Vascular Smooth Muscle Cell Lymphotoxin β Receptors

PubMed Central

Hu, Desheng; Mohanta, Sarajo K.; Yin, Changjun; Peng, Li; Ma, Zhe; Srikakulapu, Prasad; Grassia, Gianluca; MacRitchie, Neil; Dever, Gary; Gordon, Peter; Burton, Francis L.; Ialenti, Armando; Sabir, Suleman R.; McInnes, Iain B.; Brewer, James M.; Garside, Paul; Weber, Christian; Lehmann, Thomas; Teupser, Daniel; Habenicht, Livia; Beer, Michael; Grabner, Rolf; Maffia, Pasquale; Weih, Falk; Habenicht, Andreas J.R.

2015-01-01

Summary Tertiary lymphoid organs (TLOs) emerge during nonresolving peripheral inflammation, but their impact on disease progression remains unknown. We have found in aged Apoe−/− mice that artery TLOs (ATLOs) controlled highly territorialized aorta T cell responses. ATLOs promoted T cell recruitment, primed CD4+ T cells, generated CD4+, CD8+, T regulatory (Treg) effector and central memory cells, converted naive CD4+ T cells into induced Treg cells, and presented antigen by an unusual set of dendritic cells and B cells. Meanwhile, vascular smooth muscle cell lymphotoxin β receptors (VSMC-LTβRs) protected against atherosclerosis by maintaining structure, cellularity, and size of ATLOs though VSMC-LTβRs did not affect secondary lymphoid organs: Atherosclerosis was markedly exacerbated in Apoe−/−Ltbr−/− and to a similar extent in aged Apoe−/−Ltbrfl/flTagln-cre mice. These data support the conclusion that the immune system employs ATLOs to organize aorta T cell homeostasis during aging and that VSMC-LTβRs participate in atherosclerosis protection via ATLOs. PMID:26084025

Comparison of clinical and physics scoring of PET images when image reconstruction parameters are varied.

PubMed

Walsh, C; Johnston, C; Sheehy, N; O' Reilly, G

2013-02-01

In this study the quantitative and qualitative image quality (IQ) measurements with clinical judgement of IQ in positron emission tomography (PET) were compared. The limitations of IQ metrics and the proposed criteria of acceptability for PET scanners are discussed. Phantom and patient images were reconstructed using seven different iterative reconstruction protocols. For each reconstructed set of images, IQ was scored based both on the visual analysis and on the quantitative metrics. The quantitative physics metrics did not rank the reconstruction protocols in the same order as the clinicians' scoring of perceived IQ (R(s)=-0.54). Better agreement was achieved when comparing the clinical perception of IQ to the physicist's visual assessment of IQ in the phantom images (R(s)=+0.59). The closest agreement was seen between the quantitative physics metrics and the measurement of the standard uptake values (SUVs) in small tumours (R(s)=+0.92). Given the disparity between the clinical perception of IQ and the physics metrics a cautious approach to use of IQ measurements for determining suspension levels is warranted.

Surface enhanced Raman spectroscopic studies on aspirin : An experimental and theoretical approach

NASA Astrophysics Data System (ADS)

Premkumar, R.; Premkumar, S.; Rekha, T. N.; Parameswari, A.; Mathavan, T.; Benial, A. Milton Franklin

2016-05-01

Surface enhanced Raman scattering (SERS) studies on aspirin molecule adsorbed on silver nanoparticles (AgNPs) were investigated by experimental and density functional theory approach. The AgNPs were synthesized by the solution-combustion method and characterized by the X-ray diffraction and high resolution-transmission electron microscopy techniques. The averaged particle size of synthesized AgNPs was calculated as ˜55 nm. The normal Raman spectrum (nRs) and SERS spectrum of the aspirin were recorded. The molecular structure of the aspirin and aspirin adsorbed on silver cluster were optimized by the DFT/ B3PW91 method with LanL2DZ basis set. The vibrational frequencies were calculated and assigned on the basis of potential energy distribution calculation. The calculated nRs and SERS frequencies were correlated well with the observed frequencies. The flat-on orientation was predicted from the nRs and SERS spectra, when the aspirin adsorbed on the AgNPs. Hence, the present studies lead to the understanding of adsorption process of aspirin on the AgNPs, which paves the way for biomedical applications.

Surface enhanced Raman spectroscopic studies on aspirin : An experimental and theoretical approach

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

Premkumar, R.; Premkumar, S.; Parameswari, A.

Surface enhanced Raman scattering (SERS) studies on aspirin molecule adsorbed on silver nanoparticles (AgNPs) were investigated by experimental and density functional theory approach. The AgNPs were synthesized by the solution-combustion method and characterized by the X-ray diffraction and high resolution-transmission electron microscopy techniques. The averaged particle size of synthesized AgNPs was calculated as ∼55 nm. The normal Raman spectrum (nRs) and SERS spectrum of the aspirin were recorded. The molecular structure of the aspirin and aspirin adsorbed on silver cluster were optimized by the DFT/ B3PW91 method with LanL2DZ basis set. The vibrational frequencies were calculated and assigned on the basismore » of potential energy distribution calculation. The calculated nRs and SERS frequencies were correlated well with the observed frequencies. The flat-on orientation was predicted from the nRs and SERS spectra, when the aspirin adsorbed on the AgNPs. Hence, the present studies lead to the understanding of adsorption process of aspirin on the AgNPs, which paves the way for biomedical applications.« less

Association between ADAM metallopeptidase domain 33 gene polymorphism and risk of childhood asthma: a meta-analysis.

PubMed

Sun, F J; Zou, L Y; Tong, D M; Lu, X Y; Li, J; Deng, C B

2017-08-31

This study aimed to investigate the association between ADAM metallopeptidase domain 33 (ADAM33) gene polymorphisms and the risk of childhood asthma. The relevant studies about the relationship between ADAM33 gene polymorphisms and childhood asthma were searched from electronic databases and the deadline of retrieval was May 2016. The single nucleotide polymorphisms (SNPs) of ADAM33 (rs511898, rs2280092, rs3918396, rs528557, rs2853209, rs44707, rs2280091 and rs2280089) were analyzed based on several models including the allele, codominant, recessive and dominant models. The results showed that the ADAM33 rs2280091 polymorphism in all four genetic models was associated with an increased risk of childhood asthma. Positive associations were also found between the polymorphisms rs2280090, rs2787094, rs44707 and rs528557 and childhood asthma in some genetic models. This meta-analysis suggested that ADAM33 polymorphisms rs2280091, rs2280090, rs2787094, rs44707 and rs528557 were significantly associated with a high risk of childhood asthma.

Association between Six CETP Polymorphisms and Metabolic Syndrome in Uyghur Adults from Xinjiang, China

PubMed Central

Hou, Huixian; Ma, Rulin; Guo, Heng; He, Jia; Hu, Yunhua; Mu, Lati; Yan, Yizhong; Ma, Jiaolong; Li, Shugang; Zhang, Jingyu; Ding, Yusong; Zhang, Mei; Niu, Qiang; Liu, Jiaming; Guo, Shuxia

2017-01-01

Objective: To explore the association between CETP gene polymorphisms and metabolic syndrome (MS), as well as the relationship between the CETP gene polymorphisms and each component of MS. Methods: A total of 571 individuals which were randomly selected from 5692 Uyghur adults were subdivided into two groups, including 280 patients with MS and 291 control subjects, using the group-matching method after matching for gender. We detected CETP polymorphisms (rs5882, rs1800775, rs3764261, rs12149545, rs711752, and rs708272) by using the Snapshot method. Results: (1) Significant differences were found involving the frequency distribution of genotypes and alleles of rs1800775, rs3764261, rs12149545, rs711752, and rs708272 between the control and MS groups (all p < 0.05). (2) rs1800775, rs3764261, rs12149545, rs711752, and rs708272 polymorphisms were significantly related to the risk of MS (all p < 0.05). (3) The rs1800775 polymorphism was associated with high fasting blood glucose levels and low high density lipoprotein cholesterol (HDL-C); rs3764261 and rs12149545 polymorphisms were associated with all components of MS except high blood pressure; rs711752 and rs708272 polymorphisms were associated with low HDL-C (all p < 0.05). (4) Complete linkage disequilibrium (LD) was identified for two pairs of single nucleotide polymorphisms (SNPs) (rs3764261 and rs12149545 (D’ = 1.000, r2 = 0.931), rs711752 and rs708272 (D’ = 1.000, r2 = 0.996)). (5) The A-G-G-G-C (p = 0.013, odds ratio [OR] = 0.622, 95% confidence interval [95% CI] = 0.427–0.906) and A-T-A-A-T (p < 0.001, OR = 0.519, 95% CI = 0.386–0.697) haplotypes were more frequent in the control group than in the case group. Conclusions: The rs1800775, rs3764261, rs12149545, rs711752, and rs708272 polymorphisms of CETP were associated with MS and its components among the Uyghur ethnic group. Complete LD was found between two pairs of SNPs (rs3764261 and rs12149545, rs711752, and rs708272). The A-G-G-G-C and A-T-A-A-T haplotypes might be protective factors for MS. PMID:28629169

Association analysis of the SLC22A11 (organic anion transporter 4) and SLC22A12 (urate transporter 1) urate transporter locus with gout in New Zealand case-control sample sets reveals multiple ancestral-specific effects

PubMed Central

2013-01-01

Introduction There is inconsistent association between urate transporters SLC22A11 (organic anion transporter 4 (OAT4)) and SLC22A12 (urate transporter 1 (URAT1)) and risk of gout. New Zealand (NZ) Māori and Pacific Island people have higher serum urate and more severe gout than European people. The aim of this study was to test genetic variation across the SLC22A11/SLC22A12 locus for association with risk of gout in NZ sample sets. Methods A total of 12 single nucleotide polymorphism (SNP) variants in four haplotype blocks were genotyped using TaqMan® and Sequenom MassArray in 1003 gout cases and 1156 controls. All cases had gout according to the 1977 American Rheumatism Association criteria. Association analysis of single markers and haplotypes was performed using PLINK and Stata. Results A haplotype block 1 SNP (rs17299124) (upstream of SLC22A11) was associated with gout in less admixed Polynesian sample sets, but not European Caucasian (odds ratio; OR = 3.38, P = 6.1 × 10-4; OR = 0.91, P = 0.40, respectively) sample sets. A protective block 1 haplotype caused the rs17299124 association (OR = 0.28, P = 6.0 × 10-4). Within haplotype block 2 (SLC22A11) we could not replicate previous reports of association of rs2078267 with gout in European Caucasian (OR = 0.98, P = 0.82) sample sets, however this SNP was associated with gout in Polynesian (OR = 1.51, P = 0.022) sample sets. Within haplotype block 3 (including SLC22A12) analysis of haplotypes revealed a haplotype with trans-ancestral protective effects (OR = 0.80, P = 0.004), and a second haplotype conferring protection in less admixed Polynesian sample sets (OR = 0.63, P = 0.028) but risk in European Caucasian samples (OR = 1.33, P = 0.039). Conclusions Our analysis provides evidence for multiple ancestral-specific effects across the SLC22A11/SLC22A12 locus that presumably influence the activity of OAT4 and URAT1 and risk of gout. Further fine mapping of the association signal is needed using trans-ancestral re-sequence data. PMID:24360580

Actigraphy for the Assessment of Sleep Measures in Parkinson's Disease

PubMed Central

Maglione, Jeanne E.; Liu, Lianqi; Neikrug, Ariel B.; Poon, Tina; Natarajan, Loki; Calderon, Joanna; Avanzino, Julie A.; Corey-Bloom, Jody; Palmer, Barton W.; Loredo, Jose S.; Ancoli-Israel, Sonia

2013-01-01

Objectives: To assess the usefulness of actigraphy for assessment of nighttime sleep measures in patients with Parkinson's disease (PD). Design: Participants underwent overnight sleep assessment simultaneously by polysomnography (PSG) and actigraphy. Setting: Overnight sleep study in academic sleep research laboratory. Participants: Sixty-one patients (mean age 67.74 ± 8.88 y) with mild to moderate PD. Measurements: Sleep measures including total sleep time (TST), sleep efficiency (SE), wake after sleep onset (WASO), and sleep onset latency (SOL) were calculated independently from data derived from PSG and from actigraphy. Different actigraphy scoring settings were compared. Results: No single tested actigraphy scoring setting was optimal for all sleep measures. A customized setting of an activity threshold of 10, with five consecutive immobile minutes for sleep onset, yielded the combination of mean TST, SE, and WASO values that best approximated mean values determined by PSG with differences of 6.05 ± 85.67 min for TST, 1.1 ± 0.641% for SE, and 4.35 ± 59.56 min for WASO. There were significant but moderate correlations between actigraphy and PSG measurements (rs = 0.496, P < 0.001 for TST, rs = 0.384, P = 0.002 for SE, and rs = 0.400, P = 0.001 for WASO) using these settings. Greater disease stage was associated with greater differences between TST (R2 = 0.099, beta = 0.315, P = 0.018), SE (R2 = 0.107, beta = 0.327, P = 0.014), and WASO (R2 = 0.094, beta = 0.307, P = 0.021) values derived by actigraphy and PSG explaining some of the variability. Using a setting of 10 immobile min for sleep onset yielded a mean SOL that was within 1 min of that estimated by PSG. However SOL values determined by actigraphy and PSG were not significantly correlated at any tested setting. Conclusions: Our results suggest that actigraphy may be useful for measurement of mean TST, SE, and WASO values in groups of patients with mild to moderate Parkinson's disease. However, there is a significant degree of variability in accuracy among individual patients. The importance of determining optimal scoring parameters for each population studied is underscored. Citation: Maglione JE; Liu L; Neikrug AB; Poon T; Natarajan L; Calderon J; Avanzino JA; Corey-Bloom J; Palmer BW; Loredo JS; Ancoli-Israel S. Actigraphy for the assessment of sleep measures in Parkinson's disease. SLEEP 2013;36(8):1209-1217. PMID:23904681

Costs analysis of a population level rabies control programme in Tamil Nadu, India.

PubMed

Abbas, Syed Shahid; Kakkar, Manish; Rogawski, Elizabeth Tacket

2014-02-01

The study aimed to determine costs to the state government of implementing different interventions for controlling rabies among the entire human and animal populations of Tamil Nadu. This built upon an earlier assessment of Tamil Nadu's efforts to control rabies. Anti-rabies vaccines were made available at all health facilities. Costs were estimated for five different combinations of animal and human interventions using an activity-based costing approach from the provider perspective. Disease and population data were sourced from the state surveillance data, human census and livestock census. Program costs were extrapolated from official documents. All capital costs were depreciated to estimate annualized costs. All costs were inflated to 2012 Rupees. Sensitivity analysis was conducted across all major cost centres to assess their relative impact on program costs. It was found that the annual costs of providing Anti-rabies vaccine alone and in combination with Immunoglobulins was $0.7 million (Rs 36 million) and $2.2 million (Rs 119 million), respectively. For animal sector interventions, the annualised costs of rolling out surgical sterilisation-immunization, injectable immunization and oral immunizations were estimated to be $ 44 million (Rs 2,350 million), $23 million (Rs 1,230 million) and $ 11 million (Rs 590 million), respectively. Dog bite incidence, health systems coverage and cost of rabies biologicals were found to be important drivers of costs for human interventions. For the animal sector interventions, the size of dog catching team, dog population and vaccine costs were found to be driving the costs. Rabies control in Tamil Nadu seems a costly proposition the way it is currently structured. Policy makers in Tamil Nadu and other similar settings should consider the long-term financial sustainability before embarking upon a state or nation-wide rabies control programme.

Evidence for gene-gene epistatic interactions among susceptibility loci for systemic lupus erythematosus.

PubMed

Hughes, Travis; Adler, Adam; Kelly, Jennifer A; Kaufman, Kenneth M; Williams, Adrienne H; Langefeld, Carl D; Brown, Elizabeth E; Alarcón, Graciela S; Kimberly, Robert P; Edberg, Jeffrey C; Ramsey-Goldman, Rosalind; Petri, Michelle; Boackle, Susan A; Stevens, Anne M; Reveille, John D; Sanchez, Elena; Martín, Javier; Niewold, Timothy B; Vilá, Luis M; Scofield, R Hal; Gilkeson, Gary S; Gaffney, Patrick M; Criswell, Lindsey A; Moser, Kathy L; Merrill, Joan T; Jacob, Chaim O; Tsao, Betty P; James, Judith A; Vyse, Timothy J; Alarcón-Riquelme, Marta E; Harley, John B; Richardson, Bruce C; Sawalha, Amr H

2012-02-01

Several confirmed genetic susceptibility loci for lupus have been described. To date, no clear evidence for genetic epistasis in lupus has been established. The aim of this study was to test for gene-gene interactions in a number of known lupus susceptibility loci. Eighteen single-nucleotide polymorphisms tagging independent and confirmed lupus susceptibility loci were genotyped in a set of 4,248 patients with lupus and 3,818 normal healthy control subjects of European descent. Epistasis was tested by a 2-step approach using both parametric and nonparametric methods. The false discovery rate (FDR) method was used to correct for multiple testing. We detected and confirmed gene-gene interactions between the HLA region and CTLA4, IRF5, and ITGAM and between PDCD1 and IL21 in patients with lupus. The most significant interaction detected by parametric analysis was between rs3131379 in the HLA region and rs231775 in CTLA4 (interaction odds ratio 1.19, Z = 3.95, P = 7.8 × 10(-5) [FDR ≤0.05], P for multifactor dimensionality reduction = 5.9 × 10(-45)). Importantly, our data suggest that in patients with lupus, the presence of the HLA lupus risk alleles in rs1270942 and rs3131379 increases the odds of also carrying the lupus risk allele in IRF5 (rs2070197) by 17% and 16%, respectively (P = 0.0028 and P = 0.0047, respectively). We provide evidence for gene-gene epistasis in systemic lupus erythematosus. These findings support a role for genetic interaction contributing to the complexity of lupus heritability. Copyright © 2012 by the American College of Rheumatology.

Resting-state functional connectivity predicts the strength of hemispheric lateralization for language processing in temporal lobe epilepsy and normals.

PubMed

Doucet, Gaëlle E; Pustina, Dorian; Skidmore, Christopher; Sharan, Ashwini; Sperling, Michael R; Tracy, Joseph I

2015-01-01

In temporal lobe epilepsy (TLE), determining the hemispheric specialization for language before surgery is critical to preserving a patient's cognitive abilities post-surgery. To date, the major techniques utilized are limited by the capacity of patients to efficiently realize the task. We determined whether resting-state functional connectivity (rsFC) is a reliable predictor of language hemispheric dominance in right and left TLE patients, relative to controls. We chose three subregions of the inferior frontal cortex (pars orbitalis, pars triangularis, and pars opercularis) as the seed regions. All participants performed both a verb generation task and a resting-state fMRI procedure. Based on the language task, we computed a laterality index (LI) for the resulting network. This revealed that 96% of the participants were left-hemisphere dominant, although there remained a large degree of variability in the strength of left lateralization. We tested whether LI correlated with rsFC values emerging from each seed. We revealed a set of regions that was specific to each group. Unique correlations involving the epileptic mesial temporal lobe were revealed for the right and left TLE patients, but not for the controls. Importantly, for both TLE groups, the rsFC emerging from a contralateral seed was the most predictive of LI. Overall, our data depict the broad patterns of rsFC that support strong versus weak left hemisphere language laterality. This project provides the first evidence that rsFC data may potentially be used on its own to verify the strength of hemispheric dominance for language in impaired or pathologic populations. © 2014 Wiley Periodicals, Inc.

Association Analysis of FOXO3 Longevity Variants With Blood Pressure and Essential Hypertension

PubMed Central

Chen, Randi; Donlon, Timothy A.; Evans, Daniel S.; Tranah, Gregory J.; Parimi, Neeta; Ehret, Georg B.; Newton-Cheh, Christopher; Seto, Todd; Willcox, D. Craig; Masaki, Kamal H.; Kamide, Kei; Ryuno, Hirochika; Oguro, Ryosuke; Nakama, Chikako; Kabayama, Mai; Yamamoto, Koichi; Sugimoto, Ken; Ikebe, Kazunori; Masui, Yukie; Arai, Yasumichi; Ishizaki, Tatsuro; Gondo, Yasuyuki; Rakugi, Hiromi; Willcox, Bradley J.

2016-01-01

BACKGROUND The minor alleles of 3 FOXO3 single nucleotide polymorphisms (SNPs)—rs2802292, rs2253310, and rs2802288—are associated with human longevity. The aim of the present study was to test these SNPs for association with blood pressure (BP) and essential hypertension (EHT). METHODS In a primary study involving Americans of Japanese ancestry drawn from the Family Blood Pressure Program II we genotyped 411 female and 432 male subjects aged 40–79 years and tested for statistical association by contingency table analysis and generalized linear models that included logistic regression adjusting for sibling correlation in the data set. Replication of rs2802292 with EHT was attempted in Japanese SONIC study subjects and of each SNP in a meta-analysis of genome-wide association studies of BP in individuals of European ancestry. RESULTS In Americans of Japanese ancestry, women homozygous for the longevity-associated (minor) allele of each FOXO3 SNP had 6mm Hg lower systolic BP and 3mm Hg lower diastolic BP compared with major allele homozygotes (Bonferroni corrected P < 0.05 and >0.05, respectively). Frequencies of minor allele homozygotes were 3.3–3.9% in women with EHT compared with 9.5–9.6% in normotensive women (P = 0.03–0.04; haplotype analysis P = 0.0002). No association with BP or EHT was evident in males. An association with EHT was seen for the minor allele of rs2802292 in the Japanese SONIC cohort (P = 0.03), while in European subjects the minor allele of each SNP was associated with higher systolic and diastolic BP. CONCLUSION Longevity-associated FOXO3 variants may be associated with lower BP and EHT in Japanese women. PMID:26476085

Association Analysis of FOXO3 Longevity Variants With Blood Pressure and Essential Hypertension.

PubMed

Morris, Brian J; Chen, Randi; Donlon, Timothy A; Evans, Daniel S; Tranah, Gregory J; Parimi, Neeta; Ehret, Georg B; Newton-Cheh, Christopher; Seto, Todd; Willcox, D Craig; Masaki, Kamal H; Kamide, Kei; Ryuno, Hirochika; Oguro, Ryosuke; Nakama, Chikako; Kabayama, Mai; Yamamoto, Koichi; Sugimoto, Ken; Ikebe, Kazunori; Masui, Yukie; Arai, Yasumichi; Ishizaki, Tatsuro; Gondo, Yasuyuki; Rakugi, Hiromi; Willcox, Bradley J

2016-11-01

The minor alleles of 3 FOXO3 single nucleotide polymorphisms (SNPs)- rs2802292 , rs2253310 , and rs2802288 -are associated with human longevity. The aim of the present study was to test these SNPs for association with blood pressure (BP) and essential hypertension (EHT). In a primary study involving Americans of Japanese ancestry drawn from the Family Blood Pressure Program II we genotyped 411 female and 432 male subjects aged 40-79 years and tested for statistical association by contingency table analysis and generalized linear models that included logistic regression adjusting for sibling correlation in the data set. Replication of rs2802292 with EHT was attempted in Japanese SONIC study subjects and of each SNP in a meta-analysis of genome-wide association studies of BP in individuals of European ancestry. In Americans of Japanese ancestry, women homozygous for the longevity-associated (minor) allele of each FOXO3 SNP had 6mm Hg lower systolic BP and 3mm Hg lower diastolic BP compared with major allele homozygotes (Bonferroni corrected P < 0.05 and >0.05, respectively). Frequencies of minor allele homozygotes were 3.3-3.9% in women with EHT compared with 9.5-9.6% in normotensive women ( P = 0.03-0.04; haplotype analysis P = 0.0002). No association with BP or EHT was evident in males. An association with EHT was seen for the minor allele of rs2802292 in the Japanese SONIC cohort ( P = 0.03), while in European subjects the minor allele of each SNP was associated with higher systolic and diastolic BP. Longevity-associated FOXO3 variants may be associated with lower BP and EHT in Japanese women.

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

Matthews, Q; Lum, JJ; Isabelle, M

Purpose: To use label-free Raman spectroscopy (RS) for early treatment monitoring of tumour cell radioresistance. Methods: Three human tumour cell lines, two radioresistant (H460, SF{sub 2} = 0.57 and MCF7, SF{sub 2} = 0.70) and one radiosensitive (LNCaP, SF{sub 2} = 0.36), were irradiated with single fractions of 2, 4, 6, 8 or 10 Gy. In additional experiments, H460 and MCF7 cells were irradiated under co-treatment with the anti-diabetic drug metformin, a known radiosensitizing agent. Treated and control cultures were analyzed with RS daily for 3 days post-treatment. Single-cell Raman spectra were acquired from 20 live cells per sample, andmore » experiments were repeated in triplicate. The combined data sets were analyzed with principal component analysis using standard algorithms. Cells from each culture were also subjected to standard assays for viability, proliferation, cell cycle, and radiation clonogenic survival. Results: The radioresistant cells (H460, MCF7) exhibited a RS molecular radiation response signature, detectable as early as 1 day post-treatment, of which radiation-induced glycogen synthesis is a significant contributor. The radiosensitive cells (LNCaP) exhibited negligible glycogen synthesis. Co-treatment with metformin in MCF7 cells blocked glycogen synthesis, reduced viability and proliferation, and increased radiosensitivity. Conversely, metformin co-treatment in H460 cells did not produce these same effects; importantly, both radiation-induced synthesis of glycogen and radiosensitivity were unaffected. Conclusions: Label-free RS can detect early glycogen synthesis post-irradiation, a previously undocumented metabolic mechanism associated with tumour cell radioresistance that can be targeted to increase radiosensitivity. RS monitoring of intratumoral glycogen may provide new opportunities for personalized combined modality radiotherapy treatments.« less

Impact of genomic risk factors on survival after haematopoietic stem cell transplantation for patients with acute leukaemia.

PubMed

Pearce, K F; Balavarca, Y; Norden, J; Jackson, G; Holler, E; Dressel, R; Greinix, H; Toubert, A; Gluckman, E; Hromadnikova, I; Sedlacek, P; Wolff, D; Holtick, U; Bickeböller, H; Dickinson, A M

2016-12-01

The EBMT risk score is an established tool successfully used in the prognosis of survival post-HSCT and is applicable for a range of haematological disorders. One of its main advantages is that score generation involves summation of clinical parameters that are available pretransplant. However, the EBMT risk score is recognized as not being optimal. Previous analyses, involving patients with various diagnoses, have shown that non-HLA gene polymorphisms influence outcome after allogeneic HSCT. This study is novel as it focuses only on patients having acute leukaemia (N = 458) and attempts to demonstrate how non-HLA gene polymorphisms can be added to the EBMT risk score in a Cox regression model to improve prognostic ability for overall survival. The results of the study found that three genetic factors improved EBMT risk score. The presence of MAL (rs8177374) allele T in the patient, absence of glucocorticoid receptor haplotype (consisting of rs6198, rs33389 and rs33388) ACT in the patient and absence of heat-shock protein 70-hom (+2437) (rs2227956) allele C in the patient were associated with decreased survival time. When compared to the EBMT risk score, the scores combining EBMT risk score with the genetic factors had an improved correlation with clinical outcome and better separation of risk groups. A bootstrapping technique, involving repeated testing of a model using multiple validation sets, also revealed that the newly proposed model had improved predictive value when compared to the EBMT risk score alone. Results support the view that non-HLA polymorphisms could be useful for pretransplant clinical assessment and provide evidence that polymorphisms in the recipient genotype may influence incoming donor cells, suppressing the initiation of the graft versus leukaemia effect and reducing survival. © 2016 John Wiley & Sons Ltd.

fabp4 is central to eight obesity associated genes: a functional gene network-based polymorphic study.

PubMed

Bag, Susmita; Ramaiah, Sudha; Anbarasu, Anand

2015-01-07

Network study on genes and proteins offers functional basics of the complexity of gene and protein, and its interacting partners. The gene fatty acid-binding protein 4 (fabp4) is found to be highly expressed in adipose tissue, and is one of the most abundant proteins in mature adipocytes. Our investigations on functional modules of fabp4 provide useful information on the functional genes interacting with fabp4, their biochemical properties and their regulatory functions. The present study shows that there are eight set of candidate genes: acp1, ext2, insr, lipe, ostf1, sncg, usp15, and vim that are strongly and functionally linked up with fabp4. Gene ontological analysis of network modules of fabp4 provides an explicit idea on the functional aspect of fabp4 and its interacting nodes. The hierarchal mapping on gene ontology indicates gene specific processes and functions as well as their compartmentalization in tissues. The fabp4 along with its interacting genes are involved in lipid metabolic activity and are integrated in multi-cellular processes of tissues and organs. They also have important protein/enzyme binding activity. Our study elucidated disease-associated nsSNP prediction for fabp4 and it is interesting to note that there are four rsID׳s (rs1051231, rs3204631, rs140925685 and rs141169989) with disease allelic variation (T104P, T126P, G27D and G90V respectively). On the whole, our gene network analysis presents a clear insight about the interactions and functions associated with fabp4 gene network. Copyright © 2014 Elsevier Ltd. All rights reserved.

Costs Analysis of a Population Level Rabies Control Programme in Tamil Nadu, India

PubMed Central

Abbas, Syed Shahid; Kakkar, Manish; Rogawski, Elizabeth Tacket

2014-01-01

The study aimed to determine costs to the state government of implementing different interventions for controlling rabies among the entire human and animal populations of Tamil Nadu. This built upon an earlier assessment of Tamil Nadu's efforts to control rabies. Anti-rabies vaccines were made available at all health facilities. Costs were estimated for five different combinations of animal and human interventions using an activity-based costing approach from the provider perspective. Disease and population data were sourced from the state surveillance data, human census and livestock census. Program costs were extrapolated from official documents. All capital costs were depreciated to estimate annualized costs. All costs were inflated to 2012 Rupees. Sensitivity analysis was conducted across all major cost centres to assess their relative impact on program costs. It was found that the annual costs of providing Anti-rabies vaccine alone and in combination with Immunoglobulins was $0.7 million (Rs 36 million) and $2.2 million (Rs 119 million), respectively. For animal sector interventions, the annualised costs of rolling out surgical sterilisation-immunization, injectable immunization and oral immunizations were estimated to be $ 44 million (Rs 2,350 million), $23 million (Rs 1,230 million) and $ 11 million (Rs 590 million), respectively. Dog bite incidence, health systems coverage and cost of rabies biologicals were found to be important drivers of costs for human interventions. For the animal sector interventions, the size of dog catching team, dog population and vaccine costs were found to be driving the costs. Rabies control in Tamil Nadu seems a costly proposition the way it is currently structured. Policy makers in Tamil Nadu and other similar settings should consider the long-term financial sustainability before embarking upon a state or nation-wide rabies control programme. PMID:24587471

PPARD rs2016520 polymorphism affects repaglinide response in Chinese Han patients with type 2 diabetes mellitus.

PubMed

Song, Jin-Fang; Wang, Tao; Zhu, Jing; Zhou, Xue-Yan; Lu, Qian; Guo, Hao; Zhang, Fan; Wang, Yan; Li, Wei; Wang, Dan-Dan; Cui, Ya-Wen; Lv, Dong-Mei; Yin, Xiao-Xing

2015-01-01

Repaglinide is a short-acting insulin secretagogue, which often results in considerable interindividual variability in therapeutic efficacy when widely used in a clinical setting. Among various reasons under discussion is genetic polymorphism, especially the genes related to insulin secretion and resistance. Recent studies have described the importance of PPARD in regulating the secretion and resistance of insulin. However, little is known about the impacts of PPARD genetic polymorphism on the efficacy of repaglinide. Therefore, the current study was designed to investigate the associations of PPARD rs2016520 polymorphism with type 2 diabetes mellitus (T2DM) susceptibility and repaglinide therapeutic efficacy in Chinese Han T2DM patients. A total of 338 T2DM patients and 200 healthy subjects were genotyped for PPARD rs2016520 polymorphism by polymerase chain reaction-restriction fragment length polymorphism assay. A total of 84 patients with the same genotypes of CYP2C8*3 139Arg and OATP1B1 521TT were randomized to orally take repaglinide for 8 weeks. Then the pharmacodynamic parameters of repaglinide and biochemical indicators were determined before and after repaglinide treatment. No significant difference was found in either allelic frequency (P = 0.298) or genotype distribution (P = 0.151) of PPARD rs2016520 between T2DM patients and healthy subjects. However, T2DM patients carrying genotype TC showed a significantly lower increase in postprandial serum insulin (mU/L) than those with wild-type TT (P < 0.05). These findings suggest that PPARD rs2016520 polymorphism might influence the therapeutic effect of repaglinide rather than T2DM susceptibility in Chinese Han T2DM patients. © 2014 Wiley Publishing Asia Pty Ltd.

CFH Variants Affect Structural and Functional Brain Changes and Genetic Risk of Alzheimer's Disease.

PubMed

Zhang, Deng-Feng; Li, Jin; Wu, Huan; Cui, Yue; Bi, Rui; Zhou, He-Jiang; Wang, Hui-Zhen; Zhang, Chen; Wang, Dong; Kong, Qing-Peng; Li, Tao; Fang, Yiru; Jiang, Tianzi; Yao, Yong-Gang

2016-03-01

The immune response is highly active in Alzheimer's disease (AD). Identification of genetic risk contributed by immune genes to AD may provide essential insight for the prognosis, diagnosis, and treatment of this neurodegenerative disease. In this study, we performed a genetic screening for AD-related top immune genes identified in Europeans in a Chinese cohort, followed by a multiple-stage study focusing on Complement Factor H (CFH) gene. Effects of the risk SNPs on AD-related neuroimaging endophenotypes were evaluated through magnetic resonance imaging scan, and the effects on AD cerebrospinal fluid biomarkers (CSF) and CFH expression changes were measured in aged and AD brain tissues and AD cellular models. Our results showed that the AD-associated top immune genes reported in Europeans (CR1, CD33, CLU, and TREML2) have weak effects in Chinese, whereas CFH showed strong effects. In particular, rs1061170 (P(meta)=5.0 × 10(-4)) and rs800292 (P(meta)=1.3 × 10(-5)) showed robust associations with AD, which were confirmed in multiple world-wide sample sets (4317 cases and 16 795 controls). Rs1061170 (P=2.5 × 10(-3)) and rs800292 (P=4.7 × 10(-4)) risk-allele carriers have an increased entorhinal thickness in their young age and a higher atrophy rate as the disease progresses. Rs800292 risk-allele carriers have higher CSF tau and Aβ levels and severe cognitive decline. CFH expression level, which was affected by the risk-alleles, was increased in AD brains and cellular models. These comprehensive analyses suggested that CFH is an important immune factor in AD and affects multiple pathological changes in early life and during disease progress.

Radiation Therapy Overcomes Adverse Prognostic Role of Cyclooxygenase-2 Expression on Reed-Sternberg Cells in Early Hodgkin Lymphoma

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

Mestre, Francisco; Gutiérrez, Antonio, E-mail: antoniom.gutierrez@ssib.es; Rodriguez, Jose

Purpose: To analyze the role of radiation therapy (RT) on the adverse prognostic influence of cyclooxygenase-2 (COX-2) expression on Reed-Sternberg (RS) cells, in the setting of early Hodgkin lymphoma (HL) treated with ABVD (adriamycin, vinblastine, bleomycin, dacarbazine). Methods and Materials: In the present study we retrospectively investigated the prognostic value of COX-2 expression in a large (n=143), uniformly treated early HL population from the Spanish Network of HL using tissue microarrays. Univariate and multivariate analyses were done, including the most recognized clinical variables and the potential role of administration of adjuvant RT. Results: Median age was 31 years; the expression of COX-2more » defined a subgroup with significantly worse prognosis. Considering COX-2{sup +} patients, those who received RT had significantly better 5-year progression-free survival (PFS) (80% vs 54% if no RT; P=.008). In contrast, COX-2{sup −} patients only had a modest, nonsignificant benefit from RT in terms of 5-year PFS (90% vs 79%; P=.13). When we compared the outcome of patients receiving RT considering the expression of COX-2 on RS cells, we found a nonsignificant 10% difference in terms of PFS between COX-2{sup +} and COX-2{sup −} patients (P=.09), whereas the difference between the 2 groups was important (25%) in patients not receiving RT (P=.04). Conclusions: Cyclooxygenase-2 RS cell expression is an adverse independent prognostic factor in early HL. Radiation therapy overcomes the worse prognosis associated with COX-2 expression on RS cells, acting in a chemotherapy-independent way. Cyclooxygenase-2 RS cell expression may be useful for determining patient candidates with early HL to receive consolidation with RT.« less

Metabolic Characterization of a Rare Genetic Variation Within APOC3 and Its Lipoprotein Lipase-Independent Effects.

PubMed

Drenos, Fotios; Davey Smith, George; Ala-Korpela, Mika; Kettunen, Johannes; Würtz, Peter; Soininen, Pasi; Kangas, Antti J; Dale, Caroline; Lawlor, Debbie A; Gaunt, Tom R; Casas, Juan-Pablo; Timpson, Nicholas J

2016-06-01

Plasma triglyceride levels have been implicated in atherosclerosis and coronary heart disease. Apolipoprotein C-III (APOC3) plays a key role in the hydrolysis of triglyceride-rich lipoproteins to remnant particles by lipoprotein lipase (LPL) and their uptake by the liver. A rare variant in APOC3(rs138326449) has been associated with triglyceride, very low-density lipoprotein, and high-density lipoprotein levels, as well as risk of coronary heart disease. We aimed to characterize the impact of this locus across a broad set of mainly lipids-focused metabolic measures. A high-throughput serum nuclear magnetic resonance metabolomics platform was used to quantify 225 metabolic measures in 13 285 participants from 2 European population cohorts. We analyzed the effect of the APOC3 variant on the metabolic measures and used the common LPL(rs12678919) polymorphism to test for LPL-independent effects. Eighty-one metabolic measures showed evidence of association with APOC3(rs138326449). In addition to previously reported triglyceride and high-density lipoprotein associations, the variant was also associated with very low-density lipoprotein and high-density lipoprotein composition measures, other cholesterol measures, and fatty acids. Comparison of the APOC3 and LPL associations revealed that APOC3 association results for medium and very large very low-density lipoprotein composition are unlikely to be solely predictable by the action of APOC3 through LPL. We characterized the effects of the rare APOC3(rs138326449) loss of function mutation in lipoprotein metabolism, as well as the effects of LPL(rs12678919). Our results improve our understanding of the role of APOC3 in triglyceride metabolism, its LPL independent action, and the complex and correlated nature of human metabolites. © 2016 The Authors.

Metabolic Characterization of a Rare Genetic Variation Within APOC3 and Its Lipoprotein Lipase–Independent Effects

PubMed Central

Davey Smith, George; Ala-Korpela, Mika; Kettunen, Johannes; Würtz, Peter; Soininen, Pasi; Kangas, Antti J.; Dale, Caroline; Lawlor, Debbie A.; Gaunt, Tom R.; Casas, Juan-Pablo

2016-01-01

Background— Plasma triglyceride levels have been implicated in atherosclerosis and coronary heart disease. Apolipoprotein C-III (APOC3) plays a key role in the hydrolysis of triglyceride-rich lipoproteins to remnant particles by lipoprotein lipase (LPL) and their uptake by the liver. A rare variant in APOC3(rs138326449) has been associated with triglyceride, very low–density lipoprotein, and high-density lipoprotein levels, as well as risk of coronary heart disease. We aimed to characterize the impact of this locus across a broad set of mainly lipids-focused metabolic measures. Methods and Results— A high-throughput serum nuclear magnetic resonance metabolomics platform was used to quantify 225 metabolic measures in 13 285 participants from 2 European population cohorts. We analyzed the effect of the APOC3 variant on the metabolic measures and used the common LPL(rs12678919) polymorphism to test for LPL-independent effects. Eighty-one metabolic measures showed evidence of association with APOC3(rs138326449). In addition to previously reported triglyceride and high-density lipoprotein associations, the variant was also associated with very low–density lipoprotein and high-density lipoprotein composition measures, other cholesterol measures, and fatty acids. Comparison of the APOC3 and LPL associations revealed that APOC3 association results for medium and very large very low–density lipoprotein composition are unlikely to be solely predictable by the action of APOC3 through LPL. Conclusions— We characterized the effects of the rare APOC3(rs138326449) loss of function mutation in lipoprotein metabolism, as well as the effects of LPL(rs12678919). Our results improve our understanding of the role of APOC3 in triglyceride metabolism, its LPL independent action, and the complex and correlated nature of human metabolites. PMID:27114411

Identifying Rodent Resting-State Brain Networks with Independent Component Analysis

PubMed Central

Bajic, Dusica; Craig, Michael M.; Mongerson, Chandler R. L.; Borsook, David; Becerra, Lino

2017-01-01

Rodent models have opened the door to a better understanding of the neurobiology of brain disorders and increased our ability to evaluate novel treatments. Resting-state functional magnetic resonance imaging (rs-fMRI) allows for in vivo exploration of large-scale brain networks with high spatial resolution. Its application in rodents affords researchers a powerful translational tool to directly assess/explore the effects of various pharmacological, lesion, and/or disease states on known neural circuits within highly controlled settings. Integration of animal and human research at the molecular-, systems-, and behavioral-levels using diverse neuroimaging techniques empowers more robust interrogations of abnormal/ pathological processes, critical for evolving our understanding of neuroscience. We present a comprehensive protocol to evaluate resting-state brain networks using Independent Component Analysis (ICA) in rodent model. Specifically, we begin with a brief review of the physiological basis for rs-fMRI technique and overview of rs-fMRI studies in rodents to date, following which we provide a robust step-by-step approach for rs-fMRI investigation including data collection, computational preprocessing, and brain network analysis. Pipelines are interwoven with underlying theory behind each step and summarized methodological considerations, such as alternative methods available and current consensus in the literature for optimal results. The presented protocol is designed in such a way that investigators without previous knowledge in the field can implement the analysis and obtain viable results that reliably detect significant differences in functional connectivity between experimental groups. Our goal is to empower researchers to implement rs-fMRI in their respective fields by incorporating technical considerations to date into a workable methodological framework. PMID:29311770

Tribological Properties of PVD Ti/C-N Nanocoatnigs

NASA Astrophysics Data System (ADS)

Leitans, A.; Lungevics, J.; Rudzitis, J.; Filipovs, A.

2017-04-01

The present paper discusses and analyses tribological properties of various coatings that increase surface wear resistance. Four Ti/C-N nanocoatings with different coating deposition settings are analysed. Tribological and metrological tests on the samples are performed: 2D and 3D parameters of the surface roughness are measured with modern profilometer, and friction coefficient is measured with CSM Instruments equipment. Roughness parameters Ra, Sa, Sz, Str, Sds, Vmp, Vmc and friction coefficient at 6N load are determined during the experiment. The examined samples have many pores, which is the main reason for relatively large values of roughness parameter. A slight wear is identified in all four samples as well; its friction coefficient values range from 0,.21 to 0.29. Wear rate values are not calculated for the investigated coatings, as no expressed tribotracks are detected on the coating surface.

Reduction of Surface Roughness by Means of Laser Processing over Additive Manufacturing Metal Parts.

PubMed

Alfieri, Vittorio; Argenio, Paolo; Caiazzo, Fabrizia; Sergi, Vincenzo

2016-12-31

Optimization of processing parameters and exposure strategies is usually performed in additive manufacturing to set up the process; nevertheless, standards for roughness may not be evenly matched on a single complex part, since surface features depend on the building direction of the part. This paper aims to evaluate post processing treating via laser surface modification by means of scanning optics and beam wobbling to process metal parts resulting from selective laser melting of stainless steel in order to improve surface topography. The results are discussed in terms of roughness, geometry of the fusion zone in the cross-section, microstructural modification, and microhardness so as to assess the effects of laser post processing. The benefits of beam wobbling over linear scanning processing are shown, as heat effects in the base metal are proven to be lower.

Reduction of Surface Roughness by Means of Laser Processing over Additive Manufacturing Metal Parts

PubMed Central

Alfieri, Vittorio; Argenio, Paolo; Caiazzo, Fabrizia; Sergi, Vincenzo

2016-01-01

Optimization of processing parameters and exposure strategies is usually performed in additive manufacturing to set up the process; nevertheless, standards for roughness may not be evenly matched on a single complex part, since surface features depend on the building direction of the part. This paper aims to evaluate post processing treating via laser surface modification by means of scanning optics and beam wobbling to process metal parts resulting from selective laser melting of stainless steel in order to improve surface topography. The results are discussed in terms of roughness, geometry of the fusion zone in the cross-section, microstructural modification, and microhardness so as to assess the effects of laser post processing. The benefits of beam wobbling over linear scanning processing are shown, as heat effects in the base metal are proven to be lower. PMID:28772380

Comprehensive Search for Alzheimer Disease Susceptibility Loci in the APOE Region

PubMed Central

Jun, Gyungah; Vardarajan, Badri N.; Buros, Jacqueline; Yu, Chang-En; Hawk, Michele V.; Dombroski, Beth A.; Crane, Paul K.; Larson, Eric B.; Mayeux, Richard; Haines, Jonathan L.; Lunetta, Kathryn L.; Pericak-Vance, Margaret A.; Schellenberg, Gerard D.; Farrer, Lindsay A.

2013-01-01

Objective To evaluate the association of risk and age at onset (AAO) of Alzheimer disease (AD) with single-nucleotide polymorphisms (SNPs) in the chromosome 19 region including apolipoprotein E (APOE) and a repeat-length polymorphism in TOMM40 (poly-T, rs10524523). Design Conditional logistic regression models and survival analysis. Setting Fifteen genome-wide association study data sets assembled by the Alzheimer's Disease Genetics Consortium. Participants Eleven thousand eight hundred forty AD cases and 10 931 cognitively normal elderly controls. Main Outcome Measures Association of AD risk and AAO with genotyped and imputed SNPs located in an 800-Mb region including APOE in the entire Alzheimer's Disease Genetics Consortium data set and with the TOMM40 poly-T marker genotyped in a subset of 1256 cases and 1605 controls. Results In models adjusting for APOE ε4, no SNPs in the entire region were significantly associated with AAO at P<.001. Rs10524523 was not significantly associated with AD or AAO in models adjusting for APOE genotype or within the subset of ε3/ε3 subjects. Conclusions APOE alleles ε2, ε3, and ε4 account for essentially all the inherited risk of AD associated with this region. Other variants including a poly-T track in TOMM40 are not independent risk or AAO loci. PMID:22869155

On the stability of von Kármán rotating-disk boundary layers with radial anisotropic surface roughness

NASA Astrophysics Data System (ADS)

Garrett, S. J.; Cooper, A. J.; Harris, J. H.; Özkan, M.; Segalini, A.; Thomas, P. J.

2016-01-01

We summarise results of a theoretical study investigating the distinct convective instability properties of steady boundary-layer flow over rough rotating disks. A generic roughness pattern of concentric circles with sinusoidal surface undulations in the radial direction is considered. The goal is to compare predictions obtained by means of two alternative, and fundamentally different, modelling approaches for surface roughness for the first time. The motivating rationale is to identify commonalities and isolate results that might potentially represent artefacts associated with the particular methodologies underlying one of the two modelling approaches. The most significant result of practical relevance obtained is that both approaches predict overall stabilising effects on type I instability mode of rotating disk flow. This mode leads to transition of the rotating-disk boundary layer and, more generally, the transition of boundary-layers with a cross-flow profile. Stabilisation of the type 1 mode means that it may be possible to exploit surface roughness for laminar-flow control in boundary layers with a cross-flow component. However, we also find differences between the two sets of model predictions, some subtle and some substantial. These will represent criteria for establishing which of the two alternative approaches is more suitable to correctly describe experimental data when these become available.

A Fractal Interpretation of Controlled-Source Helicopter Electromagnetic Survey Data: Seco Creek, Edwards Aquifer, TX

NASA Astrophysics Data System (ADS)

Decker, K. T.; Everett, M. E.

2009-12-01

The Edwards aquifer lies in the structurally complex Balcones fault zone and supplies water to the growing city of San Antonio. To ensure that future demands for water are met, the hydrological and geophysical properties of the aquifer must be well-understood. In most settings, fracture lengths and displacements occur in power-law distributions. Fracture distribution plays an important role in determining electrical and hydraulic current flowpaths. 1-D synthetic models of the controlled-source electromagnetic (CSEM) response for layered models with a fractured layer at depth described by the roughness parameter βV, such that 0≤βV<1, associated with the power-law length-scale dependence of electrical conductivity are developed. A value of βV = 0 represents homogeneous, continuous media, while a value of 0<βV<1 shows that roughness exists. The Seco Creek frequency-domain helicopter electromagnetic survey data set is analyzed by introducing the similarly defined roughness parameter βH to detect lateral roughness along survey lines. Fourier transforming the apparent resistivity as a function of position along flight line into wavenumber domain using a 256-point sliding window gives the power spectral density (PSD) plot for each line. The value of βH is the slope of the least squares regression for the PSD in each 256-point window. Changes in βH with distance along the flight line are plotted. Large values of βH are found near well-known large fractures and maps of βH produced by interpolating values of βH along survey lines suggest previously undetected structure at depth.

Quantification of tillage, plant cover, and cumulative rainfall effects on soil surface microrelief by statistical, geostatistical and fractal indices

NASA Astrophysics Data System (ADS)

Paz-Ferreiro, J.; Bertol, I.; Vidal Vázquez, E.

2008-07-01

Changes in soil surface microrelief with cumulative rainfall under different tillage systems and crop cover conditions were investigated in southern Brazil. Surface cover was none (fallow) or the crop succession maize followed by oats. Tillage treatments were: 1) conventional tillage on bare soil (BS), 2) conventional tillage (CT), 3) minimum tillage (MT) and 4) no tillage (NT) under maize and oats. Measurements were taken with a manual relief meter on small rectangular grids of 0.234 and 0.156 m2, throughout growing season of maize and oats, respectively. Each data set consisted of 200 point height readings, the size of the smallest cells being 3×5 cm during maize and 2×5 cm during oats growth periods. Random Roughness (RR), Limiting Difference (LD), Limiting Slope (LS) and two fractal parameters, fractal dimension (D) and crossover length (l) were estimated from the measured microtopographic data sets. Indices describing the vertical component of soil roughness such as RR, LD and l generally decreased with cumulative rain in the BS treatment, left fallow, and in the CT and MT treatments under maize and oats canopy. However, these indices were not substantially affected by cumulative rain in the NT treatment, whose surface was protected with previous crop residues. Roughness decay from initial values was larger in the BS treatment than in CT and MT treatments. Moreover, roughness decay generally tended to be faster under maize than under oats. The RR and LD indices decreased quadratically, while the l index decreased exponentially in the tilled, BS, CT and MT treatments. Crossover length was sensitive to differences in soil roughness conditions allowing a description of microrelief decay due to rainfall in the tilled treatments, although better correlations between cumulative rainfall and the most commonly used indices RR and LD were obtained. At the studied scale, parameters l and D have been found to be useful in interpreting the configuration properties of the soil surface microrelief.

Contact stiffness of regularly patterned multi-asperity interfaces

NASA Astrophysics Data System (ADS)

Li, Shen; Yao, Quanzhou; Li, Qunyang; Feng, Xi-Qiao; Gao, Huajian

2018-02-01

Contact stiffness is a fundamental mechanical index of solid surfaces and relevant to a wide range of applications. Although the correlation between contact stiffness, contact size and load has long been explored for single-asperity contacts, our understanding of the contact stiffness of rough interfaces is less clear. In this work, the contact stiffness of hexagonally patterned multi-asperity interfaces is studied using a discrete asperity model. We confirm that the elastic interaction among asperities is critical in determining the mechanical behavior of rough contact interfaces. More importantly, in contrast to the common wisdom that the interplay of asperities is solely dictated by the inter-asperity spacing, we show that the number of asperities in contact (or equivalently, the apparent size of contact) also plays an indispensable role. Based on the theoretical analysis, we propose a new parameter for gauging the closeness of asperities. Our theoretical model is validated by a set of experiments. To facilitate the application of the discrete asperity model, we present a general equation for contact stiffness estimation of regularly rough interfaces, which is further proved to be applicable for interfaces with single-scale random roughness.

The Applicant Based Training Model Setting Conditions for Recruiting Success

DTIC Science & Technology

2002-07-01

the RS XO is another critical 32. function that falls into the scope of their responsibly and requires specific training in marketing and advertising . During...Phase I require a solid working knowledge of marketing and advertising . OpsO: Phase II actions require the OpsO receive advanced training in data

Identification and characterization of MicroRNAs expressed in chicken skeletal muscle

USDA-ARS?s Scientific Manuscript database

MicroRNAs (miRNAs, miRs) encompass a class of small noncoding RNAs that negatively regulate gene expression. MicroRNAs play an essential role in skeletal muscle, determining the proper development and maintenance of this tissue. In comparison to other organs and tissues, the full set of muscle miRNA...

Dr. Overhead's Elixir of Learning, or Where Have All the Experts Gone?

ERIC Educational Resources Information Center

Berger, Peter N.

1995-01-01

Claims that many education workshops are run by "experts" who have not set foot in a classroom in years. Suggests that teaching is not a science--it is and will remain an art and a craft. Argues that education is absorbed in "cultic obsessions with empty expertise and patent remedies." (RS)

Germline and somatic genetic predictors of pathological response in neoadjuvant settings of rectal and esophageal cancers: systematic review and meta-analysis.

PubMed

Salnikova, L E; Kolobkov, D S

2016-06-01

Oncologists have pointed out an urgent need for biomarkers that can be useful for clinical application to predict the susceptibility of patients to preoperative therapy. This review collects, evaluates and combines data on the influence of reported somatic and germline genetic variations on histological tumor regression in neoadjuvant settings of rectal and esophageal cancers. Five hundred and twenty-seven articles were identified, 204 retrieved and 61 studies included. Among 24 and 14 genetic markers reported for rectal and esophageal cancers, respectively, significant associations in meta-analyses were demonstrated for the following markers. In rectal cancer, major response was more frequent in carriers of the TYMS genotype 2 R/2 R-2 R/3 R (rs34743033), MTHFR genotype 677C/C (rs1801133), wild-type TP53 and KRAS genes. In esophageal cancer, successful therapy appeared to correlate with wild-type TP53. These results may be useful for future research directions to translate reported data into practical clinical use.

Make your enemies your allies.

PubMed

Uzzi, Brian; Dunlap, Shannon

2012-05-01

Rivalries in the workplace can be destructive to both personal career growth and group success. Many attempts to reverse rivalries fail because of the complex way emotion and reason operate in the building of trust. Using a method called the 3Rs, an effective leader can turn a rival into a collaborator, setting the stage for a healthy work life while driving fresh thinking within an organization. Step 1 of the method is redirection, shifting a rival's negative emotions away from the adversarial relationship. This creates an opening for Step 2, reciprocity, through which a relationship can be established. Here, the essential principle is to give before you ask--offering a rival something of clear benefit and "priming the pump" for a future return that requires little effort on the rival's part. Step 3, rationality, sets expectations of the new relationship so that efforts made using the previous steps don't come off as disingenuous. A rival is encouraged to see collaborative opportunities from a reasoned standpoint. A key advantage of the 3Rs is that the method can work to reverse all kinds of rivalries, including those with subordinates, peers, and superiors.

Comparative Evaluation of Conventional and Accelerated Castings on Marginal Fit and Surface Roughness

PubMed Central

Jadhav, Vivek Dattatray; Motwani, Bhagwan K.; Shinde, Jitendra; Adhapure, Prasad

2017-01-01

Aims: The aim of this study was to evaluate the marginal fit and surface roughness of complete cast crowns made by a conventional and an accelerated casting technique. Settings and Design: This study was divided into three parts. In Part I, the marginal fit of full metal crowns made by both casting techniques in the vertical direction was checked, in Part II, the fit of sectional metal crowns in the horizontal direction made by both casting techniques was checked, and in Part III, the surface roughness of disc-shaped metal plate specimens made by both casting techniques was checked. Materials and Methods: A conventional technique was compared with an accelerated technique. In Part I of the study, the marginal fit of the full metal crowns as well as in Part II, the horizontal fit of sectional metal crowns made by both casting techniques was determined, and in Part III, the surface roughness of castings made with the same techniques was compared. Statistical Analysis Used: The results of the t-test and independent sample test do not indicate statistically significant differences in the marginal discrepancy detected between the two casting techniques. Results: For the marginal discrepancy and surface roughness, crowns fabricated with the accelerated technique were significantly different from those fabricated with the conventional technique. Conclusions: Accelerated casting technique showed quite satisfactory results, but the conventional technique was superior in terms of marginal fit and surface roughness. PMID:29042726