Linking initial microstructure and local response during quasistatic granular compaction

DOE PAGES

Hurley, R. C.; Lind, J.; Pagan, D. C.; ...

2017-07-24

In this study, we performed experiments combining three-dimensional x-ray diffraction and x-ray computed tomography to explore the relationship between microstructure and local force and strain during quasistatic granular compaction. We found that initial void space around a grain and contact coordination number before compaction can be used to predict regions vulnerable to above-average local force and strain at later stages of compaction. We also found correlations between void space around a grain and coordination number, and between grain stress and maximum interparticle force, at all stages of compaction. Finally, we observed grains that fracture to have an above-average initial localmore » void space and a below-average initial coordination number. In conclusion, our findings provide (1) a detailed description of microstructure evolution during quasistatic granular compaction, (2) an approach for identifying regions vulnerable to large values of strain and interparticle force, and (3) methods for identifying regions of a material with large interparticle forces and coordination numbers from measurements of grain stress and local porosity.« less

Litter size at birth in purebred dogs--a retrospective study of 224 breeds.

PubMed

Borge, Kaja Sverdrup; Tønnessen, Ragnhild; Nødtvedt, Ane; Indrebø, Astrid

2011-03-15

Despite the long history of purebred dogs and the large number of existing breeds, few studies of canine litter size based upon a large number of breeds exist. Previous studies are either old or include only one or a few selected breeds. The aim of this large-scale retrospective study was to estimate the mean litter size in a large population of purebred dogs and to describe some factors that might influence the litter size. A total of 10,810 litters of 224 breeds registered in the Norwegian Kennel Club from 2006 to 2007 were included in the study. The overall mean litter size at birth was 5.4 (± 0.025). A generalized linear mixed model with a random intercept for breed revealed that the litter size was significantly influenced by the size of the breed, the method of mating and the age of the bitch. A significant interaction between breed size and age was detected, in that the expected number of puppies born decreased more for older bitches of large breeds. Mean litter size increased with breed size, from 3.5 (± 0.04) puppies in miniature breeds to 7.1 (± 0.13) puppies in giant breeds. No effect on litter size was found for the season of birth or the parity of the bitch. The large number of breeds and the detail of the registered information on the litters in this study are unique. In conclusion, the size of the breed, the age of the bitch and the method of mating were found to influence litter size in purebred dogs when controlling for breed, with the size of the breed as the strongest determinant. Copyright © 2011 Elsevier Inc. All rights reserved.

A replacement for islet equivalents with improved reliability and validity.

PubMed

Huang, Han-Hung; Ramachandran, Karthik; Stehno-Bittel, Lisa

2013-10-01

Islet equivalent (IE), the standard estimate of isolated islet volume, is an essential measure to determine the amount of transplanted islet tissue in the clinic and is used in research laboratories to normalize results, yet it is based on the false assumption that all islets are spherical. Here, we developed and tested a new easy-to-use method to quantify islet volume with greater accuracy. Isolated rat islets were dissociated into single cells, and the total cell number per islet was determined by using computer-assisted cytometry. Based on the cell number per islet, we created a regression model to convert islet diameter to cell number with a high R2 value (0.8) and good validity and reliability with the same model applicable to young and old rats and males or females. Conventional IE measurements overestimated the tissue volume of islets. To compare results obtained using IE or our new method, we compared Glut2 protein levels determined by Western Blot and proinsulin content via ELISA between small (diameter≤100 μm) and large (diameter≥200 μm) islets. When normalized by IE, large islets showed significantly lower Glut2 level and proinsulin content. However, when normalized by cell number, large and small islets had no difference in Glut2 levels, but large islets contained more proinsulin. In conclusion, normalizing islet volume by IE overestimated the tissue volume, which may lead to erroneous results. Normalizing by cell number is a more accurate method to quantify tissue amounts used in islet transplantation and research.

Melanocytic nevi, nevus genes and melanoma risk in a large case-control study in the United Kingdom

PubMed Central

Newton-Bishop, Julia A; Chang, Yu-Mei; Iles, Mark M; Taylor, John C; Bakker, Bert; Chan, May; Leake, Susan; Karpavicius, Birute; Haynes, Sue; Fitzgibbon, Elaine; Elliott, Faye; Kanetsky, Peter A.; Harland, Mark; Barrett, Jennifer H; Bishop, D Timothy

2010-01-01

Background Increased number of melanocytic nevi is a potent melanoma risk factor. We have carried out a large population-based case-control study to explore the environmental and genetic determinants of nevi and the relationship with melanoma risk. Methods We report nevus phenotype in relation to differing patterns of sun exposure, inherited variation at loci shown in recent genome-wide association studies to be nevus genes, and risk. Results Increased numbers of nevi were associated with holiday sun exposure, particularly on intermittently sun-exposed body sites (test for trend p<0.0001). Large nevi were also associated with holiday sun exposure (p=0.002). Single nucleotide polymorphisms (SNPs) on chromosomes 9 and 22 were associated with increased numbers of nevi (p=0.04 and p=0.002 respectively) and larger nevi (p=0.03 and p=0.002), whereas that on chromosome 6 was associated only with large nevi (p=0.01). Melanoma risk was associated with increased nevus count, large nevi and atypical nevi for tumors in all body sites (including rare sites) irrespective of age. The risk persisted when adjusted for inheritance of nevus SNPs. Conclusions The at-risk nevus phenotype is associated with behaviors known to increase melanoma risk (holiday sun exposure). Although SNPs on chromosomes 6, 9 and 22 were shown to be nevus genes they explained only a small proportion of melanoma risk and nevus phenotype; therefore a number of nevus genes likely remain to be identified. Impact This paper confirms the importance of nevi in melanoma pathogenesis and increases understanding of their genetic determinants. PMID:20647408

Overview of Emerging Contaminants and Associated Human Health Effects

PubMed Central

Lei, Meng; Zhang, Lun; Lei, Jianjun; Zong, Liang; Li, Jiahui; Wu, Zheng; Wang, Zheng

2015-01-01

In recent decades, because of significant progress in the analysis and detection of trace pollutants, emerging contaminants have been discovered and quantified in living beings and diverse environmental substances; however, the adverse effects of environmental exposure on the general population are largely unknown. This review summarizes the conclusions of the comprehensive epidemic literature and representative case reports relevant to emerging contaminants and the human body to address concerns about potential harmful health effects in the general population. The most prevalent emerging contaminants include perfluorinated compounds, water disinfection byproducts, gasoline additives, manufactured nanomaterials, human and veterinary pharmaceuticals, and UV-filters. Rare but statistically meaningful connections have been reported for a number of contaminants and cancer and reproductive risks. Because of contradictions in the outcomes of some investigations and the limited number of articles, no significant conclusions regarding the relationship between adverse effects on humans and extents of exposure can be drawn at this time. Here, we report that the current evidence is not conclusive and comprehensive and suggest prospective cohort studies in the future to evaluate the associations between human health outcomes and emerging environmental contaminants. PMID:26713315

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

PubMed Central

2012-01-01

Background For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching the spectra against an increasingly large database of sequences and their post-translational modifications with known masses. Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed. Results We present a sequence database search engine that is specifically designed to run efficiently on the Hadoop MapReduce distributed computing framework. The search engine implements the K-score algorithm, generating comparable output for the same input files as the original implementation. The scalability of the system is shown, and the architecture required for the development of such distributed processing is discussed. Conclusion The software is scalable in its ability to handle a large peptide database, numerous modifications and large numbers of spectra. Performance scales with the number of processors in the cluster, allowing throughput to expand with the available resources. PMID:23216909

Benchmarking the pseudopotential and fixed-node approximations in diffusion Monte Carlo calculations of molecules and solids

DOE PAGES

Nazarov, Roman; Shulenburger, Luke; Morales, Miguel A.; ...

2016-03-28

We performed diffusion Monte Carlo (DMC) calculations of the spectroscopic properties of a large set of molecules, assessing the effect of different approximations. In systems containing elements with large atomic numbers, we show that the errors associated with the use of nonlocal mean-field-based pseudopotentials in DMC calculations can be significant and may surpass the fixed-node error. In conclusion, we suggest practical guidelines for reducing these pseudopotential errors, which allow us to obtain DMC-computed spectroscopic parameters of molecules and equation of state properties of solids in excellent agreement with experiment.

Benchmarking the pseudopotential and fixed-node approximations in diffusion Monte Carlo calculations of molecules and solids

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

Nazarov, Roman; Shulenburger, Luke; Morales, Miguel A.

We performed diffusion Monte Carlo (DMC) calculations of the spectroscopic properties of a large set of molecules, assessing the effect of different approximations. In systems containing elements with large atomic numbers, we show that the errors associated with the use of nonlocal mean-field-based pseudopotentials in DMC calculations can be significant and may surpass the fixed-node error. In conclusion, we suggest practical guidelines for reducing these pseudopotential errors, which allow us to obtain DMC-computed spectroscopic parameters of molecules and equation of state properties of solids in excellent agreement with experiment.

Externally blown flap noise research

NASA Technical Reports Server (NTRS)

Dorsch, R. G.

1974-01-01

The Lewis Research Center cold-flow model externally blown flap (EBF) noise research test program is summarized. Both engine under-the-wing and over-the-wing EBF wing section configurations were studied. Ten large scale and nineteen small scale EBF models were tested. A limited number of forward airspeed effect and flap noise suppression tests were also run. The key results and conclusions drawn from the flap noise tests are summarized and discussed.

Contribution to Terminology Internationalization by Word Alignment in Parallel Corpora

PubMed Central

Deléger, Louise; Merkel, Magnus; Zweigenbaum, Pierre

2006-01-01

Background and objectives Creating a complete translation of a large vocabulary is a time-consuming task, which requires skilled and knowledgeable medical translators. Our goal is to examine to which extent such a task can be alleviated by a specific natural language processing technique, word alignment in parallel corpora. We experiment with translation from English to French. Methods Build a large corpus of parallel, English-French documents, and automatically align it at the document, sentence and word levels using state-of-the-art alignment methods and tools. Then project English terms from existing controlled vocabularies to the aligned word pairs, and examine the number and quality of the putative French translations obtained thereby. We considered three American vocabularies present in the UMLS with three different translation statuses: the MeSH, SNOMED CT, and the MedlinePlus Health Topics. Results We obtained several thousand new translations of our input terms, this number being closely linked to the number of terms in the input vocabularies. Conclusion Our study shows that alignment methods can extract a number of new term translations from large bodies of text with a moderate human reviewing effort, and thus contribute to help a human translator obtain better translation coverage of an input vocabulary. Short-term perspectives include their application to a corpus 20 times larger than that used here, together with more focused methods for term extraction. PMID:17238328

Clinical research in Finland in 2002 and 2007: quantity and type

PubMed Central

2013-01-01

Background Regardless of worries over clinical research and various initiatives to overcome problems, few quantitative data on the numbers and type of clinical research exist. This article aims to describe the volume and type of clinical research in 2002 and 2007 in Finland. Methods The research law in Finland requires all medical research to be submitted to regional ethics committees (RECs). Data from all new projects in 2002 and 2007 were collected from REC files and the characteristics of clinical projects (76% of all submissions) were analyzed. Results The number of clinical projects was large, but declining: 794 in 2002 and 762 in 2007. Drug research (mainly trials) represented 29% and 34% of the clinical projects; their total number had not declined, but those without a commercial sponsor had. The number of different principal investigators was large (630 and 581). Most projects were observational, while an experimental design was used in 43% of projects. Multi-center studies were common. In half of the projects, the main funder was health care or was done as unpaid work; 31% had industry funding as the main source. There was a clear difference in the type of research by sponsorship. Industry-funded research was largely drug research, international multi-center studies, with randomized controlled or other experimental design. The findings for the two years were similar, but a university hospital as the main research site became less common between 2002 and 2007. Conclusions Clinical research projects were common, but numbers are declining; research was largely funded by health care, with many physicians involved. Drug trials were a minority, even though most research promotion efforts and regulation concerns them. PMID:23680289

Technical considerations on using the large Nancay radio telescope for SETI

NASA Technical Reports Server (NTRS)

Gulkis, S.; Biraud, F.; Heidmann, J.; Tarter, J.

1990-01-01

The Nancay decimetric Radio Telescope (NRT) in Nancay, France, is described, and its potential use for Search for Extraterrestrial Intelligence (SETI) observations is discussed. The conclusion reached is that the NRT is well suited for SETI observations because of its large collecting area, its large sky coverage, and its wideband frequency capability. However, a number of improvements are necessary in order to take full advantage of the system in carrying out an efficient SETI program. In particular, system sensitivity should be increased. This can be achieved through a series of improvements to the system, including lowering the ground pickup noise through the use of ground reflectors and more efficient feed design, and by using low-noise amplifier front ends.

Syringe Exchange, Injecting and Intranasal Drug Use

PubMed Central

Arasteh, Kamyar; McKnight, Courtney; Ringer, Martin; Friedman, Samuel R.

2016-01-01

Objective To assess trends in injecting and non-injecting drug use after implementation of large-scale syringe exchange in New York City. The belief that implementation of syringe exchange will lead to increased drug injecting has been a persistent argument against syringe exchange. Methods Administrative data on route of administration for primary drug of abuse among patients entering the Beth Israel methadone maintenance program from 1995 – 2007. Approximately 2000 patients enter the program each year. Results During and after the period of large scale implementation of syringe exchange, the numbers of methadone program entrants reporting injecting drug use decreased while the numbers of entrants reporting intranasal drug use increased (p < .001). Conclusion While assessing possible effects of syringe exchange on trends in injecting drug use is inherently difficult, this may be the strongest data collected to date showing a lack of increase in drug injecting following implementation of syringe exchange. PMID:19891668

Segregation of large granules from close-packed cluster of small granules due to buoyancy.

PubMed

Yang, Xian-qing; Zhou, Kun; Qiu, Kang; Zhao, Yue-min

2006-03-01

Segregation of large granules in a vibrofluidized granular bed with inhomogeneous granular number density distribution is studied by an event-driven algorithm. Simulation results show that the mean vertical position of large granules decreases with the increase of the density ration of the large granules to the small ones. This conclusion is consistent with the explanation that the net pressure due to the small surrounding particle impacts balances the large granular weight, and indict that the upward movement of the large granules is driven by the buoyancy. The values of temperature, density, and pressure of the systems are also computed by changing the conditions such as heating temperature on the bottom and restitution coefficient of particles. These results indicate that the segregation of large granules also happen in the systems with density inversion or even close-packed cluster of particles floating on a low-density fluid, due to the buoyancy. An equation of state is proposed to explain the buoyancy.

Zel'dovich Λ and Weinberg's relation: an explanation for the cosmological coincidences

NASA Astrophysics Data System (ADS)

Alfonso-Faus, Antonio

2008-11-01

In 1937 Dirac proposed the large number hypothesis (LNH). The idea was to explain that these numbers were large because the Universe is old. A time variation of certain “constants” was assumed. So far, no experimental evidence has significantly supported this time variation. Here we present a simplified cosmological model. We propose a new cosmological system of units, including a cosmological Planck’s constant that “absorbs” the well known large number 10120. With this new Planck’s constant no large numbers appear at the cosmological level. They appear at lower levels, e.g. at the quantum world. We note here that Zel’dovich formula, for the cosmological constant Λ, is equivalent to the Weinberg’s relation. The immediate conclusion is that the speed of light c must be proportional to the Hubble parameter H, and therefore decrease with time. We find that the gravitational radius of the Universe and its size are one and the same constant (Mach’s principle). The usual cosmological Ω’s parameters for mass, lambda and curvature turn out to be all constants of order one. The anthropic principle is not necessary in this theory. It is shown that a factor of 1061 converts in this theory a Planck fluctuation (a quantum black hole) into a cosmological quantum black hole: the Universe today. General relativity and quantum mechanics give the same local solution of an expanding Universe with the law a( t)≈constṡ t. This constant is just the speed of light today. Then the Hubble parameter is exactly H= a( t)'/ a( t)=1/ t.

Maximum likelihood inference implies a high, not a low, ancestral haploid chromosome number in Araceae, with a critique of the bias introduced by ‘x’

PubMed Central

Cusimano, Natalie; Sousa, Aretuza; Renner, Susanne S.

2012-01-01

Background and Aims For 84 years, botanists have relied on calculating the highest common factor for series of haploid chromosome numbers to arrive at a so-called basic number, x. This was done without consistent (reproducible) reference to species relationships and frequencies of different numbers in a clade. Likelihood models that treat polyploidy, chromosome fusion and fission as events with particular probabilities now allow reconstruction of ancestral chromosome numbers in an explicit framework. We have used a modelling approach to reconstruct chromosome number change in the large monocot family Araceae and to test earlier hypotheses about basic numbers in the family. Methods Using a maximum likelihood approach and chromosome counts for 26 % of the 3300 species of Araceae and representative numbers for each of the other 13 families of Alismatales, polyploidization events and single chromosome changes were inferred on a genus-level phylogenetic tree for 113 of the 117 genera of Araceae. Key Results The previously inferred basic numbers x = 14 and x = 7 are rejected. Instead, maximum likelihood optimization revealed an ancestral haploid chromosome number of n = 16, Bayesian inference of n = 18. Chromosome fusion (loss) is the predominant inferred event, whereas polyploidization events occurred less frequently and mainly towards the tips of the tree. Conclusions The bias towards low basic numbers (x) introduced by the algebraic approach to inferring chromosome number changes, prevalent among botanists, may have contributed to an unrealistic picture of ancestral chromosome numbers in many plant clades. The availability of robust quantitative methods for reconstructing ancestral chromosome numbers on molecular phylogenetic trees (with or without branch length information), with confidence statistics, makes the calculation of x an obsolete approach, at least when applied to large clades. PMID:22210850

Density of Indoor Tanning Facilities in 116 Large U.S. Cities

PubMed Central

Hoerster, Katherine D.; Garrow, Rebecca L.; Mayer, Joni A.; Clapp, Elizabeth J.; Weeks, John R.; Woodruff, Susan I.; Sallis, James F.; Slymen, Donald J.; Patel, Minal R.; Sybert, Stephanie A.

2009-01-01

Background U.S. adolescents and young adults are using indoor tanning at high rates, even though it has been linked to both melanoma and squamous cell cancer. Because the availability of commercial indoor tanning facilities may influence use, data are needed on the number and density of such facilities. Methods In March 2006, commercial indoor tanning facilities in 116 large U.S. cities were identified, and the number and density (per 100,000 population) were computed for each city. Bivariate and multivariate analyses conducted in 2008 tested the association between tanning-facility density and selected geographic, climatologic, demographic, and legislative variables. Results Mean facility number and density across cities were 41.8 (SD=30.8) and 11.8 (SD=6.0), respectively. In multivariate analysis, cities with higher percentages of whites and lower ultraviolet (UV)index scores had significantly higher facility densities than those with lower percentages of whites and higher UV index scores. Conclusions These data indicate that commercial indoor tanning is widely available in the urban U.S., and this availability may help explain the high usage of indoor tanning. PMID:19215849

Is the place cell a "supple" engram?

PubMed

Routtenberg, Aryeh

2015-06-01

This short note, which honors Nobelists O'Keefe and the Mosers, asks how the patterning of inputs to a single place cell regulates its firing. Because the combination of inputs to a single CA1 place cell is very large, the generally accepted view is rejected that inputs to a place cell are relatively restricted, near identical repetition upon re-presentation of the environment. The alternative proposed here is that when any 100 excitatory inputs are fired activating a subset combination, which is a large number, selected from the 30,000 synapses, this leads to CA1 cell firing. The selection of the combination of inputs is a very large number it nonetheless leads to the conclusion that even though the same cell dutifully fires when the animal is in an identical location, the inputs that fire the place cell are nonetheless obligatorily non-identical. This CA1 input combinatorial proposal may help us understand the physiological underpinnings of the memory mechanism arising from supple synapses (Routtenberg (2013), Hippocampus 23:202-206). © 2015 Wiley Periodicals, Inc.

Impacts of savanna trees on forage quality for a large African herbivore

PubMed Central

De Kroon, Hans; Prins, Herbert H. T.

2008-01-01

Recently, cover of large trees in African savannas has rapidly declined due to elephant pressure, frequent fires and charcoal production. The reduction in large trees could have consequences for large herbivores through a change in forage quality. In Tarangire National Park, in Northern Tanzania, we studied the impact of large savanna trees on forage quality for wildebeest by collecting samples of dominant grass species in open grassland and under and around large Acacia tortilis trees. Grasses growing under trees had a much higher forage quality than grasses from the open field indicated by a more favourable leaf/stem ratio and higher protein and lower fibre concentrations. Analysing the grass leaf data with a linear programming model indicated that large savanna trees could be essential for the survival of wildebeest, the dominant herbivore in Tarangire. Due to the high fibre content and low nutrient and protein concentrations of grasses from the open field, maximum fibre intake is reached before nutrient requirements are satisfied. All requirements can only be satisfied by combining forage from open grassland with either forage from under or around tree canopies. Forage quality was also higher around dead trees than in the open field. So forage quality does not reduce immediately after trees die which explains why negative effects of reduced tree numbers probably go initially unnoticed. In conclusion our results suggest that continued destruction of large trees could affect future numbers of large herbivores in African savannas and better protection of large trees is probably necessary to sustain high animal densities in these ecosystems. PMID:18309522

Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat.

PubMed

Würschum, Tobias; Boeven, Philipp H G; Langer, Simon M; Longin, C Friedrich H; Leiser, Willmar L

2015-07-29

Copy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown. Here, we employed a large worldwide panel of 1110 winter wheat varieties to assess the frequency and the geographic distribution of copy number variants at the Photoperiod-B1 (Ppd-B1) and the Vernalization-A1 (Vrn-A1) loci as well as their effects on flowering time under field conditions. We identified a novel four copy variant of Vrn-A1 and based on the phylogenetic relationships among the lines show that the higher copy variants at both loci are likely to have arisen independently multiple times. In addition, we found that the frequency of the different copy number variants at both loci reflects the environmental conditions in the varieties' region of origin and based on multi-location field trials show that Ppd-B1 copy number has a substantial effect on the fine-tuning of flowering time. In conclusion, our results show the importance of copy number variation at Ppd-B1 and Vrn-A1 for the global adaptation of wheat making it a key factor for wheat success in a broad range of environments and in a wider context substantiate the significant role of copy number variation in crops.

Methanol production from Eucalyptus wood chips. Working Document 2. Vegetative propagation of Eucalypts

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

Fishkind, H.H.

1982-04-01

The feasibility of large-scale plantation establishment by various methods was examined, and the following conclusions were reached: seedling plantations are limited in potential yield due to genetic variation among the planting stock and often inadequate supplies of appropriate seed; vegetative propagation by rooted cuttings can provide good genetic uniformity of select hybrid planting stock; however, large-scale production requires establishment and maintenance of extensive cutting orchards. The collection of shoots and preparation of cuttings, although successfully implemented in the Congo and Brazil, would not be economically feasible in Florida for large-scale plantations; tissue culture propagation of select hybrid eucalypts offers themore » only opportunity to produce the very large number of trees required to establish the energy plantation. The cost of tissue culture propagation, although higher than seedling production, is more than off-set by the increased productivity of vegetative plantations established from select hybrid Eucalyptus.« less

The Hagen-Poiseuille, Plane Couette and Poiseuille Flows Linear Instability and Rogue Waves Excitation Mechanism

NASA Astrophysics Data System (ADS)

Chefranov, Sergey; Chefranov, Alexander

2016-04-01

Linear hydrodynamic stability theory for the Hagen-Poiseuille (HP) flow yields a conclusion of infinitely large threshold Reynolds number, Re, value. This contradiction to the observation data is bypassed using assumption of the HP flow instability having hard type and possible for sufficiently high-amplitude disturbances. HP flow disturbance evolution is considered by nonlinear hydrodynamic stability theory. Similar is the case of the plane Couette (PC) flow. For the plane Poiseuille (PP) flow, linear theory just quantitatively does not agree with experimental data defining the threshold Reynolds number Re= 5772 ( S. A. Orszag, 1971), more than five-fold exceeding however the value observed, Re=1080 (S. J. Davies, C. M. White, 1928). In the present work, we show that the linear stability theory conclusions for the HP and PC on stability for any Reynolds number and evidently too high threshold Reynolds number estimate for the PP flow are related with the traditional use of the disturbance representation assuming the possibility of separation of the longitudinal (along the flow direction) variable from the other spatial variables. We show that if to refuse from this traditional form, conclusions on the linear instability for the HP and PC flows may be obtained for finite Reynolds numbers (for the HP flow, for Re>704, and for the PC flow, for Re>139). Also, we fit the linear stability theory conclusion on the PP flow to the experimental data by getting an estimate of the minimal threshold Reynolds number as Re=1040. We also get agreement of the minimal threshold Reynolds number estimate for PC with the experimental data of S. Bottin, et.al., 1997, where the laminar PC flow stability threshold is Re = 150. Rogue waves excitation mechanism in oppositely directed currents due to the PC flow linear instability is discussed. Results of the new linear hydrodynamic stability theory for the HP, PP, and PC flows are published in the following papers: 1. S.G. Chefranov, A.G. Chefranov, JETP, v.119, No.2, 331, 2014 2. S.G. Chefranov, A.G. Chefranov, Doklady Physics, vol.60, No.7, 327-332, 2015 3. S.G. Chefranov, A. G. Chefranov, arXiv: 1509.08910v1 [physics.flu-dyn] 29 Sep 2015 (accepted to JETP)

Inhalation Conscious Sedation with Nitrous Oxide and Oxygen as Alternative to General Anesthesia in Precooperative, Fearful, and Disabled Pediatric Dental Patients: A Large Survey on 688 Working Sessions.

PubMed

Galeotti, Angela; Garret Bernardin, Annelyse; D'Antò, Vincenzo; Ferrazzano, Gianmaria Fabrizio; Gentile, Tina; Viarani, Valeria; Cassabgi, Giorgio; Cantile, Tiziana

2016-01-01

Aim . To evaluate the effectiveness and the tolerability of the nitrous oxide sedation for dental treatment on a large pediatric sample constituting precooperative, fearful, and disabled patients. Methods . 472 noncooperating patients (aged 4 to 17) were treated under conscious sedation. The following data were calculated: average age; gender distribution; success/failure; adverse effects; number of treatments; kind of dental procedure undertaken; number of dental procedures for each working session; number of working sessions for each patient; differences between males and females and between healthy and disabled patients in relation to success; success in relation to age; and level of cooperation using Venham score. Results . 688 conscious sedations were carried out. The success was 86.3%. Adverse effects occurred in 2.5%. 1317 dental procedures were performed. In relation to the success, there was a statistically significant difference between healthy and disabled patients. Sex and age were not significant factors for the success. Venham score was higher at the first contact with the dentist than during the treatment. Conclusions . Inhalation conscious sedation represented an effective and safe method to obtain cooperation, even in very young patients, and it could reduce the number of pediatric patients referred to hospitals for general anesthesia.

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

PubMed Central

Menten, Björn; Pattyn, Filip; De Preter, Katleen; Robbrecht, Piet; Michels, Evi; Buysse, Karen; Mortier, Geert; De Paepe, Anne; van Vooren, Steven; Vermeesch, Joris; Moreau, Yves; De Moor, Bart; Vermeulen, Stefan; Speleman, Frank; Vandesompele, Jo

2005-01-01

Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at . PMID:15910681

Inhalation Conscious Sedation with Nitrous Oxide and Oxygen as Alternative to General Anesthesia in Precooperative, Fearful, and Disabled Pediatric Dental Patients: A Large Survey on 688 Working Sessions

PubMed Central

Galeotti, Angela; Garret Bernardin, Annelyse; D'Antò, Vincenzo; Viarani, Valeria; Cassabgi, Giorgio

2016-01-01

Aim. To evaluate the effectiveness and the tolerability of the nitrous oxide sedation for dental treatment on a large pediatric sample constituting precooperative, fearful, and disabled patients. Methods. 472 noncooperating patients (aged 4 to 17) were treated under conscious sedation. The following data were calculated: average age; gender distribution; success/failure; adverse effects; number of treatments; kind of dental procedure undertaken; number of dental procedures for each working session; number of working sessions for each patient; differences between males and females and between healthy and disabled patients in relation to success; success in relation to age; and level of cooperation using Venham score. Results. 688 conscious sedations were carried out. The success was 86.3%. Adverse effects occurred in 2.5%. 1317 dental procedures were performed. In relation to the success, there was a statistically significant difference between healthy and disabled patients. Sex and age were not significant factors for the success. Venham score was higher at the first contact with the dentist than during the treatment. Conclusions. Inhalation conscious sedation represented an effective and safe method to obtain cooperation, even in very young patients, and it could reduce the number of pediatric patients referred to hospitals for general anesthesia. PMID:27747238

Survey of gene splicing algorithms based on reads.

PubMed

Si, Xiuhua; Wang, Qian; Zhang, Lei; Wu, Ruo; Ma, Jiquan

2017-11-02

Gene splicing is the process of assembling a large number of unordered short sequence fragments to the original genome sequence as accurately as possible. Several popular splicing algorithms based on reads are reviewed in this article, including reference genome algorithms and de novo splicing algorithms (Greedy-extension, Overlap-Layout-Consensus graph, De Bruijn graph). We also discuss a new splicing method based on the MapReduce strategy and Hadoop. By comparing these algorithms, some conclusions are drawn and some suggestions on gene splicing research are made.

Azimuth orientation of the dragonfly (Sympetrum)

NASA Technical Reports Server (NTRS)

Hisada, M.

1972-01-01

Evidence is presented of directional orientation by an alighting dragonfly relative to the azimuth of the sun. The effects of wind direction on this orientation are analyzed. It was concluded that wind does not play a major role in orientation but may have some secondary function in helping greater numbers of dragonflies face windward more often than leeward. A search was made to find the principle sensory receptor for orientation. Two possibilities, the large compound eye and the frontal ocelli, were noted; however, no conclusive evidence could be found.

Podocyte Number in Children and Adults: Associations with Glomerular Size and Numbers of Other Glomerular Resident Cells

PubMed Central

Puelles, Victor G.; Douglas-Denton, Rebecca N.; Cullen-McEwen, Luise A.; Li, Jinhua; Hughson, Michael D.; Hoy, Wendy E.; Kerr, Peter G.

2015-01-01

Increases in glomerular size occur with normal body growth and in many pathologic conditions. In this study, we determined associations between glomerular size and numbers of glomerular resident cells, with a particular focus on podocytes. Kidneys from 16 male Caucasian-Americans without overt renal disease, including 4 children (≤3 years old) to define baseline values of early life and 12 adults (≥18 years old), were collected at autopsy in Jackson, Mississippi. We used a combination of immunohistochemistry, confocal microscopy, and design-based stereology to estimate individual glomerular volume (IGV) and numbers of podocytes, nonepithelial cells (NECs; tuft cells other than podocytes), and parietal epithelial cells (PECs). Podocyte density was calculated. Data are reported as medians and interquartile ranges (IQRs). Glomeruli from children were small and contained 452 podocytes (IQR=335–502), 389 NECs (IQR=265–498), and 146 PECs (IQR=111–206). Adult glomeruli contained significantly more cells than glomeruli from children, including 558 podocytes (IQR=431–746; P<0.01), 1383 NECs (IQR=998–2042; P<0.001), and 367 PECs (IQR=309–673; P<0.001). However, large adult glomeruli showed markedly lower podocyte density (183 podocytes per 106 µm3) than small glomeruli from adults and children (932 podocytes per 106 µm3; P<0.001). In conclusion, large adult glomeruli contained more podocytes than small glomeruli from children and adults, raising questions about the origin of these podocytes. The increased number of podocytes in large glomeruli does not match the increase in glomerular size observed in adults, resulting in relative podocyte depletion. This may render hypertrophic glomeruli susceptible to pathology. PMID:25568174

Association between Air Pollution and Hemoptysis

PubMed Central

Garcia-Olive, Ignasi; Radua, Joaquim; Fiz, Jose Antonio; Sanz-Santos, Jose; Ruiz-Manzano, Juan

2016-01-01

Background. The relationship between air pollution and exacerbation of respiratory diseases is well established. Nevertheless, its association with hemoptysis has been poorly investigated. This paper describes the relationship of air pollutants with severe hemoptysis. Methods. All consecutive subjects with severe hemoptysis during a 5-year period were included. The relationship between the contamination measurements and the frequency of embolizations was analyzed using Poisson regressions. In these regressions, the dependent variable was the monthly number of embolizations in a given month and the independent variable was either the concentration of an air contaminant during the same month, the concentration of the air contaminant during the previous month, or the difference between the two. Results. A higher total number of embolizations per month were observed over the months with increases in the concentration of NO. The number of embolizations was 2.0 in the 33 months with no increases in the concentration of NO, 2.1 in the 12 months with small increases, 2.2 in the 5 months with moderate increases, 2.5 in the 4 months with large increases, and 4.0 in the 5 months with very large increases. Conclusion. There is association between hemoptysis and increases in the concentration of atmospheric NO in Badalona (Spain). PMID:27445569

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Influence of Blurred Ways on Pattern Recognition of a Scale-Free Hopfield Neural Network

NASA Astrophysics Data System (ADS)

Chang, Wen-Li

2010-01-01

We investigate the influence of blurred ways on pattern recognition of a Barabási-Albert scale-free Hopfield neural network (SFHN) with a small amount of errors. Pattern recognition is an important function of information processing in brain. Due to heterogeneous degree of scale-free network, different blurred ways have different influences on pattern recognition with same errors. Simulation shows that among partial recognition, the larger loading ratio (the number of patterns to average degree P/langlekrangle) is, the smaller the overlap of SFHN is. The influence of directed (large) way is largest and the directed (small) way is smallest while random way is intermediate between them. Under the ratio of the numbers of stored patterns to the size of the network P/N is less than 0. 1 conditions, there are three families curves of the overlap corresponding to directed (small), random and directed (large) blurred ways of patterns and these curves are not associated with the size of network and the number of patterns. This phenomenon only occurs in the SFHN. These conclusions are benefit for understanding the relation between neural network structure and brain function.

Serotonin-producing enterochromaffin (EC) cells of gastrointestinal mucosa in dexamethasone-treated rats.

PubMed

Glisić, Radmila; Koko, Vesna; Todorović, Vera; Drndarević, Neda; Cvijić, Gordana

2006-09-11

The aim of our study was to investigate the morphological, immunohistochemical and ultrastructural changes of rat serotonin-producing enterochromaffin (EC) cells of gastrointestinal mucosa in dexamethasone-treated rats (D). After 12-daily intraperitoneal administration of 2 mg/kg dexamethasone, rats developed diabetes similar to human diabetes type 2. Stomach, small and large intestines were examined. Large serotonin positive EC cells appeared in the corpus mucosa epithelium of D group of rats, although these cells were not present in control (C) rats. Both volume fraction and the number of EC cells per mm(2) of mucosa were significantly increased only in the duodenum. However, the number of EC cells per circular sections of both antrum and small intestine was increased, but reduced both in the ascending and descending colon in D group. The dexamethasone treatment caused a strong reduction in number of granules in the antral EC cells, while it was gradually increased beginning from the jejunum to descending colon. The mean granular content was reduced in the antral EC cells but increased in the jejunal EC cells in D group. In conclusion, the present study showed that morphological changes in gut serotonin-producing EC cells occurred in diabetic rats.

Progress, pitfalls and parallel universes: a history of insect phylogenetics

PubMed Central

Simon, Chris; Yavorskaya, Margarita; Beutel, Rolf G.

2016-01-01

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985–2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed. PMID:27558853

An approach to radiation safety department benchmarking in academic and medical facilities.

PubMed

Harvey, Richard P

2015-02-01

Based on anecdotal evidence and networking with colleagues at other facilities, it has become evident that some radiation safety departments are not adequately staffed and radiation safety professionals need to increase their staffing levels. Discussions with management regarding radiation safety department staffing often lead to similar conclusions. Management acknowledges the Radiation Safety Officer (RSO) or Director of Radiation Safety's concern but asks the RSO to provide benchmarking and justification for additional full-time equivalents (FTEs). The RSO must determine a method to benchmark and justify additional staffing needs while struggling to maintain a safe and compliant radiation safety program. Benchmarking and justification are extremely important tools that are commonly used to demonstrate the need for increased staffing in other disciplines and are tools that can be used by radiation safety professionals. Parameters that most RSOs would expect to be positive predictors of radiation safety staff size generally are and can be emphasized in benchmarking and justification report summaries. Facilities with large radiation safety departments tend to have large numbers of authorized users, be broad-scope programs, be subject to increased controls regulations, have large clinical operations, have significant numbers of academic radiation-producing machines, and have laser safety responsibilities.

Feeding damage to plants increases with plant size across 21 Brassicaceae species.

PubMed

Schlinkert, Hella; Westphal, Catrin; Clough, Yann; Ludwig, Martin; Kabouw, Patrick; Tscharntke, Teja

2015-10-01

Plant size is a major predictor of ecological functioning. We tested the hypothesis that feeding damage to plants increases with plant size, as the conspicuousness of large plants makes resource finding and colonisation easier. Further, large plants can be attractive to herbivores, as they offer greater amounts and ranges of resources and niches, but direct evidence from experiments testing size effects on feeding damage and consequently on plant fitness is so far missing. We established a common garden experiment with a plant size gradient (10-130 cm height) using 21 annual Brassicaceae species, and quantified plant size, biomass and number of all aboveground components (flowers, fruits, leaves, stems) and their proportional feeding damage. Plant reproductive fitness was measured using seed number, 1000 seed weight and total seed weight. Feeding damage to the different plant components increased with plant size or component biomass, with mean damage levels being approximately 30 % for flowers, 5 % for fruits and 1 % for leaves and stems. Feeding damage affected plant reproductive fitness depending on feeding damage type, with flower damage having the strongest effect, shown by greatly reduced seed number, 1000 seed weight and total seed weight. Finally, we found an overall negative effect of plant size on 1000 seed weight, but not on seed number and total seed weight. In conclusion, being conspicuous and attractive to herbivores causes greater flower damage leading to higher fitness costs for large plants, which might be partly counterbalanced by benefits such as enhanced competitive/compensatory abilities or more mutualistic pollinator visits.

Antidepressant Efficacy for Depression in Children and Adolescents: Industry- and NIMH-Funded Studies.

PubMed

Walkup, John T

2017-05-01

Significant controversy surrounds the efficacy of the newer antidepressants for children and adolescents with depression. The controversy largely hinges on meta-analyses of studies that suggest that antidepressants are minimally effective, not effective, or equivalent to placebo. In this review, the author discusses several scientific and clinical complexities that are important to understand in reviewing the antidepressant literature: the strengths and weaknesses of meta-analyses; the scientific and regulatory context for the large number of antidepressant trials in the late 1990s and early 2000s; and the distinction between a negative trial, where the treatment does not demonstrate efficacy, and a failed trial, where methodological problems make it impossible to draw any conclusion about efficacy. It is the premise of this review that meta-analyses that include the large number of industry-sponsored antidepressant trials distort the picture of antidepressant efficacy for teen depression. Industry-sponsored child and adolescent depression trials suffer from a number of implementation challenges and should be considered failed trials that are largely uninformative and not eligible to be included in efficacy meta-analyses. In contrast to the industry-sponsored trials, depression trials funded by the National Institute of Mental Health (NIMH) (N=2) are characterized by many methodological strengths, lower placebo response rates (30%-35%), and meaningful between-group differences (25%-30%) that support antidepressant efficacy. The NIMH-funded trials, taken together with the demonstrated efficacy of the serotonin reuptake inhibitors for childhood-onset obsessive-compulsive disorder and the anxiety disorders, suggest a broad and important role for antidepressant medications in pediatric internalizing conditions.

The Caenorhabditis chemoreceptor gene families

PubMed Central

Thomas, James H; Robertson, Hugh M

2008-01-01

Background Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species. Results Based on manual curation and sequence comparisons among putative G-protein-coupled chemoreceptor genes in the nematode Caenorhabditis elegans, we identified approximately 1300 genes and 400 pseudogenes in the 19 largest gene families, most of which fall into larger superfamilies. In the related species C. briggsae and C. remanei, we identified most or all genes in each of the 19 families. For most families, C. elegans has the largest number of genes and C. briggsae the smallest number, suggesting changes in the importance of chemoperception among the species. Protein trees reveal family-specific and species-specific patterns of gene duplication and gene loss. The frequency of strict orthologs varies among the families, from just over 50% in two families to less than 5% in three families. Several families include large species-specific expansions, mostly in C. elegans and C. remanei. Conclusion Chemoreceptor gene families in Caenorhabditis species are large and evolutionarily dynamic as a result of gene duplication and gene loss. These dynamics shape the chemoreceptor gene complements in Caenorhabditis species and define the receptor space available for chemosensory responses. To explain these patterns, we propose the gray pawn hypothesis: individual genes are of little significance, but the aggregate of a large number of diverse genes is required to cover a large phenotype space. PMID:18837995

Evolution of the lithium morphology from cycling of thin film solid state batteries

DOE PAGES

Dudney, Nancy J.

2017-03-11

Thin film batteries with a Lipon electrolyte and Li metal anode can be cycled thousands of times. During this time there is a gradual redistribution of the lithium at the top surface; the morphology that develops depends on a number of factors but is largely driven by dewetting. In this work, this redistribution is characterized as functions of the cycle number, duty cycle, cathode composition, and protective coating over the lithium. Observations of wrinkled and pitted surfaces are discussed considering the effects of defects and diffusion in the lithium and influences of film stresses and surface energy. In conclusion, similarmore » processes may impact solid state lithium batteries with higher energy per active area.« less

Evolution of the lithium morphology from cycling of thin film solid state batteries

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

Dudney, Nancy J.

Thin film batteries with a Lipon electrolyte and Li metal anode can be cycled thousands of times. During this time there is a gradual redistribution of the lithium at the top surface; the morphology that develops depends on a number of factors but is largely driven by dewetting. In this work, this redistribution is characterized as functions of the cycle number, duty cycle, cathode composition, and protective coating over the lithium. Observations of wrinkled and pitted surfaces are discussed considering the effects of defects and diffusion in the lithium and influences of film stresses and surface energy. In conclusion, similarmore » processes may impact solid state lithium batteries with higher energy per active area.« less

Comparison of molecular dynamics and superfamily spaces of protein domain deformation

PubMed Central

Velázquez-Muriel, Javier A; Rueda, Manuel; Cuesta, Isabel; Pascual-Montano, Alberto; Orozco, Modesto; Carazo, José-María

2009-01-01

Background It is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. Technically, protein flexibility exploration is an essential task in many applications, such as protein structure prediction and modeling. In this contribution we have compared two different approaches to explore the flexibility space of protein domains: i) molecular dynamics (MD-space), and ii) the study of the structural changes within superfamily (SF-space). Results Our analysis indicates that the MD-space and the SF-space display a significant overlap, but are still different enough to be considered as complementary. The SF-space space is wider but less complex than the MD-space, irrespective of the number of members in the superfamily. Also, the SF-space does not sample all possibilities offered by the MD-space, but often introduces very large changes along just a few deformation modes, whose number tend to a plateau as the number of related folds in the superfamily increases. Conclusion Theoretically, we obtained two conclusions. First, that function restricts the access to some flexibility patterns to evolution, as we observe that when a superfamily member changes to become another, the path does not completely overlap with the physical deformability. Second, that conformational changes from variation in a superfamily are larger and much simpler than those allowed by physical deformability. Methodologically, the conclusion is that both spaces studied are complementary, and have different size and complexity. We expect this fact to have application in fields as 3D-EM/X-ray hybrid models or ab initio protein folding. PMID:19220918

Dense baryon matter with isospin and chiral imbalance in the framework of a NJL4 model at large Nc: Duality between chiral symmetry breaking and charged pion condensation

NASA Astrophysics Data System (ADS)

Khunjua, T. G.; Klimenko, K. G.; Zhokhov, R. N.

2018-03-01

In this paper the phase structure of dense quark matter has been investigated at zero temperature in the presence of baryon, isospin and chiral isospin chemical potentials in the framework of massless (3 +1 )-dimensional Nambu-Jona-Lasinio model with two quark flavors. It has been shown that in the large-Nc limit (Nc is the number of colors of quarks) there exists a duality correspondence between the chiral symmetry breaking phase and the charged pion condensation one. The key conclusion of our studies is the fact that chiral isospin chemical potential generates charged pion condensation in dense quark matter with isotopic asymmetry.

Software Engineering for Scientific Computer Simulations

NASA Astrophysics Data System (ADS)

Post, Douglass E.; Henderson, Dale B.; Kendall, Richard P.; Whitney, Earl M.

2004-11-01

Computer simulation is becoming a very powerful tool for analyzing and predicting the performance of fusion experiments. Simulation efforts are evolving from including only a few effects to many effects, from small teams with a few people to large teams, and from workstations and small processor count parallel computers to massively parallel platforms. Successfully making this transition requires attention to software engineering issues. We report on the conclusions drawn from a number of case studies of large scale scientific computing projects within DOE, academia and the DoD. The major lessons learned include attention to sound project management including setting reasonable and achievable requirements, building a good code team, enforcing customer focus, carrying out verification and validation and selecting the optimum computational mathematics approaches.

Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae

PubMed Central

2013-01-01

Background The sequenced genomes of cucumber, melon and watermelon have relatively few R-genes, with 70, 75 and 55 copies only, respectively. The mechanism for low copy number of R-genes in Cucurbitaceae genomes remains unknown. Results Manual annotation of R-genes in the sequenced genomes of Cucurbitaceae species showed that approximately half of them are pseudogenes. Comparative analysis of R-genes showed frequent loss of R-gene loci in different Cucurbitaceae species. Phylogenetic analysis, data mining and PCR cloning using degenerate primers indicated that Cucurbitaceae has limited number of R-gene lineages (subfamilies). Comparison between R-genes from Cucurbitaceae and those from poplar and soybean suggested frequent loss of R-gene lineages in Cucurbitaceae. Furthermore, the average number of R-genes per lineage in Cucurbitaceae species is approximately 1/3 that in soybean or poplar. Therefore, both loss of lineages and deficient duplications in extant lineages accounted for the low copy number of R-genes in Cucurbitaceae. No extensive chimeras of R-genes were found in any of the sequenced Cucurbitaceae genomes. Nevertheless, one lineage of R-genes from Trichosanthes kirilowii, a wild Cucurbitaceae species, exhibits chimeric structures caused by gene conversions, and may contain a large number of distinct R-genes in natural populations. Conclusions Cucurbitaceae species have limited number of R-gene lineages and each genome harbors relatively few R-genes. The scarcity of R-genes in Cucurbitaceae species was due to frequent loss of R-gene lineages and infrequent duplications in extant lineages. The evolutionary mechanisms for large variation of copy number of R-genes in different plant species were discussed. PMID:23682795

Global Statistics of Bolides in the Terrestrial Atmosphere

NASA Astrophysics Data System (ADS)

Chernogor, L. F.; Shevelyov, M. B.

2017-06-01

Purpose: Evaluation and analysis of distribution of the number of meteoroid (mini asteroid) falls as a function of glow energy, velocity, the region of maximum glow altitude, and geographic coordinates. Design/methodology/approach: The satellite database on the glow of 693 mini asteroids, which were decelerated in the terrestrial atmosphere, has been used for evaluating basic meteoroid statistics. Findings: A rapid decrease in the number of asteroids with increasing of their glow energy is confirmed. The average speed of the celestial bodies is equal to about 17.9 km/s. The altitude of maximum glow most often equals to 30-40 km. The distribution law for a number of meteoroids entering the terrestrial atmosphere in longitude and latitude (after excluding the component in latitudinal dependence due to the geometry) is approximately uniform. Conclusions: Using a large enough database of measurements, the meteoroid (mini asteroid) statistics has been evaluated.

The interstellar redding law in the ultraviolet deduced from filter photometry obtained by the OAO-2 satellite

NASA Technical Reports Server (NTRS)

Laget, M.

1972-01-01

Filter photometry has been obtained of 16 BO stars at ten effective wavelengths in the range 4250-1430 A. The wavelength dependence of the interstellar reddening law, deduced from a least squares fit of the observed values to the reddening line at each band, is found in satisfactory agreement with that derived by Bless and Savage (1972). Toward the shorter wavelengths the increase of the computed probable error of the slope of the mean reddening line suggests that large fluctuations in the law may occur from star to star. Similar computations, separating main-sequence stars and supergiants, indicate that the large fluctuations of the law appear to be well related to the luminosity of the stars; the supergiants show systematically less extinction, this deficiency becoming large toward the far UV. The small number in the sample however, does not allow a general conclusion to be drawn.

Search for dark matter and other new phenomena in events with an energetic jet and large missing transverse momentum using the ATLAS detector

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

Aaboud, M.; Aad, G.; Abbott, B.

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses proton-proton collision data corresponding to an integrated luminosity of 36.1 fb -1 at a centre-of-mass energy of 13 TeV collected in 2015 and 2016 with the ATLAS detector at the Large Hadron Collider. Events are required to have at least one jet with a transverse momentum above 250 GeV and no leptons (e or μ). Several signal regions are considered with increasing requirements on the missing transverse momentum above 250 GeV. Good agreement is observed betweenmore » the number of events in data and Standard Model predictions. In conclusion, the results are translated into exclusion limits in models with pair-produced weakly interacting dark-matter candidates, large extra spatial dimensions, and supersymmetric particles in several compressed scenarios.« less

Search for dark matter and other new phenomena in events with an energetic jet and large missing transverse momentum using the ATLAS detector

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2018-01-25

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses proton-proton collision data corresponding to an integrated luminosity of 36.1 fb -1 at a centre-of-mass energy of 13 TeV collected in 2015 and 2016 with the ATLAS detector at the Large Hadron Collider. Events are required to have at least one jet with a transverse momentum above 250 GeV and no leptons (e or μ). Several signal regions are considered with increasing requirements on the missing transverse momentum above 250 GeV. Good agreement is observed betweenmore » the number of events in data and Standard Model predictions. In conclusion, the results are translated into exclusion limits in models with pair-produced weakly interacting dark-matter candidates, large extra spatial dimensions, and supersymmetric particles in several compressed scenarios.« less

International Migration of Doctors, and Its Impact on Availability of Psychiatrists in Low and Middle Income Countries

PubMed Central

Jenkins, Rachel; Kydd, Robert; Mullen, Paul; Thomson, Kenneth; Sculley, James; Kuper, Susan; Carroll, Joanna; Gureje, Oye; Hatcher, Simon; Brownie, Sharon; Carroll, Christopher; Hollins, Sheila; Wong, Mai Luen

2010-01-01

Background Migration of health professionals from low and middle income countries to rich countries is a large scale and long-standing phenomenon, which is detrimental to the health systems in the donor countries. We sought to explore the extent of psychiatric migration. Methods In our study, we use the respective professional databases in each country to establish the numbers of psychiatrists currently registered in the UK, US, New Zealand, and Australia who originate from other countries. We also estimate the impact of this migration on the psychiatrist population ratios in the donor countries. Findings We document large numbers of psychiatrists currently registered in the UK, US, New Zealand and Australia originating from India (4687 psychiatrists), Pakistan (1158), Bangladesh (149) , Nigeria (384) , Egypt (484), Sri Lanka (142), Philippines (1593). For some countries of origin, the numbers of psychiatrists currently registered within high-income countries' professional databases are very small (e.g., 5 psychiatrists of Tanzanian origin registered in the 4 high-income countries we studied), but this number is very significant compared to the 15 psychiatrists currently registered in Tanzania). Without such emigration, many countries would have more than double the number of psychiatrists per 100, 000 population (e.g. Bangladesh, Myanmar, Afghanistan, Egypt, Syria, Lebanon); and some countries would have had five to eight times more psychiatrists per 100,000 (e.g. Philippines, Pakistan, Sri Lanka, Liberia, Nigeria and Zambia). Conclusions Large numbers of psychiatrists originating from key low and middle income countries are currently registered in the UK, US, New Zealand and Australia, with concomitant impact on the psychiatrist/population ratio n the originating countries. We suggest that creative international policy approaches are needed to ensure the individual migration rights of health professionals do not compromise societal population rights to health, and that there are public and fair agreements between countries within an internationally agreed framework. PMID:20140216

Molecular counting by photobleaching in protein complexes with many subunits: best practices and application to the cellulose synthesis complex

DOE PAGES

Chen, Yalei; Deffenbaugh, Nathan C.; Anderson, Charles T.; ...

2014-09-17

The constituents of large, multisubunit protein complexes dictate their functions in cells, but determining their precise molecular makeup in vivo is challenging. One example of such a complex is the cellulose synthesis complex (CSC), which in plants synthesizes cellulose, the most abundant biopolymer on Earth. In growing plant cells, CSCs exist in the plasma membrane as six-lobed rosettes that contain at least three different cellulose synthase (CESA) isoforms, but the number and stoichiometry of CESAs in each CSC are unknown. To begin to address this question, we performed quantitative photobleaching of GFP-tagged AtCESA3-containing particles in living Arabidopsis thaliana cells usingmore » variable-angle epifluorescence microscopy and developed a set of information-based step detection procedures to estimate the number of GFP molecules in each particle. The step detection algorithms account for changes in signal variance due to changing numbers of fluorophores, and the subsequent analysis avoids common problems associated with fitting multiple Gaussian functions to binned histogram data. The analysis indicates that at least 10 GFP-AtCESA3 molecules can exist in each particle. In conclusion, these procedures can be applied to photobleaching data for any protein complex with large numbers of fluorescently tagged subunits, providing a new analytical tool with which to probe complex composition and stoichiometry.« less

Genetic Structures of Copy Number Variants Revealed by Genotyping Single Sperm

PubMed Central

Luo, Minjie; Cui, Xiangfeng; Fredman, David; Brookes, Anthony J.; Azaro, Marco A.; Greenawalt, Danielle M.; Hu, Guohong; Wang, Hui-Yun; Tereshchenko, Irina V.; Lin, Yong; Shentu, Yue; Gao, Richeng; Shen, Li; Li, Honghua

2009-01-01

Background Copy number variants (CNVs) occupy a significant portion of the human genome and may have important roles in meiotic recombination, human genome evolution and gene expression. Many genetic diseases may be underlain by CNVs. However, because of the presence of their multiple copies, variability in copy numbers and the diploidy of the human genome, detailed genetic structure of CNVs cannot be readily studied by available techniques. Methodology/Principal Findings Single sperm samples were used as the primary subjects for the study so that CNV haplotypes in the sperm donors could be studied individually. Forty-eight CNVs characterized in a previous study were analyzed using a microarray-based high-throughput genotyping method after multiplex amplification. Seventeen single nucleotide polymorphisms (SNPs) were also included as controls. Two single-base variants, either allelic or paralogous, could be discriminated for all markers. Microarray data were used to resolve SNP alleles and CNV haplotypes, to quantitatively assess the numbers and compositions of the paralogous segments in each CNV haplotype. Conclusions/Significance This is the first study of the genetic structure of CNVs on a large scale. Resulting information may help understand evolution of the human genome, gain insight into many genetic processes, and discriminate between CNVs and SNPs. The highly sensitive high-throughput experimental system with haploid sperm samples as subjects may be used to facilitate detailed large-scale CNV analysis. PMID:19384415

The use of single-date MODIS imagery for estimating large-scale urban impervious surface fraction with spectral mixture analysis and machine learning techniques

NASA Astrophysics Data System (ADS)

Deng, Chengbin; Wu, Changshan

2013-12-01

Urban impervious surface information is essential for urban and environmental applications at the regional/national scales. As a popular image processing technique, spectral mixture analysis (SMA) has rarely been applied to coarse-resolution imagery due to the difficulty of deriving endmember spectra using traditional endmember selection methods, particularly within heterogeneous urban environments. To address this problem, we derived endmember signatures through a least squares solution (LSS) technique with known abundances of sample pixels, and integrated these endmember signatures into SMA for mapping large-scale impervious surface fraction. In addition, with the same sample set, we carried out objective comparative analyses among SMA (i.e. fully constrained and unconstrained SMA) and machine learning (i.e. Cubist regression tree and Random Forests) techniques. Analysis of results suggests three major conclusions. First, with the extrapolated endmember spectra from stratified random training samples, the SMA approaches performed relatively well, as indicated by small MAE values. Second, Random Forests yields more reliable results than Cubist regression tree, and its accuracy is improved with increased sample sizes. Finally, comparative analyses suggest a tentative guide for selecting an optimal approach for large-scale fractional imperviousness estimation: unconstrained SMA might be a favorable option with a small number of samples, while Random Forests might be preferred if a large number of samples are available.

The issue of cavitation number value in studies of water treatment by hydrodynamic cavitation.

PubMed

Šarc, Andrej; Stepišnik-Perdih, Tadej; Petkovšek, Martin; Dular, Matevž

2017-01-01

Within the last years there has been a substantial increase in reports of utilization of hydrodynamic cavitation in various applications. It has came to our attention that many times the results are poorly repeatable with the main reason being that the researchers put significant emphasis on the value of the cavitation number when describing the conditions at which their device operates. In the present paper we firstly point to the fact that the cavitation number cannot be used as a single parameter that gives the cavitation condition and that large inconsistencies in the reports exist. Then we show experiments where the influences of the geometry, the flow velocity, the medium temperature and quality on the size, dynamics and aggressiveness of cavitation were assessed. Finally we show that there are significant inconsistencies in the definition of the cavitation number itself. In conclusions we propose a number of parameters, which should accompany any report on the utilization of hydrodynamic cavitation, to make it repeatable and to enable faster progress of science and technology development. Copyright © 2016 Elsevier B.V. All rights reserved.

Perturbations of the Richardson number field by gravity waves

NASA Technical Reports Server (NTRS)

Wurtele, M. G.; Sharman, R. D.

1985-01-01

An analytic solution is presented for a stratified fluid of arbitrary constant Richardson number. By computer aided analysis the perturbation fields, including that of the Richardson number can be calculated. The results of the linear analytic model were compared with nonlinear simulations, leading to the following conclusions: (1) the perturbations in the Richardson number field, when small, are produced primarily by the perturbations of the shear; (2) perturbations of in the Richardson number field, even when small, are not symmetric, the increase being significantly larger than the decrease (the linear analytic solution and the nonlinear simulations both confirm this result); (3) as the perturbations grow, this asymmetry increases, but more so in the nonlinear simulations than in the linear analysis; (4) for large perturbations of the shear flow, the static stability, as represented by N2, is the dominating mechanism, becoming zero or negative, and producing convective overturning; and (5) the convectional measure of linearity in lee wave theory, NH/U, is no longer the critical parameter (it is suggested that (H/u sub 0) (du sub 0/dz) takes on this role in a shearing flow).

Statistical properties of the Jukes-Holmquist method of estimating the number of nucleotide substitutions: reply to Holmquist and Conroy's criticism.

PubMed

Nei, M; Tateno, Y

1981-01-01

Conducting computer simulations, Nei and Tateno (1978) have shown that Jukes and Holmquist's (1972) method of estimating the number of nucleotide substitutions tends to give an overestimate and the estimate obtained has a large variance. Holmquist and Conroy (1980) repeated some parts of our simulation and claim that the overestimation of nucleotide substitutions in our paper occurred mainly because we used selected data. Examination of Holmquist and Conroy's simulation indicates that their results are essentially the same as ours when the Jukes-Holmquist method is used, but since they used a different method of computation their estimates of nucleotide substitutions differed substantially from ours. Another problem in Holmquist and Conroy's Letter is that they confused the expected number of nucleotide substitution with the number in a sample. This confusion has resulted in a number of unnecessary arguments. They also criticized our X2 measure, but this criticism is apparently due to a misunderstanding of the assumptions of our method and a failure to use our method in the way we described. We believe that our earlier conclusions remain unchanged.

Extreme Task-Specificity in Writer’s Cramp

PubMed Central

Shamim, Ejaz A.; Chu, Jason; Scheider, Linda H.; Savitt, Joseph; Jinnah, H. A.; Hallett, Mark

2011-01-01

Background Focal hand dystonia may be task-specific as is the case with writer’s cramp (WC). In early stages, the task-specificity can be so specific that it may be mistaken for a psychogenic movement disorder. Methods We describe four patients who showed extreme task specificity in WC. They initially only had problems writing either a single letter or number. Although they were largely thought to be psychogenic, they progressed to typical WC. Conclusions Early recognition of this condition may provide an opportunity for early initiation of treatment. PMID:21714006

Citation patterns of online and print journals in the digital ageEC

PubMed Central

De Groote, Sandra L.

2008-01-01

Purpose: The research assesses the impact of online journals on citation patterns by examining whether researchers were more likely to limit the resources they cited to those journals available online rather than those only in print. Setting: Publications from a large urban university with a medical college at an urban location and at a smaller regional location were examined. The number of online journals available to authors on either campus was the same. The number of print journals available on the large campus was much greater than the print journals available at the small campus. Methodology: Searches by author affiliation from 1996 to 2005 were performed in the Web of Science to find all articles written by affiliated members in the college of medicine at the selected institution. Cited references from randomly selected articles were recorded, and the cited journals were coded into five categories based on their availability at the study institution: print only, print and online, online only, not owned, and dropped. Results were analyzed using SPSS. The age of articles cited for selected years as well as for 2006 and 2007 was also examined. Results: The number of journals cited each year continued to increase. On the large urban campus, researchers were not more likely to cite journals available online or less likely to cite journals only in print. At the regional location, at which the number of print-only journals was minimal, use of print-only journals significantly decreased. Conclusion/discussion: The citation of print-only journals by researchers with access to a library with a large print and electronic collection appeared to continue, despite the availability of potential alternatives in the online collection. Journals available in electronic format were cited more frequently in publications from the campus whose library had a small print collection, and the citation of journals available in both print and electronic formats generally increased over the years studied. PMID:18974814

Screening for Lung Cancer

PubMed Central

Mazzone, Peter J.; Naidich, David P.; Bach, Peter B.

2013-01-01

Background: Lung cancer is by far the major cause of cancer deaths largely because in the majority of patients it is at an advanced stage at the time it is discovered, when curative treatment is no longer feasible. This article examines the data regarding the ability of screening to decrease the number of lung cancer deaths. Methods: A systematic review was conducted of controlled studies that address the effectiveness of methods of screening for lung cancer. Results: Several large randomized controlled trials (RCTs), including a recent one, have demonstrated that screening for lung cancer using a chest radiograph does not reduce the number of deaths from lung cancer. One large RCT involving low-dose CT (LDCT) screening demonstrated a significant reduction in lung cancer deaths, with few harms to individuals at elevated risk when done in the context of a structured program of selection, screening, evaluation, and management of the relatively high number of benign abnormalities. Whether other RCTs involving LDCT screening are consistent is unclear because data are limited or not yet mature. Conclusions: Screening is a complex interplay of selection (a population with sufficient risk and few serious comorbidities), the value of the screening test, the interval between screening tests, the availability of effective treatment, the risk of complications or harms as a result of screening, and the degree with which the screened individuals comply with screening and treatment recommendations. Screening with LDCT of appropriate individuals in the context of a structured process is associated with a significant reduction in the number of lung cancer deaths in the screened population. Given the complex interplay of factors inherent in screening, many questions remain on how to effectively implement screening on a broader scale. PMID:23649455

Structure-activity models of oral clearance, cytotoxicity, and LD50: a screen for promising anticancer compounds

PubMed Central

Boik, John C; Newman, Robert A

2008-01-01

Background Quantitative structure-activity relationship (QSAR) models have become popular tools to help identify promising lead compounds in anticancer drug development. Few QSAR studies have investigated multitask learning, however. Multitask learning is an approach that allows distinct but related data sets to be used in training. In this paper, a suite of three QSAR models is developed to identify compounds that are likely to (a) exhibit cytotoxic behavior against cancer cells, (b) exhibit high rat LD50 values (low systemic toxicity), and (c) exhibit low to modest human oral clearance (favorable pharmacokinetic characteristics). Models were constructed using Kernel Multitask Latent Analysis (KMLA), an approach that can effectively handle a large number of correlated data features, nonlinear relationships between features and responses, and multitask learning. Multitask learning is particularly useful when the number of available training records is small relative to the number of features, as was the case with the oral clearance data. Results Multitask learning modestly but significantly improved the classification precision for the oral clearance model. For the cytotoxicity model, which was constructed using a large number of records, multitask learning did not affect precision but did reduce computation time. The models developed here were used to predict activities for 115,000 natural compounds. Hundreds of natural compounds, particularly in the anthraquinone and flavonoids groups, were predicted to be cytotoxic, have high LD50 values, and have low to moderate oral clearance. Conclusion Multitask learning can be useful in some QSAR models. A suite of QSAR models was constructed and used to screen a large drug library for compounds likely to be cytotoxic to multiple cancer cell lines in vitro, have low systemic toxicity in rats, and have favorable pharmacokinetic properties in humans. PMID:18554402

Evidence from the Cochrane Collaboration for Traditional Chinese Medicine Therapies

PubMed Central

Wieland, Susan; Kimbrough, Elizabeth; Cheng, Ker; Berman, Brian M.

2009-01-01

Abstract Background The Cochrane Collaboration, an international not-for-profit organization that prepares and maintains systematic reviews of randomized trials of health care therapies, has produced reviews summarizing much of the evidence on Traditional Chinese Medicine (TCM). Our objective was to review the evidence base according to Cochrane systematic reviews. Methods In order to detect reviews focusing on TCM, we searched the titles and abstracts of all reviews in Issue 4, 2008 of the Cochrane Database of Systematic Reviews. For each review, we extracted data on the number of trials included and the total number of participants. We provided an indication of the strength of the review findings by assessing the reviewers' abstract conclusions statement. We supplemented our assessment of the abstract conclusions statements with a listing of the comparisons and outcomes showing statistically significant meta-analyses results. Results We identified 70 Cochrane systematic reviews of TCM, primarily acupuncture (n = 26) and Chinese herbal medicine (n = 42), and 1 each of moxibustion and t'ai chi. Nineteen (19) of 26 acupuncture reviews and 22/42 herbal medicine reviews concluded that there was not enough good quality trial evidence to make any conclusion about the efficacy of the evaluated treatment, while the remaining 7 acupuncture and 20 herbal medicine reviews and each of the moxibustion and t'ai chi reviews indicated a suggestion of benefit, which was qualified by a caveat about the poor quality and quantity of studies. Most reviews included many distinct interventions, controls, outcomes, and populations, and a large number of different comparisons were made, each with a distinct forest plot. Conclusions Most Cochrane systematic reviews of TCM are inconclusive, due specifically to the poor methodology and heterogeneity of the studies reviewed. Some systematic reviews provide preliminary evidence of Chinese medicine's benefits to certain patient populations, underscoring the importance and appropriateness of further research. These preliminary findings should be considered tentative and need to be confirmed with rigorous randomized controlled trials. PMID:19757977

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files

PubMed Central

Gao, Jingjing; Jin, Peng; Eng, Celeste; Burchard, Esteban G; Beaty, Terri H; Ruczinski, Ingo; Mathias, Rasika A; Barnes, Kathleen; Wang, Fusheng

2018-01-01

Abstract Background Sorted merging of genomic data is a common data operation necessary in many sequencing-based studies. It involves sorting and merging genomic data from different subjects by their genomic locations. In particular, merging a large number of variant call format (VCF) files is frequently required in large-scale whole-genome sequencing or whole-exome sequencing projects. Traditional single-machine based methods become increasingly inefficient when processing large numbers of files due to the excessive computation time and Input/Output bottleneck. Distributed systems and more recent cloud-based systems offer an attractive solution. However, carefully designed and optimized workflow patterns and execution plans (schemas) are required to take full advantage of the increased computing power while overcoming bottlenecks to achieve high performance. Findings In this study, we custom-design optimized schemas for three Apache big data platforms, Hadoop (MapReduce), HBase, and Spark, to perform sorted merging of a large number of VCF files. These schemas all adopt the divide-and-conquer strategy to split the merging job into sequential phases/stages consisting of subtasks that are conquered in an ordered, parallel, and bottleneck-free way. In two illustrating examples, we test the performance of our schemas on merging multiple VCF files into either a single TPED or a single VCF file, which are benchmarked with the traditional single/parallel multiway-merge methods, message passing interface (MPI)–based high-performance computing (HPC) implementation, and the popular VCFTools. Conclusions Our experiments suggest all three schemas either deliver a significant improvement in efficiency or render much better strong and weak scalabilities over traditional methods. Our findings provide generalized scalable schemas for performing sorted merging on genetics and genomics data using these Apache distributed systems. PMID:29762754

Comparative Evaluation of Different Optimization Algorithms for Structural Design Applications

NASA Technical Reports Server (NTRS)

Patnaik, Surya N.; Coroneos, Rula M.; Guptill, James D.; Hopkins, Dale A.

1996-01-01

Non-linear programming algorithms play an important role in structural design optimization. Fortunately, several algorithms with computer codes are available. At NASA Lewis Research Centre, a project was initiated to assess the performance of eight different optimizers through the development of a computer code CometBoards. This paper summarizes the conclusions of that research. CometBoards was employed to solve sets of small, medium and large structural problems, using the eight different optimizers on a Cray-YMP8E/8128 computer. The reliability and efficiency of the optimizers were determined from the performance of these problems. For small problems, the performance of most of the optimizers could be considered adequate. For large problems, however, three optimizers (two sequential quadratic programming routines, DNCONG of IMSL and SQP of IDESIGN, along with Sequential Unconstrained Minimizations Technique SUMT) outperformed others. At optimum, most optimizers captured an identical number of active displacement and frequency constraints but the number of active stress constraints differed among the optimizers. This discrepancy can be attributed to singularity conditions in the optimization and the alleviation of this discrepancy can improve the efficiency of optimizers.

Residual fields from extinct dynamos

NASA Astrophysics Data System (ADS)

Parker, E. N.

The generation of magnetic fields in convective zones of declining vigor and/or thickness is considered, the goal being to explain the magnetic fields observed in A-stars. The investigation is restricted to kinematical dynamos in order to show some of the many possibilities, which depend on the assumed conditions of decline of the convection. The examples illustrate the quantitative detail required to describe the convection in order to extract any firm conclusions concerning specific stars. The first example treats the basic problem of diffusion from a layer of declining thickness. The second has a buoyant rise added to the field in the layer. The third deals with plane dynamo waves in a region with declining eddy diffusivity, dynamo coefficient, and large-scale shear. It is noted that the dynamo number may increase or decrease with declining convection, with an increase expected if the large-scale shear does not decline as rapidly as the eddy diffusivity. It is shown that one of the components of the field may increase without bound even when the dynamo number declines to zero.

Performance Trend of Different Algorithms for Structural Design Optimization

NASA Technical Reports Server (NTRS)

Patnaik, Surya N.; Coroneos, Rula M.; Guptill, James D.; Hopkins, Dale A.

1996-01-01

Nonlinear programming algorithms play an important role in structural design optimization. Fortunately, several algorithms with computer codes are available. At NASA Lewis Research Center, a project was initiated to assess performance of different optimizers through the development of a computer code CometBoards. This paper summarizes the conclusions of that research. CometBoards was employed to solve sets of small, medium and large structural problems, using different optimizers on a Cray-YMP8E/8128 computer. The reliability and efficiency of the optimizers were determined from the performance of these problems. For small problems, the performance of most of the optimizers could be considered adequate. For large problems however, three optimizers (two sequential quadratic programming routines, DNCONG of IMSL and SQP of IDESIGN, along with the sequential unconstrained minimizations technique SUMT) outperformed others. At optimum, most optimizers captured an identical number of active displacement and frequency constraints but the number of active stress constraints differed among the optimizers. This discrepancy can be attributed to singularity conditions in the optimization and the alleviation of this discrepancy can improve the efficiency of optimizers.

Managing protected health information in distributed research network environments: automated review to facilitate collaboration

PubMed Central

2013-01-01

Background Multi-site health sciences research is becoming more common, as it enables investigation of rare outcomes and diseases and new healthcare innovations. Multi-site research usually involves the transfer of large amounts of research data between collaborators, which increases the potential for accidental disclosures of protected health information (PHI). Standard protocols for preventing release of PHI are extremely vulnerable to human error, particularly when the shared data sets are large. Methods To address this problem, we developed an automated program (SAS macro) to identify possible PHI in research data before it is transferred between research sites. The macro reviews all data in a designated directory to identify suspicious variable names and data patterns. The macro looks for variables that may contain personal identifiers such as medical record numbers and social security numbers. In addition, the macro identifies dates and numbers that may identify people who belong to small groups, who may be identifiable even in the absences of traditional identifiers. Results Evaluation of the macro on 100 sample research data sets indicated a recall of 0.98 and precision of 0.81. Conclusions When implemented consistently, the macro has the potential to streamline the PHI review process and significantly reduce accidental PHI disclosures. PMID:23521861

Genomic diversity of the human intestinal parasite Entamoeba histolytica

PubMed Central

2012-01-01

Background Entamoeba histolytica is a significant cause of disease worldwide. However, little is known about the genetic diversity of the parasite. We re-sequenced the genomes of ten laboratory cultured lines of the eukaryotic pathogen Entamoeba histolytica in order to develop a picture of genetic diversity across the genome. Results The extreme nucleotide composition bias and repetitiveness of the E. histolytica genome provide a challenge for short-read mapping, yet we were able to define putative single nucleotide polymorphisms in a large portion of the genome. The results suggest a rather low level of single nucleotide diversity, although genes and gene families with putative roles in virulence are among the more polymorphic genes. We did observe large differences in coverage depth among genes, indicating differences in gene copy number between genomes. We found evidence indicating that recombination has occurred in the history of the sequenced genomes, suggesting that E. histolytica may reproduce sexually. Conclusions E. histolytica displays a relatively low level of nucleotide diversity across its genome. However, large differences in gene family content and gene copy number are seen among the sequenced genomes. The pattern of polymorphism indicates that E. histolytica reproduces sexually, or has done so in the past, which has previously been suggested but not proven. PMID:22630046

Technical Note: Improved CT number stability across patient size using dual-energy CT virtual monoenergetic imaging

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

Michalak, Gregory; Grimes, Joshua; Fletcher, Joel

2016-01-15

Purpose: The purpose of this study was to evaluate, over a wide range of phantom sizes, CT number stability achieved using two techniques for generating dual-energy computed tomography (DECT) virtual monoenergetic images. Methods: Water phantoms ranging in lateral diameter from 15 to 50 cm and containing a CT number test object were scanned on a DSCT scanner using both single-energy (SE) and dual-energy (DE) techniques. The SE tube potentials were 70, 80, 90, 100, 110, 120, 130, 140, and 150 kV; the DE tube potential pairs were 80/140, 70/150Sn, 80/150Sn, 90/150Sn, and 100/150Sn kV (Sn denotes that the 150 kVmore » beam was filtered with a 0.6 mm tin filter). Virtual monoenergetic images at energies ranging from 40 to 140 keV were produced from the DECT data using two algorithms, monoenergetic (mono) and monoenergetic plus (mono+). Particularly in large phantoms, water CT number errors and/or artifacts were observed; thus, datasets with water CT numbers outside ±10 HU or with noticeable artifacts were excluded from the study. CT numbers were measured to determine CT number stability across all phantom sizes. Results: Data exclusions were generally limited to cases when a SE or DE technique with a tube potential of less than 90 kV was used to scan a phantom larger than 30 cm. The 90/150Sn DE technique provided the most accurate water background over the large range of phantom sizes evaluated. Mono and mono+ provided equally improved CT number stability as a function of phantom size compared to SE; the average deviation in CT number was only 1.4% using 40 keV and 1.8% using 70 keV, while SE had an average deviation of 11.8%. Conclusions: The authors’ report demonstrates, across all phantom sizes, the improvement in CT number stability achieved with mono and mono+ relative to SE.« less

Assessing nonlinear structures in real exchange rates using recurrence plot strategies

NASA Astrophysics Data System (ADS)

Belaire-Franch, Jorge; Contreras, Dulce; Tordera-Lledó, Lorena

2002-11-01

Purchasing power parity (PPP) is an important theory at the basis of a large number of economic models. However, the implication derived from the theory that real exchange rates must follow stationary processes is not conclusively supported by empirical studies. In a recent paper, Serletis and Gogas [Appl. Finance Econ. 10 (2000) 615] show evidence of deterministic chaos in several OECD exchange rates. As a consequence, PPP rejections could be spurious. In this work, we follow a two-stage testing procedure to test for nonlinearities and chaos in real exchange rates, using a new set of techniques designed by Webber and Zbilut [J. Appl. Physiol. 76 (1994) 965], called recurrence quantification analysis (RQA). Our conclusions differ slightly from Serletis and Gogas [Appl. Finance Econ. 10 (2000) 615], but they are also supportive of chaos for some exchange rates.

Modified social force model based on information transmission toward crowd evacuation simulation

NASA Astrophysics Data System (ADS)

Han, Yanbin; Liu, Hong

2017-03-01

In this paper, the information transmission mechanism is introduced into the social force model to simulate pedestrian behavior in an emergency, especially when most pedestrians are unfamiliar with the evacuation environment. This modified model includes a collision avoidance strategy and an information transmission model that considers information loss. The former is used to avoid collision among pedestrians in a simulation, whereas the latter mainly describes how pedestrians obtain and choose directions appropriate to them. Simulation results show that pedestrians can obtain the correct moving direction through information transmission mechanism and that the modified model can simulate actual pedestrian behavior during an emergency evacuation. Moreover, we have drawn four conclusions to improve evacuation based on the simulation results; and these conclusions greatly contribute in optimizing a number of efficient emergency evacuation schemes for large public places.

Pipeline issues

NASA Technical Reports Server (NTRS)

Eisley, Joe T.

1990-01-01

The declining pool of graduates, the lack of rigorous preparation in science and mathematics, and the declining interest in science and engineering careers at the precollege level promises a shortage of technically educated personnel at the college level for industry, government, and the universities in the next several decades. The educational process, which starts out with a large number of students at the elementary level, but with an ever smaller number preparing for science and engineering at each more advanced educational level, is in a state of crisis. These pipeline issues, so called because the educational process is likened to a series of ever smaller constrictions in a pipe, were examined in a workshop at the Space Grant Conference and a summary of the presentations and the results of the discussion, and the conclusions of the workshop participants are reported.

Robotic surgery - advance or gimmick?

PubMed

De Wilde, Rudy L; Herrmann, Anja

2013-06-01

Robotic surgery is increasingly implemented as a minimally invasive approach to a variety of gynaecological procedures. The use of conventional laparoscopy by a broad range of surgeons, especially in complex procedures, is hampered by several drawbacks. Robotic surgery was created with the aim of overcoming some of the limitations. Although robotic surgery has many advantages, it is also associated with clear disadvantages. At present, the proof of superiority over access by laparotomy or laparoscopy through large randomised- controlled trials is still lacking. Until results of such trials are present, a firm conclusion about the usefulness of robotic surgery cannot be drawn. Robotic surgery is promising, making the advantages of minimally invasive surgery potentially available to a large number of surgeons and patients in the future. Copyright © 2013 Elsevier Ltd. All rights reserved.

Quadruplex MAPH: improvement of throughput in high-resolution copy number screening

PubMed Central

Tyson, Jess; Majerus, Tamsin MO; Walker, Susan; Armour, John AL

2009-01-01

Background Copy number variation (CNV) in the human genome is recognised as a widespread and important source of human genetic variation. Now the challenge is to screen for these CNVs at high resolution in a reliable, accurate and cost-effective way. Results Multiplex Amplifiable Probe Hybridisation (MAPH) is a sensitive, high-resolution technology appropriate for screening for CNVs in a defined region, for a targeted population. We have developed MAPH to a highly multiplexed format ("QuadMAPH") that allows the user a four-fold increase in the number of loci tested simultaneously. We have used this method to analyse a genomic region of 210 kb, including the MSH2 gene and 120 kb of flanking DNA. We show that the QuadMAPH probes report copy number with equivalent accuracy to simplex MAPH, reliably demonstrating diploid copy number in control samples and accurately detecting deletions in Hereditary Non-Polyposis Colorectal Cancer (HNPCC) samples. Conclusion QuadMAPH is an accurate, high-resolution method that allows targeted screening of large numbers of subjects without the expense of genome-wide approaches. Whilst we have applied this technique to a region of the human genome, it is equally applicable to the genomes of other organisms. PMID:19785739

Hyperhomocysteinemia Associates with Small Vessel Disease More Closely Than Large Vessel Disease

PubMed Central

Feng, Chao; Bai, Xue; Xu, Yu; Hua, Ting; Huang, Jing; Liu, Xue-Yuan

2013-01-01

Background: Hyperhomocysteinemia was believed to be an independent risk factor for stroke and associate with small vessel disease (SVD) related stroke and large vessel disease (LVD) related stroke differently. However it's still unclear which type of stroke associated with homocysteine (HCY) more strongly because the conclusions of previous studies were contradictory. In this study we focused on the subclinical angiopathies of stroke, i.e., SVD and LVD instead of stroke subtypes and sought to compare the associations between HCY level and different angiopathies. Methods: 324 non-stroke patients were enrolled. Sex, age, HCY level and other vascular risk factors were collected. MRI and angiographies were used to determine the type of angiopathies and their severity, i.e., the scores of leukoaraiosis (LA), plaques and numbers of silent brain infarctions (SBI). LVD was defined as the presence of atherosclerotic plaques of cerebral arteries. SVD was defined as the presence of either LA or SBI. 230 patients were deemed to have LVD; 180 patients were deemed to have SVD. Spearman's correlation test and logistic regression were used to analyze the association between HCY level and different angiopathies. Results: The correlation between HCY level and scores of plaques was weaker than that of the scores of LA and numbers of SBI. Hyperhomocysteinemia was an independent risk factor for SVD (OR = 1.315, P <0.001), whereas the association between HCY level and LVD was not that significant (OR = 1.058, P = 0.075). Conclusion: HCY level associated with SVD more strongly than LVD. PMID:23471237

Calculus domains modelled using an original bool algebra based on polygons

NASA Astrophysics Data System (ADS)

Oanta, E.; Panait, C.; Raicu, A.; Barhalescu, M.; Axinte, T.

2016-08-01

Analytical and numerical computer based models require analytical definitions of the calculus domains. The paper presents a method to model a calculus domain based on a bool algebra which uses solid and hollow polygons. The general calculus relations of the geometrical characteristics that are widely used in mechanical engineering are tested using several shapes of the calculus domain in order to draw conclusions regarding the most effective methods to discretize the domain. The paper also tests the results of several CAD commercial software applications which are able to compute the geometrical characteristics, being drawn interesting conclusions. The tests were also targeting the accuracy of the results vs. the number of nodes on the curved boundary of the cross section. The study required the development of an original software consisting of more than 1700 computer code lines. In comparison with other calculus methods, the discretization using convex polygons is a simpler approach. Moreover, this method doesn't lead to large numbers as the spline approximation did, in that case being required special software packages in order to offer multiple, arbitrary precision. The knowledge resulted from this study may be used to develop complex computer based models in engineering.

Mayday - integrative analytics for expression data

PubMed Central

2010-01-01

Background DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files. Results We have rewritten large parts of Mayday's core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved. Conclusions We present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well as the extension possibilities using compiled plugins and ad-hoc scripting allow for the rapid adaption of Mayday also to very specialized data exploration. Mayday is available at http://microarray-analysis.org. PMID:20214778

Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers

PubMed Central

2013-01-01

Background Many large-scale studies analyzed high-throughput genomic data to identify altered pathways essential to the development and progression of specific types of cancer. However, no previous study has been extended to provide a comprehensive analysis of pathways disrupted by copy number alterations across different human cancers. Towards this goal, we propose a network-based method to integrate copy number alteration data with human protein-protein interaction networks and pathway databases to identify pathways that are commonly disrupted in many different types of cancer. Results We applied our approach to a data set of 2,172 cancer patients across 16 different types of cancers, and discovered a set of commonly disrupted pathways, which are likely essential for tumor formation in majority of the cancers. We also identified pathways that are only disrupted in specific cancer types, providing molecular markers for different human cancers. Analysis with independent microarray gene expression datasets confirms that the commonly disrupted pathways can be used to identify patient subgroups with significantly different survival outcomes. We also provide a network view of disrupted pathways to explain how copy number alterations affect pathways that regulate cell growth, cycle, and differentiation for tumorigenesis. Conclusions In this work, we demonstrated that the network-based integrative analysis can help to identify pathways disrupted by copy number alterations across 16 types of human cancers, which are not readily identifiable by conventional overrepresentation-based and other pathway-based methods. All the results and source code are available at http://compbio.cs.umn.edu/NetPathID/. PMID:23822816

SU-E-T-230: Creating a Large Number of Focused Beams with Variable Patient Head Tilt to Improve Dose Fall-Off for Brain Radiosurgery

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

Chiu, J; Ma, L

2015-06-15

Purpose: To develop a treatment delivery and planning strategy by increasing the number of beams to minimize dose to brain tissue surrounding a target, while maximizing dose coverage to the target. Methods: We analyzed 14 different treatment plans via Leksell PFX and 4C. For standardization, single tumor cases were chosen. Original treatment plans were compared with two optimized plans. The number of beams was increased in treatment plans by varying tilt angles of the patient head, while maintaining original isocenter and the beam positions in the x-, y- and z-axes, collimator size, and beam blocking. PFX optimized plans increased beammore » numbers with three pre-set tilt angles, 70, 90, 110, and 4C optimized plans increased beam numbers with tilt angles increasing arbitrarily from range of 30 to 150 degrees. Optimized treatment plans were compared dosimetrically with original treatment plans. Results: Comparing total normal tissue isodose volumes between original and optimized plans, the low-level percentage isodose volumes decreased in all plans. Despite the addition of multiple beams up to a factor of 25, beam-on times for 1 tilt angle versus 3 or more tilt angles were comparable (<1 min.). In 64% (9/14) of the studied cases, the volume percentage decrease by >5%, with the highest value reaching 19%. The addition of more tilt angles correlates to a greater decrease in normal brain irradiated volume. Selectivity and coverage for original and optimized plans remained comparable. Conclusion: Adding large number of additional focused beams with variable patient head tilt shows improvement for dose fall-off for brain radiosurgery. The study demonstrates technical feasibility of adding beams to decrease target volume.« less

On the challenges of drawing conclusions from p-values just below 0.05

PubMed Central

2015-01-01

In recent years, researchers have attempted to provide an indication of the prevalence of inflated Type 1 error rates by analyzing the distribution of p-values in the published literature. De Winter & Dodou (2015) analyzed the distribution (and its change over time) of a large number of p-values automatically extracted from abstracts in the scientific literature. They concluded there is a ‘surge of p-values between 0.041–0.049 in recent decades’ which ‘suggests (but does not prove) questionable research practices have increased over the past 25 years.’ I show the changes in the ratio of fractions of p-values between 0.041–0.049 over the years are better explained by assuming the average power has decreased over time. Furthermore, I propose that their observation that p-values just below 0.05 increase more strongly than p-values above 0.05 can be explained by an increase in publication bias (or the file drawer effect) over the years (cf. Fanelli, 2012; Pautasso, 2010, which has led to a relative decrease of ‘marginally significant’ p-values in abstracts in the literature (instead of an increase in p-values just below 0.05). I explain why researchers analyzing large numbers of p-values need to relate their assumptions to a model of p-value distributions that takes into account the average power of the performed studies, the ratio of true positives to false positives in the literature, the effects of publication bias, and the Type 1 error rate (and possible mechanisms through which it has inflated). Finally, I discuss why publication bias and underpowered studies might be a bigger problem for science than inflated Type 1 error rates, and explain the challenges when attempting to draw conclusions about inflated Type 1 error rates from a large heterogeneous set of p-values. PMID:26246976

Productivity trends and collaboration patterns: A diachronic study in the eating disorders field

PubMed Central

Valderrama-Zurián, Juan-Carlos; Aguilar-Moya, Remedios; Cepeda-Benito, Antonio; Navarro-Moreno, María-Ángeles; Gandía-Balaguer, Asunción; Aleixandre-Benavent, Rafael

2017-01-01

Objective The present study seeks to extend previous bibliometric studies on eating disorders (EDs) by including a time-dependent analysis of the growth and evolution of multi-author collaborations and their correlation with ED publication trends from 1980 to 2014 (35 years). Methods Using standardized practices, we searched Web of Science (WoS) Core Collection (WoSCC) (indexes: Science Citation Index-Expanded [SCIE], & Social Science Citation Index [SSCI]) and Scopus (areas: Health Sciences, Life Sciences, & Social Sciences and Humanities) to identify a large sample of articles related to EDs. We then submitted our sample of articles to bibliometric and graph theory analyses to identify co-authorship and social network patterns. Results We present a large number of detailed findings, including a clear pattern of scientific growth measured as number of publications per five-year period or quinquennium (Q), a tremendous increase in the number of authors attracted by the ED subject, and a very high and steady growth in collaborative work. Conclusions We inferred that the noted publication growth was likely driven by the noted increase in the number of new authors per Q. Social network analyses suggested that collaborations within ED follow patters of interaction that are similar to well established and recognized disciplines, as indicated by the presence of a “giant cluster”, high cluster density, and the replication of the “small world” phenomenon—the principle that we are all linked by short chains of acquaintances. PMID:28850569

Phenotypic Association Analyses With Copy Number Variation in Recurrent Depressive Disorder.

PubMed

Rucker, James J H; Tansey, Katherine E; Rivera, Margarita; Pinto, Dalila; Cohen-Woods, Sarah; Uher, Rudolf; Aitchison, Katherine J; Craddock, Nick; Owen, Michael J; Jones, Lisa; Jones, Ian; Korszun, Ania; Barnes, Michael R; Preisig, Martin; Mors, Ole; Maier, Wolfgang; Rice, John; Rietschel, Marcella; Holsboer, Florian; Farmer, Anne E; Craig, Ian W; Scherer, Stephen W; McGuffin, Peter; Breen, Gerome

2016-02-15

Defining the molecular genomic basis of the likelihood of developing depressive disorder is a considerable challenge. We previously associated rare, exonic deletion copy number variants (CNV) with recurrent depressive disorder (RDD). Sex chromosome abnormalities also have been observed to co-occur with RDD. In this reanalysis of our RDD dataset (N = 3106 cases; 459 screened control samples and 2699 population control samples), we further investigated the role of larger CNVs and chromosomal abnormalities in RDD and performed association analyses with clinical data derived from this dataset. We found an enrichment of Turner's syndrome among cases of depression compared with the frequency observed in a large population sample (N = 34,910) of live-born infants collected in Denmark (two-sided p = .023, odds ratio = 7.76 [95% confidence interval = 1.79-33.6]), a case of diploid/triploid mosaicism, and several cases of uniparental isodisomy. In contrast to our previous analysis, large deletion CNVs were no more frequent in cases than control samples, although deletion CNVs in cases contained more genes than control samples (two-sided p = .0002). After statistical correction for multiple comparisons, our data do not support a substantial role for CNVs in RDD, although (as has been observed in similar samples) occasional cases may harbor large variants with etiological significance. Genetic pleiotropy and sample heterogeneity suggest that very large sample sizes are required to study conclusively the role of genetic variation in mood disorders. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Perilobar nephrogenic rests are non-obligate molecular genetic precursor lesions of IGF2-associated Wilms tumours

PubMed Central

Vuononvirta, Raisa; Sebire, Neil J.; Dallosso, Anthony R.; Reis-Filho, Jorge S.; Williams, Richard D.; Mackay, Alan; Fenwick, Kerry; Grigoriadis, Anita; Ashworth, Alan; Pritchard-Jones, Kathy; Brown, Keith W.; Vujanic, Gordan M.; Jones, Chris

2009-01-01

Purpose: Perilobar nephrogenic rests (PLNRs) are abnormally persistent foci of embryonal immature blastema that have been associated with dysregulation at the 11p15 locus by genetic/epigenetic means, and are thought to be precursor lesions of Wilms tumour. The precise genomic events are, however, largely unknown. Experimental Design: We used arrayCGH to analyse a series of 50 PLNRs and 25 corresponding Wilms tumours characterised for 11p15 genetic/epigenetic alterations and IGF2 expression. Results: The genomic profiles of PLNRs could be subdivided into three categories: those with no copy number changes (22/50, 44%), those with single, whole chromosome alterations (8/50, 16%), and those with multiple gains/losses (20/50, 40%). The most frequent aberrations included 1p- (7/50, 14%) +18 (6/50, 12%), +13 (5/50, 10%) and +12 (3/50, 6%). For the majority (19/25, 76%) of cases, the rest harboured a subset of the copy number changes in the associated Wilms tumour. We identified a temporal order of genomic changes which occur during the IGF2/PLNR pathway of Wilms tumorigenesis, with large scale chromosomal alterations such as 1p-, +12, +13 and +18 regarded as ‘early’ events. In some of the cases (24%), the PLNRs harboured large-scale copy number changes not observed in the concurrent Wilms tumour, including +10p, +14q and +18. Conclusions: These data suggest that although the evidence for PLNRs as precursors is compelling, not all lesions must necessarily undergo malignant transformation. PMID:19047088

Individual differences in non-symbolic numerical abilities predict mathematical achievements but contradict ATOM.

PubMed

Agrillo, Christian; Piffer, Laura; Adriano, Andrea

2013-07-01

A significant debate surrounds the nature of the cognitive mechanisms involved in non-symbolic number estimation. Several studies have suggested the existence of the same cognitive system for estimation of time, space, and number, called "a theory of magnitude" (ATOM). In addition, researchers have proposed the theory that non-symbolic number abilities might support our mathematical skills. Despite the large number of studies carried out, no firm conclusions can be drawn on either topic. In the present study, we correlated the performance of adults on non-symbolic magnitude estimations and symbolic numerical tasks. Non-symbolic magnitude abilities were assessed by asking participants to estimate which auditory tone lasted longer (time), which line was longer (space), and which group of dots was more numerous (number). To assess symbolic numerical abilities, participants were required to perform mental calculations and mathematical reasoning. We found a positive correlation between non-symbolic and symbolic numerical abilities. On the other hand, no correlation was found among non-symbolic estimations of time, space, and number. Our study supports the idea that mathematical abilities rely on rudimentary numerical skills that predate verbal language. By contrast, the lack of correlation among non-symbolic estimations of time, space, and number is incompatible with the idea that these magnitudes are entirely processed by the same cognitive system.

Cluster randomised trials in the medical literature: two bibliometric surveys

PubMed Central

Bland, J Martin

2004-01-01

Background Several reviews of published cluster randomised trials have reported that about half did not take clustering into account in the analysis, which was thus incorrect and potentially misleading. In this paper I ask whether cluster randomised trials are increasing in both number and quality of reporting. Methods Computer search for papers on cluster randomised trials since 1980, hand search of trial reports published in selected volumes of the British Medical Journal over 20 years. Results There has been a large increase in the numbers of methodological papers and of trial reports using the term 'cluster random' in recent years, with about equal numbers of each type of paper. The British Medical Journal contained more such reports than any other journal. In this journal there was a corresponding increase over time in the number of trials where subjects were randomised in clusters. In 2003 all reports showed awareness of the need to allow for clustering in the analysis. In 1993 and before clustering was ignored in most such trials. Conclusion Cluster trials are becoming more frequent and reporting is of higher quality. Perhaps statistician pressure works. PMID:15310402

Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision

PubMed Central

2011-01-01

Background Data fusion methods are widely used in virtual screening, and make the implicit assumption that the more often a molecule is retrieved in multiple similarity searches, the more likely it is to be active. This paper tests the correctness of this assumption. Results Sets of 25 searches using either the same reference structure and 25 different similarity measures (similarity fusion) or 25 different reference structures and the same similarity measure (group fusion) show that large numbers of unique molecules are retrieved by just a single search, but that the numbers of unique molecules decrease very rapidly as more searches are considered. This rapid decrease is accompanied by a rapid increase in the fraction of those retrieved molecules that are active. There is an approximately log-log relationship between the numbers of different molecules retrieved and the number of searches carried out, and a rationale for this power-law behaviour is provided. Conclusions Using multiple searches provides a simple way of increasing the precision of a similarity search, and thus provides a justification for the use of data fusion methods in virtual screening. PMID:21824430

Building application of solar energy. Study no. 4: Scenarios for the utilization of solar energy in southern California buildings, change 1

NASA Technical Reports Server (NTRS)

Davis, E. S.; French, R. L.; Hirshberg, A. S.

1976-01-01

Plausible future market scenarios for solar heating and cooling systems into buildings in the area served by the Southern California Edison Company. A range of plausible estimates for the number of solar systems which might be installed and the electrical energy which might be displaced by energy from these systems are provided. The effect on peak electrical load was not explicitly calculated but preliminary conclusions concerning peak load can be inferred from the estimates presented. Two markets are investigated: the single family market and the large power commercial market.

First Case Report of Sinusitis with Lophomonas blattarum from Iran

PubMed Central

Berenji, Fariba; Parian, Mahmoud; Fata, Abdolmajid; Bakhshaee, Mahdi; Fattahi, Fereshte

2016-01-01

Introduction. Lophomonas blattarum is a rare cause of bronchopulmonary and sinus infection. This paper presents a rare case of Lophomonas sinusitis. Case Presentation. The patient was a 31-year-old woman who was admitted because of a history of upper respiratory infection and sinusitis. Direct microscopic examination of the sputum and nasal discharge showed large numbers of living Lophomonas blattarum with irregular movement of flagella. The patient was successfully treated by Metronidazole 750 mg t.i.d. for 30 days. Conclusions. This is the first case report of Lophomonas blattarum sinusitis from Iran. PMID:26966601

First Case Report of Sinusitis with Lophomonas blattarum from Iran.

PubMed

Berenji, Fariba; Parian, Mahmoud; Fata, Abdolmajid; Bakhshaee, Mahdi; Fattahi, Fereshte

2016-01-01

Introduction. Lophomonas blattarum is a rare cause of bronchopulmonary and sinus infection. This paper presents a rare case of Lophomonas sinusitis. Case Presentation. The patient was a 31-year-old woman who was admitted because of a history of upper respiratory infection and sinusitis. Direct microscopic examination of the sputum and nasal discharge showed large numbers of living Lophomonas blattarum with irregular movement of flagella. The patient was successfully treated by Metronidazole 750 mg t.i.d. for 30 days. Conclusions. This is the first case report of Lophomonas blattarum sinusitis from Iran.

Guidelines for the Effective Use of Entity-Attribute-Value Modeling for Biomedical Databases

PubMed Central

Dinu, Valentin; Nadkarni, Prakash

2007-01-01

Purpose To introduce the goals of EAV database modeling, to describe the situations where Entity-Attribute-Value (EAV) modeling is a useful alternative to conventional relational methods of database modeling, and to describe the fine points of implementation in production systems. Methods We analyze the following circumstances: 1) data are sparse and have a large number of applicable attributes, but only a small fraction will apply to a given entity; 2) numerous classes of data need to be represented, each class has a limited number of attributes, but the number of instances of each class is very small. We also consider situations calling for a mixed approach where both conventional and EAV design are used for appropriate data classes. Results and Conclusions In robust production systems, EAV-modeled databases trade a modest data sub-schema for a complex metadata sub-schema. The need to design the metadata effectively makes EAV design potentially more challenging than conventional design. PMID:17098467

The effects of frequent electroejaculation on the semen characteristics of a captive Siberian tiger (Panthera tigris altaica).

PubMed

Fukui, Daisuke; Nagano, Masashi; Nakamura, Ryohei; Bando, Gen; Nakata, Shinichi; Kosuge, Masao; Sakamoto, Hideyuki; Matsui, Motozumi; Yanagawa, Yojiro; Takahashi, Yoshiyuki

2013-10-01

Artificial insemination (AI) can help to avoid inbreeding and genetic degeneration for sustaining genetically healthy populations of endangered species in captivity. Collection of a sufficient quantity of viable sperm is an essential first step in the AI process. In the present study, we examined the effects of frequent electroejaculation on semen characteristics in a Siberian tiger. We collected semen in all 17 trials during 6 breeding seasons (6 years). The mean number of sperm and the percentage of motile sperm were 294.3 ± 250.2 × 10⁶/ejaculate and 82.4 ± 11.4%, respectively. The number of motile sperm tended to increase during frequent electroejaculation in the same breeding season. Semen collection by electroejaculation can be performed effectively up to the fourth sequential ejaculate, which contained the most sperm in the study. In conclusion, frequent collection of sperm by electroejaculation from tigers may be effective for collection of a large number of motile sperm.

Optical touch sensing: practical bounds for design and performance

NASA Astrophysics Data System (ADS)

Bläßle, Alexander; Janbek, Bebart; Liu, Lifeng; Nakamura, Kanna; Nolan, Kimberly; Paraschiv, Victor

2013-02-01

Touch sensitive screens are used in many applications ranging in size from smartphones and tablets to display walls and collaborative surfaces. In this study, we consider optical touch sensing, a technology best suited for large-scale touch surfaces. Optical touch sensing utilizes cameras and light sources placed along the edge of the display. Within this framework, we first find a sufficient number of cameras necessary for identifying a convex polygon touching the screen, using a continuous light source on the boundary of a circular domain. We then find the number of cameras necessary to distinguish between two circular objects in a circular or rectangular domain. Finally, we use Matlab to simulate the polygonal mesh formed from distributing cameras and light sources on a circular domain. Using this, we compute the number of polygons in the mesh and the maximum polygon area to give us information about the accuracy of the configuration. We close with summary and conclusions, and pointers to possible future research directions.

How long will asteroids on retrograde orbits survive?

NASA Astrophysics Data System (ADS)

Kankiewicz, Paweł; Włodarczyk, Ireneusz

2018-05-01

Generally, a common scenario for the origin of minor planets with high orbital inclinations does not exist. This applies especially to objects whose orbital inclinations are much greater than 90° (retrograde asteroids). Since the discovery of Dioretsa in 1999, approximately 100 small bodies now are classified as retrograde asteroids. A small number of them were reclassified as comets, due to cometary activity. There are only 25 multi-opposition retrograde asteroids, with a relatively large number of observations and well-determined orbits. We studied the orbital evolution of numbered and multi-opposition retrograde asteroids by numerical integration up to 1 Gy forward and backward in time. Additionally, we analyzed the propagation of orbital elements with the observational errors, determined dynamical lifetimes and studied their chaotic properties. Conclusively, we obtained quantitative parameters describing the long-term stability of orbits relating to the past and the future. In turn, we were able to estimate their lifetimes and how long these objects will survive in the Solar System.

The value of qualitative conclusions for the interpretation of Super Soft Source grating spectra

NASA Astrophysics Data System (ADS)

Ness, J.

2017-10-01

High-resolution (grating) X-ray spectra of Super Soft Sources (SSS) contain a large amount of information. Main-stream interpretation approaches apply radiation transport models that, if uniquely constrained by the data, would provide information about temperature and mass of the underlying white dwarf and chemical composition of the ejecta. The complexity of the grating spectra has so far prohibited unique conclusions because realistic effects such as inhomogeneous density distribution, asymmetric ejecta, expansion etc open up an almost infinite number of dimensions to the problem. Further development of models are with no doubt needed, but unbiased inspection of the observed spectra is needed to narrow down where new developments are needed. In this presentation I illustrate how much we can already conclude without any models and remind of the value of qualitative conclusions. I show examples of past and recent observations and how comparisons with other observations help us to reveal common mechanisms. Albeit the high degree of complexity, some astonishing similarities between very different systems are found which can tailor the development of new models.

Criteria for retrograde rotation of accreting black holes

NASA Astrophysics Data System (ADS)

Mikhailov, A. G.; Piotrovich, M. Yu; Gnedin, Yu N.; Natsvlishvili, T. M.; Buliga, S. D.

2018-06-01

Rotating supermassive black holes produce jets and their origin is connected to the magnetic field that is generated by accreting matter flow. There is a point of view that electromagnetic fields around rotating black holes are brought to the hole by accretion. In this situation the prograde accreting discs produce weaker large-scale black hole threading magnetic fields, implying weaker jets than in retrograde regimes. The basic goal of this paper is to find the best candidates for retrograde accreting systems in observed active galactic nuclei. We show that active galactic nuclei with low Eddington ratio are really the best candidates for retrograde systems. This conclusion is obtained for kinetically dominated Fanaroff-Riley class II radio galaxies, flat-spectrum radio-loud narrow-line Seyfert I galaxies and a number of nearby galaxies. Our conclusion is that the best candidates for retrograde systems are the noticeable population of active galactic nuclei in the Universe. This result corresponds to the conclusion that in the merging process the interaction of merging black holes with a retrograde circumbinary disc is considerably more effective for shrinking the binary system.

Large-Scale Advanced Prop-Fan (LAP)

NASA Technical Reports Server (NTRS)

Degeorge, C. L.

1988-01-01

In recent years, considerable attention has been directed toward improving aircraft fuel efficiency. Analytical studies and research with wind tunnel models have demonstrated that the high inherent efficiency of low speed turboprop propulsion systems may now be extended to the Mach .8 flight regime of today's commercial airliners. This can be accomplished with a propeller, employing a large number of thin highly swept blades. The term Prop-Fan has been coined to describe such a propulsion system. In 1983 the NASA-Lewis Research Center contracted with Hamilton Standard to design, build and test a near full scale Prop-Fan, designated the Large Scale Advanced Prop-Fan (LAP). This report provides a detailed description of the LAP program. The assumptions and analytical procedures used in the design of Prop-Fan system components are discussed in detail. The manufacturing techniques used in the fabrication of the Prop-Fan are presented. Each of the tests run during the course of the program are also discussed and the major conclusions derived from them stated.

Pushing configuration-interaction to the limit: Towards massively parallel MCSCF calculations

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

Vogiatzis, Konstantinos D.; Ma, Dongxia; Olsen, Jeppe

A new large-scale parallel multiconfigurational self-consistent field (MCSCF) implementation in the open-source NWChem computational chemistry code is presented. The generalized active space approach is used to partition large configuration interaction (CI) vectors and generate a sufficient number of batches that can be distributed to the available cores. Massively parallel CI calculations with large active spaces can be performed. The new parallel MCSCF implementation is tested for the chromium trimer and for an active space of 20 electrons in 20 orbitals, which can now routinely be performed. Unprecedented CI calculations with an active space of 22 electrons in 22 orbitals formore » the pentacene systems were performed and a single CI iteration calculation with an active space of 24 electrons in 24 orbitals for the chromium tetramer was possible. In conclusion, the chromium tetramer corresponds to a CI expansion of one trillion Slater determinants (914 058 513 424) and is the largest conventional CI calculation attempted up to date.« less

Pushing configuration-interaction to the limit: Towards massively parallel MCSCF calculations

DOE PAGES

Vogiatzis, Konstantinos D.; Ma, Dongxia; Olsen, Jeppe; ...

2017-11-14

A new large-scale parallel multiconfigurational self-consistent field (MCSCF) implementation in the open-source NWChem computational chemistry code is presented. The generalized active space approach is used to partition large configuration interaction (CI) vectors and generate a sufficient number of batches that can be distributed to the available cores. Massively parallel CI calculations with large active spaces can be performed. The new parallel MCSCF implementation is tested for the chromium trimer and for an active space of 20 electrons in 20 orbitals, which can now routinely be performed. Unprecedented CI calculations with an active space of 22 electrons in 22 orbitals formore » the pentacene systems were performed and a single CI iteration calculation with an active space of 24 electrons in 24 orbitals for the chromium tetramer was possible. In conclusion, the chromium tetramer corresponds to a CI expansion of one trillion Slater determinants (914 058 513 424) and is the largest conventional CI calculation attempted up to date.« less

Influenza newspaper reports and the influenza epidemic: an observational study in Fukuoka City, Japan

PubMed Central

Hagihara, Akihito; Onozuka, Daisuke; Miyazaki, Shougo; Abe, Takeru

2015-01-01

Objectives We examined whether the weekly number of newspaper articles reporting on influenza was related to the incidence of influenza in a large city. Design Prospective, non-randomised, observational study. Setting Registry data of influenza cases in Fukuoka City, Japan. Participants A total of 83 613 cases of influenza cases that occurred between October 1999 and March 2007 in Fukuoka City, Japan. Main outcome measure A linear model with autoregressive time series errors was fitted to time series data on the incidence of influenza and the accumulated number of influenza-related newspaper articles with different time lags in Fukuoka City, Japan. In order to obtain further evidence that the number of newspaper articles a week with specific time lags is related to the incidence of influenza, Granger causality was also tested. Results Of the 16 models including ‘number of newspaper articles’ with different time lags between 2 and 17 weeks (xt-2 to t-17), the β coefficients of ‘number of newspaper articles’ at time lags between t-5 and t-13 were significant. However, the β coefficients of ‘number of newspaper articles’ that are significant with respect to the Granger causality tests (p<0.05) were the weekly number of newspaper articles at time lags between t-6 and t-10 (time shift of 10 weeks, β=−0.301, p<0.01; time shift of 9 weeks, β=−0.200, p<0.01; time shift of 8 weeks, β=−0.156, p<0.01; time shift of 7 weeks, β=−0.122, p<0.05; time shift of 6 weeks, β=−0.113, p<0.05). Conclusions We found that the number of newspaper articles reporting on influenza in a week was related to the incidence of influenza 6–10 weeks after media coverage in a large city in Japan. PMID:26719323

Experimental Non-Violation of the Bell Inequality

NASA Astrophysics Data System (ADS)

Palmer, Tim

2018-05-01

A finite non-classical framework for physical theory is described which challenges the conclusion that the Bell Inequality has been shown to have been violated experimentally, even approximately. This framework postulates the universe as a deterministic locally causal system evolving on a measure-zero fractal-like geometry $I_U$ in cosmological state space. Consistent with the assumed primacy of $I_U$, and $p$-adic number theory, a non-Euclidean (and hence non-classical) metric $g_p$ is defined on cosmological state space, where $p$ is a large but finite Pythagorean prime. Using number-theoretic properties of spherical triangles, the inequalities violated experimentally are shown to be $g_p$-distant from the CHSH inequality, whose violation would rule out local realism. This result fails in the singular limit $p=\\infty$, at which $g_p$ is Euclidean. Broader implications are discussed.

Stimulated neutrino transformation with sinusoidal density profiles

DOE PAGES

Kneller, J. P.; McLaughlin, G. C.; Patton, K. M.

2013-03-28

Large amplitude oscillations between the states of a quantum system can be stimulated by sinusoidal external potentials with frequencies that are similar to the energy level splitting of the states or a fraction thereof. Situations where the applied frequency is equal to an integer fraction of the energy level splittings are known as parametric resonances. We investigate this effect for neutrinos both analytically and numerically for the case of arbitrary numbers of neutrino flavors. We look for environments where the effect may be observed and find that supernovae are the one realistic possibility due to the necessity of both largemore » densities and large amplitude fluctuations. In conclusion, the comparison of numerical and analytical results of neutrino propagation through a model supernova reveals that it is possible to predict the locations and strengths of the stimulated transitions that occur.« less

Phylogenetic search through partial tree mixing

PubMed Central

2012-01-01

Background Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques. Results When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda Conclusions The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution. PMID:23320449

Functional analysis of a large set of BRCA2 exon 7 variants highlights the predictive value of hexamer scores in detecting alterations of exonic splicing regulatory elements.

PubMed

Di Giacomo, Daniela; Gaildrat, Pascaline; Abuli, Anna; Abdat, Julie; Frébourg, Thierry; Tosi, Mario; Martins, Alexandra

2013-11-01

Exonic variants can alter pre-mRNA splicing either by changing splice sites or by modifying splicing regulatory elements. Often these effects are difficult to predict and are only detected by performing RNA analyses. Here, we analyzed, in a minigene assay, 26 variants identified in the exon 7 of BRCA2, a cancer predisposition gene. Our results revealed eight new exon skipping mutations in this exon: one directly altering the 5' splice site and seven affecting potential regulatory elements. This brings the number of splicing regulatory mutations detected in BRCA2 exon 7 to a total of 11, a remarkably high number considering the total number of variants reported in this exon (n = 36), all tested in our minigene assay. We then exploited this large set of splicing data to test the predictive value of splicing regulator hexamers' scores recently established by Ke et al. (). Comparisons of hexamer-based predictions with our experimental data revealed high sensitivity in detecting variants that increased exon skipping, an important feature for prescreening variants before RNA analysis. In conclusion, hexamer scores represent a promising tool for predicting the biological consequences of exonic variants and may have important applications for the interpretation of variants detected by high-throughput sequencing. © 2013 WILEY PERIODICALS, INC.

Sperm competition dynamics: ejaculate fertilising efficiency changes differentially with time

PubMed Central

2008-01-01

Background A fundamental challenge in evolutionary biology is to resolve the mechanisms that maintain paternity a hypervariable fitness component. Because females are often sexually promiscuous, this challenge hinges on establishing the mechanisms through which the ejaculates of different males compete for fertilisation (sperm competition). The competitive quality of an ejaculate is mediated by the relative number of live sperm and their motile performance. The differential rate at which rival ejaculates lose their fertilising efficiency over time is therefore expected to influence the outcome of sperm competition. Results Here, we artificially inseminated into sets of replicate domestic hens, Gallus gallus domesticus, experimentally engineered heterospermic ejaculates containing a large number of low-quality sperm from one male, and a lower number of high-quality sperm from another male. Large, low-quality ejaculates fertilised the first eggs produced after insemination, but small, high-quality ejaculates prevailed in the long run despite their numerical disadvantage. Conclusion Together, these results provide the first experimental demonstration that the relative competitive value of an ejaculate changes drastically over the time during which competing ejaculates are stored within the reproductive tract of a female, resulting in a marked temporal pattern of variation in paternity. A high level of replication makes these results robust. However, our study was restricted to few males of a well characterised study population, and future work should explore the generality of these results. PMID:19087292

Variability of dental cone beam CT grey values for density estimations

PubMed Central

Pauwels, R; Nackaerts, O; Bellaiche, N; Stamatakis, H; Tsiklakis, K; Walker, A; Bosmans, H; Bogaerts, R; Jacobs, R; Horner, K

2013-01-01

Objective The aim of this study was to investigate the use of dental cone beam CT (CBCT) grey values for density estimations by calculating the correlation with multislice CT (MSCT) values and the grey value error after recalibration. Methods A polymethyl methacrylate (PMMA) phantom was developed containing inserts of different density: air, PMMA, hydroxyapatite (HA) 50 mg cm−3, HA 100, HA 200 and aluminium. The phantom was scanned on 13 CBCT devices and 1 MSCT device. Correlation between CBCT grey values and CT numbers was calculated, and the average error of the CBCT values was estimated in the medium-density range after recalibration. Results Pearson correlation coefficients ranged between 0.7014 and 0.9996 in the full-density range and between 0.5620 and 0.9991 in the medium-density range. The average error of CBCT voxel values in the medium-density range was between 35 and 1562. Conclusion Even though most CBCT devices showed a good overall correlation with CT numbers, large errors can be seen when using the grey values in a quantitative way. Although it could be possible to obtain pseudo-Hounsfield units from certain CBCTs, alternative methods of assessing bone tissue should be further investigated. Advances in knowledge The suitability of dental CBCT for density estimations was assessed, involving a large number of devices and protocols. The possibility for grey value calibration was thoroughly investigated. PMID:23255537

Conflict of Interest Policies for Organizations Producing a Large Number of Clinical Practice Guidelines

PubMed Central

Norris, Susan L.; Holmer, Haley K.; Burda, Brittany U.; Ogden, Lauren A.; Fu, Rongwei

2012-01-01

Background Conflict of interest (COI) of clinical practice guideline (CPG) sponsors and authors is an important potential source of bias in CPG development. The objectives of this study were to describe the COI policies for organizations currently producing a significant number of CPGs, and to determine if these policies meet 2011 Institute of Medicine (IOM) standards. Methodology/Principal Findings We identified organizations with five or more guidelines listed in the National Guideline Clearinghouse between January 1, 2009 and November 5, 2010. We obtained the COI policy for each organization from publicly accessible sources, most often the organization's website, and compared those polices to IOM standards related to COI. 37 organizations fulfilled our inclusion criteria, of which 17 (46%) had a COI policy directly related to CPGs. These COI policies varied widely with respect to types of COI addressed, from whom disclosures were collected, monetary thresholds for disclosure, approaches to management, and updating requirements. Not one organization's policy adhered to all seven of the IOM standards that were examined, and nine organizations did not meet a single one of the standards. Conclusions/Significance COI policies among organizations producing a large number of CPGs currently do not measure up to IOM standards related to COI disclosure and management. CPG developers need to make significant improvements in these policies and their implementation in order to optimize the quality and credibility of their guidelines. PMID:22629391

Efficient discovery of responses of proteins to compounds using active learning

PubMed Central

2014-01-01

Background Drug discovery and development has been aided by high throughput screening methods that detect compound effects on a single target. However, when using focused initial screening, undesirable secondary effects are often detected late in the development process after significant investment has been made. An alternative approach would be to screen against undesired effects early in the process, but the number of possible secondary targets makes this prohibitively expensive. Results This paper describes methods for making this global approach practical by constructing predictive models for many target responses to many compounds and using them to guide experimentation. We demonstrate for the first time that by jointly modeling targets and compounds using descriptive features and using active machine learning methods, accurate models can be built by doing only a small fraction of possible experiments. The methods were evaluated by computational experiments using a dataset of 177 assays and 20,000 compounds constructed from the PubChem database. Conclusions An average of nearly 60% of all hits in the dataset were found after exploring only 3% of the experimental space which suggests that active learning can be used to enable more complete characterization of compound effects than otherwise affordable. The methods described are also likely to find widespread application outside drug discovery, such as for characterizing the effects of a large number of compounds or inhibitory RNAs on a large number of cell or tissue phenotypes. PMID:24884564

THE RESULTS OF THE SERUM TREATMENT IN THIRTEEN HUNDRED CASES OF EPIDEMIC MENINGITIS

PubMed Central

Flexner, Simon

1913-01-01

The data brought together in this report have been gathered from a wide territory and for a period extending over several years. The antimeningitis serum was first employed in 1906 and the latest figures relating to its use included in this report were furnished in 1912. There is no longer doubt that the serum has come to be applied under conditions fairly representing all known manifestations of epidemic meningitis. Hence the test of the serum treatment may be regarded as having been a rigorous one. The initial difficulties surrounding the administration by direct subdural injection have been largely overcome and doubtless will be still further mastered. Already the serum is being successfully applied in private as well as in hospital practice. This gain will probably be reflected in a still further diminution of the mortality since early injection plays such a large part in determining the results achieved. The 1,300 cases studied in this report are a part only of a far greater number of cases actually treated with the serum supplied by the Rockefeller Institute. It was not found possible to secure histories of all the cases treated; but there is no reason to suppose that the results of the analysis would have been essentially different if reports of a still larger number of cases had been returned. The decision arrived at is not based upon statistical computations alone, but upon objective data as well that are not readily misinterpreted. The conclusion that follows was first stated in 1909 as the result of an analysis of 400 serum-treated cases. It is supported by the study of the larger series of cases just presented. "In view of the various considerations presented, the conclusion may be drawn that the antimeningitis serum, when used by the subdural method of injection, in suitable doses and at proper intervals, is capable of reducing the period of illness; of preventing, in large measure, the chronic lesions and types of the infection; of bringing about complete restoration of health, in all but a very small number of the recovered, thus lessening the serious, deforming, and permanent consequences of meningitis; and of greatly diminishing the fatalities due to the disease." PMID:19867668

CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations

PubMed Central

Wang, Xihong; Zheng, Zhuqing; Cai, Yudong; Chen, Ting; Li, Chao; Fu, Weiwei

2017-01-01

Abstract Background The increasing amount of sequencing data available for a wide variety of species can be theoretically used for detecting copy number variations (CNVs) at the population level. However, the growing sample sizes and the divergent complexity of nonhuman genomes challenge the efficiency and robustness of current human-oriented CNV detection methods. Results Here, we present CNVcaller, a read-depth method for discovering CNVs in population sequencing data. The computational speed of CNVcaller was 1–2 orders of magnitude faster than CNVnator and Genome STRiP for complex genomes with thousands of unmapped scaffolds. CNV detection of 232 goats required only 1.4 days on a single compute node. Additionally, the Mendelian consistency of sheep trios indicated that CNVcaller mitigated the influence of high proportions of gaps and misassembled duplications in the nonhuman reference genome assembly. Furthermore, multiple evaluations using real sheep and human data indicated that CNVcaller achieved the best accuracy and sensitivity for detecting duplications. Conclusions The fast generalized detection algorithms included in CNVcaller overcome prior computational barriers for detecting CNVs in large-scale sequencing data with complex genomic structures. Therefore, CNVcaller promotes population genetic analyses of functional CNVs in more species. PMID:29220491

FOUNTAIN: A JAVA open-source package to assist large sequencing projects

PubMed Central

Buerstedde, Jean-Marie; Prill, Florian

2001-01-01

Background Better automation, lower cost per reaction and a heightened interest in comparative genomics has led to a dramatic increase in DNA sequencing activities. Although the large sequencing projects of specialized centers are supported by in-house bioinformatics groups, many smaller laboratories face difficulties managing the appropriate processing and storage of their sequencing output. The challenges include documentation of clones, templates and sequencing reactions, and the storage, annotation and analysis of the large number of generated sequences. Results We describe here a new program, named FOUNTAIN, for the management of large sequencing projects . FOUNTAIN uses the JAVA computer language and data storage in a relational database. Starting with a collection of sequencing objects (clones), the program generates and stores information related to the different stages of the sequencing project using a web browser interface for user input. The generated sequences are subsequently imported and annotated based on BLAST searches against the public databases. In addition, simple algorithms to cluster sequences and determine putative polymorphic positions are implemented. Conclusions A simple, but flexible and scalable software package is presented to facilitate data generation and storage for large sequencing projects. Open source and largely platform and database independent, we wish FOUNTAIN to be improved and extended in a community effort. PMID:11591214

Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders

PubMed Central

Pfundt, Rolph; del Rosario, Marisol; Vissers, Lisenka E.L.M.; Kwint, Michael P.; Janssen, Irene M.; de Leeuw, Nicole; Yntema, Helger G.; Nelen, Marcel R.; Lugtenberg, Dorien; Kamsteeg, Erik-Jan; Wieskamp, Nienke; Stegmann, Alexander P.A.; Stevens, Servi J.C.; Rodenburg, Richard J.T.; Simons, Annet; Mensenkamp, Arjen R.; Rinne, Tuula; Gilissen, Christian; Scheffer, Hans; Veltman, Joris A.; Hehir-Kwa, Jayne Y.

2017-01-01

Purpose: Copy-number variation is a common source of genomic variation and an important genetic cause of disease. Microarray-based analysis of copy-number variants (CNVs) has become a first-tier diagnostic test for patients with neurodevelopmental disorders, with a diagnostic yield of 10–20%. However, for most other genetic disorders, the role of CNVs is less clear and most diagnostic genetic studies are generally limited to the study of single-nucleotide variants (SNVs) and other small variants. With the introduction of exome and genome sequencing, it is now possible to detect both SNVs and CNVs using an exome- or genome-wide approach with a single test. Methods: We performed exome-based read-depth CNV screening on data from 2,603 patients affected by a range of genetic disorders for which exome sequencing was performed in a diagnostic setting. Results: In total, 123 clinically relevant CNVs ranging in size from 727 bp to 15.3 Mb were detected, which resulted in 51 conclusive diagnoses and an overall increase in diagnostic yield of ~2% (ranging from 0 to –5.8% per disorder). Conclusions: This study shows that CNVs play an important role in a broad range of genetic disorders and that detection via exome-based CNV profiling results in an increase in the diagnostic yield without additional testing, bringing us closer to single-test genomics. Genet Med advance online publication 27 October 2016 PMID:28574513

Optimizing agent-based transmission models for infectious diseases.

PubMed

Willem, Lander; Stijven, Sean; Tijskens, Engelbert; Beutels, Philippe; Hens, Niel; Broeckhove, Jan

2015-06-02

Infectious disease modeling and computational power have evolved such that large-scale agent-based models (ABMs) have become feasible. However, the increasing hardware complexity requires adapted software designs to achieve the full potential of current high-performance workstations. We have found large performance differences with a discrete-time ABM for close-contact disease transmission due to data locality. Sorting the population according to the social contact clusters reduced simulation time by a factor of two. Data locality and model performance can also be improved by storing person attributes separately instead of using person objects. Next, decreasing the number of operations by sorting people by health status before processing disease transmission has also a large impact on model performance. Depending of the clinical attack rate, target population and computer hardware, the introduction of the sort phase decreased the run time from 26% up to more than 70%. We have investigated the application of parallel programming techniques and found that the speedup is significant but it drops quickly with the number of cores. We observed that the effect of scheduling and workload chunk size is model specific and can make a large difference. Investment in performance optimization of ABM simulator code can lead to significant run time reductions. The key steps are straightforward: the data structure for the population and sorting people on health status before effecting disease propagation. We believe these conclusions to be valid for a wide range of infectious disease ABMs. We recommend that future studies evaluate the impact of data management, algorithmic procedures and parallelization on model performance.

Current and future worldwide prevalence of dependency, its relationship to total population, and dependency ratios.

PubMed Central

Harwood, Rowan H.; Sayer, Avan Aihie; Hirschfeld, Miriam

2004-01-01

OBJECTIVE: To estimate the number of people worldwide requiring daily assistance from another person in carrying out health, domestic or personal tasks. METHODS: Data from the Global Burden of Disease Study were used to calculate the prevalence of severe levels of disability, and consequently, to estimate dependency. Population projections were used to forecast changes over the next 50 years. FINDINGS: The greatest burden of dependency currently falls in sub-Saharan Africa, where the "dependency ratio" (ratio of dependent people to the population of working age) is about 10%, compared with 7-8% elsewhere. Large increases in prevalence are predicted in sub-Saharan Africa, the Middle East, Asia and Latin America of up to 5-fold or 6-fold in some cases. These increases will occur in the context of generally increasing populations, and dependency ratios will increase modestly to about 10%. The dependency ratio will increase more in China (14%) and India (12%) than in other areas with large prevalence increases. Established market economies, especially Europe and Japan, will experience modest increases in the prevalence of dependency (30%), and in the dependency ratio (up to 10%). Former Socialist economies of Europe will have static or declining numbers of dependent people, but will have large increases in the dependency ratio (up to 13%). CONCLUSION: Many countries will be greatly affected by the increasing number of dependent people and will need to identify the human and financial resources to support them. Much improved collection of data on disability and on the needs of caregivers is required. The prevention of disability and provision of support for caregivers needs greater priority. PMID:15259253

Retinal Pigment Epithelial Tears in the Era of Intravitreal Pharmacotherapy: Risk Factors, Pathogenesis, Prognosis and Treatment (An American Ophthalmological Society Thesis)

PubMed Central

Sarraf, David; Joseph, Anthony; Rahimy, Ehsan

2014-01-01

Purpose: To describe the risk factors, pathogenesis, and prognosis of retinal pigment epithelial (RPE) tears and to demonstrate our hypothesis that continued anti–vascular endothelial growth factor (VEGF) therapy after an RPE tear has occurred correlates with improved long-term visual and anatomical outcomes. Methods: We searched a database of 10,089 patients and retrospectively identified a large case series of 56 eyes with neovascular age-related macular degeneration (AMD) complicated by an RPE tear over an 8-year period. Baseline visual acuity (VA) was tabulated and analysis of the RPE tear was performed with multimodal imaging. Follow-up VA, progression of the tear, and severity of fibrosis were evaluated, and each was correlated with number of anti-VEGF injections. Results: Average follow-up for the 56 eyes was 42 months, and mean logMAR VA at baseline was 0.88 (Snellen VA 20/150) with minimal decline over 3 years. LogMAR VA plotted against number of anti-VEGF injections demonstrated that more frequent and cumulative injections correlated with better VA (P<.0001). A greater number of anti-VEGF injections was associated with minimal progression of the RPE tear, reduced fibrosis, and lower risk of a large, end-stage exudative disciform scar. Conclusions: Fifteen to 20% of vascularized pigment epithelial detachments (PEDs) may develop RPE tears after anti-VEGF therapy due to progressive contraction of the type 1 choroidal neovascular membrane in a PED at risk. Continued monitoring of RPE tears for exudative changes warranting anti-VEGF therapy may stabilize VA, improve anatomical outcomes, reduce fibrosis, and decrease the risk of developing a large blinding end-stage exudative disciform scar. PMID:25646033

Acoustic evaluation of the Helmholtz resonator treatment in the NASA Lewis 8- by 6-foot supersonic wind tunnel

NASA Technical Reports Server (NTRS)

Heidelberg, Laurence J.; Gordon, Elliot B.

1989-01-01

The acoustic consequences of sealing the Helmholtz resonators of the NASA Lewis 8- by 6-Foot Supersonic Wind Tunnel (8x6 SWT) were experimentally evaluated. This resonator sealing was proposed in order to avoid entrapment of hydrogen during tests of advanced hydrogen-fueled engines. The resonators were designed to absorb energy in the 4- to 20-Hz range; thus, this investigation is primarily concerned with infrasound. Limited internal and external noise measurements were made at tunnel Mach numbers ranging from 0.5 to 2.0. Although the resonators were part of the acoustic treatment installed because of a community noise problem their sealing did not seem to indicate a reoccurrence of the problem would result. Two factors were key to this conclusion: (1) A large bulk treatment muffler downstream of the resonators was able to make up for much of the attenuation originally provided by the resonators, and (2) there was no noise source in the tunnel test section. The previous community noise problem occurred when a large ramjet was tested in an open-loop tunnel configuration. If a propulsion system producing high noise levels at frequencies of less than 10 Hz were tested, the conclusion on community noise would have to be reevaluated.

Establishing Substantial Equivalence: Metabolomics

NASA Astrophysics Data System (ADS)

Beale, Michael H.; Ward, Jane L.; Baker, John M.

Modern ‘metabolomic’ methods allow us to compare levels of many structurally diverse compounds in an automated fashion across a large number of samples. This technology is ideally suited to screening of populations of plants, including trials where the aim is the determination of unintended effects introduced by GM. A number of metabolomic methods have been devised for the determination of substantial equivalence. We have developed a methodology, using [1H]-NMR fingerprinting, for metabolomic screening of plants and have applied it to the study of substantial equivalence of field-grown GM wheat. We describe here the principles and detail of that protocol as applied to the analysis of flour generated from field plots of wheat. Particular emphasis is given to the downstream data processing and comparison of spectra by multivariate analysis, from which conclusions regarding metabolome changes due to the GM can be assessed against the background of natural variation due to environment.

Quantitative assessment of relative roles of drivers of acute respiratory diseases

PubMed Central

Goswami, Prashant; Baruah, Jurismita

2014-01-01

Several thousands of people, including children, suffer from acute respiratory disease (ARD) every year worldwide. Pro-active planning and mitigation for these diseases require identification of the major drivers in a location-specific manner. While the importance of air pollutants in ARD has been extensively studied and emphasized, the role of weather variables has been less explored. With Delhi with its large population and pollution as a test case, we examine the relative roles of air pollution and weather (cold days) in ARD. It is shown that both the number of cold days and air pollution play important roles in ARD load; however, the number of cold days emerges as the major driver. These conclusions are consistent with analyses for several other states in India. The robust association between ARD load and cold days provides basis for estimating and predicting ARD load through dynamical model, as well as impact of climate change. PMID:25322687

Metallic phases from disordered (2+1)-dimensional quantum electrodynamics

DOE PAGES

Goswami, Pallab; Goldman, Hart; Raghu, S.

2017-06-15

Metallic phases have been observed in several disordered two-dimensional (2D) systems, including thin films near superconductor-insulator transitions and quantum Hall systems near plateau transitions. The existence of 2D metallic phases at zero temperature generally requires an interplay of disorder and interaction effects. Consequently, experimental observations of 2D metallic behavior have largely defied explanation. We formulate a general stability criterion for strongly interacting, massless Dirac fermions against disorder, which describe metallic ground states with vanishing density of states. We show that (2+1)-dimensional quantum electrodynamics (QED 3) with a large, even number of fermion flavors remains metallic in the presence of weakmore » scalar potential disorder due to the dynamic screening of disorder by gauge fluctuations. In conclusion, we also show that QED 3 with weak mass disorder exhibits a stable, dirty metallic phase in which both interactions and disorder play important roles.« less

Handwritten recognition of Tamil vowels using deep learning

NASA Astrophysics Data System (ADS)

Ram Prashanth, N.; Siddarth, B.; Ganesh, Anirudh; Naveen Kumar, Vaegae

2017-11-01

We come across a large volume of handwritten texts in our daily lives and handwritten character recognition has long been an important area of research in pattern recognition. The complexity of the task varies among different languages and it so happens largely due to the similarity between characters, distinct shapes and number of characters which are all language-specific properties. There have been numerous works on character recognition of English alphabets and with laudable success, but regional languages have not been dealt with very frequently and with similar accuracies. In this paper, we explored the performance of Deep Belief Networks in the classification of Handwritten Tamil vowels, and conclusively compared the results obtained. The proposed method has shown satisfactory recognition accuracy in light of difficulties faced with regional languages such as similarity between characters and minute nuances that differentiate them. We can further extend this to all the Tamil characters.

A progress report on estuary modeling by the finite-element method

USGS Publications Warehouse

Gray, William G.

1978-01-01

Various schemes are investigated for finite-element modeling of two-dimensional surface-water flows. The first schemes investigated combine finite-element spatial discretization with split-step time stepping schemes that have been found useful in finite-difference computations. Because of the large number of numerical integrations performed in space and the large sparse matrices solved, these finite-element schemes were found to be economically uncompetitive with finite-difference schemes. A very promising leapfrog scheme is proposed which, when combined with a novel very fast spatial integration procedure, eliminates the need to solve any matrices at all. Additional problems attacked included proper propagation of waves and proper specification of the normal flow-boundary condition. This report indicates work in progress and does not come to a definitive conclusion as to the best approach for finite-element modeling of surface-water problems. The results presented represent findings obtained between September 1973 and July 1976. (Woodard-USGS)

Natural polyreactive IgA antibodies coat the intestinal microbiota

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

Bunker, Jeffrey J.; Erickson, Steven A.; Flynn, Theodore M.

Large quantities of immunoglobulin A (IgA) are constitutively secreted by intestinal plasma cells to coat and contain the commensal microbiota, yet the specificity of these antibodies remains elusive. In this paper, we profiled the reactivities of single murine IgA plasma cells by cloning and characterizing large numbers of monoclonal antibodies. IgAs were not specific to individual bacterial taxa but rather polyreactive, with broad reactivity to a diverse, but defined, subset of microbiota. These antibodies arose at low frequencies among naïve B cells and were selected into the IgA repertoire upon recirculation in Peyer’s patches. This selection process occurred independent ofmore » microbiota or dietary antigens. Furthermore, although some IgAs acquired somatic mutations, these did not substantially influence their reactivity. In conclusion, these findings reveal an endogenous mechanism driving homeostatic production of polyreactive IgAs with innate specificity to microbiota.« less

Propulsion of space ships by nuclear explosion

NASA Astrophysics Data System (ADS)

Linhart, J. G.; Kravárik, J.

2005-01-01

Recent progress in the research on deuterium-tritium (D-T) inertially confined microexplosions encourages one to reconsider the nuclear propulsion of spaceships based on the concept originally proposed in the Orion project. We discuss first the acceleration of medium-sized spaceships by D-T explosions whose output is in the range of 0.1 10 t of TNT. The launching of such a ship into an Earth orbit or beyond by a large nuclear explosion in an underground cavity is sketched out in the second section of the paper, and finally we consider a hypothetical Mars mission based on these concepts. In the conclusion it is argued that propulsion based on the Orion concept only is not the best method for interplanetary travel owing to the very large number of nuclear explosion required. A combination of a super gun and subsequent rocket propulsion using advanced chemical fuels appears to be the best solution for space flights of the near future.

TabSQL: a MySQL tool to facilitate mapping user data to public databases

PubMed Central

2010-01-01

Background With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. Results We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. Conclusions TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data. PMID:20573251

Natural polyreactive IgA antibodies coat the intestinal microbiota

DOE PAGES

Bunker, Jeffrey J.; Erickson, Steven A.; Flynn, Theodore M.; ...

2017-09-28

Large quantities of immunoglobulin A (IgA) are constitutively secreted by intestinal plasma cells to coat and contain the commensal microbiota, yet the specificity of these antibodies remains elusive. In this paper, we profiled the reactivities of single murine IgA plasma cells by cloning and characterizing large numbers of monoclonal antibodies. IgAs were not specific to individual bacterial taxa but rather polyreactive, with broad reactivity to a diverse, but defined, subset of microbiota. These antibodies arose at low frequencies among naïve B cells and were selected into the IgA repertoire upon recirculation in Peyer’s patches. This selection process occurred independent ofmore » microbiota or dietary antigens. Furthermore, although some IgAs acquired somatic mutations, these did not substantially influence their reactivity. In conclusion, these findings reveal an endogenous mechanism driving homeostatic production of polyreactive IgAs with innate specificity to microbiota.« less

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

Goswami, Pallab; Goldman, Hart; Raghu, S.

Metallic phases have been observed in several disordered two-dimensional (2D) systems, including thin films near superconductor-insulator transitions and quantum Hall systems near plateau transitions. The existence of 2D metallic phases at zero temperature generally requires an interplay of disorder and interaction effects. Consequently, experimental observations of 2D metallic behavior have largely defied explanation. We formulate a general stability criterion for strongly interacting, massless Dirac fermions against disorder, which describe metallic ground states with vanishing density of states. We show that (2+1)-dimensional quantum electrodynamics (QED 3) with a large, even number of fermion flavors remains metallic in the presence of weakmore » scalar potential disorder due to the dynamic screening of disorder by gauge fluctuations. In conclusion, we also show that QED 3 with weak mass disorder exhibits a stable, dirty metallic phase in which both interactions and disorder play important roles.« less

Thermoelectric properties of semiconductor nanowire networks

DOE PAGES

Roslyak, Oleksiy; Piryatinski, Andrei

2016-03-28

To examine the thermoelectric (TE) properties of a semiconductor nanowire (NW) network, we propose a theoretical approach mapping the TE network on a two-port network. In contrast to a conventional single-port (i.e., resistor)network model, our model allows for large scale calculations showing convergence of TE figure of merit, ZT, with an increasing number of junctions. Using this model, numerical simulations are performed for the Bi 2Te 3 branched nanowire (BNW) and Cayley tree NW (CTNW) network. We find that the phonon scattering at the network junctions plays a dominant role in enhancing the network ZT. Specifically, disordered BNW and CTNWmore » demonstrate an order of magnitude higher ZT enhancement compared to their ordered counterparts. Formation of preferential TE pathways in CTNW makes the network effectively behave as its BNW counterpart. In conclusion, we provide formalism for simulating large scale nanowire networks hinged upon experimentally measurable TE parameters of a single T-junction.« less

Rapidly Measuring the Speed of Unconscious Learning: Amnesics Learn Quickly and Happy People Slowly

PubMed Central

Dienes, Zoltan; Baddeley, Roland J.; Jansari, Ashok

2012-01-01

Background We introduce a method for quickly determining the rate of implicit learning. Methodology/Principal Findings The task involves making a binary prediction for a probabilistic sequence over 10 minutes; from this it is possible to determine the influence of events of a different number of trials in the past on the current decision. This profile directly reflects the learning rate parameter of a large class of learning algorithms including the delta and Rescorla-Wagner rules. To illustrate the use of the method, we compare a person with amnesia with normal controls and we compare people with induced happy and sad moods. Conclusions/Significance Learning on the task is likely both associative and implicit. We argue theoretically and demonstrate empirically that both amnesia and also transient negative moods can be associated with an especially large learning rate: People with amnesia can learn quickly and happy people slowly. PMID:22457759

Extremes in Otolaryngology Resident Surgical Case Numbers: An Update.

PubMed

Baugh, Tiffany P; Franzese, Christine B

2017-06-01

Objectives The purpose of this study is to examine the effect of minimum case numbers on otolaryngology resident case log data and understand differences in minimum, mean, and maximum among certain procedures as a follow-up to a prior study. Study Design Cross-sectional survey using a national database. Setting Academic otolaryngology residency programs. Subjects and Methods Review of otolaryngology resident national data reports from the Accreditation Council for Graduate Medical Education (ACGME) resident case log system performed from 2004 to 2015. Minimum, mean, standard deviation, and maximum values for total number of supervisor and resident surgeon cases and for specific surgical procedures were compared. Results The mean total number of resident surgeon cases for residents graduating from 2011 to 2015 ranged from 1833.3 ± 484 in 2011 to 2072.3 ± 548 in 2014. The minimum total number of cases ranged from 826 in 2014 to 1004 in 2015. The maximum total number of cases increased from 3545 in 2011 to 4580 in 2015. Multiple key indicator procedures had less than the required minimum reported in 2015. Conclusion Despite the ACGME instituting required minimum numbers for key indicator procedures, residents have graduated without meeting these minimums. Furthermore, there continues to be large variations in the minimum, mean, and maximum numbers for many procedures. Variation among resident case numbers is likely multifactorial. Ensuring proper instruction on coding and case role as well as emphasizing frequent logging by residents will ensure programs have the most accurate data to evaluate their case volume.

Customer relationship management in the contract pharmaceutical industry: an exploratory study for measuring success.

PubMed

Kros, John F; Nadler, Scott; Molis, Justin

2007-01-01

Managing customer relationships is a very important issue in business-to-business markets. This research investigates the growing number of available resources defining Customer Relationship Management (CRM) efforts, and how they are being applied within the Contract Pharmaceutical Manufacturing industry. Exploratory study results using face-to-face and telephone questionnaires based on four criteria for rating a company's CRM efforts are presented. Data was collected from large Contract Pharmaceutical Manufacturing companies in the US market. The results and conclusions are discussed relating how the Contract Pharmaceutical Manufacturing industry is implementing CRM including some potential steps to take when considering a CRM initiative.

Laser Embossing of Micro-and Submicrometer Surface Structures in Copper

NASA Astrophysics Data System (ADS)

Ehrhardt, Martin; Lorenz, Pierre; Frost, Frank; Zimmer, Klaus

Micro- and submicrometer structures have been transferred from nickel foils into solid copper surfaces by laser microembossing. The developed arrangement for laser microembossing allows a large-area replication using multi- pulse laser scanning scheme, guaranties a low contamination of the embossed surface and enables the utilization of thick workpieces. In the micrometer range the replicated patterns feature a high accuracy regarding the shape. A significant difference between the master and the replication pattern could be observed for the laser embossing of submicrometer patterns. In conclusion, the results show that the proposed laser embossing process is a promising method with a number of applications in microengineering.

Nd and Sm isotopic composition of spent nuclear fuels from three material test reactors

DOE PAGES

Sharp, Nicholas; Ticknor, Brian W.; Bronikowski, Michael; ...

2016-11-17

Rare earth elements such as neodymium and samarium are ideal for probing the neutron environment that spent nuclear fuels are exposed to in nuclear reactors. The large number of stable isotopes can provide distinct isotopic signatures for differentiating the source material for nuclear forensic investigations. The rare-earth elements were isolated from the high activity fuel matrix via ion exchange chromatography in a shielded cell. The individual elements were then separated using cation exchange chromatography. In conclusion, the neodymium and samarium aliquots were analyzed via MC–ICP–MS, resulting in isotopic compositions with a precision of 0.01–0.3%.

Nd and Sm isotopic composition of spent nuclear fuels from three material test reactors

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

Sharp, Nicholas; Ticknor, Brian W.; Bronikowski, Michael

Rare earth elements such as neodymium and samarium are ideal for probing the neutron environment that spent nuclear fuels are exposed to in nuclear reactors. The large number of stable isotopes can provide distinct isotopic signatures for differentiating the source material for nuclear forensic investigations. The rare-earth elements were isolated from the high activity fuel matrix via ion exchange chromatography in a shielded cell. The individual elements were then separated using cation exchange chromatography. In conclusion, the neodymium and samarium aliquots were analyzed via MC–ICP–MS, resulting in isotopic compositions with a precision of 0.01–0.3%.

Objective comparison of particle tracking methods.

PubMed

Chenouard, Nicolas; Smal, Ihor; de Chaumont, Fabrice; Maška, Martin; Sbalzarini, Ivo F; Gong, Yuanhao; Cardinale, Janick; Carthel, Craig; Coraluppi, Stefano; Winter, Mark; Cohen, Andrew R; Godinez, William J; Rohr, Karl; Kalaidzidis, Yannis; Liang, Liang; Duncan, James; Shen, Hongying; Xu, Yingke; Magnusson, Klas E G; Jaldén, Joakim; Blau, Helen M; Paul-Gilloteaux, Perrine; Roudot, Philippe; Kervrann, Charles; Waharte, François; Tinevez, Jean-Yves; Shorte, Spencer L; Willemse, Joost; Celler, Katherine; van Wezel, Gilles P; Dan, Han-Wei; Tsai, Yuh-Show; Ortiz de Solórzano, Carlos; Olivo-Marin, Jean-Christophe; Meijering, Erik

2014-03-01

Particle tracking is of key importance for quantitative analysis of intracellular dynamic processes from time-lapse microscopy image data. Because manually detecting and following large numbers of individual particles is not feasible, automated computational methods have been developed for these tasks by many groups. Aiming to perform an objective comparison of methods, we gathered the community and organized an open competition in which participating teams applied their own methods independently to a commonly defined data set including diverse scenarios. Performance was assessed using commonly defined measures. Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to notable practical conclusions for users and developers.

Too much of a good thing? An observational study of prolific authors.

PubMed

Wager, Elizabeth; Singhvi, Sanjay; Kleinert, Sabine

2015-01-01

Introduction. Researchers' productivity is usually measured in terms of their publication output. A minimum number of publications is required for some medical qualifications and professional appointments. However, authoring an unfeasibly large number of publications might indicate disregard of authorship criteria or even fraud. We therefore examined publication patterns of highly prolific authors in 4 medical specialties. Methods. We analysed Medline publications from 2008-12 using bespoke software to disambiguate individual authors focusing on 4 discrete topics (to further reduce the risk of combining publications from authors with the same name and affiliation). This enabled us to assess the number and type of publications per author per year. Results. While 99% of authors were listed on fewer than 20 publications in the 5-year period, 24 authors in the chosen areas were listed on at least 25 publications in a single year (i.e., >1 publication per 10 working days). Types of publication by the prolific authors varied but included substantial numbers of original research papers (not simply editorials or letters). Conclusions. Institutions and funders should be alert to unfeasibly prolific authors when measuring and creating incentives for researcher productivity.

Optimal spatial sampling techniques for ground truth data in microwave remote sensing of soil moisture

NASA Technical Reports Server (NTRS)

Rao, R. G. S.; Ulaby, F. T.

1977-01-01

The paper examines optimal sampling techniques for obtaining accurate spatial averages of soil moisture, at various depths and for cell sizes in the range 2.5-40 acres, with a minimum number of samples. Both simple random sampling and stratified sampling procedures are used to reach a set of recommended sample sizes for each depth and for each cell size. Major conclusions from statistical sampling test results are that (1) the number of samples required decreases with increasing depth; (2) when the total number of samples cannot be prespecified or the moisture in only one single layer is of interest, then a simple random sample procedure should be used which is based on the observed mean and SD for data from a single field; (3) when the total number of samples can be prespecified and the objective is to measure the soil moisture profile with depth, then stratified random sampling based on optimal allocation should be used; and (4) decreasing the sensor resolution cell size leads to fairly large decreases in samples sizes with stratified sampling procedures, whereas only a moderate decrease is obtained in simple random sampling procedures.

Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae).

PubMed

Krahulcová, Anna; Trávnícek, Pavel; Krahulec, František; Rejmánek, Marcel

2017-04-01

Aesculus L. (horse chestnut, buckeye) is a genus of 12-19 extant woody species native to the temperate Northern Hemisphere. This genus is known for unusually large seeds among angiosperms. While chromosome counts are available for many Aesculus species, only one has had its genome size measured. The aim of this study is to provide more genome size data and analyse the relationship between genome size and seed mass in this genus. Chromosome numbers in root tip cuttings were confirmed for four species and reported for the first time for three additional species. Flow cytometric measurements of 2C nuclear DNA values were conducted on eight species, and mean seed mass values were estimated for the same taxa. The same chromosome number, 2 n = 40, was determined in all investigated taxa. Original measurements of 2C values for seven Aesculus species (eight taxa), added to just one reliable datum for A. hippocastanum , confirmed the notion that the genome size in this genus with relatively large seeds is surprisingly low, ranging from 0·955 pg 2C -1 in A. parviflora to 1·275 pg 2C -1 in A. glabra var. glabra. The chromosome number of 2 n = 40 seems to be conclusively the universal 2 n number for non-hybrid species in this genus. Aesculus genome sizes are relatively small, not only within its own family, Sapindaceae, but also within woody angiosperms. The genome sizes seem to be distinct and non-overlapping among the four major Aesculus clades. These results provide an extra support for the most recent reconstruction of Aesculus phylogeny. The correlation between the 2C values and seed masses in examined Aesculus species is slightly negative and not significant. However, when the four major clades are treated separately, there is consistent positive association between larger genome size and larger seed mass within individual lineages. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

MR-guided focused ultrasound robot for performing experiments on large animals

NASA Astrophysics Data System (ADS)

Mylonas, N.; Damianou, C.

2011-09-01

Introduction: In this paper an experimental MRI-guided focused ultrasound robot for large animals is presented. Materials and methods: A single element spherically focused transducer of 4 cm diameter, focusing at 10 cm and operating at 1 MHz was used. A positioning device was developed in order to scan the ultrasound transducer for performing MR-guided focused ultrasound experiments in large animals such as pig, sheep and dog. The positioning device incorporates only MRI compatible materials such as piezoelectric motors, Acrylonitrile Butadiene Styrene (ABS) plastic, brass screws, and brass pulleys. The system is manufactured automatically using a rapid prototyping system. Results: The system was tested successfully in a number of animals for various tasks (creation of single lesions, creation of overlapping lesions, and MR compatibility). Conclusions: A simple, cost effective, portable positioning device has been developed which can be used in virtually any clinical MRI scanner since it can be sited on the scanner's table. The propagation of HIFU can be via a lateral or superior-inferior approach. This system has the potential to be marketed as a cost effective solution for performing experiments in small and large animals.

Enhancing the Accuracy of Platelet to Lymphocyte Ratio after Adjustment for Large Platelet Count: A Pilot Study in Breast Cancer Patients

PubMed Central

Seretis, Charalampos; Seretis, Fotios; Lagoudianakis, Emmanuel; Politou, Marianna; Gemenetzis, George; Salemis, Nikolaos S.

2012-01-01

Background. The objective of our study is to investigate the potential effect of adjusting preoperative platelet to lymphocyte ratio, an emerging biomarker of survival in cancer patients, for the fraction of large platelets. Methods. A total of 79 patients with breast neoplasias, 44 with fibroadenomas, and 35 with invasive ductal carcinoma were included in the study. Both conventional platelet to lymphocyte ratio (PLR) and the adjusted marker, large platelet to lymphocyte ratio (LPLR), were correlated with laboratory and histopathological parameters of the study sample. Results. LPLR elevation was significantly correlated with the presence of malignancy, advanced tumor stage, metastatic spread in the axillary nodes and HER2/neu overexpression, while PLR was only correlated with the number of infiltrated lymph nodes. Conclusions. This is the first study evaluating the effect of adjustment for large platelet count on improving PLR accuracy, when correlated with the basic independent markers of survival in a sample of breast cancer patients. Further studies are needed in order to assess the possibility of applying our adjustment as standard in terms of predicting survival rates in cancer. PMID:23304480

Enhancing the accuracy of platelet to lymphocyte ratio after adjustment for large platelet count: a pilot study in breast cancer patients.

PubMed

Seretis, Charalampos; Seretis, Fotios; Lagoudianakis, Emmanuel; Politou, Marianna; Gemenetzis, George; Salemis, Nikolaos S

2012-01-01

Background. The objective of our study is to investigate the potential effect of adjusting preoperative platelet to lymphocyte ratio, an emerging biomarker of survival in cancer patients, for the fraction of large platelets. Methods. A total of 79 patients with breast neoplasias, 44 with fibroadenomas, and 35 with invasive ductal carcinoma were included in the study. Both conventional platelet to lymphocyte ratio (PLR) and the adjusted marker, large platelet to lymphocyte ratio (LPLR), were correlated with laboratory and histopathological parameters of the study sample. Results. LPLR elevation was significantly correlated with the presence of malignancy, advanced tumor stage, metastatic spread in the axillary nodes and HER2/neu overexpression, while PLR was only correlated with the number of infiltrated lymph nodes. Conclusions. This is the first study evaluating the effect of adjustment for large platelet count on improving PLR accuracy, when correlated with the basic independent markers of survival in a sample of breast cancer patients. Further studies are needed in order to assess the possibility of applying our adjustment as standard in terms of predicting survival rates in cancer.

CoCoNUT: an efficient system for the comparison and analysis of genomes

PubMed Central

2008-01-01

Background Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons. Results Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit) that allows solving several different tasks in a unified framework: (1) finding regions of high similarity among multiple genomic sequences and aligning them, (2) comparing two draft or multi-chromosomal genomes, (3) locating large segmental duplications in large genomic sequences, and (4) mapping cDNA/EST to genomic sequences. Conclusion CoCoNUT is competitive with other software tools w.r.t. the quality of the results. The use of state of the art algorithms and data structures allows CoCoNUT to solve comparative genomics tasks more efficiently than previous tools. With the improved user interface (including an interactive visualization component), CoCoNUT provides a unified, versatile, and easy-to-use software tool for large scale studies in comparative genomics. PMID:19014477

Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array.

PubMed

van Geest, Geert; Voorrips, Roeland E; Esselink, Danny; Post, Aike; Visser, Richard Gf; Arens, Paul

2017-08-07

Cultivated chrysanthemum is an outcrossing hexaploid (2n = 6× = 54) with a disputed mode of inheritance. In this paper, we present a single nucleotide polymorphism (SNP) selection pipeline that was used to design an Affymetrix Axiom array with 183 k SNPs from RNA sequencing data (1). With this array, we genotyped four bi-parental populations (with sizes of 405, 53, 76 and 37 offspring plants respectively), and a cultivar panel of 63 genotypes. Further, we present a method for dosage scoring in hexaploids from signal intensities of the array based on mixture models (2) and validation of selection steps in the SNP selection pipeline (3). The resulting genotypic data is used to draw conclusions on the mode of inheritance in chrysanthemum (4), and to make an inference on allelic expression bias (5). With use of the mixture model approach, we successfully called the dosage of 73,936 out of 183,130 SNPs (40.4%) that segregated in any of the bi-parental populations. To investigate the mode of inheritance, we analysed markers that segregated in the large bi-parental population (n = 405). Analysis of segregation of duplex x nulliplex SNPs resulted in evidence for genome-wide hexasomic inheritance. This evidence was substantiated by the absence of strong linkage between markers in repulsion, which indicated absence of full disomic inheritance. We present the success rate of SNP discovery out of RNA sequencing data as affected by different selection steps, among which SNP coverage over genotypes and use of different types of sequence read mapping software. Genomic dosage highly correlated with relative allele coverage from the RNA sequencing data, indicating that most alleles are expressed according to their genomic dosage. The large population, genotyped with a very large number of markers, is a unique framework for extensive genetic analyses in hexaploid chrysanthemum. As starting point, we show conclusive evidence for genome-wide hexasomic inheritance.

Trial Sequential Analysis in systematic reviews with meta-analysis.

PubMed

Wetterslev, Jørn; Jakobsen, Janus Christian; Gluud, Christian

2017-03-06

Most meta-analyses in systematic reviews, including Cochrane ones, do not have sufficient statistical power to detect or refute even large intervention effects. This is why a meta-analysis ought to be regarded as an interim analysis on its way towards a required information size. The results of the meta-analyses should relate the total number of randomised participants to the estimated required meta-analytic information size accounting for statistical diversity. When the number of participants and the corresponding number of trials in a meta-analysis are insufficient, the use of the traditional 95% confidence interval or the 5% statistical significance threshold will lead to too many false positive conclusions (type I errors) and too many false negative conclusions (type II errors). We developed a methodology for interpreting meta-analysis results, using generally accepted, valid evidence on how to adjust thresholds for significance in randomised clinical trials when the required sample size has not been reached. The Lan-DeMets trial sequential monitoring boundaries in Trial Sequential Analysis offer adjusted confidence intervals and restricted thresholds for statistical significance when the diversity-adjusted required information size and the corresponding number of required trials for the meta-analysis have not been reached. Trial Sequential Analysis provides a frequentistic approach to control both type I and type II errors. We define the required information size and the corresponding number of required trials in a meta-analysis and the diversity (D 2 ) measure of heterogeneity. We explain the reasons for using Trial Sequential Analysis of meta-analysis when the actual information size fails to reach the required information size. We present examples drawn from traditional meta-analyses using unadjusted naïve 95% confidence intervals and 5% thresholds for statistical significance. Spurious conclusions in systematic reviews with traditional meta-analyses can be reduced using Trial Sequential Analysis. Several empirical studies have demonstrated that the Trial Sequential Analysis provides better control of type I errors and of type II errors than the traditional naïve meta-analysis. Trial Sequential Analysis represents analysis of meta-analytic data, with transparent assumptions, and better control of type I and type II errors than the traditional meta-analysis using naïve unadjusted confidence intervals.

Accreting transition discs with large cavities created by X-ray photoevaporation in C and O depleted discs

NASA Astrophysics Data System (ADS)

Ercolano, Barbara; Weber, Michael L.; Owen, James E.

2018-01-01

Circumstellar discs with large dust depleted cavities and vigorous accretion on to the central star are often considered signposts for (multiple) giant planet formation. In this Letter, we show that X-ray photoevaporation operating in discs with modest (factors 3-10) gas-phase depletion of carbon and oxygen at large radii ( > 15 au) yields the inner radius and accretion rates for most of the observed discs, without the need to invoke giant planet formation. We present one-dimensional viscous evolution models of discs affected by X-ray photoevaporation assuming moderate gas-phase depletion of carbon and oxygen, well within the range reported by recent observations. Our models use a simplified prescription for scaling the X-ray photoevaporation rates and profiles at different metallicity, and our quantitative result depends on this scaling. While more rigorous hydrodynamical modelling of mass-loss profiles at low metallicities is required to constrain the observational parameter space that can be explained by our models, the general conclusion that metal sequestering at large radii may be responsible for the observed diversity of transition discs is shown to be robust. Gap opening by giant planet formation may still be responsible for a number of observed transition discs with large cavities and very high accretion rate.

Role of optometry school in single day large scale school vision testing

PubMed Central

Anuradha, N; Ramani, Krishnakumar

2015-01-01

Background: School vision testing aims at identification and management of refractive errors. Large-scale school vision testing using conventional methods is time-consuming and demands a lot of chair time from the eye care professionals. A new strategy involving a school of optometry in single day large scale school vision testing is discussed. Aim: The aim was to describe a new approach of performing vision testing of school children on a large scale in a single day. Materials and Methods: A single day vision testing strategy was implemented wherein 123 members (20 teams comprising optometry students and headed by optometrists) conducted vision testing for children in 51 schools. School vision testing included basic vision screening, refraction, frame measurements, frame choice and referrals for other ocular problems. Results: A total of 12448 children were screened, among whom 420 (3.37%) were identified to have refractive errors. 28 (1.26%) children belonged to the primary, 163 to middle (9.80%), 129 (4.67%) to secondary and 100 (1.73%) to the higher secondary levels of education respectively. 265 (2.12%) children were referred for further evaluation. Conclusion: Single day large scale school vision testing can be adopted by schools of optometry to reach a higher number of children within a short span. PMID:25709271

SU-E-T-352: Why Is the Survival Rate Low in Oropharyngeal Squamous Cell Carcinoma?

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

Huang, Z; Feng, Y; Rasmussen, K

2014-06-01

Purpose: Tumors are composed of a large number of clonogens that have the capability of indefinite reproduction. Even when there is complete clinical or radiographic regression of the gross tumor mass after treatment, tumor recurrence can occur if the clonogens are not completely eradicated by radiotherapy. This study was to investigate the colonogen number and its association with the tumor control probability (TCP) in oropharyngeal squamous cell carcinoma (OSCCA). Methods: A literature search was conducted to collect clinical information of patients with OSCCA, including the prescription dose, tumor volume and survival rate. The linear-quadratic (LQ) model was incorporated into TCPmore » model for clinical data analysis. The total dose ranged from 60 to 70 Gy and tumor volume ranged from 10 to 50 cc. The TCP was calculated for each group according to tumor size and dose. The least χ{sup 2} method was used to fit the TCP calculation to clinical data while other LQ model parameters (α, β) were adopted from the literature, due to the limited patient data. Results: A total of 190 patients with T2–T4 OSCCA were included. The association with HPV was not available for all the patients. The 3-year survival rate was about 82% for T2 squamous cell carcinoma and 40% for advanced tumors. Fitting the TCP model to the survival data, the average clonogen number was 1.56×10{sup 12}. For the prescription dose of 70 Gy, the calculated TCP ranged from 40% to 90% when the tumor volume varied from 10 to 50 cc. Conclusion: Our data suggests variation between the clonogen number and TCP in OSCCA. Tumors with larger colonogen number tend to have lower TCP and therefore dose escalation above 70 Gy may be indicated in order to improve the TCP and survival rate. Our result will require future confirmation with a large number of patients.« less

On the Challenge of Interpreting Census Data: Insights from a Study of an Endangered Pinniped

PubMed Central

Trillmich, Fritz; Meise, Kristine; Kalberer, Stephanie; Mueller, Birte; Piedrahita, Paolo; Pörschmann, Ulrich; Wolf, Jochen B. W.; Krüger, Oliver

2016-01-01

Population monitoring is vital for conservation and management. However, simple counts of animals can be misleading and this problem is exacerbated in seals (pinnipeds) where individuals spend much time foraging away from colonies. We analyzed a 13-year-series of census data of Galapagos sea lions (Zalophus wollebaeki) from the colony of Caamaño, an islet in the center of the Galapagos archipelago where a large proportion of animals was individually marked. Based on regular resighting efforts during the cold, reproductive (cold-R; August to January) and the warm, non-reproductive (warm-nR; February to May) season, we document changes in numbers for different sex and age classes. During the cold-R season the number of adults increased as the number of newborn pups increased. Numbers were larger in the morning and evening than around mid-day and not significantly influenced by tide levels. More adults frequented the colony during the warm-nR season than the cold-R season. Raw counts suggested a decline in numbers over the 13 years, but Lincoln-Petersen (LP-) estimates (assuming a closed population) did not support that conclusion. Raw counts and LP estimates were not significantly correlated, demonstrating the overwhelming importance of variability in attendance patterns of individuals. The probability of observing a given adult in the colony varied between 16% (mean for cold-R season) and 23% (warm-nR season) and may be much less for independent 2 to 4 year olds. Dependent juveniles (up to the age of about 2 years) are observed much more frequently ashore (35% during the cold-R and 50% during the warm-nR seasons). Simple counts underestimate real population size by a factor of 4–6 and may lead to erroneous conclusions about trends in population size. PMID:27148735

Taking OSCE examiner training on the road: reaching the masses.

PubMed

Reid, Katharine; Smallwood, David; Collins, Margo; Sutherland, Ruth; Dodds, Agnes

2016-01-01

Background To ensure the rigour of objective structured clinical examinations (OSCEs) in assessing medical students, medical school educators must educate examiners with a view to standardising examiner assessment behaviour. Delivering OSCE examiner training is a necessary yet challenging part of the OSCE process. A novel approach to implementing training for current and potential OSCE examiners was trialled by delivering large-group education sessions at major teaching hospitals. Methods The 'OSCE Roadshow' comprised a short training session delivered in the context of teaching hospital 'Grand Rounds' to current and potential OSCE examiners. The training was developed to educate clinicians about OSCE processes, clarify the examiners' role and required behaviours, and to review marking guides and mark allocation in an effort to standardise OSCE processes and encourage consistency in examiner marking behaviour. A short exercise allowed participants to practise marking a mock OSCE to investigate examiner marking behaviour after the training. Results OSCE Roadshows at four metropolitan and one rural teaching hospital were well received and well attended by 171 clinicians across six sessions. Unexpectedly, medical students also attended in large numbers (n=220). After training, participants' average scores for the mock OSCE clustered closely around the ideal score of 28 (out of 40), and the average scores did not differ according to the levels of clinical experience. Conclusion The OSCE Roadshow demonstrated the potential of brief familiarisation training in reaching large numbers of current and potential OSCE examiners in a time and cost-effective manner to promote standardisation of OSCE processes.

Msn2 Coordinates a Stoichiometric Gene Expression Program

PubMed Central

Stewart-Ornstein, Jacob; Nelson, Christopher; DeRisi, Joe; Weissman, Jonathan S.; El-Samad, Hana

2014-01-01

Summary Background Many cellular processes operate in an “analog” regime in which the magnitude of the response is precisely tailored to the intensity of the stimulus. In order to maintain the coherence of such responses, the cell must provide for proportional expression of multiple target genes across a wide dynamic range of induction states. Our understanding of the strategies used to achieve graded gene regulation is limited. Results In this work, we document a relationship between stress responsive gene expression and the transcription factor Msn2 that is graded over a large range of Msn2 cocnentrations. We use computational modeling, in vivo, and in vitro analysis to dissect the roots of this relationship. Our studies reveal a simple and general strategy based on non-cooperative low-affinity interactions between Msn2 and its cognate binding sites, as well as competition over a large number of Msn2 binding sites in the genome relative to the number of Msn2 molecules. Conclusions In addition to enabling precise tuning of gene expression to the state of the environment, this strategy ensures co-linear activation of target genes, allowing for stoichiometric expression of large groups of genes without extensive promoter tuning. Furthermore, such a strategy enables precise modulation of the activity of any given promoter by addition of binding sites without altering the qualitative relationship between different genes in a regulon. This feature renders a given regulon highly ‘evolvable’. PMID:24210615

[The consequences of passive smoking in adults].

PubMed

Trédaniel, J; Savinelli, F; Vignot, S; Bousquet, G; Le Maignan, C; Misset, J-L

2006-04-01

Passive smoking is the involuntary inhalation by a non-smoker of smoke generated in his neighbourhood by one or more smokers. The effect of this exposure is already generally recognised in children. In adults the induction of chronic obstructive lung disease has not been demonstrated. This is no longer the case for ischaemic heart disease and lung cancer where the effect of passive exposure of non-smokers to cigarette smoke is recognised. The biological plausibility together with the concordance of results obtained over successive years, as well as the large numbers of patients included in the studies, lead to a confident conclusion that the risks in adult non-smokers are increased by the order of 25%. There is no evidence that bias affects the conclusions reached and the World Health Organisation has recently classified passive smoking as being carcinogenic in man. As a result of these data prevention of passive exposure to cigarette smoke should be part of a larger framework of smoking prevention, especially among the young.

Community-Partnered Research Conference Model: The Experience of Community Partners in Care Study

PubMed Central

Khodyakov, Dmitry; Pulido, Esmeralda; Ramos, Ana; Dixon, Elizabeth

2013-01-01

The Problem Conducting community-partnered research conferences is a powerful yet underutilized approach to translating research into practice and improving result dissemination and intervention sustainability strategies. Nonetheless, detailed descriptions of conference features and ways to use them in empirical research are rare. Purpose of Article We describe how community-partnered conferences may be integrated into research projects by using an example of Community Partners in Care, a large cluster-randomized controlled trial that uses Community Partnered Participatory Research principles. Key Points Our conceptual model illustrates the role community-partnered research conferences may play in three study phases and describes how different conference features may increase community engagement, build two-way capacity, and ensure equal project ownership. Conclusion(s) As the number of community-partnered studies grows, so too does the need for practical tools to support this work. Community-partnered research conferences may be effectively employed in translational research to increase two-way capacity-building and promote long-term intervention success. PMID:24859106

To the Large Nucleolar Bodies in Apoptotic Leukaemic Granulocytic Progenitors without Further Differentiation. Are Large Nucleoli Always Present in Proliferating Cells?

PubMed

Smetana, K; Kuželová, K; Zápotocký, M; Hrkal, Z

2017-01-01

Large nucleoli have generally been believed to be present in less differentiated and proliferating cells including the malignant ones. Such nucleoli have also been considered to be active in the biosynthetic process and major cell developmental activities. In contrast, after cytostatic treatment, apoptotic leukaemic progenitors still containing nuclei did not exhibit substantial reduction of the nucleolar size but displayed decreased nucleolar biosynthetic activity. The present study was undertaken to provide more information on the large nucleoli in spontaneously occurring apoptotic leukaemic progenitors without further differentiation. Leukaemic progenitors of established cell lineages originating from leukaemic patients represented a very convenient model for such study. Some of them exhibit morphological signs of the spontaneously occurring apoptotic process. Since such signs are expressed by nuclear and cytoplasmic morphological variability, the present study dealt with spontaneously occurring apoptotic progenitors with preserved nuclei characterized by heavy chromatin condensation and occasional fragmentation. Based of nucleolar body and nuclear maximal diameter measurements it seems to be clear that the nucleolar size in these cells was not substantially reduced, contrary to that of the nucleus. However, large nucleolar bodies in spontaneously occurring apoptotic cells were characterized by markedly reduced biosynthetic activity, as expressed by the decreased number of nucleolar transcription markers such as nucleolar fibrillar centres. In conclusion, large nucleoli may be present not only in proliferating, but also in spontaneously occurring apoptotic cells.

Data submission and quality in microarray-based microRNA profiling

PubMed Central

Witwer, Kenneth W.

2014-01-01

Background Public sharing of scientific data has assumed greater importance in the ‘omics’ era. Transparency is necessary for confirmation and validation, and multiple examiners aid in extracting maximal value from large datasets. Accordingly, database submission and provision of the Minimum Information About a Microarray Experiment (MIAME) are required by most journals as a prerequisite for review or acceptance. Methods In this study, the level of data submission and MIAME compliance was reviewed for 127 articles that included microarray-based microRNA profiling and that were published from July, 2011 through April, 2012 in the journals that published the largest number of such articles—PLOS ONE, the Journal of Biological Chemistry, Blood, and Oncogene—along with articles from nine other journals, including Clinical Chemistry, that published smaller numbers of array-based articles. Results Overall, data submission was reported at publication for less than 40% of all articles, and almost 75% of articles were MIAME-noncompliant. On average, articles that included full data submission scored significantly higher on a quality metric than articles with limited or no data submission, and studies with adequate description of methods disproportionately included larger numbers of experimental repeats. Finally, for several articles that were not MIAME-compliant, data re-analysis revealed less than complete support for the published conclusions, in one case leading to retraction. Conclusions These findings buttress the hypothesis that reluctance to share data is associated with low study quality and suggest that most miRNA array investigations are underpowered and/or potentially compromised by a lack of appropriate reporting and data submission. PMID:23358751

Comparison of molecular dynamics and superfamily spaces of protein domain deformation.

PubMed

Velázquez-Muriel, Javier A; Rueda, Manuel; Cuesta, Isabel; Pascual-Montano, Alberto; Orozco, Modesto; Carazo, José-María

2009-02-17

It is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. Technically, protein flexibility exploration is an essential task in many applications, such as protein structure prediction and modeling. In this contribution we have compared two different approaches to explore the flexibility space of protein domains: i) molecular dynamics (MD-space), and ii) the study of the structural changes within superfamily (SF-space). Our analysis indicates that the MD-space and the SF-space display a significant overlap, but are still different enough to be considered as complementary. The SF-space space is wider but less complex than the MD-space, irrespective of the number of members in the superfamily. Also, the SF-space does not sample all possibilities offered by the MD-space, but often introduces very large changes along just a few deformation modes, whose number tend to a plateau as the number of related folds in the superfamily increases. Theoretically, we obtained two conclusions. First, that function restricts the access to some flexibility patterns to evolution, as we observe that when a superfamily member changes to become another, the path does not completely overlap with the physical deformability. Second, that conformational changes from variation in a superfamily are larger and much simpler than those allowed by physical deformability. Methodologically, the conclusion is that both spaces studied are complementary, and have different size and complexity. We expect this fact to have application in fields as 3D-EM/X-ray hybrid models or ab initio protein folding.

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing

PubMed Central

2013-01-01

Background Technical improvements have decreased sequencing costs and, as a result, the size and number of genomic datasets have increased rapidly. Because of the lower cost, large amounts of sequence data are now being produced by small to midsize research groups. Crossbow is a software tool that can detect single nucleotide polymorphisms (SNPs) in whole-genome sequencing (WGS) data from a single subject; however, Crossbow has a number of limitations when applied to multiple subjects from large-scale WGS projects. The data storage and CPU resources that are required for large-scale whole genome sequencing data analyses are too large for many core facilities and individual laboratories to provide. To help meet these challenges, we have developed Rainbow, a cloud-based software package that can assist in the automation of large-scale WGS data analyses. Results Here, we evaluated the performance of Rainbow by analyzing 44 different whole-genome-sequenced subjects. Rainbow has the capacity to process genomic data from more than 500 subjects in two weeks using cloud computing provided by the Amazon Web Service. The time includes the import and export of the data using Amazon Import/Export service. The average cost of processing a single sample in the cloud was less than 120 US dollars. Compared with Crossbow, the main improvements incorporated into Rainbow include the ability: (1) to handle BAM as well as FASTQ input files; (2) to split large sequence files for better load balance downstream; (3) to log the running metrics in data processing and monitoring multiple Amazon Elastic Compute Cloud (EC2) instances; and (4) to merge SOAPsnp outputs for multiple individuals into a single file to facilitate downstream genome-wide association studies. Conclusions Rainbow is a scalable, cost-effective, and open-source tool for large-scale WGS data analysis. For human WGS data sequenced by either the Illumina HiSeq 2000 or HiSeq 2500 platforms, Rainbow can be used straight out of the box. Rainbow is available for third-party implementation and use, and can be downloaded from http://s3.amazonaws.com/jnj_rainbow/index.html. PMID:23802613

Epidemiology and eradication of infectious bovine rhinotracheitis/infectious pustular vulvovaginitis (IBR/IPV) virus in Finland

PubMed Central

Nuotio, Lasse; Neuvonen, Erkki; Hyytiäinen, Mauno

2007-01-01

Background Infectious bovine rhinotracheitis/infectious pustular vulvovaginitis (IBR/IPV) is a significant disease among domestic and wild cattle. The BHV-1 infection was first detected in Finland in 1970; presumably it was imported in 1968. The infection reappeared in the large-scale bulk-tank milk surveillances which started in 1990, and was eradicated in 1994. Our aim is to describe the epidemiology of this infection in Finland, and its eradication. Materials and methods The official sources of pertinent information, the legal basis for the disease control and the serological methods for the detection of the infection are described. Results and conclusion Ten AI bulls were found to be seropositive in 1970–1971. The total number of herds with BHV-1 antibody positive animals in the large-scale surveillance in 1990 and subsequent epidemiological investigations in 1991 was five, and the total number of seropositive animals was 90. The five herds formed three epidemiological units; semen of at least one bull seropositive in 1971 had been used in each unit. This remained the only plausible route of infection in each of the three units. Using the 'test and slaughter' approach and total stamping out in one herd the infection was eradicated in 1994. PMID:17222341

Predicted trends in the supply and demand of veterinarians in Japan.

PubMed

Kimura, S; Shinkawa, S; Mago, J; Yamamoto, M; Sakai, M; Sugisaki, T; Karaki, H; Sugiura, K

2008-12-01

Currently in Japan, there are 32,000 active veterinarians, mainly engaged in small and large animal practice and public animal health and public health services. In the face of the notable increase in recent years in the proportion of female students enrolled in veterinary schools and in the number of households with companion animals, a model was developed to predict the supply and demand of veterinarians toward 2040 in Japan. Surveys were conducted on sampled households and veterinarians to estimate input variables used in the supply and demand model. From this data it is predicted that there might be somewhere between a shortage of 1,000 to an over-supply of 3,700 veterinarians engaged in small animal practice in 2040. This, however, will depend on possible changes in the number of visits made to veterinarians by small animal owners and the efficiency of practices in the future. The model also predicts that there will be a shortage of around 1,100 veterinarians in large animal practice in 2040. Considering the many assumptions made to estimate the input variables used in the model, the results of this study do not provide definitive conclusions, but provide a base for discussions on what will be needed in the veterinary profession in the future.

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity

PubMed Central

Carrara, Matteo; Beccuti, Marco; Lazzarato, Fulvio; Cavallo, Federica; Cordero, Francesca; Donatelli, Susanna; Calogero, Raffaele A.

2013-01-01

Background. Gene fusions arising from chromosomal translocations have been implicated in cancer. RNA-seq has the potential to discover such rearrangements generating functional proteins (chimera/fusion). Recently, many methods for chimeras detection have been published. However, specificity and sensitivity of those tools were not extensively investigated in a comparative way. Results. We tested eight fusion-detection tools (FusionHunter, FusionMap, FusionFinder, MapSplice, deFuse, Bellerophontes, ChimeraScan, and TopHat-fusion) to detect fusion events using synthetic and real datasets encompassing chimeras. The comparison analysis run only on synthetic data could generate misleading results since we found no counterpart on real dataset. Furthermore, most tools report a very high number of false positive chimeras. In particular, the most sensitive tool, ChimeraScan, reports a large number of false positives that we were able to significantly reduce by devising and applying two filters to remove fusions not supported by fusion junction-spanning reads or encompassing large intronic regions. Conclusions. The discordant results obtained using synthetic and real datasets suggest that synthetic datasets encompassing fusion events may not fully catch the complexity of RNA-seq experiment. Moreover, fusion detection tools are still limited in sensitivity or specificity; thus, there is space for further improvement in the fusion-finder algorithms. PMID:23555082

A singular value decomposition approach for improved taxonomic classification of biological sequences

PubMed Central

2011-01-01

Background Singular value decomposition (SVD) is a powerful technique for information retrieval; it helps uncover relationships between elements that are not prima facie related. SVD was initially developed to reduce the time needed for information retrieval and analysis of very large data sets in the complex internet environment. Since information retrieval from large-scale genome and proteome data sets has a similar level of complexity, SVD-based methods could also facilitate data analysis in this research area. Results We found that SVD applied to amino acid sequences demonstrates relationships and provides a basis for producing clusters and cladograms, demonstrating evolutionary relatedness of species that correlates well with Linnaean taxonomy. The choice of a reasonable number of singular values is crucial for SVD-based studies. We found that fewer singular values are needed to produce biologically significant clusters when SVD is employed. Subsequently, we developed a method to determine the lowest number of singular values and fewest clusters needed to guarantee biological significance; this system was developed and validated by comparison with Linnaean taxonomic classification. Conclusions By using SVD, we can reduce uncertainty concerning the appropriate rank value necessary to perform accurate information retrieval analyses. In tests, clusters that we developed with SVD perfectly matched what was expected based on Linnaean taxonomy. PMID:22369633

Atrial fibrillation and silent stroke: links, risks, and challenges.

PubMed

Hahne, Kathrin; Mönnig, Gerold; Samol, Alexander

2016-01-01

Atrial fibrillation (AF) is the most common cardiac arrhythmia, with a projected number of 1 million affected subjects in Germany. Changes in age structure of the Western population allow for the assumption that the number of concerned people is going to be doubled, maybe tripled, by the year 2050. Large epidemiological investigations showed that AF leads to a significant increase in mortality and morbidity. Approximately one-third of all strokes are caused by AF and, due to thromboembolic cause, these strokes are often more severe than those caused by other etiologies. Silent brain infarction is defined as the presence of cerebral infarction in the absence of corresponding clinical symptomatology. Progress in imaging technology simplifies diagnostic procedures of these lesions and leads to a large amount of diagnosed lesions, but there is still no final conclusion about frequency, risk factors, and clinical relevance of these infarctions. The prevalence of silent strokes in patients with AF is higher compared to patients without AF, and several studies reported high incidence rates of silent strokes after AF ablation procedures. While treatment strategies to prevent clinically apparent strokes in patients with AF are well investigated, the role of anticoagulatory treatment for prevention of silent infarctions is unclear. This paper summarizes developments in diagnosis of silent brain infarction and its context to AF.

Detailed kinetics and regulation of mammalian 2-oxoglutarate dehydrogenase

PubMed Central

2011-01-01

Background Mitochondrial 2-oxoglutarate (α-ketoglutarate) dehydrogenase complex (OGDHC), a key regulatory point of tricarboxylic acid (TCA) cycle, plays vital roles in multiple pathways of energy metabolism and biosynthesis. The catalytic mechanism and allosteric regulation of this large enzyme complex are not fully understood. Here computer simulation is used to test possible catalytic mechanisms and mechanisms of allosteric regulation of the enzyme by nucleotides (ATP, ADP), pH, and metal ion cofactors (Ca2+ and Mg2+). Results A model was developed based on an ordered ter-ter enzyme kinetic mechanism combined with con-formational changes that involve rotation of one lipoic acid between three catalytic sites inside the enzyme complex. The model was parameterized using a large number of kinetic data sets on the activity of OGDHC, and validated by comparison of model predictions to independent data. Conclusions The developed model suggests a hybrid rapid-equilibrium ping-pong random mechanism for the kinetics of OGDHC, consistent with previously reported mechanisms, and accurately describes the experimentally observed regulatory effects of cofactors on the OGDHC activity. This analysis provides a single consistent theoretical explanation for a number of apparently contradictory results on the roles of phosphorylation potential, NAD (H) oxidation-reduction state ratio, as well as the regulatory effects of metal ions on ODGHC function. PMID:21943256

Ten Years of Addressing Children’s Health through Regulatory Policy at the U.S. Environmental Protection Agency

PubMed Central

Payne-Sturges, Devon; Kemp, Debra

2008-01-01

Background Executive Order (EO) 13045, Protection of Children From Environmental Health Risks and Safety Risks, directs each federal agency to ensure that its policies, programs, activities, and standards address disproportionate environmental health and safety risks to children. Objectives We reviewed regulatory actions published by U.S. Environmental Protection Agency (EPA) in the Federal Register from April 1998 through December 2006 to evaluate applicability of EO 13045 to U.S. EPA actions and consideration of children’s health issues in U.S. EPA rulemakings. Discussion Although virtually all actions discussed EO 13045, fewer than two regulations per year, on average, were subject to the EO requirement to evaluate children’s environmental health risks. Nonetheless, U.S. EPA considered children’s environmental health in all actions addressing health or safety risks that may disproportionately affect children. Conclusion The EO does not apply to a broad enough set of regulatory actions to ensure protection of children’s health and safety risks, largely because of the small number of rules that are economically significant. However, given the large number of regulations that consider children’s health issues despite not being subject to the EO, other statutory requirements and agency policies reach a larger set of regulations to ensure protection of children’s environmental health. PMID:19079726

Obtaining evidence for use by healthcare payers on the success of chronic obstructive pulmonary disease management.

PubMed

Mapel, D; Pearson, M

2002-08-01

Healthcare payers make decisions on funding for treatments for diseases, such as chronic obstructive pulmonary disease (COPD), on a population level, so require evidence of treatment success in appropriate populations, using usual routine care as the comparison for alternative management approaches. Such health outcomes evidence can be obtained from a number of sources. The 'gold standard' method for obtaining evidence of treatment success is usually taken as the randomized controlled prospective clinical trial. Yet the value of such studies in providing evidence for decision-makers can be questioned due to the restricted entry criteria limiting the ability to generalize to real life populations, narrow focus on individual parameters, use of placebo for comparison rather than usual therapy and unrealistic intense monitoring of patients. Evidence obtained from retrospective and observational studies can supplement that from randomized clinical trials, providing that care is taken to guard against bias and confounders. However, very large numbers of patients must be investigated if small differences between drugs and treatment approaches are to be detected. Administrative databases from healthcare systems provide an opportunity to obtain observational data on large numbers of patients. Such databases have shown that high healthcare costs in patients with COPD are associated with co-morbid conditions and current smoking status. Analysis of an administrative database has also shown that elderly patients with COPD who received inhaled corticosteroids within 90 days of discharge from hospital had 24% fewer repeat hospitalizations for COPD and were 29% less likely to die during the 1-year follow-up period. In conclusion, there are a number of sources of meaningful evidence of the health outcomes arising from different therapeutic approaches that should be of value to healthcare payers making decisions on resource allocation.

Increasing Incidence and Severity of Coccidioidomycosis at a Naval Air Station

PubMed Central

Lee, Rachel U; Crum-Cianflone, Nancy F

2009-01-01

Background Increasing rates of coccidioidomycosis among the general population are being described. Given the large number of military personnel stationed and training in endemic areas, data regarding infection trends among military members would be informative. Methods We performed a retrospective epidemiologic study concerning the incidence and severity of clinical cases of coccidioidomycosis at a Naval base located in an endemic area in California. Results Eighty-two military beneficiaries at the base were diagnosed with coccidioidomycosis from January 2002 to December 2006. Among active duty personnel, the rate of coccidioidomycosis rose 10-fold during the five-year study period: 29.88 to 313.71 cases per 100,000 person-years. The incidence of coccidioidal infections occurring in active duty members was higher than other military beneficiaries at the base. The median age of patients with a coccidioidal infection was 28 years, and 73% were male. Sixty-six had primary pulmonary disease, and 14 had disseminated disease; data were unavailable for two cases. The number of disseminated cases increased significantly over time; by 2006, 30% of the diagnosed cases were disseminated disease. Among cases of dissemination, 43% occurred among white/non-Hispanics. Disseminated disease was associated with high complement fixation titers and a more recent year of diagnosis. Although the sample size was small, we found no differences in rates of disseminated disease by race, likely due to the large number of cases among Caucasians. Conclusions Coccidioidomycosis incidence rates have significantly increased during the last five years among military beneficiaries. Active duty members were more likely to develop coccidioidomycosis than dependents or retirees, perhaps related to the number and intensity of exposures in this group. PMID:18751595

Body fat mass and the proportion of very large adipocytes in pregnant women are associated with gestational insulin resistance

PubMed Central

Svensson, H; Wetterling, L; Bosaeus, M; Odén, B; Odén, A; Jennische, E; Edén, S; Holmäng, A; Lönn, M

2016-01-01

Background/Objectives: Pregnancy is accompanied by fat gain and insulin resistance. Changes in adipose tissue morphology and function during pregnancy and factors contributing to gestational insulin resistance are incompletely known. We sought to characterize adipose tissue in trimesters 1 and 3 (T1/T3) in normal weight (NW) and obese pregnant women, and identify adipose tissue-related factors associated with gestational insulin resistance. Subjects/Methods: Twenty-two NW and 11 obese women were recruited early in pregnancy for the Pregnancy Obesity Nutrition and Child Health study. Examinations and sampling of blood and abdominal adipose tissue were performed longitudinally in T1/T3 to determine fat mass (air-displacement plethysmography); insulin resistance (homeostasis model assessment of insulin resistance, HOMA-IR); size, number and lipolytic activity of adipocytes; and adipokine release and density of immune cells and blood vessels in adipose tissue. Results: Fat mass and HOMA-IR increased similarly between T1 and T3 in the groups; all remained normoglycemic. Adipocyte size increased in NW women. Adipocyte number was not influenced, but proportions of small and large adipocytes changed oppositely in the groups. Lipolytic activity and circulating adipocyte fatty acid-binding protein increased in both groups. Adiponectin release was reduced in NW women. Fat mass and the proportion of very large adipocytes were most strongly associated with T3 HOMA-IR by multivariable linear regression (R2=0.751, P<0.001). Conclusions: During pregnancy, adipose tissue morphology and function change comprehensively. NW women accumulated fat in existing adipocytes, accompanied by reduced adiponectin release. In comparison with the NW group, obese women had signs of adipocyte recruitment and maintained adiponectin levels. Body fat and large adipocytes may contribute significantly to gestational insulin resistance. PMID:26563815

ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles

PubMed Central

2009-01-01

Background Sequence identification of ESTs from non-model species offers distinct challenges particularly when these species have duplicated genomes and when they are phylogenetically distant from sequenced model organisms. For the common carp, an environmental model of aquacultural interest, large numbers of ESTs remained unidentified using BLAST sequence alignment. We have used the expression profiles from large-scale microarray experiments to suggest gene identities. Results Expression profiles from ~700 cDNA microarrays describing responses of 7 major tissues to multiple environmental stressors were used to define a co-expression landscape. This was based on the Pearsons correlation coefficient relating each gene with all other genes, from which a network description provided clusters of highly correlated genes as 'mountains'. We show that these contain genes with known identities and genes with unknown identities, and that the correlation constitutes evidence of identity in the latter. This procedure has suggested identities to 522 of 2701 unknown carp ESTs sequences. We also discriminate several common carp genes and gene isoforms that were not discriminated by BLAST sequence alignment alone. Precision in identification was substantially improved by use of data from multiple tissues and treatments. Conclusion The detailed analysis of co-expression landscapes is a sensitive technique for suggesting an identity for the large number of BLAST unidentified cDNAs generated in EST projects. It is capable of detecting even subtle changes in expression profiles, and thereby of distinguishing genes with a common BLAST identity into different identities. It benefits from the use of multiple treatments or contrasts, and from the large-scale microarray data. PMID:19939286

Thermocapillary Bubble Migration: Thermal Boundary Layers for Large Marangoni Numbers

NASA Technical Reports Server (NTRS)

Balasubramaniam, R.; Subramanian, R. S.

1996-01-01

The migration of an isolated gas bubble in an immiscible liquid possessing a temperature gradient is analyzed in the absence of gravity. The driving force for the bubble motion is the shear stress at the interface which is a consequence of the temperature dependence of the surface tension. The analysis is performed under conditions for which the Marangoni number is large, i.e. energy is transferred predominantly by convection. Velocity fields in the limit of both small and large Reynolds numbers are used. The thermal problem is treated by standard boundary layer theory. The outer temperature field is obtained in the vicinity of the bubble. A similarity solution is obtained for the inner temperature field. For both small and large Reynolds numbers, the asymptotic values of the scaled migration velocity of the bubble in the limit of large Marangoni numbers are calculated. The results show that the migration velocity has the same scaling for both low and large Reynolds numbers, but with a different coefficient. Higher order thermal boundary layers are analyzed for the large Reynolds number flow field and the higher order corrections to the migration velocity are obtained. Results are also presented for the momentum boundary layer and the thermal wake behind the bubble, for large Reynolds number conditions.

Accuracy and differential bias in copy number measurement of CCL3L1 in association studies with three auto-immune disorders

PubMed Central

2011-01-01

Background Copy number variation (CNV) contributes to the variation observed between individuals and can influence human disease progression, but the accurate measurement of individual copy numbers is technically challenging. In the work presented here we describe a modification to a previously described paralogue ratio test (PRT) method for genotyping the CCL3L1/CCL4L1 copy variable region, which we use to ascertain CCL3L1/CCL4L1 copy number in 1581 European samples. As the products of CCL3L1 and CCL4L1 potentially play a role in autoimmunity we performed case control association studies with Crohn's disease, rheumatoid arthritis and psoriasis clinical cohorts. Results We evaluate the PRT methodology used, paying particular attention to accuracy and precision, and highlight the problems of differential bias in copy number measurements. Our PRT methods for measuring copy number were of sufficient precision to detect very slight but systematic differential bias between results from case and control DNA samples in one study. We find no evidence for an association between CCL3L1 copy number and Crohn's disease, rheumatoid arthritis or psoriasis. Conclusions Differential bias of this small magnitude, but applied systematically across large numbers of samples, would create a serious risk of false positive associations in copy number, if measured using methods of lower precision, or methods relying on single uncorroborated measurements. In this study the small differential bias detected by PRT in one sample set was resolved by a simple pre-treatment by restriction enzyme digestion. PMID:21851606

Potential and Limitations of Cochrane Reviews in Pediatric Cardiology: A Systematic Analysis.

PubMed

Poryo, Martin; Khosrawikatoli, Sara; Abdul-Khaliq, Hashim; Meyer, Sascha

2017-04-01

Evidence-based medicine has contributed substantially to the quality of medical care in pediatric and adult cardiology. However, our impression from the bedside is that a substantial number of Cochrane reviews generate inconclusive data that are of limited clinical benefit. We performed a systematic synopsis of Cochrane reviews published between 2001 and 2015 in the field of pediatric cardiology. Main outcome parameters were the number and percentage of conclusive, partly conclusive, and inconclusive reviews as well as their recommendations and their development over three a priori defined intervals. In total, 69 reviews were analyzed. Most of them examined preterm and term neonates (36.2%), whereas 33.3% included also non-pediatric patients. Leading topics were pharmacological issues (71.0%) followed by interventional (10.1%) and operative procedures (2.9%). The majority of reviews were inconclusive (42.9%), while 36.2% were conclusive and 21.7% partly conclusive. Although the number of published reviews increased during the three a priori defined time intervals, reviews with "no specific recommendations" remained stable while "recommendations in favor of an intervention" clearly increased. Main reasons for missing recommendations were insufficient data (n = 41) as well as an insufficient number of trials (n = 22) or poor study quality (n = 19). There is still need for high-quality research, which will likely yield a greater number of Cochrane reviews with conclusive results.

The Application Law of Large Numbers That Predicts The Amount of Actual Loss in Insurance of Life

NASA Astrophysics Data System (ADS)

Tinungki, Georgina Maria

2018-03-01

The law of large numbers is a statistical concept that calculates the average number of events or risks in a sample or population to predict something. The larger the population is calculated, the more accurate predictions. In the field of insurance, the Law of Large Numbers is used to predict the risk of loss or claims of some participants so that the premium can be calculated appropriately. For example there is an average that of every 100 insurance participants, there is one participant who filed an accident claim, then the premium of 100 participants should be able to provide Sum Assured to at least 1 accident claim. The larger the insurance participant is calculated, the more precise the prediction of the calendar and the calculation of the premium. Life insurance, as a tool for risk spread, can only work if a life insurance company is able to bear the same risk in large numbers. Here apply what is called the law of large number. The law of large numbers states that if the amount of exposure to losses increases, then the predicted loss will be closer to the actual loss. The use of the law of large numbers allows the number of losses to be predicted better.

Zero-gravity cloud physics.

NASA Technical Reports Server (NTRS)

Hollinden, A. B.; Eaton, L. R.; Vaughan, W. W.

1972-01-01

The first results of an ongoing preliminary-concept and detailed-feasibility study of a zero-gravity earth-orbital cloud physics research facility are reviewed. Current planning and thinking are being shaped by two major conclusions of this study: (1) there is a strong requirement for and it is feasible to achieve important and significant research in a zero-gravity cloud physics facility; and (2) some very important experiments can be accomplished with 'off-the-shelf' type hardware by astronauts who have no cloud-physics background; the most complicated experiments may require sophisticated observation and motion subsystems and the astronaut may need graduate level cloud physics training; there is a large number of experiments whose complexity varies between these two extremes.

Electric Dipole Theory of Chemical Synaptic Transmission

PubMed Central

Wei, Ling Y.

1968-01-01

In this paper we propose that chemicals such as acetylcholine are electric dipoles which when oriented and arranged in a large array could produce an electric field strong enough to drive positive ions over the junction barrier of the post-synaptic membrane and thus initiate excitation or produce depolarization. This theory is able to explain a great number of facts such as cleft size, synaptic delay, nonregeneration, subthreshold integration, facilitation with repetition, and the calcium and magnesium effects. It also shows why and how acetylcholine could act as excitatory or inhibitory transmitters under different circumstances. Our conclusion is that the nature of synaptic transmission is essentially electrical, be it mediated by electrical or chemical transmitters. PMID:4296121

Anatomy and Biomechanics of the Unstable Shoulder

PubMed Central

Cuéllar, Ricardo; Ruiz-Ibán, Miguel Angel; Cuéllar, Adrián

2017-01-01

Purpose: To review the anatomy of the shoulder joint and of the physiology of glenohumeral stability is essential to manage correctly shoulder instability. Methods: It was reviewed a large number of recently published research studies related to the shoulder instability that received a higher Level of Evidence grade. Results: It is reviewed the bony anatomy, the anatomy and function of the ligaments that act on this joint, the physiology and physiopathology of glenohumeral instability and the therapeutic implications of the injured structures. Conclusion: This knowledge allows the surgeon to evaluate the possible causes of instability, to assess which are the structures that must be reconstructed and to decide which surgical technique must be performed. PMID:28979600

Objective comparison of particle tracking methods

PubMed Central

Chenouard, Nicolas; Smal, Ihor; de Chaumont, Fabrice; Maška, Martin; Sbalzarini, Ivo F.; Gong, Yuanhao; Cardinale, Janick; Carthel, Craig; Coraluppi, Stefano; Winter, Mark; Cohen, Andrew R.; Godinez, William J.; Rohr, Karl; Kalaidzidis, Yannis; Liang, Liang; Duncan, James; Shen, Hongying; Xu, Yingke; Magnusson, Klas E. G.; Jaldén, Joakim; Blau, Helen M.; Paul-Gilloteaux, Perrine; Roudot, Philippe; Kervrann, Charles; Waharte, François; Tinevez, Jean-Yves; Shorte, Spencer L.; Willemse, Joost; Celler, Katherine; van Wezel, Gilles P.; Dan, Han-Wei; Tsai, Yuh-Show; de Solórzano, Carlos Ortiz; Olivo-Marin, Jean-Christophe; Meijering, Erik

2014-01-01

Particle tracking is of key importance for quantitative analysis of intracellular dynamic processes from time-lapse microscopy image data. Since manually detecting and following large numbers of individual particles is not feasible, automated computational methods have been developed for these tasks by many groups. Aiming to perform an objective comparison of methods, we gathered the community and organized, for the first time, an open competition, in which participating teams applied their own methods independently to a commonly defined data set including diverse scenarios. Performance was assessed using commonly defined measures. Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to important practical conclusions for users and developers. PMID:24441936

“ENHANCING LIFE AFTER CANCER IN DIVERSE COMMUNITIES”

PubMed Central

Kaur, Judith S.; Coe, Kathryn; Rowland, Julia; Braun, Kathryn L.; Conde, Francisco A.; Burhansstipanov, Linda; Heiney, Sue; Kagawa-Singer, Marjorie; Lu, Qian; Witte, Catherine

2012-01-01

Background Although large numbers of cancer survivors exist in every community, including minority communities, there is a significant gap in knowledge about best practices for these patients. Methods Community Networks Programs (CNPs) funded by the National Cancer Institute’s Center to Reduce Cancer Health Disparities, have developed and tested unique services for these communities. These programs have utilized community based participatory research techniques under a framework of diffusion of innovation and communications theory. Results This article describes some specifically tailored interventions that may be useful to a wide range of providers working with the underserved Conclusions Enhancing life after cancer can be achieved in underserved communities by supplementing local resources. PMID:22434384

Magnetic circuit modifications in resonant vibration harvesters

NASA Astrophysics Data System (ADS)

Szabo, Zoltan; Fiala, Pavel; Dohnal, Premysl

2018-01-01

The paper discusses the conclusions obtained from a research centered on a vibration-powered milli- or micro generator (MG) operating as a harvester to yield the maximum amount of energy transferred by the vibration of an independent system. The investigation expands on the results proposed within papers that theoretically define the properties characterizing the basic configurations of a generator based on applied Faraday's law of induction. We compared two basic principles of circuit closing in a magnetic circuit that, fully or partially, utilizes a ferromagnetic material, and a large number of generator design solutions were examined and tested. In the given context, the article brings a compact survey of the rules facilitating energy transformation and the designing of harvesters.

Why did ISO 9001:2008 system fail to deliver?

PubMed

Langford, Melvyn

2014-02-01

This article is based on an actual investigation undertaken, and summarises the subsequent report's findings and observations. It has been anonymised for obvious reasons. In May 2013 an analysis was undertaken by a multidisciplinary team that compared an NHS Trust estates department's managerial systems against the NHS national recommendations. The conclusions stated that: 'There was a systemic failure across a large number of topics generating intolerable/substantial risks to the organisation, its staff, and patients; this despite the department's managerial systems being accredited to the International Standard ISO 9001:2008'. The natural question raised when presented with this demonstrable and auditable evidence was: 'Why did the ISO 9001:2008 system fail?'

A recent history of science cases for optical interferometry

NASA Astrophysics Data System (ADS)

Defrère, Denis; Aerts, Conny; Kishimoto, Makoto; Léna, Pierre

2018-04-01

Optical long-baseline interferometry is a unique and powerful technique for astronomical research. Since the 1980's (with I2T, GI2T, Mark I to III, SUSI, ...), optical interferometers have produced an increasing number of scientific papers covering various fields of astrophysics. As current interferometric facilities are reaching their maturity, we take the opportunity in this paper to summarize the conclusions of a few key meetings, workshops, and conferences dedicated to interferometry. We present the most persistent recommendations related to science cases and discuss some key technological developments required to address them. In the era of extremely large telescopes, optical long-baseline interferometers will remain crucial to probe the smallest spatial scales and make breakthrough discoveries.

From K giants to G dwarfs: stellar lifetime effects on metallicity distributions derived from red giants

NASA Astrophysics Data System (ADS)

Manning, Ellen M.; Cole, Andrew A.

2017-11-01

We examine the biases inherent to chemical abundance distributions when targets are selected from the red giant branch (RGB), using simulated giant branches created from isochrones. We find that even when stars are chosen from the entire colour range of RGB stars and over a broad range of magnitudes, the relative numbers of stars of different ages and metallicities, integrated over all stellar types, are not accurately represented in the giant branch sample. The result is that metallicity distribution functions derived from RGB star samples require a correction before they can be fitted by chemical evolution models. We derive simple correction factors for over- and under-represented populations for the limiting cases of single-age populations with a broad range of metallicities and of continuous star formation at constant metallicity; an important general conclusion is that intermediate-age populations (≈1-4 Gyr) are over-represented in RGB samples. We apply our models to the case of the Large Magellanic Cloud bar and show that the observed metallicity distribution underestimates the true number of metal-poor stars by more than 25 per cent; as a result, the inferred importance of gas flows in chemical evolution models could potentially be overestimated. The age- and metallicity-dependences of RGB lifetimes require careful modelling if they are not to lead to spurious conclusions about the chemical enrichment history of galaxies.

Does information from ClinicalTrials.gov increase transparency and reduce bias? Results from a five-report case series.

PubMed

Adam, Gaelen P; Springs, Stacey; Trikalinos, Thomas; Williams, John W; Eaton, Jennifer L; Von Isenburg, Megan; Gierisch, Jennifer M; Wilson, Lisa M; Robinson, Karen A; Viswanathan, Meera; Middleton, Jennifer Cook; Forman-Hoffman, Valerie L; Berliner, Elise; Kaplan, Robert M

2018-04-16

We investigated whether information in ClinicalTrials.gov would impact the conclusions of five ongoing systematic reviews. We considered five reviews that included 495 studies total. Each review team conducted a search of ClinicalTrials.gov up to the date of the review's last literature search, screened the records using the review's eligibility criteria, extracted information, and assessed risk of bias and applicability. Each team then evaluated the impact of the evidence found in ClinicalTrials.gov on the conclusions in the review. Across the five reviews, the number of studies that had both a registry record and a publication varied widely, from none in one review to 43% of all studies identified in another. Among the studies with both a record and publication, there was also wide variability in the match between published outcomes and those listed in ClinicalTrials.gov. Of the 173 total ClinicalTrials.gov records identified across the five projects, between 11 and 43% did not have an associated publication. In the 14% of records that contained results, the new data provided in the ClinicalTrials.gov records did not change the results or conclusions of the reviews. Finally, a large number of published studies were not registered in ClinicalTrials.gov, but many of these were published before ClinicalTrials.gov's inception date of 2000. Improved prospective registration of trials and consistent reporting of results in ClinicalTrials.gov would help make ClinicalTrials.gov records more useful in finding unpublished information and identifying potential biases. In addition, consistent indexing in databases, such as MEDLINE, would allow for better matching of records and publications, leading to increased utility of these searches for systematic review projects.

Performance of HIV Prevention of Mother-To-Child Transmission Programs in Sub-Saharan Africa: Longitudinal Assessment of 64 Nevirapine-Based Programs Implemented in 25 Countries, 2000-2011

PubMed Central

Ladner, Joël; Besson, Marie-Hélène; Rodrigues, Mariana; Saba, Joseph; Audureau, Etienne

2015-01-01

Background To evaluate the performance and to identify predictive factors of performance in prevention of mother-to-child HIV transmission programs (PMTCT) in sub-Saharan African countries. Methods From 2000 to 2011, PMTCT programs included in the Viramune Donation Programme (VDP) were prospectively followed. Each institution included in the VDP provided data on program implementation, type of management institution, number of PMTCT sites, key programs outputs (HIV counseling and testing, NVP regimens received by mothers and newborns). Nevirapine Coverage Ratio (NCR), defined as the number of women who should have received nevirapine (observed HIV prevalence x number of women in antenatal care), was used to measure performance. Included programs were followed every six months through progress reports. Results A total of 64 programs in 25 sub-Saharan African countries were included. The mean program follow-up was 48.0 months (SD = 24.5); 20,084,490 women attended in antenatal clinics were included. The overall mean NCR was 0.52 (SD = 0.25), with an increase from 0.37 to 0.57 between the first and last progress reports (p<.0001); NCR increased by 3.26% per year-program. Between the first and the last report, the number of women counseled and tested increased from 64.3% to 86.0% (p<.0001), the number of women post-counseled from 87.5% to 91.3% (p = 0.08). After mixed linear regression analysis, type of responsible institution, number of women attended in ANC, and program initiation in 2005-2006 were significant predictive factors associated with the NCR. The effect of the time period increased from earlier to later periods. Conclusion A longitudinal assessment of large PMTCT programs shows that scaling-up of programs was increased in sub-Saharan African countries. The PMTCT coverage increased throughout the study period, especially after 2006. Performance may be better for programs with a small or medium number of women attended in ANC. Identification of factors that predict PMTCT program performance may help in the development and expansion of additional large PMTCT services in sub-Saharan Africa. PMID:26098311

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

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

Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.« less

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

DOE PAGES

Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.; ...

2016-05-25

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.« less

Large- and small-scale environmental factors drive distributions of cool-adapted plants in karstic microrefugia

PubMed Central

Vojtkó, András; Farkas, Tünde; Szabó, Anna; Havadtői, Krisztina; Vojtkó, Anna E.; Tölgyesi, Csaba; Cseh, Viktória; Erdős, László; Maák, István Elek; Keppel, Gunnar

2017-01-01

Background and aims Dolines are small- to large-sized bowl-shaped depressions of karst surfaces. They may constitute important microrefugia, as thermal inversion often maintains cooler conditions within them. This study aimed to identify the effects of large- (macroclimate) and small-scale (slope aspect and vegetation type) environmental factors on cool-adapted plants in karst dolines of East-Central Europe. We also evaluated the potential of these dolines to be microrefugia that mitigate the effects of climate change on cool-adapted plants in both forest and grassland ecosystems. Methods We compared surveys of plant species composition that were made between 2007 and 2015 in 21 dolines distributed across four mountain ranges (sites) in Hungary and Romania. We examined the effects of environmental factors on the distribution and number of cool-adapted plants on three scales: (1) regional (all sites); (2) within sites and; (3) within dolines. Generalized linear models and non-parametric tests were used for the analyses. Key Results Macroclimate, vegetation type and aspect were all significant predictors of the diversity of cool-adapted plants. More cool-adapted plants were recorded in the coolest site, with only few found in the warmest site. At the warmest site, the distribution of cool-adapted plants was restricted to the deepest parts of dolines. Within sites of intermediate temperature and humidity, the effect of vegetation type and aspect on the diversity of cool-adapted plants was often significant, with more taxa being found in grasslands (versus forests) and on north-facing slopes (versus south-facing slopes). Conclusions There is large variation in the number and spatial distribution of cool-adapted plants in karst dolines, which is related to large- and small-scale environmental factors. Both macro- and microrefugia are therefore likely to play important roles in facilitating the persistence of cool-adapted plants under global warming. PMID:28025290

A shrunken-2 Transgene Increases Maize Yield by Acting in Maternal Tissues to Increase the Frequency of Seed Development[W

PubMed Central

Hannah, L. Curtis; Futch, Brandon; Bing, James; Shaw, Janine R.; Boehlein, Susan; Stewart, Jon D.; Beiriger, Robert; Georgelis, Nikolaos; Greene, Thomas

2012-01-01

The maize (Zea mays) shrunken-2 (Sh2) gene encodes the large subunit of the rate-limiting starch biosynthetic enzyme, ADP-glucose pyrophosphorylase. Expression of a transgenic form of the enzyme with enhanced heat stability and reduced phosphate inhibition increased maize yield up to 64%. The extent of the yield increase is dependent on temperatures during the first 4 d post pollination, and yield is increased if average daily high temperatures exceed 33°C. As found in wheat (Triticum aestivum) and rice (Oryza sativa), this transgene increases maize yield by increasing seed number. This result was surprising, since an entire series of historic observations at the whole-plant, enzyme, gene, and physiological levels pointed to Sh2 playing an important role only in the endosperm. Here, we present several lines of evidence that lead to the conclusion that the Sh2 transgene functions in maternal tissue to increase seed number and, in turn, yield. Furthermore, the transgene does not increase ovary number; rather, it increases the probability that a seed will develop. Surprisingly, the number of fully developed seeds is only ∼50% of the number of ovaries in wild-type maize. This suggests that increasing the frequency of seed development is a feasible agricultural target, especially under conditions of elevated temperatures. PMID:22751213

A large-scale survey of genetic copy number variations among Han Chinese residing in Taiwan

PubMed Central

Lin, Chien-Hsing; Li, Ling-Hui; Ho, Sheng-Feng; Chuang, Tzu-Po; Wu, Jer-Yuarn; Chen, Yuan-Tsong; Fann, Cathy SJ

2008-01-01

Background Copy number variations (CNVs) have recently been recognized as important structural variations in the human genome. CNVs can affect gene expression and thus may contribute to phenotypic differences. The copy number inferring tool (CNIT) is an effective hidden Markov model-based algorithm for estimating allele-specific copy number and predicting chromosomal alterations from single nucleotide polymorphism microarrays. The CNIT algorithm, which was constructed using data from 270 HapMap multi-ethnic individuals, was applied to identify CNVs from 300 unrelated Han Chinese individuals in Taiwan. Results Using stringent selection criteria, 230 regions with variable copy numbers were identified in the Han Chinese population; 133 (57.83%) had been reported previously, 64 displayed greater than 1% CNV allele frequency. The average size of the CNV regions was 322 kb (ranging from 1.48 kb to 5.68 Mb) and covered a total of 2.47% of the human genome. A total of 196 of the CNV regions were simple deletions and 27 were simple amplifications. There were 449 genes and 5 microRNAs within these CNV regions; some of these genes are known to be associated with diseases. Conclusion The identified CNVs are characteristic of the Han Chinese population and should be considered when genetic studies are conducted. The CNV distribution in the human genome is still poorly characterized, and there is much diversity among different ethnic populations. PMID:19108714

The base number of ‘loxoscaphoid’ Asplenium species and its implication for cytoevolution in Aspleniaceae

PubMed Central

Bellefroid, Elke; Rambe, S. Khadijah; Leroux, Olivier; Viane, Ronald L. L.

2010-01-01

Background and Aims ‘Loxoscaphoid’ Asplenium species are morphologically a remarkably distinct group of Aspleniaceae. Except for two preliminary chromosome counts of Asplenium theciferum, the cytology of this group of species has, however, been largely unstudied. Methods Chromosome counts were obtained by acetocarmine squash preparations of one mitotic cell and several meiotic cells. Relative DNA content of gametophytic and sporophytic cells was determined by flow cytometry. The phylogenetic placement of A. loxoscaphoides, A. rutifolium s.l. and A. theciferum s.l. was investigated through an analysis of rbcL sequences. Key Results The dysploid base number is reported to be x = 35 in Asplenium centrafricanum, A. loxoscaphoides, A. sertularioides and A. theciferum. Analysis of rbcL sequences confirms that ‘loxoscaphoids’ nest robustly within Asplenium. Several high ploidy levels exceeding the tetraploid level were found in A. theciferum s.l. and A. rutifolium s.l. All taxa proved to be sexual. Conclusions Four base numbers are known at present for Aspleniaceae: x = 39, 38, 36 and 35. The dysploid base number x = 35 found in the ‘loxoscaphoid’ Asplenium spp. sheds a novel light on the cytoevolution of the whole family. We postulate a recurrent descending dysploid evolution within Aspleniaceae, leading to speciation at the (sub)generic and species/group level. PMID:20498038

Diffusion of an Evidence-Based Smoking Cessation Intervention Through Facebook: A Randomized Controlled Trial

PubMed Central

Cobb, Nathan K.; Jacobs, Megan A.; Wileyto, Paul; Valente, Thomas

2016-01-01

Objectives. To examine the diffusion of an evidence-based smoking cessation application (“app”) through Facebook social networks and identify specific intervention components that accelerate diffusion. Methods. Between December 2012 and October 2013, we recruited adult US smokers (“seeds”) via Facebook advertising and randomized them to 1 of 12 app variants using a factorial design. App variants targeted components of diffusion: duration of use (t), “contagiousness” (β), and number of contacts (Z). The primary outcome was the reproductive ratio (R), defined as the number of individuals installing the app (“descendants”) divided by the number of a seed participant’s Facebook friends. Results. We randomized 9042 smokers. App utilization metrics demonstrated between-variant differences in expected directions. The highest level of diffusion (R = 0.087) occurred when we combined active contagion strategies with strategies to increase duration of use (incidence rate ratio = 9.99; 95% confidence interval = 5.58, 17.91; P < .001). Involving nonsmokers did not affect diffusion. Conclusions. The maximal R value (0.087) is sufficient to increase the numbers of individuals receiving treatment if applied on a large scale. Online interventions can be designed a priori to spread through social networks. PMID:27077358

Titan's interior constrained from its obliquity and tidal Love number

NASA Astrophysics Data System (ADS)

Baland, Rose-Marie; Coyette, Alexis; Yseboodt, Marie; Beuthe, Mikael; Van Hoolst, Tim

2016-04-01

In the last few years, the Cassini-Huygens mission to the Saturn system has measured the shape, the obliquity, the static gravity field, and the tidally induced gravity field of Titan. The large values of the obliquity and of the k2 Love number both point to the existence of a global internal ocean below the icy crust. In order to constrain interior models of Titan, we combine the above-mentioned data as follows: (1) we build four-layer density profiles consistent with Titan's bulk properties; (2) we determine the corresponding internal flattening compatible with the observed gravity and topography; (3) we compute the obliquity and tidal Love number for each interior model; (4) we compare these predictions with the observations. Previously, we found that Titan is more differentiated than expected (assuming hydrostatic equilibrium), and that its ocean is dense and less than 100 km thick. Here, we revisit these conclusions using a more complete Cassini state model, including: (1) gravitational and pressure torques due to internal tidal deformations; (2) atmosphere/lakes-surface exchange of angular momentum; (3) inertial torque due to Poincaré flow. We also adopt faster methods to evaluate Love numbers (i.e. the membrane approach) in order to explore a larger parameter space.

Dendroscope: An interactive viewer for large phylogenetic trees

PubMed Central

Huson, Daniel H; Richter, Daniel C; Rausch, Christian; Dezulian, Tobias; Franz, Markus; Rupp, Regula

2007-01-01

Background Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems. Results We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP. Conclusion Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets. PMID:18034891

Differential foraging preferences on seed size by rodents result in higher dispersal success of medium-sized seeds.

PubMed

Cao, Lin; Wang, Zhenyu; Yan, Chuan; Chen, Jin; Guo, Cong; Zhang, Zhibin

2016-11-01

Rodent preference for scatter-hoarding large seeds has been widely considered to favor the evolution of large seeds. Previous studies supporting this conclusion were primarily based on observations at earlier stages of seed dispersal, or on a limited sample of successfully established seedlings. Because seed dispersal comprises multiple dispersal stages, we hypothesized that differential foraging preference on seed size by animal dispersers at different dispersal stages would ultimately result in medium-sized seeds having the highest dispersal success rates. In this study, by tracking a large number of seeds for 5 yr, we investigated the effects of seed size on seed fates from seed removal to seedling establishment of a dominant plant Pittosporopsis kerrii (Icacinaceae) dispersed by scatter-hoarding rodents in tropical forest in southwest China. We found that small seeds had a lower survival rate at the early dispersal stage where more small seeds were predated at seed stations and after removal; large seeds had a lower survival rate at the late dispersal stage, more large seeds were recovered, predated after being cached, or larder-hoarded. Medium-sized seeds experienced the highest dispersal success. Our study suggests that differential foraging preferences by scatter-hoarding rodents at different stages of seed dispersal could result in conflicting selective pressures on seed size and higher dispersal success of medium-sized seeds. © 2016 by the Ecological Society of America.

Evaluating the feasibility of using candidate DNA barcodes in discriminating species of the large Asteraceae family

PubMed Central

2010-01-01

Background Five DNA regions, namely, rbcL, matK, ITS, ITS2, and psbA-trnH, have been recommended as primary DNA barcodes for plants. Studies evaluating these regions for species identification in the large plant taxon, which includes a large number of closely related species, have rarely been reported. Results The feasibility of using the five proposed DNA regions was tested for discriminating plant species within Asteraceae, the largest family of flowering plants. Among these markers, ITS2 was the most useful in terms of universality, sequence variation, and identification capability in the Asteraceae family. The species discriminating power of ITS2 was also explored in a large pool of 3,490 Asteraceae sequences that represent 2,315 species belonging to 494 different genera. The result shows that ITS2 correctly identified 76.4% and 97.4% of plant samples at the species and genus levels, respectively. In addition, ITS2 displayed a variable ability to discriminate related species within different genera. Conclusions ITS2 is the best DNA barcode for the Asteraceae family. This approach significantly broadens the application of DNA barcoding to resolve classification problems in the family Asteraceae at the genera and species levels. PMID:20977734

A Survey of Residents' Perceptions of the Effect of Large-Scale Economic Developments on Perceived Safety, Violence, and Economic Benefits

PubMed Central

Geller, Ruth; Bear, Todd M.; Foulds, Abigail L.; Duell, Jessica; Sharma, Ravi

2015-01-01

Background. Emerging research highlights the promise of community- and policy-level strategies in preventing youth violence. Large-scale economic developments, such as sports and entertainment arenas and casinos, may improve the living conditions, economics, public health, and overall wellbeing of area residents and may influence rates of violence within communities. Objective. To assess the effect of community economic development efforts on neighborhood residents' perceptions on violence, safety, and economic benefits. Methods. Telephone survey in 2011 using a listed sample of randomly selected numbers in six Pittsburgh neighborhoods. Descriptive analyses examined measures of perceived violence and safety and economic benefit. Responses were compared across neighborhoods using chi-square tests for multiple comparisons. Survey results were compared to census and police data. Results. Residents in neighborhoods with the large-scale economic developments reported more casino-specific and arena-specific economic benefits. However, 42% of participants in the neighborhood with the entertainment arena felt there was an increase in crime, and 29% of respondents from the neighborhood with the casino felt there was an increase. In contrast, crime decreased in both neighborhoods. Conclusions. Large-scale economic developments have a direct influence on the perception of violence, despite actual violence rates. PMID:26273310

TIME DISTRIBUTIONS OF LARGE AND SMALL SUNSPOT GROUPS OVER FOUR SOLAR CYCLES

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

Kilcik, A.; Yurchyshyn, V. B.; Abramenko, V.

2011-04-10

Here we analyze solar activity by focusing on time variations of the number of sunspot groups (SGs) as a function of their modified Zurich class. We analyzed data for solar cycles 20-23 by using Rome (cycles 20 and 21) and Learmonth Solar Observatory (cycles 22 and 23) SG numbers. All SGs recorded during these time intervals were separated into two groups. The first group includes small SGs (A, B, C, H, and J classes by Zurich classification), and the second group consists of large SGs (D, E, F, and G classes). We then calculated small and large SG numbers frommore » their daily mean numbers as observed on the solar disk during a given month. We report that the time variations of small and large SG numbers are asymmetric except for solar cycle 22. In general, large SG numbers appear to reach their maximum in the middle of the solar cycle (phases 0.45-0.5), while the international sunspot numbers and the small SG numbers generally peak much earlier (solar cycle phases 0.29-0.35). Moreover, the 10.7 cm solar radio flux, the facular area, and the maximum coronal mass ejection speed show better agreement with the large SG numbers than they do with the small SG numbers. Our results suggest that the large SG numbers are more likely to shed light on solar activity and its geophysical implications. Our findings may also influence our understanding of long-term variations of the total solar irradiance, which is thought to be an important factor in the Sun-Earth climate relationship.« less

Glycosylation Focuses Sequence Variation in the Influenza A Virus H1 Hemagglutinin Globular Domain

PubMed Central

Hensley, Scott E.; Hurt, Darrell E.; Bennink, Jack R.; Yewdell, Jonathan W.

2010-01-01

Antigenic drift in the influenza A virus hemagglutinin (HA) is responsible for seasonal reformulation of influenza vaccines. Here, we address an important and largely overlooked issue in antigenic drift: how does the number and location of glycosylation sites affect HA evolution in man? We analyzed the glycosylation status of all full-length H1 subtype HA sequences available in the NCBI influenza database. We devised the “flow index” (FI), a simple algorithm that calculates the tendency for viruses to gain or lose consensus glycosylation sites. The FI predicts the predominance of glycosylation states among existing strains. Our analyses show that while the number of glycosylation sites in the HA globular domain does not influence the overall magnitude of variation in defined antigenic regions, variation focuses on those regions unshielded by glycosylation. This supports the conclusion that glycosylation generally shields HA from antibody-mediated neutralization, and implies that fitness costs in accommodating oligosaccharides limit virus escape via HA hyperglycosylation. PMID:21124818

Weight optimization of large span steel truss structures with genetic algorithm

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

Mojolic, Cristian; Hulea, Radu; Pârv, Bianca Roxana

2015-03-10

The paper presents the weight optimization process of the main steel truss that supports the Slatina Sport Hall roof. The structure was loaded with self-weight, dead loads, live loads, snow, wind and temperature, grouped in eleven load cases. The optimization of the structure was made using genetic algorithms implemented in a Matlab code. A total number of four different cases were taken into consideration when trying to determine the lowest weight of the structure, depending on the types of connections with the concrete structure ( types of supports, bearing modes), and the possibility of the lower truss chord nodes tomore » change their vertical position. A number of restrictions for tension, maximum displacement and buckling were enforced on the elements, and the cross sections are chosen by the program from a user data base. The results in each of the four cases were analyzed in terms of weight, element tension, element section and displacement. The paper presents the optimization process and the conclusions drawn.« less

Radiology workstation for mammography: preliminary observations, eyetracker studies, and design

NASA Astrophysics Data System (ADS)

Beard, David V.; Johnston, Richard E.; Pisano, Etta D.; Hemminger, Bradley M.; Pizer, Stephen M.

1991-07-01

For the last four years, the UNC FilmPlane project has focused on constructing a radiology workstation facilitating CT interpretations equivalent to those with film and viewbox. Interpretation of multiple CT studies was originally chosen because handling such large numbers of images was considered to be one of the most difficult tasks that could be performed with a workstation. The authors extend the FilmPlane design to address mammography. The high resolution and contrast demands coupled with the number of images often cross- compared make mammography a difficult challenge for the workstation designer. This paper presents the results of preliminary work with workstation interpretation of mammography. Background material is presented to justify why the authors believe electronic mammographic workstations could improve health care delivery. The results of several observation sessions and a preliminary eyetracker study of multiple-study mammography interpretations are described. Finally, tentative conclusions of what a mammographic workstation might look like and how it would meet clinical demand to be effective are presented.

High-resolution single-nucleotide polymorphism array-profiling in myeloproliferative neoplasms identifies novel genomic aberrations

PubMed Central

Stegelmann, Frank; Bullinger, Lars; Griesshammer, Martin; Holzmann, Karlheinz; Habdank, Marianne; Kuhn, Susanne; Maile, Carmen; Schauer, Stefanie; Döhner, Hartmut; Döhner, Konstanze

2010-01-01

Single-nucleotide polymorphism arrays allow for genome-wide profiling of copy-number alterations and copy-neutral runs of homozygosity at high resolution. To identify novel genetic lesions in myeloproliferative neoplasms, a large series of 151 clinically well characterized patients was analyzed in our study. Copy-number alterations were rare in essential thrombocythemia and polycythemia vera. In contrast, approximately one third of myelofibrosis patients exhibited small genomic losses (less than 5 Mb). In 2 secondary myelofibrosis cases the tumor suppressor gene NF1 in 17q11.2 was affected. Sequencing analyses revealed a mutation in the remaining NF1 allele of one patient. In terms of copy-neutral aberrations, no chromosomes other than 9p were recurrently affected. In conclusion, novel genomic aberrations were identified in our study, in particular in patients with myelofibrosis. Further analyses on single-gene level are necessary to uncover the mechanisms that are involved in the pathogenesis of myeloproliferative neoplasms. PMID:20015882

[Mineralocorticoid receptor antagonists in chronic kidney disease - pros and cons].

PubMed

Jędras, Mirosław; Filipowicz, Ewa

2017-01-01

Aldosterone takes part in the regulation of body fluid volume, blood pressure and kalemia. In a number of pathological conditions, including chronic kidney disease (CKD), secondary hyperaldosteronism occurs, leading to development of edema, hypervolemia and hypertension. Aldosterone has also a proinflammatory action, leading to heart and blood vessels damage, and is an independent risk factor of death. Some of the research conducted to confirm the expected benefits of angiotensin converting enzyme inhibitors (ACEi) and angiotensin II receptor blockers (ARB) therapy in CKD patients did not yield positive results, probably due to "aldosterone escape". Mineralocorticoid receptor antagonists (MRA) are being introduced also in the treatment of CKD patients, although the risk of developing hyperkalemia exists. A number of papers suggest a positive influence of MRA on slowing down the progression of renal failure, reduction of cardiovascular risk, and decreasing mortality, with relative safety of treatment, however the data are based on small and heterogenous groups of patients, therefore conclusive information is expected from large trials which are currently being conducted (BARACK D, ALCHEMIST).

Effect of special Hungarian probiotic kefir on faecal microflora

PubMed Central

Figler, Mária; Mózsik, Gyula; Schaffer, Béla; Gasztonyi, Beáta; Ács, Pongrác; Szili, Béla; Rab, Regina; Szakály, Sándor

2006-01-01

AIM: To investigate the effect of a four-week consumption of a special Hungarian probiotic agent (Biofir®) on the faecal microflora in human healthy subjects. METHODS: The effect of Biofir® with 106/cm3 initial germs on the faecal microflora was studied in 120 healthy volunteers (71 females, 49 males). The traditional Russian type kefir was used as control. The various germ groups and pH values were determined in wk 2, 4 and 6. RESULTS: The number of all microbes increased during the 4-week probiotic treatment. The number of microbes increased 4.3-fold in the control group and 6.8-fold in Biofir-treated group. The probiotic kefir caused multiplication of the probiotic flora, meanwhile the undesired bacteria multiplied in the control group. No significant change of pH values of the faeces was found in both groups. CONCLUSION: The Hungarian probiotic kefir (Biofir®) is capable of promoting multiplication of probiotic bacterial flora in the large bowel. PMID:16534858

Interpreting Epidemiological Evidence in the Presence of Multiple Endpoints: An Alternative Analytic Approach using the 9-Year Follow-up of the Seychelles Child Development Study

PubMed Central

van Wijngaarden, Edwin; Myers, Gary J.; Thurston, Sally W.; Shamlaye, Conrad F.; Davidson, Philip W.

2012-01-01

Purpose The potential for ill-informed causal inference is a major concern in published longitudinal studies evaluating impaired neurological function in children prenatally exposed to background levels of methyl mercury (MeHg). These studies evaluate a large number of developmental tests. We propose an alternative analysis strategy that reduces the number of comparisons tested in these studies. Methods Using data from the 9-year follow-up of 643 children in the Seychelles Child Development Study (SCDS), we grouped 18 individual endpoints into one overall ordinal outcome variable as well as by developmental domains. Subsequently, ordinal logistic regression analyses were performed. Results We did not find an association between prenatal MeHg exposure and developmental outcomes at 9 years of age. Conclusion Our proposed framework is more likely to result in a balanced interpretation of a posteriori associations. In addition, this new strategy should facilitate the use of complex epidemiological data in quantitative risk assessment. PMID:19205720

Constraining the baryon-dark matter relative velocity with the large-scale 3-point correlation function of the SDSS BOSS DR12 CMASS galaxies

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

Slepian, Zachary; Slosar, Anze; Eisenstein, Daniel J.

We search for a galaxy clustering bias due to a modulation of galaxy number with the baryon-dark matter relative velocity resulting from recombination-era physics. We find no detected signal and place the constraint bv <0.01 on the relative velocity bias for the CMASS galaxies. This bias is an important potential systematic of Baryon Acoustic Oscillation (BAO) method measurements of the cosmic distance scale using the 2-point clustering. Our limit on the relative velocity bias indicates a systematic shift of no more than 0.3% rms in the distance scale inferred from the BAO feature in the BOSS 2-point clustering, well belowmore » the 1% statistical error of this measurement. In conclusion, this constraint is the most stringent currently available and has important implications for the ability of upcoming large-scale structure surveys such as DESI to self-protect against the relative velocity as a possible systematic.« less

Large-scale GWAS identifies multiple loci for hand grip strength providing biological insights into muscular fitness.

PubMed

Willems, Sara M; Wright, Daniel J; Day, Felix R; Trajanoska, Katerina; Joshi, Peter K; Morris, John A; Matteini, Amy M; Garton, Fleur C; Grarup, Niels; Oskolkov, Nikolay; Thalamuthu, Anbupalam; Mangino, Massimo; Liu, Jun; Demirkan, Ayse; Lek, Monkol; Xu, Liwen; Wang, Guan; Oldmeadow, Christopher; Gaulton, Kyle J; Lotta, Luca A; Miyamoto-Mikami, Eri; Rivas, Manuel A; White, Tom; Loh, Po-Ru; Aadahl, Mette; Amin, Najaf; Attia, John R; Austin, Krista; Benyamin, Beben; Brage, Søren; Cheng, Yu-Ching; Cięszczyk, Paweł; Derave, Wim; Eriksson, Karl-Fredrik; Eynon, Nir; Linneberg, Allan; Lucia, Alejandro; Massidda, Myosotis; Mitchell, Braxton D; Miyachi, Motohiko; Murakami, Haruka; Padmanabhan, Sandosh; Pandey, Ashutosh; Papadimitriou, Ioannis; Rajpal, Deepak K; Sale, Craig; Schnurr, Theresia M; Sessa, Francesco; Shrine, Nick; Tobin, Martin D; Varley, Ian; Wain, Louise V; Wray, Naomi R; Lindgren, Cecilia M; MacArthur, Daniel G; Waterworth, Dawn M; McCarthy, Mark I; Pedersen, Oluf; Khaw, Kay-Tee; Kiel, Douglas P; Pitsiladis, Yannis; Fuku, Noriyuki; Franks, Paul W; North, Kathryn N; van Duijn, Cornelia M; Mather, Karen A; Hansen, Torben; Hansson, Ola; Spector, Tim; Murabito, Joanne M; Richards, J Brent; Rivadeneira, Fernando; Langenberg, Claudia; Perry, John R B; Wareham, Nick J; Scott, Robert A

2017-07-12

Hand grip strength is a widely used proxy of muscular fitness, a marker of frailty, and predictor of a range of morbidities and all-cause mortality. To investigate the genetic determinants of variation in grip strength, we perform a large-scale genetic discovery analysis in a combined sample of 195,180 individuals and identify 16 loci associated with grip strength (P<5 × 10 -8 ) in combined analyses. A number of these loci contain genes implicated in structure and function of skeletal muscle fibres (ACTG1), neuronal maintenance and signal transduction (PEX14, TGFA, SYT1), or monogenic syndromes with involvement of psychomotor impairment (PEX14, LRPPRC and KANSL1). Mendelian randomization analyses are consistent with a causal effect of higher genetically predicted grip strength on lower fracture risk. In conclusion, our findings provide new biological insight into the mechanistic underpinnings of grip strength and the causal role of muscular strength in age-related morbidities and mortality.

Electrical detection of single viruses

NASA Astrophysics Data System (ADS)

Patolsky, Fernando; Zheng, Gengfeng; Hayden, Oliver; Lakadamyali, Melike; Zhuang, Xiaowei; Lieber, Charles M.

2004-09-01

We report direct, real-time electrical detection of single virus particles with high selectivity by using nanowire field effect transistors. Measurements made with nanowire arrays modified with antibodies for influenza A showed discrete conductance changes characteristic of binding and unbinding in the presence of influenza A but not paramyxovirus or adenovirus. Simultaneous electrical and optical measurements using fluorescently labeled influenza A were used to demonstrate conclusively that the conductance changes correspond to binding/unbinding of single viruses at the surface of nanowire devices. pH-dependent studies further show that the detection mechanism is caused by a field effect, and that the nanowire devices can be used to determine rapidly isoelectric points and variations in receptor-virus binding kinetics for different conditions. Lastly, studies of nanowire devices modified with antibodies specific for either influenza or adenovirus show that multiple viruses can be selectively detected in parallel. The possibility of large-scale integration of these nanowire devices suggests potential for simultaneous detection of a large number of distinct viral threats at the single virus level.

IMS applications analysis

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

RODACY,PHILIP J.; REBER,STEPHEN D.; SIMONSON,ROBERT J.

This report examines the market potential of a miniature, hand-held Ion Mobility Spectrometer. Military and civilian markets are discussed, as well as applications in a variety of diverse fields. The strengths and weaknesses of competing technologies are discussed. An extensive Ion Mobility Spectrometry (IMS) bibliography is included. The conclusions drawn from this study are: (1) There are a number of competing technologies that are capable of detecting explosives, drugs, biological, or chemical agents. The IMS system currently represents the best available compromise regarding sensitivity, specificity, and portability. (2) The military market is not as large as the commercial market, butmore » the military services are more likely to invest R and D funds in the system. (3) Military applications should be addressed before commercial applications are addressed. (4) There is potentially a large commercial market for rugged, hand-held Ion Mobility Spectrometer systems. Commercial users typically do not invest R and D funds in this type of equipment rather, they wait for off-the-shelf availability.« less

Deficiency of ''Thin'' Stellar Bars in Seyfert Host Galaxies

NASA Technical Reports Server (NTRS)

Shlosman, Isaac; Peletier, Reynier F.; Knapen, Johan

1999-01-01

Using all available major samples of Seyfert galaxies and their corresponding control samples of closely matched non-active galaxies, we find that the bar ellipticities (or axial ratios) in Seyfert galaxies are systematically different from those in non-active galaxies. Overall, there is a deficiency of bars with large ellipticities (i.e., 'fat' or 'weak' bars) in Seyferts, compared to non-active galaxies. Accompanied with a large dispersion due to small number statistics, this effect is strictly speaking at the 2 sigma level. To obtain this result, the active galaxy samples of near-infrared surface photometry were matched to those of normal galaxies in type, host galaxy ellipticity, absolute magnitude, and, to some extent, in redshift. We discuss possible theoretical explanations of this phenomenon within the framework of galactic evolution, and, in particular, of radial gas redistribution in barred galaxies. Our conclusions provide further evidence that Seyfert hosts differ systematically from their non-active counterparts on scales of a few kpc.

Mitochondrial DNA sequence variation and phylogeography of the scarlet kingsnake (Lampropeltis elapsoides).

PubMed

Friedman, Michael; Schaffer, Les

2011-02-01

BACKGROUND AND AIMS. With the goal of assessing population structure and geographic distribution of haplotype lineages among Lampropeltis elapsoides, we sequenced the ND4 mitochondrial DNA locus from 96 specimens of this snake across its area of distribution. MATERIALS AND METHODS. We relied heavily on formalin-fixed museum specimens to accomplish this analysis. RESULTS. The sequence alignment consisted of 491 bp of the selected gene, with 28% missing data. A simulation used to assess the effect of missing data on population genetic and phylogenetic resolution indicated increased character conflict, but with minimal loss of phylogenetic structure. CONCLUSION. This limited dataset suggests that L. elapsoides constitutes a largely unstructured population, with both widespread haplotypes and large number of private haplotypes, a moderate level of nucleotide diversity, and a low, but significant, degree of north-south population differentiation. Haplotype structure and frequency, nucleotide frequency, and values for Tajima's D and Fu's F(S) indicate a recent range or population expansion following a historic bottleneck.

Constraining the baryon-dark matter relative velocity with the large-scale 3-point correlation function of the SDSS BOSS DR12 CMASS galaxies

DOE PAGES

Slepian, Zachary; Slosar, Anze; Eisenstein, Daniel J.; ...

2017-10-24

We search for a galaxy clustering bias due to a modulation of galaxy number with the baryon-dark matter relative velocity resulting from recombination-era physics. We find no detected signal and place the constraint bv <0.01 on the relative velocity bias for the CMASS galaxies. This bias is an important potential systematic of Baryon Acoustic Oscillation (BAO) method measurements of the cosmic distance scale using the 2-point clustering. Our limit on the relative velocity bias indicates a systematic shift of no more than 0.3% rms in the distance scale inferred from the BAO feature in the BOSS 2-point clustering, well belowmore » the 1% statistical error of this measurement. In conclusion, this constraint is the most stringent currently available and has important implications for the ability of upcoming large-scale structure surveys such as DESI to self-protect against the relative velocity as a possible systematic.« less

An Evaluation of Systematic Tuberculosis Screening at Private Facilities in Karachi, Pakistan

PubMed Central

Creswell, Jacob; Khowaja, Saira; Codlin, Andrew; Hashmi, Rabia; Rasheed, Erum; Khan, Mubashir; Durab, Irfan; Mergenthaler, Christina; Hussain, Owais; Khan, Faisal; Khan, Aamir J.

2014-01-01

Background In Pakistan, like many Asian countries, a large proportion of healthcare is provided through the private sector. We evaluated a systematic screening strategy to identify people with tuberculosis in private facilities in Karachi and assessed the approaches' ability to diagnose patients earlier in their disease progression. Methods and Findings Lay workers at 89 private clinics and a large hospital outpatient department screened all attendees for tuberculosis using a mobile phone-based questionnaire during one year. The number needed to screen to detect a case of tuberculosis was calculated. To evaluate early diagnosis, we tested for differences in cough duration and smear grading by screening facility. 529,447 people were screened, 1,010 smear-positive tuberculosis cases were detected and 942 (93.3%) started treatment, representing 58.7% of all smear-positive cases notified in the intervention area. The number needed to screen to detect a smear-positive case was 124 (prevalence 806/100,000) at the hospital and 763 (prevalence 131/100,000) at the clinics; however, ten times the number of individuals were screened in clinics. People with smear-positive TB detected at the hospital were less likely to report cough lasting 2–3 weeks (RR 0.66 95%CI [0.49–0.90]) and more likely to report cough duration >3 weeks (RR 1.10 95%CI [1.03–1.18]). Smear-positive cases at the clinics were less likely to have a +3 grade (RR 0.76 95%CI [0.63–0.92]) and more likely to have +1 smear grade (RR 1.24 95%CI [1.02–1.51]). Conclusions Tuberculosis screening at private facilities is acceptable and can yield large numbers of previously undiagnosed cases. Screening at general practitioner clinics may find cases earlier than at hospitals although more people must be screened to identify a case of tuberculosis. Limitations include lack of culture testing, therefore underestimating true TB prevalence. Using more sensitive and specific screening and diagnostic tests such as chest x-ray and Xpert MTB/RIF may improve results. PMID:24705600

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

PubMed Central

2010-01-01

Background Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome. Results We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes. Conclusions ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such as a different Chromatin immunoprecipitation (ChIP) preparation and a dataset from literature, or existing annotation packages, such as GenomicFeatures and BSgenome, provides flexibility. Tight integration to the biomaRt package enables up-to-date annotation retrieval from the BioMart database. PMID:20459804

Food bodies in Cissus verticillata (Vitaceae): ontogenesis, structure and functional aspects

PubMed Central

Paiva, Elder Antônio Sousa; Buono, Rafael Andrade; Lombardi, Julio Antonio

2009-01-01

Background and Aims The distinction between pearl bodies (or pearl glands) and food bodies (FBs) is not clear; neither is our understanding of what these structures really represent. The present work examined the ontogenesis, structure, ultrastructure and histochemical aspects of the protuberances in Cissus verticillata, which have been described since the beginning of the 19th century as pearl glands or pearl bodies, in order to establish a relationship between their structure and function. Methods Segments of stems and leaves in different stages of development were collected and fixed for study under light microscopy as well as electron transmission and scanning microscopy. Samples of FBs were subjected to chemical analysis using thin-layer chromatography. Key Results The FBs in C. verticillata are globose and attached to the plant by a short peduncle. These structures are present along the entire stem during primary growth, and on the inflorescence axis and the abaxial face of the leaves. The FBs were observed to be of mixed origin, with the participation of both the epidermis and the underlying parenchymatic cells. The epidermis is uniseriate with a thin cuticle, and the cells have dense cytoplasm and a large nucleus. The internal parenchymatic cells have thin walls; in the young structures these cells have dense cytoplasm with a predominance of mitochondria and plastids. In the mature FBs, the parenchymatic cells accumulate oils and soluble sugars; dictyosomes and rough endoplasmic reticulum predominate in the cytoplasm; the vacuoles are ample. Removal of the FBs appears to stimulate the formation of new ones, at the same place. Conclusions The vegetative vigour of the plant seems to influence the number of FBs produced, with more vigorous branches having greater densities of FBs. The results allow the conclusion that the structures traditionally designated pearl glands or pearl bodies in C. verticillata constitute FBs that can recruit large numbers of ants. PMID:19049986

Low-lying intruder and tensor-driven structures in 82As revealed by β decay at a new movable-tape-based experimental setup

NASA Astrophysics Data System (ADS)

Etilé, A.; Verney, D.; Arsenyev, N. N.; Bettane, J.; Borzov, I. N.; Cheikh Mhamed, M.; Cuong, P. V.; Delafosse, C.; Didierjean, F.; Gaulard, C.; Van Giai, Nguyen; Goasduff, A.; Ibrahim, F.; Kolos, K.; Lau, C.; Niikura, M.; Roccia, S.; Severyukhin, A. P.; Testov, D.; Tusseau-Nenez, S.; Voronov, V. V.

2015-06-01

The β decay of 82Ge Ge was re-investigated using the newly commissioned tape station BEDO at the electron-driven ISOL (isotope separation on line) facility ALTO operated by the Institut de Physique Nucléaire, Orsay. The original motivation of this work was focused on the sudden occurrence in the light N =49 odd-odd isotonic chain of a large number of J ≤1 states (positive or negative parity) in 80Ga by providing a reliable intermediate example, viz., 82As. The extension of the 82As level scheme towards higher energies from the present work has revealed three potential 1+ states above the already known one at 1092 keV. In addition our data allow ruling out the hypothesis that the 843 keV level could be a 1+ state. A detailed analysis of the level scheme using both an empirical core-particle coupling model and a fully microscopic treatment within a Skyrme-QRPA (quasiparticle random-phase approximation) approach using the finite-rank separable approximation was performed. From this analysis two conclusions can be drawn: (i) the presence of a large number of low-lying low-spin negative parity states is due to intruder states stemming from above the N =50 shell closure, and (ii) the sudden increase, from 82As to 80Ga, of the number of low-lying 1+ states and the corresponding Gamow-Teller fragmentation are naturally reproduced by the inclusion of tensor correlations and couplings to 2p-2h excitations.

Spatio-temporal optimization of sampling for bluetongue vectors (Culicoides) near grazing livestock

PubMed Central

2013-01-01

Background Estimating the abundance of Culicoides using light traps is influenced by a large variation in abundance in time and place. This study investigates the optimal trapping strategy to estimate the abundance or presence/absence of Culicoides on a field with grazing animals. We used 45 light traps to sample specimens from the Culicoides obsoletus species complex on a 14 hectare field during 16 nights in 2009. Findings The large number of traps and catch nights enabled us to simulate a series of samples consisting of different numbers of traps (1-15) on each night. We also varied the number of catch nights when simulating the sampling, and sampled with increasing minimum distances between traps. We used resampling to generate a distribution of different mean and median abundance in each sample. Finally, we used the hypergeometric distribution to estimate the probability of falsely detecting absence of vectors on the field. The variation in the estimated abundance decreased steeply when using up to six traps, and was less pronounced when using more traps, although no clear cutoff was found. Conclusions Despite spatial clustering in vector abundance, we found no effect of increasing the distance between traps. We found that 18 traps were generally required to reach 90% probability of a true positive catch when sampling just one night. But when sampling over two nights the same probability level was obtained with just three traps per night. The results are useful for the design of vector monitoring programmes on fields with grazing animals. PMID:23705770

Nuclear exoticism

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

Penionzhkevich, Yu. E., E-mail: pyuer@mail.ru

2016-07-15

Extreme states of nuclearmatter (such that feature high spins, large deformations, high density and temperature, or a large excess of neutrons and protons) play an important role in studying fundamental properties of nuclei and are helpful in solving the problem of constructing the equation of state for nuclear matter. The synthesis of neutron-rich nuclei near the nucleon drip lines and investigation of their properties permit drawing conclusions about the positions of these boundaries and deducing information about unusual states of such nuclei and about their decays. At the present time, experimental investigations along these lines can only be performed viamore » the cooperation of leading research centers that possess powerful heavy-ion accelerators, such as the Large Hadron Collider (LHC) at CERN and the heavy-ion cyclotrons at the Joint Institute for Nuclear Research (JINR, Dubna), where respective experiments are being conducted by physicists from about 20 JINR member countries. The present article gives a survey of the most recent results in the realms of super neutron-rich nuclei. Implications of the change in the structure of such nuclei near the nucleon drip lines are discussed. Information about the results obtained by measuring the masses (binding energies) of exotic nuclei, the nucleon-distribution radii (neutron halo) and momentum distributions in them, and their deformations and quantum properties is presented. It is shown that the properties of nuclei lying near the stability boundaries differ strongly from the properties of other nuclei. The problem of the stability of nuclei that is associated with the magic numbers of 20 and 28 is discussed along with the effect of new magic numbers.« less

Diffusion Kurtosis Imaging of Acute Infarction: Comparison with Routine Diffusion and Follow-up MR Imaging.

PubMed

Yin, Jianzhong; Sun, Haizhen; Wang, Zhiyun; Ni, Hongyan; Shen, Wen; Sun, Phillip Zhe

2018-05-01

Purpose To determine the relationship between diffusion-weighted imaging (DWI) and diffusion kurtosis imaging (DKI) in patients with acute stroke at admission and the tissue outcome 1 month after onset of stroke. Materials and Methods Patients with stroke underwent DWI (b values = 0, 1000 sec/mm 2 along three directions) and DKI (b values = 0, 1000, 2000 sec/mm 2 along 20 directions) within 24 hours after symptom onset and 1 month after symptom onset. For large lesions (diameter ≥ 1 cm), acute lesion volumes at DWI and DKI were compared with those at follow-up T2-weighted imaging by using Spearman correlation analysis. For small lesions (diameter < 1 cm), the number of acute lesions at DWI and DKI and follow-up T2-weighted imaging was counted and compared by using the McNemar test. Results Thirty-seven patients (mean age, 58 years; range, 35-82 years) were included. There were 32 large lesions and 138 small lesions. For large lesions, the volumes of acute lesions on kurtosis maps showed no difference from those on 1-month follow-up T2-weighted images (P = .532), with a higher correlation coefficient than those on the apparent diffusion coefficient and mean diffusivity maps (R 2 = 0.730 vs 0.479 and 0.429). For small lesions, the number of acute lesions on DKI, but not on DWI, images was consistent with that on the follow-up T2-weighted images (P = .125). Conclusion DKI complements DWI for improved prediction of outcome of acute ischemic stroke. © RSNA, 2018.

Taking OSCE examiner training on the road: reaching the masses

PubMed Central

Reid, Katharine; Smallwood, David; Collins, Margo; Sutherland, Ruth; Dodds, Agnes

2016-01-01

Background To ensure the rigour of objective structured clinical examinations (OSCEs) in assessing medical students, medical school educators must educate examiners with a view to standardising examiner assessment behaviour. Delivering OSCE examiner training is a necessary yet challenging part of the OSCE process. A novel approach to implementing training for current and potential OSCE examiners was trialled by delivering large-group education sessions at major teaching hospitals. Methods The ‘OSCE Roadshow’ comprised a short training session delivered in the context of teaching hospital ‘Grand Rounds’ to current and potential OSCE examiners. The training was developed to educate clinicians about OSCE processes, clarify the examiners’ role and required behaviours, and to review marking guides and mark allocation in an effort to standardise OSCE processes and encourage consistency in examiner marking behaviour. A short exercise allowed participants to practise marking a mock OSCE to investigate examiner marking behaviour after the training. Results OSCE Roadshows at four metropolitan and one rural teaching hospital were well received and well attended by 171 clinicians across six sessions. Unexpectedly, medical students also attended in large numbers (n=220). After training, participants’ average scores for the mock OSCE clustered closely around the ideal score of 28 (out of 40), and the average scores did not differ according to the levels of clinical experience. Conclusion The OSCE Roadshow demonstrated the potential of brief familiarisation training in reaching large numbers of current and potential OSCE examiners in a time and cost-effective manner to promote standardisation of OSCE processes. PMID:27687287

Tracking the NGS revolution: managing life science research on shared high-performance computing clusters

PubMed Central

2018-01-01

Abstract Background Next-generation sequencing (NGS) has transformed the life sciences, and many research groups are newly dependent upon computer clusters to store and analyze large datasets. This creates challenges for e-infrastructures accustomed to hosting computationally mature research in other sciences. Using data gathered from our own clusters at UPPMAX computing center at Uppsala University, Sweden, where core hour usage of ∼800 NGS and ∼200 non-NGS projects is now similar, we compare and contrast the growth, administrative burden, and cluster usage of NGS projects with projects from other sciences. Results The number of NGS projects has grown rapidly since 2010, with growth driven by entry of new research groups. Storage used by NGS projects has grown more rapidly since 2013 and is now limited by disk capacity. NGS users submit nearly twice as many support tickets per user, and 11 more tools are installed each month for NGS projects than for non-NGS projects. We developed usage and efficiency metrics and show that computing jobs for NGS projects use more RAM than non-NGS projects, are more variable in core usage, and rarely span multiple nodes. NGS jobs use booked resources less efficiently for a variety of reasons. Active monitoring can improve this somewhat. Conclusions Hosting NGS projects imposes a large administrative burden at UPPMAX due to large numbers of inexperienced users and diverse and rapidly evolving research areas. We provide a set of recommendations for e-infrastructures that host NGS research projects. We provide anonymized versions of our storage, job, and efficiency databases. PMID:29659792

Physical activity and obesity: what we know and what we need to know.

PubMed

Chin, S-H; Kahathuduwa, C N; Binks, M

2016-12-01

Creating a negative energy balance by decreasing caloric consumption and increasing physical activity is a common strategy used to treat obesity. A large number of review and original research papers have considered the role of physical activity in weight loss and maintenance. However, their conclusions are at times conflicting. In this review, we have critically evaluated the findings of systematic reviews and meta-analyses and supplemented their conclusions with recently published, high-quality clinical trials. We have eliminated studies that were methodologically flawed in an attempt to reduce the ambiguity in the literature. We further sought, through selective review of these publications, to isolate the effects of various types of exercise, independent of dietary interventions, to further clarify their independent contributions. Thus, our review describes (i) combined calorie restriction with physical activity interventions, (ii) physical activity interventions without calorie restriction and (iii) the role of physical activity on maintenance of weight loss. Through this critical examination of the literature, we have provided conclusions to address certain ambiguities regarding the role of physical activity in obesity treatment that will inform clinical practice. We have also identified several long-standing gaps in knowledge that will inform future research. © 2016 The Authors. Obesity Reviews published by John Wiley & Sons Ltd on behalf of World Obesity Federation.

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

PubMed Central

2010-01-01

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size. PMID:20565983

Efficacy and safety of Suanzaoren decoction for primary insomnia: a systematic review of randomized controlled trials

PubMed Central

2013-01-01

Background Insomnia is a widespread human health problem, but there currently are the limitations of conventional therapies available. Suanzaoren decoction (SZRD) is a well known classic Chinese herbal prescription for insomnia and has been treating people’s insomnia for more than thousand years. The objective of this study was to evaluate the efficacy and safety of SZRD for insomnia. Methods A systematic literature search was performed for 6 databases up to July of 2012 to identify randomized control trials (RCTs) involving SZRD for insomniac patients. The methodological quality of RCTs was assessed independently using the Cochrane Handbook for Systematic Reviews of Interventions. Results Twelve RCTs with total of 1376 adult participants were identified. The methodological quality of all included trials are no more than 3/8 score. Majority of the RCTs concluded that SZRD was more significantly effective than benzodiazepines for treating insomnia. Despite these positive outcomes, there were many methodological shortcomings in the studies reviewed, including insufficient information about randomization generation and absence of allocation concealment, lack of blinding and no placebo control, absence of intention-to-treat analysis and lack of follow-ups, selective publishing and reporting, and small number of sample sizes. A number of clinical heterogeneity such as diagnosis, intervention, control, and outcome measures were also reviewed. Only 3 trials reported adverse events, whereas the other 9 trials did not provide the safety information. Conclusions Despite the apparent reported positive findings, there is insufficient evidence to support efficacy of SZRD for insomnia due to the poor methodological quality and the small number of trials of the included studies. SZRD seems generally safe, but is insufficient evidence to make conclusions on the safety because fewer studies reported the adverse events. Further large sample-size and well-designed RCTs are needed. PMID:23336848

SU-F-J-193: Efficient Dose Extinction Method for Water Equivalent Path Length (WEPL) of Real Tissue Samples for Validation of CT HU to Stopping Power Conversion

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

Zhang, R; Baer, E; Jee, K

Purpose: For proton therapy, an accurate model of CT HU to relative stopping power (RSP) conversion is essential. In current practice, validation of these models relies solely on measurements of tissue substitutes with standard compositions. Validation based on real tissue samples would be much more direct and can address variations between patients. This study intends to develop an efficient and accurate system based on the concept of dose extinction to measure WEPL and retrieve RSP in biological tissue in large number of types. Methods: A broad AP proton beam delivering a spread out Bragg peak (SOBP) is used to irradiatemore » the samples with a Matrixx detector positioned immediately below. A water tank was placed on top of the samples, with the water level controllable in sub-millimeter by a remotely controlled dosing pump. While gradually lowering the water level with beam on, the transmission dose was recorded at 1 frame/sec. The WEPL were determined as the difference between the known beam range of the delivered SOBP (80%) and the water level corresponding to 80% of measured dose profiles in time. A Gammex 467 phantom was used to test the system and various types of biological tissue was measured. Results: RSP for all Gammex inserts, expect the one made with lung-450 material (<2% error), were determined within ±0.5% error. Depends on the WEPL of investigated phantom, a measurement takes around 10 min, which can be accelerated by a faster pump. Conclusion: Based on the concept of dose extinction, a system was explored to measure WEPL efficiently and accurately for a large number of samples. This allows the validation of CT HU to stopping power conversions based on large number of samples and real tissues. It also allows the assessment of beam uncertainties due to variations over patients, which issue has never been sufficiently studied before.« less

Integrative Approach to Quality Assessment of Medical Journals Using Impact Factor, Eigenfactor, and Article Influence Scores

PubMed Central

Rizkallah, Jacques; Sin, Don D.

2010-01-01

Background Impact factor (IF) is a commonly used surrogate for assessing the scientific quality of journals and articles. There is growing discontent in the medical community with the use of this quality assessment tool because of its many inherent limitations. To help address such concerns, Eigenfactor (ES) and Article Influence scores (AIS) have been devised to assess scientific impact of journals. The principal aim was to compare the temporal trends in IF, ES, and AIS on the rank order of leading medical journals over time. Methods The 2001 to 2008 IF, ES, AIS, and number of citable items (CI) of 35 leading medical journals were collected from the Institute of Scientific Information (ISI) and the http://www.eigenfactor.org databases. The journals were ranked based on the published 2008 ES, AIS, and IF scores. Temporal score trends and variations were analyzed. Results In general, the AIS and IF values provided similar rank orders. Using ES values resulted in large changes in the rank orders with higher ranking being assigned to journals that publish a large volume of articles. Since 2001, the IF and AIS of most journals increased significantly; however the ES increased in only 51% of the journals in the analysis. Conversely, 26% of journals experienced a downward trend in their ES, while the rest experienced no significant changes (23%). This discordance between temporal trends in IF and ES was largely driven by temporal changes in the number of CI published by the journals. Conclusion The rank order of medical journals changes depending on whether IF, AIS or ES is used. All of these metrics are sensitive to the number of citable items published by journals. Consumers should thus consider all of these metrics rather than just IF alone in assessing the influence and importance of medical journals in their respective disciplines. PMID:20419115

An empirical study using permutation-based resampling in meta-regression

PubMed Central

2012-01-01

Background In meta-regression, as the number of trials in the analyses decreases, the risk of false positives or false negatives increases. This is partly due to the assumption of normality that may not hold in small samples. Creation of a distribution from the observed trials using permutation methods to calculate P values may allow for less spurious findings. Permutation has not been empirically tested in meta-regression. The objective of this study was to perform an empirical investigation to explore the differences in results for meta-analyses on a small number of trials using standard large sample approaches verses permutation-based methods for meta-regression. Methods We isolated a sample of randomized controlled clinical trials (RCTs) for interventions that have a small number of trials (herbal medicine trials). Trials were then grouped by herbal species and condition and assessed for methodological quality using the Jadad scale, and data were extracted for each outcome. Finally, we performed meta-analyses on the primary outcome of each group of trials and meta-regression for methodological quality subgroups within each meta-analysis. We used large sample methods and permutation methods in our meta-regression modeling. We then compared final models and final P values between methods. Results We collected 110 trials across 5 intervention/outcome pairings and 5 to 10 trials per covariate. When applying large sample methods and permutation-based methods in our backwards stepwise regression the covariates in the final models were identical in all cases. The P values for the covariates in the final model were larger in 78% (7/9) of the cases for permutation and identical for 22% (2/9) of the cases. Conclusions We present empirical evidence that permutation-based resampling may not change final models when using backwards stepwise regression, but may increase P values in meta-regression of multiple covariates for relatively small amount of trials. PMID:22587815

Integration of eHealth Tools in the Process of Workplace Health Promotion: Proposal for Design and Implementation

PubMed Central

2018-01-01

Background Electronic health (eHealth) and mobile health (mHealth) tools can support and improve the whole process of workplace health promotion (WHP) projects. However, several challenges and opportunities have to be considered while integrating these tools in WHP projects. Currently, a large number of eHealth tools are developed for changing health behavior, but these tools can support the whole WHP process, including group administration, information flow, assessment, intervention development process, or evaluation. Objective To support a successful implementation of eHealth tools in the whole WHP processes, we introduce a concept of WHP (life cycle model of WHP) with 7 steps and present critical and success factors for the implementation of eHealth tools in each step. Methods We developed a life cycle model of WHP based on the World Health Organization (WHO) model of healthy workplace continual improvement process. We suggest adaptations to the WHO model to demonstrate the large number of possibilities to implement eHealth tools in WHP as well as possible critical points in the implementation process. Results eHealth tools can enhance the efficiency of WHP in each of the 7 steps of the presented life cycle model of WHP. Specifically, eHealth tools can support by offering easier administration, providing an information and communication platform, supporting assessments, presenting and discussing assessment results in a dashboard, and offering interventions to change individual health behavior. Important success factors include the possibility to give automatic feedback about health parameters, create incentive systems, or bring together a large number of health experts in one place. Critical factors such as data security, anonymity, or lack of management involvement have to be addressed carefully to prevent nonparticipation and dropouts. Conclusions Using eHealth tools can support WHP, but clear regulations for the usage and implementation of these tools at the workplace are needed to secure quality and reach sustainable results. PMID:29475828

Using Modelling to Disentangle the Relative Contributions of Zoonotic and Anthroponotic Transmission: The Case of Lassa Fever

PubMed Central

Lo Iacono, Giovanni; Cunningham, Andrew A.; Fichet-Calvet, Elisabeth; Garry, Robert F.; Grant, Donald S.; Khan, Sheik Humarr; Leach, Melissa; Moses, Lina M.; Schieffelin, John S.; Shaffer, Jeffrey G.; Webb, Colleen T.; Wood, James L. N.

2015-01-01

Background Zoonotic infections, which transmit from animals to humans, form the majority of new human pathogens. Following zoonotic transmission, the pathogen may already have, or may acquire, the ability to transmit from human to human. With infections such as Lassa fever (LF), an often fatal, rodent-borne, hemorrhagic fever common in areas of West Africa, rodent-to-rodent, rodent-to-human, human-to-human and even human-to-rodent transmission patterns are possible. Indeed, large hospital-related outbreaks have been reported. Estimating the proportion of transmission due to human-to-human routes and related patterns (e.g. existence of super-spreaders), in these scenarios is challenging, but essential for planned interventions. Methodology/Principal Findings Here, we make use of an innovative modeling approach to analyze data from published outbreaks and the number of LF hospitalized patients to Kenema Government Hospital in Sierra Leone to estimate the likely contribution of human-to-human transmission. The analyses show that almost of the cases at KGH are secondary cases arising from human-to-human transmission. However, we found much of this transmission is associated with a disproportionally large impact of a few individuals (‘super-spreaders’), as we found only of human cases result in an effective reproduction number (i.e. the average number of secondary cases per infectious case) , with a maximum value up to . Conclusions/Significance This work explains the discrepancy between the sizes of reported LF outbreaks and a clinical perception that human-to-human transmission is low. Future assessment of risks of LF and infection control guidelines should take into account the potentially large impact of super-spreaders in human-to-human transmission. Our work highlights several neglected topics in LF research, the occurrence and nature of super-spreading events and aspects of social behavior in transmission and detection. PMID:25569707

MO-FG-202-05: Identifying Treatment Planning System Errors in IROC-H Phantom Irradiations

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

Kerns, J; Followill, D; Howell, R

Purpose: Treatment Planning System (TPS) errors can affect large numbers of cancer patients receiving radiation therapy. Using an independent recalculation system, the Imaging and Radiation Oncology Core-Houston (IROC-H) can identify institutions that have not sufficiently modelled their linear accelerators in their TPS model. Methods: Linear accelerator point measurement data from IROC-H’s site visits was aggregated and analyzed from over 30 linear accelerator models. Dosimetrically similar models were combined to create “classes”. The class data was used to construct customized beam models in an independent treatment dose verification system (TVS). Approximately 200 head and neck phantom plans from 2012 to 2015more » were recalculated using this TVS. Comparison of plan accuracy was evaluated by comparing the measured dose to the institution’s TPS dose as well as the TVS dose. In cases where the TVS was more accurate than the institution by an average of >2%, the institution was identified as having a non-negligible TPS error. Results: Of the ∼200 recalculated plans, the average improvement using the TVS was ∼0.1%; i.e. the recalculation, on average, slightly outperformed the institution’s TPS. Of all the recalculated phantoms, 20% were identified as having a non-negligible TPS error. Fourteen plans failed current IROC-H criteria; the average TVS improvement of the failing plans was ∼3% and 57% were found to have non-negligible TPS errors. Conclusion: IROC-H has developed an independent recalculation system to identify institutions that have considerable TPS errors. A large number of institutions were found to have non-negligible TPS errors. Even institutions that passed IROC-H criteria could be identified as having a TPS error. Resolution of such errors would improve dose delivery for a large number of IROC-H phantoms and ultimately, patients.« less

Variables Associated with Infections of Cattle by Brucella abortus., Leptospira spp. and Neospora spp. in Amazon Region in Brazil.

PubMed

Chiebao, D P; Valadas, S Y O B; Minervino, A H H; Castro, V; Romaldini, A H C N; Calhau, A S; De Souza, R A B; Gennari, S M; Keid, L B; Soares, R M

2015-10-01

The frequency of Neospora spp., Leptospira spp. and Brucella abortus infections in adult cattle was determined in herds of the State of Pará, Brazil, which is an important region for cattle production located in the Amazon region. A total of 3466 adult female cattle from 176 herds were tested, leading to a frequency of seropositive animals of 14.7%, 3.7% and 65.5% and a herd positivity of 87.4%, 41.3% and 98.8% for infections caused by Neospora spp., B. abortus and Leptospira spp., respectively. The five most frequently diagnosed serologic responses to Leptospira spp. were those against serovars hardjo, wolfii, grippotyphosa, hebdomadis and shermani. The following associations were found: practice of artificial insemination, large farm size, large herd size, large number of dogs and high number of total abortions per year with the presence of antibodies against serovar hardjo; positive results to serovar grippotyphosa with the presence of dogs; inappropriate disposal of aborted foetuses with positivity to serovar hebdomadis. Serovar grippotyphosa was also associated with number of episodes of abortions. Neospora spp. positive herds were associated with episodes of abortion and B. abortus infection with the disposal of dead animals and aborted foetuses on pastures and with the use of artificial insemination. In conclusion, the high frequency of brucellosis, leptospirosis and neosporosis in the region may be a consequence of social, natural and raising conditions as: (i) climate conditions that favour the survival and spread of pathogens in the environment; (ii) farms located in regions bordering forest areas; (iii) farms in areas of difficult access to the veterinary service; (iv) extensive beef herds raised at pastures with different age and productive groups inter-mingled; and (v) minimal concerns regarding hygiene practices and disease prevention measures. © 2013 Blackwell Verlag GmbH.

A simulation analysis to characterize the dynamics of vaccinating behaviour on contact networks

PubMed Central

2009-01-01

Background Human behavior influences infectious disease transmission, and numerous "prevalence-behavior" models have analyzed this interplay. These previous analyses assumed homogeneously mixing populations without spatial or social structure. However, spatial and social heterogeneity are known to significantly impact transmission dynamics and are particularly relevant for certain diseases. Previous work has demonstrated that social contact structure can change the individual incentive to vaccinate, thus enabling eradication of a disease under a voluntary vaccination policy when the corresponding homogeneous mixing model predicts that eradication is impossible due to free rider effects. Here, we extend this work and characterize the range of possible behavior-prevalence dynamics on a network. Methods We simulate transmission of a vaccine-prevetable infection through a random, static contact network. Individuals choose whether or not to vaccinate on any given day according to perceived risks of vaccination and infection. Results We find three possible outcomes for behavior-prevalence dynamics on this type of network: small final number vaccinated and final epidemic size (due to rapid control through voluntary ring vaccination); large final number vaccinated and significant final epidemic size (due to imperfect voluntary ring vaccination), and little or no vaccination and large final epidemic size (corresponding to little or no voluntary ring vaccination). We also show that the social contact structure enables eradication under a broad range of assumptions, except when vaccine risk is sufficiently high, the disease risk is sufficiently low, or individuals vaccinate too late for the vaccine to be effective. Conclusion For populations where infection can spread only through social contact network, relatively small differences in parameter values relating to perceived risk or vaccination behavior at the individual level can translate into large differences in population-level outcomes such as final size and final number vaccinated. The qualitative outcome of rational, self interested behaviour under a voluntary vaccination policy can vary substantially depending on interactions between social contact structure, perceived vaccine and disease risks, and the way that individual vaccination decision-making is modelled. PMID:19476616

Deriving semantic structure from category fluency: clustering techniques and their pitfalls

PubMed Central

Voorspoels, Wouter; Storms, Gert; Longenecker, Julia; Verheyen, Steven; Weinberger, Daniel R.; Elvevåg, Brita

2013-01-01

Assessing verbal output in category fluency tasks provides a sensitive indicator of cortical dysfunction. The most common metrics are the overall number of words produced and the number of errors. Two main observations have been made about the structure of the output, first that there is a temporal component to it with words being generated in spurts, and second that the clustering pattern may reflect a search for meanings such that the ‘clustering’ is attributable to the activation of a specific semantic field in memory. A number of sophisticated approaches to examining the structure of this clustering have been developed, and a core theme is that the similarity relations between category members will reveal the mental semantic structure of the category underlying an individual’s responses, which can then be visualized by a number of algorithms, such as MDS, hierarchical clustering, ADDTREE, ADCLUS or SVD. Such approaches have been applied to a variety of neurological and psychiatric populations, and the general conclusion has been that the clinical condition systematically distorts the semantic structure in the patients, as compared to the healthy controls. In the present paper we explore this approach to understanding semantic structure using category fluency data. On the basis of a large pool of patients with schizophrenia (n=204) and healthy control participants (n=204), we find that the methods are problematic and unreliable to the extent that it is not possible to conclude that any putative difference reflects a systematic difference between the semantic representations in patients and controls. Moreover, taking into account the unreliability of the methods, we find that the most probable conclusion to be made is that no difference in underlying semantic representation exists. The consequences of these findings to understanding semantic structure, and the use of category fluency data, in cortical dysfunction are discussed. PMID:24275165

Enhancing growth and yield of grey oyster mushroom (Pleurotus sajor-caju) using sound treatment at different intervals

NASA Astrophysics Data System (ADS)

Roshita, I.; Mukhlis, A. Amir; Ain, M. S. Nur; Fern, C. Shi; Zarina, Z.

2017-09-01

Mushrooms are famous for their use as source of nutrient and medicinal purposes. Wild mushrooms grew in a large number in the nature after a heavy down pour. Some believes that the thunderstorm and lightning can have effects on the growth of mushrooms. Hence, this study was conducted to investigate the impact of different acoustic sound treatment intervals towards the growth of grey oyster mushroom (Pleurotus sajor-caju). Five different sound treatment intervals involved which were; no treatment (control), 5-day, 10-day, 15-day and 20 day. The variables investigated were mycelium growth rate, growth stage performance (durations for mycelium filling up the bags, pinhead emergence and fruiting bodies formation), yield (number of fruiting bodies, total weight of fruiting bodies and percentage of biological efficiency) and physical analyses (pileus size, colour and texture). There were significant differences (P<0.05) observed in the mycelium growth rate, mycelium filling up the bags and number of fruiting bodies formation among different treatment intervals. As conclusion, the sound treated at different intervals have significant impact on the growth and yield of mushroom production where treatment at 5-day intervals was found to be the best treatment interval.

Dynamic Stall Control Using Plasma Actuators

NASA Astrophysics Data System (ADS)

Webb, Nathan; Singhal, Achal; Castaneda, David; Samimy, Mo

2017-11-01

Dynamic stall occurs in many applications, including sharp maneuvers of fixed wing aircraft, wind turbines, and rotorcraft and produces large unsteady aerodynamic loads that can lead to flutter and mechanical failure. This work uses flow control to reduce the unsteady loads by excitation of instabilities in the shear layer over the separated region using nanosecond pulse driven dielectric barrier discharge (NS-DBD) plasma actuators. These actuators have been shown to effectively delay or mitigate static stall. A wide range of flow parameters were explored in the current work: Reynolds number (Re = 167,000 to 500,000), reduced frequency (k = 0.025 to 0.075), and excitation Strouhal number (Ste = 0 to 10). Based on the results, three major conclusions were drawn: (a) Low Strouhal number excitation (Ste <0.5) results in oscillatory aerodynamic loads in the stalled stage of dynamic stall; (b) All excitation resulted in earlier flow reattachment; and (c) Excitation at progressively higher Ste weakened and eventually eliminated the dynamic stall vortex (DSV), thereby dramatically reducing the unsteady loading. The decrease in the strength of the DSV is achieved by the formation of shear layer coherent structures that bleed the leading-edge vorticity prior to the ejection of the DSV.

Number and Impact of Published Scholarly Works by Pharmacy Practice Faculty Members at Accredited US Colleges and Schools of Pharmacy (2001-2003)

PubMed Central

Coleman, Craig I.; Schlesselman, Lauren S.; Lao, Eang

2007-01-01

Objective To evaluate the quantity and quality of published literature conducted by pharmacy practice faculty members in US colleges and schools of pharmacy for the years 2001-2003. Methods The Web of Science bibliographic database was used to identify publication citations for the years 2001-2003, which were then evaluated in a number of different ways. Faculty members were identified using American Association of Colleges of Pharmacy rosters for the 2000-2001, 2001-2002, and 2002-2003 academic years. Results Two thousand three hundred seventy-four pharmacy practice faculty members generated 1,896 publications in Web of Science searchable journals. A small number of faculty members (2.1%) were responsible for a large proportion of publications (30.6%), and only 4.9% of faculty members published 2 or more publications in these journals per year. The average impact factor for the top 200 publications was 7.6. Conclusion Pharmacy practice faculty members contributed substantially to the biomedical literature and their work has had an important impact. A substantial portion of this work has come from a small subset of faculty members. PMID:17619644

The effect of the Syrian crisis on organ transplantation in Syria.

PubMed

Saeed, Bassam

2015-04-01

The war in Syria that started in March 2011 has destroyed much of the country's infrastructure including many hospitals. The total number of kidney transplants performed in Syria in 2010 was 385 transplants before the number gradually declined to 154 transplants in 2013, a decrease of 60%. In addition, the number of operational kidney transplant centers has decreased from 8 to 4 centers. Unrelated-donor kidney transplant decreased from 70% during the years that preceded the crisis to 47% in 2013. More than 50% of physicians and surgeons involved in kidney transplant are not practicing transplant currently in their centers. Difficulties in the provision of immunosuppressive drugs for all patients in all provinces constitute a major challenge for the health authorities and transplant patients, especially patients who cannot arrange an alternate source. The project to initiate liver transplant came to a halt because foreign trainers could not visit Syria. The autologous bone marrow transplant program continued to function, but in a smaller and irregular manner. The commitment of transplant teams despite the large challenges was, and still is, extraordinary. In conclusion, all aspects of organ transplant have been affected, paralyzing new projects and negatively affecting existing programs.

Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico.

PubMed

Aguilar-Meléndez, Araceli; Morrell, Peter L; Roose, Mikeal L; Kim, Seung-Chul

2009-06-01

The chile of Mesoamerica, Capsicum annuum, is one of five domesticated chiles in the Americas. Among the chiles, it varies the most in size, form, and color of its fruits. Together with maize, C. annuum is one of the principal elements of the neotropical diets of Mesoamerican civilizations. Despite the great economic and cultural importance of C. annuum both worldwide and in Mexico, however, very little is known about its geographic origin and number of domestications. Here we sampled a total of 80 accessions from Mexico (58 semiwild and 22 domesticated) and examined nucleotide sequence diversity at three single- or low-copy nuclear loci, Dhn, G3pdh, and Waxy. Across the three loci, we found an average reduction of ca. 10% in the diversity of domesticates relative to semiwild chiles and geographic structure within Mexican populations. The Yucatan Peninsula contained a large number of haplotypes, many of which were unique, suggesting an important region of chile domestication and center of diversity. The present sampling of loci did not conclusively resolve the number and location of domestications, but several lines of evidence suggest multiple independent domestications from widely distributed progenitor populations.

Magnetic beads (Dynabead) toxicity to endothelial cells at high bead concentration: implication for tissue engineering of vascular prosthesis.

PubMed

Tiwari, A; Punshon, G; Kidane, A; Hamilton, G; Seifalian, A M

2003-10-01

Magnetic beads (Dynabeads) have been used for the purification of endothelial cells. One application for this procedure may be for single-stage seeding of bypass grafts. The number of endothelial cells (EC) isolated is crucial and therefore to increase the number of cells extracted, a higher number of Dynabeads per cell may need to be used. The effect of large numbers of CD31 Dynabeads on cell proliferation/metabolism is unknown. We undertook this study using CD31-coated Dynabeads and EC from human umbilical vein. EC were coated at concentrations of 4, 10, or 50 beads per cell. The cells were cultured for 6 days with control being normal EC. Cellular proliferation was assessed by trypsinization of cells and metabolism assessed with an Alamar blue viability assay. In a further experiment a compliant polyurethane graft was single-stage seeded with both coated Dynabeads and normal EC. The results showed that using a higher number of beads per cell resulted in a reduction in cell proliferation and a reduction in cell metabolism. The total number of Dynabeads-coated cells in culture compared to controls (%) by day 6 were 30.7 +/- 2.56, 41.3 +/- 9.8 and 59.2 +/- 7.3 for 50, 10, and 4 beads per cell, respectively. The corresponding results for Alamar blue were 43.7 +/- 1.2, 61.8 +/- 1.4, and 72.1 +/- 4.3. The seeded grafts showed reduced metabolism with the Dynabeads-coated EC. In conclusion, high numbers of beads per cell have a late detrimental effect on cell proliferation and metabolism. Therefore for single-stage seeding lower numbers of Dynabeads will need to be used with resultant reduction in the number of available EC.

Copy Number Variations of TBK1 in Australian Patients With Primary Open-Angle Glaucoma

PubMed Central

AWADALLA, MONA S.; FINGERT, JOHN H.; ROOS, BENJAMIN E.; CHEN, SIMON; HOLMES, RICHARD; GRAHAM, STUART L.; CHEHADE, MARK; GALANOPOLOUS, ANNA; RIDGE, BRONWYN; SOUZEAU, EMMANUELLE; ZHOU, TIGER; SIGGS, OWEN M.; HEWITT, ALEX W.; MACKEY, DAVID A.; BURDON, KATHRYN P.; CRAIG, JAMIE E.

2015-01-01

PURPOSE To investigate the presence of TBK1 copy number variations in a large, well-characterized Australian cohort of patients with glaucoma comprising both normal-tension glaucoma and high-tension glaucoma cases. DESIGN A retrospective cohort study. METHODS DNA samples from patients with normal-tension glaucoma and high-tension glaucoma and unaffected controls were screened for TBK1 copy number variations using real-time quantitative polymerase chain reaction. Samples with additional copies of the TBK1 gene were further tested using custom comparative genomic hybridization arrays. RESULTS Four out of 334 normal-tension glaucoma cases (1.2%) were found to carry TBK1 copy number variations using quantitative polymerase chain reaction. One extra dose of the TBK1 gene (duplication) was detected in 3 normal-tension glaucoma patients, while 2 extra doses of the gene (triplication) were detected in a fourth normal-tension glaucoma patient. The results were further confirmed by custom comparative genomic hybridization arrays. Further, the TBK1 copy number variation segregated with normal-tension glaucoma in the family members of the probands, showing an autosomal dominant pattern of inheritance. No TBK1 copy number variations were detected in 1045 Australian patients with high-tension glaucoma or in 254 unaffected controls. CONCLUSION We report the presence of TBK1 copy number variations in our Australian normal-tension glaucoma cohort, including the first example of more than 1 extra copy of this gene in glaucoma patients (gene triplication). These results confirm TBK1 to be an important cause of normal-tension glaucoma, but do not suggest common involvement in high-tension glaucoma. PMID:25284765

The Chandra Source Catalog : Automated Source Correlation

NASA Astrophysics Data System (ADS)

Hain, Roger; Evans, I. N.; Evans, J. D.; Glotfelty, K. J.; Anderson, C. S.; Bonaventura, N. R.; Chen, J. C.; Davis, J. E.; Doe, S. M.; Fabbiano, G.; Galle, E.; Gibbs, D. G.; Grier, J. D.; Hall, D. M.; Harbo, P. N.; He, X.; Houck, J. C.; Karovska, M.; Lauer, J.; McCollough, M. L.; McDowell, J. C.; Miller, J. B.; Mitschang, A. W.; Morgan, D. L.; Nichols, J. S.; Nowak, M. A.; Plummer, D. A.; Primini, F. A.; Refsdal, B. L.; Rots, A. H.; Siemiginowska, A. L.; Sundheim, B. A.; Tibbetts, M. S.; Van Stone, D. W.; Winkelman, S. L.; Zografou, P.

2009-01-01

Chandra Source Catalog (CSC) master source pipeline processing seeks to automatically detect sources and compute their properties. Since Chandra is a pointed mission and not a sky survey, different sky regions are observed for a different number of times at varying orientations, resolutions, and other heterogeneous conditions. While this provides an opportunity to collect data from a potentially large number of observing passes, it also creates challenges in determining the best way to combine different detection results for the most accurate characterization of the detected sources. The CSC master source pipeline correlates data from multiple observations by updating existing cataloged source information with new data from the same sky region as they become available. This process sometimes leads to relatively straightforward conclusions, such as when single sources from two observations are similar in size and position. Other observation results require more logic to combine, such as one observation finding a single, large source and another identifying multiple, smaller sources at the same position. We present examples of different overlapping source detections processed in the current version of the CSC master source pipeline. We explain how they are resolved into entries in the master source database, and examine the challenges of computing source properties for the same source detected multiple times. Future enhancements are also discussed. This work is supported by NASA contract NAS8-03060 (CXC).

EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

PubMed Central

Nahum, Laila A; Reynolds, Matthew T; Wang, Zhengyuan O; Faith, Jeremiah J; Jonna, Rahul; Jiang, Zhi J; Meyer, Thomas J; Pollock, David D

2006-01-01

Background Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; ) to begin to address this. Description EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs. Conclusion EGenBio was designed to serve as a platform for tools and resources to ease combined analysis in evolution, genomics, and biodiversity. PMID:17118150

Next-Generation Sequencing of the Chrysanthemum nankingense (Asteraceae) Transcriptome Permits Large-Scale Unigene Assembly and SSR Marker Discovery

PubMed Central

Wang, Haibin; Jiang, Jiafu; Chen, Sumei; Qi, Xiangyu; Peng, Hui; Li, Pirui; Song, Aiping; Guan, Zhiyong; Fang, Weimin; Liao, Yuan; Chen, Fadi

2013-01-01

Background Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST) sequences have been acquired to date, so the number of available EST-SSR markers is very low. Methodology/Principal Findings Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59%) unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all) of the assays were transferable across species and that they exposed a significant amount of allelic diversity. Conclusions/Significance SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera. PMID:23626799

Application of a Multivariant, Caucasian-Specific, Genotyped Donor Panel for Performance Validation of MDmulticard®, ID-System®, and Scangel® RhD/ABO Serotyping

PubMed Central

Gassner, Christoph; Rainer, Esther; Pircher, Elfriede; Markut, Lydia; Körmöczi, Günther F.; Jungbauer, Christof; Wessin, Dietmar; Klinghofer, Roswitha; Schennach, Harald; Schwind, Peter; Schönitzer, Diether

2009-01-01

Summary Background Validations of routinely used serological typing methods require intense performance evaluations typically including large numbers of samples before routine application. However, such evaluations could be improved considering information about the frequency of standard blood groups and their variants. Methods Using RHD and ABO population genetic data, a Caucasian-specific donor panel was compiled for a performance comparison of the three RhD and ABO serological typing methods MDmulticard (Medion Diagnostics), ID-System (DiaMed) and ScanGel (Bio-Rad). The final test panel included standard and variant RHD and ABO genotypes, e.g. RhD categories, partial and weak RhDs, RhD DELs, and ABO samples, mainly to interpret weak serological reactivity for blood group A specificity. All samples were from individuals recorded in our local DNA blood group typing database. Results For ‘standard’ blood groups, results of performance were clearly interpretable for all three serological methods compared. However, when focusing on specific variant phenotypes, pronounced differences in reaction strengths and specificities were observed between them. Conclusions A genetically and ethnically predefined donor test panel consisting of 93 individual samples only, delivered highly significant results for serological performance comparisons. Such small panels offer impressive representative powers, higher as such based on statistical chances and large numbers only. PMID:21113264

D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements

PubMed Central

2013-01-01

Background The binding of transcription factors to DNA plays an essential role in the regulation of gene expression. Numerous experiments elucidated binding sequences which subsequently have been used to derive statistical models for predicting potential transcription factor binding sites (TFBS). The rapidly increasing number of genome sequence data requires sophisticated computational approaches to manage and query experimental and predicted TFBS data in the context of other epigenetic factors and across different organisms. Results We have developed D-Light, a novel client-server software package to store and query large amounts of TFBS data for any number of genomes. Users can add small-scale data to the server database and query them in a large scale, genome-wide promoter context. The client is implemented in Java and provides simple graphical user interfaces and data visualization. Here we also performed a statistical analysis showing what a user can expect for certain parameter settings and we illustrate the usage of D-Light with the help of a microarray data set. Conclusions D-Light is an easy to use software tool to integrate, store and query annotation data for promoters. A public D-Light server, the client and server software for local installation and the source code under GNU GPL license are available at http://biwww.che.sbg.ac.at/dlight. PMID:23617301

Extended Twin Study of Alcohol Use in Virginia and Australia.

PubMed

Verhulst, Brad; Neale, Michael C; Eaves, Lindon J; Medland, Sarah E; Heath, Andrew C; Martin, Nicholas G; Maes, Hermine H

2018-06-01

Drinking alcohol is a normal behavior in many societies, and prior studies have demonstrated it has both genetic and environmental sources of variation. Using two very large samples of twins and their first-degree relatives (Australia ≈ 20,000 individuals from 8,019 families; Virginia ≈ 23,000 from 6,042 families), we examine whether there are differences: (1) in the genetic and environmental factors that influence four interrelated drinking behaviors (quantity, frequency, age of initiation, and number of drinks in the last week), (2) between the twin-only design and the extended twin design, and (3) the Australian and Virginia samples. We find that while drinking behaviors are interrelated, there are substantial differences in the genetic and environmental architectures across phenotypes. Specifically, drinking quantity, frequency, and number of drinks in the past week have large broad genetic variance components, and smaller but significant environmental variance components, while age of onset is driven exclusively by environmental factors. Further, the twin-only design and the extended twin design come to similar conclusions regarding broad-sense heritability and environmental transmission, but the extended twin models provide a more nuanced perspective. Finally, we find a high level of similarity between the Australian and Virginian samples, especially for the genetic factors. The observed differences, when present, tend to be at the environmental level. Implications for the extended twin model and future directions are discussed.

Large-scale microsatellite development in grasspea (Lathyrus sativus L.), an orphan legume of the arid areas

PubMed Central

2014-01-01

Background Grasspea (Lathyrus sativus L., 2n = 14), a member of the family Leguminosae, holds great agronomic potential as grain and forage legume crop in the arid areas for its superb resilience to abiotic stresses such as drought, flood and salinity. The crop could not make much progress through conventional breeding in the past, and there are hardly any detailed molecular biology studies due to paucity of reliable molecular markers representative of the entire genome. Results Using the 454 FLX Titanium pyrosequencing technique, 651,827 simple sequence repeat (SSR) loci were identified and 50,144 nonredundant primer pairs were successfully designed, of which 288 were randomly selected for validation among 23 L. sativus and one L. cicera accessions of diverse provenance. 74 were polymorphic, 70 monomorphic, and 144 with no PCR product. The number of observed alleles ranged from two to five, the observed heterozygosity from 0 to 0.9545, and Shannon’s information index ranged from 0.1013 to 1.0980, respectively. The dendrogram constructed by using unweighted pair group method with arithmetic mean (UPGMA) based on Nei's genetic distance, showed obvious distinctions and understandable relationships among the 24 accessions. Conclusions The large number of SSR primer pairs developed in this study would make a significant contribution to genomics enabled improvement of grasspea. PMID:24635905

Linkage of osteoporosis to chromosome 20p12 and association to BMP2.

PubMed

Styrkarsdottir, Unnur; Cazier, Jean-Baptiste; Kong, Augustine; Rolfsson, Ottar; Larsen, Helene; Bjarnadottir, Emma; Johannsdottir, Vala D; Sigurdardottir, Margret S; Bagger, Yu; Christiansen, Claus; Reynisdottir, Inga; Grant, Struan F A; Jonasson, Kristjan; Frigge, Michael L; Gulcher, Jeffrey R; Sigurdsson, Gunnar; Stefansson, Kari

2003-12-01

Osteoporotic fractures are a major cause of morbidity and mortality in ageing populations. Osteoporosis, defined as low bone mineral density (BMD) and associated fractures, have significant genetic components that are largely unknown. Linkage analysis in a large number of extended osteoporosis families in Iceland, using a phenotype that combines osteoporotic fractures and BMD measurements, showed linkage to Chromosome 20p12.3 (multipoint allele-sharing LOD, 5.10; p value, 6.3 x 10(-7)), results that are statistically significant after adjusting for the number of phenotypes tested and the genome-wide search. A follow-up association analysis using closely spaced polymorphic markers was performed. Three variants in the bone morphogenetic protein 2 (BMP2) gene, a missense polymorphism and two anonymous single nucleotide polymorphism haplotypes, were determined to be associated with osteoporosis in the Icelandic patients. The association is seen with many definitions of an osteoporotic phenotype, including osteoporotic fractures as well as low BMD, both before and after menopause. A replication study with a Danish cohort of postmenopausal women was conducted to confirm the contribution of the three identified variants. In conclusion, we find that a region on the short arm of Chromosome 20 contains a gene or genes that appear to be a major risk factor for osteoporosis and osteoporotic fractures, and our evidence supports the view that BMP2 is at least one of these genes.

New collector efficiency equation for colloid filtration in both natural and engineered flow conditions

NASA Astrophysics Data System (ADS)

Nelson, Kirk E.; Ginn, Timothy R.

2011-05-01

A new equation for the collector efficiency (η) of the colloid filtration theory (CFT) is developed via nonlinear regression on the numerical data generated by a large number of Lagrangian simulations conducted in Happel's sphere-in-cell porous media model over a wide range of environmentally relevant conditions. The new equation expands the range of CFT's applicability in the natural subsurface primarily by accommodating departures from power law dependence of η on the Peclet and gravity numbers, a necessary but as of yet unavailable feature for applying CFT to large-scale field transport (e.g., of nanoparticles, radionuclides, or genetically modified organisms) under low groundwater velocity conditions. The new equation also departs from prior equations for colloids in the nanoparticle size range at all fluid velocities. These departures are particularly relevant to subsurface colloid and colloid-facilitated transport where low permeabilities and/or hydraulic gradients lead to low groundwater velocities and/or to nanoparticle fate and transport in porous media in general. We also note the importance of consistency in the conceptualization of particle flux through the single collector model on which most η equations are based for the purpose of attaining a mechanistic understanding of the transport and attachment steps of deposition. A lack of sufficient data for small particles and low velocities warrants further experiments to draw more definitive and comprehensive conclusions regarding the most significant discrepancies between the available equations.

Identification of Rare, Single-Nucleotide Mutations in NDE1 and Their Contributions to Schizophrenia Susceptibility

PubMed Central

Kimura, Hiroki; Tsuboi, Daisuke; Wang, Chenyao; Kushima, Itaru; Koide, Takayoshi; Ikeda, Masashi; Iwayama, Yoshimi; Toyota, Tomoko; Yamamoto, Noriko; Kunimoto, Shohko; Nakamura, Yukako; Yoshimi, Akira; Banno, Masahiro; Xing, Jingrui; Takasaki, Yuto; Yoshida, Mami; Aleksic, Branko; Uno, Yota; Okada, Takashi; Iidaka, Tetsuya; Inada, Toshiya; Suzuki, Michio; Ujike, Hiroshi; Kunugi, Hiroshi; Kato, Tadafumi; Yoshikawa, Takeo; Iwata, Nakao; Kaibuchi, Kozo; Ozaki, Norio

2015-01-01

Background: Nuclear distribution E homolog 1 (NDE1), located within chromosome 16p13.11, plays an essential role in microtubule organization, mitosis, and neuronal migration and has been suggested by several studies of rare copy number variants to be a promising schizophrenia (SCZ) candidate gene. Recently, increasing attention has been paid to rare single-nucleotide variants (SNVs) discovered by deep sequencing of candidate genes, because such SNVs may have large effect sizes and their functional analysis may clarify etiopathology. Methods and Results: We conducted mutation screening of NDE1 coding exons using 433 SCZ and 145 pervasive developmental disorders samples in order to identify rare single nucleotide variants with a minor allele frequency ≤5%. We then performed genetic association analysis using a large number of unrelated individuals (3554 SCZ, 1041 bipolar disorder [BD], and 4746 controls). Among the discovered novel rare variants, we detected significant associations between SCZ and S214F (P = .039), and between BD and R234C (P = .032). Furthermore, functional assays showed that S214F affected axonal outgrowth and the interaction between NDE1 and YWHAE (14-3-3 epsilon; a neurodevelopmental regulator). Conclusions: This study strengthens the evidence for association between rare variants within NDE1 and SCZ, and may shed light into the molecular mechanisms underlying this severe psychiatric disorder. PMID:25332407

Multi-agent systems and their applications

DOE PAGES

Xie, Jing; Liu, Chen-Ching

2017-07-14

The number of distributed energy components and devices continues to increase globally. As a result, distributed control schemes are desirable for managing and utilizing these devices, together with the large amount of data. In recent years, agent-based technology becomes a powerful tool for engineering applications. As a computational paradigm, multi agent systems (MASs) provide a good solution for distributed control. Here in this paper, MASs and applications are discussed. A state-of-the-art literature survey is conducted on the system architecture, consensus algorithm, and multi-agent platform, framework, and simulator. In addition, a distributed under-frequency load shedding (UFLS) scheme is proposed using themore » MAS. Simulation results for a case study are presented. The future of MASs is discussed in the conclusion.« less

Recent developments in Geant4

DOE PAGES

Allison, J.; Amako, K.; Apostolakis, J.; ...

2016-07-01

Geant4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection. Over the past several years, major changes have been made to the toolkit in order to accommodate the needs of these user communities, and to efficiently exploit the growth of computing power made available by advances in technology. In conclusion, the adaptation of Geant4 to multithreading, advances in physics, detector modeling and visualization, extensions tomore » the toolkit, including biasing and reverse Monte Carlo, and tools for physics and release validation are discussed here.« less

Multi-agent systems and their applications

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

Xie, Jing; Liu, Chen-Ching

The number of distributed energy components and devices continues to increase globally. As a result, distributed control schemes are desirable for managing and utilizing these devices, together with the large amount of data. In recent years, agent-based technology becomes a powerful tool for engineering applications. As a computational paradigm, multi agent systems (MASs) provide a good solution for distributed control. Here in this paper, MASs and applications are discussed. A state-of-the-art literature survey is conducted on the system architecture, consensus algorithm, and multi-agent platform, framework, and simulator. In addition, a distributed under-frequency load shedding (UFLS) scheme is proposed using themore » MAS. Simulation results for a case study are presented. The future of MASs is discussed in the conclusion.« less

What can we learn from fitness landscapes?

PubMed

Hartl, Daniel L

2014-10-01

A combinatorially complete data set consists of studies of all possible combinations of a set of mutant sites in a gene or mutant alleles in a genome. Among the most robust conclusions from these studies is that epistasis between beneficial mutations often shows a pattern of diminishing returns, in which favorable mutations are less fit when combined than would be expected. Another robust inference is that the number of adaptive evolutionary paths is often limited to a relatively small fraction of the theoretical possibilities, owing largely to sign epistasis requiring evolutionary steps that would entail a decrease in fitness. Here we summarize these and other results while also examining issues that remain unresolved and future directions that seem promising. Copyright © 2014 Elsevier Ltd. All rights reserved.

Tables of E2 transition probabilities from the first 2 + states in even-even nuclei [B(E2) evaluation for 0 + 1 → 2 + 1 transitions in even-even nuclei

DOE PAGES

Pritychenko, B.; Birch, M.; Singh, B.; ...

2015-11-03

A complete B(E2)↑ evaluation and compilation for even-even nuclei has been presented. The present paper is a continuation of P.H. Stelson and L. Grodzins, and S. Raman et al. nuclear data evaluations and was motivated by a large number of new measurements. It extends the list of evaluated nuclides from 328 to 452, includes an extended list of nuclear reaction kinematics parameters and comprehensive shell model analysis. Evaluation policies for analysis of experimental data have been discussed and conclusions are given. Moreover, future plans for B(E2)↑ systematics and experimental technique analyses of even-even nuclei are outlined.

Can we obtain the coefficient of restitution from the sound of a bouncing ball?

NASA Astrophysics Data System (ADS)

Heckel, Michael; Glielmo, Aldo; Gunkelmann, Nina; Pöschel, Thorsten

2016-03-01

The coefficient of restitution may be determined from the sound signal emitted by a sphere bouncing repeatedly off the ground. Although there is a large number of publications exploiting this method, so far, there is no quantitative discussion of the error related to this type of measurement. Analyzing the main error sources, we find that even tiny deviations of the shape from the perfect sphere may lead to substantial errors that dominate the overall error of the measurement. Therefore, we come to the conclusion that the well-established method to measure the coefficient of restitution through the emitted sound is applicable only for the case of nearly perfect spheres. For larger falling height, air drag may lead to considerable error, too.

Tight-binding calculation studies of vacancy and adatom defects in graphene

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

Zhang, Wei; Lu, Wen-Cai; Zhang, Hong-Xing

2016-02-19

Computational studies of complex defects in graphene usually need to deal with a larger number of atoms than the current first-principles methods can handle. We show a recently developed three-center tight-binding potential for carbon is very efficient for large scale atomistic simulations and can accurately describe the structures and energies of various defects in graphene. Using the three-center tight-binding potential, we have systematically studied the stable structures and formation energies of vacancy and embedded-atom defects of various sizes up to 4 vacancies and 4 embedded atoms in graphene. In conclusion, our calculations reveal low-energy defect structures and provide a moremore » comprehensive understanding of the structures and stability of defects in graphene.« less

[The neurobiology of antisocial behaviour].

PubMed

Loomans, M M; Tulen, J H M; van Marle, H J C

2010-01-01

Neuro-imaging is being used increasingly to provide explanations for antisocial behaviour. To make a neurobiological contribution to the diagnosis of many types of antisocial behaviour. The literature was searched using PubMed and combinations of the keywords 'psychopathy', 'antisocial', 'neurobiology' and 'neuro-anatomy' for the period 1990-2009. Impairments in the prefrontal cortex, amygdala, hippocampus, superior temporal gyrus, corpus callosum and anterior cingulate cortex provide a possible explanation for a large number of the symptoms associated with antisocial behaviour. The concept of psychopathy is connected mainly with impairments in a prefrontal-temporal-limbic system. CONCLUSION Combinations of deficiencies in the associated brain areas and malfunctioning of the communication between the various brain structures seem to play a more important role than deficiencies in the separate brain structures.

Small and Large Number Processing in Infants and Toddlers with Williams Syndrome

ERIC Educational Resources Information Center

Van Herwegen, Jo; Ansari, Daniel; Xu, Fei; Karmiloff-Smith, Annette

2008-01-01

Previous studies have suggested that typically developing 6-month-old infants are able to discriminate between small and large numerosities. However, discrimination between small numerosities in young infants is only possible when variables continuous with number (e.g. area or circumference) are confounded. In contrast, large number discrimination…

Factors influencing piglet pre-weaning mortality in 47 commercial swine herds in Thailand.

PubMed

Nuntapaitoon, Morakot; Tummaruk, Padet

2018-01-01

The present study aims to determine the occurrence of piglet pre-weaning mortality in commercial swine herds in Thailand in relation to piglet, sow, and environmental factors. Data were collected from the database of the computerized recording system from 47 commercial swine herds in Thailand. The raw data were carefully scrutinized for accuracy. Litters with a lactation length < 16 days or >28 days were excluded. In total, 199,918 litters from 74,088 sows were included in the analyses. Piglet pre-weaning mortality at the individual sow level was calculated as piglet pre-weaning mortality (%) = (number of littermate pigs - number of piglets at weaning) / number of littermate pigs. Litters were classified according to sow parity numbers (1, 2-5, and 6-9), average birth weight of the piglets (0.80-1.29, 1.30-1.79, 1.80-2.50 kg), number of littermate pigs (5-7, 8-10, 11-12, and 13-15 piglets), and size of the herd (small, medium, and large). Pearson correlations were conducted to analyze the associations between piglet pre-weaning mortality and reproductive parameters. Additionally, a general linear model procedure was performed to analyze the various factors influencing piglet pre-weaning mortality. On average, piglet pre-weaning mortality was 11.2% (median = 9.1%) and varied among herds from 4.8 to 19.2%. Among all the litters, 62.1, 18.1, and 19.8% of the litters had a piglet pre-weaning mortality rate of 0-10, 11-20, and greater than 20%, respectively. As the number of littermate pigs increased, piglet pre-weaning mortality also increased (r = 0.390, P < 0.001). Litters with 13-16 littermate pigs had a higher piglet pre-weaning mortality than litters with 5-7, 8-10, and 11-12 littermate pigs (20.8, 7.8, 7.2, and 11.2%, respectively; P < 0.001). Piglet pre-weaning mortality in large-sized herds was higher than that in small- and medium-sized herds (13.6, 10.6, and 11.2%, respectively; P < 0.001). Interestingly, in all categories of herd size, piglet pre-weaning mortality was increased almost two times when the number of littermates increased from 11-12 to 13-16 piglets. Furthermore, piglets with birth weights of 0.80-1.29 kg in large-sized herds had a higher risk of mortality than those in small- and medium-sized herds (15.3, 10.9, and 12.2%, respectively, P < 0.001). In conclusion, in commercial swine herds in the tropics, piglet pre-weaning mortality averaged 11.2% and varied among herds from 4.8 to 19.2%. The litters with 13-16 littermate pigs had piglet pre-weaning mortality of up to 20.8%. Piglets with low birth weight (0.80-1.29 kg) had a higher risk of pre-weaning mortality. Management strategies for reducing piglet pre-weaning mortality in tropical climates should be emphasized in litters with a high number of littermate pigs, low piglet birth weights, and large herd sizes.

Introducing student inquiry in large introductory genetics classes.

PubMed Central

Pukkila, Patricia J

2004-01-01

An appreciation of genetic principles depends upon understanding the individual curiosity that sparked particular investigations, the creativity involved in imagining alternative outcomes and designing experiments to eliminate these outcomes, and the clarity of thought necessary to convince one's scientific peers of the validity of the conclusions. At large research universities, students usually begin their study of genetics in large lecture classes. It is widely assumed that the lecture format, coupled with the pressures to be certain that students become familiar with the principal conclusions of genetics investigations, constrains most if not all departures from the formats textbooks used to explain these conclusions. Here I present several examples of mechanisms to introduce meaningful student inquiry in an introductory genetics course and to evaluate student creative effort. Most of the examples involve altered student preparation prior to class and additional in-class activities, while a few depend upon a smaller recitation section, which accompanies the course from which the examples have been drawn. I conclude that large introductory classes are suitable venues to teach students how to identify scientific claims, determine the evidence that is essential to eliminate alternative conclusions, and convince their peers of the validity of their arguments. PMID:15020401

Comment on 'The Global Resurfacing of Venus' by R. G. Strom, G.G. Schaber, and D.D. Dawson

NASA Technical Reports Server (NTRS)

Herrick, Robert R.; Izenberg, Noam; Phillips, Roger J.

1995-01-01

The distribution of impact craters on Venus has been the subject of a great deal of analysis since the return of Magellan data. Phillips el al. (1992) performed Monte Carlo two-dimensional (2-D) modeling of the areal distribution of craters, and the results of that exercise allowed a restricted, but still quite large, range of possible planetary resurfacing histories, including the possibility that the crater, were emplaced on a geologically inactive planet. However, the nonrandom distribution of embayed and deformed craters (Phillips el al., 1992), the hypsometric distribution of craters (Herrick and Phillips, 1994), the varied degradation states of craters (Izenberg et al., 1994), their nonrandom distribution with different geologic terrain types (Namiki and Solomon, 1994; Price et al, 1994), and three-dimensional resurfacing modeling (Bullock el al., 1993) all seem to argue against that particular possibility. In contrast, Strom el al. (1994) have collected a refined and more comprehensive data set of impact features, and they input these data into more sophisticated 2-D Monte Carlo modeling and statistical analyses of the areal distribution of craters, the hypsometric distribution of craters, and the number of embayed craters. They concluded that 'Venus experienced a global resurfacing event about 300 m.y. ago followed by a dramatic reduction of volcanism and tectonism. This global resurfacing event ended abruptly (less than 10 m.y.). The present crater population has accumulated since then and remains largely intact . . . only about 4%-6% of the planet has been volcanically resurfaced since the global event . . .' If these conclusions are well-founded, this work certainly represents a significant advancement in restricting tile number of plausible resurfacing histories for the planet. If Strom et al. (1994) are correct, it would also mean that all of the other aforementioned works are in error to various degrees, or at least represent overzealous interpretation of the data. However, we have identified apparent flaws in the observations, modeling, and interpretations presented by Strom el al. (1994) that lead us to question whether their conclusions are warranted. We limit our comments to three areas of their analysis: (1) observations pertaining to the number and area of disrupted and pristine craters and crater-related features, (2) modeling of the areal and elevation distribution of craters, and (3) interpretations of resurfacing models.

Discovery of quantitative trait loci for resistance to parasitic nematode infection in sheep: I. Analysis of outcross pedigrees

PubMed Central

Crawford, Allan M; Paterson, Korena A; Dodds, Ken G; Diez Tascon, Cristina; Williamson, Penny A; Roberts Thomson, Meredith; Bisset, Stewart A; Beattie, Anne E; Greer, Gordon J; Green, Richard S; Wheeler, Roger; Shaw, Richard J; Knowler, Kevin; McEwan, John C

2006-01-01

Background Currently most pastoral farmers rely on anthelmintic drenches to control gastrointestinal parasitic nematodes in sheep. Resistance to anthelmintics is rapidly increasing in nematode populations such that on some farms none of the drench families are now completely effective. It is well established that host resistance to nematode infection is a moderately heritable trait. This study was undertaken to identify regions of the genome, quantitative trait loci (QTL) that contain genes affecting resistance to parasitic nematodes. Results Rams obtained from crossing nematode parasite resistant and susceptible selection lines were used to derive five large half-sib families comprising between 348 and 101 offspring per sire. Total offspring comprised 940 lambs. Extensive measurements for a range of parasite burden and immune function traits in all offspring allowed each lamb in each pedigree to be ranked for relative resistance to nematode parasites. Initially the 22 most resistant and 22 most susceptible progeny from each pedigree were used in a genome scan that used 203 microsatellite markers spread across all sheep autosomes. This study identified 9 chromosomes with regions showing sufficient linkage to warrant the genotyping of all offspring. After genotyping all offspring with markers covering Chromosomes 1, 3, 4, 5, 8, 12, 13, 22 and 23, the telomeric end of chromosome 8 was identified as having a significant QTL for parasite resistance as measured by the number of Trichostrongylus spp. adults in the abomasum and small intestine at the end of the second parasite challenge. Two further QTL for associated immune function traits of total serum IgE and T. colubiformis specific serum IgG, at the end of the second parasite challenge, were identified on chromosome 23. Conclusion Despite parasite resistance being a moderately heritable trait, this large study was able to identify only a single significant QTL associated with it. The QTL concerned adult parasite burdens at the end of the second parasite challenge when the lambs were approximately 6 months old. Our failure to discover more QTL suggests that most of the genes controlling this trait are of relatively small effect. The large number of suggestive QTL discovered (more than one per family per trait than would be expected by chance) also supports this conclusion. PMID:16846521

Estimating Large Numbers

ERIC Educational Resources Information Center

Landy, David; Silbert, Noah; Goldin, Aleah

2013-01-01

Despite their importance in public discourse, numbers in the range of 1 million to 1 trillion are notoriously difficult to understand. We examine magnitude estimation by adult Americans when placing large numbers on a number line and when qualitatively evaluating descriptions of imaginary geopolitical scenarios. Prior theoretical conceptions…

The Intuitiveness of the Law of Large Numbers

ERIC Educational Resources Information Center

Lem, Stephanie

2015-01-01

In this paper two studies are reported in which two contrasting claims concerning the intuitiveness of the law of large numbers are investigated. While Sedlmeier and Gigerenzer ("J Behav Decis Mak" 10:33-51, 1997) claim that people have an intuition that conforms to the law of large numbers, but that they can only employ this intuition…

An investigation of small scales of turbulence in a boundary layer at high Reynolds numbers

NASA Technical Reports Server (NTRS)

Wallace, James M.; Ong, L.; Balint, J.-L.

1993-01-01

The assumption that turbulence at large wave-numbers is isotropic and has universal spectral characteristics which are independent of the flow geometry, at least for high Reynolds numbers, has been a cornerstone of closure theories as well as of the most promising recent development in the effort to predict turbulent flows, viz. large eddy simulations. This hypothesis was first advanced by Kolmogorov based on the supposition that turbulent kinetic energy cascades down the scales (up the wave-numbers) of turbulence and that, if the number of these cascade steps is sufficiently large (i.e. the wave-number range is large), then the effects of anisotropies at the large scales are lost in the energy transfer process. Experimental attempts were repeatedly made to verify this fundamental assumption. However, Van Atta has recently suggested that an examination of the scalar and velocity gradient fields is necessary to definitively verify this hypothesis or prove it to be unfounded. Of course, this must be carried out in a flow with a sufficiently high Reynolds number to provide the necessary separation of scales in order unambiguously to provide the possibility of local isotropy at large wave-numbers. An opportunity to use our 12-sensor hot-wire probe to address this issue directly was made available at the 80'x120' wind tunnel at the NASA Ames Research Center, which is normally used for full-scale aircraft tests. An initial report on this high Reynolds number experiment and progress toward its evaluation is presented.

Evaluation of Genetic Algorithm Concepts using Model Problems. Part 1; Single-Objective Optimization

NASA Technical Reports Server (NTRS)

Holst, Terry L.; Pulliam, Thomas H.

2003-01-01

A genetic-algorithm-based optimization approach is described and evaluated using a simple hill-climbing model problem. The model problem utilized herein allows for the broad specification of a large number of search spaces including spaces with an arbitrary number of genes or decision variables and an arbitrary number hills or modes. In the present study, only single objective problems are considered. Results indicate that the genetic algorithm optimization approach is flexible in application and extremely reliable, providing optimal results for all problems attempted. The most difficult problems - those with large hyper-volumes and multi-mode search spaces containing a large number of genes - require a large number of function evaluations for GA convergence, but they always converge.

Comparative analyses of the neuron numbers and volumes of the amygdaloid complex in old and new world primates.

PubMed

Carlo, C N; Stefanacci, L; Semendeferi, K; Stevens, C F

2010-04-15

The amygdaloid complex (AC), a key component of the limbic system, is a brain region critical for the detection and interpretation of emotionally salient information. Therefore, changes in its structure and function are likely to provide correlates of mood and emotion disorders, diseases that afflict a large portion of the human population. Previous gross comparisons of the AC in control and diseased individuals have, however, mainly failed to discover these expected correlations with diseases. We have characterized AC nuclei in different nonhuman primate species to establish a baseline for more refined comparisons between the normal and the diseased amygdala. AC nuclei volume and neuron number in 19 subdivisions are reported from 13 Old and New World primate brains, spanning five primate species, and compared with corresponding data from humans. Analysis of the four largest AC nuclei revealed that volume and neuron number of one component, the central nucleus, has a negative allometric relationship with total amygdala volume and neuron number, which is in contrast with the isometric relationship found in the other AC nuclei (for both neuron number and volume). Neuron density decreases across all four nuclei according to a single power law with an exponent of about minus one-half. Because we have included quantitative comparisons with great apes and humans, our conclusions apply to human brains, and our scaling laws can potentially be used to study the anatomical correlates of the amygdala in disorders involving pathological emotion processing. (c) 2009 Wiley-Liss, Inc.

[Evaluation of the Global Research Architecture Regarding Diabetic Retinopathy].

PubMed

Schöffel, N; Wahrlich, N; Groneberg, D A; Bundschuh, M; Ohlendorf, D; Bendels, M H K

2017-02-01

Aims and Scope: Diabetic retinopathy (DR) is of major scientific and socioeconomic interest in most of the industrialized countries due to increasing prevalence. This interest is reflected by a marked increase in the number of publications since the 1990 s. It is therefore difficult for a single author to obtain an overview of the topic. Material and Methods: The total number of published items on DR was determined in the Web of Science database. All bibliometric data were collected for the period 1900 to 2008 (search term:"diabet* retinopath*" and "diabet* macul*"). A number of different scientometric methods were applied in accordance with the NewQIS protocol, e.g. state of the art visualisation techniques such as density equalising maps and network diagrams. Results: A total of 15,624 publications were identified. The U. S. A. leads in the overall number of publications (4,689). The most productive and the most prolific institutions, authors and publications are all in the U. S. A. The University of Wisconsin (i.e. Ronald Klein and his wife Barbara Eden Kobrin Klein) have established an international network with a large number of institutions publishing important work. Nevertheless, many other important institutions can be identified, e.g. the Joslin Diabetes Center, which has published many articles on VEGF. Conclusion: The results reveal that the scientific interest on the topic DR is continuously increasing. International collaboration is of growing importance in this field. Georg Thieme Verlag KG Stuttgart · New York.

The Endocytic Adaptor Eps15 Controls Marginal Zone B Cell Numbers

PubMed Central

Pozzi, Benedetta; Amodio, Stefania; Lucano, Caterina; Sciullo, Anna; Ronzoni, Simona; Castelletti, Daniela; Adler, Thure; Treise, Irina; Betsholtz, Ingrid Holmberg; Rathkolb, Birgit; Busch, Dirk H.; Wolf, Eckhard; Fuchs, Helmut; Gailus-Durner, Valérie; de Angelis, Martin Hrabě; Betsholtz, Christer; Casola, Stefano; Di Fiore, Pier Paolo; Offenhäuser, Nina

2012-01-01

Eps15 is an endocytic adaptor protein involved in clathrin and non-clathrin mediated endocytosis. In Caenorhabditis elegans and Drosophila melanogaster lack of Eps15 leads to defects in synaptic vesicle recycling and synapse formation. We generated Eps15-KO mice to investigate its function in mammals. Eps15-KO mice are born at the expected Mendelian ratio and are fertile. Using a large-scale phenotype screen covering more than 300 parameters correlated to human disease, we found that Eps15-KO mice did not show any sign of disease or neural deficits. Instead, altered blood parameters pointed to an immunological defect. By competitive bone marrow transplantation we demonstrated that Eps15-KO hematopoietic precursor cells were more efficient than the WT counterparts in repopulating B220+ bone marrow cells, CD19− thymocytes and splenic marginal zone (MZ) B cells. Eps15-KO mice showed a 2-fold increase in MZ B cell numbers when compared with controls. Using reverse bone marrow transplantation, we found that Eps15 regulates MZ B cell numbers in a cell autonomous manner. FACS analysis showed that although MZ B cells were increased in Eps15-KO mice, transitional and pre-MZ B cell numbers were unaffected. The increase in MZ B cell numbers in Eps15 KO mice was not dependent on altered BCR signaling or Notch activity. In conclusion, in mammals, the endocytic adaptor protein Eps15 is a regulator of B-cell lymphopoiesis. PMID:23226392

Changes in Characteristics and Practice Patterns of Ontario Psychiatrists

PubMed Central

Zaheer, Juveria; Cheng, Joyce; Rudoler, David; Mulsant, Benoit H.

2016-01-01

Objective: The objective of this study was to evaluate the changes in demographic, geographic, and practice characteristics of all Ontario psychiatrists between 2003 and 2013 and their implication for access to psychiatrists. Methods: We included all psychiatrists who were clinically active in Ontario in any year from 2003 to 2013. For each psychiatrist, we reported age, sex, years since medical school graduation, geographic practice region, and practice characteristics such as total number of inpatients, outpatients, and outpatient visit frequencies. Results: In 2013, there were 2070 psychiatrists, with nearly half (47%) more than 30 years since medical school graduation. Female psychiatrists comprised 41% of all psychiatrists in 2013 but 56% of all psychiatrists within 15 years of medical school graduation. Between 2003 and 2013, there was a 17% increase in the total number of psychiatrists, with the largest growth in psychiatrists occurring in the group more than 30 years from medical school graduation. Over these 11 years, the mean (SD) number of unique outpatients seen by a psychiatrist annually increased from 208 (228) to 249 (275) (19.5%; P = 0.001), with male psychiatrists, on average, seeing more outpatients annually than female psychiatrists. Conclusion: The number of outpatients seen by psychiatrists is slowly increasing. However, the large proportion of aging psychiatrists, the high concentration of psychiatrists in urban settings, and the increase in the number of female psychiatrists with smaller practices suggest that without radical changes to the way psychiatrists practice, access to psychiatrists will remain a challenge in Ontario. PMID:27550804

A large increase of sour taste receptor cells in Skn-1-deficient mice does not alter the number of their sour taste signal-transmitting gustatory neurons.

PubMed

Maeda, Naohiro; Narukawa, Masataka; Ishimaru, Yoshiro; Yamamoto, Kurumi; Misaka, Takumi; Abe, Keiko

2017-05-01

The connections between taste receptor cells (TRCs) and innervating gustatory neurons are formed in a mutually dependent manner during development. To investigate whether a change in the ratio of cell types that compose taste buds influences the number of innervating gustatory neurons, we analyzed the proportion of gustatory neurons that transmit sour taste signals in adult Skn-1a -/- mice in which the number of sour TRCs is greatly increased. We generated polycystic kidney disease 1 like 3-wheat germ agglutinin (pkd1l3-WGA)/Skn-1a +/+ and pkd1l3-WGA/Skn-1a -/- mice by crossing Skn-1a -/- mice and pkd1l3-WGA transgenic mice, in which neural pathways of sour taste signals can be visualized. The number of WGA-positive cells in the circumvallate papillae is 3-fold higher in taste buds of pkd1l3-WGA/Skn-1a -/- mice relative to pkd1l3-WGA/Skn-1a +/+ mice. Intriguingly, the ratio of WGA-positive neurons to P2X 2 -expressing gustatory neurons in nodose/petrosal ganglia was similar between pkd1l3-WGA/Skn-1a +/+ and pkd1l3-WGA/Skn-1a -/- mice. In conclusion, an alteration in the ratio of cell types that compose taste buds does not influence the number of gustatory neurons that transmit sour taste signals. Copyright © 2017. Published by Elsevier B.V.

Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults

PubMed Central

Chen, Fang; He, Jing; Zhang, Jianqi; Chen, Gary K.; Thomas, Venetta; Ambrosone, Christine B.; Bandera, Elisa V.; Berndt, Sonja I.; Bernstein, Leslie; Blot, William J.; Cai, Qiuyin; Carpten, John; Casey, Graham; Chanock, Stephen J.; Cheng, Iona; Chu, Lisa; Deming, Sandra L.; Driver, W. Ryan; Goodman, Phyllis; Hayes, Richard B.; Hennis, Anselm J. M.; Hsing, Ann W.; Hu, Jennifer J.; Ingles, Sue A.; John, Esther M.; Kittles, Rick A.; Kolb, Suzanne; Leske, M. Cristina; Monroe, Kristine R.; Murphy, Adam; Nemesure, Barbara; Neslund-Dudas, Christine; Nyante, Sarah; Ostrander, Elaine A; Press, Michael F.; Rodriguez-Gil, Jorge L.; Rybicki, Ben A.; Schumacher, Fredrick; Stanford, Janet L.; Signorello, Lisa B.; Strom, Sara S.; Stevens, Victoria; Van Den Berg, David; Wang, Zhaoming; Witte, John S.; Wu, Suh-Yuh; Yamamura, Yuko; Zheng, Wei; Ziegler, Regina G.; Stram, Alexander H.; Kolonel, Laurence N.; Marchand, Loïc Le; Henderson, Brian E.; Haiman, Christopher A.; Stram, Daniel O.

2015-01-01

Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44.7% (se: 3.7%) for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1) whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2) whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported) height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the variability of height, and by implication other complex phenotypes. Our overall conclusions are that when study sizes are quite large (5,000 or so) the additive heritability estimate for height is not apparently biased upwards using the linear mixed model; however there is evidence in our simulation that a very large number of causal variants (many thousands) each with very small effect on phenotypic variance will need to be discovered to fill the gap between the heritability explained by known versus unknown causal variants. We conclude that today's GWAS data will remain useful in the future for causal variant prediction, but that finding the causal variants that need to be predicted may be extremely laborious. PMID:26125186

Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults.

PubMed

Chen, Fang; He, Jing; Zhang, Jianqi; Chen, Gary K; Thomas, Venetta; Ambrosone, Christine B; Bandera, Elisa V; Berndt, Sonja I; Bernstein, Leslie; Blot, William J; Cai, Qiuyin; Carpten, John; Casey, Graham; Chanock, Stephen J; Cheng, Iona; Chu, Lisa; Deming, Sandra L; Driver, W Ryan; Goodman, Phyllis; Hayes, Richard B; Hennis, Anselm J M; Hsing, Ann W; Hu, Jennifer J; Ingles, Sue A; John, Esther M; Kittles, Rick A; Kolb, Suzanne; Leske, M Cristina; Millikan, Robert C; Monroe, Kristine R; Murphy, Adam; Nemesure, Barbara; Neslund-Dudas, Christine; Nyante, Sarah; Ostrander, Elaine A; Press, Michael F; Rodriguez-Gil, Jorge L; Rybicki, Ben A; Schumacher, Fredrick; Stanford, Janet L; Signorello, Lisa B; Strom, Sara S; Stevens, Victoria; Van Den Berg, David; Wang, Zhaoming; Witte, John S; Wu, Suh-Yuh; Yamamura, Yuko; Zheng, Wei; Ziegler, Regina G; Stram, Alexander H; Kolonel, Laurence N; Le Marchand, Loïc; Henderson, Brian E; Haiman, Christopher A; Stram, Daniel O

2015-01-01

Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44.7% (se: 3.7%) for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1) whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2) whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported) height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the variability of height, and by implication other complex phenotypes. Our overall conclusions are that when study sizes are quite large (5,000 or so) the additive heritability estimate for height is not apparently biased upwards using the linear mixed model; however there is evidence in our simulation that a very large number of causal variants (many thousands) each with very small effect on phenotypic variance will need to be discovered to fill the gap between the heritability explained by known versus unknown causal variants. We conclude that today's GWAS data will remain useful in the future for causal variant prediction, but that finding the causal variants that need to be predicted may be extremely laborious.

An ontology-based search engine for protein-protein interactions

PubMed Central

2010-01-01

Background Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. Results We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Conclusion Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology. PMID:20122195

ADOPTION OF MELD SCORE INCREASES THE NUMBER OF LIVER TRANSPLANT

PubMed Central

NACIF, Lucas Souto; ANDRAUS, Wellington; MARTINO, Rodrigo Bronze; SANTOS, Vinicius Rocha; PINHEIRO, Rafael Soares; HADDAD, Luciana BP; D'ALBUQUERQUE, Luiz Carneiro

2014-01-01

Background Liver transplantation is performed at large transplant centers worldwide as a therapeutic intervention for patients with end-stage liver diseases. Aim To analyze the outcomes and incidence of liver transplantation performed at the University of São Paulo and to compare those with the State of São Paulo before and after adoption of the Model for End-Stage Liver Disease (MELD) score. Method Evaluation of the number of liver transplantations before and after adoption of the MELD score. Mean values and standard deviations were used to analyze normally distributed variables. The incidence results were compared with those of the State of São Paulo. Results There was a high prevalence of male patients, with a predominance of middle-aged. The main indication for liver transplantation was hepatitis C cirrhosis. The mean and median survival rates and overall survival over ten and five years were similar between the groups (p>0.05). The MELD score increased over the course of the study period for patients who underwent liver transplantation (p>0.05). There were an increased number of liver transplants after adoption of the MELD score at this institution and in the State of São Paulo (p<0.001). Conclusion The adoption of the MELD score led to increase the number of liver transplants performed in São Paulo. PMID:25184772

Survey of quantitative antimicrobial consumption per production stage in farrow-to-finish pig farms in Spain

PubMed Central

Moreno, Miguel A.

2014-01-01

Objectives To characterise antimicrobial use (AMU) per production stage in terms of drugs, routes of application, indications, duration and exposed animals in farrow-to-finish pig farms in Spain. Design Survey using a questionnaire on AMU during the six months prior to the interview, administered in face-to-face interviews completed from April to October 2010. Participants 108 potentially eligible farms covering all the country were selected using a multistage sampling methodology; of these, 33 were excluded because they did not fulfil the participation criteria and 49 were surveyed. Results The rank of the most used antimicrobials per farm and production stage and administration route started with polymyxins (colistin) by feed during the growing and the preweaning phases, followed by β-lactams by feed during the growing and the preweaning phases and by injection during the preweaning phase. Conclusions The study demonstrates that the growing stage (from weaning to the start of finishing) has the highest AMU according to different quantitative indicators (number of records, number of antimicrobials used, percentage of farms reporting use, relative number of exposed animals per farm and duration of exposure); feed is the administration route that produces the highest antimicrobial exposure based on the higher number of exposed animals and the longer duration of treatment; and there are large differences in AMU among individual pig farms. PMID:26392868

Genetic and environmental factors affecting cryptic variations in gene regulatory networks

PubMed Central

2013-01-01

Background Cryptic genetic variation (CGV) is considered to facilitate phenotypic evolution by producing visible variations in response to changes in the internal and/or external environment. Several mechanisms enabling the accumulation and release of CGVs have been proposed. In this study, we focused on gene regulatory networks (GRNs) as an important mechanism for producing CGVs, and examined how interactions between GRNs and the environment influence the number of CGVs by using individual-based simulations. Results Populations of GRNs were allowed to evolve under various stabilizing selections, and we then measured the number of genetic and phenotypic variations that had arisen. Our results showed that CGVs were not depleted irrespective of the strength of the stabilizing selection for each phenotype, whereas the visible fraction of genetic variation in a population decreased with increasing strength of selection. On the other hand, increasing the number of different environments that individuals encountered within their lifetime (i.e., entailing plastic responses to multiple environments) suppressed the accumulation of CGVs, whereas the GRNs with more genes and interactions were favored in such heterogeneous environments. Conclusions Given the findings that the number of CGVs in a population was largely determined by the size (order) of GRNs, we propose that expansion of GRNs and adaptation to novel environments are mutually facilitating and sustainable sources of evolvability and hence the origins of biological diversity and complexity. PMID:23622056

[Publication activity at Aalborg Hospital].

PubMed

Andersen, Jens Peter; Skrubbeltrang, Conni; Gregersen, Hans

2010-04-26

In 2003 Aalborg Hospital became part of Aarhus University Hospital and in that context focus on research activities was increased. This article investigates whether the increased focus has led to changes in the quantity and/or quality of research publications in the following period. All scientific articles published by Aalborg Hospital in the period 2002-2008, as well as information about author affiliations comprise the data material for the analysis. Different levels of journal groups are created based on Journal Performance Indicators combined with peer-reviewing as a measure of publication quality, awarding publications in highly esteemed journals a higher score than those published in less recognized journals. Together with the number of publications, a measure of research quality and quantity is thereby achieved. This method is compared to the more traditional journal impact factor method. Data show an increase in total publications per year while the mean number of points per publication decreases during the period. Results also show a relation between the score level of publications and the number of collaborations for the publication, i.e. large collaborations are more frequently published in top journals. The study shows that the increased focus on research has led to increased publication activity without loss of quality, as the decrease in points per publication is associated with the increased mean number of collaborators. The results indicate that the method would benefit from a revision to facilitate clearer conclusions.

Structured Product Labeling Improves Detection of Drug-intolerance Issues

PubMed Central

Schadow, Gunther

2009-01-01

Objectives This study sought to assess the value of the Health Level 7/U.S. Food and Drug Administration Structured Product Labeling (SPL) drug knowledge representation standard and its associated terminology sources for drug-intolerance (allergy) decision support in computerized provider order entry (CPOE) systems. Design The Regenstrief Institute CPOE drug-intolerance issue detection system and its knowledge base was compared with a method based on existing SPL label content enriched with knowledge sources used with SPL (NDF-RT/MeSH). Both methods were applied to a large set of drug-intolerance (allergy) records, drug orders, and medication dispensing records covering >50,000 patients over 30 years. Measurements The number of drug-intolerance issues detected by both methods was counted, as well as the number of patients with issues, number of distinct drugs, and number of distinct intolerances. The difference between drug-intolerance issues detected or missed by either method was qualitatively analyzed. Results Although <70% of terms were mapped to SPL, the new approach detected four times as many drug-intolerance issues on twice as many patients. Conclusion The SPL-based approach is more sensitive and suggests that mapping local dictionaries to SPL, and enhancing the depth and breadth of coverage of SPL content are worth accelerating. The study also highlights specificity problems known to trouble drug-intolerance decision support and suggests how terminology and methods of recording drug intolerances could be improved. PMID:18952933

Genes commonly deleted in childhood B-cell precursor acute lymphoblastic leukemia: association with cytogenetics and clinical features

PubMed Central

Schwab, Claire J.; Chilton, Lucy; Morrison, Heather; Jones, Lisa; Al-Shehhi, Halima; Erhorn, Amy; Russell, Lisa J.; Moorman, Anthony V.; Harrison, Christine J.

2013-01-01

In childhood B-cell precursor acute lymphoblastic leukemia, cytogenetics is important in diagnosis and as an indicator of response to therapy, thus playing a key role in risk stratification of patients for treatment. Little is known of the relationship between different cytogenetic subtypes in B-cell precursor acute lymphoblastic leukemia and the recently reported copy number abnormalities affecting significant leukemia associated genes. In a consecutive series of 1427 childhood B-cell precursor acute lymphoblastic leukemia patients, we have determined the incidence and type of copy number abnormalities using multiplex ligation-dependent probe amplification. We have shown strong links between certain deletions and cytogenetic subtypes, including the novel association between RB1 deletions and intrachromosomal amplification of chromosome 21. In this study, we characterized the different copy number abnormalities and show heterogeneity of PAX5 and IKZF1 deletions and the recurrent nature of RB1 deletions. Whole gene losses are often indicative of larger deletions, visible by conventional cytogenetics. An increased number of copy number abnormalities is associated with NCI high risk, specifically deletions of IKZF1 and CDKN2A/B, which occur more frequently among these patients. IKZF1 deletions and rearrangements of CRLF2 among patients with undefined karyotypes may point to the poor risk BCR-ABL1-like group. In conclusion, this study has demonstrated in a large representative cohort of children with B-cell precursor acute lymphoblastic leukemia that the pattern of copy number abnormalities is highly variable according to the primary genetic abnormality. PMID:23508010

Breaking evolutionary and pleiotropic constraints in mammals: On sloths, manatees and homeotic mutations

PubMed Central

2011-01-01

Background Mammals as a rule have seven cervical vertebrae, except for sloths and manatees. Bateson proposed that the change in the number of cervical vertebrae in sloths is due to homeotic transformations. A recent hypothesis proposes that the number of cervical vertebrae in sloths is unchanged and that instead the derived pattern is due to abnormal primaxial/abaxial patterning. Results We test the detailed predictions derived from both hypotheses for the skeletal patterns in sloths and manatees for both hypotheses. We find strong support for Bateson's homeosis hypothesis. The observed vertebral and rib patterns cannot be explained by changes in primaxial/abaxial patterning. Vertebral patterns in sloths and manatees are similar to those in mice and humans with abnormal numbers of cervical vertebrae: incomplete and asymmetric homeotic transformations are common and associated with skeletal abnormalities. In sloths the homeotic vertebral shift involves a large part of the vertebral column. As such, similarity is greatest with mice mutant for genes upstream of Hox. Conclusions We found no skeletal abnormalities in specimens of sister taxa with a normal number of cervical vertebrae. However, we always found such abnormalities in conspecifics with an abnormal number, as in many of the investigated dugongs. These findings strongly support the hypothesis that the evolutionary constraints on changes of the number of cervical vertebrae in mammals is due to deleterious pleitropic effects. We hypothesize that in sloths and manatees low metabolic and activity rates severely reduce the usual stabilizing selection, allowing the breaking of the pleiotropic constraints. This probably also applies to dugongs, although to a lesser extent. PMID:21548920

The reasons why Pakistan might be at high risk of Crimean Congo haemorrhagic fever epidemic; a scoping review of the literature.

PubMed

Atif, Muhammad; Saqib, Anum; Ikram, Raazeyah; Sarwar, Muhammad Rehan; Scahill, Shane

2017-03-23

Pakistan has faced a number of significant healthcare challenges over the past decade. In 2000, one of these events - a deadly epidemic of Crimean Congo Haemorrhagic Fever (CCHF) - struck Pakistan. The people of Pakistan are at a very high risk of acquiring CCHF, due to a number of factors which emerge from a scoping review of the literature. First, the underdeveloped healthcare system of the country is currently not prepared to cope with challenges of this nature. Healthcare professionals and medical institutes are not sufficiently equipped to properly diagnose, manage and prevent CCHF. Second, a large percentage of the general public is unaware of the spread and control of the vector. The agricultural sector of Pakistan is vast and thus many people are involved in animal husbandry and the handling of livestock which can lead to the transmission of the CCHF virus. Even in urban areas the risk of transmission is significantly higher around the time of Eid-ul-Azha, when Muslims slaughter animals. Finally, the political upheavals faced by the country have also increased Pakistan's vulnerability because a large number of refugees from Afghanistan, a CCHF endemic country, have migrated to Pakistan as a result of the Afghan war. Most of the refugees and their animals settle in Baluchistan and Khyber Pakhtunkhwa provinces, which consequently have a higher prevalence of CCHF. This scoping review of the literature highlights the potential causes of high risk CCHF and draws conclusions and makes recommendations that policy-makers in Pakistan may wish to consider in-order to improve on the current situation.

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data

PubMed Central

2015-01-01

Background Investigations into novel biomarkers using omics techniques generate large amounts of data. Due to their size and numbers of attributes, these data are suitable for analysis with machine learning methods. A key component of typical machine learning pipelines for omics data is feature selection, which is used to reduce the raw high-dimensional data into a tractable number of features. Feature selection needs to balance the objective of using as few features as possible, while maintaining high predictive power. This balance is crucial when the goal of data analysis is the identification of highly accurate but small panels of biomarkers with potential clinical utility. In this paper we propose a heuristic for the selection of very small feature subsets, via an iterative feature elimination process that is guided by rule-based machine learning, called RGIFE (Rule-guided Iterative Feature Elimination). We use this heuristic to identify putative biomarkers of osteoarthritis (OA), articular cartilage degradation and synovial inflammation, using both proteomic and transcriptomic datasets. Results and discussion Our RGIFE heuristic increased the classification accuracies achieved for all datasets when no feature selection is used, and performed well in a comparison with other feature selection methods. Using this method the datasets were reduced to a smaller number of genes or proteins, including those known to be relevant to OA, cartilage degradation and joint inflammation. The results have shown the RGIFE feature reduction method to be suitable for analysing both proteomic and transcriptomics data. Methods that generate large ‘omics’ datasets are increasingly being used in the area of rheumatology. Conclusions Feature reduction methods are advantageous for the analysis of omics data in the field of rheumatology, as the applications of such techniques are likely to result in improvements in diagnosis, treatment and drug discovery. PMID:25923811

Triplet supertree heuristics for the tree of life

PubMed Central

Lin, Harris T; Burleigh, J Gordon; Eulenstein, Oliver

2009-01-01

Background There is much interest in developing fast and accurate supertree methods to infer the tree of life. Supertree methods combine smaller input trees with overlapping sets of taxa to make a comprehensive phylogenetic tree that contains all of the taxa in the input trees. The intrinsically hard triplet supertree problem takes a collection of input species trees and seeks a species tree (supertree) that maximizes the number of triplet subtrees that it shares with the input trees. However, the utility of this supertree problem has been limited by a lack of efficient and effective heuristics. Results We introduce fast hill-climbing heuristics for the triplet supertree problem that perform a step-wise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. To realize time efficient heuristics we designed the first nontrivial algorithms for two standard search problems, which greatly improve on the time complexity to the best known (naïve) solutions by a factor of n and n2 (the number of taxa in the supertree). These algorithms enable large-scale supertree analyses based on the triplet supertree problem that were previously not possible. We implemented hill-climbing heuristics that are based on our new algorithms, and in analyses of two published supertree data sets, we demonstrate that our new heuristics outperform other standard supertree methods in maximizing the number of triplets shared with the input trees. Conclusion With our new heuristics, the triplet supertree problem is now computationally more tractable for large-scale supertree analyses, and it provides a potentially more accurate alternative to existing supertree methods. PMID:19208181

A quantification of the effectiveness of EPID dosimetry and software-based plan verification systems in detecting incidents in radiotherapy

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

Bojechko, Casey; Phillps, Mark; Kalet, Alan

Purpose: Complex treatments in radiation therapy require robust verification in order to prevent errors that can adversely affect the patient. For this purpose, the authors estimate the effectiveness of detecting errors with a “defense in depth” system composed of electronic portal imaging device (EPID) based dosimetry and a software-based system composed of rules-based and Bayesian network verifications. Methods: The authors analyzed incidents with a high potential severity score, scored as a 3 or 4 on a 4 point scale, recorded in an in-house voluntary incident reporting system, collected from February 2012 to August 2014. The incidents were categorized into differentmore » failure modes. The detectability, defined as the number of incidents that are detectable divided total number of incidents, was calculated for each failure mode. Results: In total, 343 incidents were used in this study. Of the incidents 67% were related to photon external beam therapy (EBRT). The majority of the EBRT incidents were related to patient positioning and only a small number of these could be detected by EPID dosimetry when performed prior to treatment (6%). A large fraction could be detected by in vivo dosimetry performed during the first fraction (74%). Rules-based and Bayesian network verifications were found to be complimentary to EPID dosimetry, able to detect errors related to patient prescriptions and documentation, and errors unrelated to photon EBRT. Combining all of the verification steps together, 91% of all EBRT incidents could be detected. Conclusions: This study shows that the defense in depth system is potentially able to detect a large majority of incidents. The most effective EPID-based dosimetry verification is in vivo measurements during the first fraction and is complemented by rules-based and Bayesian network plan checking.« less

Prevalence of Food and Beverage Brands in Movies: 1996–2005

PubMed Central

Sutherland, Lisa A.; MacKenzie, Todd; Purvis, Lisa A.; Dalton, Madeline

2010-01-01

OBJECTIVE The objective of this study was to describe food and beverage brand placements in a large representative sample of popular movies. METHODS We identified and coded brand placements for foods, beverages, and food retail establishments in the top 20 US box office movie hits for each year from 1996 to 2005. We also coded general movie characteristics (Motion Picture Association of America rating, run time, genre, and information about major characters). We summarized the number and types of food, beverage, and food retail establishment brands by movie characteristics and also identified manufacturers that are associated with each of the brands. RESULTS Of the 200 movies coded, 138 (69%) contained at least 1 food, beverage, or food retail establishment brand. Movies rated PG-13 and R were significantly more likely to have brand placements compared with movies in other rating categories. Comedies, action/adventures, and horror films had more brand placements than other genres. We did not detect a significant difference in the number of movies with brand placements or mean number of placements per movie by year of movie release. A total of 1180 brand placements were identified and verified, including 427 food, 425 beverage, and 328 food retail establishment brand placements. Candy/confections (26%) and salty snacks (21%) were the most prevalent food brands, sugar-sweetened beverages (76%) were the most prevalent beverage brands, and fast food composed two thirds of the food retail establishment brand placements. CONCLUSIONS Food, beverage, and food retail establishment brands are frequently portrayed in movies, and most of the brand placements are for energy-dense, nutrient-poor foods or product lines. Movies are a potent source of advertising to children, which has been largely overlooked. PMID:20142289

An observational study of retail availability and in-store marketing of e-cigarettes in London: potential to undermine recent tobacco control gains?

PubMed Central

Hsu, Robert; Myers, Allison E; Ribisl, Kurt M; Marteau, Theresa M

2013-01-01

Objectives E-cigarette companies and vendors claim the potential of e-cigarettes to help smokers reduce or quit tobacco use. E-cigarettes also have the potential to renormalise smoking. The purpose of this study was to describe the availability and in-store marketing of e-cigarettes in London, UK stores selling tobacco and alcohol. Design Observational study. Setting Small and large stores selling alcohol and tobacco in London, UK. Primary and secondary outcome measures The number of stores selling e-cigarettes, the number of stores with an interior or exterior e-cigarette advertisement, the number of stores with an e-cigarette point-of-sale movable display, store size, deprivation index score for store's corresponding lower super output area. Results Audits were completed in 108 of 128 selected stores. 62 of the audited stores (57%) sold e-cigarettes. E-cigarette availability was unrelated to store size. There was a statistically non-significant trend towards increased availability in more deprived areas (p=0.069). 31 of the 62 stores (50%) selling e-cigarettes had a point-of-sale movable display, with all but one found in small stores. Two small stores had interior advertisements and eight had exterior advertisements. No advertisements were observed in large stores. Conclusions This audit revealed widespread availability of e-cigarettes and in-store marketing in London, UK. Even if e-cigarettes prove to be an effective cessation aid, their sale and use are resulting in an increasing public presence of cigarette-like images and smoking behaviour. After decades of work to denormalise smoking, these findings raise the question of whether e-cigarettes are renormalising smoking. PMID:24366581

PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County

PubMed Central

2010-01-01

Background Because they are a closed founder population, the Old Order Amish (OOA) of Lancaster County have been the subject of many medical genetics studies. We constructed four versions of Anabaptist Genealogy Database (AGDB) using three sources of genealogies and multiple updates. In addition, we developed PedHunter, a suite of query software that can solve pedigree-related problems automatically and systematically. Methods We report on how we have used new features in PedHunter to quantify the number and expected genetic contribution of founders to the OOA. The queries and utility of PedHunter programs are illustrated by examples using AGDB in this paper. For example, we calculated the number of founders expected to be contributing genetic material to the present-day living OOA and estimated the mean relative founder representation for each founder. New features in PedHunter also include pedigree trimming and pedigree renumbering, which should prove useful for studying large pedigrees. Results With PedHunter version 2.0 querying AGDB version 4.0, we identified 34,160 presumed living OOA individuals and connected them into a 14-generation pedigree descending from 554 founders (332 females and 222 males) after trimming. From the analysis of cumulative mean relative founder representation, 128 founders (78 females and 50 males) accounted for over 95% of the mean relative founder contribution among living OOA descendants. Discussion/Conclusions The OOA are a closed founder population in which a modest number of founders account for the genetic variation present in the current OOA population. Improvements to the PedHunter software will be useful in future studies of both the OOA and other populations with large and computerized genealogies. PMID:20433770

What is the degree of innovation routinely implemented in Dutch radiotherapy centres? A multicentre cross-sectional study

PubMed Central

Boersma, Liesbeth; Dekker, Andre; Bosmans, Geert; van Merode, Frits; Verhaegen, Frank; de Ruysscher, Dirk; Swart, Rachelle; Kengen, Cindy; Lambin, Philippe

2016-01-01

Objective: To study the implementation of innovation activities in Dutch radiotherapy (RT) centres in a broad sense (product, technological, market and organizational innovations). Methods: A descriptive cross-sectional study was conducted in 15 Dutch RT centres. A list of innovations implemented from 2011 to 2013 was drawn up for each centre using semi-structured interviews. These innovations were classified into innovation categories according to previously defined innovation indicators. Where applicable, each innovation was rated by each centre on the effort required to implement it and on its expected effects, to get an impression of how far reaching and radical the innovations were and to be able to compare the number of innovations between centres. Results: The participating RT centres in the Netherlands implemented 12 innovations per year on average (range 5–25); this number was not significantly different for academic (n = 13) or non-academic centres (n = 10). Several centres were dealing with the same innovations at the same time. The average required effort and expected output did not differ significantly between product, technological and organizational innovation or between academic and non-academic centres. Conclusion: The number of innovations observed per centre varied across a large range, with a large overlap in terms of the type of innovations that were implemented. Registering innovations using the innovation indicators applied in our study would make it possible to improve collaboration between centres, e.g. with common training modules, to avoid duplication of work. Advances in knowledge: This study is the first of its kind investigating innovation implementation in RT in a broad sense. PMID:27660890

A checklist of macroparasites of Liza haematocheila (Temminck & Schlegel) (Teleostei: Mugilidae)

PubMed Central

Kostadinova, Aneta

2008-01-01

Background The mugilid fish Liza haematocheila (syn. Mugil soiuy), native to the Western North Pacific, provides opportunities to examine the changes of its parasite fauna after its translocation to the Sea of Azov and subsequent establishment in the Black Sea. However, the information on macroparasites of this host in both ranges of its current distribution comes from isolated studies published in difficult-to-access literature sources. Materials and methods Data from 53 publications, predominantly in Chinese, Russian and Ukrainian, were compiled from an extensive search of the literature and the Host-Parasite Database maintained up to 2005 at the Natural History Museum, London. Results The complete checklist of the metazoan parasites of L. haematocheila throughout its distributional range comprises summarised information for 69 nominal species of helminth and ectoparasitic crustacean parasites, from 45 genera and 27 families (370 host-parasite records in total) and includes the name of the parasite species, the area/locality of the host capture, and the author and date of the published record. The taxonomy is updated and the validity of the records and synonymies are critically evaluated. A comparison of the parasite faunas based on the records in the native and introduced/invasive range of L. haematocheila suggests that a large number of parasite species was 'lost' in the new distributional range whereas an even greater number was 'gained'. Conclusion Although the present checklist provides information that will facilitate future studies, the interesting question of macroparasite faunal diversity in L. haematocheila in its natural and introduced/invasive ranges cannot be dealt with the current data because of unreliability associated with the large number of non-documented and questionable records. This stresses the importance of data quality analysis in using host-parasite database and checklist data. PMID:19117506

Absenteeism and Employer Costs Associated With Chronic Diseases and Health Risk Factors in the US Workforce

PubMed Central

Roy, Kakoli; Lang, Jason E.; Payne, Rebecca L.; Howard, David H.

2016-01-01

Introduction Employers may incur costs related to absenteeism among employees who have chronic diseases or unhealthy behaviors. We examined the association between employee absenteeism and 5 conditions: 3 risk factors (smoking, physical inactivity, and obesity) and 2 chronic diseases (hypertension and diabetes). Methods We identified 5 chronic diseases or risk factors from 2 data sources: MarketScan Health Risk Assessment and the Medical Expenditure Panel Survey (MEPS). Absenteeism was measured as the number of workdays missed because of sickness or injury. We used zero-inflated Poisson regression to estimate excess absenteeism as the difference in the number of days missed from work by those who reported having a risk factor or chronic disease and those who did not. Covariates included demographics (eg, age, education, sex) and employment variables (eg, industry, union membership). We quantified absenteeism costs in 2011 and adjusted them to reflect growth in employment costs to 2015 dollars. Finally, we estimated absenteeism costs for a hypothetical small employer (100 employees) and a hypothetical large employer (1,000 employees). Results Absenteeism estimates ranged from 1 to 2 days per individual per year depending on the risk factor or chronic disease. Except for the physical inactivity and obesity estimates, disease- and risk-factor–specific estimates were similar in MEPS and MarketScan. Absenteeism increased with the number of risk factors or diseases reported. Nationally, each risk factor or disease was associated with annual absenteeism costs greater than $2 billion. Absenteeism costs ranged from $16 to $81 (small employer) and $17 to $286 (large employer) per employee per year. Conclusion Absenteeism costs associated with chronic diseases and health risk factors can be substantial. Employers may incur these costs through lower productivity, and employees could incur costs through lower wages. PMID:27710764

Psychometric Properties of the Problematic Internet Use Questionnaire Short-Form (PIUQ-SF-6) in a Nationally Representative Sample of Adolescents.

PubMed

Demetrovics, Zsolt; Király, Orsolya; Koronczai, Beatrix; Griffiths, Mark D; Nagygyörgy, Katalin; Elekes, Zsuzsanna; Tamás, Domokos; Kun, Bernadette; Kökönyei, Gyöngyi; Urbán, Róbert

2016-01-01

Despite the large number of measurement tools developed to assess problematic Internet use, numerous studies use measures with only modest investigation into their psychometric properties. The goal of the present study was to validate the short (6-item) version of the Problematic Internet Use Questionnaire (PIUQ) on a nationally representative adolescent sample (n = 5,005; mean age 16.4 years, SD = 0.87) and to determine a statistically established cut-off value. Data were collected within the framework of the European School Survey Project on Alcohol and Other Drugs project. Results showed an acceptable fit of the original three-factor structure to the data. In addition, a MIMIC model was carried out to justify the need for three distinct factors. The sample was divided into users at-risk of problematic Internet use and those with no-risk using a latent profile analysis. Two latent classes were obtained with 14.4% of adolescents belonging to the at-risk group. Concurrent and convergent validity were tested by comparing the two groups across a number of variables (i.e., time spent online, academic achievement, self-esteem, depressive symptoms, and preferred online activities). Using the at-risk latent profile analysis class as the gold standard, a cut-off value of 15 (out of 30) was suggested based on sensitivity and specificity analyses. In conclusion, the brief version of the (6-item) PIUQ also appears to be an appropriate measure to differentiate between Internet users at risk of developing problematic Internet use and those not at risk. Furthermore, due to its brevity, the shortened PIUQ is advantageous to utilize within large-scale surveys assessing many different behaviors and/or constructs by reducing the overall number of survey questions, and as a consequence, likely increasing completion rates.

Measurement of contact-angle hysteresis for droplets on nanopillared surface and in the Cassie and Wenzel states: a molecular dynamics simulation study.

PubMed

Koishi, Takahiro; Yasuoka, Kenji; Fujikawa, Shigenori; Zeng, Xiao Cheng

2011-09-27

We perform large-scale molecular dynamics simulations to measure the contact-angle hysteresis for a nanodroplet of water placed on a nanopillared surface. The water droplet can be in either the Cassie state (droplet being on top of the nanopillared surface) or the Wenzel state (droplet being in contact with the bottom of nanopillar grooves). To measure the contact-angle hysteresis in a quantitative fashion, the molecular dynamics simulation is designed such that the number of water molecules in the droplets can be systematically varied, but the number of base nanopillars that are in direct contact with the droplets is fixed. We find that the contact-angle hysteresis for the droplet in the Cassie state is weaker than that in the Wenzel state. This conclusion is consistent with the experimental observation. We also test a different definition of the contact-angle hysteresis, which can be extended to estimate hysteresis between the Cassie and Wenzel state. The idea is motivated from the appearance of the hysteresis loop typically seen in computer simulation of the first-order phase transition, which stems from the metastability of a system in different thermodynamic states. Since the initial shape of the droplet can be controlled arbitrarily in the computer simulation, the number of base nanopillars that are in contact with the droplet can be controlled as well. We show that the measured contact-angle hysteresis according to the second definition is indeed very sensitive to the initial shape of the droplet. Nevertheless, the contact-angle hystereses measured based on the conventional and new definition seem converging in the large droplet limit. © 2011 American Chemical Society

Urinary incontinence in Moroccan and Turkish women: a qualitative study on impact and preferences for treatment

PubMed Central

van den Muijsenbergh, Maria ETC; Lagro-Janssen, Toine ALM

2006-01-01

Aim To gain insight into the impact of urinary incontinence on the daily lives of Moroccan and Turkish women and their preferences for treatment. Design of study A qualitative analysis of data from semi-structured in depth interviews with 30 Moroccan and Turkish migrant women with urinary incontinence. Setting Six general practices with large numbers of immigrant families in four cities in the Netherlands. Method Semi-structured in depth interviews were conducted with Moroccan and Turkish migrant women, who presented with complaints of urinary incontinence in six general practices with large numbers of immigrant families on the practice list in four different cities in the Netherlands. Results All the women adhered closely to bodily cleanliness and considered incontinence to be dirty. As Muslims, they were obliged to perform ritual prayers preceded by ablution five times per day and the urinary incontinence breached their status of ritual purity. Therefore, they had to wash more often and experienced this as a heavy burden. In a number of the women, shame formed a reason why they could not talk to anybody about the incontinence, not even with the doctor. One-third of the women felt that their GP had not taken them seriously. Knowledge about anatomy, physiology and available treatments was mostly lacking. In addition, the women did not understand the aim of the exercises from the physiotherapist. The majority of women gave preference to help from a female doctor. Conclusion Urinary incontinence in Moroccan and Turkish migrant women formed a considerable problem in their daily following of the Islam faith. Shame on the part of the patient and miscommunication at the doctor's surgery led to inadequate care. PMID:17132383

Characterising the progress in HIV/AIDS research in the Middle East and North Africa

PubMed Central

Saba, Hanan F; Kouyoumjian, Silva P; Mumtaz, Ghina R; Abu-Raddad, Laith J

2013-01-01

Objectives The Middle East and North Africa (MENA) region is perceived to have limited HIV data. The objective of this study was to quantitatively characterise the progress in HIV research in this region since the discovery of the epidemic. Methods Four indices were defined and implemented to measure the progress of HIV research using the PubMed, Embase, MENA HIV/AIDS Epidemiology Synthesis Project and US Census Bureau HIV/AIDS Surveillance databases. The four indices provide complementary measures to characterise different aspects of the progress of HIV research. Results A total of 2118, 2352, 683 and 4889 records were identified through the PubMed, the Embase, the Synthesis Project and the HIV Prevalence indices, respectively. The proportion of the total global HIV records that relate to MENA is 1.2%. Overall, the indices show steady progress in the number of new records every year, with an accelerated pace in the last few years. The rate of progress in MENA was also higher than the rate of progress in HIV records globally. There is no evidence so far of stabilisation or a peak in the number of new records year by year. About half of the records were produced after the year 2005. The number of records shows large heterogeneity across countries. Conclusions MENA has witnessed a rapid growth in HIV research over the last decade. However, there are still large gaps in HIV scientific evidence in the region, and the progress is far from being uniform across countries. Ongoing and future research needs to be geared towards academic standard and production of scientific publications. PMID:23596206

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

PubMed Central

2010-01-01

Background Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. Results This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Conclusions Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service. PMID:21034504

Percentile Ranking and Citation Impact of a Large Cohort of NHLBI-funded Cardiovascular R01 Grants

PubMed Central

Danthi, Narasimhan; Wu, Colin O.; Shi, Peibei; Lauer, Michael

2014-01-01

Rationale Funding decisions for cardiovascular R01 grant applications at NHLBI largely hinge on percentile rankings. It is not known whether this approach enables the highest impact science. Objective To conduct an observational analysis of percentile rankings and bibliometric outcomes for a contemporary set of funded NHLBI cardiovascular R01 grants. Methods and results We identified 1492 investigator-initiated de novo R01 grant applications that were funded between 2001 and 2008, and followed their progress for linked publications and citations to those publications. Our co-primary endpoints were citations received per million dollars of funding, citations obtained within 2-years of publication, and 2-year citations for each grant’s maximally cited paper. In 7654 grant-years of funding that generated $3004 million of total NIH awards, the portfolio yielded 16,793 publications that appeared between 2001 and 2012 (median per grant 8, 25th and 75th percentiles 4 and 14, range 0 – 123), which received 2,224,255 citations (median per grant 1048, 25th and 75th percentiles 492 and 1,932, range 0 – 16,295). We found no association between percentile ranking and citation metrics; the absence of association persisted even after accounting for calendar time, grant duration, number of grants acknowledged per paper, number of authors per paper, early investigator status, human versus non-human focus, and institutional funding. An exploratory machine-learning analysis suggested that grants with the very best percentile rankings did yield more maximally cited papers. Conclusions In a large cohort of NHLBI-funded cardiovascular R01 grants, we were unable to find a monotonic association between better percentile ranking and higher scientific impact as assessed by citation metrics. PMID:24406983

On the use of total aerobic spore bacteria to make treatment decisions due to Cryptosporidium risk at public water system wells.

PubMed

Berger, Philip; Messner, Michael J; Crosby, Jake; Vacs Renwick, Deborah; Heinrich, Austin

2018-05-01

Spore reduction can be used as a surrogate measure of Cryptosporidium natural filtration efficiency. Estimates of log10 (log) reduction were derived from spore measurements in paired surface and well water samples in Casper Wyoming and Kearney Nebraska. We found that these data were suitable for testing the hypothesis (H 0 ) that the average reduction at each site was 2 log or less, using a one-sided Student's t-test. After establishing data quality objectives for the test (expressed as tolerable Type I and Type II error rates), we evaluated the test's performance as a function of the (a) true log reduction, (b) number of paired samples assayed and (c) variance of observed log reductions. We found that 36 paired spore samples are sufficient to achieve the objectives over a wide range of variance, including the variances observed in the two data sets. We also explored the feasibility of using smaller numbers of paired spore samples to supplement bioparticle counts for screening purposes in alluvial aquifers, to differentiate wells with large volume surface water induced recharge from wells with negligible surface water induced recharge. With key assumptions, we propose a normal statistical test of the same hypothesis (H 0 ), but with different performance objectives. As few as six paired spore samples appear adequate as a screening metric to supplement bioparticle counts to differentiate wells in alluvial aquifers with large volume surface water induced recharge. For the case when all available information (including failure to reject H 0 based on the limited paired spore data) leads to the conclusion that wells have large surface water induced recharge, we recommend further evaluation using additional paired biweekly spore samples. Published by Elsevier GmbH.

SLC25A13 Gene Analysis in Citrin Deficiency: Sixteen Novel Mutations in East Asian Patients, and the Mutation Distribution in a Large Pediatric Cohort in China

PubMed Central

Song, Yuan-Zong; Zhang, Zhan-Hui; Lin, Wei-Xia; Zhao, Xin-Jing; Deng, Mei; Ma, Yan-Li; Guo, Li; Chen, Feng-Ping; Long, Xiao-Ling; He, Xiang-Ling; Sunada, Yoshihide; Soneda, Shun; Nakatomi, Akiko; Dateki, Sumito; Ngu, Lock-Hock; Kobayashi, Keiko; Saheki, Takeyori

2013-01-01

Background The human SLC25A13 gene encodes citrin, the liver-type mitochondrial aspartate/glutamate carrier isoform 2 (AGC2), and SLC25A13 mutations cause citrin deficiency (CD), a disease entity that encompasses different age-dependant clinical phenotypes such as Adult-onset Citrullinemia Type II (CTLN2) and Neonatal Intrahepatic Cholestasis caused by Citrin Deficiency (NICCD). The analyses of SLC25A13 gene and its protein/mRNA products remain reliable tools for the definitive diagnoses of CD patients, and so far, the SLC25A13 mutation spectrum in Chinese CD patients has not been well-characterized yet. Methods and Results By means of direct DNA sequencing, cDNA cloning and SNP analyses, 16 novel pathogenic mutations, including 9 missense, 4 nonsense, 1 splice-site, 1 deletion and 1 large transposal insertion IVS4ins6kb (GenBank accession number KF425758), were identified in CTLN2 or NICCD patients from China, Japan and Malaysia, respectively, making the SLC25A13 variations worldwide reach the total number of 81. A large NICCD cohort of 116 Chinese cases was also established, and the 4 high-frequency mutations contributed a much larger proportion of the mutated alleles in the patients from south China than in those from the north (χ2 = 14.93, P<0.01), with the latitude of 30°N as the geographic dividing line in mainland China. Conclusions This paper further enriched the SLC25A13 variation spectrum worldwide, and formed a substantial contribution to the in-depth understanding of the genotypic feature of Chinese CD patients. PMID:24069319

Branching habit and the allocation of reproductive resources in conifers

PubMed Central

Leslie, Andrew B.

2012-01-01

Background and Aims Correlated relationships between branch thickness, branch density, and twig and leaf size have been used extensively to study the evolution of plant canopy architecture, but fewer studies have explored the impact of these relationships on the allocation of reproductive resources. This study quantifies pollen cone production in conifers, which have similar basic reproductive biology but vary dramatically in branching habit, in order to test how differences in branch diameter influence pollen cone size and the density with which they are deployed in the canopy. Methods Measurements of canopy branch density, the number of cones per branch and cone size were used to estimate the amount of pollen cone tissues produced by 16 species in three major conifer clades. The number of pollen grains produced was also estimated using direct counts from individual pollen cones. Key Results The total amount of pollen cone tissues in the conifer canopy varied little among species and clades, although vegetative traits such as branch thickness, branch density and pollen cone size varied over several orders of magnitude. However, branching habit controls the way these tissues are deployed: taxa with small branches produce small pollen cones at a high density, while taxa with large branches produce large cones relatively sparsely. Conclusions Conifers appear to invest similar amounts of energy in pollen production independent of branching habit. However, similar associations between branch thickness, branch density and pollen cone size are seen across conifers, including members of living and extinct groups not directly studied here. This suggests that reproductive features relating to pollen cone size are in large part a function of the evolution of vegetative morphology and branching habit. PMID:22782240

Prevalence and predictors of Axis I disorders in a large sample of treatment-seeking victims of sexual abuse and incest

PubMed Central

McElroy, Eoin; Shevlin, Mark; Elklit, Ask; Hyland, Philip; Murphy, Siobhan; Murphy, Jamie

2016-01-01

Background Childhood sexual abuse (CSA) is a common occurrence and a robust, yet non-specific, predictor of adult psychopathology. While many demographic and abuse factors have been shown to impact this relationship, their common and specific effects remain poorly understood. Objective This study sought to assess the prevalence of Axis I disorders in a large sample of help-seeking victims of sexual trauma, and to examine the common and specific effects of demographic and abuse characteristics across these different diagnoses. Method The participants were attendees at four treatment centres in Denmark that provide psychological therapy for victims of CSA (N=434). Axis I disorders were assessed using the Millon Clinical Multiaxial Inventory-III (MCMI-III). Multivariate logistic regression analysis was used to examine the associations between CSA characteristics (age of onset, duration, number of abusers, number of abusive acts) and 10 adult clinical syndromes. Results There was significant variation in the prevalence of disorders and the abuse characteristics were differentially associated with the outcome variables. Having experienced sexual abuse from more than one perpetrator was the strongest predictor of psychopathology. Conclusions The relationship between CSA and adult psychopathology is complex. Abuse characteristics have both unique and shared effects across different diagnoses. Highlights of the article The prevalence of Axis I disorders were assessed in a large sample of sexual abuse and incest survivors. The impact of demographic and abuse characteristics were also examined. There was significant variation in the prevalence of disorders. Abuse characteristics were differentially associated with the disorders. Abuse from multiple perpetrators was the strongest overall predictor of psychopathology. PMID:27064976

A Theoretical Investigation of Optical Emission in Solar Flares

NASA Astrophysics Data System (ADS)

Abbett, William Paul

A dynamic theoretical model of a flare loop from its footpoints in the photosphere to its apex in the corona is presented, and the effects of non-thermal heating of the lower atmosphere by accelerated electrons and soft X-ray irradiation from the flare heated transition region and corona are investigated. Important transitions of hydrogen, helium, and singly ionized calcium and magnesium are treated in non-LTE. Three main conclusions are drawn from the models. First, even the strongest of impulsive events can be described as having two phases: a gentle phase characterized by a state of near equilibrium, and an explosive phase characterized by large material flows, and strong hydrodynamic waves and shocks. During the gentle phase, one or possibly two temperature 'plateaus' form in the upper chromosphere. The line emission generated in these regions produces profiles that are generally symmetric and undistorted, in contrast to emission produced during the explosive phase, where large velocity gradients that occur in the upper atmosphere produce line profiles that are highly asymmetric and show large emission peaks and troughs. Second, a significant continuum (or 'white light') brightening results from increased hydrogen recombination radiation in the upper chromosphere at the point where the accelerated electrons deposit the bulk of their energy. Third, there exists a measurable time lag between the brightening of the near wings of Hα and the brightening of the Paschen continuum. This delay is controlled by the amount of time it takes for electron densities in the upper chromosphere to become high enough, and the densities of hydrogen atoms in high energy bound states to become low enough, to allow the number of recombinations to dominate the number of photoionizations in the region.

PLANNING AND RESPONSE IN THE AFTERMATH OF A LARGE CRISIS: AN AGENT-BASED INFORMATICS FRAMEWORK*

PubMed Central

Barrett, Christopher; Bisset, Keith; Chandan, Shridhar; Chen, Jiangzhuo; Chungbaek, Youngyun; Eubank, Stephen; Evrenosoğlu, Yaman; Lewis, Bryan; Lum, Kristian; Marathe, Achla; Marathe, Madhav; Mortveit, Henning; Parikh, Nidhi; Phadke, Arun; Reed, Jeffrey; Rivers, Caitlin; Saha, Sudip; Stretz, Paula; Swarup, Samarth; Thorp, James; Vullikanti, Anil; Xie, Dawen

2014-01-01

We present a synthetic information and modeling environment that can allow policy makers to study various counter-factual experiments in the event of a large human-initiated crisis. The specific scenario we consider is a ground detonation caused by an improvised nuclear device in a large urban region. In contrast to earlier work in this area that focuses largely on the prompt effects on human health and injury, we focus on co-evolution of individual and collective behavior and its interaction with the differentially damaged infrastructure. This allows us to study short term secondary and tertiary effects. The present environment is suitable for studying the dynamical outcomes over a two week period after the initial blast. A novel computing and data processing architecture is described; the architecture allows us to represent multiple co-evolving infrastructures and social networks at a highly resolved temporal, spatial, and individual scale. The representation allows us to study the emergent behavior of individuals as well as specific strategies to reduce casualties and injuries that exploit the spatial and temporal nature of the secondary and tertiary effects. A number of important conclusions are obtained using the modeling environment. For example, the studies decisively show that deploying ad hoc communication networks to reach individuals in the affected area is likely to have a significant impact on the overall casualties and injuries. PMID:25580055

PLANNING AND RESPONSE IN THE AFTERMATH OF A LARGE CRISIS: AN AGENT-BASED INFORMATICS FRAMEWORK*

PubMed

Barrett, Christopher; Bisset, Keith; Chandan, Shridhar; Chen, Jiangzhuo; Chungbaek, Youngyun; Eubank, Stephen; Evrenosoğlu, Yaman; Lewis, Bryan; Lum, Kristian; Marathe, Achla; Marathe, Madhav; Mortveit, Henning; Parikh, Nidhi; Phadke, Arun; Reed, Jeffrey; Rivers, Caitlin; Saha, Sudip; Stretz, Paula; Swarup, Samarth; Thorp, James; Vullikanti, Anil; Xie, Dawen

2013-01-01

We present a synthetic information and modeling environment that can allow policy makers to study various counter-factual experiments in the event of a large human-initiated crisis. The specific scenario we consider is a ground detonation caused by an improvised nuclear device in a large urban region. In contrast to earlier work in this area that focuses largely on the prompt effects on human health and injury, we focus on co-evolution of individual and collective behavior and its interaction with the differentially damaged infrastructure. This allows us to study short term secondary and tertiary effects. The present environment is suitable for studying the dynamical outcomes over a two week period after the initial blast. A novel computing and data processing architecture is described; the architecture allows us to represent multiple co-evolving infrastructures and social networks at a highly resolved temporal, spatial, and individual scale. The representation allows us to study the emergent behavior of individuals as well as specific strategies to reduce casualties and injuries that exploit the spatial and temporal nature of the secondary and tertiary effects. A number of important conclusions are obtained using the modeling environment. For example, the studies decisively show that deploying ad hoc communication networks to reach individuals in the affected area is likely to have a significant impact on the overall casualties and injuries.

Developing Young Children's Multidigit Number Sense.

ERIC Educational Resources Information Center

Diezmann, Carmel M.; English, Lyn D.

2001-01-01

This article describes a series of enrichment experiences designed to develop young (ages 5 to 8) gifted children's understanding of large numbers, central to their investigation of space travel. It describes activities designed to teach reading of large numbers and exploring numbers to a thousand and then a million. (Contains ten references.) (DB)

No Winglets: What a Drag...Argument for Adding Winglets to Large Air Force Aircraft

DTIC Science & Technology

2008-01-01

22134-5068 MASTER OF MILITARY STUDIES NO WINGLETS : WHAT A DRAG... ARGUMENT FOR ADDING WINGLETS TO LARGE AIR FORCE AIRCRAFT ,SUBMITTED IN PARTIAL...currently valid OMB control number. 1. REPORT DATE 2008 2. REPORT TYPE 3. DATES COVERED 00-00-2008 to 00-00-2008 4. TITLE AND SUBTITLE No Winglets ...What a Drag...Argument for Adding Winglets to Large Air Force Aircraft 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR

Percolation on fitness landscapes: effects of correlation, phenotype, and incompatibilities

PubMed Central

Gravner, Janko; Pitman, Damien; Gavrilets, Sergey

2009-01-01

We study how correlations in the random fitness assignment may affect the structure of fitness landscapes, in three classes of fitness models. The first is a phenotype space in which individuals are characterized by a large number n of continuously varying traits. In a simple model of random fitness assignment, viable phenotypes are likely to form a giant connected cluster percolating throughout the phenotype space provided the viability probability is larger than 1/2n. The second model explicitly describes genotype-to-phenotype and phenotype-to-fitness maps, allows for neutrality at both phenotype and fitness levels, and results in a fitness landscape with tunable correlation length. Here, phenotypic neutrality and correlation between fitnesses can reduce the percolation threshold, and correlations at the point of phase transition between local and global are most conducive to the formation of the giant cluster. In the third class of models, particular combinations of alleles or values of phenotypic characters are “incompatible” in the sense that the resulting genotypes or phenotypes have zero fitness. This setting can be viewed as a generalization of the canonical Bateson-Dobzhansky-Muller model of speciation and is related to K- SAT problems, prominent in computer science. We analyze the conditions for the existence of viable genotypes, their number, as well as the structure and the number of connected clusters of viable genotypes. We show that analysis based on expected values can easily lead to wrong conclusions, especially when fitness correlations are strong. We focus on pairwise incompatibilities between diallelic loci, but we also address multiple alleles, complex incompatibilities, and continuous phenotype spaces. In the case of diallelic loci, the number of clusters is stochastically bounded and each cluster contains a very large sub-cube. Finally, we demonstrate that the discrete NK model shares some signature properties of models with high correlations. PMID:17692873

Sterile flowers increase pollinator attraction and promote female success in the Mediterranean herb Leopoldia comosa

PubMed Central

Morales, Carolina L.; Traveset, Anna; Harder, Lawrence D.

2013-01-01

Background and Aims Large floral displays have opposing consequences for animal-pollinated angiosperms: they attract more pollinators but also enable elevated among-flower self-pollination (geitonogamy). The presence of sterile flowers as pollinator signals may enhance attraction while allowing displays of fewer open fertile flowers, limiting geitonogamy. The simultaneous contributions of fertile and non-fertile display components to pollinator attraction and reproductive output remain undetermined. Methods The simultaneous effects of the presence of sterile flowers and fertile-flower display size in two populations of Leopoldia comosa were experimentally assessed. Pollinator behaviour, pollen removal and deposition, and fruit and seed production were compared between intact plants and plants with sterile flowers removed. Key Results The presence of sterile flowers almost tripled pollinator attraction, supplementing the positive effect of the number of fertile flowers on the number of bees approaching inflorescences. Although attracted bees visited more flowers on larger inflorescences, the number visited did not additionally depend on the presence of sterile flowers. The presence of sterile flowers improved all aspects of plant performance, the magnitude of plant benefit being context dependent. During weather favourable to pollinators, the presence of sterile flowers increased pollen deposition on stigmas of young flowers, but this difference was not evident in older flowers, probably because of autonomous self-pollination in poorly visited flowers. Total pollen receipt per stigma decreased with increasing fertile display size. In the population with more pollinators, the presence of sterile flowers increased fruit number but not seed set or mass, whereas in the other population sterile flowers enhanced seeds per fruit, but not fruit production. These contrasts are consistent with dissimilar cross-pollination and autonomous self-pollination, coupled with the strong predispersal inbreeding depression exhibited by L. comosa populations. Conclusions Sterile flowers enrich pollination quality by promoting pollen export and import, while limiting the mating costs of geitonogamy associated with large fertile displays. PMID:23131298

Effectiveness of controlled internal drug release device treatment to alleviate reproductive seasonality in anestrus lactating or dry Barki and Rahmani ewes during non-breeding season.

PubMed

El-Mokadem, M Y; Nour El-Din, Anm; Ramadan, T A; Rashad, A M; Taha, T A; Samak, M A; Salem, M H

2018-04-01

This study aimed to evaluate the effectiveness of hormonal treatments on ovarian activity and reproductive performance in Barki and Rahmani ewes during non-breeding season. Forty-eight multiparous ewes, 24 Barki and 24 Rahmani ewes were divided into two groups, 12 lactating and 12 dry ewes for each breed. Controlled internal drug release (CIDR) device was inserted in all ewes for 14 days in conjunction with intramuscular 500 IU equine chronic gonadotrophin (eCG) at day of CIDR removal. Data were analysed using PROC MIXED of SAS for repeated measures. Breed, physiological status and days were used as fixed effects and individual ewes as random effects. Barki ewes recorded higher (p < .05) total number of follicles, number of large follicles, serum estradiol concentration and estradiol: progesterone (E 2 :P 4 ) ratio compared to Rahmani ewes. Lactating ewes recorded higher (p < .05) number of small follicles and lower concentration of total antioxidant capacity (TAC) compared to dry ewes. Number and diameter of large follicles recorded the highest (p < .05) values accompanied with disappearance of corpora lutea at day of mating. Serum progesterone concentration recorded lower (p < .05) value at day of mating and the highest (p < .05) value at day 35 after mating. CIDR-eCG protocol induced 100% oestrous behaviour in both breeds, but Rahmani ewes recorded longer (p < .05) oestrous duration compared to Barki. Conception failure was higher (p < .05) in Barki compared to Rahmani ewes. In conclusion, CIDR-eCG protocol was more potent in improving ovarian activity in Barki compared to Rahmani ewes, but this protocol seems to induce hormonal imbalance in Barki ewes that resulted in increasing conception failure compared to Rahmani ewes. © 2017 Blackwell Verlag GmbH.

Using Benchmarking Techniques and the 2011 Maternity Practices Infant Nutrition and Care (mPINC) Survey to Improve Performance among Peer Groups across the United States

PubMed Central

Edwards, Roger A.; Dee, Deborah; Umer, Amna; Perrine, Cria G.; Shealy, Katherine R.; Grummer-Strawn, Laurence M.

2015-01-01

Background A substantial proportion of US maternity care facilities engage in practices that are not evidence-based and that interfere with breastfeeding. The CDC Survey of Maternity Practices in Infant Nutrition and Care (mPINC) showed significant variation in maternity practices among US states. Objective The purpose of this article is to use benchmarking techniques to identify states within relevant peer groups that were top performers on mPINC survey indicators related to breastfeeding support. Methods We used 11 indicators of breastfeeding-related maternity care from the 2011 mPINC survey and benchmarking techniques to organize and compare hospital-based maternity practices across the 50 states and Washington, DC. We created peer categories for benchmarking first by region (grouping states by West, Midwest, South, and Northeast) and then by size (grouping states by the number of maternity facilities and dividing each region into approximately equal halves based on the number of facilities). Results Thirty-four states had scores high enough to serve as benchmarks, and 32 states had scores low enough to reflect the lowest score gap from the benchmark on at least 1 indicator. No state served as the benchmark on more than 5 indicators and no state was furthest from the benchmark on more than 7 indicators. The small peer group benchmarks in the South, West, and Midwest were better than the large peer group benchmarks on 91%, 82%, and 36% of the indicators, respectively. In the West large, the Midwest large, the Midwest small, and the South large peer groups, 4–6 benchmarks showed that less than 50% of hospitals have ideal practice in all states. Conclusion The evaluation presents benchmarks for peer group state comparisons that provide potential and feasible targets for improvement. PMID:24394963

Intensity of Territorial Marking Predicts Wolf Reproduction: Implications for Wolf Monitoring

PubMed Central

García, Emilio J.

2014-01-01

Background The implementation of intensive and complex approaches to monitor large carnivores is resource demanding, restricted to endangered species, small populations, or small distribution ranges. Wolf monitoring over large spatial scales is difficult, but the management of such contentious species requires regular estimations of abundance to guide decision-makers. The integration of wolf marking behaviour with simple sign counts may offer a cost-effective alternative to monitor the status of wolf populations over large spatial scales. Methodology/Principal Findings We used a multi-sampling approach, based on the collection of visual and scent wolf marks (faeces and ground scratching) and the assessment of wolf reproduction using howling and observation points, to test whether the intensity of marking behaviour around the pup-rearing period (summer-autumn) could reflect wolf reproduction. Between 1994 and 2007 we collected 1,964 wolf marks in a total of 1,877 km surveyed and we searched for the pups' presence (1,497 howling and 307 observations points) in 42 sampling sites with a regular presence of wolves (120 sampling sites/year). The number of wolf marks was ca. 3 times higher in sites with a confirmed presence of pups (20.3 vs. 7.2 marks). We found a significant relationship between the number of wolf marks (mean and maximum relative abundance index) and the probability of wolf reproduction. Conclusions/Significance This research establishes a real-time relationship between the intensity of wolf marking behaviour and wolf reproduction. We suggest a conservative cutting point of 0.60 for the probability of wolf reproduction to monitor wolves on a regional scale combined with the use of the mean relative abundance index of wolf marks in a given area. We show how the integration of wolf behaviour with simple sampling procedures permit rapid, real-time, and cost-effective assessments of the breeding status of wolf packs with substantial implications to monitor wolves at large spatial scales. PMID:24663068

Assessing Agreement between Multiple Raters with Missing Rating Information, Applied to Breast Cancer Tumour Grading

PubMed Central

Ellis, Ian O.; Green, Andrew R.; Hanka, Rudolf

2008-01-01

Background We consider the problem of assessing inter-rater agreement when there are missing data and a large number of raters. Previous studies have shown only ‘moderate’ agreement between pathologists in grading breast cancer tumour specimens. We analyse a large but incomplete data-set consisting of 24177 grades, on a discrete 1–3 scale, provided by 732 pathologists for 52 samples. Methodology/Principal Findings We review existing methods for analysing inter-rater agreement for multiple raters and demonstrate two further methods. Firstly, we examine a simple non-chance-corrected agreement score based on the observed proportion of agreements with the consensus for each sample, which makes no allowance for missing data. Secondly, treating grades as lying on a continuous scale representing tumour severity, we use a Bayesian latent trait method to model cumulative probabilities of assigning grade values as functions of the severity and clarity of the tumour and of rater-specific parameters representing boundaries between grades 1–2 and 2–3. We simulate from the fitted model to estimate, for each rater, the probability of agreement with the majority. Both methods suggest that there are differences between raters in terms of rating behaviour, most often caused by consistent over- or under-estimation of the grade boundaries, and also considerable variability in the distribution of grades assigned to many individual samples. The Bayesian model addresses the tendency of the agreement score to be biased upwards for raters who, by chance, see a relatively ‘easy’ set of samples. Conclusions/Significance Latent trait models can be adapted to provide novel information about the nature of inter-rater agreement when the number of raters is large and there are missing data. In this large study there is substantial variability between pathologists and uncertainty in the identity of the ‘true’ grade of many of the breast cancer tumours, a fact often ignored in clinical studies. PMID:18698346

Response of Moose Hunters to Predation following Wolf Return in Sweden

PubMed Central

Wikenros, Camilla; Sand, Håkan; Bergström, Roger; Liberg, Olof; Chapron, Guillaume

2015-01-01

Background Predation and hunter harvest constitute the main mortality factors affecting the size and dynamics of many exploited populations. The re-colonization by wolves (Canis lupus) of the Scandinavian Peninsula may therefore substantially reduce hunter harvest of moose (Alces alces), the main prey of wolves. Methodology/Principal findings We examined possible effects of wolf presence on hunter harvest in areas where we had data before and after wolf establishment (n = 25), and in additional areas that had been continuously exposed to wolf predation during at least ten years (n = 43). There was a general reduction in the total number of moose harvested (n = 31,827) during the ten year study period in all areas irrespective of presence of wolves or not. However, the reduction in hunter harvest was stronger within wolf territories compared to control areas without wolves. The reduction in harvest was larger in small (500-800 km2) compared to large (1,200-1,800 km2) wolf territories. In areas with newly established wolf territories moose management appeared to be adaptive with regard to both managers (hunting quotas) and to hunters (actual harvest). In these areas an instant reduction in moose harvest over-compensated the estimated number of moose killed annually by wolves and the composition of the hunted animals changed towards a lower proportion of adult females. Conclusions/Significance We show that the re-colonization of wolves may result in an almost instant functional response by another large predator—humans—that reduced the potential for a direct numerical effect on the density of wolves’ main prey, the moose. Because most of the worlds’ habitat that will be available for future colonization by large predators are likely to be strongly influenced by humans, human behavioural responses may constitute a key trait that govern the impact of large predators on their prey. PMID:25853570

Differential Expression Patterns in Chemosensory and Non-Chemosensory Tissues of Putative Chemosensory Genes Identified by Transcriptome Analysis of Insect Pest the Purple Stem Borer Sesamia inferens (Walker)

PubMed Central

Zhang, Ya-Nan; Jin, Jun-Yan; Jin, Rong; Xia, Yi-Han; Zhou, Jing-Jiang; Deng, Jian-Yu; Dong, Shuang-Lin

2013-01-01

Background A large number of insect chemosensory genes from different gene subfamilies have been identified and annotated, but their functional diversity and complexity are largely unknown. A systemic examination of expression patterns in chemosensory organs could provide important information. Methodology/Principal Findings We identified 92 putative chemosensory genes by analysing the transcriptome of the antennae and female sex pheromone gland of the purple stem borer Sesamia inferens, among them 87 are novel in this species, including 24 transcripts encoding for odorant binding proteins (OBPs), 24 for chemosensory proteins (CSPs), 2 for sensory neuron membrane proteins (SNMPs), 39 for odorant receptors (ORs) and 3 for ionotropic receptors (IRs). The transcriptome analyses were validated and quantified with a detailed global expression profiling by Reverse Transcription-PCR for all 92 transcripts and by Quantitative Real Time RT-PCR for selected 16 ones. Among the chemosensory gene subfamilies, CSP transcripts are most widely and evenly expressed in different tissues and stages, OBP transcripts showed a clear antenna bias and most of OR transcripts are only detected in adult antennae. Our results also revealed that some OR transcripts, such as the transcripts of SNMP2 and 2 IRs were expressed in non-chemosensory tissues, and some CSP transcripts were antenna-biased expression. Furthermore, no chemosensory transcript is specific to female sex pheromone gland and very few are found in the heads. Conclusion Our study revealed that there are a large number of chemosensory genes expressed in S. inferens, and some of them displayed unusual expression profile in non-chemosensory tissues. The identification of a large set of putative chemosensory genes of each subfamily from a single insect species, together with their different expression profiles provide further information in understanding the functions of these chemosensory genes in S. inferens as well as other insects. PMID:23894529

Glyoxalase 1 copy number variation in patients with well differentiated gastro-entero-pancreatic neuroendocrine tumours (GEP-NET)

PubMed Central

Xue, Mingzhan; Shafie, Alaa; Qaiser, Talha; Rajpoot, Nasir M.; Kaltsas, Gregory; James, Sean; Gopalakrishnan, Kishore; Fisk, Adrian; Dimitriadis, Georgios K.; Grammatopoulos, Dimitris K.; Rabbani, Naila; Thornalley, Paul J.; Weickert, Martin O.

2017-01-01

Background The glyoxalase-1 gene (GLO1) is a hotspot for copy-number variation (CNV) in human genomes. Increased GLO1 copy-number is associated with multidrug resistance in tumour chemotherapy, but prevalence of GLO1 CNV in gastro-entero-pancreatic neuroendocrine tumours (GEP-NET) is unknown. Methods GLO1 copy-number variation was measured in 39 patients with GEP-NET (midgut NET, n = 25; pancreatic NET, n = 14) after curative or debulking surgical treatment. Primary tumour tissue, surrounding healthy tissue and, where applicable, additional metastatic tumour tissue were analysed, using real time qPCR. Progression and survival following surgical treatment were monitored over 4.2 ± 0.5 years. Results In the pooled GEP-NET cohort, GLO1 copy-number in healthy tissue was 2.0 in all samples but significantly increased in primary tumour tissue in 43% of patients with pancreatic NET and in 72% of patients with midgut NET, mainly driven by significantly higher GLO1 copy-number in midgut NET. In tissue from additional metastases resection (18 midgut NET and one pancreatic NET), GLO1 copy number was also increased, compared with healthy tissue; but was not significantly different compared with primary tumour tissue. During mean 3 - 5 years follow-up, 8 patients died and 16 patients showed radiological progression. In midgut NET, a high GLO1 copy-number was associated with earlier progression. In NETs with increased GLO1 copy number, there was increased Glo1 protein expression compared to non-malignant tissue. Conclusions GLO1 copy-number was increased in a large percentage of patients with GEP-NET and correlated positively with increased Glo1 protein in tumour tissue. Analysis of GLO1 copy-number variation particularly in patients with midgut NET could be a novel prognostic marker for tumour progression. PMID:29100361

Cram

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

Gamblin, T.

2014-08-29

Large-scale systems like Sequoia allow running small numbers of very large (1M+ process) jobs, but their resource managers and schedulers do not allow large numbers of small (4, 8, 16, etc.) process jobs to run efficiently. Cram is a tool that allows users to launch many small MPI jobs within one large partition, and to overcome the limitations of current resource management software for large ensembles of jobs.

Aging and Visual Counting

PubMed Central

Li, Roger W.; MacKeben, Manfred; Chat, Sandy W.; Kumar, Maya; Ngo, Charlie; Levi, Dennis M.

2010-01-01

Background Much previous work on how normal aging affects visual enumeration has been focused on the response time required to enumerate, with unlimited stimulus duration. There is a fundamental question, not yet addressed, of how many visual items the aging visual system can enumerate in a “single glance”, without the confounding influence of eye movements. Methodology/Principal Findings We recruited 104 observers with normal vision across the age span (age 21–85). They were briefly (200 ms) presented with a number of well- separated black dots against a gray background on a monitor screen, and were asked to judge the number of dots. By limiting the stimulus presentation time, we can determine the maximum number of visual items an observer can correctly enumerate at a criterion level of performance (counting threshold, defined as the number of visual items at which ≈63% correct rate on a psychometric curve), without confounding by eye movements. Our findings reveal a 30% decrease in the mean counting threshold of the oldest group (age 61–85: ∼5 dots) when compared with the youngest groups (age 21–40: 7 dots). Surprisingly, despite decreased counting threshold, on average counting accuracy function (defined as the mean number of dots reported for each number tested) is largely unaffected by age, reflecting that the threshold loss can be primarily attributed to increased random errors. We further expanded this interesting finding to show that both young and old adults tend to over-count small numbers, but older observers over-count more. Conclusion/Significance Here we show that age reduces the ability to correctly enumerate in a glance, but the accuracy (veridicality), on average, remains unchanged with advancing age. Control experiments indicate that the degraded performance cannot be explained by optical, retinal or other perceptual factors, but is cortical in origin. PMID:20976149

Consumption with Large Sip Sizes Increases Food Intake and Leads to Underestimation of the Amount Consumed

PubMed Central

Bolhuis, Dieuwerke P.; Lakemond, Catriona M. M.; de Wijk, Rene A.; Luning, Pieternel A.; de Graaf, Cees

2013-01-01

Background A number of studies have shown that bite and sip sizes influence the amount of food intake. Consuming with small sips instead of large sips means relatively more sips for the same amount of food to be consumed; people may believe that intake is higher which leads to faster satiation. This effect may be disturbed when people are distracted. Objective The objective of the study is to assess the effects of sip size in a focused state and a distracted state on ad libitum intake and on the estimated amount consumed. Design In this 3×2 cross-over design, 53 healthy subjects consumed ad libitum soup with small sips (5 g, 60 g/min), large sips (15 g, 60 g/min), and free sips (where sip size was determined by subjects themselves), in both a distracted and focused state. Sips were administered via a pump. There were no visual cues toward consumption. Subjects then estimated how much they had consumed by filling soup in soup bowls. Results Intake in the small-sip condition was ∼30% lower than in both the large-sip and free-sip conditions (P<0.001). In addition, subjects underestimated how much they had consumed in the large-sip and free-sip conditions (P<0.03). Distraction led to a general increase in food intake (P = 0.003), independent of sip size. Distraction did not influence sip size or estimations. Conclusions Consumption with large sips led to higher food intake, as expected. Large sips, that were either fixed or chosen by subjects themselves led to underestimations of the amount consumed. This may be a risk factor for over-consumption. Reducing sip or bite sizes may successfully lower food intake, even in a distracted state. PMID:23372657

Adults Who Order Sugar-Sweetened Beverages

PubMed Central

Taksler, Glen B.; Kiszko, Kamila; Abrams, Courtney; Elbel, Brian

2016-01-01

Introduction Approximately 30% of adults consume sugar-sweetened beverages (SSBs) daily, many at fast food restaurants. Researchers examined fast food purchases to better understand which consumers order SSBs, particularly large SSBs. Methods Fast food customers in New York City and New Jersey provided receipts and participated in a survey during 2013–2014 (N=11,614). Logistic regression analyses predicted three outcomes: ordering no beverage or a non-SSB, a small/medium SSB, or a large SSB. Among respondents who ordered a beverage (n=3,775), additional analyses predicted number of beverage calories and odds of ordering an SSB. Covariates included demographic and behavioral factors. Results Respondents aged 18–29 years were 88% more likely to order a large SSB than a non-SSB or no beverage, as compared with respondents aged ≥50 years (p<0.001). Among respondents who purchased a beverage, respondents ordered more beverage calories with a large combination meal (+85.13 kcal, p=0.001) or if the restaurant had a large cup size >30 ounces (+36.07 kcal, p=0.001). Hispanic and Asian respondents were less likely to order a large SSB (AOR=0.49 and 0.52, respectively, both p≤0.026) than non-Hispanic white respondents. Odds of ordering a large SSB were higher for respondents who ate in the restaurant (AOR=1.66, p<0.001) or stated that they chose beverage based on price (AOR=2.02, p<0.001). Conclusions Young adults and customers of restaurants with a larger cup size were more likely to purchase SSBs, and their beverage calories increased with meal size. Increased understanding of these factors is an important step toward limiting unhealthy SSB consumption. PMID:27662697

Protein folding: the optically induced electronic excitations model

NASA Astrophysics Data System (ADS)

Jeknić-Dugić, J.

2009-07-01

The large-molecules conformational transitions problem (the 'protein folding problem') is an open issue of vivid current science research work of fundamental importance for a number of modern science disciplines as well as for nanotechnology. Here, we elaborate the recently proposed quantum-decoherence-based approach to the issue. First, we emphasize a need for detecting the elementary quantum mechanical processes (whose combinations may give a proper description of the realistic experimental situations) and then we design such a model. As distinct from the standard approach that deals with the conformation system, we investigate the optically induced transitions in the molecule electrons system that, in effect, may give rise to a conformation change in the molecule. Our conclusion is that such a model may describe the comparatively slow conformational transitions.

Morphometric analysis of cisplatin-induced neurite outgrowth in N1E-115 neuroblastoma cells.

PubMed

Konings, P N; Philipsen, R L; van den Broek, J H; Ruigt, G S

1994-08-29

Cisplatin, a widely used cytostatic drug for the control of a variety of neoplastic tumors, unexpectedly induced neurite outgrowth in N1E-115 neuroblastoma cells and this phenomenon was studied further in detail with morphometric analysis. As expected, cisplatin dose-dependently reduced cell number. At the same time, however, cisplatin affected the morphology of the neuroblastoma cells that changed from small rounded cell bodies into large flat cell bodies with neurites. The neurite length/cell as a function of cisplatin concentration showed a bell-shaped curve. The maximal effect (1200% of control) on neurite length/cell was observed at 1 microgram/ml cisplatin. In conclusion, cisplatin induced cellular differentiation in N1E-115 neuroblastoma cells at and just above threshold doses for cytostatic activity.

Comparison of two leading uniform theories of edge diffraction with the exact uniform asymptotic solution

NASA Technical Reports Server (NTRS)

Boersma, J.; Rahmat-Samii, Y.

1980-01-01

The diffraction of an arbitrary cylindrical wave by a half-plane has been treated by Rahmat-Samii and Mittra who used a spectral domain approach. In this paper, their exact solution for the total field is expressed in terms of a new integral representation. For large wave number k, two rigorous procedures are described for the exact uniform asymptotic expansion of the total field solution. The uniform expansions obtained are valid in the entire space, including transition regions around the shadow boundaries. The final results are compared with the formulations of two leading uniform theories of edge diffraction, namely, the uniform asymptotic theory and the uniform theory of diffraction. Some unique observations and conclusions are made in relating the two theories.

Array-based Hierarchical Mesh Generation in Parallel

DOE PAGES

Ray, Navamita; Grindeanu, Iulian; Zhao, Xinglin; ...

2015-11-03

In this paper, we describe an array-based hierarchical mesh generation capability through uniform refinement of unstructured meshes for efficient solution of PDE's using finite element methods and multigrid solvers. A multi-degree, multi-dimensional and multi-level framework is designed to generate the nested hierarchies from an initial mesh that can be used for a number of purposes such as multi-level methods to generating large meshes. The capability is developed under the parallel mesh framework “Mesh Oriented dAtaBase” a.k.a MOAB. We describe the underlying data structures and algorithms to generate such hierarchies and present numerical results for computational efficiency and mesh quality. Inmore » conclusion, we also present results to demonstrate the applicability of the developed capability to a multigrid finite-element solver.« less

Comparing barrier algorithms

NASA Technical Reports Server (NTRS)

Arenstorf, Norbert S.; Jordan, Harry F.

1987-01-01

A barrier is a method for synchronizing a large number of concurrent computer processes. After considering some basic synchronization mechanisms, a collection of barrier algorithms with either linear or logarithmic depth are presented. A graphical model is described that profiles the execution of the barriers and other parallel programming constructs. This model shows how the interaction between the barrier algorithms and the work that they synchronize can impact their performance. One result is that logarithmic tree structured barriers show good performance when synchronizing fixed length work, while linear self-scheduled barriers show better performance when synchronizing fixed length work with an imbedded critical section. The linear barriers are better able to exploit the process skew associated with critical sections. Timing experiments, performed on an eighteen processor Flex/32 shared memory multiprocessor, that support these conclusions are detailed.

Application of Factor Analysis on the Financial Ratios of Indian Cement Industry and Validation of the Results by Cluster Analysis

NASA Astrophysics Data System (ADS)

De, Anupam; Bandyopadhyay, Gautam; Chakraborty, B. N.

2010-10-01

Financial ratio analysis is an important and commonly used tool in analyzing financial health of a firm. Quite a large number of financial ratios, which can be categorized in different groups, are used for this analysis. However, to reduce number of ratios to be used for financial analysis and regrouping them into different groups on basis of empirical evidence, Factor Analysis technique is being used successfully by different researches during the last three decades. In this study Factor Analysis has been applied over audited financial data of Indian cement companies for a period of 10 years. The sample companies are listed on the Stock Exchange India (BSE and NSE). Factor Analysis, conducted over 44 variables (financial ratios) grouped in 7 categories, resulted in 11 underlying categories (factors). Each factor is named in an appropriate manner considering the factor loads and constituent variables (ratios). Representative ratios are identified for each such factor. To validate the results of Factor Analysis and to reach final conclusion regarding the representative ratios, Cluster Analysis had been performed.

Long-term physical and psychological effects of the Vajont disaster

PubMed Central

Zaetta, Cristina; Santonastaso, Paolo; Favaro, Angela

2011-01-01

Background Few studies to date investigated the long-term consequences of disasters on physical health. Objective The aim of the present report was to study the consequence on physical health of exposure to the Vajont disaster after 40 years. We also explored the effects of severity of trauma, posttraumatic stress disorder (PTSD), and major depression disorder on physical health and health-related quality of life. Method Sixty survivors of the Vajont disaster and 48 control subjects of similar gender, education, and age participated in the study. Physician-reported and subjective measures of physical health have been employed. Results Survivors reported a greater number of physical complaints than controls (p<0.001), and some type of diseases showed a significant relationship with PTSD or PTSD symptoms. Quality of life differed between the two groups as regards the perception of physical health. The number of intrusive PTSD symptoms showed a significant negative effect on the quality of life of survivors. Conclusions Our study shows that large-scale disasters such as the Vajont one may have deleterious effects on both psychological and physical health. PMID:22893826

Survey and analysis of multiresolution methods for turbulence data

DOE PAGES

Pulido, Jesus; Livescu, Daniel; Woodring, Jonathan; ...

2015-11-10

This paper compares the effectiveness of various multi-resolution geometric representation methods, such as B-spline, Daubechies, Coiflet and Dual-tree wavelets, curvelets and surfacelets, to capture the structure of fully developed turbulence using a truncated set of coefficients. The turbulence dataset is obtained from a Direct Numerical Simulation of buoyancy driven turbulence on a 512 3 mesh size, with an Atwood number, A = 0.05, and turbulent Reynolds number, Re t = 1800, and the methods are tested against quantities pertaining to both velocities and active scalar (density) fields and their derivatives, spectra, and the properties of constant density surfaces. The comparisonsmore » between the algorithms are given in terms of performance, accuracy, and compression properties. The results should provide useful information for multi-resolution analysis of turbulence, coherent feature extraction, compression for large datasets handling, as well as simulations algorithms based on multi-resolution methods. In conclusion, the final section provides recommendations for best decomposition algorithms based on several metrics related to computational efficiency and preservation of turbulence properties using a reduced set of coefficients.« less

The reproductive outcome of female patients with myotonic dystrophy type 1 (DM1) undergoing PGD is not affected by the size of the expanded CTG repeat tract

PubMed Central

Seneca, Sara; De Rademaeker, Marjan; Sermon, Karen; De Rycke, Martine; De Vos, Michel; Haentjens, Patrick; Devroey, Paul; Liebaers, Ingeborg

2010-01-01

Purpose This study aims to analyze the relationship between trinucleotide repeat length and reproductive outcome in a large cohort of DM1 patients undergoing ICSI and PGD. Methods Prospective cohort study. The effect of trinucleotide repeat length on reproductive outcome per patient was analyzed using bivariate analysis (T-test) and multivariate analysis using Kaplan-Meier and Cox regression analysis. Results Between 1995 and 2005, 205 cycles of ICSI and PGD were carried out for DM1 in 78 couples. The number of trinucleotide repeats does not have an influence on reproductive outcome when adjusted for age, BMI, basal FSH values, parity, infertility status and male or female affected. Cox regression analysis indicates that cumulative live birth rate is not influenced by the number of trinucleotide repeats. The only factor with a significant effect is age (p < 0.05). Conclusion There is no evidence of an effect of trinucleotide repeat length on reproductive outcome in patients undergoing ICSI and PGD. PMID:20221684

The Cognitive Advantages of Counting Specifically: A Representational Analysis of Verbal Numeration Systems in Oceanic Languages.

PubMed

Bender, Andrea; Schlimm, Dirk; Beller, Sieghard

2015-10-01

The domain of numbers provides a paradigmatic case for investigating interactions of culture, language, and cognition: Numerical competencies are considered a core domain of knowledge, and yet the development of specifically human abilities presupposes cultural and linguistic input by way of counting sequences. These sequences constitute systems with distinct structural properties, the cross-linguistic variability of which has implications for number representation and processing. Such representational effects are scrutinized for two types of verbal numeration systems-general and object-specific ones-that were in parallel use in several Oceanic languages (English with its general system is included for comparison). The analysis indicates that the object-specific systems outperform the general systems with respect to counting and mental arithmetic, largely due to their regular and more compact representation. What these findings reveal on cognitive diversity, how the conjectures involved speak to more general issues in cognitive science, and how the approach taken here might help to bridge the gap between anthropology and other cognitive sciences is discussed in the conclusion. Copyright © 2015 Cognitive Science Society, Inc.

Urban Form and Extreme Heat Events: Are Sprawling Cities More Vulnerable to Climate Change Than Compact Cities?

PubMed Central

Stone, Brian; Hess, Jeremy J.; Frumkin, Howard

2010-01-01

Background Extreme heat events (EHEs) are increasing in frequency in large U.S. cities and are responsible for a greater annual number of climate-related fatalities, on average, than any other form of extreme weather. In addition, low-density, sprawling patterns of urban development have been associated with enhanced surface temperatures in urbanized areas. Objectives In this study. we examined the association between urban form at the level of the metropolitan region and the frequency of EHEs over a five-decade period. Methods We employed a widely published sprawl index to measure the association between urban form in 2000 and the mean annual rate of change in EHEs between 1956 and 2005. Results We found that the rate of increase in the annual number of EHEs between 1956 and 2005 in the most sprawling metropolitan regions was more than double the rate of increase observed in the most compact metropolitan regions. Conclusions The design and management of land use in metropolitan regions may offer an important tool for adapting to the heat-related health effects associated with ongoing climate change. PMID:21114000

Analysis of factors which determine the existence of Yersinia pseudotuberculosis in a saprophytic phase.

PubMed

Litvin VYu; Maksimenkova, I A; Pushkareva, V I; Shustrova, N M

1990-01-01

Data are presented on the effects of a variety of abiotic and biotic environmental factors on the existence and changes in the numbers of Y. pseudotuberculosis. Experiments with sterile soil showed that Y. pseudotuberculosis populations were resistant over a wide range of major abiotic factors: temperature (0-30 degrees C), humidity (15-50%), pH (5.9-9.0). Although exerting some effect on the duration of different growth phases, the above abiotic factors did not influence, within the tested range, the general nature of populational dynamics of the microbe. Comparative experiments carried out in sterile and natural soil specimens using an RNA-polymerase mutant warranted the conclusion that the numbers of Y. pseudotuberculosis in soil (water) are largely controlled by the biotic components of ecosystems, including microflora and microfauna. Y. pseudotuberculosis was shown to exist in the environment (vegetable storehouses and substrate of rodent nests) in association with bacteria belonging to the family Enterobacteriaceae as well as the genera Acinetobacter and Pseudomonas. Endosymbiotic relationships are described between Y. pseudotuberculosis and the free-living infusorian Tetrahymena pyriformis which sustains microbial populations in the soil (water).

Is Health Education at University Associated with Students' Health Literacy? Evidence from Cross-Sectional Study Applying HLS-EU-Q

PubMed Central

Ossowsky, Zbigniew Marcin

2017-01-01

Background Despite the large number of studies assessing health literacy, little research has been conducted with young adults. Since health literacy is related to the setting in which health information is provided, our study aim was to measure health literacy competencies in a sample of university students and to evaluate the relationships between these competencies and their university health education. Methods A total of 912 university students (aged 18–24 years) completed the 47-item European Health Literacy Survey Questionnaire (HLS-EU-Q47). Results Perceived difficulties with health information were related to gender, with male students reporting significantly lower health literacy scores. Studying more health education-related subjects was associated with a higher health literacy competency, due to these students' higher rates of accessing and understanding health information in the health promotion domain. Conclusion Health literacy among young adult university students is insufficient. The subjects they study are related to their university health education; in particular, the number of health-related subjects they study is positively related to students' health promotion domain-based competencies. PMID:29130048

Allergic contact dermatitis from allyl isothiocyanate in a Danish cohort of 259 selected patients.

PubMed

Lerbaek, Anne; Rastogi, Suresh Chandra; Menné, Torkil

2004-08-01

Allyl isothiocyanate is present in many plants. Allergic contact dermatitis from allyl isothiocyanate is well known but infrequently reported. The aim of this study was to investigate the prevalence of contact allergy to allyl isothiocyanate in patients with suspected contact dermatitis from vegetables and food. 259 such patients were tested at the Department of Dermatology, Gentofte Hospital, Denmark, from 1994 to 2003. Only 2 patients (0.8%) had a positive reaction (+) to allyl isothiocyanate and 43 patients (16.6%) had a ?+ reaction. One of the patients with a positive reaction provided samples of margarine, salad cream, oil and mayonnaise. These were analysed with high-performance liquid chromatography, and a moderate concentration of allyl isothiocyanate (2.5 ppm) was detected in the sample of margarine. This patient was a professional sandwich maker presenting with fingertip dermatitis mimicking 'tulip fingers' or allergic contact dermatitis from garlic and onions. In conclusion, allergic contact dermatitis from allyl isothiocyanate occurs in only a limited number of cases, despite frequent exposure. The large number of ?+ reactions raises the question as to whether the recommended patch test concentration is too low.

Metformin in cancer.

PubMed

Mallik, Ritwika; Chowdhury, Tahseen A

2018-05-26

Metformin is a lipophilic biguanide which inhibits hepatic gluconeogenesis and improves peripheral utilization of glucose. It is the first line pharmacotherapy for glucose control in patients with Type 2 diabetes due to its safety, efficacy and tolerability. Metformin exhibits pleotropic effects, which may have beneficial effects on a variety of tissues independent of glucose control. A potential anti-tumourigenic effect of metformin may be mediated by its role in activating AMP-kinase, which in turn inhibits mammalian target of rapamycin (mTOR). Non-AMPK dependent protective pathways may include reduction of insulin, insulin-like growth factor-1, leptin, inflammatory pathways and potentiation of adiponectin, all of which may have a role in tumourigenesis. A role in inhibiting cancer stem cells is also postulated. A number of large scale observational and cohort studies suggest metformin is associated with a reduced risk of a number of cancers, although the data is not conclusive. Recent randomised studies reporting use of metformin in treatment of cancer have revealed mixed results, and the results of much larger randomised trials of metformin as an adjuvant therapy in breast and colorectal cancers are awaited. Copyright © 2018 Elsevier B.V. All rights reserved.

netPICOmag: from Design to Network Implementation

NASA Astrophysics Data System (ADS)

Schofield, I.; Connors, M.; Russell, C.

2009-05-01

netPICOmag is the successful conclusion of a design effort involving networking based on Rabbit microcontrollers, PIC microcontrollers, and pulsed magnetometer sensors. GPS timing allows both timestamping of data and the precision counting of the number of pulses produced by the sensor heads in one second. Power over Ethernet, use of DHCP, and broadcast of UDP packets mean a very simple local installation, with one wire leading to a relatively small integrated sensor package which is vertically placed in the ground. Although we continue to make improvements, including through investigating new sensor types, we regard the design as mature and well tested. Here we focus on the need for yet denser magnetometer networks, technological applications which become practical using sensitive yet inexpensive magnetometers, and deployment methods for large numbers of sensors. With careful calibration, netPICOmags overlap with research grade magnetometers. Without it, they still sensitively detect magnetic variations and can be used for an education or outreach program. Due to their low cost, such an application allows many students to be directly involved in gathering data that can be very relevant to them personally when they witness auroras.

Comparison of the clinical effects of white brand toothbrushes versus Vitis Suave®

PubMed Central

Segarra-Vidal, Marta; Lucas-Alcahuz, Eduardo; López-Roldán, Andrés; Gil-Loscos, Francisco; Alpiste-Illueca, Francisco

2015-01-01

Background There has been an increase in the use of white label manual toothbrushes and a greater increase in inquiries for discomfort of the gingiva and mucosa. Material and Methods A randomized, double-blind, cross-over clinical trial was made of four white brand toothbrushes versus a control brush (Vitis Suave®), with the recording of plaque index, bleeding upon probing, and gingival abrasions following utilization of the different brushes. Results All the brushes except Deliplus® were equally effective in terms of plaque removal (p<0.05). Vitis Suave® and Veckia® were the brushes associated to the greatest increase in minor abrasions (p<0.01), while Veckia®, Carrefour® and Deluxe® significantly increased the number of medium intensity abrasions (p<0.05). These brushes also increased the number of large abrasions, though statistical significance was not reached in this case. Conclusions The white brand brushes proved effective in controlling bacterial plaque, but were associated to more intense soft tissue abrasion. Key words:Gingival abrasions, manual tooth brushing, white brand, clinical effects. PMID:26535095

The impact of condom availability [correction of distribution] in Seattle schools on sexual behavior and condom use.

PubMed Central

Kirby, D; Brener, N D; Brown, N L; Peterfreund, N; Hillard, P; Harrist, R

1999-01-01

OBJECTIVES: Ten Seattle high schools made condoms available through vending machines, baskets in school clinics, or both. This study measured the number of condoms that students obtained and subsequent changes in sexual behavior and condom use. METHODS: Schoolwide surveys were administered in spring 1993 and in spring 1995, before and during the condom availability program. These data were compared with data from nationally representative surveys administered at the same time. RESULTS: Seattle students obtained an average of 4.6 condoms per year, the vast majority from baskets and very few from vending machines. Relative to the national samples, the percentage of Seattle students who had ever had sex remained stable after the program began; current sexual activity decreased significantly; and the percentage of sexually experienced students who used a condom the last time they had sex decreased significantly, particularly in the 5 schools with baskets of condoms in clinics. CONCLUSIONS: Making condoms available in Seattle schools enabled students to obtain relatively large numbers of condoms but did not lead to increases in either sexual activity or condom use. PMID:9949746

Health-service Use in Women with Binge Eating Disorders

PubMed Central

Dickerson, John; DeBar, Lynn; Perrin, Nancy A.; Lynch, Frances; Wilson, G. Terence; Rosselli, Francine; Kraemer, Helena C.; Striegel-Moore, Ruth H.

2014-01-01

Objective To compare health-care utilization between participants who met DSM-IV criteria for Binge Eating Disorder (BED) and those engaged in Recurrent Binge Eating (RBE) and to evaluate whether objective binge eating (OBE) days, a key measurement for diagnosing BED, predicted health-care costs. Method We obtained utilization and cost data from electronic medical records to augment patient reported data for 100 adult female members of a large health maintenance organization (HMO) who were enrolled in a randomized clinical trial to treat binge eating. Results Total costs did not differ between the BED and RBE groups (β=−0.117, z=−0.48, p=0.629), nor did the number of OBE days predictor total costs (β= −0.017, z=−1.01, p=0.313). Conclusions Findings suggest that the medical impairment, as assessed through health care costs, caused by BED may not be greater than impairment caused by RBE. The current threshold number of two OBE days/week as a criterion for BED may need to be reconsidered PMID:21823138

Sagace: A web-based search engine for biomedical databases in Japan

PubMed Central

2012-01-01

Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/. PMID:23110816

Burn Injury and Explosions: An Australian Perspective

PubMed Central

Greenwood, John E.

2009-01-01

Objectives: Increasingly (but not exclusively), terrorist activity and the use of explosive devices have enjoyed the focus of the global media. This paper aims to bring a range of issues to attention, to highlight how burn injuries are sustained in such incidents and why burn injuries (and thus burn disasters) are so complicated to manage. Materials and Methods: The author's experience with burn injury caused during explosions and his involvement in burn disaster situations has been summarized to form the basis of the article. This has been expanded upon with discussion points which provide a strategy for planning for such events and by a broad sample of the literature. Results: Several strategies are suggested to facilitate planning for burn disasters and to illustrate to those not directly involved why forward planning is pivotal to success when these incidents occur. Conclusions: Disasters generating large numbers of burn-injured are relatively frequent. Explosive devices are widespread in their use both in military and increasingly in civilian fields. Encompassing a large range of aetiologies, geographical sites, populations, and resources; burn disaster management is difficult and planning essential. PMID:19834533

On the Cutting Performance of Segmented Diamond Blades when Dry-Cutting Concrete

PubMed Central

Martynenko, V.; Martínez Krahmer, D.; Benítez, A.; Genovese, G.

2018-01-01

The objective of the present study is to analyze and compare the cutting performance of segmented diamond blades when dry-cutting concrete. A cutting criteria is proposed to characterize the wear of the blades by measuring the variation of the external diameter and the weight loss of the blade. The results exhibit the cutting blade SB-A, which has twice the density of diamonds and large contact area, exhibits less wear even though the material removal rate is higher compared with the other two cutting blades. Additionally, the surface topography of the different blades is evaluated to examine the impact of wear depending on the surface profile and the distribution of the diamonds in the blade’s matrix. Large number of diamonds pull-out are found in blades type SB-C, which additionally shows the worst wear resistant capability. As a conclusion, the cutting efficiency of the blade is found to be related to the density of embedded diamonds and the type of the surface profile of the cutting blade after reaching the stop criteria. PMID:29425125

The Reality of Neandertal Symbolic Behavior at the Grotte du Renne, Arcy-sur-Cure, France

PubMed Central

Caron, François; d'Errico, Francesco; Del Moral, Pierre; Santos, Frédéric; Zilhão, João

2011-01-01

Background The question of whether symbolically mediated behavior is exclusive to modern humans or shared with anatomically archaic populations such as the Neandertals is hotly debated. At the Grotte du Renne, Arcy-sur-Cure, France, the Châtelperronian levels contain Neandertal remains and large numbers of personal ornaments, decorated bone tools and colorants, but it has been suggested that this association reflects intrusion of the symbolic artifacts from the overlying Protoaurignacian and/or of the Neandertal remains from the underlying Mousterian. Methodology/Principal Findings We tested these hypotheses against the horizontal and vertical distributions of the various categories of diagnostic finds and statistically assessed the probability that the Châtelperronian levels are of mixed composition. Our results reject that the associations result from large or small scale, localized or generalized post-depositional displacement, and they imply that incomplete sample decontamination is the parsimonious explanation for the stratigraphic anomalies seen in the radiocarbon dating of the sequence. Conclusions/Significance The symbolic artifacts in the Châtelperronian of the Grotte du Renne are indeed Neandertal material culture. PMID:21738702

A search for AGN activity in Infrared-Faint Radio Sources (IFRS)

NASA Astrophysics Data System (ADS)

Lenc, Emil; Middelberg, Enno; Norris, Ray; Mao, Minnie

2009-04-01

We propose to observe a large sample of radio sources from the ATLAS (Australia Telescope Large Area Survey) source catalogue with the LBA, to determine their compactness. The sample consists of 36 sources with no counterpart in the co-located SWIRE survey (3.6 um to 160 um), carried out with the Spitzer Space Telescope. This rare class of sources, dubber Infrared-Faint Radio Sources (IFRS), is inconsistent with current galaxy evolution models. VLBI observations are an essential way to obtain further clues on what these objects are and why they are hidden from infrared observations. We will measure the flux densities on long baselines to determine their compactness. Only five IFRS have been previously targeted with VLBI observations (resulting in two detections). We propose using single baseline (Parkes-ATCA) eVLBI observations with the LBA at 1 Gbps to maximise sensitivity. With the observations proposed here we will increase the number of VLBI-observed IFRS from 5 to 36, allowing us to draw statistical conclusions about this intriguing new class of objects.

A search for AGN activity in Infrared-Faint Radio Sources (IFRS)

NASA Astrophysics Data System (ADS)

Lenc, Emil; Middelberg, Enno; Norris, Ray; Mao, Minnie

2010-04-01

We propose to observe a large sample of radio sources from the ATLAS (Australia Telescope Large Area Survey) source catalogue with the LBA, to determine their compactness. The sample consists of 36 sources with no counterpart in the co-located SWIRE survey (3.6 um to 160 um), carried out with the Spitzer Space Telescope. This rare class of sources, dubber Infrared-Faint Radio Sources (IFRS), is inconsistent with current galaxy evolution models. VLBI observations are an essential way to obtain further clues on what these objects are and why they are hidden from infrared observations. We will measure the flux densities on long baselines to determine their compactness. Only five IFRS have been previously targeted with VLBI observations (resulting in two detections). We propose using single baseline (Parkes-ATCA) eVLBI observations with the LBA at 1 Gbps to maximise sensitivity. With the observations proposed here we will increase the number of VLBI-observed IFRS from 5 to 36, allowing us to draw statistical conclusions about this intriguing new class of objects.

A perspective on coherent structures and conceptual models for turbulent boundary layer physics

NASA Technical Reports Server (NTRS)

Robinson, Stephen K.

1990-01-01

Direct numerical simulations of turbulent boundary layers have been analyzed to develop a unified conceptual model for the kinematics of coherent motions in low Reynolds number canonical turbulent boundary layers. All classes of coherent motions are considered in the model, including low-speed streaks, ejections and sweeps, vortical structures, near-wall and outer-region shear layers, sublayer pockets, and large-scale outer-region eddies. The model reflects the conclusions from the study of the simulated boundary layer that vortical structures are directly associated with the production of turbulent shear stresses, entrainment, dissipation of turbulence kinetic energy, and the fluctuating pressure field. These results, when viewed from the perspective of the large body of published work on the subject of coherent motions, confirm that vortical structures may be considered the central dynamic element in the maintenance of turbulence in the canonical boundary layer. Vortical structures serve as a framework on which to construct a unified picture of boundary layer structure, providing a means to relate the many known structural elements in a consistent way.

On the Cutting Performance of Segmented Diamond Blades when Dry-Cutting Concrete.

PubMed

Sánchez Egea, A J; Martynenko, V; Martínez Krahmer, D; López de Lacalle, L N; Benítez, A; Genovese, G

2018-02-09

The objective of the present study is to analyze and compare the cutting performance of segmented diamond blades when dry-cutting concrete. A cutting criteria is proposed to characterize the wear of the blades by measuring the variation of the external diameter and the weight loss of the blade. The results exhibit the cutting blade SB-A, which has twice the density of diamonds and large contact area, exhibits less wear even though the material removal rate is higher compared with the other two cutting blades. Additionally, the surface topography of the different blades is evaluated to examine the impact of wear depending on the surface profile and the distribution of the diamonds in the blade's matrix. Large number of diamonds pull-out are found in blades type SB-C, which additionally shows the worst wear resistant capability. As a conclusion, the cutting efficiency of the blade is found to be related to the density of embedded diamonds and the type of the surface profile of the cutting blade after reaching the stop criteria.

Synchronization of Large Josephson-Junction Arrays by Traveling Electromagnetic Waves

NASA Astrophysics Data System (ADS)

Galin, M. A.; Borodianskyi, E. A.; Kurin, V. V.; Shereshevskiy, I. A.; Vdovicheva, N. K.; Krasnov, V. M.; Klushin, A. M.

2018-05-01

Mutual synchronization of many Josephson junctions is required for superradiant enhancement of the emission power. However, the larger the junction array is, the more difficult is the synchronization, especially when the array size becomes much larger than the emitted wavelength. Here, we study experimentally Josephson emission from such larger-than-the-wavelength Nb /NbSi /Nb junction arrays. For one of the arrays we observe a clear superradiant enhancement of emission above a threshold number of active junctions. The arrays exhibit strong geometrical resonances, seen as steps in current-voltage characteristics. However, radiation patterns of the arrays have forward-backward asymmetry, which is inconsistent with the solely geometrical resonance (standing-wave) mechanism of synchronization. We argue that the asymmetry provides evidence for an alternative mechanism of synchronization mediated by unidirectional traveling-wave propagation along the array (such as a surface plasmon). In this case, emission occurs predominantly in the direction of propagation of the traveling wave. Our conclusions are supported by numerical modeling of Josephson traveling-wave antenna. We argue that such a nonresonant mechanism of synchronization opens a possibility for phase locking of very large arrays of oscillators.

The Nimrod computational workbench: a case study in desktop metacomputing

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

Abramson, D.; Sosic, R.; Foster, I.

The coordinated use of geographically distributed computers, or metacomputing, can in principle provide more accessible and cost- effective supercomputing than conventional high-performance systems. However, we lack evidence that metacomputing systems can be made easily usable, or that there exist large numbers of applications able to exploit metacomputing resources. In this paper, we present work that addresses both these concerns. The basis for this work is a system called Nimrod that provides a desktop problem-solving environment for parametric experiments. We describe how Nimrod has been extended to support the scheduling of computational resources located in a wide-area environment, and report onmore » an experiment in which Nimrod was used to schedule a large parametric study across the Australian Internet. The experiment provided both new scientific results and insights into Nimrod capabilities. We relate the results of this experiment to lessons learned from the I-WAY distributed computing experiment, and draw conclusions as to how Nimrod and I-WAY- like computing environments should be developed to support desktop metacomputing.« less

Preterm Cord Blood Contains a Higher Proportion of Immature Hematopoietic Progenitors Compared to Term Samples

PubMed Central

Podestà, Marina; Bruschettini, Matteo; Cossu, Claudia; Sabatini, Federica; Dagnino, Monica; Romantsik, Olga; Spaggiari, Grazia Maria; Ramenghi, Luca Antonio; Frassoni, Francesco

2015-01-01

Background Cord blood contains high number of hematopoietic cells that after birth disappear. In this paper we have studied the functional properties of the umbilical cord blood progenitor cells collected from term and preterm neonates to establish whether quantitative and/or qualitative differences exist between the two groups. Methods and Results Our results indicate that the percentage of total CD34+ cells was significantly higher in preterm infants compared to full term: 0.61% (range 0.15–4.8) vs 0.3% (0.032–2.23) p = 0.0001 and in neonates <32 weeks of gestational age (GA) compared to those ≥32 wks GA: 0.95% (range 0.18–4.8) and 0.36% (0.15–3.2) respectively p = 0.0025. The majority of CD34+ cells co-expressed CD71 antigen (p<0.05 preterm vs term) and grew in vitro large BFU-E, mostly in the second generation. The subpopulations CD34+CD38- and CD34+CD45- resulted more represented in preterm samples compared to term, conversely, Side Population (SP) did not show any difference between the two group. The absolute number of preterm colonies (CFCs/10microL) resulted higher compared to term (p = 0.004) and these progenitors were able to grow until the third generation maintaining an higher proportion of CD34+ cells (p = 0.0017). The number of colony also inversely correlated with the gestational age (Pearson r = -0.3001 p<0.0168). Conclusions We found no differences in the isolation and expansion capacity of Endothelial Colony Forming Cells (ECFCs) from cord blood of term and preterm neonates: both groups grew in vitro large number of endothelial cells until the third generation and showed a transitional phenotype between mesenchymal stem cells and endothelial progenitors (CD73, CD31, CD34 and CD144)The presence, in the cord blood of preterm babies, of high number of immature hematopoietic progenitors and endothelial/mesenchymal stem cells with high proliferative potential makes this tissue an important source of cells for developing new cells therapies. PMID:26417990

An experimental and numerical study of the inwardly-propagating premixed flame

NASA Astrophysics Data System (ADS)

Ibarreta, Alfonso F.

Flame stretch, described as the time rate of change of the flame surface area, can cause large changes in burning velocity of laminar premixed flames. Many experimental studies have been conducted to quantify the effects of flame stretch, but most only deal with the hydrodynamic strain component of stretch rate. In this thesis, a new experimental technique was used to study the inwardly-propagating premixed flame. This flame configuration is significant because it is subjected to the curvature component of stretch rate without the competing effects of hydrodynamic strain. Inwardly-propagating premixed flames were formed using a vortex to wrinkle a flame and create a pocket of reactants. Experiments using lean propane/air mixtures were run at both one-g and microgravity conditions to optimize the formation of large pockets of reactants. Numerical simulations of the inwardly-propagating flame (IPF) and outwardly-propagating flame (OPF) were performed for lean propane/air, methane/air and hydrogen/air mixtures. Complex chemistry as well as three different one-step reaction models were employed. Markstein numbers obtained from the experiments and computations were compared to OPF experimental data available in the literature. Researchers have used different definitions of flame location and burning velocity; the effects of these differences on the Markstein number were assessed. Experimental and numerical results indicate that the Markstein numbers obtained for the IPF are typically two to three times larger than those for the OPF. It was concluded that the observed difference in Markstein number was not caused by the IPF flame-flame interaction or the presence of intermediate species. Analysis of results obtained from the one-step reaction models identified the reasons for the difference between IPFs and OPFs: (A) the thermo-diffusive mechanism, (B) the pure curvature mechanism and (C) gas expansion. The consumption speed (Sc) was found to depend only on the thermo-diffusive mechanism and to be less sensitive to the flame geometry than the displacement velocity (Su). Observed differences between IPF and OPF results lead to the conclusion that the effects of curvature and strain cannot be grouped into a single term, but two separate Markstein numbers should be defined, one for curvature and one for strain.

Risk Factors for Oxaliplatin-Induced Hypersensitivity Reactions in Japanese Patients with Advanced Colorectal Cancer

PubMed Central

Seki, Kyoko; Senzaki, Kenzou; Tsuduki, Yasuo; Ioroi, Takeshi; Fujii, Michiko; Yamauchi, Hiroko; Shiraishi, Yukinari; Nakata, Izumi; Nishiguchi, Kohshi; Matsubayashi, Teruhisa; Takakubo, Yoshihide; Okamura, Noboru; Yamamori, Motohiro; Tamura, Takao; Sakaeda, Toshiyuki

2011-01-01

Objective: Previously, we suggested that oxaliplatin (L-OHP)-related grade 3/4 hypersensitivity reactions occurred immediately after the initiation, but grade 1/2 reactions did not. This study was conducted to clarify the risk factors for L-OHP-related hypersensitivity reactions. Methods: Clinical data from 108 Japanese patients with colorectal cancer were analyzed, who were treated with L-OHP-containing regimens, FOLFOX4 and/or mFOLFOX6. The risk factors examined included demographic data, preexisting allergies, laboratory test data, treatment regimen, treatment line of therapy, pretreatment with steroids, total number of cycles and cumulative amount of L-OHP. Results: The incidence of grade 1/2 and grade 3/4 hypersensitivity reactions were found at 13.0% (14/108) and 9.3% (10/108), respectively. Female (P=0.037), preexisting allergies (P=0.004) and lower level of lactate dehydrogenase (P=0.003) were risk factors for grade 1/2 hypersensitivity reactions, and higher neutrophil count (P=0.043) and lower monocyte count (P=0.007) were for grade 3/4 reactions. Total number of cycles were larger in the patients with grade 3/4 reactions than those without reactions (P=0.049). Conclusions: Further extensive examination with a large number of patients is needed to establish a patient management strategy. PMID:21448307

The precision-recall plot is more informative than the ROC plot when evaluating binary classifiers on imbalanced datasets.

PubMed

Saito, Takaya; Rehmsmeier, Marc

2015-01-01

Binary classifiers are routinely evaluated with performance measures such as sensitivity and specificity, and performance is frequently illustrated with Receiver Operating Characteristics (ROC) plots. Alternative measures such as positive predictive value (PPV) and the associated Precision/Recall (PRC) plots are used less frequently. Many bioinformatics studies develop and evaluate classifiers that are to be applied to strongly imbalanced datasets in which the number of negatives outweighs the number of positives significantly. While ROC plots are visually appealing and provide an overview of a classifier's performance across a wide range of specificities, one can ask whether ROC plots could be misleading when applied in imbalanced classification scenarios. We show here that the visual interpretability of ROC plots in the context of imbalanced datasets can be deceptive with respect to conclusions about the reliability of classification performance, owing to an intuitive but wrong interpretation of specificity. PRC plots, on the other hand, can provide the viewer with an accurate prediction of future classification performance due to the fact that they evaluate the fraction of true positives among positive predictions. Our findings have potential implications for the interpretation of a large number of studies that use ROC plots on imbalanced datasets.

Enumeration of small collections violates Weber's law.

PubMed

Choo, H; Franconeri, S L

2014-02-01

In a phenomenon called subitizing, we can immediately generate exact counts of small collections (one to three objects), in contrast to larger collections, for which we must either create rough estimates or serially count. A parsimonious explanation for this advantage for small collections is that noisy representations of small collections are more tolerable, due to the larger relative differences between consecutive numbers (e.g., 2 vs. 3 is a 50 % increase, but 10 vs. 11 is only a 10 % increase). In contrast, the advantage could stem from the fact that small-collection enumeration is more precise, relying on a unique mechanism. Here, we present two experiments that conclusively showed that the enumeration of small collections is indeed "superprecise." Participants compared numerosity within either small or large visual collections in conditions in which the relative differences were controlled (e.g., performance for 2 vs. 3 was compared with performance for 20 vs. 30). Small-number comparison was still faster and more accurate, across both "more-fewer" judgments (Exp. 1), and "same-different" judgments (Exp. 2). We then reviewed the remaining potential mechanisms that might underlie this superprecision for small collections, including the greater diagnostic value of visual features that correlate with number and a limited capacity for visually individuating objects.

Identifying the Factors Affecting Papers’ Citability in the Field of Medicine: an Evidence-based Approach Using 200 Highly and Lowly-cited Papers

PubMed Central

Yaminfirooz, Mousa; Ardali, Farzaneh Raeesi

2018-01-01

Introduction: Nowadays, publishing highly-cited papers is important for researchers and editors. In this evidence-based study, the factors influencing the citability of published papers in the field of medicine have been identified. Material and Methods: 200 papers indexed in Scopus (in two groups: highly-cited and lowly-cited) with 100 papers in each were studied. Needed data were manually collected with a researcher-made checklist. Data analysis was done in SPSS using descriptive and inferential statistics. Results: Variables such as journal IF, journal rank, journal subject quartile, the first/corresponding author’s h-index, the number of documents produced by the first/corresponding author, SJR and SNIP had significantly positive correlation with paper citability (p< .05). Other variables, including among others, paper age, paper type, the number of references, the number of authors, indexing institute and journal kind had not any relationship with paper citability (p> .05). Conclusion: the factors affecting the citability are among indicators relating to authors, publishing journals and published papers. Determining the extent to which these factors influence the citability of a paper needs further large-scaled research. Authors and editors searching for high-citedness should consider these factors when authoring and publishing papers. PMID:29719306

One Small Step for Manuals: Computer-Assisted Training in Twelve-Step Facilitation*

PubMed Central

Sholomskas, Diane E.; Carroll, Kathleen M.

2008-01-01

Objective The burgeoning number of empirically validated therapies has not been met with systematic evaluation of practical, inexpensive means of teaching large numbers of clinicians to use these treatments effectively. An interactive, computer-assisted training program that sought to impart skills associated with the Project MATCH (Matching Alcoholism Treatments to Client Heterogeneity) Twelve-Step Facilitation (TSF) manual was developed to address this need. Method Twenty-five community-based substance use-treatment clinicians were randomized to one of two training conditions: (1) access to the computer-assisted training program plus the TSF manual or (2) access to the manual only. The primary outcome measure was change from pre- to posttraining in the clinicians' ability to demonstrate key TSF skills. Results The data suggested that the clinicians' ability to implement TSF, as assessed by independent ratings of adherence and skill for the key TSF interventions, was significantly higher after training for those who had access to the computerized training condition than those who were assigned to the manual-only condition. Those assigned to the computer-assisted training condition also demonstrated greater gains in a knowledge test assessing familiarity with concepts presented in the TSF manual. Conclusions Computer-based training may be a feasible and effective means of training larger numbers of clinicians in empirically supported, manual-guided therapies. PMID:17061013

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems.

PubMed

Smith, Robert W; van Rosmalen, Rik P; Martins Dos Santos, Vitor A P; Fleck, Christian

2018-06-19

Models of metabolism are often used in biotechnology and pharmaceutical research to identify drug targets or increase the direct production of valuable compounds. Due to the complexity of large metabolic systems, a number of conclusions have been drawn using mathematical methods with simplifying assumptions. For example, constraint-based models describe changes of internal concentrations that occur much quicker than alterations in cell physiology. Thus, metabolite concentrations and reaction fluxes are fixed to constant values. This greatly reduces the mathematical complexity, while providing a reasonably good description of the system in steady state. However, without a large number of constraints, many different flux sets can describe the optimal model and we obtain no information on how metabolite levels dynamically change. Thus, to accurately determine what is taking place within the cell, finer quality data and more detailed models need to be constructed. In this paper we present a computational framework, DMPy, that uses a network scheme as input to automatically search for kinetic rates and produce a mathematical model that describes temporal changes of metabolite fluxes. The parameter search utilises several online databases to find measured reaction parameters. From this, we take advantage of previous modelling efforts, such as Parameter Balancing, to produce an initial mathematical model of a metabolic pathway. We analyse the effect of parameter uncertainty on model dynamics and test how recent flux-based model reduction techniques alter system properties. To our knowledge this is the first time such analysis has been performed on large models of metabolism. Our results highlight that good estimates of at least 80% of the reaction rates are required to accurately model metabolic systems. Furthermore, reducing the size of the model by grouping reactions together based on fluxes alters the resulting system dynamics. The presented pipeline automates the modelling process for large metabolic networks. From this, users can simulate their pathway of interest and obtain a better understanding of how altering conditions influences cellular dynamics. By testing the effects of different parameterisations we are also able to provide suggestions to help construct more accurate models of complete metabolic systems in the future.

Assemblages of saproxylic beetles on large downed trunks of oak.

PubMed

Milberg, Per; Bergman, Karl-Olof; Sancak, Kerem; Jansson, Nicklas

2016-03-01

Old living oaks (Quercus robur) are known as a very species-rich habitat for saproxylic beetles, but it is less clear to what extent such veteran trees differ from an even rarer feature: downed trunks of large oaks. In this study, we set out to sample this habitat, using window traps, with two aims: (1) to describe the variation of assemblages among downed trunks of different type and (2) to compare beetles on downed oaks with data from veteran standing trees. The results showed that trunk volume and sun exposure better explained assemblages as well as species numbers on downed trunks than did decay stage. Furthermore, species classified as facultative saproxylic species showed weak or no differentiation among downed trunks. Species with different feeding habits showed no apparent differentiation among downed trunks. Furthermore, species composition on dead, downed oak trunks differed sharply from that of living, veteran oaks. Wood or bark feeders were more common on veterans than downed trunks, but there was no difference for those species feeding on fungi or those feeding on insects and their remains. In conclusion, for a successful conservation of the saproxylic beetle fauna it is important to keep downed oak trunks, and particularly large ones, in forest and pastures as they constitute a saproxylic habitat that differs from that of living trees.

Galactic supernova remnant candidates discovered by THOR

NASA Astrophysics Data System (ADS)

Anderson, L. D.; Wang, Y.; Bihr, S.; Rugel, M.; Beuther, H.; Bigiel, F.; Churchwell, E.; Glover, S. C. O.; Goodman, A. A.; Henning, Th.; Heyer, M.; Klessen, R. S.; Linz, H.; Longmore, S. N.; Menten, K. M.; Ott, J.; Roy, N.; Soler, J. D.; Stil, J. M.; Urquhart, J. S.

2017-09-01

Context. There is a considerable deficiency in the number of known supernova remnants (SNRs) in the Galaxy compared to that expected. This deficiency is thought to be caused by a lack of sensitive radio continuum data. Searches for extended low-surface brightness radio sources may find new Galactic SNRs, but confusion with the much larger population of H II regions makes identifying such features challenging. SNRs can, however, be separated from H II regions using their significantly lower mid-infrared (MIR) to radio continuum intensity ratios. Aims: Our goal is to find missing SNR candidates in the Galactic disk by locating extended radio continuum sources that lack MIR counterparts. Methods: We use the combination of high-resolution 1-2 GHz continuum data from The HI, OH, Recombination line survey of the Milky Way (THOR) and lower-resolution VLA 1.4 GHz Galactic Plane Survey (VGPS) continuum data, together with MIR data from the Spitzer GLIMPSE, Spitzer MIPSGAL, and WISE surveys to identify SNR candidates. To ensure that the candidates are not being confused with H II regions, we exclude radio continuum sources from the WISE Catalog of Galactic H II Regions, which contains all known and candidate H II regions in the Galaxy. Results: We locate 76 new Galactic SNR candidates in the THOR and VGPS combined survey area of 67.4° > ℓ > 17.5°, | b | ≤ 1.25° and measure the radio flux density for 52 previously-known SNRs. The candidate SNRs have a similar spatial distribution to the known SNRs, although we note a large number of new candidates near ℓ ≃ 30°, the tangent point of the Scutum spiral arm. The candidates are on average smaller in angle compared to the known regions, 6.4' ± 4.7' versus 11.0' ± 7.8', and have lower integrated flux densities. Conclusions: The THOR survey shows that sensitive radio continuum data can discover a large number of SNR candidates, and that these candidates can be efficiently identified using the combination of radio and MIR data. If the 76 candidates are confirmed as true SNRs, for example using radio polarization measurements or by deriving radio spectral indices, this would more than double the number of known Galactic SNRs in the survey area. This large increase would still, however, leave a discrepancy between the known and expected SNR populations of about a factor of two.

25 CFR 17.7 - Limiting number of witnesses.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 25 Indians 1 2014-04-01 2014-04-01 false Limiting number of witnesses. 17.7 Section 17.7 Indians... Limiting number of witnesses. When the evidence seems clear and conclusive, the special attorney may, in his discretion, limit the number of witnesses to be examined formally upon any matter. ...

Reading the World through Very Large Numbers

ERIC Educational Resources Information Center

Greer, Brian; Mukhopadhyay, Swapna

2010-01-01

One original, and continuing, source of interest in large numbers is observation of the natural world, such as trying to count the stars on a clear night or contemplation of the number of grains of sand on the seashore. Indeed, a search of the internet quickly reveals many discussions of the relative numbers of stars and grains of sand. Big…

Low Reynolds number numerical solutions of chaotic flow

NASA Technical Reports Server (NTRS)

Pulliam, Thomas H.

1989-01-01

Numerical computations of two-dimensional flow past an airfoil at low Mach number, large angle of attack, and low Reynolds number are reported which show a sequence of flow states leading from single-period vortex shedding to chaos via the period-doubling mechanism. Analysis of the flow in terms of phase diagrams, Poincare sections, and flowfield variables are used to substantiate these results. The critical Reynolds number for the period-doubling bifurcations is shown to be sensitive to mesh refinement and the influence of large amounts of numerical dissipation. In extreme cases, large amounts of added dissipation can delay or completely eliminate the chaotic response. The effect of artificial dissipation at these low Reynolds numbers is to produce a new effective Reynolds number for the computations.

Forecasting distribution of numbers of large fires

Treesearch

Haiganoush K. Preisler; Jeff Eidenshink; Stephen Howard; Robert E. Burgan

2015-01-01

Systems to estimate forest fire potential commonly utilize one or more indexes that relate to expected fire behavior; however they indicate neither the chance that a large fire will occur, nor the expected number of large fires. That is, they do not quantify the probabilistic nature of fire danger. In this work we use large fire occurrence information from the...

77 FR 60133 - Agency Information Collection Activities: Deferral of Duty on Large Yachts Imported for Sale

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-02

... Activities: Deferral of Duty on Large Yachts Imported for Sale AGENCY: U.S. Customs and Border Protection... collection requirement concerning Deferral of Duty on Large Yachts Imported for Sale. This request for...: Title: Deferral of Duty on Large Yachts Imported for Sale. OMB Number: 1651-0080. Form Number: None...

Disorders of sex development: a genetic study of patients in a multidisciplinary clinic

PubMed Central

Laino, Luigi; Majore, Silvia; Preziosi, Nicoletta; Grammatico, Barbara; De Bernardo, Carmelilia; Scommegna, Salvatore; Rapone, Anna Maria; Marrocco, Giacinto; Bottillo, Irene; Grammatico, Paola

2014-01-01

Sex development is a process under genetic control directing both the bi-potential gonads to become either a testis or an ovary, and the consequent differentiation of internal ducts and external genitalia. This complex series of events can be altered by a large number of genetic and non-genetic factors. Disorders of sex development (DSD) are all the medical conditions characterized by an atypical chromosomal, gonadal, or phenotypical sex. Incomplete knowledge of the genetic mechanisms involved in sex development results in a low probability of determining the molecular definition of the genetic defect in many of the patients. In this study, we describe the clinical, cytogenetic, and molecular study of 88 cases with DSD, including 29 patients with 46,XY and disorders in androgen synthesis or action, 18 with 46,XX and disorders in androgen excess, 17 with 46,XY and disorders of gonadal (testicular) development, 11 classified as 46,XX other, eight with 46,XX and disorders of gonadal (ovarian) development, and five with sex chromosome anomalies. In total, we found a genetic variant in 56 out of 88 of them, leading to the clinical classification of every patient, and we outline the different steps required for a coherent genetic testing approach. In conclusion, our results highlight the fact that each category of DSD is related to a large number of different DNA alterations, thus requiring multiple genetic studies to achieve a precise etiological diagnosis for each patient. PMID:25248670

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

Ting Yuan-Sen; Conroy, Charlie; Cargile, Phillip

Understanding the evolution of the Milky Way calls for the precise abundance determination of many elements in many stars. A common perception is that deriving more than a few elemental abundances ([Fe/H], [ α /Fe], perhaps [C/H], [N/H]) requires medium-to-high spectral resolution, R ≳ 10,000, mostly to overcome the effects of line blending. In a recent work, we presented an efficient and practical way to model the full stellar spectrum, even when fitting a large number of stellar labels simultaneously. In this paper, we quantify to what precision the abundances of many different elements can be recovered, as a functionmore » of spectroscopic resolution and wavelength range. In the limit of perfect spectral models and spectral normalization, we show that the precision of elemental abundances is nearly independent of resolution, for a fixed exposure time and number of detector pixels; low-resolution spectra simply afford much higher S/N per pixel and generally larger wavelength range in a single setting. We also show that estimates of most stellar labels are not strongly correlated with one another once R ≳ 1000. Modest errors in the line-spread function, as well as small radial velocity errors, do not affect these conclusions, and data-driven models indicate that spectral (continuum) normalization can be achieved well enough in practice. These results, to be confirmed with an analysis of observed low-resolution data, open up new possibilities for the design of large spectroscopic stellar surveys and for the reanalysis of archival low-resolution data sets.« less

The management of abdominal wall hernias – in search of consensus

PubMed Central

Bury, Kamil; Śmietański, Maciej

2015-01-01

Introduction Laparoscopic repair is becoming an increasingly popular alternative in the treatment of abdominal wall hernias. In spite of numerous studies evaluating this technique, indications for laparoscopic surgery have not been established. Similarly, implant selection and fixation techniques have not been unified and are the subject of scientific discussion. Aim To assess whether there is a consensus on the management of the most common ventral abdominal wall hernias among recognised experts. Material and methods Fourteen specialists representing the boards of European surgical societies were surveyed to determine their choice of surgical technique for nine typical primary ventral and incisional hernias. The access method, type of operation, mesh prosthesis and fixation method were evaluated. In addition to the laparoscopic procedures, the number of tackers and their arrangement were assessed. Results In none of the cases presented was a consensus of experts obtained. Laparoscopic and open techniques were used equally often. Especially in the group of large hernias, decisions on repair methods were characterised by high variability. The technique of laparoscopic mesh fixation was a subject of great variability in terms of both method selection and the numbers of tackers and sutures used. Conclusions Recognised experts have not reached a consensus on the management of abdominal wall hernias. Our survey results indicate the need for further research and the inclusion of large cohorts of patients in the dedicated registries to evaluate the results of different surgical methods, which would help in the development of treatment algorithms for surgical education in the future. PMID:25960793

Computational aspects in high intensity ultrasonic surgery planning.

PubMed

Pulkkinen, A; Hynynen, K

2010-01-01

Therapeutic ultrasound treatment planning is discussed and computational aspects regarding it are reviewed. Nonlinear ultrasound simulations were solved with a combined frequency domain Rayleigh and KZK model. Ultrasonic simulations were combined with thermal simulations and were used to compute heating of muscle tissue in vivo for four different focused ultrasound transducers. The simulations were compared with measurements and good agreement was found for large F-number transducers. However, at F# 1.9 the simulated rate of temperature rise was approximately a factor of 2 higher than the measured ones. The power levels used with the F# 1 transducer were too low to show any nonlinearity. The simulations were used to investigate the importance of nonlinarities generated in the coupling water, and also the importance of including skin in the simulations. Ignoring either of these in the model would lead to larger errors. Most notably, the nonlinearities generated in the water can enhance the focal temperature by more than 100%. The simulations also demonstrated that pulsed high power sonications may provide an opportunity to significantly (up to a factor of 3) reduce the treatment time. In conclusion, nonlinear propagation can play an important role in shaping the energy distribution during a focused ultrasound treatment and it should not be ignored in planning. However, the current simulation methods are accurate only with relatively large F-numbers and better models need to be developed for sharply focused transducers. Copyright 2009 Elsevier Ltd. All rights reserved.

Track and field injuries.

PubMed

Zemper, Eric D

2005-01-01

A review of the existing literature on injuries to youth (< or =18 years old) in track and field or athletics. Searches of the Medline and SPORT Discus databases for English language articles through the end of 2003, using the search terms (adolescent or youth) and (track or field or running) and injuries. Only nine prospective or retrospective studies were found dealing with track and field injuries in children and that stated injury rates or provided enough information to allow the estimation of injury rates. Differences in study design and inconsistencies in the definition of a reportable injury provided major hindrances to making comparisons or combining data across studies. Among the few conclusions that can be drawn are that the lower extremities account for the majority of injuries, and muscle strains and ligament sprains are the predominant types of injury. While a majority of injuries may occur during training, since there is much more exposure during training than during competitions, the risk of injury is about four times higher during competitions. Informed decisions with regard to preventing injuries in youth track and field are dependent upon the quality of the basic epidemiological data available, and at this time such data are, for the most part, nonexistent. Because of the large numbers of participants and the large number and variety of activities involved in track and field, adequately designed epidemiological research is difficult, but opportunities for research in this sport are available for anyone willing to take on the challenge.

Workgroup report: base stations and wireless networks-radiofrequency (RF) exposures and health consequences.

PubMed

Valberg, Peter A; van Deventer, T Emilie; Repacholi, Michael H

2007-03-01

Radiofrequency (RF) waves have long been used for different types of information exchange via the air waves--wireless Morse code, radio, television, and wireless telephone (i.e., construction and operation of telephones or telephone systems). Increasingly larger numbers of people rely on mobile telephone technology, and health concerns about the associated RF exposure have been raised, particularly because the mobile phone handset operates in close proximity to the human body, and also because large numbers of base station antennas are required to provide widespread availability of service to large populations. The World Health Organization convened an expert workshop to discuss the current state of cellular-telephone health issues, and this article brings together several of the key points that were addressed. The possibility of RF health effects has been investigated in epidemiology studies of cellular telephone users and workers in RF occupations, in experiments with animals exposed to cell-phone RF, and via biophysical consideration of cell-phone RF electric-field intensity and the effect of RF modulation schemes. As summarized here, these separate avenues of scientific investigation provide little support for adverse health effects arising from RF exposure at levels below current international standards. Moreover, radio and television broadcast waves have exposed populations to RF for > 50 years with little evidence of deleterious health consequences. Despite unavoidable uncertainty, current scientific data are consistent with the conclusion that public exposures to permissible RF levels from mobile telephone and base stations are not likely to adversely affect human health.

Workgroup Report: Base Stations and Wireless Networks—Radiofrequency (RF) Exposures and Health Consequences

PubMed Central

Valberg, Peter A.; van Deventer, T. Emilie; Repacholi, Michael H.

2007-01-01

Radiofrequency (RF) waves have long been used for different types of information exchange via the airwaves—wireless Morse code, radio, television, and wireless telephony (i.e., construction and operation of telephones or telephonic systems). Increasingly larger numbers of people rely on mobile telephone technology, and health concerns about the associated RF exposure have been raised, particularly because the mobile phone handset operates in close proximity to the human body, and also because large numbers of base station antennas are required to provide widespread availability of service to large populations. The World Health Organization convened an expert workshop to discuss the current state of cellular-telephone health issues, and this article brings together several of the key points that were addressed. The possibility of RF health effects has been investigated in epidemiology studies of cellular telephone users and workers in RF occupations, in experiments with animals exposed to cell-phone RF, and via biophysical consideration of cell-phone RF electric-field intensity and the effect of RF modulation schemes. As summarized here, these separate avenues of scientific investigation provide little support for adverse health effects arising from RF exposure at levels below current international standards. Moreover, radio and television broadcast waves have exposed populations to RF for > 50 years with little evidence of deleterious health consequences. Despite unavoidable uncertainty, current scientific data are consistent with the conclusion that public exposures to permissible RF levels from mobile telephony and base stations are not likely to adversely affect human health. PMID:17431492

Prioritizing Chemicals and Data Requirements for Screening-Level Exposure and Risk Assessment

PubMed Central

Brown, Trevor N.; Wania, Frank; Breivik, Knut; McLachlan, Michael S.

2012-01-01

Background: Scientists and regulatory agencies strive to identify chemicals that may cause harmful effects to humans and the environment; however, prioritization is challenging because of the large number of chemicals requiring evaluation and limited data and resources. Objectives: We aimed to prioritize chemicals for exposure and exposure potential and obtain a quantitative perspective on research needs to better address uncertainty in screening assessments. Methods: We used a multimedia mass balance model to prioritize > 12,000 organic chemicals using four far-field human exposure metrics. The propagation of variance (uncertainty) in key chemical information used as model input for calculating exposure metrics was quantified. Results: Modeled human concentrations and intake rates span approximately 17 and 15 orders of magnitude, respectively. Estimates of exposure potential using human concentrations and a unit emission rate span approximately 13 orders of magnitude, and intake fractions span 7 orders of magnitude. The actual chemical emission rate contributes the greatest variance (uncertainty) in exposure estimates. The human biotransformation half-life is the second greatest source of uncertainty in estimated concentrations. In general, biotransformation and biodegradation half-lives are greater sources of uncertainty in modeled exposure and exposure potential than chemical partition coefficients. Conclusions: Mechanistic exposure modeling is suitable for screening and prioritizing large numbers of chemicals. By including uncertainty analysis and uncertainty in chemical information in the exposure estimates, these methods can help identify and address the important sources of uncertainty in human exposure and risk assessment in a systematic manner. PMID:23008278

Development of an Internet-Based Obesity Prevention Program for Children

PubMed Central

Gabriele, Jeanne M.; Stewart, Tiffany M.; Sample, Alicia; Davis, Allison B.; Allen, Ray; Martin, Corby K.; Newton, Robert L.; Williamson, Donald A.

2010-01-01

Background Childhood obesity is a growing problem, particularly in rural, Louisiana school children. Traditionally, school-based obesity prevention programs have used a primary prevention approach. Finding methods to deliver secondary prevention programs to large numbers of students without singling out overweight students has been a challenge. An innovative approach to achieving this goal is through use of an Internet intervention targeted toward a student's weight status. This article describes the Louisiana (LA) Health Internet intervention, including the student Web site, the Internet counselor Web site, and the Internet counseling process. Method The LA Health Internet intervention had separate interfaces for students and Internet counselors. The main features of the student site were behavioral weight loss lessons, lesson activities, chat with an Internet counselor, and email. The Internet counselor site contained these same features, plus a student directory and various means of obtaining student information to guide counseling. Based on their baseline weight status, students received lessons and counseling that promoted either weight loss or weight maintenance. Intervention was delivered during class time, and teachers scheduled Internet counseling sessions with intervention personnel. Results The LA Health Internet intervention was initially implemented within 14 schools; 773 students were granted access to the site. From Fall 2007 to Spring 2009, 1174 hours of Internet counselor coverage was needed to implement the Internet counseling component of this intervention Conclusion The LA Health Internet intervention is an innovative and feasible method of delivering a secondary prevention program within a school setting to large numbers of students. PMID:20513340

A Reynolds Number Study of Wing Leading-Edge Effects on a Supersonic Transport Model at Mach 0.3

NASA Technical Reports Server (NTRS)

Williams, M. Susan; Owens, Lewis R., Jr.; Chu, Julio

1999-01-01

A representative supersonic transport design was tested in the National Transonic Facility (NTF) in its original configuration with small-radius leading-edge flaps and also with modified large-radius inboard leading-edge flaps. Aerodynamic data were obtained over a range of Reynolds numbers at a Mach number of 0.3 and angles of attack up to 16 deg. Increasing the radius of the inboard leading-edge flap delayed nose-up pitching moment to a higher lift coefficient. Deflecting the large-radius leading-edge flap produced an overall decrease in lift coefficient and delayed nose-up pitching moment to even higher angles of attack as compared with the undeflected large- radius leading-edge flap. At angles of attack corresponding to the maximum untrimmed lift-to-drag ratio, lift and drag coefficients decreased while lift-to-drag ratio increased with increasing Reynolds number. At an angle of attack of 13.5 deg., the pitching-moment coefficient was nearly constant with increasing Reynolds number for both the small-radius leading-edge flap and the deflected large-radius leading-edge flap. However, the pitching moment coefficient increased with increasing Reynolds number for the undeflected large-radius leading-edge flap above a chord Reynolds number of about 35 x 10 (exp 6).

Test Population Selection from Weibull-Based, Monte Carlo Simulations of Fatigue Life

NASA Technical Reports Server (NTRS)

Vlcek, Brian L.; Zaretsky, Erwin V.; Hendricks, Robert C.

2008-01-01

Fatigue life is probabilistic and not deterministic. Experimentally establishing the fatigue life of materials, components, and systems is both time consuming and costly. As a result, conclusions regarding fatigue life are often inferred from a statistically insufficient number of physical tests. A proposed methodology for comparing life results as a function of variability due to Weibull parameters, variability between successive trials, and variability due to size of the experimental population is presented. Using Monte Carlo simulation of randomly selected lives from a large Weibull distribution, the variation in the L10 fatigue life of aluminum alloy AL6061 rotating rod fatigue tests was determined as a function of population size. These results were compared to the L10 fatigue lives of small (10 each) populations from AL2024, AL7075 and AL6061. For aluminum alloy AL6061, a simple algebraic relationship was established for the upper and lower L10 fatigue life limits as a function of the number of specimens failed. For most engineering applications where less than 30 percent variability can be tolerated in the maximum and minimum values, at least 30 to 35 test samples are necessary. The variability of test results based on small sample sizes can be greater than actual differences, if any, that exists between materials and can result in erroneous conclusions. The fatigue life of AL2024 is statistically longer than AL6061 and AL7075. However, there is no statistical difference between the fatigue lives of AL6061 and AL7075 even though AL7075 had a fatigue life 30 percent greater than AL6061.

Test Population Selection from Weibull-Based, Monte Carlo Simulations of Fatigue Life

NASA Technical Reports Server (NTRS)

Vlcek, Brian L.; Zaretsky, Erwin V.; Hendricks, Robert C.

2012-01-01

Fatigue life is probabilistic and not deterministic. Experimentally establishing the fatigue life of materials, components, and systems is both time consuming and costly. As a result, conclusions regarding fatigue life are often inferred from a statistically insufficient number of physical tests. A proposed methodology for comparing life results as a function of variability due to Weibull parameters, variability between successive trials, and variability due to size of the experimental population is presented. Using Monte Carlo simulation of randomly selected lives from a large Weibull distribution, the variation in the L10 fatigue life of aluminum alloy AL6061 rotating rod fatigue tests was determined as a function of population size. These results were compared to the L10 fatigue lives of small (10 each) populations from AL2024, AL7075 and AL6061. For aluminum alloy AL6061, a simple algebraic relationship was established for the upper and lower L10 fatigue life limits as a function of the number of specimens failed. For most engineering applications where less than 30 percent variability can be tolerated in the maximum and minimum values, at least 30 to 35 test samples are necessary. The variability of test results based on small sample sizes can be greater than actual differences, if any, that exists between materials and can result in erroneous conclusions. The fatigue life of AL2024 is statistically longer than AL6061 and AL7075. However, there is no statistical difference between the fatigue lives of AL6061 and AL7075 even though AL7075 had a fatigue life 30 percent greater than AL6061.

Genotoxicity Expert Panel review: weight of evidence evaluation of the genotoxicity of glyphosate, glyphosate-based formulations, and aminomethylphosphonic acid.

PubMed

Brusick, David; Aardema, Marilyn; Kier, Larry; Kirkland, David; Williams, Gary

2016-09-01

In 2015, the International Agency for Research on Cancer (IARC) published a monograph concluding there was strong evidence for genotoxicity of glyphosate and glyphosate formulations and moderate evidence for genotoxicity of the metabolite aminomethylphosphonic acid (AMPA). These conclusions contradicted earlier extensive reviews supporting the lack of genotoxicity of glyphosate and glyphosate formulations. The IARC Monograph concluded there was strong evidence of induction of oxidative stress by glyphosate, glyphosate formulations, and AMPA. The Expert Panel reviewed the genotoxicity and oxidative stress data considered in the IARC Monograph, together with other available data not considered by IARC. The Expert Panel defined and used a weight of evidence (WoE) approach that included ranking of studies and endpoints by the strength of their linkage to events associated with carcinogenic mechanisms. Importantly, the Expert Panel concluded that there was sufficient information available from a very large number of regulatory genotoxicity studies that should have been considered by IARC. The WoE approach, the inclusion of all relevant regulatory studies, and some differences in interpretation of individual studies led to significantly different conclusions by the Expert Panel compared with the IARC Monograph. The Expert Panel concluded that glyphosate, glyphosate formulations, and AMPA do not pose a genotoxic hazard and the data do not support the IARC Monograph genotoxicity evaluation. With respect to carcinogenicity classification and mechanism, the Expert Panel concluded that evidence relating to an oxidative stress mechanism of carcinogenicity was largely unconvincing and that the data profiles were not consistent with the characteristics of genotoxic carcinogens.

Two Types of Well Followed Users in the Followership Networks of Twitter

PubMed Central

Saito, Kodai; Masuda, Naoki

2014-01-01

In the Twitter blogosphere, the number of followers is probably the most basic and succinct quantity for measuring popularity of users. However, the number of followers can be manipulated in various ways; we can even buy follows. Therefore, alternative popularity measures for Twitter users on the basis of, for example, users' tweets and retweets, have been developed. In the present work, we take a purely network approach to this fundamental question. First, we find that two relatively distinct types of users possessing a large number of followers exist, in particular for Japanese, Russian, and Korean users among the seven language groups that we examined. A first type of user follows a small number of other users. A second type of user follows approximately the same number of other users as the number of follows that the user receives. Then, we compare local (i.e., egocentric) followership networks around the two types of users with many followers. We show that the second type, which is presumably uninfluential users despite its large number of followers, is characterized by high link reciprocity, a large number of friends (i.e., those whom a user follows) for the followers, followers' high link reciprocity, large clustering coefficient, large fraction of the second type of users among the followers, and a small PageRank. Our network-based results support that the number of followers used alone is a misleading measure of user's popularity. We propose that the number of friends, which is simple to measure, also helps us to assess the popularity of Twitter users. PMID:24416209

Symbolic Numerical Distance Effect Does Not Reflect the Difference between Numbers.

PubMed

Krajcsi, Attila; Kojouharova, Petia

2017-01-01

In a comparison task, the larger the distance between the two numbers to be compared, the better the performance-a phenomenon termed as the numerical distance effect. According to the dominant explanation, the distance effect is rooted in a noisy representation, and performance is proportional to the size of the overlap between the noisy representations of the two values. According to alternative explanations, the distance effect may be rooted in the association between the numbers and the small-large categories, and performance is better when the numbers show relatively high differences in their strength of association with the small-large properties. In everyday number use, the value of the numbers and the association between the numbers and the small-large categories strongly correlate; thus, the two explanations have the same predictions for the distance effect. To dissociate the two potential sources of the distance effect, in the present study, participants learned new artificial number digits only for the values between 1 and 3, and between 7 and 9, thus, leaving out the numbers between 4 and 6. It was found that the omitted number range (the distance between 3 and 7) was considered in the distance effect as 1, and not as 4, suggesting that the distance effect does not follow the values of the numbers predicted by the dominant explanation, but it follows the small-large property association predicted by the alternative explanations.

A comparison between IMSC, PI and MIMSC methods in controlling the vibration of flexible systems

NASA Technical Reports Server (NTRS)

Baz, A.; Poh, S.

1987-01-01

A comparative study is presented between three active control algorithms which have proven to be successful in controlling the vibrations of large flexible systems. These algorithms are: the Independent Modal Space Control (IMSC), the Pseudo-inverse (PI), and the Modified Independent Modal Space Control (MIMSC). Emphasis is placed on demonstrating the effectiveness of the MIMSC method in controlling the vibration of large systems with small number of actuators by using an efficient time sharing strategy. Such a strategy favors the MIMSC over the IMSC method, which requires a large number of actuators to control equal number of modes, and also over the PI method which attempts to control large number of modes with smaller number of actuators through the use of an in-exact statistical realization of a modal controller. Numerical examples are presented to illustrate the main features of the three algorithms and the merits of the MIMSC method.

SU-E-I-20: Comprehensive Quality Assurance Test of Second Generation Toshiba Aquilion Large Bore CT Simulator Based On AAPM TG-66 Recommendations

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

Zhang, D

2015-06-15

Purpose: AAPM radiation therapy committee task group No. 66 (TG-66) published a report which described a general approach to CT simulator QA. The report outlines the testing procedures and specifications for the evaluation of patient dose, radiation safety, electromechanical components, and image quality for a CT simulator. The purpose of this study is to thoroughly evaluate the performance of a second generation Toshiba Aquilion Large Bore CT simulator with 90 cm bore size (Toshiba, Nasu, JP) based on the TG-66 criteria. The testing procedures and results from this study provide baselines for a routine QA program. Methods: Different measurements andmore » analysis were performed including CTDIvol measurements, alignment and orientation of gantry lasers, orientation of the tabletop with respect to the imaging plane, table movement and indexing accuracy, Scanogram location accuracy, high contrast spatial resolution, low contrast resolution, field uniformity, CT number accuracy, mA linearity and mA reproducibility using a number of different phantoms and measuring devices, such as CTDI phantom, ACR image quality phantom, TG-66 laser QA phantom, pencil ion chamber (Fluke Victoreen) and electrometer (RTI Solidose 400). Results: The CTDI measurements were within 20% of the console displayed values. The alignment and orientation for both gantry laser and tabletop, as well as the table movement and indexing and scanogram location accuracy were within 2mm as specified in TG66. The spatial resolution, low contrast resolution, field uniformity and CT number accuracy were all within ACR’s recommended limits. The mA linearity and reproducibility were both well below the TG66 threshold. Conclusion: The 90 cm bore size second generation Toshiba Aquilion Large Bore CT simulator that comes with 70 cm true FOV can consistently meet various clinical needs. The results demonstrated that this simulator complies with the TG-66 protocol in all aspects including electromechanical component, radiation safety component, and image quality component. Employee of Toshiba America Medical Systems.« less

Trends in Solar energy Driven Vertical Ground Source Heat Pump Systems in Sweden - An Analysis Based on the Swedish Well Database

NASA Astrophysics Data System (ADS)

Juhlin, K.; Gehlin, S.

2016-12-01

Sweden is a world leader in developing and using vertical ground source heat pump (GSHP) technology. GSHP systems extract passively stored solar energy in the ground and the Earth's natural geothermal energy. Geothermal energy is an admitted renewable energy source in Sweden since 2007 and is the third largest renewable energy source in the country today. The Geological Survey of Sweden (SGU) is the authority in Sweden that provides open access geological data of rock, soil and groundwater for the public. All wells drilled must be registered in the SGU Well Database and it is the well driller's duty to submit registration of drilled wells.Both active and passive geothermal energy systems are in use. Large GSHP systems, with at least 20 boreholes, are active geothermal energy systems. Energy is stored in the ground which allows both comfort heating and cooling to be extracted. Active systems are therefore relevant for larger properties and industrial buildings. Since 1978 more than 600 000 wells (water wells, GSHP boreholes etc) have been registered in the Well Database, with around 20 000 new registrations per year. Of these wells an estimated 320 000 wells are registered as GSHP boreholes. The vast majority of these boreholes are single boreholes for single-family houses. The number of properties with registered vertical borehole GSHP installations amounts to approximately 243 000. Of these sites between 300-350 are large GSHP systems with at least 20 boreholes. While the increase in number of new registrations for smaller homes and households has slowed down after the rapid development in the 80's and 90's, the larger installations for commercial and industrial buildings have increased in numbers over the last ten years. This poster uses data from the SGU Well Database to quantify and analyze the trends in vertical GSHP systems reported between 1978-2015 in Sweden, with special focus on large systems. From the new aggregated data, conclusions can be drawn about the development of larger vertical GSHP system installments over the years and the geographical distribution in Sweden.

The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce

PubMed Central

2013-01-01

Background The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the genomic architecture of adaptive traits in black spruce, which is a widely distributed conifer of the North American boreal forest. As an alternative to the usual candidate gene approach, a candidate SNP approach was developed for association testing. Results A genetic map containing 231 gene loci was used to identify QTL that were related to budset timing and to tree height assessed over multiple years and sites. Twenty-two unique genomic regions were identified, including 20 that were related to budset timing and 6 that were related to tree height. From results of outlier detection and bulk segregant analysis for adaptive traits using DNA pool sequencing of 434 genes, 52 candidate SNPs were identified and subsequently tested in genetic association studies for budset timing and tree height assessed over multiple years and sites. A total of 34 (65%) SNPs were significantly associated with budset timing, or tree height, or both. Although the percentages of explained variance (PVE) by individual SNPs were small, several significant SNPs were shared between sites and among years. Conclusions The sharing of genomic regions and significant SNPs between budset timing and tree height indicates pleiotropic effects. Significant QTLs and SNPs differed quite greatly among years, suggesting that different sets of genes for the same characters are involved at different stages in the tree’s life history. The functional diversity of genes carrying significant SNPs and low observed PVE further indicated that a large number of polymorphisms are involved in adaptive genetic variation. Accordingly, for undomesticated species such as black spruce with natural populations of large effective size and low linkage disequilibrium, efficient marker systems that are predictive of adaptation should require the survey of large numbers of SNPs. Candidate SNP approaches like the one developed in the present study could contribute to reducing these numbers. PMID:23724860

Meta-analyses are no substitute for registered replications: a skeptical perspective on religious priming

PubMed Central

van Elk, Michiel; Matzke, Dora; Gronau, Quentin F.; Guan, Maime; Vandekerckhove, Joachim; Wagenmakers, Eric-Jan

2015-01-01

According to a recent meta-analysis, religious priming has a positive effect on prosocial behavior (Shariff et al., 2015). We first argue that this meta-analysis suffers from a number of methodological shortcomings that limit the conclusions that can be drawn about the potential benefits of religious priming. Next we present a re-analysis of the religious priming data using two different meta-analytic techniques. A Precision-Effect Testing–Precision-Effect-Estimate with Standard Error (PET-PEESE) meta-analysis suggests that the effect of religious priming is driven solely by publication bias. In contrast, an analysis using Bayesian bias correction suggests the presence of a religious priming effect, even after controlling for publication bias. These contradictory statistical results demonstrate that meta-analytic techniques alone may not be sufficiently robust to firmly establish the presence or absence of an effect. We argue that a conclusive resolution of the debate about the effect of religious priming on prosocial behavior – and about theoretically disputed effects more generally – requires a large-scale, preregistered replication project, which we consider to be the sole remedy for the adverse effects of experimenter bias and publication bias. PMID:26441741

Is the evidence supporting dental procedures strong? A survey of Cochrane systematic reviews in oral health.

PubMed

Faggion, Clovis Mariano

2012-09-01

Every day a large number and variety of dental procedures are performed in clinical dental practice. There is, however, no information on the overall quality of evidence supporting these procedures. The objective of this study was to assess whether several common dental procedures are based on sound evidence. All Cochrane systematic reviews (CSR) published in dentistry were surveyed. The authors' conclusions about the quality of evidence supporting a specific clinical treatment were used as the measure of outcome. The evidence was considered adequate if the authors did not clearly state the evidence was weak in the conclusions while also suggesting some evidence of the effectiveness of the therapy. Of 120 CSRs assessed, in only 26 (22.0% of the reviews) was the quality of evidence regarded as adequate for supporting clinical decisions, although some methodological limitations were identified in the full text of these reviews. Moreover, the authors of most reviews reported weak or unavailable evidence. On the basis of CSRs, the overall quality of evidence can be regarded as low or nonexistent for most of the dental procedures assessed. The information reported may guide future research. Copyright © 2012 Elsevier Inc. All rights reserved.

Planetary research at Lowell Observatory

NASA Technical Reports Server (NTRS)

Baum, William A.

1988-01-01

Scientific goals include a better determination of the basic physical characteristics of cometary nuclei, a more complete understanding of the complex processes in the comae, a survey of abundances and gas/dust ratios in a large number of comets, and measurement of primordial (12)C/(13)C and (14)N/(15)N ratios. The program also includes the observation of Pluto-Charon mutual eclipses to derive dimensions. Reduction and analysis of extensive narrowband photometry of Comet Halley from Cerro Tololo Inter-American Observatory, Perth Observatory, Lowell Observatory, and Mauna Kea Observatory were completed. It was shown that the 7.4-day periodicity in the activity of Comet Halley was present from late February through at least early June 1986, but there is no conclusive evidence of periodic variability in the preperihelion data. Greatly improved NH scalelengths and lifetimes were derived from the Halley data which lead to the conclusion that the abundance of NH in comets is much higher than previously believed. Simultaneous optical and thermal infrared observations were obtained of Comet P/Temple 2 using the MKO 2.2 m telescope and the NASA IRTF. Preliminary analysis of these observations shows that the comet's nucleus is highly elongated, very dark, and quite red.

Detection of dust impacts by the Voyager planetary radio astronomy experiment

NASA Technical Reports Server (NTRS)

Evans, David R.

1993-01-01

The Planetary Radio Astronomy (PRA) instrument detected large numbers of dust particles during the Voyager 2 encounter with Neptune. The signatures of these impacts are analyzed in some detail. The major conclusions are described. PRA detects impacts from all over the spacecraft body, not just the PRA antennas. The signatures of individual impacts last substantially longer than was expected from complementary Plasma Wave Subsystem (PWS) data acquired by another Voyager experiment. The signatures of individual impacts demonstrate very rapid fluctuations in signal strength, so fast that the data are limited by the speed of response of the instrument. The PRA detects events at a rate consistently lower than does the Plasma Wave subsystem. Even so, the impact rate is so great near the inbound crossing of the ring plane that no reliable estimate of impact rate can be made for this period. The data are consistent with the presence of electrons accelerated by ions within an expanding plasma cloud from the point of impact. An ancillary conclusion is that the anomalous appearance of data acquired at 900 kHz appears to be due to an error in processing the PRA data prior to their delivery rather than due to overload of the PRA instrument.

Myenteric plexitis: A frequent feature in patients undergoing surgery for colonic diverticular disease

PubMed Central

Villanacci, Vincenzo; Sidoni, Angelo; Nascimbeni, Riccardo; Dore, Maria P; Binda, Gian A; Bandelloni, Roberto; Salemme, Marianna; Del Sordo, Rachele; Cadei, Moris; Manca, Alessandra; Bernardini, Nunzia; Maurer, Christoph A; Cathomas, Gieri

2015-01-01

Background Diverticular disease of the colon is frequent in clinical practice, and a large number of patients each year undergo surgical procedures worldwide for their symptoms. Thus, there is a need for better knowledge of the basic pathophysiologic mechanisms of this disease entity. Objectives Because patients with colonic diverticular disease have been shown to display abnormalities of the enteric nervous system, we assessed the frequency of myenteric plexitis (i.e. the infiltration of myenteric ganglions by inflammatory cells) in patients undergoing surgery for this condition. Methods We analyzed archival resection samples from the proximal resection margins of 165 patients undergoing left hemicolectomy (60 emergency and 105 elective surgeries) for colonic diverticulitis, by histology and immunochemistry. Results Overall, plexitis was present in almost 40% of patients. It was subdivided into an eosinophilic (48%) and a lymphocytic (52%) subtype. Plexitis was more frequent in younger patients; and it was more frequent in those undergoing emergency surgery (50%), compared to elective (28%) surgery (p = 0.007). All the severe cases of plexitis displayed the lymphocytic subtype. Conclusions In conclusion, myenteric plexitis is frequent in patients with colonic diverticular disease needing surgery, and it might be implicated in the pathogenesis of the disease. PMID:26668745

[Impact of chemical and physical environmental factors on the course and outcome of pregnancy].

PubMed

Slama, R; Cordier, S

2013-09-01

We review the epidemiological literature on the possible impact of chemical and physical factors on pregnancy outcome. Effects of in-utero exposures on child health are not considered here. The highest levels of evidence concern the effects of passive smoking (on fetal growth), of lead (pregnancy-induced hypertension, fetal growth), of some Polychlorinated Biphenyls (PCB; on fetal growth) and, to a lesser extent, of atmospheric pollutants (on fetal growth and preterm delivery). For the other compounds, in particular non-persistent chemicals, the literature, which is generally based on poor exposure assessment, is less informative. In conclusion, the last decades have witnessed the development of mother-child cohorts in which exposure biomarkers have been assayed, allowing a large number of publications. For some persistent compounds, for which efficient exposure assessment approaches have been used, the literature indicates a likely impact on pregnancy outcomes. With the exception of air pollutants, the literature on non-persistent compounds is little conclusive; the assay of exposure biomarkers in repeated biological samples collected at relevant time points could help further increase knowledge regarding any health impact. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Primary total hip arthroplasty in Catalonia: What is the clinical evidence that supports our prosthesis?

PubMed

Chaverri-Fierro, D; Lobo-Escolar, L; Espallargues, M; Martínez-Cruz, O; Domingo, L; Pons-Cabrafiga, M

The implementation of National Prostheses Registries allows us to obtain a large amount of data and make conclusions in order to improve the use of them. Sweden was the first country to implement a National Prostheses Registry in 1979. Catalonia has been doing this since 2005. The aim of our study is to analyse the evidence that supports primary total hip replacement in Catalonia in the last 9 years, based on the Arthroplasty Registry of Catalonia (RACat). A review of the literature was carried out of the prosthesis (acetabular cups/stems) reported in the RACat between the period 2005 to 2013 in the following databases: ODEP (Orthopaedic Data Evaluation Panel), TRIP database, PubMed, and Google Scholar. Those prostheses implanted in less than 10 units (182 acetabular components corresponding to 49 models/228 stems corresponding to 63 models) were excluded. A total of 18,634 (99%) implanted acetabular cups were analysed out of a total number of 18,816, corresponding to 74 different models. In 18 models (2527 acetabular cups) no clinical evidence to support its use was found. An analysis was performed on 19,367 (98.84%) out of a total number of 19,595 implanted stems, corresponding to 75 different models. In 16 models (1845 stems) no clinical evidence was found to support their use. Variable evidence was found in the 56 models of acetabular cups (16,107) and 59 models of stems (17,522), most of it corresponding to level iv clinical evidence. There was a significant number implanted prostheses evaluated (13.56% acetabular cups/9.5% stems) for which no clinical evidence was found. The elevated number of models is highlighted (49 types for acetabular cups/63 types for stems) with less than 10 units implanted, which corresponds to only 1% of the total implants. The use of arthroplasty registers is shown to be an extremely helpful tool that allows analyses and conclusions to be made for the follow-up and post-marketing surveillance period. Copyright © 2016 SECOT. Publicado por Elsevier España, S.L.U. All rights reserved.

Comparison of the incidence of acute decompensated heart failure before and after the major tsunami in Northeast Japan.

PubMed

Nakamura, Motoyuki; Tanaka, Fumitaka; Nakajima, Satoshi; Honma, Miho; Sakai, Toshiaki; Kawakami, Mikio; Endo, Hiroshi; Onodera, Masayuki; Niiyama, Masanobu; Komatsu, Takashi; Sakamaki, Kentaro; Onoda, Toshiyuki; Sakata, Kiyomi; Morino, Yoshihiro; Takahashi, Tomohiro; Makita, Shinji

2012-12-15

On March 11, 2011, a huge tsunami attacked the northeastern coast of Japan after a magnitude 9 earthquake. No reports have investigated the impact of tsunamis on the incidence of cardiovascular disease, especially heart failure (HF). We investigated the number and clinical characteristics of hospitalized patients with acute decompensated HF (ADHF) in the east coast of Iwate hit by the tsunami (tsunami area) for a 12-week period around the disaster. For comparison with previous years, numbers of ADHF were surveyed in the corresponding area in 2009 and 2010. In addition, to elucidate the impact of the tsunami, a similar study was performed in a remote area where the tsunami had minimal effect (control area). After the disaster, the number of patients with ADHF in the tsunami area was significantly increased compared to the predisaster period (relative risk 1.97, 95% confidence interval 1.50 to 2.59). The peak was found 3 to 4 weeks after the disaster. In contrast, in the control area, no significant change in ADHF events was observed (relative risk 1.29, 95% confidence interval 0.94 to 1.78). There was a significant correlation between changes in the number of ADHF admissions and percent tsunami flood area (r = 0.73, p <0.001) or the number of shelter evacuees (r = 0.83, p <0.001). In conclusion, these findings suggest that large and sudden changes in daily life and the trauma associated with a devastating tsunami have a significant impact on the incidence of ADHF. Copyright © 2012 Elsevier Inc. All rights reserved.

Medical Students Perceive Better Group Learning Processes when Large Classes Are Made to Seem Small

PubMed Central

Hommes, Juliette; Arah, Onyebuchi A.; de Grave, Willem; Schuwirth, Lambert W. T.; Scherpbier, Albert J. J. A.; Bos, Gerard M. J.

2014-01-01

Objective Medical schools struggle with large classes, which might interfere with the effectiveness of learning within small groups due to students being unfamiliar to fellow students. The aim of this study was to assess the effects of making a large class seem small on the students' collaborative learning processes. Design A randomised controlled intervention study was undertaken to make a large class seem small, without the need to reduce the number of students enrolling in the medical programme. The class was divided into subsets: two small subsets (n = 50) as the intervention groups; a control group (n = 102) was mixed with the remaining students (the non-randomised group n∼100) to create one large subset. Setting The undergraduate curriculum of the Maastricht Medical School, applying the Problem-Based Learning principles. In this learning context, students learn mainly in tutorial groups, composed randomly from a large class every 6–10 weeks. Intervention The formal group learning activities were organised within the subsets. Students from the intervention groups met frequently within the formal groups, in contrast to the students from the large subset who hardly enrolled with the same students in formal activities. Main Outcome Measures Three outcome measures assessed students' group learning processes over time: learning within formally organised small groups, learning with other students in the informal context and perceptions of the intervention. Results Formal group learning processes were perceived more positive in the intervention groups from the second study year on, with a mean increase of β = 0.48. Informal group learning activities occurred almost exclusively within the subsets as defined by the intervention from the first week involved in the medical curriculum (E-I indexes>−0.69). Interviews tapped mainly positive effects and negligible negative side effects of the intervention. Conclusion Better group learning processes can be achieved in large medical schools by making large classes seem small. PMID:24736272

A Search for Wave Induced Particle Precipitation from Lightning and Transmitter Sources

DTIC Science & Technology

1988-01-01

Observed and Modeled Event 50 Transmitter Whistler Sources 58 Summary 60 Chapter 4 The Wave Induced Particle Precipitation Campaign Instrumentation 63...101 ’ iii - k~rUM-rIF%9www Chapter 7 Summary and Conclusions Summary 102 Conclusions 105 Bibliography 107 iv LIST OF TABLES Number Page 1. Model ...Precipitation Bursts 56 2. X-Ray Detector Differential Channels 75 vB -- - -- - LIST OF FIGURES Number Page 1. Global Electrical circuit 2 2. Vertical

Number of Offspring and Cardiovascular Disease Risk in Men and Women

PubMed Central

Iliodromiti, Stamatina; Lawlor, Debbie A.; Catov, Janet M.; Nelson, Scott M.; Fraser, Abigail

2017-01-01

Background: Previous studies of the number of offspring and cardiovascular disease (CVD) report conflicting findings. We re-examined this association in both sexes to clarify the role of the cardiometabolic changes that women experience during pregnancy versus shared lifestyle characteristics. Methods: We studied 180,626 women and 133,259 men participating in the UK Biobank cohort who were free of CVD at baseline. CVD events were obtained from hospital and death registers. Analyses were conducted using Cox proportional hazards regression. Results: The incidence rates of overall CVD were six per 1000 person-years for women and nine per 1000 person-years for men. Number of children showed an association with risk of CVD among women; the adjusted HR (95% CI) was 1.2 (1.1, 1.3) for one, 1.1 (1.0, 1.2) for two, 1.2 (1.1, 1.3) for three, and 1.2 (1.1, 1.4) for four or more as compared to none. Number of children was also associated with CVD among men; the adjusted HR (95% CI) was 1.1 (1.0, 1.2) for one, 1.0 (0.96, 1.1) for two, 1.1 (1.0, 1.2) for three, and 1.1 (1.0, 1.3) for four or more as compared to none. There was no evidence of heterogeneity in the associations between sexes (Pinteraction = 0.80). Number of offspring also showed similar associations with ischemic heart disease and hypertensive disorders in both sexes. Conclusions: We observed similar associations between number of offspring and CVD in both sexes. The association among women might therefore be largely explained by unobserved behavioral and lifestyle characteristics. PMID:28696997

High throughput screening of human subtelomeric DNA for copy number changes using multiplex amplifiable probe hybridisation (MAPH)

PubMed Central

Hollox, E; Atia, T; Cross, G; Parkin, T; Armour, J

2002-01-01

Background: Subtelomeric regions of the human genome are gene rich, with a high level of sequence polymorphism. A number of clinical conditions, including learning disability, have been attributed to subtelomeric deletions or duplications, but screening for deletion in these regions using conventional cytogenetic methods and fluorescence in situ hybridisation (FISH) is laborious. Here we report that a new method, multiplex amplifiable probe hybridisation (MAPH), can be used to screen for copy number at subtelomeric regions. Methods: We have constructed a set of MAPH probes with each subtelomeric region represented at least once, so that one gel lane can assay copy number at all chromosome ends in one person. Each probe has been sequenced and, where possible, its position relative to the telomere determined by comparison with mapped clones. Results: The sensitivity of the probes has been characterised on a series of cytogenetically verified positive controls and 83 normal controls were used to assess the frequency of polymorphic copy number with no apparent phenotypic effect. We have also used MAPH to test a cohort of 37 people selected from males referred for fragile X syndrome testing and found six changes that were confirmed by dosage PCR. Conclusions: MAPH can be used to screen subtelomeric regions of chromosomes for deletions and duplications before confirmation by FISH or dosage PCR. The high throughput nature of this technique allows it to be used for large scale screening of subtelomeric copy number, before confirmation by FISH. In practice, the availability of a rapid and efficient screen may allow subtelomeric analysis to be applied to a wider selection of patients than is currently possible using FISH alone. PMID:12414816

Partition function of free conformal fields in 3-plet representation

NASA Astrophysics Data System (ADS)

Beccaria, Matteo; Tseytlin, Arkady A.

2017-05-01

Simplest examples of AdS/CFT duality correspond to free CFTs in d dimensions with fields in vector or adjoint representation of an internal symmetry group dual in the large N limit to a theory of massless or massless plus massive higher spins in AdS d+1. One may also study generalizations when conformal fields belong to higher dimensional representations, i.e. carry more than two internal symmetry indices. Here we consider the case of the 3-fundamental ("3-plet") representation. One motivation is a conjectured connection to multiple M5-brane theory: heuristic arguments suggest that it may be related to an (interacting) CFT of 6d (2,0) tensor multiplets in 3-plet representation of large N symmetry group that has an AdS7 dual. We compute the singlet partition function Z on S 1 × S d-1 for a free field in 3-plet representation of U( N) and analyse its novel large N behaviour. The large N limit of the low temperature expansion of Z which is convergent in the vector and adjoint cases here is only asymptotic, reflecting the much faster growth of the number of singlet operators with dimension, indicating a phase transition at very low temperature. Indeed, while the critical temperatures in the vector ( T c ˜ N γ , γ > 0) and adjoint ( T c ˜ 1) cases are finite, we find that in the 3-plet case T c ˜ (log N)-1, i.e. it approaches zero at large N. We discuss some details of large N solution for the eigenvalue distribution. Similar conclusions apply to higher p-plet representations of U( N) or O( N) and also to the free p-tensor theories invariant under [U( N)] p or [ O( N)] p with p ≥ 3.

Archival data on wild food plants used in Poland in 1948

PubMed Central

Łuczaj, Łukasz

2008-01-01

Background In 1948, Professor Józef Gajek initiated a detailed census of the wild edible plants used in Poland. The questionnaires were collected by correspondents of the Polish Folklore Society in 95 localities throughout Poland. A major part of these archival materials, including a substantial collection of herbarium specimens, had not undergone thorough analysis prior to this study, which presents a quantitative analysis of this archival set of data. Methods Herbarium specimens were identified and a database was created. Results Ninety-eight taxa identified to genus or species level, including 71 botanical species, identified using herbarium specimens, were found. On average only 11 edible plant species per locality were listed, the longest list included 39 species. No correlation between latitude and the number of edible species was found, whereas there was small but significant correlation with the longitude. Fruits were the most frequently collected part of plants. Most plants were primarily collected by women and children. Children both helped parents to collect wild fruits and also ate many species raw, which were not consumed by adults, but had often been eaten in the past. Eighteen of the taxa had not been reported in a recent comprehensive review of edible plants of Poland. Stratiotes aloides, used as a famine vegetable in the Łódź region, has never been reported as edible in any ethnobotanical literature. Conclusion The results undermine the conclusions of a recent comprehensive review of edible plants of Poland, which stated that many more wild edible plants have been collected in the Carpathians than in lowland Poland. However such results were shown to be caused by the substantially larger number of ethnographic studies undertaken in the Carpathians. In fact, large numbers of edible plant species were collected in the mid-20th century in a few regions, particularly along the eastern border, in the Carpathians and in communities originating from the expanded Soviet Union, which had been resettled to the north-west of Poland in 1945. PMID:18218132

Holographic turbulence in a large number of dimensions

NASA Astrophysics Data System (ADS)

Rozali, Moshe; Sabag, Evyatar; Yarom, Amos

2018-04-01

We consider relativistic hydrodynamics in the limit where the number of spatial dimensions is very large. We show that under certain restrictions, the resulting equations of motion simplify significantly. Holographic theories in a large number of dimensions satisfy the aforementioned restrictions and their dynamics are captured by hydrodynamics with a naturally truncated derivative expansion. Using analytic and numerical techniques we analyze two and three-dimensional turbulent flow of such fluids in various regimes and its relation to geometric data.

Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome

PubMed Central

2013-01-01

Background Copy number variation (CNV), an important source of diversity in genomic structure, is frequently found in clusters called CNV regions (CNVRs). CNVRs are strongly associated with segmental duplications (SDs), but the composition of these complex repetitive structures remains unclear. Results We conducted self-comparative-plot analysis of all mouse chromosomes using the high-speed and large-scale-homology search algorithm SHEAP. For eight chromosomes, we identified various types of large SD as tartan-checked patterns within the self-comparative plots. A complex arrangement of diagonal split lines in the self-comparative-plots indicated the presence of large homologous repetitive sequences. We focused on one SD on chromosome 13 (SD13M), and developed SHEPHERD, a stepwise ab initio method, to extract longer repetitive elements and to characterize repetitive structures in this region. Analysis using SHEPHERD showed the existence of 60 core elements, which were expected to be the basic units that form SDs within the repetitive structure of SD13M. The demonstration that sequences homologous to the core elements (>70% homology) covered approximately 90% of the SD13M region indicated that our method can characterize the repetitive structure of SD13M effectively. Core elements were composed largely of fragmented repeats of a previously identified type, such as long interspersed nuclear elements (LINEs), together with partial genic regions. Comparative genome hybridization array analysis showed that whereas 42 core elements were components of CNVR that varied among mouse strains, 8 did not vary among strains (constant type), and the status of the others could not be determined. The CNV-type core elements contained significantly larger proportions of long terminal repeat (LTR) types of retrotransposon than the constant-type core elements, which had no CNV. The higher divergence rates observed in the CNV-type core elements than in the constant type indicate that the CNV-type core elements have a longer evolutionary history than constant-type core elements in SD13M. Conclusions Our methodology for the identification of repetitive core sequences simplifies characterization of the structures of large SDs and detailed analysis of CNV. The results of detailed structural and quantitative analyses in this study might help to elucidate the biological role of one of the SDs on chromosome 13. PMID:23834397

Comparative Gene Expression Profiles Induced by PPARγ and PPARα/γ Agonists in Human Hepatocytes

PubMed Central

Rogue, Alexandra; Lambert, Carine; Jossé, Rozenn; Antherieu, Sebastien; Spire, Catherine; Claude, Nancy; Guillouzo, André

2011-01-01

Background Several glitazones (PPARγ agonists) and glitazars (dual PPARα/γ agonists) have been developed to treat hyperglycemia and, simultaneously, hyperglycemia and dyslipidemia, respectively. However, most have caused idiosyncratic hepatic or extrahepatic toxicities through mechanisms that remain largely unknown. Since the liver plays a key role in lipid metabolism, we analyzed changes in gene expression profiles induced by these two types of PPAR agonists in human hepatocytes. Methodology/Principal Findings Primary human hepatocytes and the well-differentiated human hepatoma HepaRG cells were exposed to different concentrations of two PPARγ (troglitazone and rosiglitazone) and two PPARα/γ (muraglitazar and tesaglitazar) agonists for 24 h and their transcriptomes were analyzed using human pangenomic Agilent microarrays. Principal Component Analysis, hierarchical clustering and Ingenuity Pathway Analysis® revealed large inter-individual variability in the response of the human hepatocyte populations to the different compounds. Many genes involved in lipid, carbohydrate, xenobiotic and cholesterol metabolism, as well as inflammation and immunity, were regulated by both PPARγ and PPARα/γ agonists in at least a number of human hepatocyte populations and/or HepaRG cells. Only a few genes were selectively deregulated by glitazars when compared to glitazones, indicating that PPARγ and PPARα/γ agonists share most of their target genes. Moreover, some target genes thought to be regulated only in mouse or to be expressed in Kupffer cells were also found to be responsive in human hepatocytes and HepaRG cells. Conclusions/Significance This first comprehensive analysis of gene regulation by PPARγ and PPARα/γ agonists favor the conclusion that glitazones and glitazars share most of their target genes and induce large differential changes in gene profiles in human hepatocytes depending on hepatocyte donor, the compound class and/or individual compound, thereby supporting the occurrence of idiosyncratic toxicity in some patients. PMID:21533120

A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes

PubMed Central

2009-01-01

Background Leopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East. Because of habitat fragmentation, high human population densities and the inherent adaptability of this species, they now occupy landscapes close to human settlements. As a result, they are the most common species involved in human wildlife conflict in India, necessitating their monitoring. However, their elusive nature makes such monitoring difficult. Recent advances in DNA methods along with non-invasive sampling techniques can be used to monitor populations and individuals across large landscapes including human dominated ones. In this paper, we describe a DNA-based method for leopard individual identification where we used fecal DNA samples to obtain genetic material. Further, we apply our methods to non-invasive samples collected in a human-dominated landscape to estimate the minimum number of leopards in this human-leopard conflict area in Western India. Results In this study, 25 of the 29 tested cross-specific microsatellite markers showed positive amplification in 37 wild-caught leopards. These loci revealed varied levels of polymorphism (four-12 alleles) and heterozygosity (0.05-0.79). Combining data on amplification success (including non-invasive samples) and locus specific polymorphisms, we showed that eight loci provide a sibling probability of identity of 0.0005, suggesting that this panel can be used to discriminate individuals in the wild. When this microsatellite panel was applied to fecal samples collected from a human-dominated landscape, we identified 7 individuals, with a sibling probability of identity of 0.001. Amplification success of field collected scats was up to 72%, and genotype error ranged from 0-7.4%. Conclusion Our results demonstrated that the selected panel of eight microsatellite loci can conclusively identify leopards from various kinds of biological samples. Our methods can be used to monitor leopards over small and large landscapes to assess population trends, as well as could be tested for population assignment in forensic applications. PMID:19961605

Star Formation in a Complete Spectroscopic Survey of Galaxies

NASA Astrophysics Data System (ADS)

Carter, B. J.; Fabricant, D. G.; Geller, M. J.; Kurtz, M. J.; McLean, B.

2001-10-01

The 15R-North galaxy redshift survey is a uniform spectroscopic survey (S/N~10) covering the range 3650-7400 Å for 3149 galaxies with median redshift 0.05. The sample is 90% complete to R=15.4. The median slit covering fraction is 24% of the galaxy, apparently sufficient to minimize the effects of aperture bias on the EW(Hα). Forty-nine percent of the galaxies in the survey have one or more emission lines detected at >=2 σ. In agreement with previous surveys, the fraction of absorption-line galaxies increases steeply with galaxy luminosity. We use Hβ, [O III], Hα, and [N II] to discriminate between star-forming galaxies and AGNs. At least 20% of the galaxies are star-forming, at least 17% have AGN-like emission, and 12% have unclassifiable emission. The unclassified 12% may include a ``hybrid'' population of galaxies with both star formation and AGN activity. The AGN fraction increases steeply with luminosity; the fraction of star-forming galaxies decreases. We use the EW(Hα+[N II]) to estimate the Scalo birthrate parameter, b, the ratio of the current star formation rate to the time averaged star formation rate. The median birthrate parameter is inversely correlated with luminosity in agreement with the conclusions based on smaller samples (Kennicutt, Tamblyn, & Congdon). Because our survey is large, we identify 33 vigorously star-forming galaxies with b>3. We confirm the conclusion of Jansen, Franx, & Fabricant that EW([O II]) must be used with caution as a measure of current star formation. Finally, we examine the way galaxies of different spectroscopic type trace the large-scale galaxy distribution. As expected the absorption-line fraction decreases and the star-forming emission-line fraction increases as the galaxy density decreases. The AGN fraction is insensitive to the surrounding galaxy density; the unclassified fraction declines slowly as the density increases. For the star-forming galaxies, the EW(Hα) increases very slowly as the galaxy number density decreases. Whether a galaxy forms stars or not is strongly correlated with the surrounding galaxy density averaged over a scale of a few Mpc. This dependence reflects, in large part, the morphology-density relation. However, for galaxies forming stars, the stellar birthrate parameter is remarkably insensitive to the galaxy density. This conclusion suggests that the triggering of star formation occurs on a smaller spatial scale.

Aluminum tolerance is associated with higher MATE1 gene copy-number in maize

USDA-ARS?s Scientific Manuscript database

Genome structure variation, including copy-number (CNV) and presence/absence variation (PAV), comprise a large extent of maize genetic diversity but their effect on phenotypes remains largely unexplored. Here we describe how copy-number variation in a major aluminum (Al) tolerance locus contributes ...

All Numbers Are Not Equal: An Electrophysiological Investigation of Small and Large Number Representations

ERIC Educational Resources Information Center

Hyde, Daniel C.; Spelke, Elizabeth S.

2009-01-01

Behavioral and brain imaging research indicates that human infants, humans adults, and many nonhuman animals represent large nonsymbolic numbers approximately, discriminating between sets with a ratio limit on accuracy. Some behavioral evidence, especially with human infants, suggests that these representations differ from representations of small…

Very Large Data Volumes Analysis of Collaborative Systems with Finite Number of States

ERIC Educational Resources Information Center

Ivan, Ion; Ciurea, Cristian; Pavel, Sorin

2010-01-01

The collaborative system with finite number of states is defined. A very large database is structured. Operations on large databases are identified. Repetitive procedures for collaborative systems operations are derived. The efficiency of such procedures is analyzed. (Contains 6 tables, 5 footnotes and 3 figures.)

A randomized placebo-controlled pilot study of pravastatin as an adjunctive therapy in schizophrenia patients: effect on inflammation, psychopathology, cognition and lipid metabolism

PubMed Central

Vincenzi, Brenda; Stock, Shannon; Borba, Christina P.C.; Cleary, Sarah M.; Oppenheim, Claire E.; Petruzzi, Liana J.; Fan, Xiaoduo; Copeland, Paul M.; Freudenreich, Oliver; Cather, Corinne; Henderson, David C.

2015-01-01

Objective The aim of this study was to investigate the role of pravastatin, as an adjunctive therapy, on inflammatory markers, lipid and glucose metabolism, psychopathology, and cognition in subjects with schizophrenia and schizoaffective disorder. Methods Schizophrenia or schizoaffective subjects (N=60) were randomized to receive either a 12-week supply of pravastatin 40 mg/day or placebo treatment. Anthropometric measures, lipids and glucose metabolism, inflammatory markers, psychopathology and cognitive performance were assessed at baseline, 6 weeks and 12 weeks. Results Pravastatin use was associated with a significant decrease in total cholesterol, low density lipoprotein (LDL) cholesterol and LDL particle number levels, but was not associated with any significant changes in cognition or psychopathology in the participants, except a significant decrease in the Positive and Negative Syndrome Scale (PANSS) positive symptoms score from baseline to week 6. However, this decrease failed to remain significant at 12 weeks. Interestingly, triglycerides, LDLCholesterol, Total cholesterol, LDL particle number, small LDL particle number, large very low density lipoprotein (VLDL) particle number and c-reactive protein (CRP) followed a similar pattern at 6 and 12 weeks as psychopathology. Conclusions These results suggest that a randomized trial with a larger sample size and a higher dosage of pravastatin, and would be helpful in further evaluating the anti-inflammatory properties of pravastatin, its association with improvements in cognitive symptoms, and its potential to reduce positive and negative symptoms associated with schizophrenia or schizoaffective disorders. PMID:25261882

Correlation between electric field pulse induced long-lived permeabilization and fusogenicity in cell membranes.

PubMed Central

Teissié, J; Ramos, C

1998-01-01

Electric field pulses have been reported to induce long-lived permeabilization and fusogenicity on cell membranes. The two membrane property alterations are under the control of the field strength, the pulse duration, and the number of pulses. Experiments on mammalian cells pulsed by square wave form pulses and then brought into contact randomly through centrifugation revealed an even stronger analogy between the two processes. Permeabilization was known to affect well-defined regions of the cell surface. Fusion can be obtained only when permeabilized surfaces on the two partners were brought into contact. Permeabilization was under the control of the pulse duration and of the number of pulses. A similar relationship was observed as far as fusion is concerned. But a critical level of local permeabilization must be present for fusion to take place when contacts are created. The same conclusions are obtained from previous experiments on ghosts subjected to exponentially decaying field pulses and then brought into contact by dielectrophoresis. These observations are in agreement with a model of membrane fusion in which the merging of local random defects occurs when the two membranes are brought into contact. The local defects are considered part of the structural membrane reorganization induced by the external field. Their density is dependent on the pulse duration and number of pulses. They support the long-lived permeabilization. Their number must be very large to support the occurrence of membrane fusion. PMID:9545050

Correlation between electric field pulse induced long-lived permeabilization and fusogenicity in cell membranes.

PubMed

Teissié, J; Ramos, C

1998-04-01

Electric field pulses have been reported to induce long-lived permeabilization and fusogenicity on cell membranes. The two membrane property alterations are under the control of the field strength, the pulse duration, and the number of pulses. Experiments on mammalian cells pulsed by square wave form pulses and then brought into contact randomly through centrifugation revealed an even stronger analogy between the two processes. Permeabilization was known to affect well-defined regions of the cell surface. Fusion can be obtained only when permeabilized surfaces on the two partners were brought into contact. Permeabilization was under the control of the pulse duration and of the number of pulses. A similar relationship was observed as far as fusion is concerned. But a critical level of local permeabilization must be present for fusion to take place when contacts are created. The same conclusions are obtained from previous experiments on ghosts subjected to exponentially decaying field pulses and then brought into contact by dielectrophoresis. These observations are in agreement with a model of membrane fusion in which the merging of local random defects occurs when the two membranes are brought into contact. The local defects are considered part of the structural membrane reorganization induced by the external field. Their density is dependent on the pulse duration and number of pulses. They support the long-lived permeabilization. Their number must be very large to support the occurrence of membrane fusion.

Associations between social and environmental factors and perinatal mortality in Jamaica.

PubMed

Golding, J; Greenwood, R; McCaw-Binns, A; Thomas, P

1994-04-01

Social and environmental factors in Jamaica were compared between 9919 mothers delivering in a 2-month period a singleton who survived the early neonatal period and 1847 mothers who were delivered of a singleton perinatal death in a contiguous 12-month period. Logistic regression showed independent positive statistically significant increased odds of having a perinatal death among mothers who lived in rural parishes, older mothers (aged 30 +), single parents, no other children in the household, large number of adults in the household, mother unemployed, the major wage earner of the household not being in a managerial, professional or skilled non-manual occupation, the household not having sole use of toilet facilities, smaller mothers and those classified as obese or undernourished. Variations were found for different categories of death. Intrapartum asphyxia deaths were not related to union (marital) status, occupation of major wage earner, number of adults nor to the use of the toilet. Antepartum fetal deaths did not vary significantly with occupation of major wage earner or maternal height, but did show a relationship with maternal education, mothers with lowest levels having reduced risk. Deaths from immaturity were significantly related only to occupation of major wage earner, number of children in the household, number of social amenities available (negative relationships) and maternal age (< 17 at highest risk). In conclusion there was little to indicate that social deprivation per se was related to perinatal death, although specific features of the environment showed strong relationships.

Spatial-Numerical Associations Enhance the Short-Term Memorization of Digit Locations

PubMed Central

Thevenot, Catherine; Dewi, Jasinta; Lavenex, Pamela B.; Bagnoud, Jeanne

2018-01-01

Little is known about how spatial-numerical associations (SNAs) affect the way individuals process their environment, especially in terms of learning and memory. In this study, we investigated the potential effects of SNAs in a digit memory task in order to determine whether spatially organized mental representations of numbers can influence the short-term encoding of digits positioned on an external display. To this aim, we designed a memory game in which participants had to match pairs of identical digits in a 9 × 2 matrix of cards. The nine cards of the first row had to be turned face up and then face down, one by one, to reveal a digit from 1 to 9. When a card was turned face up in the second row, the position of the matching digit in the first row had to be recalled. Our results showed that performance was better when small numbers were placed on the left side of the row and large numbers on the right side (i.e., congruent) as compared to the inverse (i.e., incongruent) or a random configuration. Our findings suggests that SNAs can enhance the memorization of digit positions and therefore that spatial mental representations of numbers can play an important role on the way humans process and encode the information around them. To our knowledge, this study is the first that reaches this conclusion in a context where digits did not have to be processed as numerical values. PMID:29867631

Multisession stereotactic radiosurgery for large benign brain tumors of >3cm- early clinical outcomes

PubMed Central

Memon, Muhammad Ali; Ahmed, Usman; Saleem, Muhammad Abid; Bhatti, Amer Iqtidar; Ahmed, Naveed; Hashim, Abdul Sattar M.

2012-01-01

Objective To evaluate the clinical outcome of linear accelerator based multisession stereotactic radiosurgery (SRS) for large benign brain tumors of >3cm. Methods Between June 2009 and May 2011, 35 patients having large benign brain tumors of >3cm (≥15 cm3) were treated by multisession stereotactic radiosurgery. This retrospective study was carried out at Neurospinal & Medical Institute Karachi. There were 17 (48.6 %) males and 18(51.4 %) females. Median age was 36 years (range: 13-65 years). Median target volume was 49.4 cm3 (range: 15-184 cm3). The median marginal dose was 25 Gy (range: 20–27.5Gy) prescribed to a median 75% isodose line (range: 65-100 %). Median number of 5 fractions were used ranging 3-5 fractions. Results All the patients tolerated treatment very well. 21 (58.3%) patients had remarkable clinical improvement of neurological symptoms, 14 (38.9%) patients had stable symptoms, and only one patient had transient worsening of symptoms. No permanent neurological damage or radiation injury was seen. Radiologically, 9 (25.7%) patients achieved reduction in size of the tumor, 26(74.3 %) patients were having stable disease, and overall control rate was found to be 100 %. Median follow-up time from the end of SRS was 6.4 months (range: 1-22.5months). Conclusion Linear accelerator based multisession stereotactic radiosurgery for large benign brain tumors of >3cm is effective and well tolerated. PMID:29296340

A scalable method for identifying frequent subtrees in sets of large phylogenetic trees

PubMed Central

2012-01-01

Background We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees. Results We develop a heuristic solution that aims to find MFASTs in sets of many, large phylogenetic trees. Our method works in multiple phases. In the first phase, it identifies small candidate subtrees from the set of input trees which serve as the seeds of larger subtrees. In the second phase, it combines these small seeds to build larger candidate MFASTs. In the final phase, it performs a post-processing step that ensures that we find a frequent agreement subtree that is not contained in a larger frequent agreement subtree. We demonstrate that this heuristic can easily handle data sets with 1000 taxa, greatly extending the estimation of MFASTs beyond current methods. Conclusions Although this heuristic does not guarantee to find all MFASTs or the largest MFAST, it found the MFAST in all of our synthetic datasets where we could verify the correctness of the result. It also performed well on large empirical data sets. Its performance is robust to the number and size of the input trees. Overall, this method provides a simple and fast way to identify strongly supported subtrees within large phylogenetic hypotheses. PMID:23033843

From the Law of Large Numbers to Large Deviation Theory in Statistical Physics: An Introduction

NASA Astrophysics Data System (ADS)

Cecconi, Fabio; Cencini, Massimo; Puglisi, Andrea; Vergni, Davide; Vulpiani, Angelo

This contribution aims at introducing the topics of this book. We start with a brief historical excursion on the developments from the law of large numbers to the central limit theorem and large deviations theory. The same topics are then presented using the language of probability theory. Finally, some applications of large deviations theory in physics are briefly discussed through examples taken from statistical mechanics, dynamical and disordered systems.

A Double-Moment Multiple-Phase Four-Class Bulk Ice Scheme. Part II: Simulations of Convective Storms in Different Large-Scale Environments and Comparisons with other Bulk Parameterizations.

NASA Astrophysics Data System (ADS)

Schoenberg Ferrier, Brad; Tao, Wei-Kuo; Simpson, Joanne

1995-04-01

Part I of this study described a detailed four-class bulk ice scheme (4ICE) developed to simulate the hydro-meteor profiles of convective and stratiform precipitation associated with mesoscale convective systems. In Part II, the 4ICE scheme is incorporated into the Goddard Cumulus Ensemble (GCE) model and applied without any `tuning' to two squall lines occurring in widely different environments, namely, one over the `Pica) ocean in the Global Atmospheric Research Program's (GARP) Atlantic Tropical Experiment (GATE) and the other over a midlatitude continent in the Cooperative Huntsville Meteorological Experiment (COHMEX). Comparisons were made both with earlier three-class ice formulations and with observations. In both cases, the 4ICE scheme interacted with the dynamics so as to resemble the observations much more closely than did the model runs with either of the three-class ice parameterizations. The following features were well simulated in the COHMEX case: a lack of stratiform rain at the surface ahead of the storm, reflectivity maxima near 60 dBZ in the vicinity of the melting level, and intense radar echoes up to near the tropopause. These features were in strong contrast with the GATE simulation, which showed extensive trailing stratiform precipitation containing a horizontally oriented radar bright band. Peak reflectivities were below the melting level, rarely exceeding 50 dBz, with a steady decrease in reflectivity with height above. With the other bulk formulations, the large stratiform rain areas were not reproduced in the GATE conditions.The microphysical structure of the model clouds in both environments were more realistic than that of earlier modeling efforts. Number concentrations of ice of O(100 L1) occurred above 6 km in the GATE model clouds as a result of ice enhancement and rime splintering in the 4ICE runs. These processes were more effective in the GATE simulation, because near the freezing level the weaker updrafts were comparable in magnitude to the fall speeds of newly frozen drops. Many of the ice crystals initiated at relatively warm temperatures (above 15°C) grew rapidly by deposition into sizes large enough to be converted to snow. In contrast, in the more intense COHMEX updrafts, very large numbers of small ice crystals were initiated at colder temperatures (below 15°C) by nucleation and stochastic freezing of droplets, such that relatively few ice crystals grew by deposition to sizes large enough to be converted to snow. In addition, the large number of frozen drops of O(5 L1) in the 4ICE run am consistent with airborne microphysical data in intense COHMEX updrafts.Numerous sensitivity experiments were made with the four-class and three-class ice schemes, varying fall speed relationships, particle characteristics, and ice collection efficiencies. These tests provide strong support to the conclusion that the 4ICE scheme gives improved resemblance to observations despite present uncertainties in a number of important microphysical parameters.

Mitochondrial Based Treatments that Prevent Post Traumatic Osteoarthritis in a Translational Large Animal Intraarticular Fracture Survival Model

DTIC Science & Technology

2015-09-01

AWARD NUMBER: W81XWH-11-1-0583 TITLE: “Mitochondrial-Based Treatments that Prevent Post-Traumatic Osteoarthritis in a Translational Large... Osteoarthritis in a Translational Large Animal Intraarticular Fracture Survival Model” 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-11-1-0583 5c. PROGRAM...upon completion of the 6- and 12- month time points. 15. SUBJECT TERMS Post-traumatic osteoarthritis , oxidative stress, mitochondria, animal model 16

Effect of External Post-tensioning in Retrofitting of RC Beams

NASA Astrophysics Data System (ADS)

Manisekar, R.

2018-05-01

There are large number of existing concrete bridges in distressed condition in India and other countries, and they need retrofitting solutions. External post-tensioning is a prime technique for bridge retrofitting. It is being applied for retrofitting of bridges in India and other countries. Although the technique is becoming popular in retrofitting, various issues regarding performance of post-retrofitting behaviour need to be studied in detail. RC beam specimens of rectangular section were distressed by means of cracks to a certain limit, and were retrofitted by external post-tensioning. Retrofitted specimens were tested to fail to study the post-retrofitting behaviour. Retrofitting has increased the ultimate load carrying capacity by 81% with reference to the control beam, and recovered the deflection. This paper intends to report the results of the experimental investigations, and conclusions.

Are C1 chondrites chemically fractionated - A trace element study

NASA Technical Reports Server (NTRS)

Ebihara, M.; Wolf, R.; Anders, E.

1982-01-01

Six C1 chondrite samples and a C2 xenolith from the Plainview H5 chondrite were analyzed by radiochemical neutron activation for a large variety of elements, including rare earths. The sample processing is described, including the irradiation, chemical procedure, rare earths separation, counting techniques, radiochemical purity check, and chemical yields. The results of consistency checks on a number of elements are discussed. Abundances for siderophiles, volatiles, and rare earths are presented and discussed. Tests are presented for fractionation of rare earths and other refractories, compositional uniformity of C1's, and interelement correlations. There is no conclusive evidence for nebular fractionation affecting C1's. Three fractionation-prone rare earths have essentially the same relative abundances in C1's and all other chondrite classes, and hence are apparently not fractionated in C1's.

Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways.

PubMed

Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P; Wheeler, Eleanor; Montasser, May E; Luan, Jian'an; Mägi, Reedik; Strawbridge, Rona J; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J; Yengo, Loïc; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C D; Jukema, J Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J; Evans, David M; Pourcain, Beate St; Wu, Ying; Andrews, Jeanette S; Hui, Jennie; Bielak, Lawrence F; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O'Connell, Jeffrey R; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tõnu; Mihailov, Evelin; Fraser, Ross M; Fall, Tove; Voight, Benjamin F; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M; Morris, Andrew P; Rayner, Nigel W; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S; Willems, Sara M; Chines, Peter S; Jackson, Anne U; Kang, Hyun Min; Stringham, Heather M; Song, Kijoung; Tanaka, Toshiko; Peden, John F; Goel, Anuj; Hicks, Andrew A; An, Ping; Müller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J; Bruinenberg, Marcel; Pankow, James S; North, Kari E; Forouhi, Nita G; Loos, Ruth J F; Edkins, Sarah; Varga, Tibor V; Hallmans, Göran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J L; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L; Rivadeneira, Fernando; Uitterlinden, Andre G; Palmer, Colin N A; Doney, Alex S F; Willemsen, Gonneke; Smit, Johannes H; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L; Fowkes, Gerard R; Kovacs, Peter; Lindström, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H; Basart, Hanneke V; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E; Boehm, Bernhard O; Peters, Annette; Pramstaller, Peter P; Province, Michael A; Borecki, Ingrid B; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M; Bergman, Richard N; Collins, Francis S; Tuomilehto, Jaakko; Watanabe, Richard M; de Geus, Eco J C; Penninx, Brenda W; Hofman, Albert; Oostra, Ben A; Psaty, Bruce M; Vollenweider, Peter; Wilson, James F; Wright, Alan F; Hovingh, G Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K E; Kyvik, Kirsten O; Kaprio, Jaakko; Price, Jackie F; Dedoussis, George V; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R; van Duijn, Cornelia M; Morris, Andrew D; Toenjes, Anke; Peyser, Patricia A; Beilby, John P; Körner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R; Schwarz, Peter E H; Lakka, Timo A; Rauramaa, Rainer; Adair, Linda S; Smith, George Davey; Spector, Tim D; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Boomsma, Dorret I; Stefansson, Kari; van der Harst, Pim; Dupuis, Josée; Pedersen, Nancy L; Sattar, Naveed; Harris, Tamara B; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J; Bouatia-Naji, Nabila; McCarthy, Mark I; Franks, Paul W; Meigs, James B; Teslovich, Tanya M; Florez, Jose C; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Inês

2012-09-01

Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin concentration showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional analysis of these newly discovered loci will further improve our understanding of glycemic control.

Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways

PubMed Central

Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P; Wheeler, Eleanor; Montasser, May E; Luan, Jian’an; Mägi, Reedik; Strawbridge, Rona J; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J; Yengo, Loïc; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C D; Jukema, J Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J; Evans, David M; Pourcain, Beate St; Wu, Ying; Andrews, Jeanette S; Hui, Jennie; Bielak, Lawrence F; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O’Connell, Jeffrey R; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tönu; Mihailov, Evelin; Fraser, Ross M; Fall, Tove; Voight, Benjamin F; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M; Morris, Andrew P; Rayner, Nigel W; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S; Willems, Sara M; Chines, Peter S; Jackson, Anne U; Kang, Hyun Min; Stringham, Heather M; Song, Kijoung; Tanaka, Toshiko; Peden, John F; Goel, Anuj; Hicks, Andrew A; An, Ping; Müller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J; Bruinenberg, Marcel; Pankow, James S; North, Kari E; Forouhi, Nita G; Loos, Ruth J F; Edkins, Sarah; Varga, Tibor V; Hallmans, Göran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J L; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L; Rivadeneira, Fernando; Uitterlinden, Andre G; Palmer, Colin N A; Doney, Alex S F; Willemsen, Gonneke; Smit, Johannes H; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L; Fowkes, Gerard R; Kovacs, Peter; Lindström, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H; Basart, Hanneke V; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E; Boehm, Bernhard O; Peters, Annette; Pramstaller, Peter P; Province, Michael A; Borecki, Ingrid B; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M; Bergman, Richard N; Collins, Francis S; Tuomilehto, Jaakko; Watanabe, Richard M; de Geus, Eco J C; Penninx, Brenda W; Hofman, Albert; Oostra, Ben A; Psaty, Bruce M; Vollenweider, Peter; Wilson, James F; Wright, Alan F; Hovingh, G Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K E; Kyvik, Kirsten O; Kaprio, Jaakko; Price, Jackie F; Dedoussis, George V; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R; van Duijn, Cornelia M; Morris, Andrew D; Toenjes, Anke; Peyser, Patricia A; Beilby, John P; Körner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R; Schwarz, Peter E H; Lakka, Timo A; Rauramaa, Rainer; Adair, Linda S; Smith, George Davey; Spector, Tim D; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Boomsma, Dorret I; Stefansson, Kari; van der Harst, Pim; Dupuis, Josée; Pedersen, Nancy L; Sattar, Naveed; Harris, Tamara B; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J; Bouatia-Naji, Nabila; McCarthy, Mark I; Franks, Paul W; Meigs, James B; Teslovich, Tanya M; Florez, Jose C; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Inês

2012-01-01

Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have raised the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional follow-up of these newly discovered loci will further improve our understanding of glycemic control. PMID:22885924

Risk of Social Media for Teens in an Urban Setting.

PubMed

Knowles, Megan; Lee, Sara Hirschfeld; O'Riordan, MaryAnn; Lazebnik, Rina

2014-01-01

Purpose. To describe the self-reported risky behaviors associated with adolescent social media use. Methods. Adolescents ages 13 to 21 years were recruited from a large, urban academic center to complete a written survey regarding social media use. Results are presented as frequencies and percentage; nominal variables were compared using χ(2) analysis. Results. Almost all participants (93%) reported belonging to a social media site. The majority of adolescents (72%) access the Internet with a phone. Nearly half (49%) of participants accept friend requests from strangers, 42% send friend requests to strangers, and 55% of participants report meeting people from social media sites in person. Conclusion. Adolescents self-report engaging in a number of risky behaviors when they use social media. Teenagers' use of social media is an additional behavior that requires attention and monitoring.

Search for the lepton flavor violating decay Z → e μ in p p collisions at s = 8 TeV with the ATLAS detector

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

Aad, G.; Abbott, B.; Abdallah, J.

2014-10-23

We use the ATLAS detector at the Large Hadron Collider to search for the lepton flavor violating process Z→eμ in pp collisions using 20.3 fb -1 of data collected at √s=8 TeV. An enhancement in the eμ invariant mass spectrum is searched for at the Z-boson mass. The number of Z bosons produced in the data sample is estimated using events of similar topology, Z→ee and μμ, significantly reducing the systematic uncertainty in the measurement. In conclusion, there is no evidence of an enhancement at the Z-boson mass, resulting in an upper limit on the branching fraction, B(Z→eμ)<7.5×10 -7 atmore » the 95% confidence level.« less

Mapping the Medical Literature for High Quality Studies and Reviews for Age-specific Clinical Specialties

PubMed Central

Stevens, Adrienne L.; Wilczynski, Nancy L.; McKibbon, K. Ann; Haynes, R. Brian

2001-01-01

Objective: To identify a journal subset that publishes reports of high quality studies and reviews relating to age-specific clinical specialties, such as pediatrics and geriatrics. Design: Handsearch of 172 journals using explicit criteria to determine methodologic quality for generating evidence for clinical practice. Main outcome measure: Frequency of high quality articles and their top yielding journals. Results: Between 17% and 33% of articles published in age-specific specialties are of high quality for clinical use. Top yielding journals for the specialties ranged from 16 to 130. Conclusion: Handsearch of the clinical literature for the year 2000 reveals that high quality articles for some age-specific specialties are concentrated in a small subset of journals (eg, obstetrics), whereas articles for other specialties are widely scattered among a large number of journals (eg, adult medicine).

Comparison of Low Energy CVV Auger transitions in Cu and Au (100) using Measured and estimated values

NASA Astrophysics Data System (ADS)

Shastry, K.; Mukherjee, S. F.; Satyal, S.; Joglekar, P. V.; Weiss, A. H.

2011-10-01

Low energy Auger lineshapes are difficult to measure because they sit on a large background due to secondary electrons arising from loss processes unrelated to the Auger mechanism. In this poster we discuss the implications of our PAES measurements of the ratio of the integrated Auger Peak and integrated low energy tail (LET) intensities for comparisons between theoretical and measured values of the Auger intensities. The experiments were carried out at university of Texas at Arlington on Cu (100) and Au (100) crystals. Our conclusions regarding the importance of the LET in determining the ratio of electrons in the Auger peak to the number of initial core holes are discussed in light of the electron stimulated Auger results obtained by Seah et.al using monte carlo simulations on various elements.

Investigation of the vibration and EMC characteristics of miniature Stirling electric coolers for space applications

NASA Astrophysics Data System (ADS)

Kondratjev, V.; Gostilo, V.; Owens, anb A.

2017-08-01

We present the results of an investigation into the detrimental effects that electromechanical coolers can have on the spectral performance of compact, large volume HPGe spectrometers for space applications. Both mechanical vibration and electromagnetic pickup effects were considered, as well as a comparative assessment between three miniature Stirling cycle coolers—two Ricor model K508 coolers and one Thales model RM3 cooler. In spite of the limited number of coolers tested, the following conclusions can be made. There are significant differences in the vibration characteristics not only between the various types of cooler but also between coolers of the same type. It was also found that compared to the noise induced by mechanical vibrations, electromagnetic interference emanating from the embedded controllers does not significantly impact the energy resolution of detectors.

Where Gibrat meets Zipf: Scale and scope of French firms

NASA Astrophysics Data System (ADS)

Bee, Marco; Riccaboni, Massimo; Schiavo, Stefano

2017-09-01

The proper characterization of the size distribution and growth of firms represents an important issue in economics and business. We use the Maximum Entropy approach to assess the plausibility of the assumption that firm size follows Lognormal or Pareto distributions, which underlies most recent works on the subject. A comprehensive dataset covering the universe of French firms allows us to draw two major conclusions. First, the Pareto hypothesis for the whole distribution should be rejected. Second, by discriminating across firms based on the number of products sold and markets served, we find that, within the class of multi-product companies active in multiple markets, the distribution converges to a Zipf's law. Conversely, Lognormal distribution is a good benchmark for small single-product firms. The size distribution of firms largely depends on firms' diversification patterns.

New insights into adipokines as potential biomarkers for type-2 diabetes mellitus.

PubMed

Olivera Santa-Catalina, Marta; Redondo, Pedro C; Cantonero, C; Granados, Maria P; Sanchez-Collado, Jose; Albarran, Letizia; Lopez, Jose Javier

2017-12-05

A large number of studies have been focused on investigating serum biomarkers associated with risk or diagnosis of type-2 diabetes mellitus. In the last decade, promising studies have shown that circulating levels of adipokines could be used as a relevant biomarker for diabetes mellitus progression as well as therapeutic future targets. Here we discuss the possible use of recent described adipokines, including apelin, omentin-1, resistin, FGF-21, neuregulin-4 and visfatin, as early biomarkers for diabetes. In addition, we also include recent findings of other well know adipokines such as leptin and adiponectin. In conclusion, further studies are needed to clarify the pathophysiological significance and clinical value of these biological factors as potential biomarkers in type-2 diabetes and related dysfunctions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A Systematic Review of the Evidence for Impaired Cognitive Theory of Mind in Maltreated Children

PubMed Central

Benarous, Xavier; Guilé, Jean-Marc; Consoli, Angèle; Cohen, David

2015-01-01

Compared to the large number of studies exploring difficulties in emotion recognition in maltreated children, few (N = 12) have explored the cognitive aspect of theory of mind (ToM), i.e., the ability to understand others’ thoughts and intentions. A systematic review of these studies shows inconsistent results regarding cognitive ToM tasks. Youths with a history of maltreatment are more likely to fail at false-belief tasks (N = 2). However, results are less conclusive regarding other tasks (perspective-taking tasks, N = 4; and hostile attribution tasks, N = 7). Additionally, only one study controlled for potential psychopathology. Measures of psychopathology and other cognitive abilities, in addition to ToM, are required to establish a specific association between maltreatment and the cognitive dimension of ToM. PMID:26283975

A Systematic Review of the Evidence for Impaired Cognitive Theory of Mind in Maltreated Children.

PubMed

Benarous, Xavier; Guilé, Jean-Marc; Consoli, Angèle; Cohen, David

2015-01-01

Compared to the large number of studies exploring difficulties in emotion recognition in maltreated children, few (N = 12) have explored the cognitive aspect of theory of mind (ToM), i.e., the ability to understand others' thoughts and intentions. A systematic review of these studies shows inconsistent results regarding cognitive ToM tasks. Youths with a history of maltreatment are more likely to fail at false-belief tasks (N = 2). However, results are less conclusive regarding other tasks (perspective-taking tasks, N = 4; and hostile attribution tasks, N = 7). Additionally, only one study controlled for potential psychopathology. Measures of psychopathology and other cognitive abilities, in addition to ToM, are required to establish a specific association between maltreatment and the cognitive dimension of ToM.

[Use of adsorption methods for plasma component apheresis].

PubMed

Bang, B; Heegaard, N H

1991-11-25

Plasma-apheresis is a nonspecific and wasteful intervention requiring the use of potentially infectious and expensive replacement fluids. Selective removal of the unwanted plasma component circumvents most of the problems. For selective binding and removal of plasma components adsorption methods based on the principles of affinity chromatography have been useful. The ideal adsorption column still does not exist, but the number of clinical applications is increasing. The results vary, but the treatment has been used with success in hypercholesterolemia, and in patients with hemophilia with antifactor antibodies and patients with antibodies directed towards HLA-antigens awaiting renal transplantation. In conclusion selective plasma component-apheresis is an improvement in some diseases as compared to conventional plasma-apheresis. The technique is still being improved but large clinical trials examining the effects of plasma-component-apheresis have not yet been published.

Seasonality of Kawasaki Disease: A Global Perspective

PubMed Central

Burns, Jane C.; Herzog, Lauren; Fabri, Olivia; Tremoulet, Adriana H.; Rodó, Xavier; Uehara, Ritei; Burgner, David; Bainto, Emelia; Pierce, David; Tyree, Mary; Cayan, Daniel

2013-01-01

Background Understanding global seasonal patterns of Kawasaki disease (KD) may provide insight into the etiology of this vasculitis that is now the most common cause of acquired heart disease in children in developed countries worldwide. Methods Data from 1970-2012 from 25 countries distributed over the globe were analyzed for seasonality. The number of KD cases from each location was normalized to minimize the influence of greater numbers from certain locations. The presence of seasonal variation of KD at the individual locations was evaluated using three different tests: time series modeling, spectral analysis, and a Monte Carlo technique. Results A defined seasonal structure emerged demonstrating broad coherence in fluctuations in KD cases across the Northern Hemisphere extra-tropical latitudes. In the extra-tropical latitudes of the Northern Hemisphere, KD case numbers were highest in January through March and approximately 40% higher than in the months of lowest case numbers from August through October. Datasets were much sparser in the tropics and the Southern Hemisphere extra-tropics and statistical significance of the seasonality tests was weak, but suggested a maximum in May through June, with approximately 30% higher number of cases than in the least active months of February, March and October. The seasonal pattern in the Northern Hemisphere extra-tropics was consistent across the first and second halves of the sample period. Conclusion Using the first global KD time series, analysis of sites located in the Northern Hemisphere extra-tropics revealed statistically significant and consistent seasonal fluctuations in KD case numbers with high numbers in winter and low numbers in late summer and fall. Neither the tropics nor the Southern Hemisphere extra-tropics registered a statistically significant aggregate seasonal cycle. These data suggest a seasonal exposure to a KD agent that operates over large geographic regions and is concentrated during winter months in the Northern Hemisphere extra-tropics. PMID:24058585

Demographic and Indication-Specific Characteristics Have Limited Association With Social Network Engagement: Evidence From 24,954 Members of Four Health Care Support Groups

PubMed Central

2017-01-01

Background Digital health social networks (DHSNs) are widespread, and the consensus is that they contribute to wellness by offering social support and knowledge sharing. The success of a DHSN is based on the number of participants and their consistent creation of externalities through the generation of new content. To promote network growth, it would be helpful to identify characteristics of superusers or actors who create value by generating positive network externalities. Objective The aim of the study was to investigate the feasibility of developing predictive models that identify potential superusers in real time. This study examined associations between posting behavior, 4 demographic variables, and 20 indication-specific variables. Methods Data were extracted from the custom structured query language (SQL) databases of 4 digital health behavior change interventions with DHSNs. Of these, 2 were designed to assist in the treatment of addictions (problem drinking and smoking cessation), and 2 for mental health (depressive disorder, panic disorder). To analyze posting behavior, 10 models were developed, and negative binomial regressions were conducted to examine associations between number of posts, and demographic and indication-specific variables. Results The DHSNs varied in number of days active (3658-5210), number of registrants (5049-52,396), number of actors (1085-8452), and number of posts (16,231-521,997). In the sample, all 10 models had low R2 values (.013-.086) with limited statistically significant demographic and indication-specific variables. Conclusions Very few variables were associated with social network engagement. Although some variables were statistically significant, they did not appear to be practically significant. Based on the large number of study participants, variation in DHSN theme, and extensive time-period, we did not find strong evidence that demographic characteristics or indication severity sufficiently explain the variability in number of posts per actor. Researchers should investigate alternative models that identify superusers or other individuals who create social network externalities. PMID:28213340

Topic modeling for cluster analysis of large biological and medical datasets

PubMed Central

2014-01-01

Background The big data moniker is nowhere better deserved than to describe the ever-increasing prodigiousness and complexity of biological and medical datasets. New methods are needed to generate and test hypotheses, foster biological interpretation, and build validated predictors. Although multivariate techniques such as cluster analysis may allow researchers to identify groups, or clusters, of related variables, the accuracies and effectiveness of traditional clustering methods diminish for large and hyper dimensional datasets. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. Its ability to reduce high dimensionality to a small number of latent variables makes it suitable as a means for clustering or overcoming clustering difficulties in large biological and medical datasets. Results In this study, three topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, are proposed and tested on the cluster analysis of three large datasets: Salmonella pulsed-field gel electrophoresis (PFGE) dataset, lung cancer dataset, and breast cancer dataset, which represent various types of large biological or medical datasets. All three various methods are shown to improve the efficacy/effectiveness of clustering results on the three datasets in comparison to traditional methods. A preferable cluster analysis method emerged for each of the three datasets on the basis of replicating known biological truths. Conclusion Topic modeling could be advantageously applied to the large datasets of biological or medical research. The three proposed topic model-derived clustering methods, highest probable topic assignment, feature selection and feature extraction, yield clustering improvements for the three different data types. Clusters more efficaciously represent truthful groupings and subgroupings in the data than traditional methods, suggesting that topic model-based methods could provide an analytic advancement in the analysis of large biological or medical datasets. PMID:25350106

Acute carbon tetrachloride feeding induces damage of large but not small cholangiocytes from BDL rat liver.

PubMed

LeSage, G D; Glaser, S S; Marucci, L; Benedetti, A; Phinizy, J L; Rodgers, R; Caligiuri, A; Papa, E; Tretjak, Z; Jezequel, A M; Holcomb, L A; Alpini, G

1999-05-01

Bile duct damage and/or loss is limited to a range of duct sizes in cholangiopathies. We tested the hypothesis that CCl4 damages only large ducts. CCl4 or mineral oil was given to bile duct-ligated (BDL) rats, and 1, 2, and 7 days later small and large cholangiocytes were purified and evaluated for apoptosis, proliferation, and secretion. In situ, we measured apoptosis by morphometric and TUNEL analysis and the number of small and large ducts by morphometry. Two days after CCl4 administration, we found an increased number of small ducts and reduced number of large ducts. In vitro apoptosis was observed only in large cholangiocytes, and this was accompanied by loss of proliferation and secretion in large cholangiocytes and loss of choleretic effect of secretin. Small cholangiocytes de novo express the secretin receptor gene and secretin-induced cAMP response. Consistent with damage of large ducts, we detected cytochrome P-4502E1 (which CCl4 converts to its radicals) only in large cholangiocytes. CCl4 induces selective apoptosis of large ducts associated with loss of large cholangiocyte proliferation and secretion.

Impact of GDP, Spending on R&D, Number of Universities and Scientific Journals on Research Publications among Asian Countries

PubMed Central

Meo, Sultan Ayoub; Al Masri, Abeer A.; Usmani, Adnan Mahmood; Memon, Almas Naeem; Zaidi, Syed Ziauddin

2013-01-01

Objectives This study aimed to compare the impact of Gross Domestic Product (GDP) per capita, spending on Research and Development (R&D), number of universities, and Indexed Scientific Journals on total number of research documents (papers), citations per document and Hirsch index (H-index) in various science and social science subjects among Asian countries. Materials and Methods In this study, 40 Asian countries were included. The information regarding Asian countries, their GDP per capita, spending on R&D, total number of universities and indexed scientific journals were collected. We recorded the bibliometric indicators, including total number of research documents, citations per document and H-index in various science and social sciences subjects during the period 1996–2011. The main sources for information were World Bank, SCI-mago/Scopus and Web of Science; Thomson Reuters. Results The mean per capita GDP for all the Asian countries is 14448.31±2854.40 US$, yearly per capita spending on R&D 0.64±0.16 US$, number of universities 72.37±18.32 and mean number of ISI indexed journal per country is 17.97±7.35. The mean of research documents published in various science and social science subjects among all the Asian countries during the period 1996–2011 is 158086.92±69204.09; citations per document 8.67±0.48; and H-index 122.8±19.21. Spending on R&D, number of universities and indexed journals have a positive correlation with number of published documents, citations per document and H-index in various science and social science subjects. However, there was no association between the per capita GDP and research outcomes. Conclusion The Asian countries who spend more on R&D have a large number of universities and scientific indexed journals produced more in research outcomes including total number of research publication, citations per documents and H-index in various science and social science subjects. PMID:23840471

United States Geological Survey fire science: fire danger monitoring and forecasting

USGS Publications Warehouse

Eidenshink, Jeff C.; Howard, Stephen M.

2012-01-01

Each day, the U.S. Geological Survey produces 7-day forecasts for all Federal lands of the distributions of number of ignitions, number of fires above a given size, and conditional probabilities of fires growing larger than a specified size. The large fire probability map is an estimate of the likelihood that ignitions will become large fires. The large fire forecast map is a probability estimate of the number of fires on federal lands exceeding 100 acres in the forthcoming week. The ignition forecast map is a probability estimate of the number of fires on Federal land greater than 1 acre in the forthcoming week. The extreme event forecast is the probability estimate of the number of fires on Federal land that may exceed 5,000 acres in the forthcoming week.

Consolidation of Customer Orders into Truckloads at a Large Manufacturer

DTIC Science & Technology

1997-08-01

Consolidation of Customer Orders into Truckloads at a Large Manufacturer G. G. Brown; D. Ronen The Journal of the Operational Research Society...AND SUBTITLE Consolidation of Customer Orders into Truckloads at a Large Manufacturer 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...All rights reserved. 0160-5682/97 $12.00 ~ Consolidation of customer orders into truckloads at a large manufacturer GG Brown1 and D Ronen2 1 Naval

The giant eyes of giant squid are indeed unexpectedly large, but not if used for spotting sperm whales.

PubMed

Nilsson, Dan-E; Warrant, Eric J; Johnsen, Sönke; Hanlon, Roger T; Shashar, Nadav

2013-09-08

We recently reported (Curr Biol 22:683-688, 2012) that the eyes of giant and colossal squid can grow to three times the diameter of the eyes of any other animal, including large fishes and whales. As an explanation to this extreme absolute eye size, we developed a theory for visual performance in aquatic habitats, leading to the conclusion that the huge eyes of giant and colossal squid are uniquely suited for detection of sperm whales, which are important squid-predators in the depths where these squid live. A paper in this journal by Schmitz et al. (BMC Evol Biol 13:45, 2013) refutes our conclusions on the basis of two claims: (1) using allometric data they argue that the eyes of giant and colossal squid are not unexpectedly large for the size of the squid, and (2) a revision of the values used for modelling indicates that large eyes are not better for detection of approaching sperm whales than they are for any other task. We agree with Schmitz et al. that their revised values for intensity and abundance of planktonic bioluminescence may be more realistic, or at least more appropriately conservative, but argue that their conclusions are incorrect because they have not considered some of the main arguments put forward in our paper. We also present new modelling to demonstrate that our conclusions remain robust, even with the revised input values suggested by Schmitz et al.

Local Diversity and Identity versus Global Interactions: Changes in the Danish Higher Education System

ERIC Educational Resources Information Center

Langberg, Kamma; Schmidt, Evanthia Kalpazidou

2010-01-01

The Danish higher education system was until recent years characterized by local diversity. It comprised, in relation to the population size, a large number of rather small institutions and a large number of universities and other research institutions. Since 1990, the Danish higher education system has changed dramatically: The number of…

Second Plateau Voltage in Nickel-cadmium Cells

NASA Technical Reports Server (NTRS)

Vasanth, K. L.

1984-01-01

Sealed nickel cadmium cells having large number of cycles on them are discharged using Hg/HgO reference electrode. The negative electrode exhibits the second plateau. A SEM of negative plates of such cells show a number of large crystals of cadmium hydroxide. The large crystals on the negative plates disappear after continuous overcharging in flooded cells.

Gonorrhoea and Syphilis Epidemiology in Flemish General Practice 2009–2013: Results from a Registry-based Retrospective Cohort Study Compared with Mandatory Notification

PubMed Central

Schweikardt, Christoph; Goderis, Geert; Elli, Steven; Coppieters, Yves

2016-01-01

Background The number of newly diagnosed gonorrhoea and syphilis cases has increased in Flanders in recent years. Our aim was to investigate, to which extent these diagnoses were registered by general practitioners (GPs), and to examine opportunities and limits of the Intego database in this regard. Methods Data from a retrospective cohort study based on the Flemish Intego general practice database was analyzed for the years 2009–2013. Case definitions were applied. Due to small case numbers obtained, cases were pooled and averaged over the observation period. Frequencies were compared with those calculated from figures of mandatory notification. Results A total of 91 gonorrhoea and 23 syphilis cases were registered. The average Intego annual frequency of gonorrhoea cases obtained was 11.9 (95% Poisson confidence interval (CI) 9.6; 14.7) per 100,000 population, and for syphilis 3.0 (CI 1.9; 4.5), respectively, while mandatory notification was calculated at 14.0 (CI: 13.6, 14.4) and 7.0 (CI: 6.7, 7.3), respectively. Conclusion In spite of limitations such as small numbers and different case definitions, comparison with mandatory notification suggests that the GP was involved in the large majority of gonorrhoea cases, while the majority of new syphilis cases did not come to the knowledge of the GP. PMID:29546196

Histological characteristics of human papilloma-virus-positive and-negative invasive and in situ squamous cell tumours of the penis

PubMed Central

Krustrup, Dorrit; Jensen, Helle Lone; van den Brule, Adriaan J C; Frisch, Morten

2009-01-01

A high prevalence of cervical cancer associated high-risk types of human papillomavirus (hrHPV) has been demonstrated in premalignant and invasive squamous cell lesions of the penis, but large studies correlating histological characteristics with HPV status are few in number. Tumour tissues from 145 patients with invasive (n = 116) or in situ (n = 29) penile squamous cell carcinoma were subjected to systematic histological evaluation and were PCR-tested for 14 hrHPV types and 23 low-risk HPV types. Around half (52%) of invasive and nine-tenths (90%) of in situ lesions were positive for an hrHPV type, of which HPV 16 was by far the predominant type (91% of hrHPV-positive lesions). In relation to histological characteristics, hrHPV positivity was statistically significantly more common in high-grade tumours, lesions dominated by small tumour cells, lesions with a high number of multinucleated cells and mitoses, and lesions with a small amount of parakeratosis. In conclusion, about half of invasive penile squamous carcinomas in this study were hrHPV-positive, most notably to HPV 16, and probably arose through in situ lesions whereas the other half of invasive penile lesions appeared to be unrelated to hrHPV. A number of histological characteristics differed significantly between hrHPV-positive and -negative invasive penile carcinomas. PMID:19335557

Projections of Trends in Overweight in the Elderly Population in Germany until 2030 and International Comparison

PubMed Central

Westphal, Christina; Doblhammer, Gabriele

2014-01-01

Background/Aims To project the numbers of pre-obese (BMI 25-29.99 kg/m²) and obese (BMI > 30 kg/m²) men and women aged 50+ in Germany until 2030 and to compare our estimates with actual figures from four European countries and the USA. Estimates are based on six scenarios encompassing improvements as well as worsenings of current trends. Methods We used pooled data from 1999 to 2009 of the German Microcensus (n = 1,472,547). Using multinomial logistic regression models we estimated age-specific probabilities of pre-obesity and obesity and applied them to the 12th population projection of the Federal Statistical Office. Results We project overall increases in absolute numbers of pre-obesity ranging between 14.2 and 18.2 million. However, the prevalence of pre-obesity is likely to decrease slightly. In contrast, absolute and relative numbers of obesity are projected to increase, ranging between 7.2 and 15.8 million. The international comparison revealed that pre-obesity prevalences will remain among the highest in Germany, while obesity is projected to fall below current levels of the UK or the USA. Conclusion Pre-obesity and, particularly, obesity are likely to become a more prominent health issue in Germany in the near future which could have large repercussions for the public health system. PMID:24525549

Order parameter re-mapping algorithm for 3D phase field model of grain growth using FEM

DOE PAGES

Permann, Cody J.; Tonks, Michael R.; Fromm, Bradley; ...

2016-01-14

Phase field modeling (PFM) is a well-known technique for simulating microstructural evolution. To model grain growth using PFM, typically each grain is assigned a unique non-conserved order parameter and each order parameter field is evolved in time. Traditional approaches using a one-to-one mapping of grains to order parameters present a challenge when modeling large numbers of grains due to the computational expense of using many order parameters. This problem is exacerbated when using an implicit finite element method (FEM), as the global matrix size is proportional to the number of order parameters. While previous work has developed methods to reducemore » the number of required variables and thus computational complexity and run time, none of the existing approaches can be applied for an implicit FEM implementation of PFM. Here, we present a modular, dynamic, scalable reassignment algorithm suitable for use in such a system. Polycrystal modeling with grain growth and stress require careful tracking of each grain’s position and orientation which is lost when using a reduced order parameter set. In conclusion, the method presented in this paper maintains a unique ID for each grain even after reassignment, to allow the PFM to be tightly coupled to calculations of the stress throughout the polycrystal. Implementation details and comparative results of our approach are presented.« less

Hepatitis A Is a Health Hazard for Iranian Pilgrims Who Go to Holly Karbala: A Preliminary Report

PubMed Central

Ghasemian, Roya; Babamahmoodi, Farhang; Ahangarkani, Fatemeh

2016-01-01

Background Iraq is a highly endemic area for the prevalence of hepatitis A and annually hosts a large number of Iranian pilgrims, most of whom are susceptible to infection with the hepatitis A virus (HAV). Objectives This study reports the health hazard of hepatitis A for Iranian pilgrims who go to holly Karbala from the Mazandaran province. Patients and Methods In this cross-sectional study, the data of all patients with acute hepatitis A admitted in the Razi teaching hospital from November 23, 2014 to January 24, 2015, with a history of recently returning from holly Karbala or being exposed to Karbala pilgrims, were registered. Results A total number of nine patients were registered. Seven patients were male and two were female. The mean age was 30.11 ± 10.09.Two patients were from the same family. All patients had typical symptoms of acute hepatitis A. None of the patients died nor did fulminant occur in any patients. In addition, all patients were treated with supportive treatment and subsequently recovered. Conclusions This number of pilgrim patients with acute hepatitis A from a single province compels us to conduct more evaluations and follow up monitoring on all persons travelling to Karbala and be sensitive to early diagnoses of the pilgrims. In the future, it is important to be mindful of administering the HAV vaccine and Ig. PMID:27630729

Readability of branding symbols in horses and histomorphological alterations at the branding site.

PubMed

Aurich, J E; Wohlsein, P; Wulf, M; Nees, M; Baumgärtner, W; Becker-Birck, M; Aurich, C

2013-03-01

Identification of horses has traditionally been facilitated by hot iron branding, but the extent by which branding symbols and numbers can be identified has not been investigated. The local pathological changes induced by branding are also unknown. This study analysed the readability of branding symbols and histomorphological alterations at the branding sites. A total of 248 horses in an equestrian championship were available for identification of symbols and numbers. A further 28 horses, euthanased for other reasons, provided histological examination of the branding site. All except one horse had evidence of histological changes at the brand site, including epidermal hyperplasia, increase of dermal collagenous fibrous tissue and loss of adnexal structures. In two foals, an ulcerative to necrotizing dermatitis was observed and interpreted as a complication of recent branding lesions. Despite the fact that hot iron branding caused lesions compatible with third degree thermal injury, it did not allow unambiguous identification of a large proportion of older horses. While the breed-specific symbol was consistently identified by three independent investigators in 84% of the horses, the double-digit branding number was read correctly by all three investigators in less than 40%. In conclusion, hot iron branding in horses causes lesions compatible with third degree thermal injury but does not always allow identification of horses. Copyright © 2012 Elsevier Ltd. All rights reserved.

Violence on Canadian Television Networks

PubMed Central

Paquette, Guy

2004-01-01

Introduction Over the past twenty years, the question of the effects of violence on television has figured prominently in public opinion and hundreds of studies have been devoted to this subject. Many researchers have determined that violence has a negative impact on behavior. The public, broadcasters and political figures all support the idea of reducing the total amount of violence on television - in particular in shows for children. A thousand programs aired between 1993 and 2001 on major non-specialty television networks in Canada were analyzed: TVA, TQS, as well as CTV and Global, private French and English networks, as well as the English CBC Radio and French Radio-Canada for the public networks. Method The methodology consists of a classic analysis of content where an act of violence constitutes a unit of analysis. Results The data collected revealed that the amount of violence has increased regularly since 1993 despite the stated willingness on the part of broadcasters to produce programs with less violence. The total number of violent acts, as well as the number of violent acts per hour, is increasing. Private networks deliver three times more violence than public networks. Researchers have also noted that a high proportion of violence occurs in programs airing before 21:00 hours, thereby exposing a large number of children to this violence. Conclusion Psychological violence is taking on a more significant role in Canadian Television. PMID:19030148

Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata)

PubMed Central

2012-01-01

Background Brassica oleracea encompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, the B. oleracea Genome Sequencing Project was launched using next generation sequencing technology. None of the available maps were detailed enough to anchor the sequence scaffolds for the Genome Sequencing Project. This report describes the development of a large number of SSR and SNP markers from the whole genome shotgun sequence data of B. oleracea, and the construction of a high-density genetic linkage map using a double haploid mapping population. Results The B. oleracea high-density genetic linkage map that was constructed includes 1,227 markers in nine linkage groups spanning a total of 1197.9 cM with an average of 0.98 cM between adjacent loci. There were 602 SSR markers and 625 SNP markers on the map. The chromosome with the highest number of markers (186) was C03, and the chromosome with smallest number of markers (99) was C09. Conclusions This first high-density map allowed the assembled scaffolds to be anchored to pseudochromosomes. The map also provides useful information for positional cloning, molecular breeding, and integration of information of genes and traits in B. oleracea. All the markers on the map will be transferable and could be used for the construction of other genetic maps. PMID:23033896

The effects of large beach debris on nesting sea turtles

USGS Publications Warehouse

Fujisaki, Ikuko; Lamont, Margaret M.

2016-01-01

A field experiment was conducted to understand the effects of large beach debris on sea turtle nesting behavior as well as the effectiveness of large debris removal for habitat restoration. Large natural and anthropogenic debris were removed from one of three sections of a sea turtle nesting beach and distributions of nests and false crawls (non-nesting crawls) in pre- (2011–2012) and post- (2013–2014) removal years in the three sections were compared. The number of nests increased 200% and the number of false crawls increased 55% in the experimental section, whereas a corresponding increase in number of nests and false crawls was not observed in the other two sections where debris removal was not conducted. The proportion of nest and false crawl abundance in all three beach sections was significantly different between pre- and post-removal years. The nesting success, the percent of successful nests in total nesting attempts (number of nests + false crawls), also increased from 24% to 38%; however the magnitude of the increase was comparably small because both the number of nests and false crawls increased, and thus the proportion of the nesting success in the experimental beach in pre- and post-removal years was not significantly different. The substantial increase in sea turtle nesting activities after the removal of large debris indicates that large debris may have an adverse impact on sea turtle nesting behavior. Removal of large debris could be an effective restoration strategy to improve sea turtle nesting.

Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data.

PubMed

Reisetter, Anna C; Muehlbauer, Michael J; Bain, James R; Nodzenski, Michael; Stevens, Robert D; Ilkayeva, Olga; Metzger, Boyd E; Newgard, Christopher B; Lowe, William L; Scholtens, Denise M

2017-02-02

Metabolomics offers a unique integrative perspective for health research, reflecting genetic and environmental contributions to disease-related phenotypes. Identifying robust associations in population-based or large-scale clinical studies demands large numbers of subjects and therefore sample batching for gas-chromatography/mass spectrometry (GC/MS) non-targeted assays. When run over weeks or months, technical noise due to batch and run-order threatens data interpretability. Application of existing normalization methods to metabolomics is challenged by unsatisfied modeling assumptions and, notably, failure to address batch-specific truncation of low abundance compounds. To curtail technical noise and make GC/MS metabolomics data amenable to analyses describing biologically relevant variability, we propose mixture model normalization (mixnorm) that accommodates truncated data and estimates per-metabolite batch and run-order effects using quality control samples. Mixnorm outperforms other approaches across many metrics, including improved correlation of non-targeted and targeted measurements and superior performance when metabolite detectability varies according to batch. For some metrics, particularly when truncation is less frequent for a metabolite, mean centering and median scaling demonstrate comparable performance to mixnorm. When quality control samples are systematically included in batches, mixnorm is uniquely suited to normalizing non-targeted GC/MS metabolomics data due to explicit accommodation of batch effects, run order and varying thresholds of detectability. Especially in large-scale studies, normalization is crucial for drawing accurate conclusions from non-targeted GC/MS metabolomics data.

Policy and Administrative Issues for Large-Scale Clinical Interventions Following Disasters

PubMed Central

Cobham, Vanessa E.; McDermott, Brett

2014-01-01

Abstract Objective: Large, programmatic mental health intervention programs for children and adolescents following disasters have become increasingly common; however, little has been written about the key goals and challenges involved. Methods: Using available data and the authors' experiences, this article reviews the factors involved in planning and implementing large-scale treatment programs following disasters. Results: These issues include funding, administration, choice of clinical targets, workforce selection, choice of treatment modalities, training, outcome monitoring, and consumer uptake. Ten factors are suggested for choosing among treatment modalities: 1) reach (providing access to the greatest number), 2) retention of patients, 3) privacy, 4) parental involvement, 5) familiarity of the modality to clinicians, 6) intensity (intervention type matches symptom acuity and impairment of patient), 7) burden to the clinician (in terms of time, travel, and inconvenience), 8) cost, 9) technology needs, and 10) effect size. Traditionally, after every new disaster, local leaders who have never done so before have had to be recruited to design, administer, and implement programs. Conclusion: As expertise in all of these areas represents a gap for most local professionals in disaster-affected areas, we propose that a central, nongovernmental agency with national or international scope be created that can consult flexibly with local leaders following disasters on both overarching and specific issues. We propose recommendations and point out areas in greatest need of innovation. PMID:24521227

Introducing the MCHF/OVRP/SDMP: Multicapacitated/Heterogeneous Fleet/Open Vehicle Routing Problems with Split Deliveries and Multiproducts

PubMed Central

Yilmaz Eroglu, Duygu; Caglar Gencosman, Burcu; Cavdur, Fatih; Ozmutlu, H. Cenk

2014-01-01

In this paper, we analyze a real-world OVRP problem for a production company. Considering real-world constrains, we classify our problem as multicapacitated/heterogeneous fleet/open vehicle routing problem with split deliveries and multiproduct (MCHF/OVRP/SDMP) which is a novel classification of an OVRP. We have developed a mixed integer programming (MIP) model for the problem and generated test problems in different size (10–90 customers) considering real-world parameters. Although MIP is able to find optimal solutions of small size (10 customers) problems, when the number of customers increases, the problem gets harder to solve, and thus MIP could not find optimal solutions for problems that contain more than 10 customers. Moreover, MIP fails to find any feasible solution of large-scale problems (50–90 customers) within time limits (7200 seconds). Therefore, we have developed a genetic algorithm (GA) based solution approach for large-scale problems. The experimental results show that the GA based approach reaches successful solutions with 9.66% gap in 392.8 s on average instead of 7200 s for the problems that contain 10–50 customers. For large-scale problems (50–90 customers), GA reaches feasible solutions of problems within time limits. In conclusion, for the real-world applications, GA is preferable rather than MIP to reach feasible solutions in short time periods. PMID:25045735

Cloud computing for comparative genomics

PubMed Central

2010-01-01

Background Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. Results We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. Conclusions The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems. PMID:20482786

Validation of hydrogen gas stratification and mixing models

DOE PAGES

Wu, Hsingtzu; Zhao, Haihua

2015-05-26

Two validation benchmarks confirm that the BMIX++ code is capable of simulating unintended hydrogen release scenarios efficiently. The BMIX++ (UC Berkeley mechanistic MIXing code in C++) code has been developed to accurately and efficiently predict the fluid mixture distribution and heat transfer in large stratified enclosures for accident analyses and design optimizations. The BMIX++ code uses a scaling based one-dimensional method to achieve large reduction in computational effort compared to a 3-D computational fluid dynamics (CFD) simulation. Two BMIX++ benchmark models have been developed. One is for a single buoyant jet in an open space and another is for amore » large sealed enclosure with both a jet source and a vent near the floor. Both of them have been validated by comparisons with experimental data. Excellent agreements are observed. The entrainment coefficients of 0.09 and 0.08 are found to fit the experimental data for hydrogen leaks with the Froude number of 99 and 268 best, respectively. In addition, the BIX++ simulation results of the average helium concentration for an enclosure with a vent and a single jet agree with the experimental data within a margin of about 10% for jet flow rates ranging from 1.21 × 10⁻⁴ to 3.29 × 10⁻⁴ m³/s. In conclusion, computing time for each BMIX++ model with a normal desktop computer is less than 5 min.« less

Medical Student Perception of Plastic Surgery and the Impact of Mainstream Media

PubMed Central

Fraser, S. J.; Al Youha, S.; Rasmussen, P. J.

2017-01-01

Background: Plastic surgery as a discipline is poorly understood by many, including primary care physicians, nurses, medical students, and the public. These misconceptions affect the specialty in a number of ways, including referral patterns and recruitment of medical students into residency programs. The reason for these commonly held misconceptions has not yet been addressed in the plastic surgery literature. As such, we assessed medical students’ knowledge and perceptions of plastic surgery as a discipline and explored factors influencing these opinions. Methods: To assess medical students’ knowledge and perceptions of plastic surgery, we conducted an online survey. A total of 231 medical students responded. Interviews were then conducted with 2 focus groups, in which we explored the survey results and reasons behind these misconceptions. Results: As with previous studies, medical students showed a gap in knowledge with respect to plastic surgery. Although they were generally aware that plastic surgeons perform cosmetic procedures and treat burns, they were largely unaware that plastic surgeons perform hand and craniofacial surgeries. Focus groups revealed that television plays a large role in shaping their ideas of plastic surgery. Conclusion: Medical students have a skewed perception of the discipline of plastic surgery, and this is largely influenced by television. Interventions aimed at educating medical students on the matter are recommended, including a greater presence in the preclerkship medical school curriculum. PMID:29026812

The scale and nature of Viking settlement in Ireland from Y-chromosome admixture analysis.

PubMed

McEvoy, Brian; Brady, Claire; Moore, Laoise T; Bradley, Daniel G

2006-12-01

The Vikings (or Norse) played a prominent role in Irish history but, despite this, their genetic legacy in Ireland, which may provide insights into the nature and scale of their immigration, is largely unexplored. Irish surnames, some of which are thought to have Norse roots, are paternally inherited in a similar manner to Y-chromosomes. The correspondence of Scandinavian patrilineal ancestry in a cohort of Irish men bearing surnames of putative Norse origin was examined using both slow mutating unique event polymorphisms and relatively rapidly changing short tandem repeat Y-chromosome markers. Irish and Scandinavian admixture proportions were explored for both systems using six different admixture estimators, allowing a parallel investigation of the impact of method and marker type in Y-chromosome admixture analysis. Admixture proportion estimates in the putative Norse surname group were highly consistent and detected little trace of Scandinavian ancestry. In addition, there is scant evidence of Scandinavian Y-chromosome introgression in a general Irish population sample. Although conclusions are largely dependent on the accurate identification of Norse surnames, the findings are consistent with a relatively small number of Norse settlers (and descendents) migrating to Ireland during the Viking period (ca. AD 800-1200) suggesting that Norse colonial settlements might have been largely composed of indigenous Irish. This observation adds to previous genetic studies that point to a flexible Viking settlement approach across North Atlantic Europe.

Vitamin D receptor gene and osteoporosis - author`s response

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

Looney, J.E.; Yoon, Hyun Koo; Fischer, M.

1996-04-01

We appreciate the comments of Dr. Nguyen et al. about our recent study, but we disagree with their suggestion that the lack of an association between low bone density and the BB VDR genotype, which we reported, is an artifact generated by the small sample size. Furthermore, our results are consistent with similar conclusions reached by a number of other investigators, as recently reported by Peacock. Peacock states {open_quotes}Taken as a whole, the results of studies outlined ... indicate that VDR alleles, cannot account for the major part of the heritable component of bone density as indicated by Morrison etmore » al.{close_quotes}. The majority of the 17 studies cited in this editorial could not confirm an association between the VDR genotype and the bone phenotype. Surely one cannot criticize this combined work as representing an artifact because of a too small sample size. We do not dispute the suggestion by Nguyen et al. that large sample sizes are required to analyze small biological effects. This is evident in both Peacock`s summary and in their own bone density studies. We did not design our study with a larger sample size because, based on the work of Morrison et al., we had hypothesized a large biological effect; large sample sizes are only needed for small biological effects. 4 refs.« less

Genomics Portals: integrative web-platform for mining genomics data

PubMed Central

2010-01-01

Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org. PMID:20070909

A depth-first search algorithm to compute elementary flux modes by linear programming

PubMed Central

2014-01-01

Background The decomposition of complex metabolic networks into elementary flux modes (EFMs) provides a useful framework for exploring reaction interactions systematically. Generating a complete set of EFMs for large-scale models, however, is near impossible. Even for moderately-sized models (<400 reactions), existing approaches based on the Double Description method must iterate through a large number of combinatorial candidates, thus imposing an immense processor and memory demand. Results Based on an alternative elementarity test, we developed a depth-first search algorithm using linear programming (LP) to enumerate EFMs in an exhaustive fashion. Constraints can be introduced to directly generate a subset of EFMs satisfying the set of constraints. The depth-first search algorithm has a constant memory overhead. Using flux constraints, a large LP problem can be massively divided and parallelized into independent sub-jobs for deployment into computing clusters. Since the sub-jobs do not overlap, the approach scales to utilize all available computing nodes with minimal coordination overhead or memory limitations. Conclusions The speed of the algorithm was comparable to efmtool, a mainstream Double Description method, when enumerating all EFMs; the attrition power gained from performing flux feasibility tests offsets the increased computational demand of running an LP solver. Unlike the Double Description method, the algorithm enables accelerated enumeration of all EFMs satisfying a set of constraints. PMID:25074068

Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish.

PubMed

Wood, Jacquelyn L A; Tezel, Defne; Joyal, Destin; Fraser, Dylan J

2015-09-01

How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Poor correlation between the removal or deposition of pollen grains and frequency of pollinator contact with sex organs

NASA Astrophysics Data System (ADS)

Sakamoto, Ryota L.; Morinaga, Shin-Ichi

2013-09-01

Pollinators deposit pollen grains on stigmas and remove pollen grains from anthers. The mechanics of these transfers can now be quantified with the use of high-speed video. We videoed hawkmoths, carpenter bees, and swallowtail butterflies pollinating Clerodendrum trichotomum. The number of grains deposited on stigmas did not vary significantly with the number of times pollinators contacted stigmas. In contrast, pollen removal from the anthers increased significantly with the number of contacts to anthers. Pollen removal varied among the three types of pollinators. Also, the three types carried pollen on different parts of their bodies. In hawkmoths and carpenter bees, a large number of contacted body part with anthers differed significantly from the body part that attached a large number of pollen grains. Our results indicate that a large number of contacts by pollinators does not increase either the male or female reproductive success of plants compared to a small number of contacts during a visit.

Complex networks with large numbers of labelable attractors

NASA Astrophysics Data System (ADS)

Mi, Yuanyuan; Zhang, Lisheng; Huang, Xiaodong; Qian, Yu; Hu, Gang; Liao, Xuhong

2011-09-01

Information storage in many functional subsystems of the brain is regarded by theoretical neuroscientists to be related to attractors of neural networks. The number of attractors is large and each attractor can be temporarily represented or suppressed easily by corresponding external stimulus. In this letter, we discover that complex networks consisting of excitable nodes have similar fascinating properties of coexistence of large numbers of oscillatory attractors, most of which can be labeled with a few nodes. According to a simple labeling rule, different attractors can be identified and the number of labelable attractors can be predicted from the analysis of network topology. With the cues of the labeling association, these attractors can be conveniently retrieved or suppressed on purpose.

Sodium content of processed foods in the United Kingdom: analysis of 44,000 foods purchased by 21,000 households123

PubMed Central

Capelin, Cathy; Dunford, Elizabeth K; Webster, Jacqueline L; Neal, Bruce C; Jebb, Susan A

2011-01-01

Background: In the United Kingdom, sodium reduction targets have been set for a large number of processed food categories. Assessment and monitoring are essential to evaluate progress. Objectives: Our aim was to determine whether household consumer panel food-purchasing data could be used to assess the sodium content of processed foods. Our further objectives were to estimate the mean sodium content of UK foods by category and undertake analyses weighted by food-purchasing volumes. Design: Data were obtained for 21,108 British households between October 2008 and September 2009. Purchasing data (product description, product weight, annual purchases) and sodium values (mg/100 g) were collated for all food categories known to be major contributors to sodium intake. Unweighted and weighted mean sodium values were calculated. Results: Data were available for 44,372 food products. The largest contributors to sodium purchases were table salt (23%), processed meat (18%), bread and bakery products (13%), dairy products (12%), and sauces and spreads (11%). More than one-third of sodium purchased (37%) was accounted for by 5 food categories: bacon, bread, milk, cheese, and sauces. For some food groups (bread and bakery, cereals and cereal products, processed meat), purchase-weighted means were 18–35% higher than unweighted means, suggesting that market leaders have higher sodium contents than the category mean. Conclusion: The targeting of sodium reduction in a small number of food categories and focusing on products sold in the highest volumes could lead to large decreases in sodium available for consumption and therefore to gains in public health. PMID:21191142

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

PubMed Central

Liebermeister, Wolfram; Klipp, Edda

2006-01-01

Background Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. Results We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. Conclusion Convenience kinetics can be used to translate a biochemical network – manually or automatically - into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases. PMID:17173669

GOSSIP: a method for fast and accurate global alignment of protein structures.

PubMed

Kifer, I; Nussinov, R; Wolfson, H J

2011-04-01

The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

Predictive equations for total lung capacity and residual volume calculated from radiographs in a random sample of the Michigan population.

PubMed Central

Kilburn, K H; Warshaw, R H; Thornton, J C; Thornton, K; Miller, A

1992-01-01

BACKGROUND: Published predicted values for total lung capacity and residual volume are often based on a small number of subjects and derive from different populations from predicted spirometric values. Equations from the only two large studies gave smaller predicted values for total lung capacity than the smaller studies. A large number of subjects have been studied from a population which has already provided predicted values for spirometry and transfer factor for carbon monoxide. METHODS: Total lung capacity was measured from standard posteroanterior and lateral chest radiographs and forced vital capacity by spirometry in a population sample of 771 subjects. Prediction equations were developed for total lung capacity (TLC), residual volume (RV) and RV/TLC in two groups--normal and total. Subjects with signs or symptoms of cardiopulmonary disease were combined with the normal subjects and equations for all subjects were also modelled. RESULTS: Prediction equations for TLC and RV in non-smoking normal men and women were square root transformations which included height and weight but not age. They included a coefficient for duration of smoking in current smokers. The predictive equation for RV/TLC included weight, age, age and duration of smoking for current smokers and ex-smokers of both sexes. For the total population the equations took the same form but the height coefficients and constants were slightly different. CONCLUSION: These population based prediction equations for TLC, RV and RV/TLC provide reference standards in a population that has provided reference standards for spirometry and single breath transfer factor for carbon monoxide. PMID:1412094

Copy number variation signature to predict human ancestry

PubMed Central

2012-01-01

Background Copy number variations (CNVs) are genomic structural variants that are found in healthy populations and have been observed to be associated with disease susceptibility. Existing methods for CNV detection are often performed on a sample-by-sample basis, which is not ideal for large datasets where common CNVs must be estimated by comparing the frequency of CNVs in the individual samples. Here we describe a simple and novel approach to locate genome-wide CNVs common to a specific population, using human ancestry as the phenotype. Results We utilized our previously published Genome Alteration Detection Analysis (GADA) algorithm to identify common ancestry CNVs (caCNVs) and built a caCNV model to predict population structure. We identified a 73 caCNV signature using a training set of 225 healthy individuals from European, Asian, and African ancestry. The signature was validated on an independent test set of 300 individuals with similar ancestral background. The error rate in predicting ancestry in this test set was 2% using the 73 caCNV signature. Among the caCNVs identified, several were previously confirmed experimentally to vary by ancestry. Our signature also contains a caCNV region with a single microRNA (MIR270), which represents the first reported variation of microRNA by ancestry. Conclusions We developed a new methodology to identify common CNVs and demonstrated its performance by building a caCNV signature to predict human ancestry with high accuracy. The utility of our approach could be extended to large case–control studies to identify CNV signatures for other phenotypes such as disease susceptibility and drug response. PMID:23270563

Years of Life and Productivity Loss from Potentially Avoidable Colorectal Cancer Deaths in U.S. Counties with Lower Educational Attainment (2008–2012)

PubMed Central

Weir, Hannah K.; Li, Chunyu; Henley, S. Jane; Joseph, Djenaba

2018-01-01

Background Educational attainment (EA) is inversely associated with colorectal cancer risk. Colorectal cancer screening can save lives if precancerous polyps or early cancers are found and successfully treated. This study aims to estimate the potential productivity loss (PPL) and associated avoidable colorectal cancer–related deaths among screen-eligible adults residing in lower EA counties in the United States. Methods Mortality and population data were used to examine colorectal cancer deaths (2008–2012) among adults aged 50 to 74 years in lower EA counties, and to estimate the expected number of deaths using the mortality experience from high EA counties. Excess deaths (observed–expected) were used to estimate potential years life lost, and the human capital method was used to estimate PPL in 2012 U.S. dollars. Results County-level colorectal cancer death rates were inversely associated with county-level EA. Of the 100,857 colorectal cancer deaths in lower EA counties, we estimated that more than 21,000 (1 in 5) was potentially avoidable and resulted in nearly $2 billion annual productivity loss. Conclusions County-level EA disparities contribute to a large number of potentially avoidable colorectal cancer–related deaths. Increased prevention and improved screening potentially could decrease deaths and help reduce the associated economic burden in lower EA communities. Increased screening could further reduce deaths in all EA groups. Impact These results estimate the large economic impact of potentially avoidable colorectal cancer–related deaths in economically disadvantaged communities, as measured by lower EA. PMID:28003180

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data.

PubMed

Bao, Yanchun; Vinciotti, Veronica; Wit, Ernst; 't Hoen, Peter A C

2013-05-30

ImmunoPrecipitation (IP) efficiencies may vary largely between different antibodies and between repeated experiments with the same antibody. These differences have a large impact on the quality of ChIP-seq data: a more efficient experiment will necessarily lead to a higher signal to background ratio, and therefore to an apparent larger number of enriched regions, compared to a less efficient experiment. In this paper, we show how IP efficiencies can be explicitly accounted for in the joint statistical modelling of ChIP-seq data. We fit a latent mixture model to eight experiments on two proteins, from two laboratories where different antibodies are used for the two proteins. We use the model parameters to estimate the efficiencies of individual experiments, and find that these are clearly different for the different laboratories, and amongst technical replicates from the same lab. When we account for ChIP efficiency, we find more regions bound in the more efficient experiments than in the less efficient ones, at the same false discovery rate. A priori knowledge of the same number of binding sites across experiments can also be included in the model for a more robust detection of differentially bound regions among two different proteins. We propose a statistical model for the detection of enriched and differentially bound regions from multiple ChIP-seq data sets. The framework that we present accounts explicitly for IP efficiencies in ChIP-seq data, and allows to model jointly, rather than individually, replicates and experiments from different proteins, leading to more robust biological conclusions.

[Variations in patient data coding affect hospital standardized mortality ratio (HSMR)].

PubMed

van den Bosch, Wim F; Silberbusch, Joseph; Roozendaal, Klaas J; Wagner, Cordula

2010-01-01

To investigate the impact of coding variations on 'hospital standardized mortality ratio' (HSMR) and to define variation reduction measures. Retrospective, descriptive. We analysed coding variations in HSMR parameters for main diagnosis, urgency of the admission and comorbidity in the national medical registration (LMR) database of admissions in 6 Dutch top clinical hospitals during 2003-2007. More than a quarter of these admission records had been included in the HSMR calculation. Admissions with ICD-9 main diagnosis codes that were excluded from HSMR calculations were investigated for inter-hospital variability and correct exclusion. Variation in coding admission type was signalled by analyzing admission records with diagnoses that had an emergency nature by their title. Variation in the average number of comorbidity diagnoses per admission was determined as an indicator for coding variation. Interviews with coding teams were used to check whether the conclusions of the analysis were correct. Over 165,000 admissions that were excluded from HSMR calculations showed large variability between hospitals. This figure was 40% of all admissions that were included. Of the admissions with a main diagnosis indicating an emergency, 34% to 93% were recorded as an emergency. The average number of comorbidity diagnoses varied between hospitals from 0.9 to 3.0 per admission. Coding of main diagnoses, urgency of admission and comorbidities showed strong inter-hospital variation with a potentially large impact on the HSMR outcomes of the hospitals. Coding variations originated from differences in interpretation of coding rules, differences in coding capacity, quality of patient records and discharge documentation and timely delivery of these.

The ecology of prescription opioid abuse in the USA: geographic variation in patients’ use of multiple prescribers (“doctor shopping”)

PubMed Central

McDonald, Douglas C.; Carlson, Kenneth E.

2016-01-01

Purpose This study estimates the prevalence in US counties of opioid patients who use large numbers of prescribers, the amounts of opioids they obtain, and the extent to which their prevalence is predicted by ecological attributes of counties, including general medical exposure to opioids. Methods Finite mixture models were used to estimate the size of an outlier subpopulation of patients with suspiciously large numbers of prescribers (probable doctor shoppers), using a sample of 146 million opioid prescriptions dispensed during 2008. Ordinary least squares regression models of county-level shopper rates included independent variables measuring ecological attributes of counties, including rates of patients prescribed opioids, socioeconomic characteristics of the resident population, supply of physicians, and measures of healthcare service utilization. Results The prevalence of shoppers varied widely by county, with rates ranging between 0.6 and 2.5 per 1000 residents. Shopper prevalence was strongly correlated with opioid prescribing for the general population, accounting for 30% of observed county variation in shopper prevalence, after adjusting for physician supply, emergency department visits, in-patient hospital days, poverty rates, percent of county residents living in urban areas, and racial/ethnic composition of resident populations. Approximately 30% of shoppers obtained prescriptions in multiple states. Conclusions The correlation between prevalence of doctor shoppers and opioid patients in a county could indicate either that easy access to legitimate medical treatment raises the risk of abuse or that drug abusers take advantage of greater opportunities in places where access is easy. Approaches to preventing excessive use of different prescribers are discussed. PMID:25111716

Evaluating a complex system-wide intervention using the difference in differences method: the Delivering Choice Programme

PubMed Central

Round, Jeff; Drake, Robyn; Kendall, Edward; Addicott, Rachael; Agelopoulos, Nicky; Jones, Louise

2015-01-01

Objectives We report the use of difference in differences (DiD) methodology to evaluate a complex, system-wide healthcare intervention. We use the worked example of evaluating the Marie Curie Delivering Choice Programme (DCP) for advanced illness in a large urban healthcare economy. Methods DiD was selected because a randomised controlled trial was not feasible. The method allows for before and after comparison of changes that occur in an intervention site with a matched control site. This enables analysts to control for the effect of the intervention in the absence of a local control. Any policy, seasonal or other confounding effects over the test period are assumed to have occurred in a balanced way at both sites. Data were obtained from primary care trusts. Outcomes were place of death, inpatient admissions, length of stay and costs. Results Small changes were identified between pre- and post-DCP outputs in the intervention site. The proportion of home deaths and median cost increased slightly, while the number of admissions per patient and the average length of stay per admission decreased slightly. None of these changes was statistically significant. Conclusions Effects estimates were limited by small numbers accessing new services and selection bias in sample population and comparator site. In evaluating the effect of a complex healthcare intervention, the choice of analysis method and output measures is crucial. Alternatives to randomised controlled trials may be required for evaluating large scale complex interventions and the DiD approach is suitable, subject to careful selection of measured outputs and control population. PMID:24644163

ETE: a python Environment for Tree Exploration

PubMed Central

2010-01-01

Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Results Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. Conclusions ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org. PMID:20070885

Multi-Reader ROC studies with Split-Plot Designs: A Comparison of Statistical Methods

PubMed Central

Obuchowski, Nancy A.; Gallas, Brandon D.; Hillis, Stephen L.

2012-01-01

Rationale and Objectives Multi-reader imaging trials often use a factorial design, where study patients undergo testing with all imaging modalities and readers interpret the results of all tests for all patients. A drawback of the design is the large number of interpretations required of each reader. Split-plot designs have been proposed as an alternative, in which one or a subset of readers interprets all images of a sample of patients, while other readers interpret the images of other samples of patients. In this paper we compare three methods of analysis for the split-plot design. Materials and Methods Three statistical methods are presented: Obuchowski-Rockette method modified for the split-plot design, a newly proposed marginal-mean ANOVA approach, and an extension of the three-sample U-statistic method. A simulation study using the Roe-Metz model was performed to compare the type I error rate, power and confidence interval coverage of the three test statistics. Results The type I error rates for all three methods are close to the nominal level but tend to be slightly conservative. The statistical power is nearly identical for the three methods. The coverage of 95% CIs fall close to the nominal coverage for small and large sample sizes. Conclusions The split-plot MRMC study design can be statistically efficient compared with the factorial design, reducing the number of interpretations required per reader. Three methods of analysis, shown to have nominal type I error rate, similar power, and nominal CI coverage, are available for this study design. PMID:23122570

The effect of post-ovulatory insemination on the subsequent embryonic loss, oestrous cycle length and vaginal discharge in sows.

PubMed

Kaeoket, K; Tantasuparuk, W; Kunavongkrit, A

2005-10-01

The aim of present study was to study the effect of post-ovulatory insemination on the subsequent embryonic loss, oestrous cycle length and vaginal discharge in sows. Ten Large White multiparous sows were divided into two groups. Group A sows were inseminated once at 15 h after ovulation. Thereafter, they were ovariohysterectomized on day 11 (n = 5, first day of standing oestrus = day 1) and flushed for recovery of embryos. Group B sows were also inseminated once at 15 h after ovulation. They were further observed for return to oestrus and vaginal discharge (n = 5) after insemination. The endometrium tissues were biopsied from sows with vaginal discharge, embedded with paraffin, stained with haematoxylin and eosin and examined under light microscope. Only two embryos were observed in one of four sows from group A. All embryos had a spherical shape but differed in size (range 1-2 mm). In group B, only one sow had a regular return to oestrus (i.e. on day 23) and another sow had an irregular return to oestrus (i.e. on day 27). The other two sows in this group had shown vaginal discharge on days 20 and 38 after standing oestrus. For the number of leucocytes in the endometrium of sows with vaginal discharge, a large number of lymphocytes and plasma cells were observed in the connective tissue of the subepithelial layer. In conclusion, post-ovulatory insemination resulted in early embryonic loss, a subsequent prolonged oestrus interval and also vaginal discharge (i.e. endometritis) in sows.

Exobiology of icy satellites

NASA Astrophysics Data System (ADS)

Simakov, M. B.

At the beginning of 2004 the total number of discovered planets near other stars was 119 All of them are massive giants and met practically in all orbits In a habitable zone from 0 8 up to 1 1 AU at less 11 planets has been found starting with HD 134987 and up to HD 4203 It would be naive to suppose existence of life in unique known to us amino-nucleic acid form on the gas-liquid giant planets Nevertheless conditions for onset and evolutions of life can be realized on hypothetical satellites extrasolar planets All giant planets of the Solar system have a big number of satellites 61 of Jupiter 52 of Saturn known in 2003 A small part of them consist very large bodies quite comparable to planets of terrestrial type but including very significant share of water ice Some from them have an atmosphere E g the mass of a column of the Titan s atmosphere exceeds 15 times the mass of the Earth atmosphere column Formation or capture of satellites is a natural phenomenon and satellite systems definitely should exist at extrasolar planets A hypothetical satellite of the planet HD 28185 with a dense enough atmosphere and hydrosphere could have biosphere of terrestrial type within the limits of our notion about an origin of terrestrial biosphere As an example we can see on Titan the largest satellite of Saturn which has a dense nitrogen atmosphere and a large quantity of liquid water under ice cover and so has a great exobiological significance The most recent models of the Titan s interior lead to the conclusion that a substantial liquid layer

Copy Number Variation in Obsessive-Compulsive Disorder and Tourette Syndrome: A Cross-Disorder Study

PubMed Central

McGrath, Lauren M.; Yu, Dongmei; Marshall, Christian; Davis, Lea K.; Thiruvahindrapuram, Bhooma; Li, Bingbin; Cappi, Carolina; Gerber, Gloria; Wolf, Aaron; Schroeder, Frederick A.; Osiecki, Lisa; O’Dushlaine, Colm; Kirby, Andrew; Illmann, Cornelia; Haddad, Stephen; Gallagher, Patience; Fagerness, Jesen A.; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Bienvenu, O. Joseph; Black, Donald W.; Bloch, Michael H.; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Cath, Danielle C.; Cavallini, Maria C.; Chouinard, Sylvain; Coric, Vladimir; Cullen, Bernadette; Delorme, Richard; Denys, Damiaan; Derks, Eske M.; Dion, Yves; Rosário, Maria C.; Eapen, Valsama; Evans, Patrick; Falkai, Peter; Fernandez, Thomas; Garrido, Helena; Geller, Daniel; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Grünblatt, Edna; Heiman, Gary A.; Hemmings, Sian M.J.; Herrera, Luis D.; Hounie, Ana G.; Jankovic, Joseph; Kennedy, James L; King, Robert A.; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Lochner, Christine; Lowe, Thomas L.; Lyon, Gholson J.; Macciardi, Fabio; Maier, Wolfgang; McCracken, James T.; McMahon, William; Murphy, Dennis L.; Naarden, Allan L; Neale, Benjamin M; Nurmi, Erika; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlos N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark; Robertson, Mary M.; Rosenberg, David; Rouleau, Guy A.; Ruhrmann, Stephan; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Tischfield, Jay A.; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Wendland, Jens R.; Shugart, Yin Yao; Miguel, Euripedes C.; Nicolini, Humberto; Oostra, Ben A.; Moessner, Rainald; Wagner, Michael; Ruiz-Linares, Andres; Heutink, Peter; Nestadt, Gerald; Freimer, Nelson; Petryshen, Tracey; Posthuma, Danielle; Jenike, Michael A.; Cox, Nancy J.; Hanna, Gregory L.; Brentani, Helena; Scherer, Stephen W.; Arnold, Paul D.; Stewart, S. Evelyn; Mathews, Carol A.; Knowles, James A.; Cook, Edwin H.; Pauls, David L.; Wang, Kai; Scharf, Jeremiah M.

2014-01-01

Objective Obsessive-compulsive disorder (OCD) and Tourette syndrome (TS) are heritable, neurodevelopmental disorders with a partially shared genetic etiology. This study represents the first genome-wide investigation of large (>500kb), rare (<1%) copy number variants (CNVs) in OCD and the largest genome-wide CNV analysis in TS to date. Method The primary analyses utilized a cross-disorder design for 2,699 patients (1,613 ascertained for OCD, 1,086 ascertained for TS) and 1,789 controls. Parental data facilitated a de novo analysis in 348 OCD trios. Results Although no global CNV burden was detected in the cross-disorder analysis or in secondary, disease-specific analyses, there was a 3.3-fold increased burden of large deletions previously associated with other neurodevelopmental disorders (p=.09). Half of these neurodevelopmental deletions were located in a single locus, 16p13.11 (5 patient deletions: 0 control deletions, p=0.08 in current study, p=0.025 compared to published controls). Three 16p13.11 deletions were confirmed de novo, providing further support to the etiological significance of this region. The overall OCD de novo rate was 1.4%, which is intermediate between published rates in controls (0.7%) and in autism or schizophrenia (2–4%). Conclusion Several converging lines of evidence implicate 16p13.11 deletions in OCD, with weaker evidence for a role in TS. The trend toward increased overall neurodevelopmental CNV burden in TS and OCD suggests that deletions previously associated with other neurodevelopmental disorders may also contribute to these phenotypes. PMID:25062598

HLA sharing among couples appears unrelated to idiopathic recurrent fetal loss in Saudi Arabia.

PubMed

Moghraby, J S; Tamim, H; Anacan, V; Al Khalaf, H; Moghraby, S A

2010-08-01

Recurrent fetal loss (RFL) is a prevalent problem affecting approximately 1% of all women of childbearing age. Many factors can lead to RFL; however, recent studies have indicated the important role of the maternal immune system in this process. The human leukocyte antigens (HLA), HLA-linked genes and regulatory factors play an important role in fetal loss and in fetal development. The current retrospective study was preformed to examine the HLA alleles shared between couples with RFL in Saudi Arabia, using a large cohort of women (having three or more RFL). Specific HLA alleles that could influence this condition, or the number of miscarriages experienced, were expected to be highlighted in this way. A total of 253 consecutive patients who visited the RFL clinic at the King AbdulAziz Medical City, National Guard Hospital in Riyadh were included in this study. They included 54 consanguineous couples, 132 non-consanguineous couples and another 67 couples shared only their tribal origin. Clinical examinations as well as laboratory investigations were carried out on each patient. Class I HLA, HLA-A, HLA-B and HLA-C, and Class II HLA, HLA-DR and HLA-DQ, were typed for each patient and their partner. No relationship was seen between sharing of HLA alleles and the number of RFL experienced by the couples, among neither consanguineous nor non-consanguineous couples. Although the results of this study suggest that HLA sharing is not an indicative factor in RFL, definitive conclusions on this topic must be based on large case-control studies.

A bacterial genome in transition - an exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus

PubMed Central

2011-01-01

Background Insertion sequence (IS) elements are important mediators of genome plasticity and are widespread among bacterial and archaeal genomes. The 1.88 Mbp genome of the obligate intracellular amoeba symbiont Amoebophilus asiaticus contains an unusually large number of transposase genes (n = 354; 23% of all genes). Results The transposase genes in the A. asiaticus genome can be assigned to 16 different IS elements termed ISCaa1 to ISCaa16, which are represented by 2 to 24 full-length copies, respectively. Despite this high IS element load, the A. asiaticus genome displays a GC skew pattern typical for most bacterial genomes, indicating that no major rearrangements have occurred recently. Additionally, the high sequence divergence of some IS elements, the high number of truncated IS element copies (n = 143), as well as the absence of direct repeats in most IS elements suggest that the IS elements of A. asiaticus are transpositionally inactive. Although we could show transcription of 13 IS elements, we did not find experimental evidence for transpositional activity, corroborating our results from sequence analyses. However, we detected contiguous transcripts between IS elements and their downstream genes at nine loci in the A. asiaticus genome, indicating that some IS elements influence the transcription of downstream genes, some of which might be important for host cell interaction. Conclusions Taken together, the IS elements in the A. asiaticus genome are currently in the process of degradation and largely represent reflections of the evolutionary past of A. asiaticus in which its genome was shaped by their activity. PMID:21943072

The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis

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

Dmytrenko, Oleg; Russell, Shelbi L.; Loo, Wesley T.

Background: Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and themore » ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Results: Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.86 Mb), GC-rich (50.4percent), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. Conclusions: The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle« less

The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis

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

Dmytrenko, Oleg; Russell, Shelbi L.; Loo, Wesley T.

Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the abilitymore » to maintain it under laboratory conditions. Here, to better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. In conclusion, the physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.« less

Rare Copy Number Variation in Treatment-Resistant Major Depressive Disorder

PubMed Central

O’Dushlaine, Colm; Ripke, Stephan; Ruderfer, Douglas M.; Hamilton, Steven P.; Fava, Maurizio; Iosifescu, Dan V.; Kohane, Isaac S.; Churchill, Susanne E.; Castro, Victor M.; Clements, Caitlin C.; Blumenthal, Sarah R.; Murphy, Shawn N.; Smoller, Jordan W.; Perlis, Roy H.

2014-01-01

Background While antidepressant treatment response appears to be partially heritable, no consistent genetic associations have been identified. Large, rare copy number variants (CNVs) play a role in other neuropsychiatric diseases, so we assessed their association with treatment-resistant depression (TRD). Methods We analyzed data from two genome-wide association studies comprising 1263 Caucasian patients with major depressive disorder. One was drawn from a large health system by applying natural language processing to electronic health records (i2b2 cohort). The second consisted of a multicenter study of sequential antidepressant treatments, Sequenced Treatment Alternatives to Relieve Depression. The Birdsuite package was used to identify rare deletions and duplications. Individuals without symptomatic remission, despite two antidepressant treatment trials, were contrasted with those who remitted with a first treatment trial. Results CNV data were derived for 778 subjects in the i2b2 cohort, including 300 subjects (37%) with TRD, and 485 subjects in Sequenced Treatment Alternatives to Relieve Depression cohort, including 152 (31%) with TRD. CNV burden analyses identified modest enrichment of duplications in cases (empirical p = .04 for duplications of 100–200 kilobase) and a particular deletion region spanning gene PABPC4L (empirical p = .02, 6 cases: 0 controls). Pathway analysis suggested enrichment of CNVs intersecting genes regulating actin cytoskeleton. However, none of these associations survived genome-wide correction. Conclusions Contribution of rare CNVs to TRD appears to be modest, individually or in aggregate. The electronic health record-based methodology demonstrated here should facilitate collection of larger TRD cohorts necessary to further characterize these effects. PMID:24529801

The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis

DOE PAGES

Dmytrenko, Oleg; Russell, Shelbi L.; Loo, Wesley T.; ...

2014-10-23

Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the abilitymore » to maintain it under laboratory conditions. Here, to better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. In conclusion, the physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.« less

Estimating large numbers.

PubMed

Landy, David; Silbert, Noah; Goldin, Aleah

2013-07-01

Despite their importance in public discourse, numbers in the range of 1 million to 1 trillion are notoriously difficult to understand. We examine magnitude estimation by adult Americans when placing large numbers on a number line and when qualitatively evaluating descriptions of imaginary geopolitical scenarios. Prior theoretical conceptions predict a log-to-linear shift: People will either place numbers linearly or will place numbers according to a compressive logarithmic or power-shaped function (Barth & Paladino, ; Siegler & Opfer, ). While about half of people did estimate numbers linearly over this range, nearly all the remaining participants placed 1 million approximately halfway between 1 thousand and 1 billion, but placed numbers linearly across each half, as though they believed that the number words "thousand, million, billion, trillion" constitute a uniformly spaced count list. Participants in this group also tended to be optimistic in evaluations of largely ineffective political strategies, relative to linear number-line placers. The results indicate that the surface structure of number words can heavily influence processes for dealing with numbers in this range, and it can amplify the possibility that analogous surface regularities are partially responsible for parallel phenomena in children. In addition, these results have direct implications for lawmakers and scientists hoping to communicate effectively with the public. Copyright © 2013 Cognitive Science Society, Inc.

CFD Validation Studies for Hypersonic Flow Prediction

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.

2001-01-01

A series of experiments to measure pressure and heating for code validation involving hypersonic, laminar, separated flows was conducted at the Calspan-University at Buffalo Research Center (CUBRC) in the Large Energy National Shock (LENS) tunnel. The experimental data serves as a focus for a code validation session but are not available to the authors until the conclusion of this session. The first set of experiments considered here involve Mach 9.5 and Mach 11.3 N2 flow over a hollow cylinder-flare with 30 degree flare angle at several Reynolds numbers sustaining laminar, separated flow. Truncated and extended flare configurations are considered. The second set of experiments, at similar conditions, involves flow over a sharp, double cone with fore-cone angle of 25 degrees and aft-cone angle of 55 degrees. Both sets of experiments involve 30 degree compressions. Location of the separation point in the numerical simulation is extremely sensitive to the level of grid refinement in the numerical predictions. The numerical simulations also show a significant influence of Reynolds number on extent of separation. Flow unsteadiness was easily introduced into the double cone simulations using aggressive relaxation parameters that normally promote convergence.

CFD Validation Studies for Hypersonic Flow Prediction

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.

2001-01-01

A series of experiments to measure pressure and heating for code validation involving hypersonic, laminar, separated flows was conducted at the Calspan-University at Buffalo Research Center (CUBRC) in the Large Energy National Shock (LENS) tunnel. The experimental data serves as a focus for a code validation session but are not available to the authors until the conclusion of this session. The first set of experiments considered here involve Mach 9.5 and Mach 11.3 N, flow over a hollow cylinder-flare with 30 deg flare angle at several Reynolds numbers sustaining laminar, separated flow. Truncated and extended flare configurations are considered. The second set of experiments, at similar conditions, involves flow over a sharp, double cone with fore-cone angle of 25 deg and aft-cone angle of 55 deg. Both sets of experiments involve 30 deg compressions. Location of the separation point in the numerical simulation is extremely sensitive to the level of grid refinement in the numerical predictions. The numerical simulations also show a significant influence of Reynolds number on extent of separation. Flow unsteadiness was easily introduced into the double cone simulations using aggressive relaxation parameters that normally promote convergence.

Use of traditional plants in management of halitosis in a Moroccan population

PubMed Central

Akkaoui, Sanae; Ennibi, Oum keltoum

2017-01-01

Introduction: The use of medicinal plants was a very spread therapeutic way. At present, several studies are moving toward this ancestral option, seen the emergence of several bacterial resistance and for the large number of side effects of some synthetic drugs. Objective: The objective of this study was to collect and evaluate information on medicinal plants commonly used in five Moroccan cities: Rabat, Salé, Témara, Khémisset, and Tiflet for the management of halitosis. Methods: This is a cross-sectional survey; conducted among 171 herbalists. The tool of the study was a questionnaire filled by herbalists. SPSS in its version 13 was used for statistical calculations. Quantitative variables were expressed as a mean and standard deviation. Categorical variables were expressed as numbers and percentage. Results: Analysis of the results of this study identified 23 plants that are used the most. The herbal knowledge herbalists prescribed on the toxicity of plants and their side effects were appreciated. Conclusions: Preliminary results presented in this work allow knowing the plants used by this population. This data could be the basis for experimental and clinical studies to promote the use of natural agents in the treatment of bad breath. PMID:28894624

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

Feather, F.

This volume was prepared in conjunction with the First Global Conference on the Future, held in Toronto, Canada, July 20-24, 1980. The conference combined the Third General Assembly of the World Future Society and the fifth annual conference of the Canadian Futures Society. The 59 papers presented here were selected from the very large number submitted to the conference committee; space limitations permitted only a small number of papers to be published in this volume. Included also are: the foreword, Mystery of the Future, by Edward R. Schreyer, Governor General of Canada; preface, A Time for Action, by Maurice F.more » Strong; introduction, Transition to Harmonic Globalism, by Frank Feather; conclusion, What We Must Do: An Agenda for Futurists; and postscript, The Challenge of the '80s, by Aurelio Peccei. The papers were presented under the following topics: The Trauma of Change (4); A Global Perspective (7); Inventorying Our Resources (7); The International Context (8); Economics: Getting Down to Business (9); Human Values: Personal, Social, Religious (6); Communications: Connecting Ourselves Together (4); Education: Learning to Meet Tomorrow (4); Health: New Approaches to Staying Fit (3); Futurism as a Way of Life (5); and Dreams into Action: Methods and Real-Life Experience (2).« less

[Development and implementation of an integrated care pathway at the POLIKUM health centers using the example of anemia].

PubMed

Bierbaum, M; Grad, M O; Wulff, H; Kewenig, S; Schöffski, O

2014-04-01

Integrated treatment pathways are an appropriate means for increasing the quality of treatment and outcome via process optimization. Taking the POLIKUM Health Centers as an example, we intend to demonstrate how the implementation can be effected for the indication of anemia. The development and implementation were executed by an interdisciplinary workgroup in several workshops. In addition, the diagnoses and hemoglobin values of all patients with requests for hemograms were obtained and analyzed at two locations. Developing the pathway required significantly greater efforts than initially planned. The biggest challenge was to adequately map the complexity of the different forms of anemia and, concomitantly, to design a pathway that can actually be realized in everyday life. Moreover, evaluation of the patient data demonstrated that there are a large number of cases where existing anemias are not reflected in the respective diagnoses. While the ultimate effects of the new pathway cannot yet be assessed conclusively, it was possible to obtain valuable findings for practical use even at this point. Despite the limitations of the sample, the surprisingly high number of undetected anemias should give physicians cause for taking diagnostic measures even in patients with mild anemia.

Safety of laparoscopic colorectal surgery in a low-volume setting: review of early and late outcome.

PubMed

Gandy, Robert C; Berney, Christophe R

2014-01-01

Background. There is increasing evidence suggesting that the laparoscopic technique is the treatment of choice for large bowel resection, including for malignancy. The purpose of the study was to assess whether general surgeons, with particular skills in advanced laparoscopy, can adequately provide safe laparoscopic colorectal resections in a low-volume setting. Methods. A retrospective review of prospectively collected case series of all laparoscopic colorectal resections performed under the care of a single general surgeon is presented. The primary endpoint was postoperative clinical outcome in terms of morbidity and mortality. Secondary endpoints were adequacy of surgical margins and number of lymph nodes harvested for colorectal cancer cases. Results. Seventy-three patients underwent 75 laparoscopic resections between March, 2003, and May, 2011. There was no elective mortality and the overall 30-day postoperative morbidity was 9.3%. Conversion and anastomotic leakage rates were both 1.3%, respectively. None of the malignant cases had positive margins and the median number of lymph nodes retrieved was 17. Conclusions. Our results support the view that general surgeons with advanced skills in minimally invasive surgery may safely perform laparoscopic colorectal resection in a low-volume setting in carefully selected patient cases.