Inter-hospital outbreak of Klebsiella pneumoniae producing KPC-2 carbapenemase in Ireland.

PubMed

Morris, Dearbháile; Boyle, Fiona; Morris, Carol; Condon, Iris; Delannoy-Vieillard, Anne-Sophie; Power, Lorraine; Khan, Aliya; Morris-Downes, Margaret; Finnegan, Cathriona; Powell, James; Monahan, Regina; Burns, Karen; O'Connell, Nuala; Boyle, Liz; O'Gorman, Alan; Humphreys, Hilary; Brisse, Sylvain; Turton, Jane; Woodford, Neil; Cormican, Martin

2012-10-01

To describe an outbreak of KPC-2-producing Klebsiella pneumoniae with inter-hospital spread and measures taken to control transmission. Between January and March 2011, 13 K. pneumoniae isolates were collected from nine patients at hospital A and two patients at hospital B. Meropenem, imipenem and ertapenem MICs were determined by Etest, carbapenemase production was confirmed by the modified Hodge method and by a disc synergy test, and confirmed carbapenemase producers were tested for the presence of carbapenemase-encoding genes by PCR. PFGE, plasmid analysis, multilocus variable-number tandem-repeat analysis (MLVA) and multilocus sequence typing (MLST) analysis were performed on all or a subset of isolates. Meropenem, imipenem and ertapenem MICs were 4 to >32, 8-32 and >16 mg/L, respectively. PCR and sequencing confirmed the presence of bla(KPC-2). PFGE identified four distinguishable (≥88%) pulsed-field profiles (PFPs). Isolates distinguishable by PFGE had identical MLVA profiles, and MLST analysis indicated all isolates belonged to the ST258 clone. Stringent infection prevention and control measures were implemented. Over a period of almost 8 months no further carbapenemase-producing Enterobacteriaceae (CPE) were isolated. However, KPC-2-producing K. pneumoniae was detected in two further patients in hospital A in August (PFP indistinguishable from previous isolates) and October 2011 (PFP similar to but distinguishable from previous isolates). Stringent infection prevention and control measures help contain CPE in the healthcare setting; however, in the case of hospital A, where CPE appears to be established in the population served, it may be virtually impossible to achieve eradication or avoid reintroduction into the hospital.

Long-Term Photometric and Spectroscopic Behavior of a Symbiotic System AG DRA

NASA Astrophysics Data System (ADS)

Gális, R.; Hric, L.; Petrík, K.

A symbiotic binary, AG Dra, is studied using long-term photometry and radial velocity measurements. New radial velocities confirm the presence of a second period, found in our previous analysis, which could be due to pulsation of the cool component of the AG Dra system.

Confirming and denying in co-construction processes: a case study of an adult with cerebral palsy and two familiar partners.

PubMed

Hörmeyer, Ina; Renner, Gregor

2013-09-01

For individuals with complex communication needs, one of the most frequent communicative strategies is the co-construction of meaning with familiar partners. This preliminary single-case study gives insight into a special sequential pattern of co-construction processes - the search sequence - particularly in relation to the processes of confirming and denying meanings proposed by familiar interaction partners. Five different conversations between an adult with cerebral palsy and complex communication needs and two familiar co-participants were videotaped and analyzed using the methodology of conversation analysis (CA). The study revealed that confirmations and denials are not simply two alternative actions, but that several possibilities to realize confirmations and denials exist that differ in their frequency and that have different consequences for the sequential context. This study of confirmations and denials demonstrates that co-construction processes are more complex than have previously been documented.

Comparative factor analysis models for an empirical study of EEG data, II: A data-guided resolution of the rotation indeterminacy.

PubMed

Rogers, L J; Douglas, R R

1984-02-01

In this paper (the second in a series), we consider a (generic) pair of datasets, which have been analyzed by the techniques of the previous paper. Thus, their "stable subspaces" have been established by comparative factor analysis. The pair of datasets must satisfy two confirmable conditions. The first is the "Inclusion Condition," which requires that the stable subspace of one of the datasets is nearly identical to a subspace of the other dataset's stable subspace. On the basis of that, we have assumed the pair to have similar generating signals, with stochastically independent generators. The second verifiable condition is that the (presumed same) generating signals have distinct ratios of variances for the two datasets. Under these conditions a small elaboration of some elementary linear algebra reduces the rotation problem to several eigenvalue-eigenvector problems. Finally, we emphasize that an analysis of each dataset by the method of Douglas and Rogers (1983) is an essential prerequisite for the useful application of the techniques in this paper. Nonempirical methods of estimating the number of factors simply will not suffice, as confirmed by simulations reported in the previous paper.

Seeing Double Old and New: Observations and Lightcurve Analysis at the Palmer Divide Observatory of Six Binary Asteroids

NASA Astrophysics Data System (ADS)

Warner, Brian D.

2013-04-01

Results of the analysis of lightcurves of six binary asteroids obtained at the Palmer Divide Observatory are reported. Of the six, three were previously known to be binary: 9069 Hovland, (26471) 2000 AS152, and 1994 XD. The remaining three are new confirmed or probable binary discoveries made at PDO: 2047 Smetana, (5646) 1990 TR, and (52316) 1992 BD.

Paragonimus westermani in Malaysian Felidae and Viverridae: probable modes of transmission in relation to host feeding habits.

PubMed

Liat, L B; Betterton, C

1977-01-01

Examination of naturally infected felids and viverrids in Malaysia confirmed previously published records which indicated that P. westermani occurred only in felid cats. Felis planiceps and F. temnickli were reported as new host records. Analysis of stomach contents revealed no crab remains in either family of cats, but confirmed that felids were strictly carnivorous while viverrids were often omnivorous. In feeding experiments, only viverrids ate the host crabs Potomiscus johorensis and Parathelphusa maculata. The probable transmission of P. westermani to felids via paratenic hosts was discussed.

Global-Mode Analysis of Full-Disk Data from the Michelson Doppler Imager and the Helioseismic and Magnetic Imager

NASA Astrophysics Data System (ADS)

Larson, Timothy P.; Schou, Jesper

2018-02-01

Building upon our previous work, in which we analyzed smoothed and subsampled velocity data from the Michelson Doppler Imager (MDI), we extend our analysis to unsmoothed, full-resolution MDI data. We also present results from the Helioseismic and Magnetic Imager (HMI), in both full resolution and processed to be a proxy for the low-resolution MDI data. We find that the systematic errors that we saw previously, namely peaks in both the high-latitude rotation rate and the normalized residuals of odd a-coefficients, are almost entirely absent in the two full-resolution analyses. Furthermore, we find that both systematic errors seem to depend almost entirely on how the input images are apodized, rather than on resolution or smoothing. Using the full-resolution HMI data, we confirm our previous findings regarding the effect of using asymmetric profiles on mode parameters, and also find that they occasionally result in more stable fits. We also confirm our previous findings regarding discrepancies between 360-day and 72-day analyses. We further investigate a six-month period previously seen in f-mode frequency shifts using the low-resolution datasets, this time accounting for solar-cycle dependence using magnetic-field data. Both HMI and MDI saw prominent six-month signals in the frequency shifts, but we were surprised to discover that the strongest signal at that frequency occurred in the mode coverage for the low-resolution proxy. Finally, a comparison of mode parameters from HMI and MDI shows that the frequencies and a-coefficients agree closely, encouraging the concatenation of the two datasets.

The role of molecular genetic analysis in the diagnosis of primary ciliary dyskinesia.

PubMed

Kim, Raymond H; A Hall, David; Cutz, Ernest; Knowles, Michael R; Nelligan, Kathleen A; Nykamp, Keith; Zariwala, Maimoona A; Dell, Sharon D

2014-03-01

Primary ciliary dyskinesia (PCD) is an autosomal recessive genetic disorder of motile cilia. The diagnosis of PCD has previously relied on ciliary analysis with transmission electron microscopy or video microscopy. However, patients with PCD may have normal ultrastructural appearance, and ciliary analysis has limited accessibility. Alternatively, PCD can be diagnosed by demonstrating biallelic mutations in known PCD genes. Genetic testing is emerging as a diagnostic tool to complement ciliary analysis where interpretation and access may delay diagnosis. To determine the diagnostic yield of genetic testing of patients with a confirmed or suspected diagnosis of PCD in a multiethnic urban center. Twenty-eight individuals with confirmed PCD on transmission electron microscopy of ciliary ultrastructure and 24 individuals with a probable diagnosis of PCD based on a classical PCD phenotype and low nasal nitric oxide had molecular analysis of 12 genes associated with PCD. Of 49 subjects who underwent ciliary biopsy, 28 (57%) were diagnosed with PCD through an ultrastructural defect. Of the 52 individuals who underwent molecular genetic analysis, 22 (42%) individuals had two mutations in known PCD genes. Twenty-four previously unreported mutations in known PCD genes were observed. Combining both diagnostic modalities of biopsy and molecular genetics, the diagnostic yield increased to 69% compared with 57% based on biopsy alone. The diagnosis of PCD is challenging and has traditionally relied on ciliary biopsy, which is unreliable as the sole criterion for a definitive diagnosis. Molecular genetic analysis can be used as a complementary test to increase the diagnostic yield.

Newly discovered Wolf-Rayet and weak emission-line central stars of planetary nebulae

NASA Astrophysics Data System (ADS)

DePew, K.; Parker, Q. A.; Miszalski, B.; De Marco, O.; Frew, D. J.; Acker, A.; Kovacevic, A. V.; Sharp, R. G.

2011-07-01

We present the spectra of 32 previously unpublished confirmed and candidate Wolf-Rayet ([WR]) and weak emission-line (WELS) central stars of planetary nebulae (CSPNe). 18 stars have been discovered in the Macquarie/AAO/Strasbourg Hα (MASH) PN survey sample, and we have also uncovered 14 confirmed and candidate [WR]s and WELS among the CSPNe of previously known PNe. Spectral classifications have been undertaken using both Acker & Neiner and Crowther, De Marco & Barlow schemes. 22 members in this sample are identified as probable [WR]s; the remaining 10 appear to be WELS. Observations undertaken as part of the MASH spectroscopic survey have now increased the number of known [WR]s by ˜30 per cent. This will permit a better analysis of [WR] subclass distribution, metallicity effects and evolutionary sequences in these uncommon objects.

Polygenic risk score analysis of pathologically confirmed Alzheimer disease.

PubMed

Escott-Price, Valentina; Myers, Amanda J; Huentelman, Matt; Hardy, John

2017-08-01

Previous estimates of the utility of polygenic risk score analysis for the prediction of Alzheimer disease have given area under the curve (AUC) estimates of <80%. However, these have been based on the genetic analysis of clinical case-control series. Here, we apply the same analytic approaches to a pathological case-control series and show a predictive AUC of 84%. We suggest that this analysis has clinical utility and that there is limited room for further improvement using genetic data. Ann Neurol 2017;82:311-314. © 2017 American Neurological Association.

Structure of native Renilla reniformis luciferin

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

Hori, K.; Charbonneau, H.; Hart, R.C.

1977-10-01

The structure of native luciferin from the bioluminescent coelenterate Renilla reniformis is shown to be 3.7-dihydro-2-(p-hydroxybenzyl)-6-(p-hydroxyphenyl)-8-benzylimidazol(1,2-a)pyrazin-3-one by mass spectral analysis of synthetic luciferin and the luciferin derived from a protein directly involved in the bioluminescent system. A previous report of the molecular weight of luciferin is shown to be incorrect by reexamination of the spectral data and by synthesis of two derivatives. Detailed analysis of kinetic, emission, and quantum yield data for the isolated and synthetic luciferins confirms this structure. Confirmation of this structure in a number of species from different phyla suggests a common substrate for a variety ofmore » bioluminescent marine organisms.« less

Preliminary Experiments with a Triple-Layer Phoswich Detector for Radioxenon Detection

DTIC Science & Technology

2008-09-01

Figure 7b; with a significant attenuation which was predicted by our MCNP modeling (Farsoni et al., 2007). The 81 keV peak in the NaI spectrum has a...analysis technique and confirmed our previous MCNP modeling. Our future work includes use of commercially available radioxenon gas (133Xe) to test

Confirmation and refinement of the heterozygous deletion of the small leucine-rich proteoglycans associated with posterior amorphous corneal dystrophy.

PubMed

Cervantes, Aleck E; Gee, Katherine M; Whiting, Martha F; Frausto, Ricardo F; Aldave, Anthony J

2018-04-19

To present the clinical and cytogenetic features of a previously unreported family with posterior amorphous corneal dystrophy (PACD) associated with a heterozygous deletion of the small leucine-rich proteoglycan (SRLP) genes on chromosome 12. Clinical characterization was performed using slit lamp biomicroscopic and optical coherence tomography (OCT) imaging. Genomic DNA was collected from affected and unaffected family members, and a cytogenomic array was used to identify copy number variations (CNV) present in the PACD locus. Three members of a Guatemalan family presented with clinical characteristics consistent with PACD: bilateral posterior stromal lamellar opacification, decreased corneal curvature, and iridocorneal adhesions. OCT imaging demonstrated decreased corneal thickness and hyperreflectivity of the posterior third of the corneal stroma. CNV analysis confirmed the presumed clinical diagnosis of PACD by revealing a 0.304 Mb heterozygous deletion in the PACD locus on chromosome 12 that included the four SLRP genes (KERA, LUM, DCN, and EPYC) deleted in each of the PACD families in which CNV analysis has been reported. This is the first report of the OCT appearance of PACD and the second confirmation of a heterozygous deletion of chromosome 12q21.33 as the cause of PACD, highlighting the utility of array-based cytogenomics to confirm the suspected clinical diagnosis of PACD. As the smallest previously reported pathogenic deletion was 0.701 Mb, the 0.304-Mb deletion we report is the smallest identified to date and reduces the size of the PACD locus to 0.275 Mb.

Reply to "Comment on `Particle path through a nested Mach-Zehnder interferometer' "

NASA Astrophysics Data System (ADS)

Griffiths, Robert B.

2018-02-01

While much of the technical analysis in the preceding Comment is correct, in the end it confirms the conclusion reached in my previous work [Phys. Rev. A 94, 032115 (2016), 10.1103/PhysRevA.94.032115]: A consistent histories analysis provides no support for the claim of counterfactual quantum communication put forward by Salih et al. [Phys. Rev. Lett. 110, 170502 (2013), 10.1103/PhysRevLett.110.170502].

Determination of the crystalline structure of scale solids from the 16H evaporator gravity drain line to tank 38H

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

Oji, L. N.

2015-10-01

August 2015, scale solids from the 16H Evaporator Gravity Drain Line (GDL) to the Tank 38H were delivered to SRNL for analysis. The desired analytical goal was to identify and confirm the crystalline structure of the scale material and determine if the form of the aluminosilicate mineral was consistent with previous analysis of the scale material from the GDL.

Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins

PubMed Central

Postmus, Iris; Trompet, Stella; Deshmukh, Harshal A.; Barnes, Michael R.; Li, Xiaohui; Warren, Helen R.; Chasman, Daniel I.; Zhou, Kaixin; Arsenault, Benoit J.; Donnelly, Louise A.; Wiggins, Kerri L.; Avery, Christy L.; Griffin, Paula; Feng, QiPing; Taylor, Kent D.; Li, Guo; Evans, Daniel S.; Smith, Albert V.; de Keyser, Catherine E.; Johnson, Andrew D.; de Craen, Anton J. M.; Stott, David J.; Buckley, Brendan M.; Ford, Ian; Westendorp, Rudi G. J.; Eline Slagboom, P.; Sattar, Naveed; Munroe, Patricia B.; Sever, Peter; Poulter, Neil; Stanton, Alice; Shields, Denis C.; O’Brien, Eoin; Shaw-Hawkins, Sue; Ida Chen, Y.-D.; Nickerson, Deborah A.; Smith, Joshua D.; Pierre Dubé, Marie; Matthijs Boekholdt, S.; Kees Hovingh, G.; Kastelein, John J. P.; McKeigue, Paul M.; Betteridge, John; Neil, Andrew; Durrington, Paul N.; Doney, Alex; Carr, Fiona; Morris, Andrew; McCarthy, Mark I.; Groop, Leif; Ahlqvist, Emma; Bis, Joshua C.; Rice, Kenneth; Smith, Nicholas L.; Lumley, Thomas; Whitsel, Eric A.; Stürmer, Til; Boerwinkle, Eric; Ngwa, Julius S.; O’Donnell, Christopher J.; Vasan, Ramachandran S.; Wei, Wei-Qi; Wilke, Russell A.; Liu, Ching-Ti; Sun, Fangui; Guo, Xiuqing; Heckbert, Susan R; Post, Wendy; Sotoodehnia, Nona; Arnold, Alice M.; Stafford, Jeanette M.; Ding, Jingzhong; Herrington, David M.; Kritchevsky, Stephen B.; Eiriksdottir, Gudny; Launer, Leonore J.; Harris, Tamara B.; Chu, Audrey Y.; Giulianini, Franco; MacFadyen, Jean G.; Barratt, Bryan J.; Nyberg, Fredrik; Stricker, Bruno H.; Uitterlinden, André G.; Hofman, Albert; Rivadeneira, Fernando; Emilsson, Valur; Franco, Oscar H.; Ridker, Paul M.; Gudnason, Vilmundur; Liu, Yongmei; Denny, Joshua C.; Ballantyne, Christie M.; Rotter, Jerome I.; Adrienne Cupples, L.; Psaty, Bruce M.; Palmer, Colin N. A.; Tardif, Jean-Claude; Colhoun, Helen M.; Hitman, Graham; Krauss, Ronald M.; Wouter Jukema, J; Caulfield, Mark J.; Donnelly, Peter; Barroso, Ines; Blackwell, Jenefer M.; Bramon, Elvira; Brown, Matthew A.; Casas, Juan P.; Corvin, Aiden; Deloukas, Panos; Duncanson, Audrey; Jankowski, Janusz; Markus, Hugh S.; Mathew, Christopher G.; Palmer, Colin N. A.; Plomin, Robert; Rautanen, Anna; Sawcer, Stephen J.; Trembath, Richard C.; Viswanathan, Ananth C.; Wood, Nicholas W.; Spencer, Chris C. A.; Band, Gavin; Bellenguez, Céline; Freeman, Colin; Hellenthal, Garrett; Giannoulatou, Eleni; Pirinen, Matti; Pearson, Richard; Strange, Amy; Su, Zhan; Vukcevic, Damjan; Donnelly, Peter; Langford, Cordelia; Hunt, Sarah E.; Edkins, Sarah; Gwilliam, Rhian; Blackburn, Hannah; Bumpstead, Suzannah J.; Dronov, Serge; Gillman, Matthew; Gray, Emma; Hammond, Naomi; Jayakumar, Alagurevathi; McCann, Owen T.; Liddle, Jennifer; Potter, Simon C.; Ravindrarajah, Radhi; Ricketts, Michelle; Waller, Matthew; Weston, Paul; Widaa, Sara; Whittaker, Pamela; Barroso, Ines; Deloukas, Panos; Mathew, Christopher G.; Blackwell, Jenefer M.; Brown, Matthew A.; Corvin, Aiden; McCarthy, Mark I.; Spencer, Chris C. A.

2014-01-01

Statins effectively lower LDL cholesterol levels in large studies and the observed interindividual response variability may be partially explained by genetic variation. Here we perform a pharmacogenetic meta-analysis of genome-wide association studies (GWAS) in studies addressing the LDL cholesterol response to statins, including up to 18,596 statin-treated subjects. We validate the most promising signals in a further 22,318 statin recipients and identify two loci, SORT1/CELSR2/PSRC1 and SLCO1B1, not previously identified in GWAS. Moreover, we confirm the previously described associations with APOE and LPA. Our findings advance the understanding of the pharmacogenetic architecture of statin response. PMID:25350695

Spinning-Up: the Case of the Symbiotic X-Ray Binary 3A 1954+319

NASA Technical Reports Server (NTRS)

Fuerst, F.; Marcu, D. M.; Pottschmidt, K.; Grinberg, V.; Wilms, J.; CadolleBel, M.

2011-01-01

We present a timing and spectral analysis of the variable X-ray source 3A 1954+319. Our analysis is mainly based on an outburst serendipitously observed during INTEGRAL Key Program observations of the Cygnus region in 2008 fall and on the Swift/BAT longterm light curve. Previous observations, though sparse, have identified the source to be one of only nine known symbiotic X-ray binaries, i.e., systems composed of an accreting neutron star orbiting in a highly inhomogeneous medium around an M-giant companion. The spectrum of3A 1954+319 above > 20 keV can be best described by a broken power law model. The extremely long pulse period of approx.5.3 hours is clearly visible in the INTEGRAL/ISGRI light curve and confirmed through an epoch folding period search. Furthermore, the light curve allows us to determine a very strong spin up of -2 x 10(exp -4) h/h during the outburst. This spin up is confirmed by the pulse period evolution calculated from Swift/BAT data. The Swift/BAT data also show a long spin-down trend prior to the 2008 outburst, which is confirmed in archival INTEGRAL/ISGRI data. We discuss possible accretion models and geometries allowing for the transfer of such large amounts of angular momentum and investigate the harder spectrum of this outburst compared to previously published results.

Spinning-Up: The Case of the Symbiotic X-Ray Binary 3A 1954+319

NASA Technical Reports Server (NTRS)

Fuerst, F.; Marcu, D. M.; Pottschmidt, K.; Grinberg, V.; Wilms, J.; Bel, M. Cadolle

2010-01-01

We present a timing and spectral analysis of the variable X-ray source 3A 1954+319, Our analysis is mainly based on an outburst serendipitously observed during INTEGRAL Key Program observations of the Cygnus region in 2008 fall and on the Swift/BAT longterm light curve, Previous observations, though sparse, have identified the source to be one of only nine known symbiotic X-ray binaries, i.e., systems composed of an accreting neutron star orbiting in a highly inhomogeneous medium around an M-giant companion. The spectrum of 3A 1954+319 above 20 keY can be best described by a broken power law model. The extremely long pulse period of approx.5.3 hours is clearly visible in the INTEGRAL/ISGRI light curve and confirmed through an epoch folding period search. Furthermore, the light curve allows us to determine a very strong spin up of -2x10(exp 4)h/h during the outburst. This spin up is confirmed by the pulse period evolution calculated from Swift/BAT data. The Swift/BAT data also show a long spin-down trend prior to the 2008 outburst. which is confirmed in archival INTEGRAL/ISGRI data. We discuss possible accretion models and geometries allowing for the transfer of such large amounts of angular momentum and investigate the harder spectrum of this outburst compared to previously published results.

Refined identification of Vibrio bacterial flora from Acanthasther planci based on biochemical profiling and analysis of housekeeping genes.

PubMed

Rivera-Posada, J A; Pratchett, M; Cano-Gomez, A; Arango-Gomez, J D; Owens, L

2011-09-09

We used a polyphasic approach for precise identification of bacterial flora (Vibrionaceae) isolated from crown-of-thorns starfish (COTS) from Lizard Island (Great Barrier Reef, Australia) and Guam (U.S.A., Western Pacific Ocean). Previous 16S rRNA gene phylogenetic analysis was useful to allocate and identify isolates within the Photobacterium, Splendidus and Harveyi clades but failed in the identification of Vibrio harveyi-like isolates. Species of the V harveyi group have almost indistinguishable phenotypes and genotypes, and thus, identification by standard biochemical tests and 16S rRNA gene analysis is commonly inaccurate. Biochemical profiling and sequence analysis of additional topA and mreB housekeeping genes were carried out for definitive identification of 19 bacterial isolates recovered from sick and wild COTS. For 8 isolates, biochemical profiles and topA and mreB gene sequence alignments with the closest relatives (GenBank) confirmed previous 16S rRNA-based identification: V. fortis and Photobacterium eurosenbergii species (from wild COTS), and V natriegens (from diseased COTS). Further phylogenetic analysis based on topA and mreB concatenated sequences served to identify the remaining 11 V harveyi-like isolates: V. owensii and V. rotiferianus (from wild COTS), and V. owensii, V. rotiferianus, and V. harveyi (from diseased COTS). This study further confirms the reliability of topA-mreB gene sequence analysis for identification of these close species, and it reveals a wider distribution range of the potentially pathogenic V. harveyi group.

Linkage analysis of autopsy-confirmed familial Alzheimer disease supports an Alzheimer disease locus in 8q24.

PubMed

Sillén, Anna; Brohede, Jesper; Forsell, Charlotte; Lilius, Lena; Andrade, Jorge; Odeberg, Jacob; Kimura, Toru; Winblad, Bengt; Graff, Caroline

2011-01-01

We have previously reported the results of an extended genome-wide scan of Swedish Alzheimer disease (AD)-affected families; in this paper, we analyzed a subset of these families with autopsy-confirmed AD. We report the fine-mapping, using both microsatellite markers and single-nucleotide polymorphisms (SNPs), in the observed maximum logarithm of the odds (LOD)-2 unit (LOD(max)-2) region under the identified linkage peak, linkage analysis of the fine-mapping data with additionally analyzed pedigrees, and association analysis of SNPs selected from candidate genes in the linked interval. The subset was made on the criterion of at least one autopsy-confirmed AD case per family, resulting in 24 families. Linkage analysis of a family subset having at least one autopsy-confirmed AD case showed a significant nonparametric single-point LOD score of 4.4 in 8q24. Fine-mapping under the linkage peak with 10 microsatellite markers yielded an increase in the multipoint (mpt) LOD score from 2.1 to 3.0. SNP genotyping was performed on 21 selected candidate transcripts of the LOD(max)-2 region. Both family-based association and linkage analysis were performed on extended material from 30 families, resulting in a suggestive linkage at peak marker rs6577853 (mpt LOD score = 2.4). The 8q24 region has been implicated to be involved in AD etiology. Copyright © 2011 S. Karger AG, Basel.

Two X-ray pulsars: 2S 1145-619 and 1E 1145.1-6141. [indentified with imaging proportional counter

NASA Technical Reports Server (NTRS)

Lamb, R. C.; Markert, T. H.; Hartman, R. C.; Thompson, D. J.; Bignami, G. F.

1980-01-01

Observations from the Einstein observatory reveal a previously unreported source, 1e1145.1-6141, within 15 arcmin of 2s1145-619 and of comparable intensity during July 1979. Periodicity analysis of the data shows a 290 + or - 2s period for the 2s source and a 298 + or - 4s period for the lE source, confirming the previous Ariel V report of two periods in this range from this region of the sky.

Repeated attempted homicide by administration of drugs documented by hair analysis.

PubMed

Baillif-Couniou, Valérie; Bartoli, Christophe; Sastre, Caroline; Chèze, Marjorie; Deveaux, Marc; Léonetti, Georges; Pélissier-Alicot, Anne-Laure

2018-02-01

Attempted murder by repeated poisoning is quite rare. The authors describe the case of a 62-year-old man who was admitted to an intensive care unit (ICU) for neurological disturbances complicated by inhalation pneumopathy. He presented a loss of consciousness while his wife was visiting him at the ICU (H0). Forty-eight hours later (H48), police officers apprehended the patient's wife pouring a liquid into his fruit salad at the hospital. Toxicological analyses of a blood sample and the infusion equipment (H0), as well as the fruit salad and its container (H48), confirmed the attempted poisoning with cyamemazine (H0) and hydrochloric acid (H48). In order to evaluate the anteriority of poisonings, hair analysis was requested and the medical records of the 6 previous months were also examined. Two 6-cm brown hair strands were sampled and the victim's medical record was seized in order to determine the treatments he had been given during the previous six months. Segmental hair testing on two 6-cm brown hair was conducted by GC-MS, LC-DAD and LC-MS/MS (0-2/2-4/4-6 cm; pg/mg). Haloperidol (9200/1391/227), amitriptyline (7450/1850/3260), venlafaxine (332/560/260), that had never been part of the victim's treatment were detected, as well as some benzodiazepines (alprazolam, bromazepam, nordazepam); cyamemazine was also detected in all the segments (9960/1610/2367) though only a single dose administration was reported in the medical records. The toxicological analyses performed at H0 and H48 confirmed the homicide attempts in the ICU. In addition, comparison of the results in hair analysis with the medical records confirmed repeated poisoning attempts over the previous six months, and thus explain the origin of the disorders presented by the victim. This case serves to remind us that repeated attempted murder can be difficult to diagnose and that hair analysis can be an effective way to detect such attempts. Copyright © 2018. Published by Elsevier Ltd.

The Effects of Education Quality on Income Growth and Mortality Decline

ERIC Educational Resources Information Center

Jamison, Eliot A.; Jamison, Dean T.; Hanushek, Eric A.

2007-01-01

Previous work shows that higher levels of education quality (as measured by international student achievement tests) increase growth rates of national income. This paper begins by confirming those findings in an analysis involving more countries over more time with additional controls. We then use the panel structure of our data to assess whether…

Pneumonic Plague Transmission, Moramanga, Madagascar, 2015

PubMed Central

Ramasindrazana, Beza; Andrianaivoarimanana, Voahangy; Rakotondramanga, Jean Marius; Birdsell, Dawn N.; Ratsitorahina, Maherisoa

2017-01-01

During a pneumonic plague outbreak in Moramanga, Madagascar, we identified 4 confirmed, 1 presumptive, and 9 suspected plague case-patients. Human-to-human transmission among close contacts was high (reproductive number 1.44) and the case fatality rate was 71%. Phylogenetic analysis showed that the Yersinia pestis isolates belonged to group q3, different from the previous outbreak. PMID:28221119

Pneumonic Plague Transmission, Moramanga, Madagascar, 2015.

PubMed

Ramasindrazana, Beza; Andrianaivoarimanana, Voahangy; Rakotondramanga, Jean Marius; Birdsell, Dawn N; Ratsitorahina, Maherisoa; Rajerison, Minoarisoa

2017-03-01

During a pneumonic plague outbreak in Moramanga, Madagascar, we identified 4 confirmed, 1 presumptive, and 9 suspected plague case-patients. Human-to-human transmission among close contacts was high (reproductive number 1.44) and the case fatality rate was 71%. Phylogenetic analysis showed that the Yersinia pestis isolates belonged to group q3, different from the previous outbreak.

Detailed Spectral Analysis of the 260 ks XMM-Newton Data of 1E 1207.4-5209 and Significance of a 2.1 keV Absorption Feature

NASA Astrophysics Data System (ADS)

Mori, Kaya; Chonko, James C.; Hailey, Charles J.

2005-10-01

We have reanalyzed the 260 ks XMM-Newton observation of 1E 1207.4-5209. There are several significant improvements over previous work. First, a much broader range of physically plausible spectral models was used. Second, we have used a more rigorous statistical analysis. The standard F-distribution was not employed, but rather the exact finite statistics F-distribution was determined by Monte Carlo simulations. This approach was motivated by the recent work of Protassov and coworkers and Freeman and coworkers. They demonstrated that the standard F-distribution is not even asymptotically correct when applied to assess the significance of additional absorption features in a spectrum. With our improved analysis we do not find a third and fourth spectral feature in 1E 1207.4-5209 but only the two broad absorption features previously reported. Two additional statistical tests, one line model dependent and the other line model independent, confirmed our modified F-test analysis. For all physically plausible continuum models in which the weak residuals are strong enough to fit, the residuals occur at the instrument Au M edge. As a sanity check we confirmed that the residuals are consistent in strength and position with the instrument Au M residuals observed in 3C 273.

Photometric, Spectroscopic, and X-ray Analysis of the Cool Algol BD+05 706

NASA Astrophysics Data System (ADS)

Torres, G.; Mader, J.; Marschall, L. A.; Neuhaeuser, R.; Duffy, A. S.

2000-12-01

BD+05 706 is an example of a rare class of a dozen or so interacting binaries called ``cool Algols", in which both components of the system are late-type stars. By contrast, the ``classical Algols" are systems in which the star transfering mass is of late spectral type, but the mass gainer is much hotter. BD+05 706 was shown previously to be eclipsing (Marschall, Torres & Neuhaeuser 1998, BAAS, 30, 835). In this paper we report our complete analysis of BVRI light curves for the system obtained at Gettysburg College Observatory, together with spectroscopy from the Harvard-Smithsonian Center for Astrophysics reported previously (Torres, Neuhaeuser & Wichmann 1998, AJ, 115, 2028), and X-ray observations obtained with the ROSAT satellite. Our light curve analysis indicates the presence of spots, most likely on the more massive, active component (primary), which change from season to season. Our results confirm the semi-detached nature of the system, and combined with the spectroscopy they have allowed us to obtain the most precise absolute masses and radii for any object of this class. Our X-ray light curve for BD+05 706 shows the primary eclipse clearly, but no sign of a secondary eclipse, confirming that the primary is the active star. Strong X-ray flares are also visible.

Intron loss from the NADH dehydrogenase subunit 4 gene of lettuce mitochondrial DNA: evidence for homologous recombination of a cDNA intermediate.

PubMed

Geiss, K T; Abbas, G M; Makaroff, C A

1994-04-01

The mitochondrial gene coding for subunit 4 of the NADH dehydrogenase complex I (nad4) has been isolated and characterized from lettuce, Lactuca sativa. Analysis of nad4 genes in a number of plants by Southern hybridization had previously suggested that the intron content varied between species. Characterization of the lettuce gene confirms this observation. Lettuce nad4 contains two exons and one group IIA intron, whereas previously sequenced nad4 genes from turnip and wheat contain three group IIA introns. Northern analysis identified a transcript of 1600 nucleotides, which represents the mature nad4 mRNA and a primary transcript of 3200 nucleotides. Sequence analysis of lettuce and turnip nad4 cDNAs was used to confirm the intron/exon border sequences and to examine RNA editing patterns. Editing is observed at the 5' and 3' ends of the lettuce transcript, but is absent from sequences that correspond to exons two, three and the 5' end of exon four in turnip and wheat. In contrast, turnip transcripts are highly edited in this region, suggesting that homologous recombination of an edited and spliced cDNA intermediate was involved in the loss of introns two and three from an ancestral lettuce nad4 gene.

Student failures on first-year medical basic science courses and the USMLE step 1: a retrospective study over a 20-year period.

PubMed

Burns, E Robert; Garrett, Judy

2015-01-01

Correlates of achievement in the basic science years in medical school and on the Step 1 of the United States Medical Licensing Examination® (USMLE®), (Step 1) in relation to preadmission variables have been the subject of considerable study. Preadmissions variables such as the undergraduate grade point average (uGPA) and Medical College Admission Test® (MCAT®) scores, solely or in combination, have previously been found to be predictors of achievement in the basic science years and/or on the Step 1. The purposes of this retrospective study were to: (1) determine if our statistical analysis confirmed previously published relationships between preadmission variables (MCAT, uGPA, and applicant pool size), and (2) study correlates of the number of failures in five M1 courses with those preadmission variables and failures on Step 1. Statistical analysis confirmed previously published relationships between all preadmission variables. Only one course, Microscopic Anatomy, demonstrated significant correlations with all variables studied including the Step 1 failures. Physiology correlated with three of the four variables studied, but not with the Step 1 failures. Analyses such as these provide a tool by which administrators will be able to identify what courses are or are not responding in appropriate ways to changes in the preadmissions variables that signal student performance on the Step 1. © 2014 American Association of Anatomists.

Breast and ovarian cancer risks to carriers of the BRCA1 5382insC and 185delAG and BRCA2 6174delT mutations: a combined analysis of 22 population based studies

PubMed Central

Antoniou, A; Pharoah, P; Narod, S; Risch, H; Eyfjord, J; Hopper, J; Olsson, H; Johannsson, O; Borg, A; Pasini, B; Radice, P; Manoukian, S; Eccles, D; Tang, N; Olah, E; Anton-Culver, H; Warner, E; Lubinski, J; Gronwald, J; Gorski, B; Tulinius, H; Thorlacius, S; Eerola, H; Nevanlinna, H; Syrjakoski, K; Kallioniemi, O; Thompson, D; Evans, C; Peto, J; Lalloo, F; Evans, D; Easton, D

2005-01-01

A recent report estimated the breast cancer risks in carriers of the three Ashkenazi founder mutations to be higher than previously published estimates derived from population based studies. In an attempt to confirm this, the breast and ovarian cancer risks associated with the three Ashkenazi founder mutations were estimated using families included in a previous meta-analysis of populatrion based studies. The estimated breast cancer risks for each of the founder BRCA1 and BRCA2 mutations were similar to the corresponding estimates based on all BRCA1 or BRCA2 mutations in the meta-analysis. These estimates appear to be consistent with the observed prevalence of the mutations in the Ashkenazi Jewish population. PMID:15994883

Isolation of Lagos bat virus from water mongoose.

PubMed

Markotter, Wanda; Kuzmin, Ivan; Rupprecht, Charles E; Randles, Jenny; Sabeta, Claude T; Wandeler, Alexander I; Nel, Louis H

2006-12-01

A genotype 2 lyssavirus, Lagos bat virus (LBV), was isolated from a terrestrial wildlife species (water mongoose) in August 2004 in the Durban area of the KwaZulu-Natal Province of South Africa. The virus isolate was confirmed as LBV by antigenic and genetic characterization, and the mongoose was identified as Atilax paludinosus by mitochondrial cytochrome b sequence analysis. Phylogenetic analysis demonstrated sequence homology with previous LBV isolates from South African bats. Studies performed in mice indicated that the peripheral pathogenicity of LBV had been underestimated in previous studies. Surveillance strategies for LBV in Africa must be improved to better understand the epidemiology of this virus and to make informed decisions on future vaccine strategies because evidence is insufficent that current rabies vaccines provide protection against LBV.

[Incidence and surgical wound infection risk factors in breast cancer surgery].

PubMed

Lefebvre, D; Penel, N; Deberles, M F; Fournier, C

2000-11-18

In order to evaluate occurrence and risk factors for wound infection (WI) in breast cancer surgery, we carried out a prospective study. From September 1996 through April 1997, an infection control physician prospectively evaluated 542 wounds of all patients having breast cancer surgery at the Oscar Lambret Cancer Center. WI was defined as a wound with pus. Antibiotic prophylaxis was given in case of immediate breast reconstruction. Statistical evaluation was performed using the c < or = test for categorial data and non-parametric Mann-Whitney test for continuous data. In univariate analysis, differences were considered significant at p < 0.01. The overall WI rate was 3.51% (19/352). In univariate analysis, risk factors for WI were: total preoperative hospital stay (p = 0.01), previous chemotherapy (p = 0.01), previous oncologic surgery (p = 0.03) and immediate breast reconstruction (p = 0.002). In mutivariate analysis, we observed two independent predictive factors for WI: previous chemotherapy (p = 0.05) and immediate breast reconstruction (p = 0.02). Previous anticancer chemotherapy was a major risk factor. In these cases, a phase III trial could confirm efficacy of standard antibiotic prophylaxis. Breast reconstruction was the second major risk factor. Standard antibiotic prophylaxis (used in our study) was insufficient.

Characterization of the Bacterial Diversity in Indo-West Pacific Loliginid and Sepiolid Squid Light Organs

PubMed Central

Guerrero-Ferreira, Ricardo; Gorman, Clayton; Chavez, Alba A.; Willie, Shantell

2013-01-01

Loliginid and sepiolid squid light organs are known to host a variety of bacterial species from the family Vibrionaceae, yet little is known about the species diversity and characteristics among different host squids. Here we present a broad-ranging molecular and physiological analysis of the bacteria colonizing light organs in loliginid and sepiolid squids from various field locations of the Indo-West Pacific (Australia and Thailand). Our PCR-RFLP analysis, physiological characterization, carbon utilization profiling, and electron microscopy data indicate that loliginid squid in the Indo-West Pacific carry a consortium of bacterial species from the families Vibrionaceae and Photobacteriaceae. This research also confirms our previous report of the presence of Vibrio harveyi as a member of the bacterial population colonizing light organs in loliginid squid. pyrH sequence data were used to confirm isolate identity, and indicates that Vibrio and Photobacterium comprise most of the light organ colonizers of squids from Australia, confirming previous reports for Australian loliginid and sepiolid squids. In addition, combined phylogenetic analysis of PCR-RFLP and 16S rDNA data from Australian and Thai isolates associated both Photobacterium and Vibrio clades with both loliginid and sepiolid strains, providing support that geographical origin does not correlate with their relatedness. These results indicate that both loliginid and sepiolid squids demonstrate symbiont specificity (Vibrionaceae), but their distribution is more likely due to environmental factors that are present during the infection process. This study adds significantly to the growing evidence for complex and dynamic associations in nature and highlights the importance of exploring symbiotic relationships in which non-virulent strains of pathogenic Vibrio species could establish associations with marine invertebrates. PMID:22885637

Analysis by plaque reduction neutralization assay of intertypic rotaviruses suggests that gene reassortment occurs in vivo.

PubMed Central

Hoshino, Y; Sereno, M M; Midthun, K; Flores, J; Chanock, R M; Kapikian, A Z

1987-01-01

The SB-1A rotavirus recovered from a diarrheic piglet in the United States is a naturally occurring intertypic rotavirus. When studied by reciprocal neutralization tests, the SB-1A virus was similar, if not identical, to the porcine Gottfried virus (serotype 4) and the porcine OSU virus (serotype 5). Analysis of reassortant viruses prepared from the SB-1A virus and the serotype 2 human DS-1 virus revealed that the antigenic specificity of the outer capsid protein VP3 of SB-1A was shared with the OSU virus, while the antigenic specificity of another outer capsid protein, VP7, of SB-1A appeared to be shared with the Gottfried virus. This suggests that SB-1A is a naturally occurring reassortant rotavirus between OSU-like and Gottfried-like porcine rotaviruses. In addition, using a genetic approach, we found evidence that the fourth gene was responsible for the predominantly one-way cross-neutralizing reactivity between canine rotavirus strain CU-1 (serotype 3) and porcine rotavirus strains SB-1A (serotypes 4 and 5) and OSU (serotype 5). Assignment of hemagglutination function to the fourth genome segment of porcine rotaviruses SB-1A and OSU and canine rotavirus CU-1 confirmed a similar previous gene assignment established for certain rotaviruses. Analysis of single gene 4 substitution reassortants confirmed our previous finding that VP3 was as potent in stimulating neutralizing antibodies as VP7. The observations confirm the need for a binary system of rotavirus classification and nomenclature similar to that used for the influenza A viruses; in such a system the neutralization specificity of both VP3 and VP7 would be indicated. Images PMID:2434522

Identification of Clinical Isolates of Actinomyces Species by Amplified 16S Ribosomal DNA Restriction Analysis

PubMed Central

Hall, Val; Talbot, P. R.; Stubbs, S. L.; Duerden, B. I.

2001-01-01

Amplified 16S ribosomal DNA (rDNA) restriction analysis (ARDRA), using enzymes HaeIII and HpaII, was applied to 176 fresh and 299 stored clinical isolates of putative Actinomyces spp. referred to the Anaerobe Reference Unit of the Public Health Laboratory Service for confirmation of identity. Results were compared with ARDRA results obtained previously for reference strains and with conventional phenotypic reactions. Identities of some strains were confirmed by analysis of partial 16S rDNA sequences. Of the 475 isolates, 331 (70%) were clearly assigned to recognized Actinomyces species, including 94 isolates assigned to six recently described species. A further 52 isolates in 12 ARDRA profiles were designated as apparently resembling recognized species, and 44 isolates, in 18 novel profiles, were confirmed as members of genera other than Actinomyces. The identities of 48 isolates in nine profiles remain uncertain, and they may represent novel species of Actinomyces. For the majority of species, phenotypic results, published reactions for the species, and ARDRA profiles concurred. However, of 113 stored isolates originally identified as A. meyeri or resembling A. meyeri by phenotypic tests, only 21 were confirmed as A. meyeri by ARDRA; 63 were reassigned as A. turicensis, 7 as other recognized species, and 22 as unidentified actinomycetes. Analyses of incidence and clinical associations of Actinomyces spp. add to the currently sparse knowledge of some recently described species. PMID:11574572

The complete genome sequence of a virus associated with cotton blue disease, cotton leafroll dwarf virus, confirms that it is a new member of the genus Polerovirus.

PubMed

Distéfano, Ana J; Bonacic Kresic, Ivan; Hopp, H Esteban

2010-11-01

Cotton blue disease is the most important virus disease of cotton in the southern part of America. The complete nucleotide sequence of the ssRNA genome of the cotton blue disease-associated virus was determined for the first time. It comprised 5,866 nucleotides, and the deduced genomic organization resembled that of members of the genus Polerovirus. Sequence homology comparison and phylogenetic analysis confirm that this virus (previous proposed name cotton leafroll dwarf virus) is a member of a new species within the genus Polerovirus.

Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila melanogaster.

PubMed

Cridland, Julie M; Thornton, Kevin R

2010-01-13

Several recent studies have focused on the evolution of recently duplicated genes in Drosophila. Currently, however, little is known about the evolutionary forces acting upon duplications that are segregating in natural populations. We used a high-throughput, paired-end sequencing platform (Illumina) to identify structural variants in a population sample of African D. melanogaster. Polymerase chain reaction and sequencing confirmation of duplications detected by multiple, independent paired-ends showed that paired-end sequencing reliably uncovered the break points of structural rearrangements and allowed us to identify a number of tandem duplications segregating within a natural population. Our confirmation experiments show that rates of confirmation are very high, even at modest coverage. Our results also compare well with previous studies using microarrays (Emerson J, Cardoso-Moreira M, Borevitz JO, Long M. 2008. Natural selection shapes genome wide patterns of copy-number polymorphism in Drosophila melanogaster. Science. 320:1629-1631. and Dopman EB, Hartl DL. 2007. A portrait of copy-number polymorphism in Drosophila melanogaster. Proc Natl Acad Sci U S A. 104:19920-19925.), which both gives us confidence in the results of this study as well as confirms previous microarray results.We were also able to identify whole-gene duplications, such as a novel duplication of Or22a, an olfactory receptor, and identify copy-number differences in genes previously known to be under positive selection, like Cyp6g1, which confers resistance to dichlorodiphenyltrichloroethane. Several "hot spots" of duplications were detected in this study, which indicate that particular regions of the genome may be more prone to generating duplications. Finally, population frequency analysis of confirmed events also showed an excess of rare variants in our population, which indicates that duplications segregating in the population may be deleterious and ultimately destined to be lost from the population.

Multiple loci on 8q24 associated with prostate cancer susceptibility.

PubMed

Al Olama, Ali Amin; Kote-Jarai, Zsofia; Giles, Graham G; Guy, Michelle; Morrison, Jonathan; Severi, Gianluca; Leongamornlert, Daniel A; Tymrakiewicz, Malgorzata; Jhavar, Sameer; Saunders, Ed; Hopper, John L; Southey, Melissa C; Muir, Kenneth R; English, Dallas R; Dearnaley, David P; Ardern-Jones, Audrey T; Hall, Amanda L; O'Brien, Lynne T; Wilkinson, Rosemary A; Sawyer, Emma; Lophatananon, Artitaya; Horwich, Alan; Huddart, Robert A; Khoo, Vincent S; Parker, Christopher C; Woodhouse, Christopher J; Thompson, Alan; Christmas, Tim; Ogden, Chris; Cooper, Colin; Donovan, Jenny L; Hamdy, Freddie C; Neal, David E; Eeles, Rosalind A; Easton, Douglas F

2009-10-01

Previous studies have identified multiple loci on 8q24 associated with prostate cancer risk. We performed a comprehensive analysis of SNP associations across 8q24 by genotyping tag SNPs in 5,504 prostate cancer cases and 5,834 controls. We confirmed associations at three previously reported loci and identified additional loci in two other linkage disequilibrium blocks (rs1006908: per-allele OR = 0.87, P = 7.9 x 10(-8); rs620861: OR = 0.90, P = 4.8 x 10(-8)). Eight SNPs in five linkage disequilibrium blocks were independently associated with prostate cancer susceptibility.

A confirmative clinimetric analysis of the 36-item Family Assessment Device.

PubMed

Timmerby, Nina; Cosci, Fiammetta; Watson, Maggie; Csillag, Claudio; Schmitt, Florence; Steck, Barbara; Bech, Per; Thastum, Mikael

2018-02-07

The Family Assessment Device (FAD) is a 60-item questionnaire widely used to evaluate self-reported family functioning. However, the factor structure as well as the number of items has been questioned. A shorter and more user-friendly version of the original FAD-scale, the 36-item FAD, has therefore previously been proposed, based on findings in a nonclinical population of adults. We aimed in this study to evaluate the brief 36-item version of the FAD in a clinical population. Data from a European multinational study, examining factors associated with levels of family functioning in adult cancer patients' families, were used. Both healthy and ill parents completed the 60-item version FAD. The psychometric analyses conducted were Principal Component Analysis and Mokken-analysis. A total of 564 participants were included. Based on the psychometric analysis we confirmed that the 36-item version of the FAD has robust psychometric properties and can be used in clinical populations. The present analysis confirmed that the 36-item version of the FAD (18 items assessing 'well-being' and 18 items assessing 'dysfunctional' family function) is a brief scale where the summed total score is a valid measure of the dimensions of family functioning. This shorter version of the FAD is, in accordance with the concept of 'measurement-based care', an easy to use scale that could be considered when the aim is to evaluate self-reported family functioning.

The gene for autosomal dominant cerebellar ataxia type II is located in a 5-cM region in 3p12-p13: genetic and physical mapping of the SCA7 locus.

PubMed

David, G; Giunti, P; Abbas, N; Coullin, P; Stevanin, G; Horta, W; Gemmill, R; Weissenbach, J; Wood, N; Cunha, S; Drabkin, H; Harding, A E; Agid, Y; Brice, A

1996-12-01

Two families with autosomal dominant cerebellar ataxia with pigmentary macular dystrophy (ADCA type II) were investigated. Analysis of 23 parent-child couples demonstrated the existence of marked anticipation, greater in paternal than in maternal transmissions, with earlier age at onset and a more rapid clinical course in successive generations. Clinical analysis revealed the presence of a great variability in age at onset, initial symptom, and associated signs, confirming the characteristic clinical heterogeneity of ADCA type II. The gene for ADCA type II previously was mapped to the spinocerebellar ataxia 7 (SCA7) locus on chromosome 3p12-p21.1. Linkage analysis of the two new families of different geographic origin confirmed the characteristic genetic homogeneity of ADCA type II, distinguishing it from ADCA type I. Haplotype analysis permitted refinement of the SCA7 region to the 5-cM interval between markers D3S1312 and D3S1600 on chromosome 3p12-p13. Eighteen sequence-tagged sites were used for the construction of an integrated map of the candidate region, based on a YACs contig. The entire candidate region is contained in a single nonchimeric YAC of 660 kb. The probable involvement of a CAG trinucleotide expansion, suggested by previous studies, should greatly facilitate the identification of the gene for ADCA type II.

The gene for autosomal dominant cerebellar ataxia type II is located in a 5-cM region in 3p12-p13: genetic and physical mapping of the SCA7 locus.

PubMed Central

David, G.; Giunti, P.; Abbas, N.; Coullin, P.; Stevanin, G.; Horta, W.; Gemmill, R.; Weissenbach, J.; Wood, N.; Cunha, S.; Drabkin, H.; Harding, A. E.; Agid, Y.; Brice, A.

1996-01-01

Two families with autosomal dominant cerebellar ataxia with pigmentary macular dystrophy (ADCA type II) were investigated. Analysis of 23 parent-child couples demonstrated the existence of marked anticipation, greater in paternal than in maternal transmissions, with earlier age at onset and a more rapid clinical course in successive generations. Clinical analysis revealed the presence of a great variability in age at onset, initial symptom, and associated signs, confirming the characteristic clinical heterogeneity of ADCA type II. The gene for ADCA type II previously was mapped to the spinocerebellar ataxia 7 (SCA7) locus on chromosome 3p12-p21.1. Linkage analysis of the two new families of different geographic origin confirmed the characteristic genetic homogeneity of ADCA type II, distinguishing it from ADCA type I. Haplotype analysis permitted refinement of the SCA7 region to the 5-cM interval between markers D3S1312 and D3S1600 on chromosome 3p12-p13. Eighteen sequence-tagged sites were used for the construction of an integrated map of the candidate region, based on a YACs contig. The entire candidate region is contained in a single nonchimeric YAC of 660 kb. The probable involvement of a CAG trinucleotide expansion, suggested by previous studies, should greatly facilitate the identification of the gene for ADCA type II. PMID:8940279

Rhythmic patterning in Malaysian and Singapore English.

PubMed

Tan, Rachel Siew Kuang; Low, Ee-Ling

2014-06-01

Previous work on the rhythm of Malaysian English has been based on impressionistic observations. This paper utilizes acoustic analysis to measure the rhythmic patterns of Malaysian English. Recordings of the read speech and spontaneous speech of 10 Malaysian English speakers were analyzed and compared with recordings of an equivalent sample of Singaporean English speakers. Analysis was done using two rhythmic indexes, the PVI and VarcoV. It was found that although the rhythm of read speech of the Singaporean speakers was syllable-based as described by previous studies, the rhythm of the Malaysian speakers was even more syllable-based. Analysis of the syllables in specific utterances showed that Malaysian speakers did not reduce vowels as much as Singaporean speakers in cases of syllables in utterances. Results of the spontaneous speech confirmed the findings for the read speech; that is, the same rhythmic patterning was found which normally triggers vowel reductions.

Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins.

PubMed

Macaulay, Iain C; Tijssen, Marloes R; Thijssen-Timmer, Daphne C; Gusnanto, Arief; Steward, Michael; Burns, Philippa; Langford, Cordelia F; Ellis, Peter D; Dudbridge, Frank; Zwaginga, Jaap-Jan; Watkins, Nicholas A; van der Schoot, C Ellen; Ouwehand, Willem H

2007-04-15

To identify previously unknown platelet receptors we compared the transcriptomes of in vitro differentiated megakaryocytes (MKs) and erythroblasts (EBs). RNA was obtained from purified, biologically paired MK and EB cultures and compared using cDNA microarrays. Bioinformatical analysis of MK-up-regulated genes identified 151 transcripts encoding transmembrane domain-containing proteins. Although many of these were known platelet genes, a number of previously unidentified or poorly characterized transcripts were also detected. Many of these transcripts, including G6b, G6f, LRRC32, LAT2, and the G protein-coupled receptor SUCNR1, encode proteins with structural features or functions that suggest they may be involved in the modulation of platelet function. Immunoblotting on platelets confirmed the presence of the encoded proteins, and flow cytometric analysis confirmed the expression of G6b, G6f, and LRRC32 on the surface of platelets. Through comparative analysis of expression in platelets and other blood cells we demonstrated that G6b, G6f, and LRRC32 are restricted to the platelet lineage, whereas LAT2 and SUCNR1 were also detected in other blood cells. The identification of the succinate receptor SUCNR1 in platelets is of particular interest, because physiologically relevant concentrations of succinate were shown to potentiate the effect of low doses of a variety of platelet agonists.

Isolation of Lagos Bat Virus from Water Mongoose

PubMed Central

Markotter, Wanda; Kuzmin, Ivan; Rupprecht, Charles E.; Randles, Jenny; Sabeta, Claude T.; Wandeler, Alexander I.

2006-01-01

A genotype 2 lyssavirus, Lagos bat virus (LBV), was isolated from a terrestrial wildlife species (water mongoose) in August 2004 in the Durban area of the KwaZulu-Natal Province of South Africa. The virus isolate was confirmed as LBV by antigenic and genetic characterization, and the mongoose was identified as Atilax paludinosus by mitochondrial cytochrome b sequence analysis. Phylogenetic analysis demonstrated sequence homology with previous LBV isolates from South African bats. Studies performed in mice indicated that the peripheral pathogenicity of LBV had been underestimated in previous studies. Surveillance strategies for LBV in Africa must be improved to better understand the epidemiology of this virus and to make informed decisions on future vaccine strategies because evidence is insufficent that current rabies vaccines provide protection against LBV. PMID:17326944

Once-Daily Amikacin Dosing in Burn Patients Treated with Continuous Venovenous Hemofiltration

DTIC Science & Technology

2011-10-01

previously documented inaccuracies with the Vitek 2 instrument (1), all Acinetobacter baumannii isolates reported as susceptible to amikacin were confirmed...to the analysis. Bacteriology. Amikacin MICs were determined for Gram-negative blood- stream isolates using the Vitek 2 instrument (bioMérieux...al. 2010. Aminoglycoside resistance and susceptibility testing errors in Acinetobacter baumannii-calcoaceticus complex. J. Clin. Microbiol. 48:1132

High symmetry effects on hydrogen bond rearrangement: The 4.1 THz vibrational band of (D2O)4

NASA Astrophysics Data System (ADS)

Brown, Mac G.; Keutsch, Frank N.; Braly, Linda B.; Saykally, Richard J.

1999-11-01

Vibration-rotation-tunneling (VRT) spectroscopy has been extended to the 4 THz spectral region through the observation of a second intermolecular vibration of (D2O)4. Analysis of the precisely measured perpendicular transition confirms the previously reported cyclic homodromic structure and reveals a dramatically increased (30×) hydrogen bond rearrangement rate in the excited state.

RAD-Seq analysis of typical and minor Citrus accessions, including Bhutanese varieties

PubMed Central

Penjor, Tshering; Mimura, Takashi; Kotoda, Nobuhiro; Matsumoto, Ryoji; Nagano, Atsushi J.; Honjo, Mie N.; Kudoh, Hiroshi; Yamamoto, Masashi; Nagano, Yukio

2016-01-01

We analyzed the reduced-representation genome sequences of Citrus species by double-digest restriction site-associated DNA sequencing (ddRAD-Seq) using 44 accessions, including typical and minor accessions, such as Bhutanese varieties. The results of this analysis using typical accessions were consistent with previous reports that citron, papeda, pummelo, and mandarin are ancestral species, and that most Citrus species are derivatives or hybrids of these four species. Citrus varieties often reproduce asexually and heterozygosity is highly conserved within each variety. Because this approach could readily detect conservation of heterozygosity, it was able to discriminate citrus varieties such as satsuma mandarin from closely related species. Thus, this method provides an inexpensive way to protect citrus varieties from unintended introduction and to prevent the provision of incorrect nursery stocks to customers. One Citrus variety in Bhutan was morphologically similar to Mexican lime and was designated as Himalayan lime. The current analysis confirmed the previous proposition that Mexican lime is a hybrid between papeda and citron, and also suggested that Himalayan lime is a probable hybrid between mandarin and citron. In addition to Himalayan lime, current analysis suggested that several accessions were formed by previously undescribed combinations. PMID:28163596

Statistical results from 10 years of Cassini Langmuir probe plasma measurements

NASA Astrophysics Data System (ADS)

Holmberg, M.; Shebanits, O.; Wahlund, J. E.; Morooka, M.; Andre, N.

2016-12-01

We use a new analysis method to obtain 10 years of Cassini RPWS Langmuir probe (LP) measurements to study the structure and dynamics of the inner plasma disk of Saturn. The LP plasma density measurements show good agreement with electron densities derived from the RPWS electric field power spectra and confirms and/or improves a number of previous findings about the structure of the plasma disk. E.g., the Enceladus plume is detected as a localised density maximum at the orbit of Enceladus, but the peak density of the inner plasma disk, excluding Enceladus plume passages, is located closer to 4.7 Rs. No density peaks are recorded at the orbits of the moons Mimas, Tethys, Dione, and Rhea. We confirm the previously detected plasma density dayside/nightside asymmetry, which is likely due to a particle drift in the dusk to dawn direction. Presented is also the LP result on the seasonal dependence of the plasma disk within Enceladus' orbit.

Independent Confirmation of the Pioneer 10 Anomalous Acceleration

NASA Technical Reports Server (NTRS)

Markwardt, Craig B.

2002-01-01

I perform an independent analysis of radio Doppler tracking data from the Pioneer 10 spacecraft for the time period 1987-1994. All of the tracking data were taken from public archive sources, and the analysis tools were developed independently by myself. I confirm that an apparent anomalous acceleration is acting on the Pioneer 10 spacecraft, which is not accounted for by present physical models of spacecraft navigation. My best fit value for the acceleration, including corrections for systematic biases and uncertainties, is (8.60 plus or minus 1.34) x 10(exp -8) centimeters per second, directed towards the Sun. This value compares favorably to previous results. I examine the robustness of my result to various perturbations of the analysis method, and find agreement to within plus or minus 5%. The anomalous acceleration is reasonably constant with time, with a characteristic variation time scale of greater than 70 yr. Such a variation timescale is still too short to rule out on-board thermal radiation effects, based on this particular Pioneer 10 data set.

Bem Sex Role Inventory Validation in the International Mobility in Aging Study.

PubMed

Ahmed, Tamer; Vafaei, Afshin; Belanger, Emmanuelle; Phillips, Susan P; Zunzunegui, Maria-Victoria

2016-09-01

This study investigated the measurement structure of the Bem Sex Role Inventory (BSRI) with different factor analysis methods. Most previous studies on validity applied exploratory factor analysis (EFA) to examine the BSRI. We aimed to assess the psychometric properties and construct validity of the 12-item short-form BSRI in a sample administered to 1,995 older adults from wave 1 of the International Mobility in Aging Study (IMIAS). We used Cronbach's alpha to assess internal consistency reliability and confirmatory factor analysis (CFA) to assess psychometric properties. EFA revealed a three-factor model, further confirmed by CFA and compared with the original two-factor structure model. Results revealed that a two-factor solution (instrumentality-expressiveness) has satisfactory construct validity and superior fit to data compared to the three-factor solution. The two-factor solution confirms expected gender differences in older adults. The 12-item BSRI provides a brief, psychometrically sound, and reliable instrument in international samples of older adults.

Effect of Previous Abdominal Surgery on Laparoscopic Liver Resection: Analysis of Feasibility and Risk Factors for Conversion.

PubMed

Cipriani, Federica; Ratti, Francesca; Fiorentini, Guido; Catena, Marco; Paganelli, Michele; Aldrighetti, Luca

2018-03-28

Previous abdominal surgery has traditionally been considered an additional element of difficulty to later laparoscopic procedures. The aim of the study is to analyze the effect of previous surgery on the feasibility and safety of laparoscopic liver resection (LLR), and its role as a risk factor for conversion. After matching, 349 LLR in patients known for previous abdominal surgery (PS group) were compared with 349 LLR on patients with a virgin abdomen (NPS group). Subgroup analysis included 161 patients with previous upper abdominal surgery (UPS subgroup). Feasibility and safety were evaluated in terms of conversion rate, reasons for conversion and outcomes, and risk factors for conversion assessed via uni/multivariable analysis. Conversion rate was 9.4%, and higher for PS patients compared with NPS patients (13.7% versus 5.1%, P = .021). Difficult adhesiolysis resulted the commonest reason for conversion in PS group (5.7%). However, operative time (P = .840), blood loss (P = .270), transfusion (P = .650), morbidity rate (P = .578), hospital stay (P = .780), and R1 rate (P = .130) were comparable between PS and NPS group. Subgroup analysis confirmed higher conversion rates for UPS patients (23%) compared with both NPS (P = .015) and PS patients (P = .041). Previous surgery emerged as independent risk factor for conversion (P = .033), alongside the postero-superior location and major hepatectomy. LLR are feasible in case of previous surgery and proved to be safe and maintain the benefits of LLR carried out in standard settings. However, a history of surgery should be considered a risk factor for conversion.

Effects of previous episodes of influenza and vaccination in preventing laboratory-confirmed influenza in Navarre, Spain, 2013/14 season.

PubMed

Castilla, Jesús; Navascués, Ana; Fernández-Alonso, Mirian; Reina, Gabriel; Albéniz, Esther; Pozo, Francisco; Álvarez, Nerea; Martínez-Baz, Iván; Guevara, Marcela; García-Cenoz, Manuel; Irisarri, Fátima; Casado, Itziar; Ezpeleta, Carmen

2016-06-02

We estimated whether previous episodes of influenza and trivalent influenza vaccination prevented laboratory-confirmed influenza in Navarre, Spain, in season 2013/14. Patients with medically-attended influenza-like illness (MA-ILI) in hospitals (n = 645) and primary healthcare (n = 525) were included. We compared 589 influenza cases and 581 negative controls. MA-ILI related to a specific virus subtype in the previous five seasons was defined as a laboratory-confirmed influenza infection with the same virus subtype or MA-ILI during weeks when more than 25% of swabs were positive for this subtype. Persons with previous MA-ILI had 30% (95% confidence interval (CI): -7 to 54) lower risk of MA-ILI, and those with previous MA-ILI related to A(H1N1)pdm09 or A(H3N2) virus, had a, respectively, 63% (95% CI: 16-84) and 65% (95% CI: 13-86) lower risk of new laboratory-confirmed influenza by the same subtype. Overall adjusted vaccine effectiveness in preventing laboratory-confirmed influenza was 31% (95% CI: 5-50): 45% (95% CI: 12-65) for A(H1N1)pdm09 and 20% (95% CI: -16 to 44) for A(H3N2). While a previous influenza episode induced high protection only against the same virus subtype, influenza vaccination provided low to moderate protection against all circulating subtypes. Influenza vaccine remains the main preventive option for high-risk populations.

Social comparison and perceived breach of psychological contract: their effects on burnout in a multigroup analysis.

PubMed

Cantisano, Gabriela Topa; Domínguez, J Francisco Morales; García, J Luis Caeiro

2007-05-01

This study focuses on the mediator role of social comparison in the relationship between perceived breach of psychological contract and burnout. A previous model showing the hypothesized effects of perceived breach on burnout, both direct and mediated, is proposed. The final model reached an optimal fit to the data and was confirmed through multigroup analysis using a sample of Spanish teachers (N = 401) belonging to preprimary, primary, and secondary schools. Multigroup analyses showed that the model fit all groups adequately.

Expression Analysis of Previously Verified Fecal and Plasma Dow-regulated MicroRNAs (miR-4478, 1295-3p, 142-3p and 26a-5p), in FFPE Tissue Samples of CRC Patients.

PubMed

Ghanbari, Reza; Rezasoltani, Sama; Hashemi, Javad; Mohamadkhani, Ashraf; Tahmasebifar, Arash; Arefian, Ehsan; Mobarra, Naser; Asadi, Jahanbakhsh; Nazemalhosseini Mojarad, Ehsan; Yazdani, Yaghoub; Knuutila, Sakari; Malekzadeh, Reza

2017-02-01

Colorectal cancer (CRC) is one of the most common causes of cancer-related mortality worldwide. Early diagnosis of this neoplasm is critical and may reduce patients' mortality. MicroRNAs are small non-coding RNA molecules whose expression pattern can be altered in various diseases such as CRC. In this study, we evaluated the expression levels of miR-142-3p, miR-26a-5p (their reduced expression in plasma samples of CRC patients was previously confirmed), miR-4478 and miR-1295-3p (their reduced expression in stool samples of CRC patients was previously confirmed) in tissue samples of CRC patients in comparison to healthy subjects. To achieve this purpose, total RNA including small RNA was extracted from 53 CRC and 35 normal subjects' Formalin-fixed, Paraffin-embedded (FFPE) tissue samples using the miRNeasy FFPE Mini Kit. The expression levels of these four selected miRNAs were measured using quantitative Reverse Transcriptase Polymerase Chain Reaction (qRT-PCR). We found that the expression levels of miR-4478 and miR-1295b-3p (two previously down-regulated fecal miRNAs) were significantly decreased in FFPE samples of CRC patients compared to healthy controls. On the other hand, no significant differences were seen in expression levels of miR-142-3p and miR-26a-5p (two previously down-regulated circulating miRNAs) in FFPE samples between these two groups. Regarding current findings, it may be concluded that to diagnose CRC patients based on the miRNAs approach, stool samples are more likely preferable to plasma samples; nevertheless, additional studies with more samples are needed to confirm the results.

Risk Factors for Developing Scoliosis in Cerebral Palsy: A Cross-Sectional Descriptive Study.

PubMed

Bertoncelli, Carlo M; Solla, Federico; Loughenbury, Peter R; Tsirikos, Athanasios I; Bertoncelli, Domenico; Rampal, Virginie

2017-06-01

This study aims to identify the risk factors leading to the development of severe scoliosis among children with cerebral palsy. A cross-sectional descriptive study of 70 children (aged 12-18 years) with severe spastic and/or dystonic cerebral palsy treated in a single specialist unit is described. Statistical analysis included Fisher exact test and logistic regression analysis to identify risk factors. Severe scoliosis is more likely to occur in patients with intractable epilepsy ( P = .008), poor gross motor functional assessment scores ( P = .018), limb spasticity ( P = .045), a history of previous hip surgery ( P = .048), and nonambulatory patients ( P = .013). Logistic regression model confirms the major risk factors are previous hip surgery ( P = .001), moderate to severe epilepsy ( P = .007), and female gender ( P = .03). History of previous hip surgery, intractable epilepsy, and female gender are predictors of developing severe scoliosis in children with cerebral palsy. This knowledge should aid in the early diagnosis of scoliosis and timely referral to specialist services.

Genetic diversity of the movement and coat protein genes of South American isolates of Prunus necrotic ringspot virus.

PubMed

Fiore, Nicola; Fajardo, Thor V M; Prodan, Simona; Herranz, María Carmen; Aparicio, Frederic; Montealegre, Jaime; Elena, Santiago F; Pallás, Vicente; Sánchez-Navarro, Jesús

2008-01-01

Prunus necrotic ringspot virus (PNRSV) is distributed worldwide, but no molecular data have been previously reported from South American isolates. The nucleotide sequences corresponding to the movement (MP) and coat (CP) proteins of 23 isolates of PNRSV from Chile, Brazil, and Uruguay, and from different Prunus species, have been obtained. Phylogenetic analysis performed with full-length MP and CP sequences from all the PNRSV isolates confirmed the clustering of the isolates into the previously reported PV32-I, PV96-II and PE5-III phylogroups. No association was found between specific sequences and host, geographic origin or symptomatology. Comparative analysis showed that both MP and CP have phylogroup-specific amino acids and all of the motifs previously characterized for both proteins. The study of the distribution of synonymous and nonsynonymous changes along both open reading frames revealed that most amino acid sites are under the effect of negative purifying selection.

XMM-Newton confirmation of a new intermediate polar: XMMU J185330.7-012815

NASA Astrophysics Data System (ADS)

Hui, C. Y.; Sriram, K.; Choi, C.-S.

2012-01-01

We report on the results of a detailed spectro-imaging and temporal analysis of an archival XMM-Newton observation of a new intermediate polar XMMU J185330.7-012815. Its X-ray spectrum can be well described by a multitemperature thermal plasma model with the K lines of heavy elements clearly detected. Possible counterparts of XMMU J185330.7-012815 have been identified in optical and ultraviolet (UV) bands. The low values of the inferred X-ray-to-UV and X-ray-to-optical flux ratios safely rule out the possibility of its being an isolated neutron star. We confirm the X-ray periodicity of ˜238 s but, differently from the previous preliminary results, we do not find any convincing evidence of phase shift in this observation. We further investigate its properties through an energy-resolved temporal analysis and find that the pulsed fraction monotonically increases with energy.

Extension and statistical analysis of the GACP aerosol optical thickness record

NASA Astrophysics Data System (ADS)

Geogdzhayev, Igor V.; Mishchenko, Michael I.; Li, Jing; Rossow, William B.; Liu, Li; Cairns, Brian

2015-10-01

The primary product of the Global Aerosol Climatology Project (GACP) is a continuous record of the aerosol optical thickness (AOT) over the oceans. It is based on channel-1 and -2 radiance data from the Advanced Very High Resolution Radiometer (AVHRR) instruments flown on successive National Oceanic and Atmospheric Administration (NOAA) platforms. We extend the previous GACP dataset by four years through the end of 2009 using NOAA-17 and -18 AVHRR radiances recalibrated against MODerate resolution Imaging Spectroradiometer (MODIS) radiance data, thereby making the GACP record almost three decades long. The temporal overlap of over three years of the new NOAA-17 and the previous NOAA-16 record reveals an excellent agreement of the corresponding global monthly mean AOT values, thereby confirming the robustness of the vicarious radiance calibration used in the original GACP product. The temporal overlap of the NOAA-17 and -18 instruments is used to introduce a small additive adjustment to the channel-2 calibration of the latter resulting in a consistent record with increased data density. The Principal Component Analysis (PCA) of the newly extended GACP record shows that most of the volcanic AOT variability can be isolated into one mode responsible for ~ 12% of the total variance. This conclusion is confirmed by a combined PCA analysis of the GACP, MODIS, and Multi-angle Imaging SpectroRadiometer (MISR) AOTs during the volcano-free period from February 2000 to December 2009. We show that the modes responsible for the tropospheric AOT variability in the three datasets agree well in terms of correlation and spatial patterns. A previously identified negative AOT trend which started in the late 1980s and continued into the early 2000s is confirmed. Its magnitude and duration indicate that it was caused by changes in tropospheric aerosols. The latest multi-satellite segment of the GACP record shows that this trend tapered off, with no noticeable AOT change after 2002. This result is consistent with the MODIS and MISR AOT records as well as with the recent gradual reversal from brightening to dimming revealed by surface flux measurements in many aerosol producing regions. Thus the robustness of the GACP record is confirmed, increasing our confidence in the validity of the negative trend. Although the nominal negative GACP AOT trend could partially be an artifact of increasing aerosol absorption, we argue that the time dependence of the GACP record, including the latest flat period, is more consistent with the actual decrease in the tropospheric AOT.

Extension and Statistical Analysis of the GACP Aerosol Optical Thickness Record.

NASA Technical Reports Server (NTRS)

Geogdzhayev, Igor V.; Mishchenko, Michael I.; Li, Jing; Rossow, William B.; Liu, Li; Cairns, Brian

2015-01-01

The primary product of the Global Aerosol Climatology Project (GACP) is a continuous record of the aerosol optical thickness (AOT) over the oceans. It is based on channel-1 and -2 radiance data from the Advanced Very High Resolution Radiometer (AVHRR) instruments flown on successive National Oceanic and Atmospheric Administration (NOAA) platforms. We extend the previous GACP dataset by four years through the end of 2009 using NOAA-17 and -18 AVHRR radiances recalibrated against MODerate resolution Imaging Spectroradiometer (MODIS) radiance data, thereby making the GACP record almost three decades long. The temporal overlap of over three years of the new NOAA-17 and the previous NOAA-16 record reveals an excellent agreement of the corresponding global monthly mean AOT values, thereby confirming the robustness of the vicarious radiance calibration used in the original GACP product. The temporal overlap of the NOAA-17 and -18 instruments is used to introduce a small additive adjustment to the channel-2 calibration of the latter resulting in a consistent record with increased data density. The Principal Component Analysis (PCA) of the newly extended GACP record shows that most of the volcanic AOT variability can be isolated into one mode responsible for 12% of the total variance. This conclusion is confirmed by a combined PCA analysis of the GACP, MODIS, andMulti-angle Imaging SpectroRadiometer (MISR) AOTs during the volcano-free period fromFebruary 2000 to December 2009.We show that the modes responsible for the tropospheric AOT variability in the three datasets agree well in terms of correlation and spatial patterns. A previously identified negative AOT trend which started in the late 1980s and continued into the early 2000s is confirmed. Its magnitude and duration indicate that it was caused by changes in tropospheric aerosols. The latest multi-satellite segment of the GACP record shows that this trend tapered off, with no noticeable AOT change after 2002. This result is consistent with the MODIS andMISR AOT records as well as with the recent gradual reversal frombrightening to dimming revealed by surface flux measurements in many aerosol producing regions. Thus the robustness of the GACP record is confirmed, increasing our confidence in the validity of the negative trend. Although the nominal negative GACP AOT trend could partially be an artifact of increasing aerosol absorption, we argue that the time dependence of the GACP record, including the latest flat period, is more consistent with the actual decrease in the tropospheric AOT.

PARK10 is a major locus for sporadic neuropathologically confirmed Parkinson disease

PubMed Central

Beecham, Gary W.; Dickson, Dennis W.; Scott, William K.; Martin, Eden R.; Schellenberg, Gerard; Nuytemans, Karen; Larson, Eric B.; Buxbaum, Joseph D.; Trojanowski, John Q.; Van Deerlin, Vivianna M.; Hurtig, Howard I.; Mash, Deborah C.; Beach, Thomas G.; Troncoso, Juan C.; Pletnikova, Olga; Frosch, Matthew P.; Ghetti, Bernardino; Foroud, Tatiana M.; Honig, Lawrence S.; Marder, Karen; Vonsattel, Jean Paul; Goldman, Samuel M.; Vinters, Harry V.; Ross, Owen A.; Wszolek, Zbigniew K.; Wang, Liyong; Dykxhoorn, Derek M.; Pericak-Vance, Margaret A.; Montine, Thomas J.; Leverenz, James B.; Dawson, Ted M.

2015-01-01

Objective: To minimize pathologic heterogeneity in genetic studies of Parkinson disease (PD), the Autopsy-Confirmed Parkinson Disease Genetics Consortium conducted a genome-wide association study using both patients with neuropathologically confirmed PD and controls. Methods: Four hundred eighty-four cases and 1,145 controls met neuropathologic diagnostic criteria, were genotyped, and then imputed to 3,922,209 variants for genome-wide association study analysis. Results: A small region on chromosome 1 was strongly associated with PD (rs10788972; p = 6.2 × 10−8). The association peak lies within and very close to the maximum linkage peaks of 2 prior positive linkage studies defining the PARK10 locus. We demonstrate that rs10788972 is in strong linkage disequilibrium with rs914722, the single nucleotide polymorphism defining the PARK10 haplotype previously shown to be significantly associated with age at onset in PD. The region containing the PARK10 locus was significantly reduced from 10.6 megabases to 100 kilobases and contains 4 known genes: TCEANC2, TMEM59, miR-4781, and LDLRAD1. Conclusions: We confirm the association of a PARK10 haplotype with the risk of developing idiopathic PD. Furthermore, we significantly reduce the size of the PARK10 region. None of the candidate genes in the new PARK10 region have been previously implicated in the biology of PD, suggesting new areas of potential research. This study strongly suggests that reducing pathologic heterogeneity may enhance the application of genetic association studies to PD. PMID:25663231

PARK10 is a major locus for sporadic neuropathologically confirmed Parkinson disease.

PubMed

Beecham, Gary W; Dickson, Dennis W; Scott, William K; Martin, Eden R; Schellenberg, Gerard; Nuytemans, Karen; Larson, Eric B; Buxbaum, Joseph D; Trojanowski, John Q; Van Deerlin, Vivianna M; Hurtig, Howard I; Mash, Deborah C; Beach, Thomas G; Troncoso, Juan C; Pletnikova, Olga; Frosch, Matthew P; Ghetti, Bernardino; Foroud, Tatiana M; Honig, Lawrence S; Marder, Karen; Vonsattel, Jean Paul; Goldman, Samuel M; Vinters, Harry V; Ross, Owen A; Wszolek, Zbigniew K; Wang, Liyong; Dykxhoorn, Derek M; Pericak-Vance, Margaret A; Montine, Thomas J; Leverenz, James B; Dawson, Ted M; Vance, Jeffery M

2015-03-10

To minimize pathologic heterogeneity in genetic studies of Parkinson disease (PD), the Autopsy-Confirmed Parkinson Disease Genetics Consortium conducted a genome-wide association study using both patients with neuropathologically confirmed PD and controls. Four hundred eighty-four cases and 1,145 controls met neuropathologic diagnostic criteria, were genotyped, and then imputed to 3,922,209 variants for genome-wide association study analysis. A small region on chromosome 1 was strongly associated with PD (rs10788972; p = 6.2 × 10(-8)). The association peak lies within and very close to the maximum linkage peaks of 2 prior positive linkage studies defining the PARK10 locus. We demonstrate that rs10788972 is in strong linkage disequilibrium with rs914722, the single nucleotide polymorphism defining the PARK10 haplotype previously shown to be significantly associated with age at onset in PD. The region containing the PARK10 locus was significantly reduced from 10.6 megabases to 100 kilobases and contains 4 known genes: TCEANC2, TMEM59, miR-4781, and LDLRAD1. We confirm the association of a PARK10 haplotype with the risk of developing idiopathic PD. Furthermore, we significantly reduce the size of the PARK10 region. None of the candidate genes in the new PARK10 region have been previously implicated in the biology of PD, suggesting new areas of potential research. This study strongly suggests that reducing pathologic heterogeneity may enhance the application of genetic association studies to PD. © 2015 American Academy of Neurology.

Imprecise intron losses are less frequent than precise intron losses but are not rare in plants.

PubMed

Ma, Ming-Yue; Zhu, Tao; Li, Xue-Nan; Lan, Xin-Ran; Liu, Heng-Yuan; Yang, Yu-Fei; Niu, Deng-Ke

2015-05-27

In this study, we identified 19 intron losses, including 11 precise intron losses (PILs), six imprecise intron losses (IILs), one de-exonization, and one exon deletion in tomato and potato, and 17 IILs in Arabidopsis thaliana. Comparative analysis of related genomes confirmed that all of the IILs have been fixed during evolution. Consistent with previous studies, our results indicate that PILs are a major type of intron loss. However, at least in plants, IILs are unlikely to be as rare as previously reported. This article was reviewed by Jun Yu and Zhang Zhang. For complete reviews, see the Reviewers' Reports section.

Implementation of a National Reference Laboratory for Buruli Ulcer Disease in Togo

PubMed Central

Badziklou, Kossi; Halatoko, Wemboo Afiwa; Maman, Issaka; Vogel, Felix; Bidjada, Bawimodom; Awoussi, Koffi Somenou; Piten, Ebekalisai; Helfrich, Kerstin; Mengele, Carolin; Nitschke, Jörg; Amekuse, Komi; Wiedemann, Franz Xaver; Diefenhardt, Adolf; Kobara, Basile; Herbinger, Karl–Heinz; Kere, Abiba Banla; Prince-David, Mireille; Löscher, Thomas; Bretzel, Gisela

2013-01-01

Background In a previous study PCR analysis of clinical samples from suspected cases of Buruli ulcer disease (BUD) from Togo and external quality assurance (EQA) for local microscopy were conducted at an external reference laboratory in Germany. The relatively poor performance of local microscopy as well as effort and time associated with shipment of PCR samples necessitated the implementation of stringent EQA measures and availability of local laboratory capacity. This study describes the approach to implementation of a national BUD reference laboratory in Togo. Methodology Large scale outreach activities accompanied by regular training programs for health care professionals were conducted in the regions “Maritime” and “Central,” standard operating procedures defined all processes in participating laboratories (regional, national and external reference laboratories) as well as the interaction between laboratories and partners in the field. Microscopy was conducted at regional level and slides were subjected to EQA at national and external reference laboratories. For PCR analysis, sample pairs were collected and subjected to a dry-reagent-based IS2404-PCR (DRB-PCR) at national level and standard IS2404 PCR followed by IS2404 qPCR analysis of negative samples at the external reference laboratory. Principal Findings The inter-laboratory concordance rates for microscopy ranged from 89% to 94%; overall, microscopy confirmed 50% of all suspected BUD cases. The inter-laboratory concordance rate for PCR was 96% with an overall PCR case confirmation rate of 78%. Compared to a previous study, the rate of BUD patients with non-ulcerative lesions increased from 37% to 50%, the mean duration of disease before clinical diagnosis decreased significantly from 182.6 to 82.1 days among patients with ulcerative lesions, and the percentage of category III lesions decreased from 30.3% to 19.2%. Conclusions High inter-laboratory concordance rates as well as case confirmation rates of 50% (microscopy), 71% (PCR at national level), and 78% (including qPCR confirmation at external reference laboratory) suggest high standards of BUD diagnostics. The increase of non-ulcerative lesions, as well as the decrease in diagnostic delay and category III lesions, prove the effect of comprehensive EQA and training measures involving also procedures outside the laboratory. PMID:23359828

Implementation of a national reference laboratory for Buruli ulcer disease in Togo.

PubMed

Beissner, Marcus; Huber, Kristina Lydia; Badziklou, Kossi; Halatoko, Wemboo Afiwa; Maman, Issaka; Vogel, Felix; Bidjada, Bawimodom; Awoussi, Koffi Somenou; Piten, Ebekalisai; Helfrich, Kerstin; Mengele, Carolin; Nitschke, Jörg; Amekuse, Komi; Wiedemann, Franz Xaver; Diefenhardt, Adolf; Kobara, Basile; Herbinger, Karl-Heinz; Kere, Abiba Banla; Prince-David, Mireille; Löscher, Thomas; Bretzel, Gisela

2013-01-01

In a previous study PCR analysis of clinical samples from suspected cases of Buruli ulcer disease (BUD) from Togo and external quality assurance (EQA) for local microscopy were conducted at an external reference laboratory in Germany. The relatively poor performance of local microscopy as well as effort and time associated with shipment of PCR samples necessitated the implementation of stringent EQA measures and availability of local laboratory capacity. This study describes the approach to implementation of a national BUD reference laboratory in Togo. Large scale outreach activities accompanied by regular training programs for health care professionals were conducted in the regions "Maritime" and "Central," standard operating procedures defined all processes in participating laboratories (regional, national and external reference laboratories) as well as the interaction between laboratories and partners in the field. Microscopy was conducted at regional level and slides were subjected to EQA at national and external reference laboratories. For PCR analysis, sample pairs were collected and subjected to a dry-reagent-based IS2404-PCR (DRB-PCR) at national level and standard IS2404 PCR followed by IS2404 qPCR analysis of negative samples at the external reference laboratory. The inter-laboratory concordance rates for microscopy ranged from 89% to 94%; overall, microscopy confirmed 50% of all suspected BUD cases. The inter-laboratory concordance rate for PCR was 96% with an overall PCR case confirmation rate of 78%. Compared to a previous study, the rate of BUD patients with non-ulcerative lesions increased from 37% to 50%, the mean duration of disease before clinical diagnosis decreased significantly from 182.6 to 82.1 days among patients with ulcerative lesions, and the percentage of category III lesions decreased from 30.3% to 19.2%. High inter-laboratory concordance rates as well as case confirmation rates of 50% (microscopy), 71% (PCR at national level), and 78% (including qPCR confirmation at external reference laboratory) suggest high standards of BUD diagnostics. The increase of non-ulcerative lesions, as well as the decrease in diagnostic delay and category III lesions, prove the effect of comprehensive EQA and training measures involving also procedures outside the laboratory.

Germline mosaicism of PHOX2B mutation accounts for familial recurrence of congenital central hypoventilation syndrome (CCHS).

PubMed

Rand, Casey M; Yu, Min; Jennings, Lawrence J; Panesar, Kelvin; Berry-Kravis, Elizabeth M; Zhou, Lili; Weese-Mayer, Debra E

2012-09-01

Congenital central hypoventilation syndrome (CCHS), a rare disorder characterized by alveolar hypoventilation and autonomic dysregulation, is caused by mutations in the PHOX2B gene. Most mutations occur de novo, but recent evidence suggests that up to 25% are inherited from asymptomatic parents with somatic mosaicism for these mutations. However, to date, germline mosaicism has not been reported. This report describes a family with recurrence of PHOX2B mutation-confirmed CCHS due to germline mosaicism. The first occurrence was a baby girl, noted on day 2 of life to have multiple episodes of apnea, bradycardia, and cyanosis while breathing room air. PHOX2B gene testing confirmed the diagnosis of CCHS with a heterozygous polyalanine repeat expansion mutation (PARM); genotype 20/27 (normal 20/20). Both parents tested negative for this mutation using fragment analysis (limit of detection<1%). Upon subsequent pregnancy [paternity confirmed using short tandem repeat (STR) analysis], amniocentesis testing identified the PHOX2B 20/27 genotype, confirmed with repeat testing. Elective abortion was performed at 21.5 weeks gestation. Testing of abortus tissue confirmed amniocentesis testing. The PHOX2B 20/27 expansion was not observed in a paternal sperm sample. This case represents the first reported family with recurrence of PHOX2B mutation-confirmed CCHS without detection of a parental carrier state or mosaicism, confirming the previously hypothesized possibility of germline mosaicism for PHOX2B mutations. This is an important finding for genetic counseling of CCHS families, suggesting that even if somatic mosaicism is not detected in parental samples, there is still reason for careful genetic counseling and consideration of prenatal testing during subsequent pregnancies. Copyright © 2012 Wiley Periodicals, Inc.

EPPUR SI MUOVE: POSITIONAL AND KINEMATIC CORRELATIONS OF SATELLITE PAIRS IN THE LOW Z UNIVERSE

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

Ibata, Rodrigo A.; Famaey, Benoit; Martin, Nicolas

2015-05-20

We have recently shown that pairs of satellite galaxies located diametrically opposite to each other around their host possess predominantly anti-correlated velocities. This is consistent with a scenario in which ≳50% of satellite galaxies belong to kinematically coherent rotating planar structures. Here we extend this analysis, examining satellites of giant galaxies drawn from an SDSS photometric redshift catalog. We find that there is a ∼17% overabundance (>3σ significance) of candidate satellites at positions diametrically opposite to a spectroscopically confirmed satellite. We show that ΛCDM cosmological simulations do not possess this property when contamination is included. After subtracting contamination, we findmore » ∼2 times more satellites diametrically opposed to a spectroscopically confirmed satellite than at 90° from it, at projected distances ranging from 100 to 150 kpc from the host. This independent analysis thus strongly supports our previous results on anti-correlated velocities. We also find that those satellite pairs with anti-correlated velocities have a strong preference (∼3:1) to align with the major axis of the host whereas those with correlated velocities display the opposite behavior. We finally show that repeating a similar analysis to Ibata et al. with same-side satellites is generally hard to interpret, but is not inconsistent with our previous results when strong quality cuts are applied on the sample. This addresses all of the concerns recently raised by Cautun et al., who did not uncover any flaw in our previous analysis, but may simply have hinted at the physical extent of planar satellite structures by pointing out that the anti-correlation signal weakens at radii >150 kpc. All these unexpected positional and kinematic correlations strongly suggest that a substantial fraction of satellite galaxies are causally linked in their formation and evolution.« less

BARNARD 59: NO EVIDENCE FOR FURTHER FRAGMENTATION

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

Roman-Zuniga, C. G.; Frau, P.; Girart, J. M.

2012-03-10

The dense molecular clump at the center of the Barnard 59 (B59) complex is the only region in the Pipe Nebula that has formed a small, stellar cluster. The previous analysis of a high-resolution near-IR dust extinction map revealed that the nuclear region in B59 is a massive, mostly quiescent clump of 18.9 M{sub Sun }. The clump shows a monolithic profile, possibly indicating that the clump is on the way to collapse, with no evident fragmentation that could lead to another group of star systems. In this paper, we present new analysis that compares the dust extinction map withmore » a new dust emission radio-continuum map of higher spatial resolution. We confirm that the clump does not show any significant evidence for prestellar fragmentation at scales smaller than those probed previously.« less

Multipole Vector Anomalies in the First-Year WMAP Data: A Cut-Sky Analysis

NASA Astrophysics Data System (ADS)

Bielewicz, P.; Eriksen, H. K.; Banday, A. J.; Górski, K. M.; Lilje, P. B.

2005-12-01

We apply the recently defined multipole vector framework to the frequency-specific first-year WMAP sky maps, estimating the low-l multipole coefficients from the high-latitude sky by means of a power equalization filter. While most previous analyses of this type have considered only heavily processed (and foreground-contaminated) full-sky maps, the present approach allows for greater control of residual foregrounds and therefore potentially also for cosmologically important conclusions. The low-l spherical harmonic coefficients and corresponding multipole vectors are tabulated for easy reference. Using this formalism, we reassess a set of earlier claims of both cosmological and noncosmological low-l correlations on the basis of multipole vectors. First, we show that the apparent l=3 and 8 correlation claimed by Copi and coworkers is present only in the heavily processed map produced by Tegmark and coworkers and must therefore be considered an artifact of that map. Second, the well-known quadrupole-octopole correlation is confirmed at the 99% significance level and shown to be robust with respect to frequency and sky cut. Previous claims are thus supported by our analysis. Finally, the low-l alignment with respect to the ecliptic claimed by Schwarz and coworkers is nominally confirmed in this analysis, but also shown to be very dependent on severe a posteriori choices. Indeed, we show that given the peculiar quadrupole-octopole arrangement, finding such a strong alignment with the ecliptic is not unusual.

Why some patients are unhappy: part 2. Relationship of nasal shape and trauma history to surgical success.

PubMed

Constantian, Mark B; Lin, Chee Paul

2014-10-01

A previous report indicated that secondary rhinoplasty patients with normal preoperative noses displayed significantly higher prevalences of depression, demanding behavior, previous aesthetic operations, and confirmed trauma (abuse/neglect) histories than patients who originally had dorsal deformities or straight noses with functional symptoms. The authors hypothesized that abuse or neglect might also influence patient satisfaction and suggest screening criteria. One hundred secondary rhinoplasty patients stratified by their original nasal shapes were examined by bivariate analysis to determine the characteristics associated with surgical satisfaction. Mediation analysis established intervening factors between total surgery number and patients' perceived success. Random forests identified important patient attributes that predicted surgical success; logistic regression confirmed these effects. Satisfied patients originally had dorsal humps, three or fewer previous operations, were not demanding or depressed, were not looking for perfect noses, and had no trauma histories. Dissatisfied patients originally had subjectively normal noses, more than three operations, were depressed, had demanding personalities, and had trauma histories. Patients who had undergone the most operations were most likely to request more surgery and least likely to be satisfied. A trauma (abuse/neglect) history was the most significant mediator between patient satisfaction and number of operations and the most prominent factor driving surgery in patients with milder deformities. Potentially causative links exist between trauma (abuse/neglect), body image disorders, and obsessive plastic surgery. Body dysmorphic disorder may be a model of the disordered adaptation to abuse or neglect, a variant of posttraumatic stress disorder. Our satisfied and dissatisfied patients shared common characteristics and therefore may be identifiable preoperatively.

Revised and extended analysis of the eighth spectrum of platinum (Pt VIII)

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

Azarov, Vladimir I., E-mail: vlad_azarov@yahoo.com; Gayasov, Robert R.

2017-05-15

The spectrum of platinum was observed in the 300–2100 Å wavelength region. Grazing and normal incidence VUV spectrographs have been used to record the spectrum. The (5d{sup 3}+5d{sup 2}6s)−5d{sup 2}6p transition array of seven times ionized platinum, Pt VIII, has been investigated. The configurations 5d{sup 3} and 5d{sup 2}6p had been previously studied, and all levels of these configurations (19 and 45 levels, respectively) had been established. The previous analysis was based on 178 classified spectral lines. In the current analysis we have confirmed identification of all previously found levels and all but 10 previously assigned spectral lines, although we havemore » detected a large (up to 35 mÅ) systematic shift in wavelength measurements used in the previous analysis. Based on new wavelength measurements, we have corrected the 5d{sup 3} and 5d{sup 2}6p energy level values (by up to 55 cm{sup −1}) and established for the first time 14 out of 16 theoretically possible 5d{sup 2}6s levels in Pt VIII. The total list of identified lines (including 180 new lines) contains 349 entries. The orthogonal operators technique was used to calculate the level structure and transition probabilities. The energy parameters have been determined by the least squares fit to the observed levels. Calculated transition probability and energy values, as well as LS-compositions obtained from the fitted parameters are presented.« less

Gene-centric Meta-analysis in 87,736 Individuals of European Ancestry Identifies Multiple Blood-Pressure-Related Loci

PubMed Central

Tragante, Vinicius; Barnes, Michael R.; Ganesh, Santhi K.; Lanktree, Matthew B.; Guo, Wei; Franceschini, Nora; Smith, Erin N.; Johnson, Toby; Holmes, Michael V.; Padmanabhan, Sandosh; Karczewski, Konrad J.; Almoguera, Berta; Barnard, John; Baumert, Jens; Chang, Yen-Pei Christy; Elbers, Clara C.; Farrall, Martin; Fischer, Mary E.; Gaunt, Tom R.; Gho, Johannes M.I.H.; Gieger, Christian; Goel, Anuj; Gong, Yan; Isaacs, Aaron; Kleber, Marcus E.; Leach, Irene Mateo; McDonough, Caitrin W.; Meijs, Matthijs F.L.; Melander, Olle; Nelson, Christopher P.; Nolte, Ilja M.; Pankratz, Nathan; Price, Tom S.; Shaffer, Jonathan; Shah, Sonia; Tomaszewski, Maciej; van der Most, Peter J.; Van Iperen, Erik P.A.; Vonk, Judith M.; Witkowska, Kate; Wong, Caroline O.L.; Zhang, Li; Beitelshees, Amber L.; Berenson, Gerald S.; Bhatt, Deepak L.; Brown, Morris; Burt, Amber; Cooper-DeHoff, Rhonda M.; Connell, John M.; Cruickshanks, Karen J.; Curtis, Sean P.; Davey-Smith, George; Delles, Christian; Gansevoort, Ron T.; Guo, Xiuqing; Haiqing, Shen; Hastie, Claire E.; Hofker, Marten H.; Hovingh, G. Kees; Kim, Daniel S.; Kirkland, Susan A.; Klein, Barbara E.; Klein, Ronald; Li, Yun R.; Maiwald, Steffi; Newton-Cheh, Christopher; O’Brien, Eoin T.; Onland-Moret, N. Charlotte; Palmas, Walter; Parsa, Afshin; Penninx, Brenda W.; Pettinger, Mary; Vasan, Ramachandran S.; Ranchalis, Jane E.; M Ridker, Paul; Rose, Lynda M.; Sever, Peter; Shimbo, Daichi; Steele, Laura; Stolk, Ronald P.; Thorand, Barbara; Trip, Mieke D.; van Duijn, Cornelia M.; Verschuren, W. Monique; Wijmenga, Cisca; Wyatt, Sharon; Young, J. Hunter; Zwinderman, Aeilko H.; Bezzina, Connie R.; Boerwinkle, Eric; Casas, Juan P.; Caulfield, Mark J.; Chakravarti, Aravinda; Chasman, Daniel I.; Davidson, Karina W.; Doevendans, Pieter A.; Dominiczak, Anna F.; FitzGerald, Garret A.; Gums, John G.; Fornage, Myriam; Hakonarson, Hakon; Halder, Indrani; Hillege, Hans L.; Illig, Thomas; Jarvik, Gail P.; Johnson, Julie A.; Kastelein, John J.P.; Koenig, Wolfgang; Kumari, Meena; März, Winfried; Murray, Sarah S.; O’Connell, Jeffery R.; Oldehinkel, Albertine J.; Pankow, James S.; Rader, Daniel J.; Redline, Susan; Reilly, Muredach P.; Schadt, Eric E.; Kottke-Marchant, Kandice; Snieder, Harold; Snyder, Michael; Stanton, Alice V.; Tobin, Martin D.; Uitterlinden, André G.; van der Harst, Pim; van der Schouw, Yvonne T.; Samani, Nilesh J.; Watkins, Hugh; Johnson, Andrew D.; Reiner, Alex P.; Zhu, Xiaofeng; de Bakker, Paul I.W.; Levy, Daniel; Asselbergs, Folkert W.; Munroe, Patricia B.; Keating, Brendan J.

2014-01-01

Blood pressure (BP) is a heritable risk factor for cardiovascular disease. To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP), we genotyped ∼50,000 SNPs in up to 87,736 individuals of European ancestry and combined these in a meta-analysis. We replicated findings in an independent set of 68,368 individuals of European ancestry. Our analyses identified 11 previously undescribed associations in independent loci containing 31 genes including PDE1A, HLA-DQB1, CDK6, PRKAG2, VCL, H19, NUCB2, RELA, HOXC@ complex, FBN1, and NFAT5 at the Bonferroni-corrected array-wide significance threshold (p < 6 × 10−7) and confirmed 27 previously reported associations. Bioinformatic analysis of the 11 loci provided support for a putative role in hypertension of several genes, such as CDK6 and NUCB2. Analysis of potential pharmacological targets in databases of small molecules showed that ten of the genes are predicted to be a target for small molecules. In summary, we identified previously unknown loci associated with BP. Our findings extend our understanding of genes involved in BP regulation, which may provide new targets for therapeutic intervention or drug response stratification. PMID:24560520

Spin Rotation of Formalism for Spin Tracking

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

Luccio,A.

The problem of which coefficients are adequate to correctly represent the spin rotation in vector spin tracking for polarized proton and deuteron beams in synchrotrons is here re-examined in the light of recent discussions. The main aim of this note is to show where some previous erroneous results originated and how to code spin rotation in a tracking code. Some analysis of a recent experiment is presented that confirm the correctness of the assumptions.

Genome-Wide Association Study of Multiple Sclerosis Confirms a Novel Locus at 5p13.1

PubMed Central

Sanna, Serena; Gayán, Javier; Urcelay, Elena; Zara, Ilenia; Pitzalis, Maristella; Cavanillas, María L.; Arroyo, Rafael; Zoledziewska, Magdalena; Marrosu, Marisa; Fernández, Oscar; Leyva, Laura; Alcina, Antonio; Fedetz, Maria; Moreno-Rey, Concha; Velasco, Juan; Real, Luis M.; Ruiz-Peña, Juan Luis; Cucca, Francesco

2012-01-01

Multiple Sclerosis (MS) is the most common progressive and disabling neurological condition affecting young adults in the world today. From a genetic point of view, MS is a complex disorder resulting from the combination of genetic and non-genetic factors. We aimed to identify previously unidentified loci conducting a new GWAS of Multiple Sclerosis (MS) in a sample of 296 MS cases and 801 controls from the Spanish population. Meta-analysis of our data in combination with previous GWAS was done. A total of 17 GWAS-significant SNPs, corresponding to three different loci were identified:HLA, IL2RA, and 5p13.1. All three have been previously reported as GWAS-significant. We confirmed our observation in 5p13.1 for rs9292777 using two additional independent Spanish samples to make a total of 4912 MS cases and 7498 controls (ORpooled = 0.84; 95%CI: 0.80–0.89; p = 1.36×10-9). This SNP differs from the one reported within this locus in a recent GWAS. Although it is unclear whether both signals are tapping the same genetic association, it seems clear that this locus plays an important role in the pathogenesis of MS. PMID:22570697

A voxel-based approach to gray matter asymmetries.

PubMed

Luders, E; Gaser, C; Jancke, L; Schlaug, G

2004-06-01

Voxel-based morphometry (VBM) was used to analyze gray matter (GM) asymmetries in a large sample (n = 60) of male and female professional musicians with and without absolute pitch (AP). We chose to examine these particular groups because previous studies using traditional region-of-interest (ROI) analyses have shown differences in hemispheric asymmetry related to AP and gender. Voxel-based methods may have advantages over traditional ROI-based methods since the analysis can be performed across the whole brain with minimal user bias. After determining that the VBM method was sufficiently sensitive for the detection of differences in GM asymmetries between groups, we found that male AP musicians were more leftward lateralized in the anterior region of the planum temporale (PT) than male non-AP musicians. This confirmed the results of previous studies using ROI-based methods that showed an association between PT asymmetry and the AP phenotype. We further observed that male non-AP musicians revealed an increased leftward GM asymmetry in the postcentral gyrus compared to female non-AP musicians, again corroborating results of a previously published study using ROI-based methods. By analyzing hemispheric GM differences across our entire sample, we were able to partially confirm findings of previous studies using traditional morphometric techniques, as well as more recent, voxel-based analyses. In addition, we found some unusually pronounced GM asymmetries in our musician sample not previously detected in subjects unselected for musical training. Since we were able to validate gender- and AP-related brain asymmetries previously described using traditional ROI-based morphometric techniques, the results of our analyses support the use of VBM for examinations of GM asymmetries.

Cyclin D1 and Ewing's sarcoma/PNET: A microarray analysis.

PubMed

Fagone, Paolo; Nicoletti, Ferdinando; Salvatorelli, Lucia; Musumeci, Giuseppe; Magro, Gaetano

2015-10-01

Recent immunohistochemical analyses have showed that cyclin D1 is expressed in soft tissue Ewing's sarcoma/peripheral neuroectodermal tumor (PNET) of childhood and adolescents, while it is undetectable in both embryonal and alveolar rhabdomyosarcoma. In the present paper, microarray analysis provided evidence of a significant upregulation of cyclin D1 in Ewing's sarcoma as compared to normal tissues. In addition, we confirmed our previous findings of a significant over-expression of cyclin D1 in Ewing sarcoma as compared to rhabdomyosarcoma. Bioinformatic analysis also allowed to identify some other genes, strongly correlated to cyclin D1, which, although not previously studied in pediatric tumors, could represent novel markers for the diagnosis and prognosis of Ewing's sarcoma/PNET. The data herein provided support not only the use of cyclin D1 as a diagnostic marker of Ewing sarcoma/PNET but also the possibility of using drugs targeting cyclin D1 as potential therapeutic strategies. Copyright © 2015 Elsevier GmbH. All rights reserved.

A chemical proteomics approach for global analysis of lysine monomethylome profiling.

PubMed

Wu, Zhixiang; Cheng, Zhongyi; Sun, Mingwei; Wan, Xuelian; Liu, Ping; He, Tieming; Tan, Minjia; Zhao, Yingming

2015-02-01

Methylation of lysine residues on histone proteins is known to play an important role in chromatin structure and function. However, non-histone protein substrates of this modification remain largely unknown. An effective approach for system-wide analysis of protein lysine methylation, particularly lysine monomethylation, is lacking. Here we describe a chemical proteomics approach for global screening for monomethyllysine substrates, involving chemical propionylation of monomethylated lysine, affinity enrichment of the modified monomethylated peptides, and HPLC/MS/MS analysis. Using this approach, we identified with high confidence 446 lysine monomethylation sites in 398 proteins, including three previously unknown histone monomethylation marks, representing the largest data set of protein lysine monomethylation described to date. Our data not only confirms previously discovered lysine methylation substrates in the nucleus and spliceosome, but also reveals new substrates associated with diverse biological processes. This method hence offers a powerful approach for dynamic study of protein lysine monomethylation under diverse cellular conditions and in human diseases. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Accuracy and usefulness of the AVOXimeter 4000 as routine analysis of carboxyhemoglobin.

PubMed

Fujihara, Junko; Kinoshita, Hiroshi; Tanaka, Naoko; Yasuda, Toshihiro; Takeshita, Haruo

2013-07-01

The measurement of blood carboxyhemoglobin (CO-Hb) is important to determine the cause of death. The AVOXimeter 4000 (AVOX), a portable CO-oximeter, has the advantages of a low purchase price and operating cost, ease of operation, and rapid results. Little information is available on the usefulness of AVOX in the forensic sample, and the previous study investigated only six samples. Therefore, in this study, we confirmed the usefulness of the AVOX through a comparison of its results with data previously obtained using the double wavelength spectrophotometric method in autopsies. Regression analysis was performed between CO-Hb levels measured by the AVOX and those measured by the conventional double wavelength spectrophotometric method in postmortem blood samples: a significant correlation was observed. This study suggests the usefulness of the AVOX to analyze postmortem blood, and the AVOX is suitable for routine forensic analysis and can be applied at the crime scene. © 2013 American Academy of Forensic Sciences.

Disseminins and Spiciferone Analogues: Polyketide-Derived Metabolites from a Fungicolous Isolate of Pestalotiopsis disseminata.

PubMed

Hwang, In Hyun; Swenson, Dale C; Gloer, James B; Wicklow, Donald T

2016-03-25

Seven new polyketide metabolites (disseminins A-E, 1-5, and spiciferones D and E, 7 and 8) were obtained from cultures of a fungicolous isolate of Pestalotiopsis disseminata (NRRL 62562), together with a related compound (6) previously known only as a semisynthetic product. Structures were determined mainly by analysis of HRMS and NMR data. Biogenetically related compounds 1 and 2 possess uncommon bis-tetrahydrofuran and dioxabicyclo[3.2.1]octane ring systems, respectively. X-ray crystallographic analysis of the p-bromobenzoate derivative of 1 confirmed the structure and enabled assignment of its absolute configuration.

Myoadenylate deaminase deficiency, hypertrophic cardiomyopathy and gigantism syndrome.

PubMed

Skyllouriotis, M L; Marx, M; Bittner, R E; Skyllouriotis, P; Gross, M; Wimmer, M

1997-07-01

We report a 20-year-old man with gigantism syndrome, hypertrophic cardiomyopathy, muscle weakness, exercise intolerance, and severe psychomotor retardation since childhood. Histochemical and biochemical analysis of skeletal muscle biopsy revealed myoadenylate deaminase deficiency; molecular genetic analysis confirmed the diagnosis of primary (inherited) myoadenylate deaminase deficiency. Plasma, urine, and muscle carnitine concentrations were reduced. L-Carnitine treatment led to gradual improvement in exercise tolerance and cognitive performance; plasma and tissue carnitine levels returned to normal, and echocardiographic evidence of left ventricular hypertrophy disappeared. The combination of inherited myoadenylate deaminase deficiency, gigantism syndrome and carnitine deficiency has not previously been described.

MRI correlates of general intelligence in neurotypical adults.

PubMed

Malpas, Charles B; Genc, Sila; Saling, Michael M; Velakoulis, Dennis; Desmond, Patricia M; O'Brien, Terence J

2016-02-01

There is growing interest in the neurobiological substrate of general intelligence. Psychometric estimates of general intelligence are reduced in a range of neurological disorders, leading to practical application as sensitive, but non-specific, markers of cerebral disorder. This study examined estimates of general intelligence in neurotypical adults using diffusion tensor imaging and resting-state functional connectivity analysis. General intelligence was related to white matter organisation across multiple brain regions, confirming previous work in older healthy adults. We also found that variation in general intelligence was related to a large functional sub-network involving all cortical lobes of the brain. These findings confirm that individual variance in general intelligence is related to diffusely represented brain networks. Copyright © 2015 Elsevier Ltd. All rights reserved.

Resistance patterns and outcomes in intensive care unit (ICU)-acquired pneumonia. Validation of European Centre for Disease Prevention and Control (ECDC) and the Centers for Disease Control and Prevention (CDC) classification of multidrug resistant organisms.

PubMed

Martin-Loeches, Ignacio; Torres, Antonio; Rinaudo, Mariano; Terraneo, Silvia; de Rosa, Francesca; Ramirez, Paula; Diaz, Emili; Fernández-Barat, Laia; Li Bassi, Gian Luigi; Ferrer, Miquel

2015-03-01

Bacterial resistance has become a major public health problem. To validate the definition of multidrug-resistant organisms (MDRO) based on the European Centre for Disease Prevention and Control (ECDC) and the Centers for Disease Control and Prevention (CDC) classification. Prospective, observational study in six medical and surgical Intensive-Care-Units (ICU) of a University hospital. Three-hundred-and-forty-three patients with ICU-acquired pneumonia (ICUAP) were prospectively enrolled, 140 patients had no microbiological confirmation (41%), 82 patients (24%) developed ICUAP for non-MDRO, whereas 121 (35%) were MDROs. Non-MDRO, MDRO and no microbiological confirmation patients did not present either a significant different previous antibiotic use (p 0.18) or previous hospital admission (p 0.17). Appropriate antibiotic therapy was associated with better ICU survival (105 [92.9%] vs. 74 [82.2%]; p = 0.03). An adjusted multivariate regression logistic analysis identified that only MDRO had a higher ICU-mortality than non-MDRO and no microbiological confirmation patients (OR 2.89; p < 0.05; 95% CI for Exp [β]. 1.02-8.21); Patients with MDRO ICUAP remained in ICU for a longer period than MDRO and no microbiological confirmation respectively (p < 0.01) however no microbiological confirmation patients had more often antibiotic consumption than culture positive ones. Patients who developed ICUAP due to MDRO showed a higher ICU-mortality than non-MDRO ones and use of ICU resources. No microbiological confirmation patients had more often antibiotic consumption than culture positive patients. Risk factors for MDRO may be important for the selection of initial antimicrobial therapy, in addition to local epidemiology. Copyright © 2014 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

[Quality of life and related factors among climacteric women from south Brazil].

PubMed

de Lorenzi, Dino R S; Saciloto, Bruno; Artico, Graziela R; Fontana, Sabrina K R

2009-01-01

This study aimed to evaluate the quality of life in climacteric and associated factor among women from Southeast Brazil. A cross-section study of 506 women aged between 45 and 60 years old attended at a university climacteric clinic from South Brazil from June to October 2002. Hysterectomized women, as well as hormonal therapy or hormonal contraceptive users were excluded. The quality of life was evaluated by the Women's Health Questionnaire (WHQ). Statistical analysis was performed with multiple linear regression analysis. The average of the age among the studied women was 51.3 (+/- 4.5) years old. About 15.4% were premenopausal, 34.4% perimenopausal and 50.2% postmenopausal women. The quality of life showed up deteriorated among the studied women. The factors related with quality of life were: the educational level (p < 0.01), the confirmation of smoking in the last year (p < 0.01), regular physical activity (p < 0.01), the confirmation of previous co-morbidities (p < 0.01) and the menopausal status (p < 0.01). A higher educational level, as well as the confirmation of regular physical activity led to a significant increase on their life quality. Smoking and previous clinical co-morbidities were responsible for the lower scores of quality of life. The pre-menopause was associated with a higher life quality level if compared to peri and post menopause. No differences in relation to the scores of life were identified among the perimenopausal and postmenopausal women. Nevertheless the menopausal status showed up associated to the quality of life, the results of the study pointed out that the climacteric is not just influenced by biological factors, but also by psychosocial and cultural factors.

Meta-analysis of gene expression profiles associated with histological classification and survival in 829 ovarian cancer samples.

PubMed

Fekete, Tibor; Rásó, Erzsébet; Pete, Imre; Tegze, Bálint; Liko, István; Munkácsy, Gyöngyi; Sipos, Norbert; Rigó, János; Györffy, Balázs

2012-07-01

Transcriptomic analysis of global gene expression in ovarian carcinoma can identify dysregulated genes capable to serve as molecular markers for histology subtypes and survival. The aim of our study was to validate previous candidate signatures in an independent setting and to identify single genes capable to serve as biomarkers for ovarian cancer progression. As several datasets are available in the GEO today, we were able to perform a true meta-analysis. First, 829 samples (11 datasets) were downloaded, and the predictive power of 16 previously published gene sets was assessed. Of these, eight were capable to discriminate histology subtypes, and none was capable to predict survival. To overcome the differences in previous studies, we used the 829 samples to identify new predictors. Then, we collected 64 ovarian cancer samples (median relapse-free survival 24.5 months) and performed TaqMan Real Time Polimerase Chain Reaction (RT-PCR) analysis for the best 40 genes associated with histology subtypes and survival. Over 90% of subtype-associated genes were confirmed. Overall survival was effectively predicted by hormone receptors (PGR and ESR2) and by TSPAN8. Relapse-free survival was predicted by MAPT and SNCG. In summary, we successfully validated several gene sets in a meta-analysis in large datasets of ovarian samples. Additionally, several individual genes identified were validated in a clinical cohort. Copyright © 2011 UICC.

Biased Target Ion Beam Deposition and Nanoskiving for Fabricating NiTi Alloy Nanowires

NASA Astrophysics Data System (ADS)

Hou, Huilong; Horn, Mark W.; Hamilton, Reginald F.

2016-12-01

Nanoskiving is a novel nanofabrication technique to produce shape memory alloy nanowires. Our previous work was the first to successfully fabricate NiTi alloy nanowires using the top-down approach, which leverages thin film technology and ultramicrotomy for ultra-thin sectioning. For this work, we utilized biased target ion beam deposition technology to fabricate nanoscale (i.e., sub-micrometer) NiTi alloy thin films. In contrast to our previous work, rapid thermal annealing was employed for heat treatment, and the B2 austenite to R-phase martensitic transformation was confirmed using stress-temperature and diffraction measurements. The ultramicrotome was programmable and facilitated sectioning the films to produce nanowires with thickness-to-width ratios ranging from 4:1 to 16:1. Energy dispersive X-ray spectroscopy analysis confirmed the elemental Ni and Ti make-up of the wires. The findings exposed the nanowires exhibited a natural ribbon-like curvature, which depended on the thickness-to-width ratio. The results demonstrate nanoskiving is a potential nanofabrication technique for producing NiTi alloy nanowires that are continuous with an unprecedented length on the order of hundreds of micrometers.

Serum S100B Is Related to Illness Duration and Clinical Symptoms in Schizophrenia—A Meta-Regression Analysis

PubMed Central

Schümberg, Katharina; Polyakova, Maryna; Steiner, Johann; Schroeter, Matthias L.

2016-01-01

S100B has been linked to glial pathology in several psychiatric disorders. Previous studies found higher S100B serum levels in patients with schizophrenia compared to healthy controls, and a number of covariates influencing the size of this effect have been proposed in the literature. Here, we conducted a meta-analysis and meta-regression analysis on alterations of serum S100B in schizophrenia in comparison with healthy control subjects. The meta-analysis followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement to guarantee a high quality and reproducibility. With strict inclusion criteria 19 original studies could be included in the quantitative meta-analysis, comprising a total of 766 patients and 607 healthy control subjects. The meta-analysis confirmed higher values of the glial serum marker S100B in schizophrenia if compared with control subjects. Meta-regression analyses revealed significant effects of illness duration and clinical symptomatology, in particular the total score of the Positive and Negative Syndrome Scale (PANSS), on serum S100B levels in schizophrenia. In sum, results confirm glial pathology in schizophrenia that is modulated by illness duration and related to clinical symptomatology. Further studies are needed to investigate mechanisms and mediating factors related to these findings. PMID:26941608

Design, analysis and verification of a knee joint oncological prosthesis finite element model.

PubMed

Zach, Lukáš; Kunčická, Lenka; Růžička, Pavel; Kocich, Radim

2014-11-01

The aim of this paper was to design a finite element model for a hinged PROSPON oncological knee endoprosthesis and to verify the model by comparison with ankle flexion angle using knee-bending experimental data obtained previously. Visible Human Project CT scans were used to create a general lower extremity bones model and to compose a 3D CAD knee joint model to which muscles and ligaments were added. Into the assembly the designed finite element PROSPON prosthesis model was integrated and an analysis focused on the PEEK-OPTIMA hinge pin bushing stress state was carried out. To confirm the stress state analysis results, contact pressure was investigated. The analysis was performed in the knee-bending position within 15.4-69.4° hip joint flexion range. The results showed that the maximum stress achieved during the analysis (46.6 MPa) did not exceed the yield strength of the material (90 MPa); the condition of plastic stability was therefore met. The stress state analysis results were confirmed by the distribution of contact pressure during knee-bending. The applicability of our designed finite element model for the real implant behaviour prediction was proven on the basis of good correlation of the analytical and experimental ankle flexion angle data. Copyright © 2014 Elsevier Ltd. All rights reserved.

High-energy variability of the Pulsar binary PSR J1311-3430

NASA Astrophysics Data System (ADS)

An, Hongjun; Fermi-LAT Collaboration

2018-01-01

We present analysis results of high-energy observations of the extreme mass-ratio black-widow millisecond pulsar binary PSR J1311-3430. Our studies in the UV, X-ray, and gamma-ray bands confirm the orbital modulation in the gamma-ray band as suggested previously. In addition, we find that the modulation is stronger in the high-energy band. In the lower-energy UV and X-ray bands, we detect flares which were observed previously and attributed to magnetic activities. We find that the optical flares are associated with the X-ray flares, suggesting common origin. We explore possible connections of the variabilities with the intrabinary shock (IBS) and magnetic activity on the low mass companion.

Lactobacillus rhamnosus GG probiotic enteric regimen does not appreciably alter the gut microbiome or provide protection against GVHD after allogeneic hematopoietic stem cell transplantation.

PubMed

Gorshein, Elan; Wei, Catherine; Ambrosy, Susan; Budney, Shanna; Vivas, Juliana; Shenkerman, Angelika; Manago, Jacqueline; McGrath, Mary Kate; Tyno, Anne; Lin, Yong; Patel, Vimal; Gharibo, Mecide; Schaar, Dale; Jenq, Robert R; Khiabanian, Hossein; Strair, Roger

2017-05-01

Graft-versus-host disease (GVHD) is a major adverse effect associated with allogeneic stem cell transplant. Previous studies in mice indicated that administration of the probiotic Lactobacillus rhamnosus GG can reduce the incidence of GVHD after hematopoietic stem cell transplant. Here we report results from the first randomized probiotic enteric regimen trial in which allogenic hematopoietic stem cell patients were supplemented with Lactobacillus rhamnosus GG. Gut microbiome analysis confirmed a previously reported gut microbiome association with GVHD. However, the clinical trial was terminated when interim analysis did not detect an appreciable probiotic-related change in the gut microbiome or incidence of GVHD. Additional studies are necessary to determine whether probiotics can alter the incidence of GVHD after allogeneic stem cell transplant. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Preprocessing with image denoising and histogram equalization for endoscopy image analysis using texture analysis.

PubMed

Hiroyasu, Tomoyuki; Hayashinuma, Katsutoshi; Ichikawa, Hiroshi; Yagi, Nobuaki

2015-08-01

A preprocessing method for endoscopy image analysis using texture analysis is proposed. In a previous study, we proposed a feature value that combines a co-occurrence matrix and a run-length matrix to analyze the extent of early gastric cancer from images taken with narrow-band imaging endoscopy. However, the obtained feature value does not identify lesion zones correctly due to the influence of noise and halation. Therefore, we propose a new preprocessing method with a non-local means filter for de-noising and contrast limited adaptive histogram equalization. We have confirmed that the pattern of gastric mucosa in images can be improved by the proposed method. Furthermore, the lesion zone is shown more correctly by the obtained color map.

Top 10 Responses to the Commentaries on Dixon, Reed, Smith et al. (2015).

PubMed

Dixon, Mark R; Reed, Derek D; Smith, Tristram; Belisle, Jordan; Jackson, Rachel E

2015-10-01

In a previous article (Dixon et al. Behavior Analysis in Practice, 8 (1), 7-15, 2015), we put forward data suggesting that most behavior analytic faculty do not publish in major behavior analytic journals, and in only about 50 % of behavior analysis programs have faculty combined to produce ten or more empirical articles. Several commentaries followed the release of our article, with content that ranged from supporting our endeavors and confirming the dangerous position our field may be in to highlighting the need for further refinement in procedures used to rank the quality of behavior analysis graduate training programs. Presented in the present article are our "top 10" responses to these commentaries.

Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome

PubMed Central

Shao, Wei; Zhao, Qiong-Yi; Wang, Xiu-Ye; Xu, Xin-Yan; Tang, Qing; Li, Muwang; Li, Xuan; Xu, Yong-Zhen

2012-01-01

Alternative splicing and trans-splicing events have not been systematically studied in the silkworm Bombyx mori. Here, the silkworm transcriptome was analyzed by RNA-seq. We identified 320 novel genes, modified 1140 gene models, and found thousands of alternative splicing and 58 trans-splicing events. Studies of three SR proteins show that both their alternative splicing patterns and mRNA products are conserved from insect to human, and one isoform of Srsf6 with a retained intron is expressed sex-specifically in silkworm gonads. Trans-splicing of mod(mdg4) in silkworm was experimentally confirmed. We identified integrations from a common 5′-gene with 46 newly identified alternative 3′-exons that are located on both DNA strands over a 500-kb region. Other trans-splicing events in B. mori were predicted by bioinformatic analysis, in which 12 events were confirmed by RT-PCR, six events were further validated by chimeric SNPs, and two events were confirmed by allele-specific RT-PCR in F1 hybrids from distinct silkworm lines of JS and L10, indicating that trans-splicing is more widespread in insects than previously thought. Analysis of the B. mori transcriptome by RNA-seq provides valuable information of regulatory alternative splicing events. The conservation of splicing events across species and newly identified trans-splicing events suggest that B. mori is a good model for future studies. PMID:22627775

Life cycle cost analysis of aging aircraft airframe maintenance

NASA Astrophysics Data System (ADS)

Sperry, Kenneth Robert

Scope and method of study. The purpose of this study was to examine the relationship between an aircraft's age and its annual airframe maintenance costs. Common life cycle costing methodology has previously not recognized the existence of this cost growth potential, and has therefor not determined the magnitude nor significance of this cost element. This study analyzed twenty-five years of DOT Form 41-airframe maintenance cost data for the Boeing 727, 737, 747 and McDonnell Douglas DC9 and DC-10 aircraft. Statistical analysis included regression analysis, Pearson's r, and t-tests to test the null hypothesis. Findings and conclusion. Airframe maintenance cost growth was confirmed to be increasing after an aircraft's age exceeded its designed service objective of approximately twenty-years. Annual airframe maintenance cost growth increases were measured ranging from 3.5% annually for a DC-9, to approximately 9% annually for a DC-10 aircraft. Average measured coefficient of determination between age and airframe maintenance, exceeded .80, confirming a strong relationship between cost: and age. The statistical significance of the difference between airframe costs sampled in 1985, compared to airframe costs sampled in 1998 was confirmed by t-tests performed on each subject aircraft group. Future cost forecasts involving aging aircraft subjects must address cost growth due to aging when attempting to model an aircraft's economic service life.

[The homogeneity of a population of yeasts from Camembert cheeses].

PubMed

Schmidt, J L; Daudin, J J

1983-01-01

Yeasts are found to a large extent in cheeses, more particularly in soft cheeses such as Camembert. The proximity between two species previously identified by standard methods was studied using a factorial discriminant analysis on 326 strains. Twenty-three fermentation and assimilation tests (discriminant variables) gave a fairly good discrimination between species. This treatment has allowed us to confirm the present tendencies noticed in yeast classification and has also enabled us to group some of the species.

A note on the effects of viscosity on the stability of a trailing-line vortex

NASA Technical Reports Server (NTRS)

Duck, Peter W.; Khorrami, Mehdi R.

1992-01-01

The linear stability of the Batchelor (1964) vortex is examined with emphasis on new viscous modes recently found numerically by Khorrami (1991). Unlike the previously reported inviscid modes of instability, these modes are destabilized by viscosity and exhibit small growth rates at large Reynolds numbers. The analysis presented here uses a combination of asymptotic and numerical techniques. The results confirm the existence of the additional modes of instability due to viscosity.

A Modified Constant-Stress Coupon for Enhanced Natural Crack Start during Fatigue Testing

DTIC Science & Technology

2016-05-01

improved numerically controlled manufacture. DSTO Research Report DSTO-RR-0340, July 2009. Wescott R, M Jones, M Heller. Stress analysis for design of...has been confirmed by Yu et al. (2014) through experimental strain measurement as well as fatigue tests under spectrum loading. However, as designed ...the results of analyses of a variety of typical non -optimal non -constant stress dog-bone coupon designs . One of those designs has in fact previously

Effects of biases in domain wall network evolution. II. Quantitative analysis

NASA Astrophysics Data System (ADS)

Correia, J. R. C. C. C.; Leite, I. S. C. R.; Martins, C. J. A. P.

2018-04-01

Domain walls form at phase transitions which break discrete symmetries. In a cosmological context, they often overclose the Universe (contrary to observational evidence), although one may prevent this by introducing biases or forcing anisotropic evolution of the walls. In a previous work [Correia et al., Phys. Rev. D 90, 023521 (2014), 10.1103/PhysRevD.90.023521], we numerically studied the evolution of various types of biased domain wall networks in the early Universe, confirming that anisotropic networks ultimately reach scaling while those with a biased potential or biased initial conditions decay. We also found that the analytic decay law obtained by Hindmarsh was in good agreement with simulations of biased potentials, but not of biased initial conditions, and suggested that the difference was related to the Gaussian approximation underlying the analytic law. Here, we extend our previous work in several ways. For the cases of biased potential and biased initial conditions, we study in detail the field distributions in the simulations, confirming that the validity (or not) of the Gaussian approximation is the key difference between the two cases. For anisotropic walls, we carry out a more extensive set of numerical simulations and compare them to the canonical velocity-dependent one-scale model for domain walls, finding that the model accurately predicts the linear scaling regime after isotropization. Overall, our analysis provides a quantitative description of the cosmological evolution of these networks.

Global population genetic structure and male-mediated gene flow in the green sea turtle (Chelonia mydas): analysis of microsatellite loci.

PubMed Central

Roberts, Mark A; Schwartz, Tonia S; Karl, Stephen A

2004-01-01

We assessed the degree of population subdivision among global populations of green sea turtles, Chelonia mydas, using four microsatellite loci. Previously, a single-copy nuclear DNA study indicated significant male-mediated gene flow among populations alternately fixed for different mitochondrial DNA haplotypes and that genetic divergence between populations in the Atlantic and Pacific Oceans was more common than subdivisions among populations within ocean basins. Even so, overall levels of variation at single-copy loci were low and inferences were limited. Here, the markedly more variable microsatellite loci confirm the presence of male-mediated gene flow among populations within ocean basins. This analysis generally confirms the genetic divergence between the Atlantic and Pacific. As with the previous study, phylogenetic analyses of genetic distances based on the microsatellite loci indicate a close genetic relationship among eastern Atlantic and Indian Ocean populations. Unlike the single-copy study, however, the results here cannot be attributed to an artifact of general low variability and likely represent recent or ongoing migration between ocean basins. Sequence analyses of regions flanking the microsatellite repeat reveal considerable amounts of cryptic variation and homoplasy and significantly aid in our understanding of population connectivity. Assessment of the allele frequency distributions indicates that at least some of the loci may not be evolving by the stepwise mutation model. PMID:15126404

Discovering genetic variants in Crohn's disease by exploring genomic regions enriched of weak association signals.

PubMed

D'Addabbo, Annarita; Palmieri, Orazio; Maglietta, Rosalia; Latiano, Anna; Mukherjee, Sayan; Annese, Vito; Ancona, Nicola

2011-08-01

A meta-analysis has re-analysed previous genome-wide association scanning definitively confirming eleven genes and further identifying 21 new loci. However, the identified genes/loci still explain only the minority of genetic predisposition of Crohn's disease. To identify genes weakly involved in disease predisposition by analysing chromosomal regions enriched of single nucleotide polymorphisms with modest statistical association. We utilized the WTCCC data set evaluating 1748 CD and 2938 controls. The identification of candidate genes/loci was performed by a two-step procedure: first of all chromosomal regions enriched of weak association signals were localized; subsequently, weak signals clustered in gene regions were identified. The statistical significance was assessed by non parametric permutation tests. The cytoband enrichment analysis highlighted 44 regions (P≤0.05) enriched with single nucleotide polymorphisms significantly associated with the trait including 23 out of 31 previously confirmed and replicated genes. Importantly, we highlight further 20 novel chromosomal regions carrying approximately one hundred genes/loci with modest association. Amongst these we find compelling functional candidate genes such as MAPT, GRB2 and CREM, LCT, and IL12RB2. Our study suggests a different statistical perspective to discover genes weakly associated with a given trait, although further confirmatory functional studies are needed. Copyright © 2011 Editrice Gastroenterologica Italiana S.r.l. All rights reserved.

Apatinib for metastatic breast cancer in non-clinical trial setting: Satisfying efficacy regardless of previous anti-angiogenic treatment.

PubMed

Lin, Ying; Wu, Zheng; Zhang, Jian; Hu, Xichun; Wang, Zhonghua; Wang, Biyun; Cao, Jun; Wang, Leiping

2017-06-01

Apatinib is a novel tyrosine kinase inhibitor targeting vascular endothelial growth factor receptor 2. This study aimed to evaluate the efficacy and safety of apatinib in metastatic breast cancer (MBC) under non-clinical trial setting, and to study the impact of previous antiangiogenic treatment to the efficacy of apatinib. 52 MBC patients treated with apatinib under non-clinical trial setting in Fudan University Shanghai Cancer Center between January 1st 2015 and October 1st 2016 were included. All patients were included in time-to-treatment failure (TTF) analysis, while 45 patients were enrolled for progression-free survival (PFS) and overall survival (OS) analysis because 7 of the patients with treatment discontinuation due to intolerable toxicities had too short time for efficacy assessment. Impact of previous exposure to antiangiogenic treatment and other factors to patients' survival were analyzed by Log-rank analysis and Cox multivariate analysis. The median PFS, median OS, and median TTF were 4.90 (95% confidence interval [CI] 3.44 - 6.36), 10.3 (unable to calculate 95% CI), and 3.93 (95% CI 1.96 - 5.90) months, respectively. Previous treatment of bevacizumab did not affect the efficacy of apatinib. Previous exposure to anthracycline, age of 60 years or older and palmar-plantar erythrodysesthesia syndrome were independent predictors for prolonged PFS. Discontinuation of treatment was more common in age group of 60 years or older than that in younger group, although the difference was not significant. Although toxicities were generally managable, a previously unrecorded grade 3~4 adverse event of dyspnea has been observed. This study confirmed the encouraging efficacy and manageable safety of apatinib on pretreated MBC patients in non-clinical trial setting. For the first time to our knowledge, this study found that previous treatment of bevacizumab did not affect the efficacy of apatinib, and reported an undocumented severe adverse effect of dyspnea.

Mutation analysis in 129 genes associated with other forms of retinal dystrophy in 157 families with retinitis pigmentosa based on exome sequencing.

PubMed

Xu, Yan; Guan, Liping; Xiao, Xueshan; Zhang, Jianguo; Li, Shiqiang; Jiang, Hui; Jia, Xiaoyun; Yang, Jianhua; Guo, Xiangming; Yin, Ye; Wang, Jun; Zhang, Qingjiong

2015-01-01

Mutations in 60 known genes were previously identified by exome sequencing in 79 of 157 families with retinitis pigmentosa (RP). This study analyzed variants in 129 genes associated with other forms of hereditary retinal dystrophy in the same cohort. Apart from the 73 genes previously analyzed, a further 129 genes responsible for other forms of hereditary retinal dystrophy were selected based on RetNet. Variants in the 129 genes determined by whole exome sequencing were selected and filtered by bioinformatics analysis. Candidate variants were confirmed by Sanger sequencing and validated by analysis of available family members and controls. A total of 90 candidate variants were present in the 129 genes. Sanger sequencing confirmed 83 of the 90 variants. Analysis of family members and controls excluded 76 of these 83 variants. The remaining seven variants were considered to be potential pathogenic mutations; these were c.899A>G, c.1814C>G, and c.2107C>T in BBS2; c.1073C>T and c.1669C>T in INPP5E; and c.3582C>G and c.5704-5C>G in CACNA1F. Six of these seven mutations were novel. The mutations were detected in five unrelated patients without a family history, including three patients with homozygous or compound heterozygous mutations in BBS2 and INPP5E, and two patients with hemizygous mutations in CACNA1F. None of the patients had mutations in the genes associated with autosome dominant retinal dystrophy. Only a small portion of patients with RP, about 3% (5/157), had causative mutations in the 129 genes associated with other forms of hereditary retinal dystrophy.

Direct analysis in real time high resolution mass spectrometry as a tool for rapid characterization of mind-altering plant materials and revelation of supplement adulteration--The case of Kanna.

PubMed

Lesiak, Ashton D; Cody, Robert B; Ubukata, Masaaki; Musah, Rabi A

2016-03-01

We demonstrate the utility of direct analysis in real time ionization coupled with high resolution time-of-flight mass spectrometry (DART-HRTOFMS) in revealing the adulteration of commercially available Sceletium tortuosum, a mind-altering plant-based drug commonly known as Kanna. Accurate masses consistent with alkaloids previously isolated from S. tortuosum plant material enabled identification of the products as Kanna, and in-source collision-induced dissociation (CID) confirmed the presence of one of these alkaloids, hordenine, while simultaneously revealing the presence of an adulterant. The stimulant ephedrine, which has been banned in herbal products and supplements, was confirmed to be present in a sample through the use of in-source CID. High-throughput DART-HRTOFMS was shown to be a powerful tool to not only screen plant-based drugs of abuse for psychotropic alkaloids, but also to reveal the presence of scheduled substances and adulterants. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Proteomic analysis of the venom from the scorpion Mesobuthus martensii.

PubMed

Xu, Xiaobo; Duan, Zhigui; Di, Zhiyong; He, Yawen; Li, Jianglin; Li, Zhongjie; Xie, Chunliang; Zeng, Xiongzhi; Cao, Zhijian; Wu, Yingliang; Liang, Songping; Li, Wenxin

2014-06-25

The scorpion Mesobuthus martensii is the most populous species in eastern Asian countries, and several toxic components have been identified from their venoms. Nevertheless, a complete proteomic profile of the venom of M. martensii is still not available. In this study, the venom of M. martensii was analyzed by comprehensive proteomic approaches. 153 fractions were isolated from the M. martensii venom by 2-DE, SDS-PAGE and RP-HPLC. The ESI-Q-TOF MS results of all fractions were used to search the scorpion genomic and transcriptomic databases. Totally, 227 non-redundant protein sequences were unambiguously identified, composed of 134 previously known and 93 previously unknown proteins. Among 134 previously known proteins, 115 proteins were firstly confirmed from the M. martensii crude venom and 19 toxins were confirmed once again, involving 43 typical toxins, 7 atypical toxins, 12 venom enzymes and 72 cell associated proteins. In typical toxins, 7 novel-toxin sequences were identified, including 3 Na(+)-channel toxins, 3K(+)-channel toxins and 1 no-annotation toxin. These results increased 230% (115/50) venom components compared with previous studies from the M. martensii venom, especially 50% (24/48) typical toxins. Additionally, a mass fingerprint obtained by MALDI-TOF MS indicated that the scorpion venom contained more than 200 different molecular mass components. This work firstly gave a systematic investigation of the M. martensii venom by combined proteomics strategy coupled with genomics and transcriptomics. A large number of protein components were unambiguously identified from the venom of M. martensii, most of which were confirmed for the first time. We also contributed 7 novel-toxin sequences and 93 protein sequences previously unknown to be part of the venom, for which we assigned potential biological functions. Besides, we obtained a mass fingerprint of the M. martensii venom. Together, our study not only provides the most comprehensive catalog of the molecular diversity of the M. martensii venom at the proteomic level, but also enriches the composition information of scorpion venom. Copyright © 2014 Elsevier B.V. All rights reserved.

Parasitological Confirmation and Analysis of Leishmania Diversity in Asymptomatic and Subclinical Infection following Resolution of Cutaneous Leishmaniasis.

PubMed

Rosales-Chilama, Mariana; Gongora, Rafael E; Valderrama, Liliana; Jojoa, Jimena; Alexander, Neal; Rubiano, Luisa C; Cossio, Alexandra; Adams, Emily R; Saravia, Nancy G; Gomez, María Adelaida

2015-12-01

The contribution of individuals with subclinical infection to the transmission and endemicity of cutaneous leishmaniasis (CL) is unknown. Immunological evidence of exposure to Leishmania in residents of endemic areas has been the basis for defining the human population with asymptomatic infection. However, parasitological confirmation of subclinical infection is lacking. We investigated the presence and viability of Leishmania in blood and non-invasive mucosal tissue samples from individuals with immunological evidence of subclinical infection in endemic areas for CL caused by Leishmania (Viannia) in Colombia. Detection of Leishmania kDNA was conducted by PCR-Southern Blot, and parasite viability was confirmed by amplification of parasite 7SLRNA gene transcripts. A molecular tool for genetic diversity analysis of parasite populations causing persistent subclinical infection based on PCR amplification and sequence analysis of an 82bp region between kDNA conserved blocks 1 and 2 was developed. Persistent Leishmania infection was demonstrated in 40% (46 of 114) of leishmanin skin test (LST) positive individuals without active disease; parasite viability was established in 59% of these (27 of 46; 24% of total). Parasite burden quantified from circulating blood monocytes, nasal, conjunctival or tonsil mucosal swab samples was comparable, and ranged between 0.2 to 22 parasites per reaction. kDNA sequences were obtained from samples from 2 individuals with asymptomatic infection and from 26 with history of CL, allowing genetic distance analysis that revealed diversity among sequences and clustering within the L. (Viannia) subgenus. Our results provide parasitological confirmation of persistent infection among residents of endemic areas of L. (Viannia) transmission who have experienced asymptomatic infection or recovered from CL, revealing a reservoir of infection that potentially contributes to the endemicity and transmission of disease. kDNA genotyping establishes proof-of-principle of the feasibility of genetic diversity analysis in previously inaccessible and unexplored parasite populations in subclinically infected individuals.

Three-dimensional structure of the submarine flanks of La Réunion inferred from geophysical data

NASA Astrophysics Data System (ADS)

Gailler, Lydie-Sarah; LéNat, Jean-FrançOis

2010-12-01

La Réunion (Indian Ocean) constitutes a huge volcanic oceanic system of which most of the volume is submerged. We present a study of its submarine part based on the interpretation of magnetic and gravity data compiled from old and recent surveys. A model of the submarine internal structure is derived from 3-D and 2-D models using constraints from previous geological and geophysical studies. Two large-scale, previously unknown, buried volcanic construction zones are discovered in continuation of the island's construction. To the east, the Alizés submarine zone is interpreted as the remnants of Les Alizés volcano eastward flank whose center is marked by a large hypovolcanic intrusion complex. To the southwest, the Etang Salé submarine zone is interpreted as an extension of Piton des Neiges, probably fed by a volcanic rift zone over a large extent. They were predominantly built during the Matuyama period and thus probably belong to early volcanism. A correlation exists between their top and seismic horizons recognized in previous studies and interpreted as the base of the volcanic edifice. Their morphology suggested a lithospheric bulging beneath La Réunion, not required to explain our data, since the seismic interfaces match the top of our volcanic constructions. The coastal shelf coincides with a negative Bouguer anomaly belt, often associated with magnetic anomalies, suggesting a shelf built by hyaloclastites. A detailed analysis of the offshore continuation of La Montagne Massif to the north confirms this hypothesis. The gravity analysis confirms that the bathymetric bulges, forming the northern, eastern, southern, and western submarine flanks, are predominantly built by debris avalanche deposits at the surface.

Hysteroscopic sterilization success in outpatient vs office setting is not affected by patient or procedural characteristics.

PubMed

Anderson, Ted L; Yunker, Amanda C; Scheib, Stacey A; Callahan, Tamara L

2013-01-01

To determine factors associated with hysteroscopic sterilization success and whether it differs between the operating room and office settings. Retrospective cohort analysis (Canadian Task Force classification II-2). Major university medical center. Six hundred thirty-eight women who underwent hysteroscopic sterilization between July 1, 2005, and June 30, 2011. Data collected included age, body mass index, previous office procedures, previous cesarean section, and presence of myomas or retroverted uterus. Place of surgery, experience of surgeon, insurance type, bilateral device placement, compliance with hysterosalpingography, and confirmation of occlusion were also recorded. Bivariate analysis of patient characteristics between groups was performed using χ(2) and independent t tests, and identified confounders and associated variables. Multivariate analysis was performed using logistic regression to assess for association and to adjust for confounders. Procedures were performed in the operating room (57%) or in the office (43%). There was no association between success in bilateral device placement or occlusion and any patient characteristic, regardless of surgery setting. Private insurance, patient age, and performance of procedures in the office setting were positively associated with likelihood of compliance with hysterosalpingography. Successful device placement and tubal occlusion are independent of patient age, body mass index, or setting of the procedure. Association between insurance type and completing hysterosalpingography illustrates an important public health problem. Patients who fail to undergo hysterosalpingography to confirm tubal occlusion may unknowingly be at risk of pregnancy and increased risk of ectopic pregnancy. Copyright © 2013 AAGL. Published by Elsevier Inc. All rights reserved.

Testing BR photocycle kinetics.

PubMed Central

Nagle, J F; Zimanyi, L; Lanyi, J K

1995-01-01

An improved K absorption spectrum in the visible is obtained from previous photocycle data for the D96N mutant of bacteriorhodopsin, and the previously obtained M absorption spectrum in the visible and the fraction cycling are confirmed at 25 degrees C. Data at lower temperatures are consistent with negligible temperature dependence in the spectra from 5 degrees C to 25 degrees C. Detailed analysis strongly indicates that there are two intermediates in addition to the first intermediate K and the last intermediate M. Assuming two of the intermediates have the same spectrum and using the L spectrum obtained previously, the best kinetic model with four intermediates that fits the time course of the intermediates is rather unusual, with two L's on a cul-de-sac. However, a previously proposed, more conventional model with five intermediates, including two L's with the same spectra and two M's with the same spectra, also fits the time course of the intermediates nearly as well. A new criterion that tests an individual proposed spectrum against data is also proposed. PMID:7787034

Matched cohort study of external cephalic version in women with previous cesarean delivery.

PubMed

Keepanasseril, Anish; Anand, Keerthana; Soundara Raghavan, Subrahmanian

2017-07-01

To evaluate the efficacy and safety of external cephalic version (ECV) among women with previous cesarean delivery. A retrospective study was conducted using data for women with previous cesarean delivery and breech presentation who underwent ECV at or after 36 weeks of pregnancy during 2011-2016. For every case, two multiparous women without previous cesarean delivery who underwent ECV and were matched for age and pregnancy duration were included. Characteristics and outcomes were compared between groups. ECV was successful for 32 (84.2%) of 38 women with previous cesarean delivery and 62 (81.6%) in the control group (P=0.728). Multivariate regression analysis confirmed that previous cesarean was not associated with ECV success (odds ratio 1.89, 95% confidence interval 0.19-18.47; P=0.244). Successful vaginal delivery after successful ECV was reported for 19 (59.4%) women in the previous cesarean delivery group and 52 (83.9%) in the control group (P<0.001). No ECV-associated complications occurred in women with previous cesarean delivery. To avoid a repeat cesarean delivery, ECV can be offered to women with breech presentation and previous cesarean delivery who are otherwise eligible for a trial of labor. © 2017 International Federation of Gynecology and Obstetrics.

Osteogenesis imperfecta presenting as aneurysmal subarachnoid haemorrhage in a 53-year-old man

PubMed Central

Kaliaperumal, Chandrasekaran; Walsh, Tom; Balasubramanian, Chandramouli; Wyse, Gerry; Fanning, Noel; Kaar, George

2011-01-01

The authors describe a case of aneurysmal subarachnoid haemorrhage in a 53-year-old man with background of osteogenesis imperfecta (OI). CT brain revealed diffuse subarachnoid haemorrhage (SAH) and cerebral angiogram subsequently confirmed vertebral artery aneurysm rupture leading to SAH. To the authors knowledge this is the first case of vertebral artery aneurysmal SAH described in OI. A previously undiagnosed OI was confirmed by genetic analysis (COL1A1 gene mutation). This aneurysm was successfully treated by endovascular route. Post interventional treatment patient developed stroke secondary to vasospasm. Communicating hydrocephalus, which developed in the process of management, was successfully treated with ventriculo-peritoneal shunt. The aetio-pathogenesis and management of this condition is described. The authors have reviewed the literature and genetic basis of this disease. PMID:22674700

Post-translational glutamylation and tyrosination in tubulin of tritrichomonads and the diplomonad Giardia intestinalis.

PubMed

Boggild, A K; Sundermann, C A; Estridge, B H

2002-01-01

Glutamylated and tyrosinated tubulin were localized in Giardia intestinalis and selected trichomonads of the Tritrichomonadinae subfamily, using specific monoclonal antibodies directed at each of the post-translational modifications. Analysis was carried out using indirect immunofluorescence microscopy. Although trichomonad tubulins remained unlabeled by anti-tyrosine tubulin (TUB-1A2), the presence of the glutamylation motif (GT 335) was confirmed and found to differ in distribution among tritrichomonads. Tritrichomonas muris was most heavily labeled with GT 335, while T. foetus was the least so. Like trichomonads, Giardia was unreactive to anti-tyrosine tubulin; however, the GT 335 antibody produced marked fluorescence in Giardia trophozoites. This study is the first to report immunofluorescent localization of tubulin glutamylation in Giardia and confirms previously reported mass spectrometry data.

Habitat Association and Seasonality in a Mosaic and Bimodal Hybrid Zone between Chorthippus brunneus and C. jacobsi (Orthoptera: Acrididae)

PubMed Central

Tatsuta, Haruki; Butlin, Roger K.

2012-01-01

Understanding why some hybrid zones are bimodal and others unimodal can aid in identifying barriers to gene exchange following secondary contact. The hybrid zone between the grasshoppers Chorthippus brunneus and C. jacobsi contains a mix of allopatric parental populations and inter-mingled bimodal and unimodal sympatric populations, and provides an ideal system to examine the roles of local selection and gene flow between populations in maintaining bimodality. However, it is first necessary to confirm, over a larger spatial scale, previously identified associations between population composition and season and habitat. Here we use cline-fitting of one morphological and one song trait along two valley transects, and intervening mountains, to confirm previously identified habitat associations (mountain versus valley) and seasonal changes in population composition. As expected from previous findings of studies on a smaller spatial scale, C. jacobsi dominated mountain habitats and mixed populations dominated valleys, and C. brunneus became more prevalent in August. Controlling for habitat and incorporating into the analysis seasonal changes in cline parameters and the standard errors of parental trait values revealed wider clines than previous studies (best estimates of 6.4 to 24.5 km in our study versus 2.8 to 4.7 km in previous studies) and increased percentage of trait variance explained (52.7% and 61.5% for transects 1 and 2 respectively, versus 17.6%). Revealing such strong and consistent patterns within a complex hybrid zone will allow more focused examination of the causes of variation in bimodality in mixed populations, in particular the roles of local selection versus habitat heterogeneity and gene flow between differentiated populations. PMID:22675485

Association of transforming growth-factor alpha gene polymorphisms with nonsyndromic cleft palate only (CPO)

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

Shiang, R.; Lidral, A.C.; Ardinger, H.H.

1993-10-01

Genetic analysis and tissue-specific expression studies support a role for transforming growth-factor alpha (TGFA) in craniofacial development. Previous studies have confirmed an association of alleles for TGFA with nonsyndromic cleft lip with or without cleft palate (CL/P) in humans. The authors carried out a retrospective association study to determine whether specific allelic variants of the TGFA gene are also associated with cleft palate only (CPO). The PCR products from 12 overlapping sets of primers to the TGFA cDNA were examined by using single-strand conformational polymorphism analysis. Four DNA polymorphic sites for TGFA were identified in the 3[prime] untranslated region ofmore » the TGFA gene. These variants, as well as previously identified RFLPs for TGFA, were characterized in case and control populations for CPO by using X[sup 2] analysis. A significant association between alleles of TGFA and CPO was identified which further supports a role for this gene as one of the genetic determinants of craniofacial development. Sequence analysis of the variants disclosed a cluster of three variable sites within 30 bp of each other in the 3[prime] untranslated region previously associated with an antisense transcript. These studies extend the role for TGFA in craniofacial morphogenesis and support an interrelated mechanism underlying nonsyndromic forms of CL/P. 46 refs., 3 figs., 3 tabs.« less

Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci.

PubMed

Tragante, Vinicius; Barnes, Michael R; Ganesh, Santhi K; Lanktree, Matthew B; Guo, Wei; Franceschini, Nora; Smith, Erin N; Johnson, Toby; Holmes, Michael V; Padmanabhan, Sandosh; Karczewski, Konrad J; Almoguera, Berta; Barnard, John; Baumert, Jens; Chang, Yen-Pei Christy; Elbers, Clara C; Farrall, Martin; Fischer, Mary E; Gaunt, Tom R; Gho, Johannes M I H; Gieger, Christian; Goel, Anuj; Gong, Yan; Isaacs, Aaron; Kleber, Marcus E; Mateo Leach, Irene; McDonough, Caitrin W; Meijs, Matthijs F L; Melander, Olle; Nelson, Christopher P; Nolte, Ilja M; Pankratz, Nathan; Price, Tom S; Shaffer, Jonathan; Shah, Sonia; Tomaszewski, Maciej; van der Most, Peter J; Van Iperen, Erik P A; Vonk, Judith M; Witkowska, Kate; Wong, Caroline O L; Zhang, Li; Beitelshees, Amber L; Berenson, Gerald S; Bhatt, Deepak L; Brown, Morris; Burt, Amber; Cooper-DeHoff, Rhonda M; Connell, John M; Cruickshanks, Karen J; Curtis, Sean P; Davey-Smith, George; Delles, Christian; Gansevoort, Ron T; Guo, Xiuqing; Haiqing, Shen; Hastie, Claire E; Hofker, Marten H; Hovingh, G Kees; Kim, Daniel S; Kirkland, Susan A; Klein, Barbara E; Klein, Ronald; Li, Yun R; Maiwald, Steffi; Newton-Cheh, Christopher; O'Brien, Eoin T; Onland-Moret, N Charlotte; Palmas, Walter; Parsa, Afshin; Penninx, Brenda W; Pettinger, Mary; Vasan, Ramachandran S; Ranchalis, Jane E; M Ridker, Paul; Rose, Lynda M; Sever, Peter; Shimbo, Daichi; Steele, Laura; Stolk, Ronald P; Thorand, Barbara; Trip, Mieke D; van Duijn, Cornelia M; Verschuren, W Monique; Wijmenga, Cisca; Wyatt, Sharon; Young, J Hunter; Zwinderman, Aeilko H; Bezzina, Connie R; Boerwinkle, Eric; Casas, Juan P; Caulfield, Mark J; Chakravarti, Aravinda; Chasman, Daniel I; Davidson, Karina W; Doevendans, Pieter A; Dominiczak, Anna F; FitzGerald, Garret A; Gums, John G; Fornage, Myriam; Hakonarson, Hakon; Halder, Indrani; Hillege, Hans L; Illig, Thomas; Jarvik, Gail P; Johnson, Julie A; Kastelein, John J P; Koenig, Wolfgang; Kumari, Meena; März, Winfried; Murray, Sarah S; O'Connell, Jeffery R; Oldehinkel, Albertine J; Pankow, James S; Rader, Daniel J; Redline, Susan; Reilly, Muredach P; Schadt, Eric E; Kottke-Marchant, Kandice; Snieder, Harold; Snyder, Michael; Stanton, Alice V; Tobin, Martin D; Uitterlinden, André G; van der Harst, Pim; van der Schouw, Yvonne T; Samani, Nilesh J; Watkins, Hugh; Johnson, Andrew D; Reiner, Alex P; Zhu, Xiaofeng; de Bakker, Paul I W; Levy, Daniel; Asselbergs, Folkert W; Munroe, Patricia B; Keating, Brendan J

2014-03-06

Blood pressure (BP) is a heritable risk factor for cardiovascular disease. To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP), we genotyped ~50,000 SNPs in up to 87,736 individuals of European ancestry and combined these in a meta-analysis. We replicated findings in an independent set of 68,368 individuals of European ancestry. Our analyses identified 11 previously undescribed associations in independent loci containing 31 genes including PDE1A, HLA-DQB1, CDK6, PRKAG2, VCL, H19, NUCB2, RELA, HOXC@ complex, FBN1, and NFAT5 at the Bonferroni-corrected array-wide significance threshold (p < 6 × 10(-7)) and confirmed 27 previously reported associations. Bioinformatic analysis of the 11 loci provided support for a putative role in hypertension of several genes, such as CDK6 and NUCB2. Analysis of potential pharmacological targets in databases of small molecules showed that ten of the genes are predicted to be a target for small molecules. In summary, we identified previously unknown loci associated with BP. Our findings extend our understanding of genes involved in BP regulation, which may provide new targets for therapeutic intervention or drug response stratification. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Phytophthora parsiana sp. nov., a new high-temperature tolerant species.

PubMed

Mostowfizadeh-Ghalamfarsa, R; Cooke, D E L; Banihashemi, Z

2008-07-01

As part of a study to examine the phylogenetic history of the taxonomically challenging species Phytophthora cryptogea and P. drechsleri, a distinct monophyletic group of isolates, previously described as P. drechsleri or P. cryptogea, were characterised. Analysis of their rDNA ITS sequences indicated that these isolates were distinct from P. drechsleri, P. cryptogea, and all members of Phytophthora ITS clades 1-8, clustering instead alongside basal groups previously described as clades 9 and 10. This group comprised six isolates all of which were isolated from woody plants, such as pistachio (Pistacia vera, Iran and USA), fig (Ficus carica, Iran), and almond (Prunus dulcis, Greece). Analysis of sequence data from nuclear (beta-tubulin and translation elongation factor 1alpha) and mitochondrial (cytochrome c oxidase subunit I) genes confirmed the ITS-based analysis as these isolates formed a distinct monophyletic group in all NJ trees. The isolates were fast growing with a relatively high optimum growth temperature of 30 degrees C and, in most cases, rapid colony growth even at 37 degrees C. The isolates produced complex colony patterns on almost all media, especially corn meal agar (CMA). Phylogenetic analysis and examination of all the other morphological and physiological data lead us to infer that this taxon has not been described previously. As this taxon was first isolated and described from Iran we propose that this taxon be formally designated as Phytophthora parsiana.

High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal Cheeses

PubMed Central

Quigley, Lisa; O'Sullivan, Orla; Beresford, Tom P.; Ross, R. Paul; Fitzgerald, Gerald F.

2012-01-01

Here, high-throughput sequencing was employed to reveal the highly diverse bacterial populations present in 62 Irish artisanal cheeses and, in some cases, associated cheese rinds. Using this approach, we revealed the presence of several genera not previously associated with cheese, including Faecalibacterium, Prevotella, and Helcococcus and, for the first time, detected the presence of Arthrobacter and Brachybacterium in goats' milk cheese. Our analysis confirmed many previously observed patterns, such as the dominance of typical cheese bacteria, the fact that the microbiota of raw and pasteurized milk cheeses differ, and that the level of cheese maturation has a significant influence on Lactobacillus populations. It was also noted that cheeses containing adjunct ingredients had lower proportions of Lactococcus species. It is thus apparent that high-throughput sequencing-based investigations can provide valuable insights into the microbial populations of artisanal foods. PMID:22685131

High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses.

PubMed

Quigley, Lisa; O'Sullivan, Orla; Beresford, Tom P; Ross, R Paul; Fitzgerald, Gerald F; Cotter, Paul D

2012-08-01

Here, high-throughput sequencing was employed to reveal the highly diverse bacterial populations present in 62 Irish artisanal cheeses and, in some cases, associated cheese rinds. Using this approach, we revealed the presence of several genera not previously associated with cheese, including Faecalibacterium, Prevotella, and Helcococcus and, for the first time, detected the presence of Arthrobacter and Brachybacterium in goats' milk cheese. Our analysis confirmed many previously observed patterns, such as the dominance of typical cheese bacteria, the fact that the microbiota of raw and pasteurized milk cheeses differ, and that the level of cheese maturation has a significant influence on Lactobacillus populations. It was also noted that cheeses containing adjunct ingredients had lower proportions of Lactococcus species. It is thus apparent that high-throughput sequencing-based investigations can provide valuable insights into the microbial populations of artisanal foods.

ABO blood groups, Rhesus negativity, and primary biliary cirrhosis

PubMed Central

Hamlyn, A. N.; Morris, J. S.; Sherlock, S.

1974-01-01

The distribution of blood groups and Rhesus negativity in 91 British patients with primary biliary cirrhosis was compared with a sample of registered blood donors. There were no significant differences from the expected proportions calculated from the control groups. Although the number of cases studied is small the analysis does not confirm previous reports of an excess of A group in the disease. If a genetic basis exists for primary biliary cirrhosis alternative markers must be found. PMID:4211827

Flash melting of tantalum in a diamond cell to 85 GPa

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

Karandikar, Amol; Boehler, Reinhard

2016-02-09

Here, we demonstrate a new level of precision in measuring melting temperatures at high pressure using laser flash-heating followed by Scanning Electron Microscopy and Focused Ion Beam Milling. Furthermore, the new measurements on tantalum put unprecedented constraints on its highly debated melting slope, calling for a reevaluation of theoretical, shock compression and diamond cell approaches to determine melting at high pressure. X-ray analysis of the recovered samples confirmed the absence of chemical reactions, which likely played a significant role in previous experiments.

Research on Capturing of Customer Requirements Based on Innovation Theory

NASA Astrophysics Data System (ADS)

junwu, Ding; dongtao, Yang; zhenqiang, Bao

To exactly and effectively capture customer requirements information, a new customer requirements capturing modeling method was proposed. Based on the analysis of function requirement models of previous products and the application of technology system evolution laws of the Theory of Innovative Problem Solving (TRIZ), the customer requirements could be evolved from existing product designs, through modifying the functional requirement unit and confirming the direction of evolution design. Finally, a case study was provided to illustrate the feasibility of the proposed approach.

Metastatic carcinoma of breast or a chordoma? A case report and clinical perspectives.

PubMed

Trivedi, Sachin; Odrazka, Karel

2015-01-01

We present a case of chordoma in a patient who had been previously treated for ductal carcinoma of the breast. The initial clinical findings and radiological studies suggested a possibility of metastases. However, the findings also adhered to the classical presentations and findings of the chordoma of the base of skull. It was only after the surgical resection and immunohistochemical confirmation that the diagnosis of chordoma could be established. Here, we discuss chordoma with the analysis of our clinical intrigue.

Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci

PubMed Central

Zhernakova, Alexandra; Stahl, Eli A.; Trynka, Gosia; Raychaudhuri, Soumya; Festen, Eleanora A.; Franke, Lude; Westra, Harm-Jan; Fehrmann, Rudolf S. N.; Kurreeman, Fina A. S.; Thomson, Brian; Gupta, Namrata; Romanos, Jihane; McManus, Ross; Ryan, Anthony W.; Turner, Graham; Brouwer, Elisabeth; Posthumus, Marcel D.; Remmers, Elaine F.; Tucci, Francesca; Toes, Rene; Grandone, Elvira; Mazzilli, Maria Cristina; Rybak, Anna; Cukrowska, Bozena; Coenen, Marieke J. H.; Radstake, Timothy R. D. J.; van Riel, Piet L. C. M.; Li, Yonghong; de Bakker, Paul I. W.; Gregersen, Peter K.; Worthington, Jane; Siminovitch, Katherine A.; Klareskog, Lars; Huizinga, Tom W. J.

2011-01-01

Epidemiology and candidate gene studies indicate a shared genetic basis for celiac disease (CD) and rheumatoid arthritis (RA), but the extent of this sharing has not been systematically explored. Previous studies demonstrate that 6 of the established non-HLA CD and RA risk loci (out of 26 loci for each disease) are shared between both diseases. We hypothesized that there are additional shared risk alleles and that combining genome-wide association study (GWAS) data from each disease would increase power to identify these shared risk alleles. We performed a meta-analysis of two published GWAS on CD (4,533 cases and 10,750 controls) and RA (5,539 cases and 17,231 controls). After genotyping the top associated SNPs in 2,169 CD cases and 2,255 controls, and 2,845 RA cases and 4,944 controls, 8 additional SNPs demonstrated P<5×10−8 in a combined analysis of all 50,266 samples, including four SNPs that have not been previously confirmed in either disease: rs10892279 near the DDX6 gene (Pcombined = 1.2×10−12), rs864537 near CD247 (Pcombined = 2.2×10−11), rs2298428 near UBE2L3 (Pcombined = 2.5×10−10), and rs11203203 near UBASH3A (Pcombined = 1.1×10−8). We also confirmed that 4 gene loci previously established in either CD or RA are associated with the other autoimmune disease at combined P<5×10−8 (SH2B3, 8q24, STAT4, and TRAF1-C5). From the 14 shared gene loci, 7 SNPs showed a genome-wide significant effect on expression of one or more transcripts in the linkage disequilibrium (LD) block around the SNP. These associations implicate antigen presentation and T-cell activation as a shared mechanism of disease pathogenesis and underscore the utility of cross-disease meta-analysis for identification of genetic risk factors with pleiotropic effects between two clinically distinct diseases. PMID:21383967

Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.

PubMed

Zhernakova, Alexandra; Stahl, Eli A; Trynka, Gosia; Raychaudhuri, Soumya; Festen, Eleanora A; Franke, Lude; Westra, Harm-Jan; Fehrmann, Rudolf S N; Kurreeman, Fina A S; Thomson, Brian; Gupta, Namrata; Romanos, Jihane; McManus, Ross; Ryan, Anthony W; Turner, Graham; Brouwer, Elisabeth; Posthumus, Marcel D; Remmers, Elaine F; Tucci, Francesca; Toes, Rene; Grandone, Elvira; Mazzilli, Maria Cristina; Rybak, Anna; Cukrowska, Bozena; Coenen, Marieke J H; Radstake, Timothy R D J; van Riel, Piet L C M; Li, Yonghong; de Bakker, Paul I W; Gregersen, Peter K; Worthington, Jane; Siminovitch, Katherine A; Klareskog, Lars; Huizinga, Tom W J; Wijmenga, Cisca; Plenge, Robert M

2011-02-01

Epidemiology and candidate gene studies indicate a shared genetic basis for celiac disease (CD) and rheumatoid arthritis (RA), but the extent of this sharing has not been systematically explored. Previous studies demonstrate that 6 of the established non-HLA CD and RA risk loci (out of 26 loci for each disease) are shared between both diseases. We hypothesized that there are additional shared risk alleles and that combining genome-wide association study (GWAS) data from each disease would increase power to identify these shared risk alleles. We performed a meta-analysis of two published GWAS on CD (4,533 cases and 10,750 controls) and RA (5,539 cases and 17,231 controls). After genotyping the top associated SNPs in 2,169 CD cases and 2,255 controls, and 2,845 RA cases and 4,944 controls, 8 additional SNPs demonstrated P<5 × 10(-8) in a combined analysis of all 50,266 samples, including four SNPs that have not been previously confirmed in either disease: rs10892279 near the DDX6 gene (P(combined) =  1.2 × 10(-12)), rs864537 near CD247 (P(combined) =  2.2 × 10(-11)), rs2298428 near UBE2L3 (P(combined) =  2.5 × 10(-10)), and rs11203203 near UBASH3A (P(combined) =  1.1 × 10(-8)). We also confirmed that 4 gene loci previously established in either CD or RA are associated with the other autoimmune disease at combined P<5 × 10(-8) (SH2B3, 8q24, STAT4, and TRAF1-C5). From the 14 shared gene loci, 7 SNPs showed a genome-wide significant effect on expression of one or more transcripts in the linkage disequilibrium (LD) block around the SNP. These associations implicate antigen presentation and T-cell activation as a shared mechanism of disease pathogenesis and underscore the utility of cross-disease meta-analysis for identification of genetic risk factors with pleiotropic effects between two clinically distinct diseases.

Real-time Raman spectroscopy for automatic in vivo skin cancer detection: an independent validation.

PubMed

Zhao, Jianhua; Lui, Harvey; Kalia, Sunil; Zeng, Haishan

2015-11-01

In a recent study, we have demonstrated that real-time Raman spectroscopy could be used for skin cancer diagnosis. As a translational study, the objective of this study is to validate previous findings through a completely independent clinical test. In total, 645 confirmed cases were included in the analysis, including a cohort of 518 cases from a previous study, and an independent cohort of 127 new cases. Multi-variant statistical data analyses including principal component with general discriminant analysis (PC-GDA) and partial least squares (PLS) were used separately for lesion classification, which generated similar results. When the previous cohort (n = 518) was used as training and the new cohort (n = 127) was used as testing, the area under the receiver operating characteristic curve (ROC AUC) was found to be 0.889 (95 % CI 0.834-0.944; PLS); when the two cohorts were combined, the ROC AUC was 0.894 (95 % CI 0.870-0.918; PLS) with the narrowest confidence intervals. Both analyses were comparable to the previous findings, where the ROC AUC was 0.896 (95 % CI 0.846-0.946; PLS). The independent study validates that real-time Raman spectroscopy could be used for automatic in vivo skin cancer diagnosis with good accuracy.

Image-Subtraction Photometry of Variable Stars in the Globular Clusters NGC 6388 and NGC 6441

NASA Technical Reports Server (NTRS)

Corwin, Michael T.; Sumerel, Andrew N.; Pritzl, Barton J.; Smith, Horace A.; Catelan, M.; Sweigart, Allen V.; Stetson, Peter B.

2006-01-01

We have applied Alard's image subtraction method (ISIS v2.1) to the observations of the globular clusters NGC 6388 and NGC 6441 previously analyzed using standard photometric techniques (DAOPHOT, ALLFRAME). In this reanalysis of observations obtained at CTIO, besides recovering the variables previously detected on the basis of our ground-based images, we have also been able to recover most of the RR Lyrae variables previously detected only in the analysis of Hubble Space Telescope WFPC2 observations of the inner region of NGC 6441. In addition, we report five possible new variables not found in the analysis of the EST observations of NGC 6441. This dramatically illustrates the capabilities of image subtraction techniques applied to ground-based data to recover variables in extremely crowded fields. We have also detected twelve new variables and six possible variables in NGC 6388 not found in our previous groundbased studies. Revised mean periods for RRab stars in NGC 6388 and NGC 6441 are 0.676 day and 0.756 day, respectively. These values are among the largest known for any galactic globular cluster. Additional probable type II Cepheids were identified in NGC 6388, confirming its status as a metal-rich globular cluster rich in Cepheids.

Gender differences in self-rated and partner-rated multiple intelligences: a Portuguese replication.

PubMed

Neto, Félix; Furnham, Adrian

2006-11-01

The authors examined gender differences and the influence of intelligence quotient (IQ) test experience in the self and partner estimation of H. Gardner's (1999) 10 multiple intelligences. Portuguese students (N = 190) completed a brief questionnaire developed on the basis of an instrument used in previous research (A. Furnham, 2001). Three of the 10 self-estimates yielded significant gender differences. Men believed they were more intelligent than were women on mathematical (logical), spatial, and naturalistic intelligence. Those who had previously completed an IQ test gave higher self-estimates on 2 of the 10 estimates. Factor analysis of the 10 and then 8 self-estimated scores did not confirm Gardner's 3-factor classification of multiple intelligences in this sample.

Analysis of chaos in high-dimensional wind power system.

PubMed

Wang, Cong; Zhang, Hongli; Fan, Wenhui; Ma, Ping

2018-01-01

A comprehensive analysis on the chaos of a high-dimensional wind power system is performed in this study. A high-dimensional wind power system is more complex than most power systems. An 11-dimensional wind power system proposed by Huang, which has not been analyzed in previous studies, is investigated. When the systems are affected by external disturbances including single parameter and periodic disturbance, or its parameters changed, chaotic dynamics of the wind power system is analyzed and chaotic parameters ranges are obtained. Chaos existence is confirmed by calculation and analysis of all state variables' Lyapunov exponents and the state variable sequence diagram. Theoretical analysis and numerical simulations show that the wind power system chaos will occur when parameter variations and external disturbances change to a certain degree.

Parsing the genetic heterogeneity of chromosome 12q susceptibility genes for Alzheimer disease by family-based association analysis.

PubMed

Lin, Ping-I; Martin, Eden R; Browning-Large, Carrie A; Schmechel, Donald E; Welsh-Bohmer, Kathleen A; Doraiswamy, P Murali; Gilbert, John R; Haines, Jonathan L; Pericak-Vance, Margaret A

2006-07-01

Previous linkage studies have suggested that chromosome 12 may harbor susceptibility genes for late-onset Alzheimer disease (LOAD). No risk genes on chromosome 12 have been conclusively identified yet. We have reported that the linkage evidence for LOAD in a 12q region was significantly increased in autopsy-confirmed families particularly for those showing no linkage to alpha-T catenin gene, a LOAD candidate gene on chromosome 10 [LOD score increased from 0.1 in the autopsy-confirmed subset to 4.19 in the unlinked subset (optimal subset); p<0.0001 for the increase in LOD score], indicating a one-LOD support interval spanning 6 Mb. To further investigate this finding and to identify potential candidate LOAD risk genes for follow-up analysis, we analyzed 99 single nucleotide polymorphisms in this region, for the overall sample, the autopsy-confirmed subset, and the optimal subset, respectively, for comparison. We saw no significant association (p<0.01) in the overall sample. In the autopsy-confirmed subset, the best finding was obtained in the activation transcription factor 7 (ATF7) gene (single-locus association, p=0.002; haplotype association global, p=0.007). In the optimal subset, the best finding was obtained in the hypothetical protein FLJ20436 (FLJ20436) gene (single-locus association, p=0.0026). These results suggest that subset and covariate analyses may be one approach to help identify novel susceptibility genes on chromosome 12q for LOAD.

Linkage and association study of late-onset Alzheimer disease families linked to 9p21.3.

PubMed

Züchner, S; Gilbert, J R; Martin, E R; Leon-Guerrero, C R; Xu, P-T; Browning, C; Bronson, P G; Whitehead, P; Schmechel, D E; Haines, J L; Pericak-Vance, M A

2008-11-01

A chromosomal locus for late-onset Alzheimer disease (LOAD) has previously been mapped to 9p21.3. The most significant results were reported in a sample of autopsy-confirmed families. Linkage to this locus has been independently confirmed in AD families from a consanguineous Israeli-Arab community. In the present study we analyzed an expanded clinical sample of 674 late-onset AD families, independently ascertained by three different consortia. Sample subsets were stratified by site and autopsy-confirmation. Linkage analysis of a dense array of SNPs across the chromosomal locus revealed the most significant results in the 166 autopsy-confirmed families of the NIMH sample. Peak HLOD scores of 4.95 at D9S741 and 2.81 at the nearby SNP rs2772677 were obtained in a dominant model. The linked region included the cyclin-dependent kinase inhibitor 2A gene (CDKN2A), which has been suggested as an AD candidate gene. By re-sequencing all exons in the vicinity of CDKN2A in 48 AD cases, we identified and genotyped four novel SNPs, including a non-synonymous, a synonymous, and two variations located in untranslated RNA sequences. Family-based allelic and genotypic association analysis yielded significant results in CDKN2A (rs11515: PDT p = 0.003, genotype-PDT p = 0.014). We conclude that CDKN2A is a promising new candidate gene potentially contributing to AD susceptibility on chromosome 9p.

Coriandrum sativum mediated synthesis of silver nanoparticles and evaluation of their biological characteristics

NASA Astrophysics Data System (ADS)

Senthilkumar, N.; Aravindhan, V.; Ruckmani, K.; Vetha Potheher, I.

2018-05-01

Silver (Ag) nanoparticles (NPs) were prepared by percolated green synthesis method using Coriandrum sativum leaf, root, seed and stem extracts and reported its antibacterial activity. The synthesized Ag NPs were confirmed by UV–visible Spectroscopy, Powder x-ray Diffraction (PXRD), Fourier Transform Infra Red (FT-IR) Spectroscopy analyzes. The Maximum absorbance observed around 400–450 nm reveal the characteristic absorbance of Ag NPs. The Dynamic Light Scattering (DLS) analysis shows the stability of synthesized NPs with average size varying from 35 to 53 nm and also zeta potential stability varying from ‑20 to ‑30 mV. The cubic structure, crystalline nature and purity of the material was confirmed by powder x-ray diffraction studies. FT-IR spectrum shows the presence of various functional groups in the resultant material. The Field Emission Scanning Electron Microscopy (FESEM) image shows the surface morphology of the synthesized NPs and the Energy Dispersive x-ray Analysis (EDAX) confirms the presence of silver metal ions. The Coriandrum sativum aqueous extract exhibited excellent antimicrobial activity against Klebsiella pneumoniae (Gram -ve) bacteria. Numerous studies have been made previously in our field of study but optimization has not been carried out by both extract (different parts like leaf, root, seed and stem) and without addition of any external source such as chemicals, heat etc.

Multi-modal management of acromegaly: a value perspective.

PubMed

Kimmell, Kristopher T; Weil, Robert J; Marko, Nicholas F

2015-10-01

The Acromegaly Consensus Group recently released updated guidelines for medical management of acromegaly patients. We subjected these guidelines to a cost analysis. We conducted a cost analysis of the recommendations based on published efficacy rates as well as publicly available cost data. The results were compared to findings from a previously reported comparative effectiveness analysis of acromegaly treatments. Using decision tree software, two models were created based on the Acromegaly Consensus Group's recommendations and the comparative effectiveness analysis. The decision tree for the Consensus Group's recommendations was subjected to multi-way tornado analysis to identify variables that most impacted the value analysis of the decision tree. The value analysis confirmed the Consensus Group's recommendations of somatostatin analogs as first line therapy for medical management. Our model also demonstrated significant value in using dopamine agonist agents as upfront therapy as well. Sensitivity analysis identified the cost of somatostatin analogs and growth hormone receptor antagonists as having the most significant impact on the cost effectiveness of medical therapies. Our analysis confirmed the value of surgery as first-line therapy for patients with surgically accessible lesions. Surgery provides the greatest value for management of patients with acromegaly. However, in accordance with the Acromegaly Consensus Group's recent recommendations, somatostatin analogs provide the greatest value and should be used as first-line therapy for patients who cannot be managed surgically. At present, the substantial cost is the most significant negative factor in the value of medical therapies for acromegaly.

Reoccurrence of retained placenta at vaginal delivery: an observational study.

PubMed

Nikolajsen, Sys; Løkkegaard, Ellen Christine Leth; Bergholt, Thomas

2013-04-01

To estimate the prevalence and validate the diagnosis of retained placenta in nulliparous women and the risk of reoccurrence at subsequent vaginal delivery. Nested cohort study. Department of Gynecology and Obstetrics, university-affiliated teaching hospital. 10 334 nulliparous singleton pregnancies who delivered vaginally at the hospital during 2000-2009. Data from a computerized database information system were used to identify 287 women who had an ICD-10 diagnosis of retained placenta and 572 randomly selected controls matched by the date of first delivery. At chart review the diagnosis was confirmed by: (1) excessive bleeding <30 minutes after delivery without placental separation, (2) placenta not separated 30 minutes after delivery or (3) confirmation of retained placental tissue >2 hours postpartum. Confirmation of the diagnosis and prevalence of retained placenta. Risk of reoccurrence in a subsequent vaginal delivery. The prevalence of retained placenta increased from 2.8 to 7.0% after confirmation according to the set criteria. Of the selected women, 48.4% had a subsequent vaginal delivery. Of these women, 25.3% (23/91) with a previous retained placenta and 5.3% (11/206) without previously retained placenta, experienced retained placenta in subsequent delivery. This corresponds to an adjusted odds ratio of 5.5 (95% confidence interval 2.6-12.7) in the multivariate analysis for recurrence of retained placenta in a subsequent vaginal delivery. The use of the ICD-10 diagnosis of retained placenta underestimated the prevalence. The risk of reoccurrence of retained placenta is significantly increased in a subsequent vaginal delivery. © 2012 The Authors Acta Obstetricia et Gynecologica Scandinavica © 2012 Nordic Federation of Societies of Obstetrics and Gynecology.

Identification of BAG3 target proteins in anaplastic thyroid cancer cells by proteomic analysis.

PubMed

Galdiero, Francesca; Bello, Anna Maria; Spina, Anna; Capiluongo, Anna; Liuu, Sophie; De Marco, Margot; Rosati, Alessandra; Capunzo, Mario; Napolitano, Maria; Vuttariello, Emilia; Monaco, Mario; Califano, Daniela; Turco, Maria Caterina; Chiappetta, Gennaro; Vinh, Joëlle; Chiappetta, Giovanni

2018-01-30

BAG3 protein is an apoptosis inhibitor and is highly expressed in Anaplastic Thyroid Cancer. We investigated the entire set of proteins modulated by BAG3 silencing in the human anaplastic thyroid 8505C cancer cells by using the Stable-Isotope Labeling by Amino acids in Cell culture strategy combined with mass spectrometry analysis. By this approach we identified 37 up-regulated and 54 down-regulated proteins in BAG3-silenced cells. Many of these proteins are reportedly involved in tumor progression, invasiveness and resistance to therapies. We focused our attention on an oncogenic protein, CAV1, and a tumor suppressor protein, SERPINB2, that had not previously been reported to be modulated by BAG3. Their expression levels in BAG3-silenced cells were confirmed by qRT-PCR and western blot analyses, disclosing two novel targets of BAG3 pro-tumor activity. We also examined the dataset of proteins obtained by the quantitative proteomics analysis using two tools, Downstream Effect Analysis and Upstream Regulator Analysis of the Ingenuity Pathways Analysis software. Our analyses confirm the association of the proteome profile observed in BAG3-silenced cells with an increase in cell survival and a decrease in cell proliferation and invasion, and highlight the possible involvement of four tumor suppressor miRNAs and TP53/63 proteins in BAG3 activity.

First reported case in the UK of acute prolonged neuropsychiatric toxicity associated with analytically confirmed recreational use of phenazepam.

PubMed

Dargan, Paul I; Davies, Susannah; Puchnarewicz, Malgorzata; Johnston, Atholl; Wood, David M

2013-03-01

There is increasing evidence from around Europe of the availability and misuse of long-acting benzodiazepines such as phenazepam. There is little information on the acute toxicity of these compounds; we describe here a case of analytically confirmed phenazepam-related acute toxicity. A 42-year-old man with no previous medical or psychiatric history was brought to the Emergency Department by his friends because he had developed prolonged ongoing confusion and disorientation following use of up to three different "legal high" powders. There was no obvious medical cause for this acute confusion and disorientation. His symptoms continued for approximately 60 h after suspected use. Subsequent toxicological analysis of a serum sample confirmed use of phenazepam (concentration 0.49 mg/L); no other drugs were detected during an extensive analytical screening. This is the second case of analytically confirmed acute toxicity related to phenazepam in Europe. This adds to the scant published information on the acute toxicity of this drug, and will provide healthcare and legislative authorities with further information on which to base advice and consideration of the need for its control.

Development and confirmation of potential gene classifiers of human clear cell renal cell carcinoma using next-generation RNA sequencing.

PubMed

Eikrem, Oystein S; Strauss, Philipp; Beisland, Christian; Scherer, Andreas; Landolt, Lea; Flatberg, Arnar; Leh, Sabine; Beisvag, Vidar; Skogstrand, Trude; Hjelle, Karin; Shresta, Anjana; Marti, Hans-Peter

2016-12-01

A previous study by this group demonstrated the feasibility of RNA sequencing (RNAseq) technology for capturing disease biology of clear cell renal cell carcinoma (ccRCC), and presented initial results for carbonic anhydrase-9 (CA9) and tumor necrosis factor-α-induced protein-6 (TNFAIP6) as possible biomarkers of ccRCC (discovery set) [Eikrem et al. PLoS One 2016;11:e0149743]. To confirm these results, the previous study is expanded, and RNAseq data from additional matched ccRCC and normal renal biopsies are analyzed (confirmation set). Two core biopsies from patients (n = 12) undergoing partial or full nephrectomy were obtained with a 16 g needle. RNA sequencing libraries were generated with the Illumina TruSeq ® Access library preparation protocol. Comparative analysis was done using linear modeling (voom/Limma; R Bioconductor). The formalin-fixed and paraffin-embedded discovery and confirmation data yielded 8957 and 11,047 detected transcripts, respectively. The two data sets shared 1193 of differentially expressed genes with each other. The average expression and the log 2 -fold changes of differentially expressed transcripts in both data sets correlated, with R²   =   .95 and R²   =   .94, respectively. Among transcripts with the highest fold changes were CA9, neuronal pentraxin-2 and uromodulin. Epithelial-mesenchymal transition was highlighted by differential expression of, for example, transforming growth factor-β 1 and delta-like ligand-4. The diagnostic accuracy of CA9 was 100% and 93.9% when using the discovery set as the training set and the confirmation data as the test set, and vice versa, respectively. These data further support TNFAIP6 as a novel biomarker of ccRCC. TNFAIP6 had combined accuracy of 98.5% in the two data sets. This study provides confirmatory data on the potential use of CA9 and TNFAIP6 as biomarkers of ccRCC. Thus, next-generation sequencing expands the clinical application of tissue analyses.

Mortality analysis by neighbourhood in a city with high levels of industrial air pollution.

PubMed

Vigotti, Maria Angela; Mataloni, Francesca; Bruni, Antonella; Minniti, Caterina; Gianicolo, Emilio A L

2014-08-01

Taranto, a city in south-eastern Italy, suffers serious environmental pollution from industrial sources. A previous cohort analysis found mortality excesses among neighbourhoods closest to industrial areas. Aim of this study was to investigate whether mortality also increased in other neighbourhoods compared to Apulia region. Standardized mortality ratios were computed. Number of deaths and of person-years at risk by neighbourhood came from the previous cohort study for 1998-2008 period. Reference population was Apulia region excluding Taranto province. A meta-analysis was conducted across less close neighbourhoods computing summary SMR estimates and evaluating heterogeneity. For the entire city higher mortality values are confirmed for all causes, all malignant neoplasms and several specific sites, neurological, cardiac, respiratory and digestive diseases. High mortality values are not confined to neighbourhoods closest to industrial areas for lung cancer, cardiac, respiratory and digestive diseases, in both sexes, and among women for all malignant neoplasms and pancreatic cancer. Increased mortality risks can also be observed in Taranto neighbourhoods not directly adjacent to industrial areas. Spatial trend, impact of socio-economic factors and duration of residence should be further explored.

Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS Culture Collection (NRRL) using multi-locus sequence analysis.

PubMed

Labeda, David P

2016-03-01

Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 strains identified as Streptomyces scabiei deposited at various times since the 1950s and these were subjected to multi-locus sequence analysis utilising partial sequences of the house-keeping genes atpD, gyrB, recA, rpoB and trpB. Phylogenetic analyses confirmed the identity of 17 of these strains as Streptomyces scabiei, 9 of the strains as the potato-pathogenic species Streptomyces europaeiscabiei and 6 strains as potentially new phytopathogenic species. Of the 16 other strains, 12 were identified as members of previously described non-pathogenic Streptomyces species while the remaining 4 strains may represent heretofore unrecognised non-pathogenic species. This study demonstrated the value of this technique for the relatively rapid, simple and sensitive molecular identification of Streptomyces strains held in culture collections.

Studies on the factors modulating indole-3-acetic acid production in endophytic bacterial isolates from Piper nigrum and molecular analysis of ipdc gene.

PubMed

Jasim, B; Jimtha John, C; Shimil, V; Jyothis, M; Radhakrishnan, E K

2014-09-01

The study mainly aimed quantitative analysis of IAA produced by endophytic bacteria under various conditions including the presence of extract from Piper nigrum. Analysis of genetic basis of IAA production was also conducted by studying the presence and diversity of the ipdc gene among the selected isolates. Five endophytic bacteria isolated previously from P. nigrum were used for the study. The effect of temperature, pH, agitation, tryptophan concentration and plant extract on modulating IAA production of selected isolates was analysed by colorimetric method. Comparative and quantitative analysis of IAA production by colorimetric isolates under optimal culture condition was analysed by HPTLC method. Presence of ipdc gene and thereby biosynthetic basis of IAA production among the selected isolates were studied by PCR-based amplification and subsequent insilico analysis of sequence obtained. Among the selected bacterial isolates from P. nigrum, isolate PnB 8 (Klebsiella pneumoniae) was found to have the maximum yield of IAA under various conditions optimized and was confirmed by colorimetric, HPLC and HPTLC analysis. Very interestingly, the study showed stimulating effect of phytochemicals from P. nigrum on IAA production by endophytic bacteria isolated from same plant. This study is unique because of the selection of endophytes from same source for comparative and quantitative analysis of IAA production under various conditions. Study on stimulatory effect of phytochemicals on bacterial IAA production as explained in the study is a novel approach. Studies on molecular basis of IAA production which was confirmed by sequence analysis of ipdc gene make the study scientifically attractive. Even though microbial production of IAA is well known, current report on detailed optimization, effect of plant extract and molecular confirmation of IAA biosynthesis is comparatively novel in its approach. © 2014 The Society for Applied Microbiology.

Confirmation of the three-factor model of problematic internet use on off-line adolescent and adult samples.

PubMed

Koronczai, Beatrix; Urbán, Róbert; Kökönyei, Gyöngyi; Paksi, Borbála; Papp, Krisztina; Kun, Bernadette; Arnold, Petra; Kállai, János; Demetrovics, Zsolt

2011-11-01

As the Internet became widely used, problems associated with its excessive use became increasingly apparent. Although for the assessment of these problems several models and related questionnaires have been elaborated, there has been little effort made to confirm them. The aim of the present study was to test the three-factor model of the previously created Problematic Internet Use Questionnaire (PIUQ) by data collection methods formerly not applied (off-line group and face-to-face settings), on the one hand, and by testing on different age groups (adolescent and adult representative samples), on the other hand. Data were collected from 438 high-school students (44.5 percent boys; mean age: 16.0 years; standard deviation=0.7 years) and also from 963 adults (49.9 percent males; mean age: 33.6 years; standard deviation=11.8 years). We applied confirmatory factor analysis to confirm the measurement model of problematic Internet use. The results of the analyses carried out inevitably support the original three-factor model over the possible one-factor solution. Using latent profile analysis, we identified 11 percent of adults and 18 percent of adolescent users characterized by problematic use. Based on exploratory factor analysis, we also suggest a short form of the PIUQ consisting of nine items. Both the original 18-item version of PIUQ and its short 9-item form have satisfactory reliability and validity characteristics, and thus, they are suitable for the assessment of problematic Internet use in future studies.

Spatio-temporal pattern of sylvatic rabies in the Sultanate of Oman, 2006-2010.

PubMed

Hussain, Muhammad Hammad; Ward, Michael P; Body, Mohammed; Al-Rawahi, Abdulmajeed; Wadir, Ali Awlad; Al-Habsi, Saif; Saqib, Muhammad; Ahmed, Mohammed Sayed; Almaawali, Mahir Gharib

2013-07-01

Rabies was first reported in the Sultanate of Oman is 1990. We analysed passive surveillance data (444 samples) collected and reported between 2006 and 2010. During this period, between 45 and 75% of samples submitted from suspect animals were subsequently confirmed (fluorescent antibody test, histopathology and reverse transcription PCR) as rabies cases. Overall, 63% of submitted samples were confirmed as rabies cases. The spatial distribution of species-specific cases were similar (centred in north-central Oman with a northeast-southwest distribution), although fox cases had a wider distribution and an east-west orientation. Clustering of cases was detected using interpolation, local spatial autocorrelation and scan statistical analysis. Several local government areas (wilayats) in north-central Oman were identified where higher than expected numbers of laboratory-confirmed rabies cases were reported. For fox rabies, more clusters (local spatial autocorrelation analysis) and a larger clustered area (scan statistical analysis) were detected. In Oman, monthly reports of fox rabies cases were highly correlated (rSP>0.5) with reports of camel, cattle, sheep and goat rabies. The best-fitting ARIMA model included a seasonality component. Fox rabies cases reported 6 months previously best explained rabies reported cases in other animal species. Despite likely reporting bias, results suggest that rabies exists as a sylvatic cycle of transmission in Oman and an opportunity still exists to prevent establishment of dog-mediated rabies. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantitative proteomic analysis of cultured skin fibroblast cells derived from patients with triglyceride deposit cardiomyovasculopathy

PubMed Central

2013-01-01

Background Triglyceride deposit cardiomyovasculopathy (TGCV) is a rare disease, characterized by the massive accumulation of triglyceride (TG) in multiple tissues, especially skeletal muscle, heart muscle and the coronary artery. TGCV is caused by mutation of adipose triglyceride lipase, which is an essential molecule for the hydrolysis of TG. TGCV is at high risk for skeletal myopathy and heart dysfunction, and therefore premature death. Development of therapeutic methods for TGCV is highly desirable. This study aims to discover specific molecules responsible for TGCV pathogenesis. Methods To identify differentially expressed proteins in TGCV patient cells, the stable isotope labeling with amino acids in cell culture (SILAC) method coupled with LC-MS/MS was performed using skin fibroblast cells derived from two TGCV patients and three healthy volunteers. Altered protein expression in TGCV cells was confirmed using the selected reaction monitoring (SRM) method. Microarray-based transcriptome analysis was simultaneously performed to identify changes in gene expression in TGCV cells. Results Using SILAC proteomics, 4033 proteins were quantified, 53 of which showed significantly altered expression in both TGCV patient cells. Twenty altered proteins were chosen and confirmed using SRM. SRM analysis successfully quantified 14 proteins, 13 of which showed the same trend as SILAC proteomics. The altered protein expression data set was used in Ingenuity Pathway Analysis (IPA), and significant networks were identified. Several of these proteins have been previously implicated in lipid metabolism, while others represent new therapeutic targets or markers for TGCV. Microarray analysis quantified 20743 transcripts, and 252 genes showed significantly altered expression in both TGCV patient cells. Ten altered genes were chosen, 9 of which were successfully confirmed using quantitative RT-PCR. Biological networks of altered genes were analyzed using an IPA search. Conclusions We performed the SILAC- and SRM-based identification-through-confirmation study using skin fibroblast cells derived from TGCV patients, and first identified altered proteins specific for TGCV. Microarray analysis also identified changes in gene expression. The functional networks of the altered proteins and genes are discussed. Our findings will be exploited to elucidate the pathogenesis of TGCV and discover clinically relevant molecules for TGCV in the near future. PMID:24360150

The Attitudes to Ageing Questionnaire: Mokken Scaling Analysis

PubMed Central

Shenkin, Susan D.; Watson, Roger; Laidlaw, Ken; Starr, John M.; Deary, Ian J.

2014-01-01

Background Hierarchical scales are useful in understanding the structure of underlying latent traits in many questionnaires. The Attitudes to Ageing Questionnaire (AAQ) explored the attitudes to ageing of older people themselves, and originally described three distinct subscales: (1) Psychosocial Loss (2) Physical Change and (3) Psychological Growth. This study aimed to use Mokken analysis, a method of Item Response Theory, to test for hierarchies within the AAQ and to explore how these relate to underlying latent traits. Methods Participants in a longitudinal cohort study, the Lothian Birth Cohort 1936, completed a cross-sectional postal survey. Data from 802 participants were analysed using Mokken Scaling analysis. These results were compared with factor analysis using exploratory structural equation modelling. Results Participants were 51.6% male, mean age 74.0 years (SD 0.28). Three scales were identified from 18 of the 24 items: two weak Mokken scales and one moderate Mokken scale. (1) ‘Vitality’ contained a combination of items from all three previously determined factors of the AAQ, with a hierarchy from physical to psychosocial; (2) ‘Legacy’ contained items exclusively from the Psychological Growth scale, with a hierarchy from individual contributions to passing things on; (3) ‘Exclusion’ contained items from the Psychosocial Loss scale, with a hierarchy from general to specific instances. All of the scales were reliable and statistically significant with ‘Legacy’ showing invariant item ordering. The scales correlate as expected with personality, anxiety and depression. Exploratory SEM mostly confirmed the original factor structure. Conclusions The concurrent use of factor analysis and Mokken scaling provides additional information about the AAQ. The previously-described factor structure is mostly confirmed. Mokken scaling identifies a new factor relating to vitality, and a hierarchy of responses within three separate scales, referring to vitality, legacy and exclusion. This shows what older people themselves consider important regarding their own ageing. PMID:24892302

Proteomics Analysis of Bladder Cancer Exosomes*

PubMed Central

Welton, Joanne L.; Khanna, Sanjay; Giles, Peter J.; Brennan, Paul; Brewis, Ian A.; Staffurth, John; Mason, Malcolm D.; Clayton, Aled

2010-01-01

Exosomes are nanometer-sized vesicles, secreted by various cell types, present in biological fluids that are particularly rich in membrane proteins. Ex vivo analysis of exosomes may provide biomarker discovery platforms and form non-invasive tools for disease diagnosis and monitoring. These vesicles have never before been studied in the context of bladder cancer, a major malignancy of the urological tract. We present the first proteomics analysis of bladder cancer cell exosomes. Using ultracentrifugation on a sucrose cushion, exosomes were highly purified from cultured HT1376 bladder cancer cells and verified as low in contaminants by Western blotting and flow cytometry of exosome-coated beads. Solubilization in a buffer containing SDS and DTT was essential for achieving proteomics analysis using an LC-MALDI-TOF/TOF MS approach. We report 353 high quality identifications with 72 proteins not previously identified by other human exosome proteomics studies. Overrepresentation analysis to compare this data set with previous exosome proteomics studies (using the ExoCarta database) revealed that the proteome was consistent with that of various exosomes with particular overlap with exosomes of carcinoma origin. Interrogating the Gene Ontology database highlighted a strong association of this proteome with carcinoma of bladder and other sites. The data also highlighted how homology among human leukocyte antigen haplotypes may confound MASCOT designation of major histocompatability complex Class I nomenclature, requiring data from PCR-based human leukocyte antigen haplotyping to clarify anomalous identifications. Validation of 18 MS protein identifications (including basigin, galectin-3, trophoblast glycoprotein (5T4), and others) was performed by a combination of Western blotting, flotation on linear sucrose gradients, and flow cytometry, confirming their exosomal expression. Some were confirmed positive on urinary exosomes from a bladder cancer patient. In summary, the exosome proteomics data set presented is of unrivaled quality. The data will aid in the development of urine exosome-based clinical tools for monitoring disease and will inform follow-up studies into varied aspects of exosome manufacture and function. PMID:20224111

Mobile Genome Express (MGE): A comprehensive automatic genetic analyses pipeline with a mobile device.

PubMed

Yoon, Jun-Hee; Kim, Thomas W; Mendez, Pedro; Jablons, David M; Kim, Il-Jin

2017-01-01

The development of next-generation sequencing (NGS) technology allows to sequence whole exomes or genome. However, data analysis is still the biggest bottleneck for its wide implementation. Most laboratories still depend on manual procedures for data handling and analyses, which translates into a delay and decreased efficiency in the delivery of NGS results to doctors and patients. Thus, there is high demand for developing an automatic and an easy-to-use NGS data analyses system. We developed comprehensive, automatic genetic analyses controller named Mobile Genome Express (MGE) that works in smartphones or other mobile devices. MGE can handle all the steps for genetic analyses, such as: sample information submission, sequencing run quality check from the sequencer, secured data transfer and results review. We sequenced an Actrometrix control DNA containing multiple proven human mutations using a targeted sequencing panel, and the whole analysis was managed by MGE, and its data reviewing program called ELECTRO. All steps were processed automatically except for the final sequencing review procedure with ELECTRO to confirm mutations. The data analysis process was completed within several hours. We confirmed the mutations that we have identified were consistent with our previous results obtained by using multi-step, manual pipelines.

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family.

PubMed

Danisman, Selahattin; van Dijk, Aalt D J; Bimbo, Andrea; van der Wal, Froukje; Hennig, Lars; de Folter, Stefan; Angenent, Gerco C; Immink, Richard G H

2013-12-01

Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein-protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein-protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family.

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family

PubMed Central

Danisman, Selahattin; de Folter, Stefan; Immink, Richard G. H.

2013-01-01

Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein–protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein–protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family. PMID:24129704

Aminoquinolines as fluorescent labels for hydrophilic interaction liquid chromatography of oligosaccharides.

PubMed

Struwe, Weston B; Rudd, Pauline M

2012-08-01

In this study, we investigated the potential of four different aminoquinoline (AQ) compounds as fluorescent labels for glycan analysis using hydrophilic interaction liquid chromatography (HILIC) and fluorescence detection (FLD). We confirmed the optimal excitation and emission wavelengths of 3-AQ and 6-AQ conjugated to glycan standards using three-dimensional fluorescent spectral scanning. The optimal excitation and emission wavelengths for 6-AQ were confirmed at λ(ex)=355 nm and λ(em)=440 nm. We concluded that the optimal wavelengths for 3-AQ were λ(ex)=355 nm and λ(em)=420 nm, which differed considerably from the wavelengths applied in previous reports. HILIC-FLD chromatograms using experimentally determined wavelengths were similar to 2-aminobenzamide controls, but the peak capacity and resolution differed significantly when published 3-AQ λ(ex/em) values were applied. Furthermore, we found that 5-AQ and 8-AQ labeled maltohexaose did not display any fluorescent properties when used as a carbohydrate tag for HPLC analysis. Finally, we applied experimentally determined wavelengths to 3-AQ labeled N-glycans released from human IgG to illustrate changes in retention time as well as to demonstrate that AQ labeling is applicable to complex sample analysis via exoglycosidase sequencing.

Long-Range Correlations in Sentence Series from A Story of the Stone

PubMed Central

Yang, Tianguang; Gu, Changgui; Yang, Huijie

2016-01-01

A sentence is the natural unit of language. Patterns embedded in series of sentences can be used to model the formation and evolution of languages, and to solve practical problems such as evaluating linguistic ability. In this paper, we apply de-trended fluctuation analysis to detect long-range correlations embedded in sentence series from A Story of the Stone, one of the greatest masterpieces of Chinese literature. We identified a weak long-range correlation, with a Hurst exponent of 0.575±0.002 up to a scale of 104. We used the structural stability to confirm the behavior of the long-range correlation, and found that different parts of the series had almost identical Hurst exponents. We found that noisy records can lead to false results and conclusions, even if the noise covers a limited proportion of the total records (e.g., less than 1%). Thus, the structural stability test is an essential procedure for confirming the existence of long-range correlations, which has been widely neglected in previous studies. Furthermore, a combination of de-trended fluctuation analysis and diffusion entropy analysis demonstrated that the sentence series was generated by a fractional Brownian motion. PMID:27648941

Long-Range Correlations in Sentence Series from A Story of the Stone.

PubMed

Yang, Tianguang; Gu, Changgui; Yang, Huijie

2016-01-01

A sentence is the natural unit of language. Patterns embedded in series of sentences can be used to model the formation and evolution of languages, and to solve practical problems such as evaluating linguistic ability. In this paper, we apply de-trended fluctuation analysis to detect long-range correlations embedded in sentence series from A Story of the Stone, one of the greatest masterpieces of Chinese literature. We identified a weak long-range correlation, with a Hurst exponent of 0.575±0.002 up to a scale of 104. We used the structural stability to confirm the behavior of the long-range correlation, and found that different parts of the series had almost identical Hurst exponents. We found that noisy records can lead to false results and conclusions, even if the noise covers a limited proportion of the total records (e.g., less than 1%). Thus, the structural stability test is an essential procedure for confirming the existence of long-range correlations, which has been widely neglected in previous studies. Furthermore, a combination of de-trended fluctuation analysis and diffusion entropy analysis demonstrated that the sentence series was generated by a fractional Brownian motion.

Confirmation of the immunoreactivity of monoclonal anti-human C-terminal EGFR antibodies in bronze Corydoras Corydoras aeneus (Callichthyidae Teleostei) by Western Blot method.

PubMed

Mytych, Jennifer; Satora, Leszek; Kozioł, Katarzyna

2018-02-01

Bronze corydoras (Corydoras aeneus) uses the distal part of the intestine as accessory respiratory organ. Our previous study showed the presence of epidermal growth factor receptor (EGFR) cytoplasmic domain in the digestive tract of the bronze corydoras. In this study, using Western Blot method, we validated the results presented in the previous research. In detail, results of Western Blot analysis on digestive and respiratory part of bronze corydoras intestine homogenates confirmed the immunoreactivity of anti-cytoplasmic domain (C-terminal) human EGFR antibodies with protein band of approximately 180kDa (EGFR molecular weight). This indicates a high homology of EGFR domain between these species and the possibility of such antibody use in bronze corydoras. Statistically significantly higher EGFR expression was observed in the respiratory part of intestine when compared to the digestive part. This implies higher proliferation activity and angiogenesis of epithelium in this part of intestine, creating conditions for air respiration. Therefore, Corydoras aeneus may be considered as a model organism for the molecular studies of the mechanisms of epithelial proliferation initiation and inhibition depending on hypoxia and normoxia. Copyright © 2017. Published by Elsevier GmbH.

Student-to-Student Confirmation in the College Classroom: The Development and Validation of the Student-to-Student Confirmation Scale

ERIC Educational Resources Information Center

LaBelle, Sara; Johnson, Zac D.

2018-01-01

Three studies were conducted to generate a valid and reliable instrument to measure student-to-student confirmation. Study One (N = 396) sought to establish a factor structure based on previous research. Study Two (N = 396) sought to confirm this factor structure and assess criterion-related validity. Study Three (N = 283) sought to assess…

Applicability of action planning and coping planning to dental flossing among Norwegian adults: a confirmatory factor analysis approach.

PubMed

Astrøm, Anne Nordrehaug

2008-06-01

Using a prospective design and a representative sample of 25-yr-old Norwegians, this study hypothesized that action planning and coping planning will add to the prediction of flossing at 4 wk of follow-up over and above the effect of intention and previous flossing. This study tested the validity of a proposed 3-factor structure of the measurement model of intention, action planning, and coping planning and for its invariance across gender. A survey was conducted in three Norwegian counties, and 1,509 out of 8,000 randomly selected individuals completed questionnaires assessing the constructs of action planning and coping planning related to daily flossing. A random subsample of 500 participants was followed up at 4 wk with a telephone interview to assess flossing. Confirmatory factor analysis (CFA) confirmed the proposed 3-factor model after respecification. Although the chi-square test was statistically significant [chi(2) = 58.501, degrees of freedom (d.f.) = 17), complementary fit indices were satisfactory [goodness-of-fit index (GFI) = 0.99, root mean squared error of approximation (RMSEA) = 0.04]. Multigroup CFA provided evidence of complete invariance of the measurement model across gender. After controlling for previous flossing, intention (beta = 0.08) and action planning (beta = 0.11) emerged as independent predictors of subsequent flossing, accounting for 2.3% of its variance. Factorial validity of intention, action planning and coping planning, and the validity of action planning in predicting flossing prospectively, was confirmed by the present study.

In vitro cell transformation assays for an integrated, alternative assessment of carcinogenicity: a data-based analysis.

PubMed

Benigni, Romualdo; Bossa, Cecilia; Tcheremenskaia, Olga

2013-01-01

The study of the chemical carcinogenesis mechanisms and the design of efficient prevention strategies and measures are of crucial importance to protect human health. The long-term carcinogenesis bioassays have played a central role in protecting human health, but for ethical and practical reasons their use is dramatically diminishing, and the genotoxicity short-term tests have taken the pivotal role in the pre-screening of carcinogenicity. However, there is evidence that this strategy is not sensitive enough to detect all genotoxic carcinogens and it cannot detect nongenotoxic carcinogens. In a previous article, we have shown that an integrated strategy consisting of the in vitro Ames and Syrian Hamster Embryo cells transformation assays, combined with structure-activity relationships, is a valid alternative to the present pre-screening strategies. Here, we expand the previous investigation by (i) including results of cell transformation assays on inorganics, together with an additional assay (Bhas 42), and (ii) considering new structural alerts for nongenotoxic carcinogenicity. We also present a new analysis on global relationships between toxicological endpoints. The new results confirm that the previously proposed integrated, alternative strategy is an efficient tool to identify both genotoxic and nongenotoxic carcinogens, with an estimated 90-95% sensitivity.

Standardization of the Hare Psychopathy Checklist-Revised in a Spanish prison sample.

PubMed

Moltó, J; Poy, R; Torrubia, R

2000-01-01

This investigation examined the reliability, validity, and factor structure of the Hare Psychopathy Checklist-Revised (PCL-R) in male adult Spanish prison populations (n = 117). The interrater reliability and internal consistency coefficients were high, and similar to those obtained in other countries. This data provides support for the homogeneity and unidimensionality of the psychopathy construct in Spanish male prison samples. The analysis of factor structure also replicated the two factor solution of previous studies. The two factors showed different patterns of intercorrelations with several self-report measures of personality, demographic, and criminal history variables, which confirmed the construct validity of PCL-R. The results confirm the psychometric properties of the PCL-R as a measure of psychopathy in Spanish male inmates, and suggest that psychopathy is a construct also observed in Southern European countries.

Erwinia mallotivora sp., a New Pathogen of Papaya (Carica papaya) in Peninsular Malaysia

PubMed Central

Amin, Noriha Mat; Bunawan, Hamidun; Redzuan, Rohaiza Ahmad; Jaganath, Indu Bala S.

2011-01-01

Erwinia mallotivora was isolated from papaya infected with dieback disease showing the typical symptoms of greasy, water-soaked lesions and spots on leaves. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belonged to the genus Erwinia and was united in a monophyletic group with E. mallotivora DSM 4565 (AJ233414). Earlier studies had indicated that the causal agent for this disease was E. papayae. However, our current studies, through Koch’s postulate, have confirmed that papaya dieback disease is caused by E. mallotivora. To our knowledge, this is the first new discovery of E. mallotivora as a causal agent of papaya dieback disease in Peninsular Malaysia. Previous reports have suggested that E. mallotivora causes leaf spot in Mallotus japonicus. However, this research confirms it also to be pathogenic to Carica papaya. PMID:21339975

Lead poisoning associated with intravenous-methamphetamine use--Oregon, 1988

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

Chandler, D.B.; Norton, R.L.; Kauffman, K.W.

1990-02-09

Between August 1 and September 6, 1988, 14 cases of non-A, non-B (NANB) hepatitis were reported in Marion County, Oregon, to the Oregon Health Division (OHD) by the county health department and private physicians. Previously, an average of less than one case per month was reported in the county. During the same period, OHD learned that eight intravenous-methamphetamine users (IVMUs) in Oregon thought to have NANB hepatitis had also been recently diagnosed with lead poisoning. A statewide media campaign describing the lead poisoning outbreak was conducted to alert IVMUs, physicians, and county health departments. In addition, OHD implemented a reportingmore » system for suspected and confirmed lead poisoning cases. Analysis of an illicit methamphetamine sample provided by one of the patients with confirmed lead poisoning detected 60% lead by weight.« less

Erwinia mallotivora sp., a new pathogen of papaya (Carica papaya) in Peninsular Malaysia.

PubMed

Amin, Noriha Mat; Bunawan, Hamidun; Redzuan, Rohaiza Ahmad; Jaganath, Indu Bala S

2010-12-24

Erwinia mallotivora was isolated from papaya infected with dieback disease showing the typical symptoms of greasy, water-soaked lesions and spots on leaves. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belonged to the genus Erwinia and was united in a monophyletic group with E. mallotivora DSM 4565 (AJ233414). Earlier studies had indicated that the causal agent for this disease was E. papayae. However, our current studies, through Koch's postulate, have confirmed that papaya dieback disease is caused by E. mallotivora. To our knowledge, this is the first new discovery of E. mallotivora as a causal agent of papaya dieback disease in Peninsular Malaysia. Previous reports have suggested that E. mallotivora causes leaf spot in Mallotus japonicus. However, this research confirms it also to be pathogenic to Carica papaya.

Phylogenetic analysis and confirmation of the endospore-forming nature of Pasteuria penetrans based on the spo0A gene.

PubMed

Trotter, James R; Bishop, Alistair H

2003-08-29

Pasteuria penetrans is an obligate parasite of plant parasitic nematodes and has yet to be grown in vitro. We have cloned the pivotal sporulation gene, spo0A, which is the first whole gene yet to come from this organism. Partial spo0A sequences were also obtained from the related bacteria, Pasteuria ramosa and Alicyclobacillus acidocaldarius. Phylogenetic analyses using the spo0A sequence data from this and previous studies confirmed the closeness of the genera Pasteuria and members of the supergenus Bacillus. A segment of the spo0A gene was also used to show that genetic heterogeneity exists within and between populations of P. penetrans. This may explain, partly at least, the variability of P. penetrans as a biological control agent of nematodes.

An Analysis of Processes in the Solar Wind in a Thin Layer Adjacent to the Front of the Shock Wave

NASA Astrophysics Data System (ADS)

Molotkov, I. A.; Atamaniuk, B.

2018-05-01

A two-dimensional stationary system of nonlinear magnetohydrodynamics (MHD) equations in a thin layer adjoining the front of the interplanetary shock wave has been solved. Previously, any available publications relied on linear transport equations. But the presence of high-energy particles in the solar wind (SW) requires taking into account the processes of self-interaction. Our analysis examines the nonlinear terms in the MHD equations. A solution has been constructed for three cases: (1) in the absence of magnetic reconnections; (2) for magnetic reconnections; and (3) with the simultaneous action of reconnections and junction of magnetic islands. In all three cases, expressions were found for the main parameters of the SW. The results obtained on the basis of the solution of the MHD equations are consistent with the conclusions based on the investigation of the particle velocity distribution functions. This makes it possible to confirm the previously established fraction of particles excited to energies above 1 MeV.

Serum protein mediators of dementia and aging proper.

PubMed

Royall, Donald R; Al-Rubaye, Safa; Bishnoi, Ram; Palmer, Raymond F

2016-12-03

The latent variable "δ" (for "dementia") appears to be uniquely responsible for the dementing aspects of cognitive impairment. Age, depressive symptoms, gender and the apolipoprotein E (APOE) ε4 allele are independently associated with δ. In this analysis, we explore serum proteins as potential mediators of age's specific association with δ in a large, ethnically diverse longitudinal cohort, the Texas Alzheimer's Research and Care Consortium (TARCC). 22 serum proteins were recognized as partial mediators of age's association with δ. These include Insulin-like Growth Factor-Binding Protein 2 (IGF-BP2), which we had previously associated with age-specific cognitive change, and both Pancreatic Polypeptide (PP) and von Willebrand Factor (vWF), previously associated with δ. Nine other δ-related proteins were not confirmed by this ethnicity adjusted analysis. Our findings suggest that age's association with the disabling fraction of cognitive performance is partially mediated by serum proteins, somatomedins and hormones. Those proteins may offer targets for the specific treatment of age-related effects on dementia severity and conversion risk.

Tetrasomy 8 in a patient with chronic lymphocytic leukemia.

PubMed

de Oliveira, Fábio Morato; Brandão, Renata Amorim; Leite-Cueva, Sabrina Dias; de Paula Careta, Francisco; Simões, Belinda Pinto; Rego, Eduardo Magalhães; Falcão, Roberto Passetto

2010-04-15

We report a case of a 47-year-old man diagnosed with chronic lymphocytic leukemia (CLL) with two extra copies of chromosome 8. Classical cytogenetic analysis by the immunostimulatory combination of DSP30 and interleukin 2 showed tetrasomy of chromosome 8 in 60% of the metaphase cells (48,XY,+8,+8[12]/46,XY[8]). Spectral karyotype analysis confirmed the abnormality previously seen by G banding. Additionally, interphase fluorescence in situ hybridization using an LSI CEP 8 probe performed on peripheral blood cells without any stimulant agent showed tetrasomy of chromosome 8 in 54% of analyzed cells (108 of 200). To our knowledge, tetrasomy 8 as the sole chromosomal abnormality in CLL has not been previously described. The prognostic significance of tetrasomy 8 in CLL remains to be elucidated. However, the patient has been followed up in the outpatient hospital since 2004 without any therapeutic intervention and has so far remained stable. Copyright 2010 Elsevier Inc. All rights reserved.

Large-scale association analyses identifies 13 new susceptibility loci for coronary artery disease

PubMed Central

Schunkert, Heribert; König, Inke R.; Kathiresan, Sekar; Reilly, Muredach P.; Assimes, Themistocles L.; Holm, Hilma; Preuss, Michael; Stewart, Alexandre F. R.; Barbalic, Maja; Gieger, Christian; Absher, Devin; Aherrahrou, Zouhair; Allayee, Hooman; Altshuler, David; Anand, Sonia S.; Andersen, Karl; Anderson, Jeffrey L.; Ardissino, Diego; Ball, Stephen G.; Balmforth, Anthony J.; Barnes, Timothy A.; Becker, Diane M.; Becker, Lewis C.; Berger, Klaus; Bis, Joshua C.; Boekholdt, S. Matthijs; Boerwinkle, Eric; Braund, Peter S.; Brown, Morris J.; Burnett, Mary Susan; Buysschaert, Ian; Carlquist, Cardiogenics, John F.; Chen, Li; Cichon, Sven; Codd, Veryan; Davies, Robert W.; Dedoussis, George; Dehghan, Abbas; Demissie, Serkalem; Devaney, Joseph M.; Do, Ron; Doering, Angela; Eifert, Sandra; El Mokhtari, Nour Eddine; Ellis, Stephen G.; Elosua, Roberto; Engert, James C.; Epstein, Stephen E.; Faire, Ulf de; Fischer, Marcus; Folsom, Aaron R.; Freyer, Jennifer; Gigante, Bruna; Girelli, Domenico; Gretarsdottir, Solveig; Gudnason, Vilmundur; Gulcher, Jeffrey R.; Halperin, Eran; Hammond, Naomi; Hazen, Stanley L.; Hofman, Albert; Horne, Benjamin D.; Illig, Thomas; Iribarren, Carlos; Jones, Gregory T.; Jukema, J.Wouter; Kaiser, Michael A.; Kaplan, Lee M.; Kastelein, John J.P.; Khaw, Kay-Tee; Knowles, Joshua W.; Kolovou, Genovefa; Kong, Augustine; Laaksonen, Reijo; Lambrechts, Diether; Leander, Karin; Lettre, Guillaume; Li, Mingyao; Lieb, Wolfgang; Linsel-Nitschke, Patrick; Loley, Christina; Lotery, Andrew J.; Mannucci, Pier M.; Maouche, Seraya; Martinelli, Nicola; McKeown, Pascal P.; Meisinger, Christa; Meitinger, Thomas; Melander, Olle; Merlini, Pier Angelica; Mooser, Vincent; Morgan, Thomas; Mühleisen, Thomas W.; Muhlestein, Joseph B.; Münzel, Thomas; Musunuru, Kiran; Nahrstaedt, Janja; Nelson, Christopher P.; Nöthen, Markus M.; Olivieri, Oliviero; Patel, Riyaz S.; Patterson, Chris C.; Peters, Annette; Peyvandi, Flora; Qu, Liming; Quyyumi, Arshed A.; Rader, Daniel J.; Rallidis, Loukianos S.; Rice, Catherine; Rosendaal, Frits R.; Rubin, Diana; Salomaa, Veikko; Sampietro, M. Lourdes; Sandhu, Manj S.; Schadt, Eric; Schäfer, Arne; Schillert, Arne; Schreiber, Stefan; Schrezenmeir, Jürgen; Schwartz, Stephen M.; Siscovick, David S.; Sivananthan, Mohan; Sivapalaratnam, Suthesh; Smith, Albert; Smith, Tamara B.; Snoep, Jaapjan D.; Soranzo, Nicole; Spertus, John A.; Stark, Klaus; Stirrups, Kathy; Stoll, Monika; Tang, W. H. Wilson; Tennstedt, Stephanie; Thorgeirsson, Gudmundur; Thorleifsson, Gudmar; Tomaszewski, Maciej; Uitterlinden, Andre G.; van Rij, Andre M.; Voight, Benjamin F.; Wareham, Nick J.; Wells, George A.; Wichmann, H.-Erich; Wild, Philipp S.; Willenborg, Christina; Witteman, Jaqueline C. M.; Wright, Benjamin J.; Ye, Shu; Zeller, Tanja; Ziegler, Andreas; Cambien, Francois; Goodall, Alison H.; Cupples, L. Adrienne; Quertermous, Thomas; März, Winfried; Hengstenberg, Christian; Blankenberg, Stefan; Ouwehand, Willem H.; Hall, Alistair S.; Deloukas, Panos; Thompson, John R.; Stefansson, Kari; Roberts, Robert; Thorsteinsdottir, Unnur; O’Donnell, Christopher J.; McPherson, Ruth; Erdmann, Jeanette; Samani, Nilesh J.

2011-01-01

We performed a meta-analysis of 14 genome-wide association studies of coronary artery disease (CAD) comprising 22,233 cases and 64,762 controls of European descent, followed by genotyping of top association signals in 60,738 additional individuals. This genomic analysis identified 13 novel loci harboring one or more SNPs that were associated with CAD at P<5×10−8 and confirmed the association of 10 of 12 previously reported CAD loci. The 13 novel loci displayed risk allele frequencies ranging from 0.13 to 0.91 and were associated with a 6 to 17 percent increase in the risk of CAD per allele. Notably, only three of the novel loci displayed significant association with traditional CAD risk factors, while the majority lie in gene regions not previously implicated in the pathogenesis of CAD. Finally, five of the novel CAD risk loci appear to have pleiotropic effects, showing strong association with various other human diseases or traits. PMID:21378990

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat.

PubMed

Yan, Honghai; Bekele, Wubishet A; Wight, Charlene P; Peng, Yuanying; Langdon, Tim; Latta, Robert G; Fu, Yong-Bi; Diederichsen, Axel; Howarth, Catherine J; Jellen, Eric N; Boyle, Brian; Wei, Yuming; Tinker, Nicholas A

2016-11-01

Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.

Genotyping-By-Sequencing (GBS) Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (Vulpes vulpes)

PubMed Central

Johnson, Jennifer L.; Wittgenstein, Helena; Mitchell, Sharon E.; Hyma, Katie E.; Temnykh, Svetlana V.; Kharlamova, Anastasiya V.; Gulevich, Rimma G.; Vladimirova, Anastasiya V.; Fong, Hiu Wa Flora; Acland, Gregory M.; Trut, Lyudmila N.; Kukekova, Anna V.

2015-01-01

The silver fox (Vulpes vulpes) offers a novel model for studying the genetics of social behavior and animal domestication. Selection of foxes, separately, for tame and for aggressive behavior has yielded two strains with markedly different, genetically determined, behavioral phenotypes. Tame strain foxes are eager to establish human contact while foxes from the aggressive strain are aggressive and difficult to handle. These strains have been maintained as separate outbred lines for over 40 generations but their genetic structure has not been previously investigated. We applied a genotyping-by-sequencing (GBS) approach to provide insights into the genetic composition of these fox populations. Sequence analysis of EcoT22I genomic libraries of tame and aggressive foxes identified 48,294 high quality SNPs. Population structure analysis revealed genetic divergence between the two strains and more diversity in the aggressive strain than in the tame one. Significant differences in allele frequency between the strains were identified for 68 SNPs. Three of these SNPs were located on fox chromosome 14 within an interval of a previously identified behavioral QTL, further supporting the importance of this region for behavior. The GBS SNP data confirmed that significant genetic diversity has been preserved in both fox populations despite many years of selective breeding. Analysis of SNP allele frequencies in the two populations identified several regions of genetic divergence between the tame and aggressive foxes, some of which may represent targets of selection for behavior. The GBS protocol used in this study significantly expanded genomic resources for the fox, and can be adapted for SNP discovery and genotyping in other canid species. PMID:26061395

Genotyping-By-Sequencing (GBS) Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (Vulpes vulpes).

PubMed

Johnson, Jennifer L; Wittgenstein, Helena; Mitchell, Sharon E; Hyma, Katie E; Temnykh, Svetlana V; Kharlamova, Anastasiya V; Gulevich, Rimma G; Vladimirova, Anastasiya V; Fong, Hiu Wa Flora; Acland, Gregory M; Trut, Lyudmila N; Kukekova, Anna V

2015-01-01

The silver fox (Vulpes vulpes) offers a novel model for studying the genetics of social behavior and animal domestication. Selection of foxes, separately, for tame and for aggressive behavior has yielded two strains with markedly different, genetically determined, behavioral phenotypes. Tame strain foxes are eager to establish human contact while foxes from the aggressive strain are aggressive and difficult to handle. These strains have been maintained as separate outbred lines for over 40 generations but their genetic structure has not been previously investigated. We applied a genotyping-by-sequencing (GBS) approach to provide insights into the genetic composition of these fox populations. Sequence analysis of EcoT22I genomic libraries of tame and aggressive foxes identified 48,294 high quality SNPs. Population structure analysis revealed genetic divergence between the two strains and more diversity in the aggressive strain than in the tame one. Significant differences in allele frequency between the strains were identified for 68 SNPs. Three of these SNPs were located on fox chromosome 14 within an interval of a previously identified behavioral QTL, further supporting the importance of this region for behavior. The GBS SNP data confirmed that significant genetic diversity has been preserved in both fox populations despite many years of selective breeding. Analysis of SNP allele frequencies in the two populations identified several regions of genetic divergence between the tame and aggressive foxes, some of which may represent targets of selection for behavior. The GBS protocol used in this study significantly expanded genomic resources for the fox, and can be adapted for SNP discovery and genotyping in other canid species.

The Pearson-Readhead Survey of Compact Extragalactic Radio Sources from Space. II. Analysis of Source Properties

NASA Astrophysics Data System (ADS)

Lister, M. L.; Tingay, S. J.; Preston, R. A.

2001-06-01

We have performed a multidimensional correlation analysis on the observed properties of a statistically complete core-selected sample of compact radio-loud active galactic nuclei based on data from the VLBI Space Observing Programme (Paper I) and previously published studies. Our sample is drawn from the well-studied Pearson-Readhead (PR) survey and is ideally suited for investigating the general effects of relativistic beaming in compact radio sources. In addition to confirming many previously known correlations, we have discovered several new trends that lend additional support to the beaming model. These trends suggest that the most highly beamed sources in core-selected samples tend to have (1) high optical polarizations; (2) large parsec- kiloparsec-scale jet misalignments; (3) prominent VLBI core components; (4) one-sided, core, or halo radio morphology on kiloparsec scales; (5) narrow emission line equivalent widths; and (6) a strong tendency for intraday variability at radio wavelengths. We have used higher resolution space and ground-based VLBI maps to confirm the bimodality of the jet misalignment distribution for the PR survey and find that the sources with aligned parsec- and kiloparsec-scale jets generally have arcsecond-scale radio emission on both sides of the core. The aligned sources also have broader emission line widths. We find evidence that the BL Lacertae objects in the PR survey are all highly beamed and have very similar properties to the high optically polarized quasars, with the exception of smaller redshifts. A cluster analysis on our data shows that after partialing out the effects of redshift, the luminosities of our sample objects in various wave bands are generally well correlated with each other but not with other source properties.

GWAS and admixture mapping identify different asthma-associated loci in Latinos: The GALA II Study

PubMed Central

Galanter, Joshua M; Gignoux, Christopher R; Torgerson, Dara G; Roth, Lindsey A; Eng, Celeste; Oh, Sam S; Nguyen, Elizabeth A; Drake, Katherine A; Huntsman, Scott; Hu, Donglei; Sen, Saunak; Davis, Adam; Farber, Harold J.; Avila, Pedro C.; Brigino-Buenaventura, Emerita; LeNoir, Michael A.; Meade, Kelley; Serebrisky, Denise; Borrell, Luisa N; Rodríguez-Cintrón, William; Estrada, Andres Moreno; Mendoza, Karla Sandoval; Winkler, Cheryl A.; Klitz, William; Romieu, Isabelle; London, Stephanie J.; Gilliland, Frank; Martinez, Fernando; Bustamante, Carlos; Williams, L Keoki; Kumar, Rajesh; Rodríguez-Santana, José R.; Burchard, and Esteban G.

2013-01-01

Background Asthma is a complex disease with both genetic and environmental causes. Genome-wide association studies of asthma have mostly involved European populations and replication of positive associations has been inconsistent. Objective To identify asthma-associated genes in a large Latino population with genome-wide association analysis and admixture mapping. Methods Latino children with asthma (n = 1,893) and healthy controls (n = 1,881) were recruited from five sites in the United States: Puerto Rico, New York, Chicago, Houston, and the San Francisco Bay Area. Subjects were genotyped on an Affymetrix World Array IV chip. We performed genome-wide association and admixture mapping to identify asthma-associated loci. Results We identified a significant association between ancestry and asthma at 6p21 (lowest p-value: rs2523924, p < 5 × 10−6). This association replicates in a meta-analysis of the EVE Asthma Consortium (p = 0.01). Fine mapping of the region in this study and the EVE Asthma Consortium suggests an association between PSORS1C1 and asthma. We confirmed the strong allelic association between the 17q21 asthma in Latinos (IKZF3, lowest p-value: rs90792, OR: 0.67, 95% CI 0.61 – 0.75, p = 6 × 10−13) and replicated associations in several genes that had previously been associated with asthma in genome-wide association studies. Conclusions Admixture mapping and genome-wide association are complementary techniques that provide evidence for multiple asthma-associated loci in Latinos. Admixture mapping identifies a novel locus on 6p21 that replicates in a meta-analysis of several Latino populations, while genome-wide association confirms the previously identified locus on 17q21. PMID:24406073

New potential markers for the detection of boldenone misuse.

PubMed

Gómez, C; Pozo, O J; Geyer, H; Marcos, J; Thevis, M; Schänzer, W; Segura, J; Ventura, R

2012-11-01

Boldenone is one of the most frequently detected anabolic androgenic steroids in doping control analysis. Boldenone misuse is commonly detected by the identification of the active drug and its main metabolite, 5β-androst-1-en-17β-ol-3-one (BM1), by gas chromatography-mass spectrometry (GC-MS), after previous hydrolysis with β-glucuronidase enzymes, extraction and derivatization steps. However, some cases of endogenous boldenone and BM1 have been reported. Nowadays, when these compounds are detected in urine at low concentrations, isotope ratio mass spectrometry (IRMS) analysis is needed to confirm their exogenous origin. The aim of the present study was to identify boldenone metabolites conjugated with sulphate and to evaluate their potential to improve the detection of boldenone misuse in sports. Boldenone was administered to a healthy volunteer and urine samples were collected up to 56h after administration. After a liquid-liquid extraction with ethyl acetate, urine extracts were analysed by liquid chromatography tandem mass spectrometry (LC-MS/MS) using electrospray ionisation in negative mode by monitoring the transition of m/z 365-350, specific for boldenone sulphate. Boldenone sulphate was identified in the excretion study urine samples and, moreover, another peak with the same transition was observed. Based on the MS/MS behaviour the metabolite was identified as epiboldenone sulphate. The identity was confirmed by isolation of the LC peak, solvolysis and comparison of the retention time and MS/MS spectra with an epiboldenone standard. These sulphated metabolites have not been previously reported in humans and although they account for less than 1% of the administered dose, they were still present in urine when the concentrations of the major metabolites, boldenone and BM1, were at the level of endogenous origin. The sulphated metabolites were also detected in 10 urine samples tested positive to boldenone and BM1 by GC-MS. In order to verify the usefulness of these new metabolites to discriminate between endogenous and exogenous origin of boldenone, four samples containing endogenous boldenone and BM1, confirmed by IRMS, were analysed. In 3 of the 4 samples, neither boldenone sulphate nor epiboldenone sulphate were detected, confirming that these metabolites were mainly detected after exogenous administration of boldenone. In contrast, boldenone sulphate and, in some cases, epiboldenone sulphate were present in samples with low concentrations of exogenous boldenone and BM1. Thus, boldenone and epiboldenone sulphates are additional markers for the exogenous origin of boldenone and they can be used to reduce the number of samples to be analysed by IRMS. In samples with boldenone and BM1 at the concentrations suspicion for endogenous origin, only if boldenone and epiboldenone sulphates are present, further analysis by IRMS will be needed to confirm exogenous origin. Copyright © 2012 Elsevier Ltd. All rights reserved.

Mutation analysis of the MECP2 gene in patients of Slavic origin with Rett syndrome: novel mutations and polymorphisms.

PubMed

Zahorakova, Daniela; Rosipal, Robert; Hadac, Jan; Zumrova, Alena; Bzduch, Vladimir; Misovicova, Nadezda; Baxova, Alice; Zeman, Jiri; Martasek, Pavel

2007-01-01

Rett syndrome (RTT), an X-linked dominant neurodevelopmental disorder in females, is caused mainly by de novo mutations in the methyl-CpG-binding protein 2 gene (MECP2). Here we report mutation analysis of the MECP2 gene in 87 patients with RTT from the Czech and Slovak Republics, and Ukraine. The patients, all girls, with classical RTT were investigated for mutations using bi-directional DNA sequencing and conformation sensitive gel electrophoresis analysis of the coding sequence and exon/intron boundaries of the MECP2 gene. Restriction fragment length polymorphism analysis was performed to confirm the mutations that cause the creation or abolition of the restriction site. Mutation-negative cases were subsequently examined by multiple ligation-dependent probe amplification (MLPA) to identify large deletions. Mutation screening revealed 31 different mutations in 68 patients and 12 non-pathogenic polymorphisms. Six mutations have not been previously published: two point mutations (323T>A, 904C>T), three deletions (189_190delGA, 816_832del17, 1069delAGC) and one deletion/inversion (1063_1236del174;1189_1231inv43). MLPA analysis revealed large deletions in two patients. The detection rate was 78.16%. Our results confirm the high frequency of MECP2 mutations in females with RTT and provide data concerning the mutation heterogeneity in the Slavic population.

Identification and characterization of near-fatal asthma phenotypes by cluster analysis.

PubMed

Serrano-Pariente, J; Rodrigo, G; Fiz, J A; Crespo, A; Plaza, V

2015-09-01

Near-fatal asthma (NFA) is a heterogeneous clinical entity and several profiles of patients have been described according to different clinical, pathophysiological and histological features. However, there are no previous studies that identify in a unbiased way--using statistical methods such as clusters analysis--different phenotypes of NFA. Therefore, the aim of the present study was to identify and to characterize phenotypes of near fatal asthma using a cluster analysis. Over a period of 2 years, 33 Spanish hospitals enrolled 179 asthmatics admitted for an episode of NFA. A cluster analysis using two-steps algorithm was performed from data of 84 of these cases. The analysis defined three clusters of patients with NFA: cluster 1, the largest, including older patients with clinical and therapeutic criteria of severe asthma; cluster 2, with an high proportion of respiratory arrest (68%), impaired consciousness level (82%) and mechanical ventilation (93%); and cluster 3, which included younger patients, characterized by an insufficient anti-inflammatory treatment and frequent sensitization to Alternaria alternata and soybean. These results identify specific asthma phenotypes involved in NFA, confirming in part previous findings observed in studies with a clinical approach. The identification of patients with a specific NFA phenotype could suggest interventions to prevent future severe asthma exacerbations. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Multivariate analysis of fears in dental phobic patients according to a reduced FSS-II scale.

PubMed

Hakeberg, M; Gustafsson, J E; Berggren, U; Carlsson, S G

1995-10-01

This study analyzed and assessed dimensions of a questionnaire developed to measure general fears and phobias. A previous factor analysis among 109 dental phobics had revealed a five-factor structure with 22 items and an explained total variance of 54%. The present study analyzed the same material using a multivariate statistical procedure (LISREL) to reveal structural latent variables. The LISREL analysis, based on the correlation matrix, yielded a chi-square of 216.6 with 195 degrees of freedom (P = 0.138) and showed a model with seven latent variables. One was a general fear factor correlated to all 22 items. The other six factors concerned "Illness & Death" (5 items), "Failures & Embarrassment" (5 items), "Social situations" (5 items), "Physical injuries" (4 items), "Animals & Natural phenomena" (4 items). One item (opposite sex) was included in both "Failures & Embarrassment" and "Social situations". The last factor, "Social interaction", combined all the items in "Failures & Embarrassment" and "Social situations" (9 items). In conclusion, this multivariate statistical analysis (LISREL) revealed and confirmed a factor structure similar to our previous study, but added two important dimensions not shown with a traditional factor analysis. This reduced FSS-II version measures general fears and phobias and may be used on a routine clinical basis as well as in dental phobia research.

Contaminations of herbal products determined by NMR fingerprint.

PubMed

Nicoletti, Marcello; Petitto, Valentina

2010-09-01

The utilisation of NMR fingerprinting is proposed as a rapid, available and reliable method to determine the contamination of herbal products. The presence of nimesulide has been reported recently as the contaminant of P.C. 28 Plus, a product based on herbal drugs marketed by the Italian company Cosval. The presence of the substance, as well as its relevant concentration (5%), was first reported by HPLC/MS analysis by other authors. The use of an NMR fingerprint confirmed the previous contamination with nimesulide in P.C. 28 Plus. The same contaminant was also found in P.C. 28 Pink. Furthermore, an analysis of Alergix Plus, another product of the same factory, evidenced the presence of bromhexin.

Glass polymorphism in amorphous germanium probed by first-principles computer simulations

NASA Astrophysics Data System (ADS)

Mancini, G.; Celino, M.; Iesari, F.; Di Cicco, A.

2016-01-01

The low-density (LDA) to high-density (HDA) transformation in amorphous Ge at high pressure is studied by first-principles molecular dynamics simulations in the framework of density functional theory. Previous experiments are accurately reproduced, including the presence of a well-defined LDA-HDA transition above 8 GPa. The LDA-HDA density increase is found to be about 14%. Pair and bond-angle distributions are obtained in the 0-16 GPa pressure range and allowed us a detailed analysis of the transition. The local fourfold coordination is transformed in an average HDA sixfold coordination associated with different local geometries as confirmed by coordination number analysis and shape of the bond-angle distributions.

Psychometrics of the preschool behavioral and emotional rating scale with children from early childhood special education settings.

PubMed

Lambert, Matthew C; Cress, Cynthia J; Epstein, Michael H

2015-01-01

In a previous study with a nationally representative sample, researchers found that the items of the Preschool Behavioral and Emotional Rating Scale can best be described by a four-factor structure model (Emotional Regulation, School Readiness, Social Confidence, and Family Involvement). The findings of this investigation replicate and extend these previous results with a national sample of children (N = 1,075) with disabilities enrolled in early childhood special education programs. Data were analyzed using classical tests theory, Rasch modeling, and confirmatory factor analysis. Results confirmed that for the most part, individual items were internally consistent within a four-factor model and showed consistent item difficulty, discrimination, and fit relative to their respective subscale scores. © 2015 Michigan Association for Infant Mental Health.

Simultaneous long-term monitoring of LS I +61°303 by OVRO and Fermi-LAT

NASA Astrophysics Data System (ADS)

Jaron, Frédéric; Massi, Maria; Kiehlmann, Sebastian; Hovatta, Talvikki

2018-07-01

Previous long-term monitorings of the γ-ray-loud X-ray binary LS I +61°303 have revealed the presence of a long-term modulation of ˜4.5 yr. After 9 yr of simultaneous monitoring of LS I +61°303 by the Owens Valley Radio Observatory and the Fermi-LAT, two cycles of the long-term period are now available. Here we perform timing analysis on the radio and the γ-ray light curves. We confirm the presence of previously detected periodicities at both radio and GeV γ-ray wavelengths. Moreover, we discover an offset of the long-term modulation between radio and γ-ray data which could imply different locations of the radio (15 GHz) and GeV emission along the precessing jet.

Human Endogenous Retrovirus HERV-Fc1 Association with Multiple Sclerosis Susceptibility: A Meta-Analysis

PubMed Central

García-Montojo, Marta; Alcina, Antonio; Fedetz, María; Alloza, Iraide; Astobiza, Ianire; Leyva, Laura; Fernández, Oscar; Izquierdo, Guillermo; Antigüedad, Alfredo; Arroyo, Rafael; Álvarez-Lafuente, Roberto; Vandenbroeck, Koen; Matesanz, Fuencisla; Urcelay, Elena

2014-01-01

Background Human endogenous retroviruses (HERVs) are repetitive sequences derived from ancestral germ-line infections by exogenous retroviruses and different HERV families have been integrated in the genome. HERV-Fc1 in chromosome X has been previously associated with multiple sclerosis (MS) in Northern European populations. Additionally, HERV-Fc1 RNA levels of expression have been found increased in plasma of MS patients with active disease. Considering the North-South latitude gradient in MS prevalence, we aimed to evaluate the role of HERV-Fc1on MS risk in three independent Spanish cohorts. Methods A single nucleotide polymorphism near HERV-Fc1, rs391745, was genotyped by Taqman chemistry in a total of 2473 MS patients and 3031 ethnically matched controls, consecutively recruited from: Northern (569 patients and 980 controls), Central (883 patients and 692 controls) and Southern (1021 patients and 1359 controls) Spain. Our results were pooled in a meta-analysis with previously published data. Results Significant associations of the HERV-Fc1 polymorphism with MS were observed in two Spanish cohorts and the combined meta-analysis with previous data yielded a significant association [rs391745 C-allele carriers: pM-H = 0.0005; ORM-H (95% CI) = 1.27 (1.11–1.45)]. Concordantly to previous findings, when the analysis was restricted to relapsing remitting and secondary progressive MS samples, a slight enhancement in the strength of the association was observed [pM-H = 0.0003, ORM-H (95% CI) = 1.32 (1.14–1.53)]. Conclusion Association of the HERV-Fc1 polymorphism rs391745 with bout-onset MS susceptibility was confirmed in Southern European cohorts. PMID:24594754

Stanford-USGS shrimp-RG ion microprobe: A new approach to determining the distribution of trace elements in coal

USGS Publications Warehouse

Kolker, A.; Wooden, J.L.; Persing, H.M.; Zielinski, R.A.

2000-01-01

The distribution of Cr and other trace metals of environmental interest in a range of widely used U.S. coals was investigated using the Stanford-USGS SHRIMP-RG ion microprobe . Using the oxygen ion source, concentrations of Cr (11 to 176 ppm), V (23 to 248 ppm), Mn (2 to 149 ppm), Ni (2 to 30 ppm), and 13 other elements were determined in illite/smectite, a group of clay minerals commonly present in coal. The results confirm previous indirect or semi-quantitative determinations indicating illite/smectite to be an important host of these metals. Calibration was achieved using doped aluminosilicate-glass synthetic standards and glasses prepared from USGS rock standards. Grains for analysis were identified optically, and confirmed by 1) precursory electron microprobe analysis and wavelength-dispersive compositional mapping, and 2) SHRIMP-RG major element data obtained concurrently with trace element results. Follow-up investigations will focus on the distribution of As and other elements that are more effectively ionized with the cesium primary beam currently being tested.

A survey of occupational cancer in the rubber and cablemaking industries: analysis of deaths occurring in 1972-74.

PubMed Central

Fox, A J; Collier, P F

1976-01-01

The records of 40 867 men employed for at least one year in the rubber and cablemaking industries have now been observed for eight years. This analysis compares the mortality pattern for 1972-74 with that previously reported for 1968-71. It indicates a significant excess of deaths due to cancer of the bladder throughout the industry including men who had not been exposed to acknowledged bladder carcinogens. This excess is in deaths occurring in 1973 and 1974 in the 45-64 and 65 years plus age groups. The two sectors of the industry where this excess is significant are footwear and footwear supplies except adhesives, and the tyre sector. The excess of all cancers taken together previously noted throughout the study population for 1968-71 is confirmed for 1972-74 as is the excess for lung cancers. The greater excess in the tyre sector is also confirmed, particularly in those men in the 55-64 year age group and those who entered the industry between 1950 and 1960. While men employed in 1967 on moulding, press, autoclave, and pan curing, and workers in finished goods, stores, packaging, and despatch continue to have more lung cancer deaths than expected for 1972-74, the excess is no longer statistically significant. An excess of cancer of the stomach which was overlooked in 1968-71 is not confirmed in 1972-74 but is nevertheless high when the total period of study 1968-74 is considered. The limitations of the study are discussed with particular reference to extrapolating the results to the whole industry. We conclude that there is a higher rate of lung cancer in the tyre sector of the industry and that immediate investigations are required to test the hypothesis concerning the recent excess of bladder cancers. Attention should now be paid to the control of exposures to all potential hazards in the industry. PMID:999799

A survey of occupational cancer in the rubber and cablemaking industries: analysis of deaths occurring in 1972-74.

PubMed

Fox, A J; Collier, P F

1976-11-01

The records of 40 867 men employed for at least one year in the rubber and cablemaking industries have now been observed for eight years. This analysis compares the mortality pattern for 1972-74 with that previously reported for 1968-71. It indicates a significant excess of deaths due to cancer of the bladder throughout the industry including men who had not been exposed to acknowledged bladder carcinogens. This excess is in deaths occurring in 1973 and 1974 in the 45-64 and 65 years plus age groups. The two sectors of the industry where this excess is significant are footwear and footwear supplies except adhesives, and the tyre sector. The excess of all cancers taken together previously noted throughout the study population for 1968-71 is confirmed for 1972-74 as is the excess for lung cancers. The greater excess in the tyre sector is also confirmed, particularly in those men in the 55-64 year age group and those who entered the industry between 1950 and 1960. While men employed in 1967 on moulding, press, autoclave, and pan curing, and workers in finished goods, stores, packaging, and despatch continue to have more lung cancer deaths than expected for 1972-74, the excess is no longer statistically significant. An excess of cancer of the stomach which was overlooked in 1968-71 is not confirmed in 1972-74 but is nevertheless high when the total period of study 1968-74 is considered. The limitations of the study are discussed with particular reference to extrapolating the results to the whole industry. We conclude that there is a higher rate of lung cancer in the tyre sector of the industry and that immediate investigations are required to test the hypothesis concerning the recent excess of bladder cancers. Attention should now be paid to the control of exposures to all potential hazards in the industry.

Visualizing conserved gene location across microbe genomes

NASA Astrophysics Data System (ADS)

Shaw, Chris D.

2009-01-01

This paper introduces an analysis-based zoomable visualization technique for displaying the location of genes across many related species of microbes. The purpose of this visualizatiuon is to enable a biologist to examine the layout of genes in the organism of interest with respect to the gene organization of related organisms. During the genomic annotation process, the ability to observe gene organization in common with previously annotated genomes can help a biologist better confirm the structure and function of newly analyzed microbe DNA sequences. We have developed a visualization and analysis tool that enables the biologist to observe and examine gene organization among genomes, in the context of the primary sequence of interest. This paper describes the visualization and analysis steps, and presents a case study using a number of Rickettsia genomes.

Multi-complexity ensemble measures for gait time series analysis: application to diagnostics, monitoring and biometrics.

PubMed

Gavrishchaka, Valeriy; Senyukova, Olga; Davis, Kristina

2015-01-01

Previously, we have proposed to use complementary complexity measures discovered by boosting-like ensemble learning for the enhancement of quantitative indicators dealing with necessarily short physiological time series. We have confirmed robustness of such multi-complexity measures for heart rate variability analysis with the emphasis on detection of emerging and intermittent cardiac abnormalities. Recently, we presented preliminary results suggesting that such ensemble-based approach could be also effective in discovering universal meta-indicators for early detection and convenient monitoring of neurological abnormalities using gait time series. Here, we argue and demonstrate that these multi-complexity ensemble measures for gait time series analysis could have significantly wider application scope ranging from diagnostics and early detection of physiological regime change to gait-based biometrics applications.

Principal components analysis of Jupiter VIMS spectra

USGS Publications Warehouse

Bellucci, G.; Formisano, V.; D'Aversa, E.; Brown, R.H.; Baines, K.H.; Bibring, J.-P.; Buratti, B.J.; Capaccioni, F.; Cerroni, P.; Clark, R.N.; Coradini, A.; Cruikshank, D.P.; Drossart, P.; Jaumann, R.; Langevin, Y.; Matson, D.L.; McCord, T.B.; Mennella, V.; Nelson, R.M.; Nicholson, P.D.; Sicardy, B.; Sotin, Christophe; Chamberlain, M.C.; Hansen, G.; Hibbits, K.; Showalter, M.; Filacchione, G.

2004-01-01

During Cassini - Jupiter flyby occurred in December 2000, Visual-Infrared mapping spectrometer (VIMS) instrument took several image cubes of Jupiter at different phase angles and distances. We have analysed the spectral images acquired by the VIMS visual channel by means of a principal component analysis technique (PCA). The original data set consists of 96 spectral images in the 0.35-1.05 ??m wavelength range. The product of the analysis are new PC bands, which contain all the spectral variance of the original data. These new components have been used to produce a map of Jupiter made of seven coherent spectral classes. The map confirms previously published work done on the Great Red Spot by using NIMS data. Some other new findings, presently under investigation, are presented. ?? 2004 Published by Elsevier Ltd on behalf of COSPAR.

ScienceCast 136: A Sudden Multiplication of Planets

NASA Image and Video Library

2014-02-26

Today, NASA announced a breakthrough addition to the catalog of new planets. Researchers using Kepler have confirmed 715 new worlds, almost quadrupling the number of planets previously confirmed by the planet-hunting spacecraft.

Epidemiological survey on pandemic influenza A (H1N1) virus infection in Kurdistan province, Islamic Republic of Iran, 2009.

PubMed

Afrasiabian, S; Mohsenpour, B; Bagheri, K H; Barari, M; Ghaderi, E; Hashemi, R; Garibi, F

2014-04-03

This study evaluated the epidemiology of suspected cases of pandemic influenza A (H1N1) virus infection in 2009-2010 in Kurdistan province, a frontier province of the Islamic Republic of Iran. A questionnaire covering demographic characteristics, clinical presentation and outcome, and history of exposure and travel was completed by patients attending health centres and hospitals in the province. Nasal and throat swabs were analysed by RT-PCR. A total of 1059 suspected cases were assessed; H1N1 influenza A was confirmed in 157 (14.8%). The highest proportion of confirmed cases was 30.0%, among children aged < 1 year. In multivariate analysis, previous contact with symptomatic influenza patients (OR = 2.17) and hospitalization (OR = 3.88) were the only significant risk factors for confirmed H1N1 infection. Age, sex, residency, presenting symptoms and history of national or international travel were not significant. Influenza A (H1N1) virus has spread in Islamic Republic of Iran; probably transmitted by travellers to Kurdistan.

High-resolution Spectroscopic Abundances of Red Giant Branch Stars in NGC 6584 and NGC 7099

NASA Astrophysics Data System (ADS)

O’Malley, Erin M.; Chaboyer, Brian

2018-04-01

We obtain high-resolution spectra of red giant branch stars in NGC 6584 and NGC 7099 to perform a detailed abundance analysis. We confirm cluster membership for these stars based on consistent radial velocities measured in this study and small pixel offsets between the observations of Sarajedini et al. and Piotto et al. We find mean metallicities of [Fe/H] = ‑1.53 ± 0.08 dex and [Fe/H] = ‑2.29 ± 0.07 dex for NGC 6584 and NGC 7099, respectively. We also find these clusters to be enhanced in their [α/Fe] ratios, consistent with what is expected for metal-poor globular clusters. Additionally, we find evidence of a statistically significant Na–O anti-correlation in both clusters. Finally, with the use of HST photometry, we compare the location of the enhanced and pristine populations in chromosome maps of the clusters to confirm previous photometric evidence of multiple stellar populations. Although we cannot confirm the nature of the polluter stars responsible for the abundance differences, our results can be used to constrain pollution models.

Transient Dynamic Mechanical Analysis of Resilin-based Elastomeric Hydrogels

NASA Astrophysics Data System (ADS)

Li, Linqing; Kiick, Kristi

2014-04-01

The outstanding high-frequency properties of emerging resilin-like polypeptides (RLPs) have motivated their development for vocal fold tissue regeneration and other applications. Recombinant RLP hydrogels show efficient gelation, tunable mechanical properties, and display excellent extensibility, but little has been reported about their transient mechanical properties. In this manuscript, we describe the transient mechanical behavior of new RLP hydrogels investigated via both sinusoidal oscillatory shear deformation and uniaxial tensile testing. Oscillatory stress relaxation and creep experiments confirm that RLP-based hydrogels display significantly reduced stress relaxation and improved strain recovery compared to PEG-based control hydrogels. Uniaxial tensile testing confirms the negligible hysteresis, reversible elasticity and superior resilience (up to 98%) of hydrated RLP hydrogels, with Young’s modulus values that compare favorably with those previously reported for resilin and that mimic the tensile properties of the vocal fold ligament at low strain (< 15%). These studies expand our understanding of the properties of these RLP materials under a variety of conditions, and confirm the unique applicability, for mechanically demanding tissue engineering applications, of a range of RLP hydrogels.

Smooth information flow in temperature climate network reflects mass transport

NASA Astrophysics Data System (ADS)

Hlinka, Jaroslav; Jajcay, Nikola; Hartman, David; Paluš, Milan

2017-03-01

A directed climate network is constructed by Granger causality analysis of air temperature time series from a regular grid covering the whole Earth. Using winner-takes-all network thresholding approach, a structure of a smooth information flow is revealed, hidden to previous studies. The relevance of this observation is confirmed by comparison with the air mass transfer defined by the wind field. Their close relation illustrates that although the information transferred due to the causal influence is not a physical quantity, the information transfer is tied to the transfer of mass and energy.

Vortex Thermometry for Turbulent Two-Dimensional Fluids.

PubMed

Groszek, Andrew J; Davis, Matthew J; Paganin, David M; Helmerson, Kristian; Simula, Tapio P

2018-01-19

We introduce a new method of statistical analysis to characterize the dynamics of turbulent fluids in two dimensions. We establish that, in equilibrium, the vortex distributions can be uniquely connected to the temperature of the vortex gas, and we apply this vortex thermometry to characterize simulations of decaying superfluid turbulence. We confirm the hypothesis of vortex evaporative heating leading to Onsager vortices proposed in Phys. Rev. Lett. 113, 165302 (2014)PRLTAO0031-900710.1103/PhysRevLett.113.165302, and we find previously unidentified vortex power-law distributions that emerge from the dynamics.

Lameness associated with tarsal haemarthrosis as the sole clinical sign of idiopathic immune-mediated thrombocytopenia in a dog.

PubMed

Walton, M B; Mardell, E; Spoor, M; Innes, J

2014-01-01

A four-year-old, male Cocker Spaniel was presented for investigation of pelvic limb stiffness. There was palpable effusion of both tarsi, and analysis of synovial fluid from these joints indicated previous haemorrhage. After further investigation a diagnosis of idiopathic immune-mediated thrombocytopenia was made. The dog responded to treatment with prednisolone and azathioprine. To the authors' knowledge, this is the first reported case of confirmed haemarthrosis as the sole presenting clinical sign for canine idiopathic immune-mediated thrombocytopenia.

Enzyme markers in inbred rat strains: genetics of new markers and strain profiles.

PubMed

Adams, M; Baverstock, P R; Watts, C H; Gutman, G A

1984-08-01

Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.

Effect of osteoporosis on fixation of osseointegrated implants in rats.

PubMed

Li, Yunfeng; He, Sheng; Hua, Yunwei; Hu, Jing

2017-11-01

The effect of osteoporosis on implant osseointegration has been widely investigated, whereas osteoporosis may also newly occur in patient with previously osseointegrated implant. This study was designed to investigate the effect of osteoporosis on implant fixation in rats after successful osseointegration had been obtained. Seventy female Sprague-Dawley rats were included, and each animal received two titanium implants in the distal metaphysis of femur bilaterally. Eight weeks later, ten rats were sacrificed to confirm the establishment of implant osseointegration. All left rats were randomly subjected to bilateral ovariectomy (OVX) or sham operation. Three, six, and twelve weeks later, implant osseointegration, peri-implant bone tissue, and biomechanical properties of implant were analyzed. Right femurs with implants were used for micro-CT and histological analysis, and left femurs with implants were used for biomechanical test. Micro-CT, histology, and biomechanical test confirmed the destructive effect of OVX on previously osseointegrated implant in rats; when compared to sham-operated rats, peri-implant bone volume, trabecular architecture, bone-to-implant contact ratio, as well as biomechanical parameters decreased progressively within 12 weeks. Results also indicated that the effect of OVX on undisturbed bone (proximal tibiae) was much stronger than that on peri-implant bone. Osteoporosis produced a progressive negative effect on previously osseointegrated implant in distal femora of rats during 12 weeks. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 2426-2432, 2017. © 2016 Wiley Periodicals, Inc.

Searching for Dark Matter annihilation in recently discovered Milky Way satellites with FERMI-LAT

DOE PAGES

Albert, A.; Anderson, B.; Bechtol, K.; ...

2017-01-06

Here, we search for excess γ-ray emission coincident with the positions of confirmed and candidate Milky Way satellite galaxies using six years of data from the Fermi Large Area Telescope (LAT). Our sample of 45 stellar systems includes 28 kinematically confirmed dark-matter-dominated dwarf spheroidal galaxies (dSphs) and 17 recently discovered systems that have photometric characteristics consistent with the population of known dSphs. For each of these targets, the relative predicted γ-ray flux due to dark matter annihilation is taken from kinematic analysis if available, and estimated from a distance-based scaling relation otherwise, assuming that the stellar systems are DM-dominated dSphs. LAT data coincident with four of the newly discovered targets show a slight preference (eachmore » $$\\sim $$2σ local) for γ-ray emission in excess of the background. However, the ensemble of derived γ-ray flux upper limits for individual targets is consistent with the expectation from analyzing random blank-sky regions, and a combined analysis of the population of stellar systems yields no globally significant excess (global significance $$\\lt 1\\sigma $$). Our analysis has increased sensitivity compared to the analysis of 15 confirmed dSphs by Ackermann et al. The observed constraints on the DM annihilation cross section are statistically consistent with the background expectation, improving by a factor of ~2 for large DM masses ($${m}_{\\mathrm{DM},b\\bar{b}}\\gtrsim 1\\,\\mathrm{TeV}$$ and $${m}_{\\mathrm{DM},{\\tau }^{+}{\\tau }^{-}}\\gtrsim 70\\,\\mathrm{GeV}$$) and weakening by a factor of ~1.5 at lower masses relative to previously observed limits.« less

Searching for Dark Matter annihilation in recently discovered Milky Way satellites with FERMI-LAT

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

Albert, A.; Anderson, B.; Bechtol, K.

Here, we search for excess γ-ray emission coincident with the positions of confirmed and candidate Milky Way satellite galaxies using six years of data from the Fermi Large Area Telescope (LAT). Our sample of 45 stellar systems includes 28 kinematically confirmed dark-matter-dominated dwarf spheroidal galaxies (dSphs) and 17 recently discovered systems that have photometric characteristics consistent with the population of known dSphs. For each of these targets, the relative predicted γ-ray flux due to dark matter annihilation is taken from kinematic analysis if available, and estimated from a distance-based scaling relation otherwise, assuming that the stellar systems are DM-dominated dSphs. LAT data coincident with four of the newly discovered targets show a slight preference (eachmore » $$\\sim $$2σ local) for γ-ray emission in excess of the background. However, the ensemble of derived γ-ray flux upper limits for individual targets is consistent with the expectation from analyzing random blank-sky regions, and a combined analysis of the population of stellar systems yields no globally significant excess (global significance $$\\lt 1\\sigma $$). Our analysis has increased sensitivity compared to the analysis of 15 confirmed dSphs by Ackermann et al. The observed constraints on the DM annihilation cross section are statistically consistent with the background expectation, improving by a factor of ~2 for large DM masses ($${m}_{\\mathrm{DM},b\\bar{b}}\\gtrsim 1\\,\\mathrm{TeV}$$ and $${m}_{\\mathrm{DM},{\\tau }^{+}{\\tau }^{-}}\\gtrsim 70\\,\\mathrm{GeV}$$) and weakening by a factor of ~1.5 at lower masses relative to previously observed limits.« less

Laparoscopic diagnosis of endometriosis.

PubMed

Wood, Carl; Kuhn, Raphael; Tsaltas, Jim

2002-08-01

To consider and explain the possibility of difficulties in diagnosis of endometriosis at previous laparoscopy Retrospective patient record review. The Endometriosis Care Centre of Australia and the private practices of authors. Two hundred and fifteen patients with clinical evidence of endometriosis examined laparoscopically between March 1999 and May 2001. Confirmation of endometriosis by histological biopsy. Endometriosis was confirmed in 168 of the 215 women. Of these women 38 had a previous negative laparoscopy within 12 months of the current laparoscopy. It is possible that in some of the patients, who previously had a negative laparoscopy, endometriosis was not recognised. Possible reasons for difficulty in diagnosis have been identified and techniques to improve diagnosis suggested. This retrospective study was performed to consider and explain the possibility of difficulties in diagnosis of endometriosis at previous laparoscopy.

Cold tolerance in rice germinating seeds revealed by deep RNAseq analysis of contrasting indica genotypes.

PubMed

Dametto, Andressa; Sperotto, Raul A; Adamski, Janete M; Blasi, Édina A R; Cargnelutti, Denise; de Oliveira, Luiz F V; Ricachenevsky, Felipe K; Fregonezi, Jeferson N; Mariath, Jorge E A; da Cruz, Renata P; Margis, Rogério; Fett, Janette P

2015-09-01

Rice productivity is largely affected by low temperature, which can be harmful throughout plant development, from germination to grain filling. Germination of indica rice cultivars under cold is slow and not uniform, resulting in irregular emergence and small plant population. To identify and characterize novel genes involved in cold tolerance during the germination stage, two indica rice genotypes (sister lines previously identified as cold-tolerant and cold-sensitive) were used in parallel transcriptomic analysis (RNAseq) under cold treatment (seeds germinating at 13 °C for 7 days). We detected 1,361 differentially expressed transcripts. Differences in gene expression found by RNAseq were confirmed for 11 selected genes using RT-qPCR. Biological processes enhanced in the cold-tolerant seedlings include: cell division and expansion (confirmed by anatomical sections of germinating seeds), cell wall integrity and extensibility, water uptake and membrane transport capacity, sucrose synthesis, generation of simple sugars, unsaturation of membrane fatty acids, wax biosynthesis, antioxidant capacity (confirmed by histochemical staining of H2O2), and hormone and Ca(2+)-signaling. The cold-sensitive seedlings respond to low temperature stress increasing synthesis of HSPs and dehydrins, along with enhanced ubiquitin/proteasome protein degradation pathway and polyamine biosynthesis. Our findings can be useful in future biotechnological approaches aiming to cold tolerance in indica rice. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

First identification of Francisella noatunensis subsp. orientalis causing mortality in Mexican tilapia Oreochromis spp.

PubMed

Ortega, Cesar; Mancera, Gerardo; Enríquez, Ricardo; Vargas, Augusto; Martínez, Simón; Fajardo, Raúl; Avendaño-Herrera, Ruben; Navarrete, María José; Romero, Alex

2016-08-09

Francisellosis, an emerging disease in tilapia Oreochromis spp., is caused by the facultative, intracellular bacterium Francisella noatunensis subsp. orientalis, which is present in various countries where tilapia farming is commercially important. We confirmed the presence of francisellosis in Mexican tilapia cultures in association with an outbreak during the second semester of 2012. Broodstock fish presented a mortality rate of approximately 40%, and disease was characterized by histologically classified granulomas, or whitish nodules, in different organs, mainly the spleen and kidney. Through DNA obtained from infected tissue and pure cultures in a cysteine heart medium supplemented with hemoglobin, F. noatunensis subsp. orientalis was initially confirmed through the amplification and analysis of the 16S rRNA gene and the internal transcribed spacer region. Phylogenetic analysis of these genes demonstrated close similarity with previously reported F. noatunensis subsp. orientalis sequences obtained from infected tilapia from various countries. The identification of this subspecies as the causative agent of the outbreak was confirmed using the iglC gene as a target sequence, which showed 99.5% identity to 2 F. noatunensis subsp. orientalis strains (Ethime-1 and Toba04). These findings represent the first documented occurrence of francisellosis in Mexican tilapia cultures, which highlights the importance of establishing preventative measures to minimize the spread of this disease within the Mexican aquaculture industry.

Wavelength dispersive X-ray fluorescence analysis using fundamental parameter approach of Catha edulis and other related plant samples

NASA Astrophysics Data System (ADS)

Shaltout, Abdallah A.; Moharram, Mohammed A.; Mostafa, Nasser Y.

2012-01-01

This work is the first attempt to quantify trace elements in the Catha edulis plant (Khat) with a fundamental parameter approach. C. edulis is a famous drug plant in east Africa and Arabian Peninsula. We have previously confirmed that hydroxyapatite represents one of the main inorganic compounds in the leaves and stalks of C. edulis. Comparable plant leaves from basil, mint and green tea were included in the present investigation as well as trifolium leaves were included as a non-related plant. The elemental analyses of the plants were done by Wavelength Dispersive X-Ray Fluorescence (WDXRF) spectroscopy. Standard-less quantitative WDXRF analysis was carried out based on the fundamental parameter approaches. According to the standard-less analysis algorithms, there is an essential need for an accurate determination of the amount of organic material in the sample. A new approach, based on the differential thermal analysis, was successfully used for the organic material determination. The obtained results based on this approach were in a good agreement with the commonly used methods. Depending on the developed method, quantitative analysis results of eighteen elements including; Al, Br, Ca, Cl, Cu, Fe, K, Na, Ni, Mg, Mn, P, Rb, S, Si, Sr, Ti and Zn were obtained for each plant. The results of the certified reference materials of green tea (NCSZC73014, China National Analysis Center for Iron and Steel, Beijing, China) confirmed the validity of the proposed method.

The Role of Rearranged Neu Genes in the Progression of Rat Mammary Tumors Induced by N-nitroso N’-methylurea.

DTIC Science & Technology

1997-08-01

anti-neu antibody response of DNA vaccine immunized mice again by indirectly flowcytometry assay, we confirm our previous finding. We also examine the... flowcytometry assay, I have confirmed my previous finding from Elisa assay. 5 I also examined the cellular immunity response of DNA immunized mice by CTL...immunized mice by indirectly flowcytometry assay. I also find mice immunized with neu DNA vaccine did not develop detectable cytotoxic T lymphocyte

Survival of gastrointestinal stromal tumor patients in the imatinib era: life raft group observational registry

PubMed Central

2012-01-01

Background Gastrointestinal stromal tumors (GIST), one of the most common mesenchymal tumors of the gastrointestinal tract, prior to routine immunohistochemical staining and the introduction of tyrosine kinase inhibitors, were often mistaken for neoplasms of smooth muscle origin such as leiomyomas, leiomyosarcomas or leiomyoblastomas. Since the advent of imatinib, GIST has been further delineated into adult- (KIT or PDGFRα mutations) and pediatric- (typified by wild-type GIST/succinate dehydrogenase deficiencies) types. Using varying gender ratios at age of diagnosis we sought to elucidate prognostic factors for each sub-type and their impact on overall survival. Methods This is a long-term retrospective analysis of a large observational study of an international open cohort of patients from a GIST research and patient advocacy's lifetime registry. Demographic and disease-specific data were voluntarily supplied by its members from May 2000-October 2010; the primary outcome was overall survival. Associations between survival and prognostic factors were evaluated by univariate Cox proportional hazard analyses, with backward selection at P < 0.05 used to identify independent factors. Results Inflections in gender ratios by age at diagnosis in years delineated two distinct groups: above and below age 35 at diagnosis. Closer analysis confirmed the above 35 age group as previously reported for adult-type GIST, typified by mixed primary tumor sites and gender, KIT or PDGFRα mutations, and shorter survival times. The pediatric group (< age 18 at diagnosis) was also as previously reported with predominantly stomach tumors, females, wild-type GIST or SDH mutations, and extended survival. "Young adults" however formed a third group aged 18-35 at diagnosis, and were a clear mix of these two previously reported distinct sub-types. Conclusions Pediatric- and adult-type GIST have been previously characterized in clinical settings and these observations confirm significant prognostic factors for each from a diverse real-world cohort. Additionally, these findings suggest that extra diligence be taken with "young adults" (aged 18-35 at diagnosis) as pediatric-type GIST may present well beyond adolescence, particularly as these distinct sub-types have different causes, and consequently respond differently to treatments. PMID:22429770

Survival of gastrointestinal stromal tumor patients in the imatinib era: life raft group observational registry.

PubMed

Call, Jerry; Walentas, Christopher D; Eickhoff, Jens C; Scherzer, Norman

2012-03-19

Gastrointestinal stromal tumors (GIST), one of the most common mesenchymal tumors of the gastrointestinal tract, prior to routine immunohistochemical staining and the introduction of tyrosine kinase inhibitors, were often mistaken for neoplasms of smooth muscle origin such as leiomyomas, leiomyosarcomas or leiomyoblastomas. Since the advent of imatinib, GIST has been further delineated into adult- (KIT or PDGFRα mutations) and pediatric- (typified by wild-type GIST/succinate dehydrogenase deficiencies) types. Using varying gender ratios at age of diagnosis we sought to elucidate prognostic factors for each sub-type and their impact on overall survival. This is a long-term retrospective analysis of a large observational study of an international open cohort of patients from a GIST research and patient advocacy's lifetime registry. Demographic and disease-specific data were voluntarily supplied by its members from May 2000-October 2010; the primary outcome was overall survival. Associations between survival and prognostic factors were evaluated by univariate Cox proportional hazard analyses, with backward selection at P < 0.05 used to identify independent factors. Inflections in gender ratios by age at diagnosis in years delineated two distinct groups: above and below age 35 at diagnosis. Closer analysis confirmed the above 35 age group as previously reported for adult-type GIST, typified by mixed primary tumor sites and gender, KIT or PDGFRα mutations, and shorter survival times. The pediatric group (< age 18 at diagnosis) was also as previously reported with predominantly stomach tumors, females, wild-type GIST or SDH mutations, and extended survival. "Young adults" however formed a third group aged 18-35 at diagnosis, and were a clear mix of these two previously reported distinct sub-types. Pediatric- and adult-type GIST have been previously characterized in clinical settings and these observations confirm significant prognostic factors for each from a diverse real-world cohort. Additionally, these findings suggest that extra diligence be taken with "young adults" (aged 18-35 at diagnosis) as pediatric-type GIST may present well beyond adolescence, particularly as these distinct sub-types have different causes, and consequently respond differently to treatments.

Visual Task Demands and the Auditory Mismatch Negativity: An Empirical Study and a Meta-Analysis

PubMed Central

Wiens, Stefan; Szychowska, Malina; Nilsson, Mats E.

2016-01-01

Because the auditory system is particularly useful in monitoring the environment, previous research has examined whether task-irrelevant, auditory distracters are processed even if subjects focus their attention on visual stimuli. This research suggests that attentionally demanding visual tasks decrease the auditory mismatch negativity (MMN) to simultaneously presented auditory distractors. Because a recent behavioral study found that high visual perceptual load decreased detection sensitivity of simultaneous tones, we used a similar task (n = 28) to determine if high visual perceptual load would reduce the auditory MMN. Results suggested that perceptual load did not decrease the MMN. At face value, these nonsignificant findings may suggest that effects of perceptual load on the MMN are smaller than those of other demanding visual tasks. If so, effect sizes should differ systematically between the present and previous studies. We conducted a selective meta-analysis of published studies in which the MMN was derived from the EEG, the visual task demands were continuous and varied between high and low within the same task, and the task-irrelevant tones were presented in a typical oddball paradigm simultaneously with the visual stimuli. Because the meta-analysis suggested that the present (null) findings did not differ systematically from previous findings, the available evidence was combined. Results of this meta-analysis confirmed that demanding visual tasks reduce the MMN to auditory distracters. However, because the meta-analysis was based on small studies and because of the risk for publication biases, future studies should be preregistered with large samples (n > 150) to provide confirmatory evidence for the results of the present meta-analysis. These future studies should also use control conditions that reduce confounding effects of neural adaptation, and use load manipulations that are defined independently from their effects on the MMN. PMID:26741815

Transcriptome Analysis in Patients with Chronic Kidney Disease on Hemodialysis Disclosing a Key Role for CD16+CX3CR1+ Monocytes

PubMed Central

Dhondt, Annemieke; De Meyer, Grim; Neirynck, Nathalie; Bernaert, Pascale; Van den Bergh, Rafael; Brouckaert, Peter; Vanholder, Raymond; Glorieux, Griet

2015-01-01

The risk for cardiovascular morbidity and mortality is increased in chronic kidney disease; in this process micro-inflammation plays an essential role. Responsible mechanisms remain to a large extent unidentified. In this pilot study transcriptome analysis of peripheral blood monocytes was used to identify in an unprejudiced manner which factors could be discriminative for cardiovascular disease in patients with chronic kidney disease on hemodialysis. Forty gender- and age-matched, non-diabetic, non-smoking subjects with CRP < 20 mg/L were recruited: 9 healthy controls, 11 patients with eGFR > 60 mL/min/1.73m2 and a history of cardiovascular event (CVE), 10 patients with chronic kidney disease stage 5 on hemodialysis without previous cardiovascular event (CKD5HD) and 10 with a previous cardiovascular event (CKD5HD/CVE). Monocytes were isolated and their mRNA was submitted to focused transcriptome analysis using a macroarray platform containing ca. 700 genes associated with macrophage functional capacity. The macroarray data indicated 9 genes (8 upregulated and 1 downregulated) with a significant differential expression in CKD5HD/CVE vs. CVE alone, after excluding genes differentially expressed in CKD5HD vs. control. For FCGR3A (CD16) and CX3CR1 (chemokine receptor) the upregulation vs. control and vs. CVE could be confirmed by quantitative RT-PCR for all CKD5HD patients. Furthermore, CX3CR1 relative expression on monocytes correlated with CRP. Flow cytometric analysis of purified monocytes confirmed a significant increase in the percentage of CD16 positive monocytes in all CKD5HD patients vs. control and CVE. The present study indicates the importance of a specific pro-inflammatory monocyte subpopulation, positive for CD16 and the co-expressed chemokine receptor, CX3CR1, discriminative for CKD5HD patients. PMID:25830914

Network analysis of knowledge and practices regarding sexual and reproductive health: a study among adolescent street girls in Kinshasa (DRC).

PubMed

Vallès, Xavier; Lusala, Patrick Lunzayiladio; Devalière, Hortense; Metsia-Thiam, Marie-Michele; Aguilar, Daniel; Cheyron, Anne-Laure; Cannet, Didier

2017-02-01

The aim of the study was to ascertain the influence of knowledge and interventions in sexual and reproductive health and contraception practices among adolescent street girls from Kinshasa, Democratic Republic of the Congo. A cross-sectional study was carried out among street girls between 12 and 21 years of age. A standardised questionnaire was used, encompassing socio-demographic data and knowledge and practices regarding sexual and reproductive health. A network analysis was carried out. The study comprised 293 street girls. The mean age was 17.1 years (range 12-21 years) and the mean time spent living on the streets was 3.9 years (range 0-15 years). Commercial sex was reported by 78.5% (95% confidence interval [CI] 73.3%, 83.2%) as the main source of their income. During their last sexual intercourse, 44.0% (95%CI 38.1%, 50.4%) had not used a condom; 29.3% (95%CI 23.3%, 35.9%) had used hormonal contraception. Previous pregnancy was reported by 62.5% (95%CI 56.7%, 68.3%) and current pregnancy by 12.3% (95%CI 8.8%, 17.2%); 24.5% of previous pregnancies ended in voluntary termination, with a higher rate among the youngest street girls (12-15 years, 50.0%; p = 0.01). Time spent living on the streets was independently associated with pregnancy (odds ratio 1.2; 95%CI 1.1, 1.4). Practices and outcomes (previous or current pregnancy) were poorly correlated with knowledge about sexual and reproductive health. The network analysis confirmed the poor influence of exposure to intervention activities on sexual and reproductive health practices and outcomes, but did confirm a centrality effect of knowledge about HIV/AIDS. Street girls in Kinshasa are extremely vulnerable with regard to their sexual and reproductive health, especially the youngest street girls. Behavioural and biomedical interventions have had limited influence. Structural and societal changes are necessary to positively impact street girls' sexual and reproductive health. Knowledge about HIV/AIDS than about risk of pregnancy had a greater influence on sexual and reproductive health practices.

RNA Seq analysis of the role of calcium chloride stress and electron transport in mitochondria for malachite green decolorization by Aspergillus niger.

PubMed

Gomaa, Ola M; Selim, Nabila S; Wee, Josephine; Linz, John E

2017-08-01

Aspergillus niger was previously demonstrated to decolorize the commercial dye malachite green (MG) and this process was enhanced under calcium chloride (CaCl 2 ) treatment. Previous data also suggested that the decolorization process is related to mitochondrial cytochrome c. In the current work, we analyzed in depth the specific relationship between CaCl 2 treatment and MG decolorization. Gene expression analysis (RNA Seq) using Next Generation Sequencing (NGS) revealed up-regulation of 28 genes that are directly or indirectly associated with stress response functions as early as 30min of CaCl 2 treatment; these data further strengthen our previous findings that CaCl 2 treatment induces a stress response in A. niger which enhances the ability to decolorize MG. A significant increase in fluorescence observed by MitoTracker dye suggests that CaCl 2 treatment also increased mitochondrial membrane potential. Isolated mitochondrial membrane protein fractions obtained from A. niger grown under standard growth conditions decolorized MG in the presence of NADH and decolorization was enhanced in samples isolated from CaCl 2 -treated A. niger cultures. Treatment of whole mitochondrial fraction with KCN which inhibits electron transport by cytochrome c oxidase and Triton-X 100 which disrupts mitochondrial membrane integrity suggests that cyanide sensitive cytochrome c oxidase activity is a key biochemical step in MG decolorization. This suggestion was confirmed by the addition of palladium α-lipoic acid complex (PLAC) which resulted in an initial increase in decolorization. Although the role of cytochrome c and cytochrome c oxidase was confirmed at the biochemical level, changes in levels of transcripts encoding these enzymes after CaCl 2 treatment were not found to be statistically significant in RNA Seq analysis. These data suggest that the regulation of cytochrome c enzymes occur predominantly at the post-transcriptional level under CaCl 2 stress. Thus, using global transcriptomics and biochemical approaches, our study provides a molecular association between fungal mitochondrial electron transfer systems and MG decolorization. Copyright © 2017 Elsevier Inc. All rights reserved.

Evolutionary history of rabies in Ghana.

PubMed

Hayman, David T S; Johnson, Nicholas; Horton, Daniel L; Hedge, Jessica; Wakeley, Philip R; Banyard, Ashley C; Zhang, Shoufeng; Alhassan, Andy; Fooks, Anthony R

2011-04-05

Rabies virus (RABV) is enzootic throughout Africa, with the domestic dog (Canis familiaris) being the principal vector. Dog rabies is estimated to cause 24,000 human deaths per year in Africa, however, this estimate is still considered to be conservative. Two sub-Saharan African RABV lineages have been detected in West Africa. Lineage 2 is present throughout West Africa, whereas Africa 1a dominates in northern and eastern Africa, but has been detected in Nigeria and Gabon, and Africa 1b was previously absent from West Africa. We confirmed the presence of RABV in a cohort of 76 brain samples obtained from rabid animals in Ghana collected over an eighteen-month period (2007-2009). Phylogenetic analysis of the sequences obtained confirmed all viruses to be RABV, belonging to lineages previously detected in sub-Saharan Africa. However, unlike earlier reported studies that suggested a single lineage (Africa 2) circulates in West Africa, we identified viruses belonging to the Africa 2 lineage and both Africa 1 (a and b) sub-lineages. Phylogeographic Bayesian Markov chain Monte Carlo analysis of a 405 bp fragment of the RABV nucleoprotein gene from the 76 new sequences derived from Ghanaian animals suggest that within the Africa 2 lineage three clades co-circulate with their origins in other West African countries. Africa 1a is probably a western extension of a clade circulating in central Africa and the Africa 1b virus a probable recent introduction from eastern Africa. We also developed and tested a novel reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of RABV in African laboratories. This RT-LAMP was shown to detect both Africa 1 and 2 viruses, including its adaptation to a lateral flow device format for product visualization. These data suggest that RABV epidemiology is more complex than previously thought in West Africa and that there have been repeated introductions of RABV into Ghana. This analysis highlights the potential problems of individual developing nations implementing rabies control programmes in the absence of a regional programme.

Confirmation of the Three-Factor Model of Problematic Internet Use on Off-Line Adolescent and Adult Samples

PubMed Central

Koronczai, Beatrix; Urbán, Róbert; Kökönyei, Gyöngyi; Paksi, Borbála; Papp, Krisztina; Kun, Bernadette; Arnold, Petra; Kállai, János

2011-01-01

Abstract As the Internet became widely used, problems associated with its excessive use became increasingly apparent. Although for the assessment of these problems several models and related questionnaires have been elaborated, there has been little effort made to confirm them. The aim of the present study was to test the three-factor model of the previously created Problematic Internet Use Questionnaire (PIUQ) by data collection methods formerly not applied (off-line group and face-to-face settings), on the one hand, and by testing on different age groups (adolescent and adult representative samples), on the other hand. Data were collected from 438 high-school students (44.5 percent boys; mean age: 16.0 years; standard deviation=0.7 years) and also from 963 adults (49.9 percent males; mean age: 33.6 years; standard deviation=11.8 years). We applied confirmatory factor analysis to confirm the measurement model of problematic Internet use. The results of the analyses carried out inevitably support the original three-factor model over the possible one-factor solution. Using latent profile analysis, we identified 11 percent of adults and 18 percent of adolescent users characterized by problematic use. Based on exploratory factor analysis, we also suggest a short form of the PIUQ consisting of nine items. Both the original 18-item version of PIUQ and its short 9-item form have satisfactory reliability and validity characteristics, and thus, they are suitable for the assessment of problematic Internet use in future studies. PMID:21711129

Hippocampal and prefrontal cortex contributions to learning and memory: analysis of lesion and aging effects on maze learning in rats.

PubMed

Winocur, G; Moscovitch, M

1990-08-01

Young adult rats with bilateral lesions to the hippocampus or prefrontal cortex, young operated controls, and normal old rats were tested on two complex mazes in the Hebb-Williams series. Approximately half the animals were previously trained on one of the mazes; the remainder received no previous training. The trained hippocampal rats showed sparing of memory for the general skill of maze learning but poor recall of the specific maze on which they had been previously trained. The opposite pattern was observed in trained prefrontal rats. In contrast, the aged rats' memory for maze-specific and maze-general information was impaired. The results confirmed the importance of the hippocampus for recalling highly specific information and pointed to a possible role for the frontal lobes in learning and remembering nonspecific skill-related information. The generalized deficit of the aged rats indicates that both types of memory were compromised and offers further evidence of frontal lobe and hippocampal dysfunction in normal aging.

Molecular Identification of Paramecium bursaria Syngens and Studies on Geographic Distribution using Mitochondrial Cytochrome C Oxidase Subunit I (COI).

PubMed

Zagata, Patrycja; Greczek-Stachura, Magdalena; Tarcz, Sebastian; Rautian, Maria

2015-01-01

Paramecium bursaria is composed of five syngens that are morphologically indistinguishable but sexually isolated. The aim of the present study was to confirm by molecular methods (analyses of mitochondrial COI) the identification of P. bursaria syngens originating from different geographical locations. Phylograms constructed using both the neighbor-joining and maximum-likelihood methods based on a comparison of 34 sequences of P. bursaria strains and P. multimicronucleatum, P. caudatum and P.calkinsi strains used as outgroups revealed five clusters which correspond to results obtained previously by mating reaction. Our analysis shows the existence of 24 haplotypes for the COI gene sequence in the studied strains. The interspecies haplotype diversity was Hd = 0.967. We confirmed genetic differentiation between strains of P. bursaria and the occurrence of a correlation between geographical distribution and the correspondent syngen.

Entamoeba struthionis n.sp. (Sarcomastigophora: Endamoebidae) from ostriches (Struthio camelus).

PubMed

Ponce Gordo, F; Martínez Díaz, R A; Herrera, S

2004-02-06

In the present work we identify the species of Entamoeba from ostriches (Struthio camelus). The complete sequence of the small subunit ribosomal RNA gene from this organism has been compared with those published for other species of the genus and clear differences have been found. These results confirm previous data which showed differences on parasite morphology and class of host with the other Entamoeba species. Taking all these data together, it can be concluded that the organism from ostriches is a new species whose proposed name is Entamoeba struthionis n.sp. This species probably infects rheas (Rhea americana), but genetic analysis of isolates from this host should be performed to confirm morphological data. Also, comparison of gene sequences with data from other authors on cysts recovered from human stool samples showed the possibility that this amoeba may affect humans. Further studies are needed to determine the risk of transmission of this new species to humans.

An Experimental Evaluation of Advanced Rotorcraft Airfoils in the NASA Ames Eleven-foot Transonic Wind Tunnel

NASA Technical Reports Server (NTRS)

Flemming, Robert J.

1984-01-01

Five full scale rotorcraft airfoils were tested in the NASA Ames Eleven-Foot Transonic Wind Tunnel for full scale Reynolds numbers at Mach numbers from 0.3 to 1.07. The models, which spanned the tunnel from floor to ceiling, included two modern baseline airfoils, the SC1095 and SC1094 R8, which have been previously tested in other facilities. Three advanced transonic airfoils, designated the SSC-A09, SSC-A07, and SSC-B08, were tested to confirm predicted performance and provide confirmation of advanced airfoil design methods. The test showed that the eleven-foot tunnel is suited to two-dimensional airfoil testing. Maximum lift coefficients, drag coefficients, pitching moments, and pressure coefficient distributions are presented. The airfoil analysis codes agreed well with the data, with the Grumman GRUMFOIL code giving the best overall performance correlation.

MGRA: Motion Gesture Recognition via Accelerometer.

PubMed

Hong, Feng; You, Shujuan; Wei, Meiyu; Zhang, Yongtuo; Guo, Zhongwen

2016-04-13

Accelerometers have been widely embedded in most current mobile devices, enabling easy and intuitive operations. This paper proposes a Motion Gesture Recognition system (MGRA) based on accelerometer data only, which is entirely implemented on mobile devices and can provide users with real-time interactions. A robust and unique feature set is enumerated through the time domain, the frequency domain and singular value decomposition analysis using our motion gesture set containing 11,110 traces. The best feature vector for classification is selected, taking both static and mobile scenarios into consideration. MGRA exploits support vector machine as the classifier with the best feature vector. Evaluations confirm that MGRA can accommodate a broad set of gesture variations within each class, including execution time, amplitude and non-gestural movement. Extensive evaluations confirm that MGRA achieves higher accuracy under both static and mobile scenarios and costs less computation time and energy on an LG Nexus 5 than previous methods.

Hereditary cardiac amyloidosis associated with the transthyretin Ile122 mutation in a white man.

PubMed

Gillmore, J D; Booth, D R; Pepys, M B; Hawkins, P N

1999-09-01

An 83 year old white man with atrial fibrillation was admitted to hospital after a cerebral infarct. Echocardiography was characteristic of cardiac amyloid deposition and subsequent tests confirmed amyloidosis of transthyretin (TTR) type, in association with the Ile122 mutation of the TTR gene; this has only been reported previously in African Americans in whom it occurs with an allele frequency of 2%. Haplotype analysis did not suggest a different founder than for the African Ile122 mutation. Cardiac amyloidosis should be considered among elderly patients presenting with cardiac failure and/or arrhythmia, particularly if they are resistant to conventional treatment; if confirmed, it should be followed by precise characterisation of amyloid fibril type. The prevalence of autosomal dominant cardiac TTR amyloidosis in elderly white people is unknown but early diagnosis and supportive treatment may prevent complications among affected family members.

Confirming a major QTL and finding additional loci responsible for field resistance to brown spot (Bipolaris oryzae) in rice.

PubMed

Sato, Hiroyuki; Matsumoto, Kengo; Ota, Chihiro; Yamakawa, Tomohiro; Kihara, Junichi; Mizobuchi, Ritsuko

2015-03-01

Brown spot is a devastating rice disease. Quantitative resistance has been observed in local varieties (e.g., 'Tadukan'), but no economically useful resistant variety has been bred. Using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) from 'Tadukan' (resistant) × 'Hinohikari' (susceptible), we previously found three QTLs (qBS2, qBS9, and qBS11) that conferred resistance in seedlings in a greenhouse. To confirm their effect, the parents and later generations of RILs were transplanted into paddy fields where brown spot severely occurred. Three new resistance QTLs (qBSfR1, qBSfR4, and qBSfR11) were detected on chromosomes 1, 4, and 11, respectively. The 'Tadukan' alleles at qBSfR1 and qBSfR11 and the 'Hinohikari' allele at qBSfR4 increased resistance. The major QTL qBSfR11 coincided with qBS11 from the previous study, whereas qBSfR1 and qBSfR4 were new but neither qBS2 nor qBS9 were detected. To verify the qBSfR1 and qBSfR11 'Tadukan' resistance alleles, near-isogenic lines (NILs) with one or both QTLs in a susceptible background ('Koshihikari') were evaluated under field conditions. NILs with qBSfR11 acquired significant field resistance; those with qBSfR1 did not. This confirms the effectiveness of qBSfR11. Genetic markers flanking qBSfR11 will be powerful tools for marker-assisted selection to improve brown spot resistance.

A combined morphological, ultrastructural, molecular, and biochemical study of the peculiar family Gomontiellaceae (Oscillatoriales) reveals a new cylindrospermopsin-producing clade of cyanobacteria.

PubMed

Bohunická, Markéta; Mareš, Jan; Hrouzek, Pavel; Urajová, Petra; Lukeš, Martin; Šmarda, Jan; Komárek, Jiří; Gaysina, Lira A; Strunecký, Otakar

2015-12-01

Members of the morphologically unusual cyanobacterial family Gomontiellaceae were studied using a polyphasic approach. Cultured strains of Hormoscilla pringsheimii, Starria zimbabweënsis, Crinalium magnum, and Crinalium epipsammum were thoroughly examined, and the type specimen of the family, Gomontiella subtubulosa, was investigated. The results of morphological observations using both light microscopy and transmission electron microscopy were consistent with previous reports and provided evidence for the unique morphological and ultrastructural traits of this family. Analysis of the 16S rRNA gene confirmed the monophyletic origin of non-marine repre-sentatives of genera traditionally classified into this family. The family was phylogenetically placed among other groups of filamentous cyanobacterial taxa. The presence of cellulose in the cell wall was analyzed and confirmed in all cultured Gomontiellaceae members using Fourier transform infrared spectroscopy and fluorescence microscopy. Evaluation of toxins produced by the studied strains revealed the hepatotoxin cylindrospermopsin (CYN) in available strains of the genus Hormoscilla. Production of this compound in both Hormoscilla strains was detected using high-performance liquid chromatography in tandem with high resolution mass spectrometry and confirmed by positive PCR amplification of the cyrJ gene from the CYN biosynthetic cluster. To our knowledge, this is the first report of CYN production by soil cyanobacteria, establishing a previously unreported CYN-producing lineage. This study indicates that cyanobacteria of the family Gomontiellaceae form a separate but coherent cluster defined by numerous intriguing morphological, ultrastructural, and biochemical features, and exhibiting a toxic potential worthy of further investigation. © 2015 Phycological Society of America.

Neandertal admixture in Eurasia confirmed by maximum-likelihood analysis of three genomes.

PubMed

Lohse, Konrad; Frantz, Laurent A F

2014-04-01

Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.

Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes

PubMed Central

Lohse, Konrad; Frantz, Laurent A. F.

2014-01-01

Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4−7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination. PMID:24532731

Metagenomic analysis of bat guano samples revealed the presence of viruses potentially carried by insects, among others by Apis mellifera in Hungary.

PubMed

Zana, Brigitta; Kemenesi, Gábor; Urbán, Péter; Földes, Fanni; Görföl, Tamás; Estók, Péter; Boldogh, Sándor; Kurucz, Kornélia; Jakab, Ferenc

2018-03-01

The predominance of dietary viruses in bat guano samples had been described recently, suggesting a new opportunity to survey the prevalence and to detect new viruses of arthropods or even plant-infecting viruses circulating locally in the ecosystem. Here we describe the diversity of viruses belonging to the order Picornavirales in Hungarian insectivorous bat guano samples. The metagenomic analysis conducted on our samples has revealed the significant predominance of aphid lethal paralysis virus (ALPV) and Big Sioux River virus (BSRV) in Hungary for the first time. Phylogenetic analysis was used to clarify the relationship to previously identified ALPV strains infecting honey bees, showing that our strain possesses a close genetic relationship with the strains that have already been described as pathogenic to honey bees. Furthermore, studies have previously confirmed the ability of these viruses to replicate in adult honey bees; however, no signs related to these viruses have been revealed yet. With the identification of two recently described possibly honey bee infecting viruses for the first time in Hungary, our results might have importance for the health conditions of Hungarian honey bee colonies in the future.

Performance of probabilistic method to detect duplicate individual case safety reports.

PubMed

Tregunno, Philip Michael; Fink, Dorthe Bech; Fernandez-Fernandez, Cristina; Lázaro-Bengoa, Edurne; Norén, G Niklas

2014-04-01

Individual case reports of suspected harm from medicines are fundamental for signal detection in postmarketing surveillance. Their effective analysis requires reliable data and one challenge is report duplication. These are multiple unlinked records describing the same suspected adverse drug reaction (ADR) in a particular patient. They distort statistical screening and can mislead clinical assessment. Many organisations rely on rule-based detection, but probabilistic record matching is an alternative. The aim of this study was to evaluate probabilistic record matching for duplicate detection, and to characterise the main sources of duplicate reports within each data set. vigiMatch™, a published probabilistic record matching algorithm, was applied to the WHO global individual case safety reports database, VigiBase(®), for reports submitted between 2000 and 2010. Reported drugs, ADRs, patient age, sex, country of origin, and date of onset were considered in the matching. Suspected duplicates for the UK, Denmark, and Spain were reviewed and classified by the respective national centre. This included evaluation to determine whether confirmed duplicates had already been identified by in-house, rule-based screening. Furthermore, each confirmed duplicate was classified with respect to the likely source of duplication. For each country, the proportions of suspected duplicates classified as confirmed duplicates, likely duplicates, otherwise related, and unrelated were obtained. The proportions of confirmed or likely duplicates that were not previously known by the national organisation were determined, and variations in the rates of suspected duplicates across subsets of reports were characterised. Overall, 2.5 % of the reports with sufficient information to be evaluated by vigiMatch were classified as suspected duplicates. The rates for the three countries considered in this study were 1.4 % (UK), 1.0 % (Denmark), and 0.7 % (Spain). Higher rates of suspected duplicates were observed for literature reports (11 %) and reports with fatal outcome (5 %), whereas a lower rate was observed for reports from consumers and non-health professionals (0.5 %). The predictive value for confirmed or likely duplicates among reports flagged as suspected duplicates by vigiMatch ranged from 86 % for the UK, to 64 % for Denmark and 33 % for Spain. The proportions of confirmed duplicates that were previously unknown to national centres ranged from 89 % for Spain, to 60 % for the UK and 38 % for Denmark, despite in-house duplicate detection processes in routine use. The proportion of unrelated cases among suspected duplicates were below 10 % for each national centre in the study. Probabilistic record matching, as implemented in vigiMatch, achieved good predictive value for confirmed or likely duplicates in each data source. Most of the false positives corresponded to otherwise related reports; less than 10 % were altogether unrelated. A substantial proportion of the correctly identified duplicates had not previously been detected by national centre activity. On one hand, vigiMatch highlighted duplicates that had been missed by rule-based methods, and on the other hand its lower total number of suspected duplicates to review improved the accuracy of manual review.

Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair.

PubMed

Liu, Fan; Chen, Yan; Zhu, Gu; Hysi, Pirro G; Wu, Sijie; Adhikari, Kaustubh; Breslin, Krystal; Pospiech, Ewelina; Hamer, Merel A; Peng, Fuduan; Muralidharan, Charanya; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Rothhammer, Francisco; Bortolini, Maria Catira; Gonzalez-Jose, Rolando; Zeng, Changqing; Xu, Shuhua; Jin, Li; Uitterlinden, André G; Ikram, M Arfan; van Duijn, Cornelia M; Nijsten, Tamar; Walsh, Susan; Branicki, Wojciech; Wang, Sijia; Ruiz-Linares, Andrés; Spector, Timothy D; Martin, Nicholas G; Medland, Sarah E; Kayser, Manfred

2018-02-01

Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P < 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62-0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans. © The Author(s) 2017. Published by Oxford University Press.

Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair

PubMed Central

Liu, Fan; Chen, Yan; Zhu, Gu; Hysi, Pirro G; Wu, Sijie; Adhikari, Kaustubh; Breslin, Krystal; Pośpiech, Ewelina; Hamer, Merel A; Peng, Fuduan; Muralidharan, Charanya; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Rothhammer, Francisco; Bortolini, Maria Catira; Gonzalez-Jose, Rolando; Zeng, Changqing; Xu, Shuhua; Jin, Li; Uitterlinden, André G; Ikram, M Arfan; van Duijn, Cornelia M; Nijsten, Tamar; Walsh, Susan; Branicki, Wojciech; Wang, Sijia; Ruiz-Linares, Andrés; Spector, Timothy D; Martin, Nicholas G; Medland, Sarah E; Kayser, Manfred

2018-01-01

Abstract Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P < 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62–0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans. PMID:29220522

Analysis of amyloid fibrils in the cheetah (Acinonyx jubatus).

PubMed

Bergström, Joakim; Ueda, Mitsuharu; Une, Yumi; Sun, Xuguo; Misumi, Shogo; Shoji, Shozo; Ando, Yukio

2006-06-01

Recently, a high prevalence of amyloid A (AA) amyloidosis has been documented among captive cheetahs worldwide. Biochemical analysis of amyloid fibrils extracted from the liver of a Japanese captive cheetah unequivocally showed that protein AA was the main fibril constituent. Further characterization of the AA fibril components by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis revealed three main protein AA bands with approximate molecular weights of 8, 10 and 12 kDa. Mass spectrometry analysis of the 12-kDa component observed in SDS-PAGE and Western blotting confirmed the molecular weight of a 12,381-Da peak. Our finding of a 12-kDa protein AA component provides evidence that the cheetah SAA sequence is longer than the previously reported 90 amino acid residues (approximately 10 kDa), and hence SAA is part of the amyloid fibril.

More powerful virus inhibitors from structure-based analysis of HEV71 capsid-binding molecules

PubMed Central

Spyrou, John A. B.; Kelly, James; Ren, Jingshan; Grimes, Jonathan; Puerstinger, Gerhard; Stonehouse, Nicola; Walter, Thomas S.; Hu, Zhongyu; Wang, Junzhi; Li, Xuemei; Peng, Wei; Rowlands, David; Fry, Elizabeth E.; Rao, Zihe; Stuart, David I.

2014-01-01

Enterovirus 71 (HEV71) epidemics amongst children and infants result mainly in mild symptoms, however, especially in the Asia-Pacific region, infection can be fatal. At present no therapies are available. We have used structural analysis of the complete virus to guide the design of HEV71 inhibitors. Analysis of complexes with four 3-(-4-pyridyl)-2-imidazolidinone derivatives with varying anti-HEV71 activities, pinpointed key structure-activity correlates. We then identified additional potentially beneficial substitutions, developed methods to reliably triage compounds by quantum mechanics-enhanced ligand docking, and synthesized two candidates. Structural analysis and in vitro assays confirmed the predicted binding modes and their ability to block viral infection. One ligand (IC50 = 25 pM) is an order of magnitude more potent than the best previously reported inhibitor, and is also more soluble. Our approach may be useful in the design of effective drugs for enterovirus infections. PMID:24509833

Two independent proteomic approaches provide a comprehensive analysis of the synovial fluid proteome response to Autologous Chondrocyte Implantation.

PubMed

Hulme, Charlotte H; Wilson, Emma L; Fuller, Heidi R; Roberts, Sally; Richardson, James B; Gallacher, Pete; Peffers, Mandy J; Shirran, Sally L; Botting, Catherine H; Wright, Karina T

2018-05-02

Autologous chondrocyte implantation (ACI) has a failure rate of approximately 20%, but it is yet to be fully understood why. Biomarkers are needed that can pre-operatively predict in which patients it is likely to fail, so that alternative or individualised therapies can be offered. We previously used label-free quantitation (LF) with a dynamic range compression proteomic approach to assess the synovial fluid (SF) of ACI responders and non-responders. However, we were able to identify only a few differentially abundant proteins at baseline. In the present study, we built upon these previous findings by assessing higher-abundance proteins within this SF, providing a more global proteomic analysis on the basis of which more of the biology underlying ACI success or failure can be understood. Isobaric tagging for relative and absolute quantitation (iTRAQ) proteomic analysis was used to assess SF from ACI responders (mean Lysholm improvement of 33; n = 14) and non-responders (mean Lysholm decrease of 14; n = 13) at the two stages of surgery (cartilage harvest and chondrocyte implantation). Differentially abundant proteins in iTRAQ and combined iTRAQ and LF datasets were investigated using pathway and network analyses. iTRAQ proteomic analysis confirmed our previous finding that there is a marked proteomic shift in response to cartilage harvest (70 and 54 proteins demonstrating ≥ 2.0-fold change and p < 0.05 between stages I and II in responders and non-responders, respectively). Further, it highlighted 28 proteins that were differentially abundant between responders and non-responders to ACI, which were not found in the LF study, 16 of which were altered at baseline. The differential expression of two proteins (complement C1s subcomponent and matrix metalloproteinase 3) was confirmed biochemically. Combination of the iTRAQ and LF proteomic datasets generated in-depth SF proteome information that was used to generate interactome networks representing ACI success or failure. Functional pathways that are dysregulated in ACI non-responders were identified, including acute-phase response signalling. Several candidate biomarkers for baseline prediction of ACI outcome were identified. A holistic overview of the SF proteome in responders and non-responders to ACI  has been profiled, providing a better understanding of the biological pathways underlying clinical outcome, particularly the differential response to cartilage harvest in non-responders.

A Streamlined Protocol for Molecular Testing of the DMD Gene within a Diagnostic Laboratory: A Combination of Array Comparative Genomic Hybridization and Bidirectional Sequence Analysis

PubMed Central

Marquis-Nicholson, Renate; Lai, Daniel; Love, Jennifer M.; Love, Donald R.

2013-01-01

Purpose. The aim of this study was to develop a streamlined mutation screening protocol for the DMD gene in order to confirm a clinical diagnosis of Duchenne or Becker muscular dystrophy in affected males and to clarify the carrier status of female family members. Methods. Sequence analysis and array comparative genomic hybridization (aCGH) were used to identify mutations in the dystrophin DMD gene. We analysed genomic DNA from six individuals with a range of previously characterised mutations and from eight individuals who had not previously undergone any form of molecular analysis. Results. We successfully identified the known mutations in all six patients. A molecular diagnosis was also made in three of the four patients with a clinical diagnosis who had not undergone prior genetic screening, and testing for familial mutations was successfully completed for the remaining four patients. Conclusion. The mutation screening protocol described here meets best practice guidelines for molecular testing of the DMD gene in a diagnostic laboratory. The aCGH method is a superior alternative to more conventional assays such as multiplex ligation-dependent probe amplification (MLPA). The combination of aCGH and sequence analysis will detect mutations in 98% of patients with the Duchenne or Becker muscular dystrophy. PMID:23476807

Contour plot assessment of existing meta-analyses confirms robust association of statin use and acute kidney injury risk.

PubMed

Chevance, Aurélie; Schuster, Tibor; Steele, Russell; Ternès, Nils; Platt, Robert W

2015-10-01

Robustness of an existing meta-analysis can justify decisions on whether to conduct an additional study addressing the same research question. We illustrate the graphical assessment of the potential impact of an additional study on an existing meta-analysis using published data on statin use and the risk of acute kidney injury. A previously proposed graphical augmentation approach is used to assess the sensitivity of the current test and heterogeneity statistics extracted from existing meta-analysis data. In addition, we extended the graphical augmentation approach to assess potential changes in the pooled effect estimate after updating a current meta-analysis and applied the three graphical contour definitions to data from meta-analyses on statin use and acute kidney injury risk. In the considered example data, the pooled effect estimates and heterogeneity indices demonstrated to be considerably robust to the addition of a future study. Supportingly, for some previously inconclusive meta-analyses, a study update might yield statistically significant kidney injury risk increase associated with higher statin exposure. The illustrated contour approach should become a standard tool for the assessment of the robustness of meta-analyses. It can guide decisions on whether to conduct additional studies addressing a relevant research question. Copyright © 2015 Elsevier Inc. All rights reserved.

The angular structure of ONC201, a TRAIL pathway-inducing compound, determines its potent anti-cancer activity

PubMed Central

Wagner, Jessica; Kline, Christina Leah; Pottorf, Richard S.; Nallaganchu, Bhaskara Rao; Olson, Gary L.; Dicker, David T.; Allen, Joshua E.; El-Deiry, Wafik S.

2014-01-01

We previously identified TRAIL-inducing compound 10 (TIC10), also known as NSC350625 or ONC201, from a NCI chemical library screen as a small molecule that has potent anti-tumor efficacy and a benign safety profile in preclinical cancer models. The chemical structure that was originally published by Stahle, et. al. in the patent literature was described as an imidazo[1,2-a]pyrido[4,3-d]pyrimidine derivative. The NCI and others generally accepted this as the correct structure, which was consistent with the mass spectrometry analysis outlined in the publication by Allen et. al. that first reported the molecule's anticancer properties. A recent publication demonstrated that the chemical structure of ONC201 material from the NCI is an angular [3,4-e] isomer of the originally disclosed, linear [4,3-d] structure. Here we confirm by NMR and X-ray structural analysis of the dihydrochloride salt form that the ONC201 material produced by Oncoceutics is the angular [3,4-e] structure and not the linear structure originally depicted in the patent literature and by the NCI. Similarly, in accordance with our biological evaluation, the previously disclosed anti-cancer activity is associated with the angular structure and not the linear isomer. Together these studies confirm that ONC201, produced by Oncoceutics or obtained from the NCI, possesses an angular [3,4-e] structure that represents the highly active anti-cancer compound utilized in prior preclinical studies and now entering clinical trials in advanced cancers. PMID:25587031

The angular structure of ONC201, a TRAIL pathway-inducing compound, determines its potent anti-cancer activity.

PubMed

Wagner, Jessica; Kline, Christina Leah; Pottorf, Richard S; Nallaganchu, Bhaskara Rao; Olson, Gary L; Dicker, David T; Allen, Joshua E; El-Deiry, Wafik S

2014-12-30

We previously identified TRAIL-inducing compound 10 (TIC10), also known as NSC350625 or ONC201, from a NCI chemical library screen as a small molecule that has potent anti-tumor efficacy and a benign safety profile in preclinical cancer models. The chemical structure that was originally published by Stahle, et. al. in the patent literature was described as an imidazo[1,2-a]pyrido[4,3-d]pyrimidine derivative. The NCI and others generally accepted this as the correct structure, which was consistent with the mass spectrometry analysis outlined in the publication by Allen et. al. that first reported the molecule's anticancer properties. A recent publication demonstrated that the chemical structure of ONC201 material from the NCI is an angular [3,4-e] isomer of the originally disclosed, linear [4,3-d] structure. Here we confirm by NMR and X-ray structural analysis of the dihydrochloride salt form that the ONC201 material produced by Oncoceutics is the angular [3,4-e] structure and not the linear structure originally depicted in the patent literature and by the NCI. Similarly, in accordance with our biological evaluation, the previously disclosed anti-cancer activity is associated with the angular structure and not the linear isomer. Together these studies confirm that ONC201, produced by Oncoceutics or obtained from the NCI, possesses an angular [3,4-e] structure that represents the highly active anti-cancer compound utilized in prior preclinical studies and now entering clinical trials in advanced cancers.

LINC00472 expression is regulated by promoter methylation and associated with disease-free survival in patients with grade 2 breast cancer

PubMed Central

Shen, Yi; Wang, Zhanwei; Loo, Lenora WM; Ni, Yan; Jia, Wei; Fei, Peiwen; Risch, Harvey A.; Katsaros, Dionyssios; Yu, Herbert

2015-01-01

Long non-coding RNAs (lncRNAs) are a class of newly recognized DNA transcripts that have diverse biological activities. Dysregulation of lncRNAs may be involved in many pathogenic processes including cancer. Recently, we found an intergenic lncRNA, LINC00472, whose expression was correlated with breast cancer progression and patient survival. Our findings were consistent across multiple clinical datasets and supported by results from in vitro experiments. To evaluate further the role of LINC00472 in breast cancer, we used various online databases to investigate possible mechanisms that might affect LINC00472 expression in breast cancer. We also analyzed associations of LINC00472 with estrogen receptor, tumor grade, and molecular subtypes in additional online datasets generated by microarray platforms different from the one we investigated previously. We found that LINC00472 expression in breast cancer was regulated more possibly by promoter methylation than by the alteration of gene copy number. Analysis of additional datasets confirmed our previous findings of high expression of LINC00472 associated with ER-positive and low-grade tumors and favorable molecular subtypes. Finally, in nine datasets, we examined the association of LINC00472 expression with disease-free survival in patients with grade 2 tumors. Meta-analysis of the datasets showed that LINC00472 expression in breast tumors predicted the recurrence of breast cancer in patients with grade 2 tumors. In summary, our analyses confirm that LINC00472 is functionally a tumor suppressor, and that assessing its expression in breast tumors may have clinical implications in breast cancer management. PMID:26564482

LINC00472 expression is regulated by promoter methylation and associated with disease-free survival in patients with grade 2 breast cancer.

PubMed

Shen, Yi; Wang, Zhanwei; Loo, Lenora W M; Ni, Yan; Jia, Wei; Fei, Peiwen; Risch, Harvey A; Katsaros, Dionyssios; Yu, Herbert

2015-12-01

Long non-coding RNAs (lncRNAs) are a class of newly recognized DNA transcripts that have diverse biological activities. Dysregulation of lncRNAs may be involved in many pathogenic processes including cancer. Recently, we found an intergenic lncRNA, LINC00472, whose expression was correlated with breast cancer progression and patient survival. Our findings were consistent across multiple clinical datasets and supported by results from in vitro experiments. To evaluate further the role of LINC00472 in breast cancer, we used various online databases to investigate possible mechanisms that might affect LINC00472 expression in breast cancer. We also analyzed associations of LINC00472 with estrogen receptor, tumor grade, and molecular subtypes in additional online datasets generated by microarray platforms different from the one we investigated previously. We found that LINC00472 expression in breast cancer was regulated more possibly by promoter methylation than by the alteration of gene copy number. Analysis of additional datasets confirmed our previous findings of high expression of LINC00472 associated with ER-positive and low-grade tumors and favorable molecular subtypes. Finally, in nine datasets, we examined the association of LINC00472 expression with disease-free survival in patients with grade 2 tumors. Meta-analysis of the datasets showed that LINC00472 expression in breast tumors predicted the recurrence of breast cancer in patients with grade 2 tumors. In summary, our analyses confirm that LINC00472 is functionally a tumor suppressor, and that assessing its expression in breast tumors may have clinical implications in breast cancer management.

The Catalina Surveys Southern periodic variable star catalogue

NASA Astrophysics Data System (ADS)

Drake, A. J.; Djorgovski, S. G.; Catelan, M.; Graham, M. J.; Mahabal, A. A.; Larson, S.; Christensen, E.; Torrealba, G.; Beshore, E.; McNaught, R. H.; Garradd, G.; Belokurov, V.; Koposov, S. E.

2017-08-01

Here, we present the results from our analysis of 6 yr of optical photometry taken by the Siding Spring Survey (SSS). This completes a search for periodic variable stars within the 30 000 deg2 of the sky covered by the Catalina Surveys. The current analysis covers 81 million sources with declinations between -20° and -75° with median magnitudes in the range 11 < V < 19.5. We find approximately 34 000 new periodic variable stars in addition to the ˜9000 RR Lyrae that we previously discovered in SSS data. This brings the total number of periodic variables identified in Catalina data to ˜110 000. The new SSS periodic variable stars mainly consist of eclipsing binaries, RR Lyrae, LPVs, RS CVn stars, δ Scutis, and Anomalous Cepheids. By cross-matching these variable stars with those from prior surveys, we find that ˜90 per cent of the sources are new discoveries and recover ˜95 per cent of the known periodic variables in the survey region. For the known sources, we find excellent agreement between our catalogue and prior values of luminosity, period, and amplitude. However, we find many variable stars that had previously been misclassified. Examining the distribution of RR Lyrae, we find a population associated with the Large Magellanic Cloud (LMC) that extends more than 20° from its centre confirming recent evidence for the existence of a very extended stellar halo in the LMC. By combining SSS photometry with Dark Energy Survey data, we identify additional LMC halo RR Lyrae, thus confirming the significance of the population.

Optimization of Anodic Porous Alumina Fabricated from Commercial Aluminum Food Foils: A Statistical Approach

PubMed Central

Riccomagno, Eva; Shayganpour, Amirreza; Salerno, Marco

2017-01-01

Anodic porous alumina is a known material based on an old industry, yet with emerging applications in nanoscience and nanotechnology. This is promising, but the nanostructured alumina should be fabricated from inexpensive raw material. We fabricated porous alumina from commercial aluminum food plate in 0.4 M aqueous phosphoric acid, aiming to design an effective manufacturing protocol for the material used as nanoporous filler in dental restorative composites, an application demonstrated previously by our group. We identified the critical input parameters of anodization voltage, bath temperature and anodization time, and the main output parameters of pore diameter, pore spacing and oxide thickness. Scanning electron microscopy and grain analysis allowed us to assess the nanostructured material, and the statistical design of experiments was used to optimize its fabrication. We analyzed a preliminary dataset, designed a second dataset aimed at clarifying the correlations between input and output parameters, and ran a confirmation dataset. Anodization conditions close to 125 V, 20 °C, and 7 h were identified as the best for obtaining, in the shortest possible time, pore diameters and spacing of 100–150 nm and 150–275 nm respectively, and thickness of 6–8 µm, which are desirable for the selected application according to previously published results. Our analysis confirmed the linear dependence of pore size on anodization voltage and of thickness on anodization time. The importance of proper control on the experiment was highlighted, since batch effects emerge when the experimental conditions are not exactly reproduced. PMID:28772776

2q37 Deletion syndrome confirmed by high-resolution cytogenetic analysis

PubMed Central

Cho, Eun-Kyung; Kim, Jinsup; Yang, Aram; Jin, Dong-Kyu

2017-01-01

Chromosome 2q37 deletion syndrome is a rare chromosomal disorder characterized by mild to moderate developmental delay, brachydactyly of the third to fifth digits or toes, short stature, obesity, hypotonia, a characteristic facial appearance, and autism spectrum disorder. Here, we report on a patient with 2q37 deletion presenting with dilated cardiomyopathy (DCMP). Congenital heart malformations have been noted in up to 20% of patients with 2q37 deletions. However, DCMP has not been reported in 2q37 deletion patients previously. The patient exhibited the characteristic facial appearance (a flat nasal bridge, deep-set eyes, arched eyebrows, and a thin upper lip), developmental delay, mild mental retardation, peripheral nerve palsy, and Albright hereditary osteodystrophy (AHO)-like phenotypes (short stature and brachydactyly). Conventional chromosomal analysis results were normal; however, microarray-based comparative genomic hybridization revealed terminal deletion at 2q37.1q37.3. In addition, the patient was confirmed to have partial growth hormone (GH) deficiency and had shown a significant increase in growth rate after substitutive GH therapy. Chromosome 2q37 deletion syndrome should be considered in the differential diagnosis of patients presenting with AHO features, especially in the presence of facial dysmorphism. When patients are suspected of having a 2q37 deletion, high-resolution cytogenetic analysis is recommended. PMID:28690993

Serological and molecular heterogeneity among Yersinia ruckeri strains isolated from farmed Atlantic salmon Salmo salar in Chile.

PubMed

Bastardo, A; Bohle, H; Ravelo, C; Toranzo, A E; Romalde, J L

2011-02-22

We investigated 11 strains of Yersinia ruckeri, the causative agent of enteric redmouth disease (ERM), that had been isolated from Atlantic salmon Salmo salar L. farmed in Chile and previously vaccinated against ERM. Phylogenetic analysis of the 16S rRNA gene sequences confirmed the identification of the salmon isolates as Y. ruckeri. A comparative analysis of the biochemical characteristics was made by means of traditional and commercial miniaturised methods. All studied isolates were motile and Tween 80 positive, and were identified as biotype 1. In addition, drug susceptibility tests determined high sensitivity to sulphamethoxazole/trimethroprim, oxytetracycline, ampicillin and enrofloxacin in all isolates. Serological assays showed the presence of O1a, O1b and O2b serotypes, with a predominance of the O1b serotype in 9 strains. Analysis of the lipopolysaccharide profiles and the correspondent immunoblot confirmed these results. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) of the outer membrane proteins revealed that all Chilean strains had profiles with a molecular weight range between 34 and 55 kDa, with 3 distinct groups based on differences in the major bands. Genotyping analyses by enterobacterial repetitive intergenic consensus (ERIC-) and repetitive extragenic palindromic (REP-)PCR techniques clearly indicated intraspecific genetic diversity among Chilean Y. ruckeri strains.

Chandra Confirmation of a Pulsar Wind Nebula in DA 495

NASA Technical Reports Server (NTRS)

Arzoumanian, Z.; Safi-Harb, S.; Landecker, T.L.; Kothes, R.; Camilo, F.

2008-01-01

As part of a multiwavelength study of the unusual radio supernova remnant DA 495, we present observations made with the Chandra X-ray Observatory. Imaging and spectroscopic analysis confirms the previously detected X-ray source at the heart of the annular radio nebula, establishing the radiative properties of two key emission components: a soft unresolved source with a blackbody temperature of 1 MK consistent with a neutron star, surrounded by a nontherma1 nebula 40" in diameter exhibiting a power-law spectrum with photon index Gamma = 1.63, typical of a pulsar wind nebula. Morphologically, the nebula appears to be slightly extended along a direction, in projection on the sky, previously demonstrated to be of significance in radio and ASCA observations; we argue that this represents the orientation of the pulsar spin axis. At smaller scales, a narrow X-ray feature is seen extending out 5" from the point source, but energetic arguments suggest that it is not the resolved termination shock of the pulsar wind against the ambient medium. Finally, we argue based on synchrotron lifetimes in the nebular magnetic field that DA 495 represents the first example of a pulsar wind nebula in which electromagnetic flux makes up a significant part, together with particle flux, of the neutron star's wind.

Chromosome analysis in embryos from young patients with previous parity.

PubMed

Kilani, Z; Magli, Mc; Qaddomi, E; Ferraretti, Ap; Shaban, M; Crippa, A; Haj Hassan, L; Shenfield, F; Gianaroli, L

2014-09-01

This study included 173 young couples of proven fertility who had previously undergone preimplantation genetic screening for chromosomes X and Y for family balancing. Several months later, when the outcome of the pregnancies was already known, the blastomeres from the corresponding embryos transferred were reanalysed by fluorescence in-situ hybridization (FISH) for chromosomes 13, 16, 18, 21, 22 with the aim of investigating correlation with embryo viability and the level of FISH sensitivity (embryos confirmed to be euploid). According to the results, informative in 152 couples, the proportion of euploid embryos was significantly lower in 53 nonpregnant women when compared with 99 women with term pregnancy (49% versus 75% respectively, P < 0.001). In addition, in 21 nonpregnant patients, all embryos transferred were found to be chromosomally abnormal. The level of FISH sensitivity was calculated in the group of term pregnancies where the number of euploid embryos was expected to exceed or match with the number of babies born. The resulting false-negative rate was 4.0% per patient and 1.9% per embryo. These findings confirmed the limited prediction power of embryo morphology on implantation but also the relevance of chromosomal abnormalities in causing embryo demise. Copyright © 2014 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Low-energy effective worldsheet theory of a non-Abelian vortex in high-density QCD revisited: A regular gauge construction

NASA Astrophysics Data System (ADS)

Chatterjee, Chandrasekhar; Nitta, Muneto

2017-04-01

Color symmetry is spontaneously broken in quark matter at high density as a consequence of di-quark condensations with exhibiting color superconductivity. Non-Abelian vortices or color magnetic flux tubes stably exist in the color-flavor locked phase at asymptotically high density. The effective worldsheet theory of a single non-Abelian vortex was previously calculated in the singular gauge to obtain the C P2 model [1,2]. Here, we reconstruct the effective theory in a regular gauge without taking a singular gauge, confirming the previous results in the singular gauge. As a byproduct of our analysis, we find that non-Abelian vortices in high-density QCD do not suffer from any obstruction for the global definition of a symmetry breaking.

Low Magnetic Fields in White Dwarfs and their Direct Progenitors?

NASA Astrophysics Data System (ADS)

Jordan, S.; Bagnulo, S.; Landstreet, J.; Fossati, L.; Valyavin, G. G.; Monin, D.; Wade, G. A.; Werner, K.; O'Toole, S. J.

2013-01-01

We have carried out a re-analysis of polarimetric data of central stars of planetary nebulae, hot subdwarfs, and white dwarfs taken with FORS1 (FOcal Reducer and low dispersion Spectrograph) on the VLT (Very Large Telescope), and added a large number of new observations in order to increase the sample. A careful analysis of the observations using only one wavelength calibration for the polarimetrically analysed spectra and for all positions of the retarder plate of the spectrograph is crucial in order to avoid spurious signals. We find that the previous detections of magnetic fields in subdwarfs and central stars could not be confirmed while about 10% of the observed white dwarfs have magnetic fields at the kilogauss level.

Foreshock waves as observed in energetic ion flux

NASA Astrophysics Data System (ADS)

Petrukovich, A. A.; Chugunova, O. M.; Inamori, T.; Kudela, K.; Stetiarova, J.

2017-05-01

Oscillations of energetic ion fluxes with periods 10-100 s are often present in the Earth's foreshock. Detailed analysis of wave properties with Time History of Events and Macroscale Interactions during Substorms data and comparisons with other data sets confirm that these oscillations are the previously unnoticed part of well-known "30 s" waves but are observed mainly for higher-speed solar wind. Simultaneous magnetic oscillations have similar periods, large amplitudes, and nonharmonic unstable waveforms or shocklet-type appearance, suggesting their nonlinearity, also typical for high solar wind speed. Analysis of the general foreshock data set of Interball project shows that the average flux of the backstreaming energetic ions increases more than 1 order of magnitude, when solar wind speed increases from 400 to 500 km/s.

Secondary analysis of teaching methods in introductory physics: A 50 k-student study

NASA Astrophysics Data System (ADS)

Von Korff, Joshua; Archibeque, Benjamin; Gomez, K. Alison; Heckendorf, Tyrel; McKagan, Sarah B.; Sayre, Eleanor C.; Schenk, Edward W.; Shepherd, Chase; Sorell, Lane

2016-12-01

Physics education researchers have developed many evidence-based instructional strategies to enhance conceptual learning of students in introductory physics courses. These strategies have historically been tested using assessments such as the Force Concept Inventory (FCI) and the Force and Motion Conceptual Evaluation (FMCE). We have performed a review and analysis of FCI and FMCE data published between 1995 and 2014. We confirm previous findings that interactive engagement teaching techniques are significantly more likely to produce high student learning gains than traditional lecture-based instruction. We also establish that interactive engagement instruction works in many settings, including those with students having a high and low level of prior knowledge, at liberal arts and research universities, and enrolled in both small and large classes.

Autonomous stress imaging cores: from concept to reality

NASA Astrophysics Data System (ADS)

van der Velden, Stephen; Rajic, Nik; Brooks, Chris; Galea, Steve

2016-04-01

The historical reliance of thermoelastic stress analysis on cooled infrared detection has created significant cost and practical impediments to the widespread use of this powerful full-field stress measurement technique. The emergence of low-cost microbolometers as a practical alternative has allowed for an expansion of the traditional role of thermoelastic stress analysis, and raises the possibility that it may in future become a viable structural health monitoring modality. Experimental results are shown to confirm that high resolution stress imagery can be obtained from an uncooled thermal camera core significantly smaller than any infrared imaging device previously applied to TSA. The paper provides a summary of progress toward the development of an autonomous stress-imaging capability based on this core.

Publication trends in Naunyn-Schmiedeberg's Archives of Pharmacology: focus on pharmacology in Egypt.

PubMed

El-Mas, Mahmoud M; El-Gowelli, Hanan M; Michel, Martin C

2013-11-01

In a previous analysis of the country of origin of papers published in Naunyn-Schmiedeberg's Archives of Pharmacology, a major shift toward contributions from emerging market countries, was noticed in comparison of 2010 to 2001 publications. Repeating such analysis for 2012 publications in the journal confirmed this trend. An interesting new trend was the emerging presence of papers from a variety of Islamic countries including Egypt. Based on this trend, we shortly review the history and current structure of pharmacology in Egypt. It appears that the presence of Egyptian pharmacology in international journals including pharmacology journals has sharply been increasing over the last two decades. Challenges for a continuation of this encouraging trend are being discussed.

Concentration analysis of breast tissue phantoms with terahertz spectroscopy

PubMed Central

Truong, Bao C. Q.; Fitzgerald, Anthony J.; Fan, Shuting; Wallace, Vincent P.

2018-01-01

Terahertz imaging has been previously shown to be capable of distinguishing normal breast tissue from its cancerous form, indicating its applicability to breast conserving surgery. The heterogeneous composition of breast tissue is among the main challenges to progressing this potential research towards a practical application. In this paper, two concentration analysis methods are proposed for analyzing phantoms mimicking breast tissue. The dielectric properties and the double Debye parameters were used to determine the phantom composition. The first method is wholly based on the conventional effective medium theory while the second one combines this theoretical model with empirical polynomial models. Through assessing the accuracy of these methods, their potential for application to quantifying breast tissue pathology was confirmed. PMID:29541525

Analysis, calculation and utilization of the k-balance attribute in interdependent networks

NASA Astrophysics Data System (ADS)

Liu, Zheng; Li, Qing; Wang, Dan; Xu, Mingwei

2018-05-01

Interdependent networks, where two networks depend on each other, are becoming more and more significant in modern systems. From previous work, it can be concluded that interdependent networks are more vulnerable than a single network. The robustness in interdependent networks deserves special attention. In this paper, we propose a metric of robustness from a new perspective-the balance. First, we define the balance-coefficient of the interdependent system. Based on precise analysis and derivation, we prove some significant theories and provide an efficient algorithm to compute the balance-coefficient. Finally, we propose an optimal solution to reduce the balance-coefficient to enhance the robustness of the given system. Comprehensive experiments confirm the efficiency of our algorithms.

Direct observation of anti-phase boundaries in heteroepitaxy of GaSb thin films grown on Si(001) by transmission electron microscopy

NASA Astrophysics Data System (ADS)

Woo, S. Y.; Hosseini Vajargah, S.; Ghanad-Tavakoli, S.; Kleiman, R. N.; Botton, G. A.

2012-10-01

Unambiguous identification of anti-phase boundaries (APBs) in heteroepitaxial films of GaSb grown on Si has been so far elusive. In this work, we present conventional transmission electron microscopy (TEM) diffraction contrast imaging using superlattice reflections, in conjunction with convergent beam electron diffraction analysis, to determine a change in polarity across APBs in order to confirm the presence of anti-phase disorder. In-depth analysis of anti-phase disorder is further supported with atomic resolution high-angle annular dark-field scanning transmission electron microscopy. The nature of APBs in GaSb is further elucidated by a comparison to previous results for GaAs epilayers grown on Si.

Approach for classification and taxonomy within family Rickettsiaceae based on the Formal Order Analysis.

PubMed

Shpynov, S; Pozdnichenko, N; Gumenuk, A

2015-01-01

Genome sequences of 36 Rickettsia and Orientia were analyzed using Formal Order Analysis (FOA). This approach takes into account arrangement of nucleotides in each sequence. A numerical characteristic, the average distance (remoteness) - "g" was used to compare of genomes. Our results corroborated previous separation of three groups within the genus Rickettsia, including typhus group, classic spotted fever group, and the ancestral group and Orientia as a separate genus. Rickettsia felis URRWXCal2 and R. akari Hartford were not in the same group based on FOA, therefore designation of a so-called transitional Rickettsia group could not be confirmed with this approach. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

A new Microbacterium species isolated from the blood of a patient with fever: Microbacterium pyrexiae sp. nov.

PubMed

Ko, Kwan Soo; Oh, Won Sup; Lee, Mi Young; Peck, Kyong Ran; Lee, Nam Yong; Song, Jae-Hoon

2007-04-01

A Gram-positive bacterium, SMC-A8265(T), which was isolated from the blood of a patient with fever but could not be identified by a conventional microbiologic method, was finally characterized by performing phenotypic and genotypic analyses. 16S rRNA gene sequence analysis revealed that the strain SMC-A8265(T) belonged to the genus Microbacterium, but it did not correspond to any of the previously described Microbacterium spp. Biochemical tests and cellular fatty acid composition analysis also confirmed that this bacterium is distinct from other Microbacterium spp. Based on the phenotypic and genotypic characteristics, we propose that the strain SMC-A8265(T) should be classified as a new species, namely, Microbacterium pyrexiae sp. nov.

Preconditioning for the Navier-Stokes equations with finite-rate chemistry

NASA Technical Reports Server (NTRS)

Godfrey, Andrew G.; Walters, Robert W.; Van Leer, Bram

1993-01-01

The preconditioning procedure for generalized finite-rate chemistry and the proper preconditioning for the one-dimensional Navier-Stokes equations are presented. Eigenvalue stiffness is resolved and convergence-rate acceleration is demonstrated over the entire Mach-number range from the incompressible to the hypersonic. Specific benefits are realized at low and transonic flow speeds. The extended preconditioning matrix accounts for thermal and chemical non-equilibrium and its implementation is explained for both explicit and implicit time marching. The effect of higher-order spatial accuracy and various flux splittings is investigated. Numerical analysis reveals the possible theoretical improvements from using proconditioning at all Mach numbers. Numerical results confirm the expectations from the numerical analysis. Representative test cases include flows with previously troublesome embedded high-condition-number regions.

Multiple host-switching of Haemosporidia parasites in bats

PubMed Central

Duval, Linda; Robert, Vincent; Csorba, Gabor; Hassanin, Alexandre; Randrianarivelojosia, Milijaona; Walston, Joe; Nhim, Thy; Goodman, Steve M; Ariey, Frédéric

2007-01-01

Background There have been reported cases of host-switching in avian and lizard species of Plasmodium (Apicomplexa, Haemosporidia), as well as in those infecting different primate species. However, no evidence has previously been found for host-swapping between wild birds and mammals. Methods This paper presents the results of the sampling of blood parasites of wild-captured bats from Madagascar and Cambodia. The presence of Haemosporidia infection in these animals is confirmed and cytochrome b gene sequences were used to construct a phylogenetic analysis. Results Results reveal at least three different and independent Haemosporidia evolutionary histories in three different bat lineages from Madagascar and Cambodia. Conclusion Phylogenetic analysis strongly suggests multiple host-switching of Haemosporidia parasites in bats with those from avian and primate hosts. PMID:18045505

[Risk factors for infection in total knee artrhoplasty, including previously unreported intraoperative fracture and deep venous thrombosis].

PubMed

de Dios, M; Cordero-Ampuero, J

2015-01-01

To carry out a statistical analysis on the significant risk factors for deep late infection (prosthetic joint infection, PJI) in patients with a knee arthroplasty (TKA). A retrospective observational case-control study was conducted on a case series of 32 consecutive knee infections, using an analysis of all the risk factors reported in the literature. A control series of 100 randomly selected patients operated in the same Department of a University General Hospital during the same period of time, with no sign of deep infection in their knee arthroplasty during follow-up. Statistical comparisons were made using Pearson for qualitative and ANOVA for quantitative variables. The significant (p>0.05) factors found in the series were: Preoperative previous knee surgery, glucocorticoids, immunosuppressants, inflammatory arthritis. prolonged surgical time, inadequate antibiotic prophylaxis, intraoperative fractures. Postoperative secretion of the wound longer than 10 days, deep palpable haematoma, need for a new surgery, and deep venous thrombosis in lower limbs. Distant infections cutaneous, generalized sepsis, urinary tract, pneumonia, abdominal. This is the first report of intraoperative fractures and deep venous thrombosis as significantly more frequent factors in infected TKAs. Other previously described risk factors for TKA PJI are also confirmed. Copyright © 2014 SECOT. Published by Elsevier Espana. All rights reserved.

Fast analysis of doping agents in urine by ultra-high-pressure liquid chromatography-quadrupole time-of-flight mass spectrometry. II: Confirmatory analysis.

PubMed

Badoud, F; Grata, E; Perrenoud, L; Saugy, M; Rudaz, S; Veuthey, J-L

2010-06-18

For doping control, analyses of samples are generally achieved in two steps: a rapid screening and, in the case of a positive result, a confirmatory analysis. A two-step methodology based on ultra-high-pressure liquid chromatography coupled to a quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) was developed to screen and confirm 103 doping agents from various classes (e.g., beta-blockers, stimulants, diuretics, and narcotics). The screening method was presented in a previous article as part I (i.e., Fast analysis of doping agents in urine by ultra-high-pressure liquid chromatography-quadrupole time-of-flight mass spectrometry. Part I: screening analysis). For the confirmatory method, basic, neutral and acidic compounds were extracted by a dedicated solid-phase extraction (SPE) in a 96-well plate format and detected by MS in the tandem mode to obtain precursor and characteristic product ions. The mass accuracy and the elemental composition of precursor and product ions were used for compound identification. After validation including matrix effect determination, the method was considered reliable to confirm suspect results without ambiguity according to the positivity criteria established by the World Anti-Doping Agency (WADA). Moreover, an isocratic method was developed to separate ephedrine from its isomer pseudoephedrine and cathine from phenylpropanolamine in a single run, what allowed their direct quantification in urine. Copyright (c) 2010 Elsevier B.V. All rights reserved.

PROGNOSTIC VALUE OF SHAPE-DESCRIPTIVE FACTORS FOR THE PROGRESSION OF GEOGRAPHIC ATROPHY SECONDARY TO AGE-RELATED MACULAR DEGENERATION.

PubMed

Pfau, Maximilian; Lindner, Moritz; Goerdt, Lukas; Thiele, Sarah; Nadal, Jennifer; Schmid, Matthias; Schmitz-Valckenberg, Steffen; Sadda, SriniVas R; Holz, Frank G; Fleckenstein, Monika

2018-05-16

To systematically compare the prognostic value of multiple shape-descriptive factors in the natural course of the disease. A total of 296 eyes of 201 patients (female patients 130; mean age: 72.2 ± 13.08 years) with a median follow-up of 2.38 years from 2 prospective, noninterventional natural history studies (Fundus-Autofluorescence-in-Age-related-Macular-Degeneration [clinicaltrials.gov identifier NCT00393692], Directional-Spread-in-Geographic-Atrophy [NCT02051998]) were included in the analysis. Serial fundus autofluorescence images were annotated using semiautomated image analysis software to determine the lesion area, circularity, perimeter, and caliper diameters. These variables and the fundus autofluorescence phenotype were evaluated for prediction of the future square root progression rates using linear mixed-effects models. For the combined model, leave-one-out cross validation on patient level (Scenario 1: previously unknown patient) resulted in a goodness-to-fit (R value) of 0.244 and leave-one-out cross validation on visit level (Scenario 2: previous observation of the patient) in a R value of 0.391. This indicated that shape-descriptive factors could explain 24.4% of the variance in geographic atrophy progression in previously unknown patients and 39.1% in patients with previous observation. These findings confirm the relevance of shape-descriptive factors and previous progression as prognostic variables for geographic atrophy progression. However, a substantial part of the remaining variation in geographic atrophy progression seems to depend on other variables, some of which are visible in optical coherence tomography.

Using passive sampling and zebrafish to identify developmental toxicants in complex mixtures.

PubMed

Bergmann, Alan J; Tanguay, Robert L; Anderson, Kim A

2017-09-01

Using effects-directed analysis, we investigated associations previously observed between polycyclic aromatic hydrocarbons (PAHs) and embryotoxicity in field-deployed low-density polyethylene (LDPE). We conducted effects-directed analysis using a zebrafish embryo assay and iterative fractionation of extracts of LDPE that were deployed in the Portland Harbor superfund megasite, Oregon (USA). Whole extracts induced toxicity including mortality, edema, and notochord distortion at 20% effect concentration (EC20) values of approximately 100, 100, and 10 mg LDPE/mL, respectively. Through fractionation, we determined that PAHs at concentrations similar to previous research did not contribute markedly to toxicity. We also eliminated pesticides, phthalates, musks, and other substances identified in toxic fractions by testing surrogate mixtures. We identified free fatty acids as lethal components of LDPE extracts and confirmed their toxicity with authentic standards. We found chromatographic evidence that dithiocarbamates are responsible for notochord and other sublethal effects, although exact matches were not obtained. Fatty acids and dithiocarbamates were previously unrecorded components of LDPE extracts and likely contribute to the toxicity of the whole mixture. The present study demonstrates the success of effects-directed analysis in nontargeted hazard identification using the zebrafish embryo test as a self-contained battery of bioassays that allows identification of multiple chemicals with different modes of action. This is the first effects-directed analysis to combine LDPE and zebrafish, approaches that are widely applicable to identifying developmental hazards in the bioavailable fraction of hydrophobic organic compounds. Environ Toxicol Chem 2017;36:2290-2298. © 2017 SETAC. © 2017 SETAC.

Childhood multidrug-resistant tuberculosis in the European Union and European Economic Area: an analysis of tuberculosis surveillance data from 2007 to 2015.

PubMed

Ködmön, Csaba; van den Boom, Martin; Zucs, Phillip; van der Werf, Marieke Johanna

2017-11-01

BackgroundConfirming tuberculosis (TB) in children and obtaining information on drug susceptibility is essential to ensure adequate treatment. We assessed whether there are gaps in diagnosis and treatment of multidrug-resistant (MDR) TB in children in the European Union and European Economic Area (EU/EEA), quantified the burden of MDR TB in children and characterised cases. Methods : We analysed surveillance data from 2007 to 2015 for paediatric cases younger than 15 years. Results : In that period, 26 EU/EEA countries reported 18,826 paediatric TB cases of whom 4,129 (21.9%) were laboratory-confirmed. Drug susceptibility testing results were available for 3,378 (17.9%), representing 81.8% of the confirmed cases. The majority (n = 2,967; 87.8%) had drug-sensitive TB, 249 (7.4%) mono-resistant TB, 64 (1.9%) poly-resistant TB, 90 (2.7%) MDR TB and eight (0.2%) had extensively drug-resistant (XDR) TB. MDR TB was more frequently reported among paediatric cases with foreign background (adjusted odds ratio (aOR) = 1.73; 95% confidence interval (95% CI): 1.12-2.67) or previous TB treatment (aOR: 6.42; 95% CI: 3.24-12.75). Successful treatment outcome was reported for 58 of 74 paediatric MDR TB cases with outcome reported from 2007 to 2013; only the group of 5-9 years-olds was significantly associated with unsuccessful treatment outcome (crude odds ratio (cOR) = 11.45; 95% CI: 1.24-106.04). Conclusions : The burden of MDR TB in children in the EU/EEA appears low, but may be underestimated owing to challenges in laboratory confirmation. Diagnostic improvements are needed for early detection and adequate treatment of MDR TB. Children previously treated for TB or of foreign origin may warrant higher attention.

Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors.

PubMed

Cau, Andrea

2017-01-01

Bayesian phylogenetic methods integrating simultaneously morphological and stratigraphic information have been applied increasingly among paleontologists. Most of these studies have used Bayesian methods as an alternative to the widely-used parsimony analysis, to infer macroevolutionary patterns and relationships among species-level or higher taxa. Among recently introduced Bayesian methodologies, the Fossilized Birth-Death (FBD) model allows incorporation of hypotheses on ancestor-descendant relationships in phylogenetic analyses including fossil taxa. Here, the FBD model is used to infer the relationships among an ingroup formed exclusively by fossil individuals, i.e., dipnoan tooth plates from four localities in the Ain el Guettar Formation of Tunisia. Previous analyses of this sample compared the results of phylogenetic analysis using parsimony with stratigraphic methods, inferred a high diversity (five or more genera) in the Ain el Guettar Formation, and interpreted it as an artifact inflated by depositional factors. In the analysis performed here, the uncertainty on the chronostratigraphic relationships among the specimens was included among the prior settings. The results of the analysis confirm the referral of most of the specimens to the taxa Asiatoceratodus , Equinoxiodus, Lavocatodus and Neoceratodus , but reject those to Ceratodus and Ferganoceratodus . The resulting phylogeny constrained the evolution of the Tunisian sample exclusively in the Early Cretaceous, contrasting with the previous scenario inferred by the stratigraphically-calibrated topology resulting from parsimony analysis. The phylogenetic framework also suggests that (1) the sampled localities are laterally equivalent, (2) but three localities are restricted to the youngest part of the section; both results are in agreement with previous stratigraphic analyses of these localities. The FBD model of specimen-level units provides a novel tool for phylogenetic inference among fossils but also for independent tests of stratigraphic scenarios.

Mesothelioma in the Quebec chrysotile mining region

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

Case, B.W.; Armstrong, B.; McDonald, J.C.

Previous studies of incidence of mesothelioma and lung tissue burden in workers and nonworkers in the Quebec chrysotile mining region showed that mesothelioma incidence is very slightly increased in the mining area, and that tremolite, or even commercial amphiboles, are responsible (and chrysotile is not). Recently, one of us (BC) noted an increase in the numbers of cases of mesothelioma coming to autopsy in the mining region. There were 19 cases, all confirmed histologically, since 1982, vs. 6 that we know of in the previous 10 y. Eighteen were occupationally exposed; one was the wife of chrysotile miner/miller. We examinedmore » lung tissue from 9 cases matched to controls of the same sex and age, dying in the same years in the same hospitals, without evidence of malignant disease. We found an excess in cases of typical asbestos bodies; tremolite fibers; and total amphiboles. In univariate linear relative risk analysis, both longer (>8 {mu}m) and shorter fibers are significant. Multivariate analysis indicates that while adjustment of chrysotile lung content for tremolite content eliminates any statistical effect of chrysotile, the reverse comparison retains significance.« less

BLAZAR SPECTRAL PROPERTIES AT 74 MHz

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

Massaro, F.; Funk, S.; Giroletti, M.

2013-10-01

Blazars are the most extreme class of active galactic nuclei. Despite a previous investigation at 102 MHz for a small sample of BL Lac objects and our recent analysis of blazars detected in the Westerbork Northern Sky Survey, a systematic study of the blazar spectral properties at frequencies below 100 MHz has been never carried out. In this paper, we present the first analysis of the radio spectral behavior of blazars based on the recent Very Large Array Low-frequency Sky Survey (VLSS) at 74 MHz. We search for blazar counterparts in the VLSS catalog, confirming that they are detected atmore » 74 MHz. We then show that blazars present radio-flat spectra (i.e., radio spectral indices of ∼0.5) when evaluated, which also about an order of magnitude in frequency lower than previous analyses. Finally, we discuss the implications of our findings in the context of the blazars-radio galaxies connection since the low-frequency radio data provide a new diagnostic tool to verify the expectations of the unification scenario for radio-loud active galaxies.« less

Measurement of θ 13 in Double Chooz using neutron captures on hydrogen with novel background rejection techniques

DOE PAGES

Abe, Y.; Appel, S.; Abrahão, T.; ...

2016-01-27

We observed a measurement of the Double Chooz collaboration and the neutrino mixing angle θ 13 using reactormore » $$\\bar{v}$$ e via the inverse beta decay reaction in which the neutron is captured on hydrogen. Our measurement is based on 462.72 live days data, approximately twice as much data as in the previous such analysis, collected with a detector positioned at an average distance of 1050 m from two reactor cores. Several novel techniques have been developed to achieve significant reductions of the backgrounds and systematic uncertainties. Accidental coincidences, the dominant background in this analysis, are suppressed by more than an order of magnitude with respect to our previous publication by a multi-variate analysis. Furthermore, these improvements demonstrate the capability of precise measurement of reactor $$\\bar{v}$$ e without gadolinium loading. Spectral distortions from the $$\\bar{v}$$ e reactor flux predictions previously reported with the neutron capture on gadolinium events are confirmed in the independent data sample presented here. A value of sin 2 2θ 13= 0.095 0.039 +0.038 (stat+syst) is obtained from a fit to the observed event rate as a function of the reactor power, a method insensitive to the energy spectrum shape. A simultaneous fit of the hydrogen capture events and of the gadolinium capture events yields a measurement of sin 2 2θ 13 = 0.088 ± 0.033(stat+syst).« less

Photoactivable caps for reactive metal nanoparticles

NASA Astrophysics Data System (ADS)

Patel, Ashish

The synthesis and stabilization of reactive metal nanoparticles is often challenging under normal atmospheric conditions. This problem can be alleviated by capping and passivation. Our lab has focused on forming polymer coatings on the surface of reactive metal nanoparticles. We discovered a convenient and effective route for stabilization of aluminum nanoparticles (Al NPs), which uses the nascent metal core as a polymerization initiator for various organic monomers. In our previous work, we used this method to passivate the Al NPs using variety of epoxides and copolymers of epoxides and alkenes. These products have demonstrated air stability for weeks to months with little to no degradation in the active Al content. Since our previously synthesized Al NP's were not beneficial for rapid and efficient thermodynamic access to the active Al core, our goal was find polymers that could easily be photochemically activated to enhance such access. Since poly(methyl methacrylate) (PMMA) has photodegrading properties, we used PMMA as a capping agent to passivate Al NPs. In this work, we present capping and stabilization of Al NPs with PMMA, and also with 1,2-epoxyhexane/ PMMA. In our previous work, we increased the stability of Al NP capped with 1,2-epoxy-9-decene by adding 1,13-tetradecadiene as a cross-linker. Here, we used the methyl methacrylate (MMA) monomer as cross-linker for Al NP capped with 1,2-epoxy-9-decene. We have also used the MMA as capping agent. We use powder x-ray diffractametry (PXRD), differential scanning calorimetry (DSC), and thermogravity analysis (TGA) to confirm the presence of elemental Al and ATR-FTIR to confirm the presence of polymers.

ECS: efficient communication scheduling for underwater sensor networks.

PubMed

Hong, Lu; Hong, Feng; Guo, Zhongwen; Li, Zhengbao

2011-01-01

TDMA protocols have attracted a lot of attention for underwater acoustic sensor networks (UWSNs), because of the unique characteristics of acoustic signal propagation such as great energy consumption in transmission, long propagation delay and long communication range. Previous TDMA protocols all allocated transmission time to nodes based on discrete time slots. This paper proposes an efficient continuous time scheduling TDMA protocol (ECS) for UWSNs, including the continuous time based and sender oriented conflict analysis model, the transmission moment allocation algorithm and the distributed topology maintenance algorithm. Simulation results confirm that ECS improves network throughput by 20% on average, compared to existing MAC protocols.

Regeneratively cooled rocket engine for space storable propellants

NASA Technical Reports Server (NTRS)

Wagner, W. R.

1973-01-01

Analysis, design, fabrication, and test efforts were performed for the existing OF2/B2H6 regeneratively cooled lK (4448 N) thrust chamber to illustrate simultaneous B2H6 fuel and OF2 oxidizer cooling and to provide results for a gaseous propellant condition injected into the combustion chamber. Data derived from performance, thermal and flow measurements confirmed predictions derived from previous test work and from concurrent analytical study. Development data derived from the experimental study were indicated to be sufficient to develop a preflight thrust chamber demonstrator prototype for future space mission objectives.

Identification of point mutations in clinical Staphylococcus aureus strains that produce small-colony variants auxotrophic for menadione.

PubMed

Dean, Melissa A; Olsen, Randall J; Long, S Wesley; Rosato, Adriana E; Musser, James M

2014-04-01

Staphylococcus aureus small-colony variants (SCVs) are implicated in chronic and relapsing infections that are difficult to diagnose and treat. Despite many years of study, the underlying molecular mechanisms and virulence effect of the small-colony phenotype remain incompletely understood. We sequenced the genomes of five S. aureus SCV strains recovered from human patients and discovered previously unidentified nonsynonymous point mutations in three genes encoding proteins in the menadione biosynthesis pathway. Analysis of genetic revertants and complementation with wild-type alleles confirmed that these mutations caused the SCV phenotype and decreased virulence for mice.

Isolation and Characterization of Three Unrecorded Zygomycete Fungi in Korea: Cunninghamella bertholletiae, Cunninghamella echinulata, and Cunninghamella elegans.

PubMed

Nguyen, Thuong T T; Choi, Young-Joon; Lee, Hyang Burm

2017-12-01

In a survey of undiscovered taxa in Korea, three zygomycete fungal strains-EML-W31, EML-HGD1-1, and EML-RUS1-1-were isolated from freshwater, grasshopper fecal, and soil samples in Korea. On the basis of the morphological characteristics and phylogenetic analysis of internal transcribed spacer and 28S rDNA, the isolates of EML-W31, EML-HGD1-1, and EML-RUS1-1 were confirmed to be Cunninghamella bertholletiae , Cunninghamella echinulata , and Cunninghamella elegans , respectively. These species have not been previously described in Korea.

Isolation and Characterization of Three Unrecorded Zygomycete Fungi in Korea: Cunninghamella bertholletiae, Cunninghamella echinulata, and Cunninghamella elegans

PubMed Central

Nguyen, Thuong T. T.; Choi, Young-Joon

2017-01-01

In a survey of undiscovered taxa in Korea, three zygomycete fungal strains–EML-W31, EML-HGD1-1, and EML-RUS1-1–were isolated from freshwater, grasshopper fecal, and soil samples in Korea. On the basis of the morphological characteristics and phylogenetic analysis of internal transcribed spacer and 28S rDNA, the isolates of EML-W31, EML-HGD1-1, and EML-RUS1-1 were confirmed to be Cunninghamella bertholletiae, Cunninghamella echinulata, and Cunninghamella elegans, respectively. These species have not been previously described in Korea. PMID:29371799

An empirical analysis of ethical and professional issues in physicians' advertising: A comparative cross-sectional study.

PubMed

Moser, H Ronald; Stevens, Robert; Loudon, David

2016-01-01

The purpose of this study is to investigate current attitudes and opinions of physicians' advertising and to compare them to the attitudes expressed 10 years previously. This study was designed to determine (a) consumers' attitudes toward advertising by physicians, and (b) whether age, occupation, income, education, or sex of consumer accounted for any significant difference in attitudes toward physicians who advertise. The study seems to confirm the belief of many marketing professionals that advertising and marketing do not have a place in the management and operation of professional services.

Multiple-step preparation and physicochemical characterization of crystalline α-germanium hydrogenphosphate

NASA Astrophysics Data System (ADS)

Romano, Ricardo; Ruiz, Ana I.; Alves, Oswaldo L.

2004-04-01

The reaction between germanium oxide and phosphoric acid has previously been described and led to impure germanium hydrogenphosphate samples with low crystallinity. A new multiple-step route involving the same reaction under refluxing and soft hydrothermal conditions is described for the preparation of pure and crystalline α-GeP. The physicochemical characterization of the samples allows accompaniment of the reaction evolution as well as determining short- and long-range structural organization. The phase purity of the α-GeP sample was confirmed by applying Rietveld's profile analysis, which also determined the cell parameters of its crystals.

ALMA Long Baseline Observations of the Dynamical Atmospheres of AGB Stars

NASA Astrophysics Data System (ADS)

Vlemmings, Wouter

2018-04-01

I will present the current status of ALMA long baseline observations of W Hya, R Leo, R Dor and Mira. We have recently obtained band 4, 6 and 7 observations of the line and continuum emission tracing the temperature and dynamics in their extended atmosphere. Our preliminary analysis confirms our previous detection of a hotspot on W Hya, and reveals unexpected lines in most of the sources, as well as possible fast rotation in the atmopshere of one of the stars. The observations show the unique power of ALMA in observing the extended stellar atmospheres.

Agony of the ecstasy: report of five cases of MDMA smuggling.

PubMed

Low, V H S; Dillon, E K

2005-10-01

The international smuggling of illicit drugs by the ingestion or rectal insertion of drug-filled packages is recognized in the trafficking of heroin and cocaine. Customs authorities, with suspicion of such activities, presented five subjects. The legally allowed radiological examination comprising one supine abdominal radiograph was performed. Radiographic findings demonstrated the presence of multiple enteric oval, capsule-shaped packages of soft tissue density. This was confirmed following supervised evacuation of bowel contents induced by the administration of laxatives. Analysis of the concealed material identified ecstasy (methylenedioxymethamphetamine (MDMA)), a substance not previously reported as transported by this route.

Toward Efficient Design of Reversible Logic Gates in Quantum-Dot Cellular Automata with Power Dissipation Analysis

NASA Astrophysics Data System (ADS)

Sasamal, Trailokya Nath; Singh, Ashutosh Kumar; Ghanekar, Umesh

2018-04-01

Nanotechnologies, remarkably Quantum-dot Cellular Automata (QCA), offer an attractive perspective for future computing technologies. In this paper, QCA is investigated as an implementation method for designing area and power efficient reversible logic gates. The proposed designs achieve superior performance by incorporating a compact 2-input XOR gate. The proposed design for Feynman, Toffoli, and Fredkin gates demonstrates 28.12, 24.4, and 7% reduction in cell count and utilizes 46, 24.4, and 7.6% less area, respectively over previous best designs. Regarding the cell count (area cover) that of the proposed Peres gate and Double Feynman gate are 44.32% (21.5%) and 12% (25%), respectively less than the most compact previous designs. Further, the delay of Fredkin and Toffoli gates is 0.75 clock cycles, which is equal to the delay of the previous best designs. While the Feynman and Double Feynman gates achieve a delay of 0.5 clock cycles, equal to the least delay previous one. Energy analysis confirms that the average energy dissipation of the developed Feynman, Toffoli, and Fredkin gates is 30.80, 18.08, and 4.3% (for 1.0 E k energy level), respectively less compared to best reported designs. This emphasizes the beneficial role of using proposed reversible gates to design complex and power efficient QCA circuits. The QCADesigner tool is used to validate the layout of the proposed designs, and the QCAPro tool is used to evaluate the energy dissipation.

LOW PRESSURE ULTRAVIOLET STUDIES FOR INACTIVATION OF GIARDIA MURIS CYSTS

EPA Science Inventory

This research was initiated to confirm and expand the current database for the inactivation of Giardia spp. using ultraviolet (UV) radiation. Initially, previous research that used in vitro excystation as the indicator for UV effectiveness was confirmed. Later, the in vitro excys...

Topography of brain glucose hypometabolism and epileptic network in glucose transporter 1 deficiency.

PubMed

Akman, Cigdem Inan; Provenzano, Frank; Wang, Dong; Engelstad, Kristin; Hinton, Veronica; Yu, Julia; Tikofsky, Ronald; Ichese, Masonari; De Vivo, Darryl C

2015-02-01

(18)F fluorodeoxyglucose positron emission tomography ((18)F FDG-PET) facilitates examination of glucose metabolism. Previously, we described regional cerebral glucose hypometabolism using (18)F FDG-PET in patients with Glucose transporter 1 Deficiency Syndrome (Glut1 DS). We now expand this observation in Glut1 DS using quantitative image analysis to identify the epileptic network based on the regional distribution of glucose hypometabolism. (18)F FDG-PET scans of 16 Glut1 DS patients and 7 healthy participants were examined using Statistical parametric Mapping (SPM). Summed images were preprocessed for statistical analysis using MATLAB 7.1 and SPM 2 software. Region of interest (ROI) analysis was performed to validate SPM results. Visual analysis of the (18)F FDG-PET images demonstrated prominent regional glucose hypometabolism in the thalamus, neocortical regions and cerebellum bilaterally. Group comparison using SPM analysis confirmed that the regional distribution of glucose hypo-metabolism was present in thalamus, cerebellum, temporal cortex and central lobule. Two mildly affected patients without epilepsy had hypometabolism in cerebellum, inferior frontal cortex, and temporal lobe, but not thalamus. Glucose hypometabolism did not correlate with age at the time of PET imaging, head circumference, CSF glucose concentration at the time of diagnosis, RBC glucose uptake, or CNS score. Quantitative analysis of (18)F FDG-PET imaging in Glut1 DS patients confirmed that hypometabolism was present symmetrically in thalamus, cerebellum, frontal and temporal cortex. The hypometabolism in thalamus correlated with the clinical history of epilepsy. Copyright © 2014. Published by Elsevier B.V.

SRG110 Stirling Generator Dynamic Simulator Vibration Test Results and Analysis Correlation

NASA Technical Reports Server (NTRS)

Suarez, Vicente J.; Lewandowski, Edward J.; Callahan, John

2006-01-01

The U.S. Department of Energy (DOE), Lockheed Martin (LM), and NASA Glenn Research Center (GRC) have been developing the Stirling Radioisotope Generator (SRG110) for use as a power system for space science missions. The launch environment enveloping potential missions results in a random input spectrum that is significantly higher than historical RPS launch levels and is a challenge for designers. Analysis presented in prior work predicted that tailoring the compliance at the generator-spacecraft interface reduced the dynamic response of the system thereby allowing higher launch load input levels and expanding the range of potential generator missions. To confirm analytical predictions, a dynamic simulator representing the generator structure, Stirling convertors and heat sources was designed and built for testing with and without a compliant interface. Finite element analysis was performed to guide the generator simulator and compliant interface design so that test modes and frequencies were representative of the SRG110 generator. This paper presents the dynamic simulator design, the test setup and methodology, test article modes and frequencies and dynamic responses, and post-test analysis results. With the compliant interface, component responses to an input environment exceeding the SRG110 qualification level spectrum were all within design allowables. Post-test analysis included finite element model tuning to match test frequencies and random response analysis using the test input spectrum. Analytical results were in good overall agreement with the test results and confirmed previous predictions that the SRG110 power system may be considered for a broad range of potential missions, including those with demanding launch environments.

SRG110 Stirling Generator Dynamic Simulator Vibration Test Results and Analysis Correlation

NASA Technical Reports Server (NTRS)

Lewandowski, Edward J.; Suarez, Vicente J.; Goodnight, Thomas W.; Callahan, John

2007-01-01

The U.S. Department of Energy (DOE), Lockheed Martin (LM), and NASA Glenn Research Center (GRC) have been developing the Stirling Radioisotope Generator (SRG110) for use as a power system for space science missions. The launch environment enveloping potential missions results in a random input spectrum that is significantly higher than historical radioisotope power system (RPS) launch levels and is a challenge for designers. Analysis presented in prior work predicted that tailoring the compliance at the generator-spacecraft interface reduced the dynamic response of the system thereby allowing higher launch load input levels and expanding the range of potential generator missions. To confirm analytical predictions, a dynamic simulator representing the generator structure, Stirling convertors and heat sources were designed and built for testing with and without a compliant interface. Finite element analysis was performed to guide the generator simulator and compliant interface design so that test modes and frequencies were representative of the SRG110 generator. This paper presents the dynamic simulator design, the test setup and methodology, test article modes and frequencies and dynamic responses, and post-test analysis results. With the compliant interface, component responses to an input environment exceeding the SRG110 qualification level spectrum were all within design allowables. Post-test analysis included finite element model tuning to match test frequencies and random response analysis using the test input spectrum. Analytical results were in good overall agreement with the test results and confirmed previous predictions that the SRG110 power system may be considered for a broad range of potential missions, including those with demanding launch environments.

Demonstration by Mass Spectrometry that Purified Native Treponema pallidum Rare Outer Membrane Protein 1 (Tromp1) Has a Cleaved Signal Peptide

PubMed Central

Blanco, David R.; Whitelegge, Julian P.; Miller, James N.; Lovett, Michael A.

1999-01-01

Purified native Tromp1 was subjected to mass spectrometric analysis in order to determine conclusively whether this protein possesses a cleaved or uncleaved signal peptide. The molecular masses of Tromp1, three Treponema pallidum lipoproteins, and a bovine serum albumin (BSA) control were determined by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. The molecular masses of all of the T. pallidum lipoproteins and BSA were within 0.7% of their respective calculated masses. The molecular mass of Tromp1 was 31,510 Da, which is consistent with a signal-less form of Tromp1, given a calculated mass of unprocessed Tromp1 of 33,571 Da, a difference of 2,061 Da (a 6.5% difference). Purified native Tromp1 was also subjected to MALDI-TOF analysis in comparison to recombinant Tromp1 following cyanogen bromide cleavage, which further confirmed the identity of Tromp1 and showed that native Tromp1 was not degraded at the carboxy terminus. These studies confirm that Tromp1 is processed and does not contain an uncleaved signal peptide as previously reported. PMID:10438785

Development of Diagnostic Biomarkers for Detecting Diabetic Retinopathy at Early Stages Using Quantitative Proteomics

PubMed Central

Min, Hophil; Kim, Sang Jin; Oh, Sohee; Kim, Kyunggon; Yu, Hyeong Gon; Park, Taesung; Kim, Youngsoo

2016-01-01

Diabetic retinopathy (DR) is a common microvascular complication caused by diabetes mellitus (DM) and is a leading cause of vision impairment and loss among adults. Here, we performed a comprehensive proteomic analysis to discover biomarkers for DR. First, to identify biomarker candidates that are specifically expressed in human vitreous, we performed data-mining on both previously published DR-related studies and our experimental data; 96 proteins were then selected. To confirm and validate the selected biomarker candidates, candidates were selected, confirmed, and validated using plasma from diabetic patients without DR (No DR) and diabetics with mild or moderate nonproliferative diabetic retinopathy (Mi or Mo NPDR) using semiquantitative multiple reaction monitoring (SQ-MRM) and stable-isotope dilution multiple reaction monitoring (SID-MRM). Additionally, we performed a multiplex assay using 15 biomarker candidates identified in the SID-MRM analysis, which resulted in merged AUC values of 0.99 (No DR versus Mo NPDR) and 0.93 (No DR versus Mi and Mo NPDR). Although further validation with a larger sample size is needed, the 4-protein marker panel (APO4, C7, CLU, and ITIH2) could represent a useful multibiomarker model for detecting the early stages of DR. PMID:26665153

Organellar proteome analyses of ricin toxin-treated HeLa cells.

PubMed

Liao, Peng; Li, Yunhu; Li, Hongyang; Liu, Wensen

2016-07-01

Apoptosis triggered by ricin toxin (RT) has previously been associated with certain cellular organellar compartments, but the diversity in the composition of the organellar proteins remains unclear. Here, we applied a shotgun proteomics strategy to examine the differential expression of proteins in the mitochondria, nuclei, and cytoplasm of HeLa cells treated and not treated with RT. Data were combined with a global bioinformatics analysis and experimental confirmations. A total of 3107 proteins were identified. Bioinformatics predictors (Proteome Analyst, WoLF PSORT, TargetP, MitoPred, Nucleo, MultiLoc, and k-nearest neighbor) and a Bayesian model that integrated these predictors were used to predict the locations of 1349 distinct organellar proteins. Our data indicate that the Bayesian model was more efficient than the individual implementation of these predictors. Additionally, a Biomolecular Interaction Network (BIN) analysis was used to identify 149 BIN subnetworks. Our experimental confirmations indicate that certain apoptosis-related proteins (e.g. cytochrome c, enolase, lamin B, Bax, and Drp1) were found to be translocated and had variable expression levels. These results provide new insights for the systematic understanding of RT-induced apoptosis responses. © The Author(s) 2014.

Further Insight on the Hypervelocity White Dwarf, LP 40–365 (GD 492): A Nearby Emissary from a Single-degenerate Type Ia Supernova

NASA Astrophysics Data System (ADS)

Raddi, R.; Hollands, M. A.; Koester, D.; Gänsicke, B. T.; Gentile Fusillo, N. P.; Hermes, J. J.; Townsley, D. M.

2018-05-01

The recently discovered hypervelocity white dwarf LP 40‑365 (aka GD 492) has been suggested as the outcome of the failed disruption of a white dwarf in a subluminous Type Ia supernova (SN Ia). We present new observations confirming GD 492 as a single star with unique spectral features. Our spectroscopic analysis suggests that a helium-dominated atmosphere, with ≃33% neon and 2% oxygen by mass, can reproduce most of the observed properties of this highly unusual star. Although our atmospheric model contrasts with the previous analysis in terms of dominant atmospheric species, we confirm that the atmosphere of GD 492 is strongly hydrogen deficient, {log}({{H}}/{He})< -5, and displays traces of 11 other α and iron-group elements (with sulfur, chromium, manganese, and titanium as new detections), indicating nuclear processing of carbon and silicon. We measure a manganese-to-iron ratio seven times larger than solar. While the observed abundances of GD 492 do not fully match any predicted nuclear yields of a partially burned supernova remnant, the manganese excess strongly favors a link with a single-degenerate SN Ia event over alternative scenarios.

Hair testing in postmortem diagnosis of substance abuse: An unusual case of slow-release oral morphine abuse in an adolescent.

PubMed

Baillif-Couniou, Valérie; Kintz, Pascal; Sastre, Caroline; Pok, Phak-Rop Pos; Chèze, Marjorie; Pépin, Gilbert; Leonetti, Georges; Pelissier-Alicot, Anne-Laure

2015-11-01

Morphine sulfate misuse is essentially observed among regular heroin injectors. To our knowledge, primary addiction to morphine sulfate is exceptional, especially among young adolescents. A 13-year-old girl, with no history of addiction, was found dead with three empty blisters of Skenan(®) LP 30 mg at her side. Opiates were detected in biological fluids and hair by chromatographic methods. Blood analyses confirmed morphine overdose (free morphine: 428 ng/mL; total morphine: 584 ng/mL) and segmental hair analysis confirmed regular exposure over several months (maximum morphine concentration 250 pg/mg). Suspecting the victim's mother of recreational use of Skenan(®), the magistrate ordered analysis of her hair, with negative results. From an epidemiological viewpoint, this case of oral morphine sulfate abuse in an adolescent with no previous history suggests the emergence of a new trend of morphine sulfate consumption. From a toxicological viewpoint, it demonstrates the value of hair testing, which documented the victim's regular exposure and made an important contribution to the police investigation. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Differentiation of clinically relevant Mucorales Rhizopus microsporus and R. arrhizus by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

PubMed

Dolatabadi, Somayeh; Kolecka, Anna; Versteeg, Matthijs; de Hoog, Sybren G; Boekhout, Teun

2015-07-01

This study addresses the usefulness of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS for reliable identification of the two most frequently occurring clinical species of Rhizopus, namely Rhizopus arrhizus with its two varieties, arrhizus and delemar, and Rhizopus microsporus. The test-set comprised 38 isolates of clinical and environmental origin previously identified by internal transcribed spacer (ITS) sequencing of rDNA. Multi-locus sequence data targeting three gene markers (ITS, ACT, TEF ) showed two monophylic clades for Rhizopus arrhizus and Rhizopus microsporus (bootstrap values of 99 %). Cluster analysis confirmed the presence of two distinct clades within Rhizopus arrhizus representing its varieties arrhizus and delemar. The MALDI Biotyper 3.0 Microflex LT platform (Bruker Daltonics) was used to confirm the distinction between Rhizopus arrhizus and Rhizopus microsporus and the presence of two varieties within the species Rhizopus arrhizus. An in-house database of 30 reference main spectra (MSPs) was initially tested for correctness using commercially available databases of Bruker Daltonics. By challenging the database with the same strains of which an in-house database was created, automatic identification runs confirmed that MALDI-TOF MS is able to recognize the strains at the variety level. Based on principal component analysis, two MSP dendrograms were created and showed concordance with the multi-locus tree; thus, MALDI-TOF MS is a useful tool for diagnostics of mucoralean species.

The three-dimensional wake of a cylinder undergoing a combination of translational and rotational oscillation in a quiescent fluid

NASA Astrophysics Data System (ADS)

Nazarinia, M.; Lo Jacono, D.; Thompson, M. C.; Sheridan, J.

2009-06-01

Previous two-dimensional numerical studies have shown that a circular cylinder undergoing both oscillatory rotational and translational motions can generate thrust so that it will actually self-propel through a stationary fluid. Although a cylinder undergoing a single oscillation has been thoroughly studied, the combination of the two oscillations has not received much attention until now. The current research reported here extends the numerical study of Blackburn et al. [Phys. Fluids 11, L4 (1999)] both experimentally and numerically, recording detailed vorticity fields in the wake and using these to elucidate the underlying physics, examining the three-dimensional wake development experimentally, and determining the three-dimensional stability of the wake through Floquet stability analysis. Experiments conducted in the laboratory are presented for a given parameter range, confirming the early results from Blackburn et al. [Phys. Fluids 11, L4 (1999)]. In particular, we confirm the thrust generation ability of a circular cylinder undergoing combined oscillatory motions. Importantly, we also find that the wake undergoes three-dimensional transition at low Reynolds numbers (Re≃100) to an instability mode with a wavelength of about two cylinder diameters. The stability analysis indicates that the base flow is also unstable to another mode at slightly higher Reynolds numbers, broadly analogous to the three-dimensional wake transition mode for a circular cylinder, despite the distinct differences in wake/mode topology. The stability of these flows was confirmed by experimental measurements.

Patterns of Novel Alleles and Genotype/Phenotype Correlations Resulting from the Analysis of 108 Previously Undetected Mutations in Patients Affected by Neurofibromatosis Type I

PubMed Central

Bonatti, Francesco; Adorni, Alessia; Matichecchia, Annalisa; Mozzoni, Paola; Uliana, Vera; Pisani, Francesco; Garavelli, Livia; Graziano, Claudio; Gnoli, Maria; Bigoni, Stefania; Boschi, Elena; Martorana, Davide; Percesepe, Antonio

2017-01-01

Neurofibromatosis type I, a genetic disorder due to mutations in the NF1 gene, is characterized by a high mutation rate (about 50% of the cases are de novo) but, with the exception of whole gene deletions associated with a more severe phenotype, no specific hotspots and few solid genotype/phenotype correlations. After retrospectively re-evaluating all NF1 gene variants found in the diagnostic activity, we studied 108 patients affected by neurofibromatosis type I who harbored mutations that had not been previously reported in the international databases, with the aim of analyzing their type and distribution along the gene and of correlating them with the phenotypic features of the affected patients. Out of the 108 previously unreported variants, 14 were inherited by one of the affected parents and 94 were de novo. Twenty-nine (26.9%) mutations were of uncertain significance, whereas 79 (73.2%) were predicted as pathogenic or probably pathogenic. No differential distribution in the exons or in the protein domains was observed and no statistically significant genotype/phenotype correlation was found, confirming previous evidences. PMID:28961165

Amplitude variations in the sdBV star PG 1605+072: Another beating time scale?

NASA Astrophysics Data System (ADS)

Pereira, T. M. D.; Lopes, I. P.

2004-10-01

PG 1605+072 has an unique and complex oscillation spectrum amongst the pulsating members of the EC 14026 stars. It has the longest periods and the richest, most puzzling frequency spectrum. We present a quantitative analysis of the photometric time-series obtained at 1-m telescope of the South African Astronomical Observatory. Thirteen oscillation parameters, frequencies, amplitudes and initial phases were determined from a 45 h time-series. Our work confirm previous observational results. The observed frequencies are within a difference smaller than 2.7% of the theoretical values, and less than 0.1% of other previous studies. We also infer the existence of variation of a periodicity of 4-5 days on the amplitude of the observed modes, similar to the yearly time-scale variation found by previous studies. Furthermore, we found a new frequency of 2133 μ Hz which has not been previously reported, its origin being yet unclear. Based on observations obtained at the South African Astronomical Observatory (SAAO). This research was supported by a grant from Fundação da Ciência e Tecnologia, grant No. PESO/P/PRO/40142/2000.

Metals and organic compounds in the biosynthesis of cannabinoids: a chemometric approach to the analysis of Cannabis sativa samples.

PubMed

Radosavljevic-Stevanovic, Natasa; Markovic, Jelena; Agatonovic-Kustrin, Snezana; Razic, Slavica

2014-01-01

Illicit production and trade of Cannabis sativa affect many societies. This drug is the most popular and easy to produce. Important information for the authorities is the production locality and the indicators of a particular production. This work is an attempt to recognise correlations between the metal content in the different parts of C. sativa L., in soils where plants were cultivated and the cannabinoids content, as a potential indicator. The organic fraction of the leaves of Cannabis plants was investigated by GC-FID analysis. In addition, the determination of Cu, Fe, Cr, Mn, Zn, Ca and Mg was realised by spectroscopic techniques (FAAS and GFAAS). In this study, numerous correlations between metal content in plants and soil, already confirmed in previous publications, were analysed applying chemometric unsupervised methods, that is, principal component analysis, factor analysis and cluster analysis, in order to highlight their role in the biosynthesis of cannabinoids.

Image analysis for the automated estimation of clonal growth and its application to the growth of smooth muscle cells.

PubMed

Gavino, V C; Milo, G E; Cornwell, D G

1982-03-01

Image analysis was used for the automated measurement of colony frequency (f) and colony diameter (d) in cultures of smooth muscle cells, Initial studies with the inverted microscope showed that number of cells (N) in a colony varied directly with d: log N = 1.98 log d - 3.469 Image analysis generated the complement of a cumulative distribution for f as a function of d. The number of cells in each segment of the distribution function was calculated by multiplying f and the average N for the segment. These data were displayed as a cumulative distribution function. The total number of colonies (fT) and the total number of cells (NT) were used to calculate the average colony size (NA). Population doublings (PD) were then expressed as log2 NA. Image analysis confirmed previous studies in which colonies were sized and counted with an inverted microscope. Thus, image analysis is a rapid and automated technique for the measurement of clonal growth.

Mosaicism of an ELANE mutation in an asymptomatic mother in a familial case of cyclic neutropenia.

PubMed

Hirata, Osamu; Okada, Satoshi; Tsumura, Miyuki; Karakawa, Shuhei; Matsumura, Itaru; Kimura, Yujiro; Maihara, Toshiro; Yasunaga, Shin'ichiro; Takihara, Yoshihiro; Ohara, Osamu; Kobayashi, Masao

2015-07-01

To confirm and characterize mosaicism of the cyclic neutropenia (CyN)-related mutation in the ELANE gene identified in the asymptomatic mother of patients with CyN. We identified sibling cases with CyN due to a novel heterozygous splicing site mutation, IVS4 +5SD G>T, in the ELANE gene, resulting in an internal in-frame deletion of 30 nucleotides (corresponding to a ten amino acid deletion, V161-F170). The mutated allele was also detected in their asymptomatic mother but at low frequency. We measured the frequency of the mutant allele from peripheral blood leukocytes (PBLs) by subcloning, and confirmed the allelic frequency of mosaicism in various cell types by massively parallel DNA sequencing (MPS) analysis. In the subcloning analysis, the mutant allele was identified in 21.36 % of PBLs from the asymptomatic mother, compared with 54.72 % of PBLs from the CyN patient. In the MPS analysis, the mutant allele was observed in approximately 30 % of mononuclear cells, CD3(+) T cells, CD14(+) monocytes and the buccal mucosa. Conversely, it was detected in low frequency in polymorphonuclear leukocytes (PLMLs) (3-4 %) and CD16(+) granulocytes (2-3 %). Mosaicism of the ELANE mutation has only previously been identified in one confirmed and one unconfirmed case of SCN. This is the first report of mosaicism of the ELANE mutation in a case of CyN. The MPS results suggest that this de novo mutation occurred during the two-cell stage of embryogenesis. PLMLs expressing the ELANE mutation were found to be actively undergoing apoptosis.

The molecular mechanism for interaction of ceruloplasmin and myeloperoxidase

NASA Astrophysics Data System (ADS)

Bakhautdin, Bakytzhan; Bakhautdin, Esen Göksöy

2016-04-01

Ceruloplasmin (Cp) is a copper-containing ferroxidase with potent antioxidant activity. Cp is expressed by hepatocytes and activated macrophages and has been known as physiologic inhibitor of myeloperoxidase (MPO). Enzymatic activity of MPO produces anti-microbial agents and strong prooxidants such as hypochlorous acid and has a potential to damage host tissue at the sites of inflammation and infection. Thus Cp-MPO interaction and inhibition of MPO has previously been suggested as an important control mechanism of excessive MPO activity. Our aim in this study was to identify minimal Cp domain or peptide that interacts with MPO. We first confirmed Cp-MPO interaction by ELISA and surface plasmon resonance (SPR). SPR analysis of the interaction yielded 30 nM affinity between Cp and MPO. We then designed and synthesized 87 overlapping peptides spanning the entire amino acid sequence of Cp. Each of the peptides was tested whether it binds to MPO by direct binding ELISA. Two of the 87 peptides, P18 and P76 strongly interacted with MPO. Amino acid sequence analysis of identified peptides revealed high sequence and structural homology between them. Further structural analysis of Cp's crystal structure by PyMOL software unfolded that both peptides represent surface-exposed sites of Cp and face nearly the same direction. To confirm our finding we raised anti-P18 antisera in rabbit and demonstrated that this antisera disrupts Cp-MPO binding and rescues MPO activity. Collectively, our results confirm Cp-MPO interaction and identify two nearly identical sites on Cp that specifically bind MPO. We propose that inhibition of MPO by Cp requires two nearly identical sites on Cp to bind homodimeric MPO simultaneously and at an angle of at least 120 degrees, which, in turn, exerts tension on MPO and results in conformational change.

Treatment of Venous Aortorenal Bypass Graft Aneurysm Using a Stent-Graft

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

Novotny, Jiri, E-mail: jino@medicon.cz; Peregrin, Jan H.; Stribrna, Jarmila

2010-02-15

We present the case of a 77-year-old male patient who had undergone a bilateral venous aortorenal bypass graft 30 years previously. Thirteen years previously, the patient was shown to have a decrease in renal function, with mild shrinking of both kidneys; additionally, a stenosis was found in the left proximal anastomosis. At the most recent follow-up visit (1 year previously), ultrasound revealed an aneurysm (42 mm in diameter) of the left renal bypass graft; the finding was confirmed by CT angiography. A significant ostial stenosis of the left renal bypass graft was also confirmed. It was decided to place amore » self-expandable stent-graft into the aneurysm while also attempting to dilate the stenosis. Proximal endoleak after stent-graft placement necessitated the implantation of another, balloon-expandable stent-graft into the bypass graft ostium. Postprocedural angiography and follow-up by CT angiography at 3 months confirmed good patency of the stent-grafts and complete thrombosis of the aneurysmal sac, with preserved kidney perfusion. Renal function remained unaltered, while the hypertension is better controlled.« less

Case control study of neuroblastoma in west-Germany after the Chernobyl accident.

PubMed

Michaelis, J; Haaf, H G; Zöllner, J; Kaatsch, P; Krummenauer, F; Berthold, F

1996-01-01

To explore possible causes of a 1988 incidence peak of infant neuroblastoma in west German regions which were contaminated with more than 6000 Bq/m2 Cs137 from the Chernobyl accident. The primary working hypothesis was that parents of the diseased children had been contaminated by an excessive intake of locally produced food, especially mushrooms or deer. Case control study with 1:2 (cases:controls) matching. Data were collected from the children's parents by questionnaires and telephone interviews. Nation-wide study (former FRG) based on the German Childhood Cancer Registry. Cases born in 1988 and reported with a neuroblastoma to the registry until March 1992. Population-based healthy controls, matched for age, sex and residence at time of diagnosis. The working hypothesis could not be confirmed by the study, because the parents of cases tended to eat less locally grown food than the parents of controls (RR = 0.63, 95% CI:0.20-1.97). Possible influence factors which previously have been described to be associated with neuroblastoma incidence could not be confirmed by the study. Parental exposure to herbicides and pesticides was associated with the occurrence of neuroblastoma (RR = 4.2, 95% CI:1.4-12.9). Neuroblastoma stage distribution in the contaminated regions was shifted towards lower stages as compared to the less contaminated regions and previous age cohorts. The study does not show additional evidence that the observed increase in neuroblastoma incidence might have been caused by exposure to fallout from the Chernobyl accident. The observed shift towards lower clinical stages may rather indicate increased diagnostic awareness. The association between neuroblastoma and parental exposure with herbicides and pesticides resulted from an extensive exploratory data analysis and needs to be confirmed in further studies.

Utilization of gene mapping and candidate gene mutation screening for diagnosing clinically equivocal conditions: a Norrie disease case study.

PubMed

Chini, Vasiliki; Stambouli, Danai; Nedelea, Florina Mihaela; Filipescu, George Alexandru; Mina, Diana; Kambouris, Marios; El-Shantil, Hatem

2014-06-01

Prenatal diagnosis was requested for an undiagnosed eye disease showing X-linked inheritance in a family. No medical records existed for the affected family members. Mapping of the X chromosome and candidate gene mutation screening identified a c.C267A[p.F89L] mutation in NPD previously described as possibly causing Norrie disease. The detection of the c.C267A[p.F89L] variant in another unrelated family confirms the pathogenic nature of the mutation for the Norrie disease phenotype. Gene mapping, haplotype analysis, and candidate gene screening have been previously utilized in research applications but were applied here in a diagnostic setting due to the scarcity of available clinical information. The clinical diagnosis and mutation identification were critical for providing proper genetic counseling and prenatal diagnosis for this family.

Initial sequence characterization of the rhabdoviruses of squamate reptiles, including a novel rhabdovirus from a caiman lizard (Dracaena guianensis)

PubMed Central

Wellehan, James F.X.; Pessier, Allan P.; Archer, Linda L.; Childress, April L.; Jacobson, Elliott R.; Tesh, Robert B.

2012-01-01

Rhabdoviruses infect a variety of hosts, including non-avian reptiles. Consensus PCR techniques were used to obtain partial RNA-dependent RNA polymerase gene sequence from five rhabdoviruses of South American lizards; Marco, Chaco, Timbo, Sena Madureira, and a rhabdovirus from a caiman lizard (Dracaena guianensis). The caiman lizard rhabdovirus formed inclusions in erythrocytes, which may be a route for infecting hematophagous insects. This is the first information on behavior of a rhabdovirus in squamates. We also obtained sequence from two rhabdoviruses of Australian lizards, confirming previous Charleville virus sequence and finding that, unlike a previous sequence report but in agreement with serologic reports, Almpiwar virus is clearly distinct from Charleville virus. Bayesian and maximum likelihood phylogenetic analysis revealed that most known rhabdoviruses of squamates cluster in the Almpiwar subgroup. The exception is Marco virus, which is found in the Hart Park group. PMID:22397930

A Unique Capsule Locus in the Newly Designated Actinobacillus pleuropneumoniae Serovar 16 and Development of a Diagnostic PCR Assay.

PubMed

Bossé, Janine T; Li, Yanwen; Sárközi, Rita; Gottschalk, Marcelo; Angen, Øystein; Nedbalcova, Katerina; Rycroft, Andrew N; Fodor, László; Langford, Paul R

2017-03-01

Actinobacillus pleuropneumoniae causes pleuropneumonia, an economically significant lung disease of pigs. Recently, isolates of A. pleuropneumoniae that were serologically distinct from the previously characterized 15 serovars were described, and a proposal was put forward that they comprised a new serovar, serovar 16. Here we used whole-genome sequencing of the proposed serovar 16 reference strain A-85/14 to confirm the presence of a unique capsular polysaccharide biosynthetic locus. For molecular diagnostics, primers were designed from the capsule locus of strain A-85/14, and a PCR was formulated that differentiated serovar 16 isolates from all 15 known serovars and other common respiratory pathogenic/commensal bacteria of pigs. Analysis of the capsule locus of strain A-85/14 combined with the previous serological data show the existence of a sixteenth serovar-designated serovar 16-of A. pleuropneumoniae . Copyright © 2017 Bossé et al.

Sequence of eruptive events in the Vesuvio area recorded in shallow-water Ionian Sea sediments

NASA Astrophysics Data System (ADS)

Taricco, C.; Alessio, S.; Vivaldo, G.

2008-01-01

The dating of the cores we drilled from the Gallipoli terrace in the Gulf of Taranto (Ionian Sea), previously obtained by tephroanalysis, is checked by applying a method to objectively recognize volcanic events. This automatic statistical procedure allows identifying pulse-like features in a series and evaluating quantitatively the confidence level at which the significant peaks are detected. We applied it to the 2000-years-long pyroxenes series of the GT89-3 core, on which the dating is based. The method confirms the dating previously performed by detecting at a high confidence level the peaks originally used and indicates a few possible undocumented eruptions. Moreover, a spectral analysis, focussed on the long-term variability of the pyroxenes series and performed by several advanced methods, reveals that the volcanic pulses are superimposed to a millennial trend and a 400 years oscillation.

Identification of mutations in Colombian patients affected with Fabry disease.

PubMed

Uribe, Alfredo; Mateus, Heidi Eliana; Prieto, Juan Carlos; Palacios, Maria Fernanda; Ospina, Sandra Yaneth; Pasqualim, Gabriela; da Silveira Matte, Ursula; Giugliani, Roberto

2015-12-15

Fabry Disease (FD) is an X-linked inborn error of glycosphingolipid catabolism, caused by a deficiency of the lisosomal α-galactosidase A (AGAL). The disorder leads to a vascular disease secondary to the involvement of kidney, heart and the central nervous system. The mutation analysis is a valuable tool for diagnosis and genetic counseling. Although more than 600 mutations have been identified, most mutations are private. Our objective was to describe the analysis of nine Colombian patients with Fabry disease by automated sequencing of the seven exons of the GLA gene. Two novel mutations were identified in two patients affected with the classical subtype of FD, in addition to other 6 mutations previously reported. The present study confirms the heterogeneity of mutations in Fabry disease and the importance of molecular analysis for genetic counseling, female heterozygotes detection as well as therapeutic decisions. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparison of NASTRAN analysis with ground vibration results of UH-60A NASA/AEFA test configuration

NASA Technical Reports Server (NTRS)

Idosor, Florentino; Seible, Frieder

1990-01-01

Preceding program flight tests, a ground vibration test and modal test analysis of a UH-60A Black Hawk helicopter was conducted by Sikorsky Aircraft to complement the UH-60A test plan and NASA/ARMY Modern Technology Rotor Airloads Program. The 'NASA/AEFA' shake test configuration was tested for modal frequencies and shapes and compared with its NASTRAN finite element model counterpart to give correlative results. Based upon previous findings, significant differences in modal data existed and were attributed to assumptions regarding the influence of secondary structure contributions in the preliminary NASTRAN modeling. An analysis of an updated finite element model including several secondary structural additions has confirmed that the inclusion of specific secondary components produces a significant effect on modal frequency and free-response shapes and improves correlations at lower frequencies with shake test data.

Familial Analysis of Seropositivity to Trypanosoma cruzi and of Clinical Forms of Chagas Disease

PubMed Central

Silva-Grecco, Roseane L.; Balarin, Marly A. S.; Correia, Dalmo; Prata, Aluízio; Rodrigues, Virmondes

2010-01-01

A cross-sectional study was carried out in Água Comprida, MG, Brazil, a region previously endemic to Chagas disease whose vectorial transmission was interrupted around 20 year ago. A total of 998 individuals were examined for anti-Trypanosoma cruzi antibodies. Seropositivity was observed in 255 subjects (25.5%), and 743 subjects were negative. Forty-one families with 5–80 individuals with similar environmental conditions were selected for familial analysis. In 15 families, seropositivity to T. cruzi was observed in > 50% of individuals. The segregation analysis confirmed family aggregation for the seropositivity to the T. cruzi. Heart commitment was the major clinical form observed, and in six families, > 50% of the individuals display cardiopathy that may be attributed to T. cruzi infection. Our results support the hypothesis that there is a family aggregation for the seropositivity but without the effect of one major gene. PMID:20064994

Gap-metric-based robustness analysis of nonlinear systems with full and partial feedback linearisation

NASA Astrophysics Data System (ADS)

Al-Gburi, A.; Freeman, C. T.; French, M. C.

2018-06-01

This paper uses gap metric analysis to derive robustness and performance margins for feedback linearising controllers. Distinct from previous robustness analysis, it incorporates the case of output unstructured uncertainties, and is shown to yield general stability conditions which can be applied to both stable and unstable plants. It then expands on existing feedback linearising control schemes by introducing a more general robust feedback linearising control design which classifies the system nonlinearity into stable and unstable components and cancels only the unstable plant nonlinearities. This is done in order to preserve the stabilising action of the inherently stabilising nonlinearities. Robustness and performance margins are derived for this control scheme, and are expressed in terms of bounds on the plant nonlinearities and the accuracy of the cancellation of the unstable plant nonlinearity by the controller. Case studies then confirm reduced conservatism compared with standard methods.

Metric for strong intrinsic fourth-order phonon anharmonicity

NASA Astrophysics Data System (ADS)

Yue, Sheng-Ying; Zhang, Xiaoliang; Qin, Guangzhao; Phillpot, Simon R.; Hu, Ming

2017-05-01

Under the framework of Taylor series expansion for potential energy, we propose a simple and robust metric, dubbed "regular residual analysis," to measure the fourth-order phonon anharmonicity in crystals. The method is verified by studying the intrinsic strong higher-order anharmonic effects in UO2 and CeO2. Comparison of the thermal conductivity results, which calculated by the anharmonic lattice dynamics method coupled with the Boltzmann transport equation and the spectral energy density method coupled with ab initio molecular dynamics simulation further validates our analysis. Analysis of the bulk Si and Ge systems confirms that the fourth-order phonon anharmonicity is enhanced and cannot be neglected at high enough temperatures, which agrees with a previous study where the four-phonon scattering was explicitly determined. This metric will facilitate evaluating and interpreting the lattice thermal conductivity of crystals with strong fourth-order phonon anharmonicity.

Molecular and Physiological Analysis of a Heat-Shock Response in Wheat 1

PubMed Central

McElwain, Elizabeth F.; Spiker, Steven

1992-01-01

We have isolated two cDNA clones from wheat (Triticum aestivum L. var Stephens), designated WHSP16.8 and WHSP16.9, that are highly similar in sequence to the low molecular weight heat-shock protein genes previously isolated from soybean. RNA blot analysis confirms that these sequences are present in heat-shocked wheat seedlings, but not in control tissues. The WHSP16.8 and WHSP16.9 cDNAs were isolated by screening a lambda gt11 expression library with antibodies to HMGc (a chromosomal protein of wheat). Immunoblot analysis has demonstrated that the antibodies raised against HMGc also recognize a group of proteins that are induced by heat shock and have molecular weights (estimated by sodium dodecyl sulfate electrophoresis) consistent with the molecular weights of the proteins deduced from the sequences of the cDNAs. ImagesFigure 3Figure 4Figure 5 PMID:16669058

The Use of Protein-DNA, Chromatin Immunoprecipitation, and Transcriptome Arrays to Describe Transcriptional Circuits in the Dehydrated Male Rat Hypothalamus

PubMed Central

Qiu, Jing; Kleineidam, Anna; Gouraud, Sabine; Yao, Song Tieng; Greenwood, Mingkwan; Hoe, See Ziau; Hindmarch, Charles

2014-01-01

The supraoptic nucleus (SON) of the hypothalamus is responsible for maintaining osmotic stability in mammals through its elaboration of the antidiuretic hormone arginine vasopressin. Upon dehydration, the SON undergoes a function-related plasticity, which includes remodeling of morphology, electrical properties, and biosynthetic activity. This process occurs alongside alterations in steady state transcript levels, which might be mediated by changes in the activity of transcription factors. In order to identify which transcription factors might be involved in changing patterns of gene expression, an Affymetrix protein-DNA array analysis was carried out. Nuclear extracts of SON from dehydrated and control male rats were analyzed for binding to the 345 consensus DNA transcription factor binding sequences of the array. Statistical analysis revealed significant changes in binding to 26 consensus elements, of which EMSA confirmed increased binding to signal transducer and activator of transcription (Stat) 1/Stat3, cellular Myelocytomatosis virus-like cellular proto-oncogene (c-Myc)-Myc-associated factor X (Max), and pre-B cell leukemia transcription factor 1 sequences after dehydration. Focusing on c-Myc and Max, we used quantitative PCR to confirm previous transcriptomic analysis that had suggested an increase in c-Myc, but not Max, mRNA levels in the SON after dehydration, and we demonstrated c-Myc- and Max-like immunoreactivities in SON arginine vasopressin-expressing cells. Finally, by comparing new data obtained from Roche-NimbleGen chromatin immunoprecipitation arrays with previously published transcriptomic data, we have identified putative c-Myc target genes whose expression changes in the SON after dehydration. These include known c-Myc targets, such as the Slc7a5 gene, which encodes the L-type amino acid transporter 1, ribosomal protein L24, histone deactylase 2, and the Rat sarcoma proto-oncogene (Ras)-related nuclear GTPase. PMID:25144923

Nonlinear forecasting analysis of inflation-deflation patterns of an active caldera (Campi Flegrei, Italy)

USGS Publications Warehouse

Cortini, M.; Barton, C.C.

1993-01-01

The ground level in Pozzuoli, Italy, at the center of the Campi Flegrei caldera, has been monitored by tide gauges. Previous work suggests that the dynamics of the Campi Flegrei system, as reconstructed from the tide gauge record, is chaotic and low dimensional. According to this suggestion, in spite of the complexity of the system, at a time scale of days the ground motion is driven by a deterministic mechanism with few degrees of freedom; however, the interactions of the system may never be describable in full detail. New analysis of the tide gauge record using Nonlinear Forecasting, confirms low-dimensional chaos in the ground elevation record at Campi Flegrei and suggests that Nonlinear Forecasting could be a useful tool in volcanic surveillance. -from Authors

High-resolution melting analysis of gyrA codon 84 and grlA codon 80 mutations conferring resistance to fluoroquinolones in Staphylococcus pseudintermedius isolates from canine clinical samples.

PubMed

Loiacono, Monica; Martino, Piera A; Albonico, Francesca; Dell'Orco, Francesca; Ferretti, Manuela; Zanzani, Sergio; Mortarino, Michele

2017-09-01

Staphylococcus pseudintermedius is an opportunistic pathogen of dogs and cats. A high-resolution melting analysis (HRMA) protocol was designed and tested on 42 clinical isolates with known fluoroquinolone (FQ) susceptibility and gyrA codon 84 and grlA codon 80 mutation status. The HRMA approach was able to discriminate between FQ-sensitive and FQ-resistant strains and confirmed previous reports that the main mutation site associated with FQ resistance in S. pseudintermedius is located at position 251 (Ser84Leu) of gyrA. Routine, HRMA-based FQ susceptibility profiles may be a valuable tool to guide therapy. The FQ resistance-predictive power of the assay should be tested in a significantly larger number of isolates.

Bianchi class B spacetimes with electromagnetic fields

NASA Astrophysics Data System (ADS)

Yamamoto, Kei

2012-02-01

We carry out a thorough analysis on a class of cosmological space-times which admit three spacelike Killing vectors of Bianchi class B and contain electromagnetic fields. Using dynamical system analysis, we show that a family of electro-vacuum plane-wave solutions of the Einstein-Maxwell equations is the stable attractor for expanding universes. Phase dynamics are investigated in detail for particular symmetric models. We integrate the system exactly for some special cases to confirm the qualitative features. Some of the obtained solutions have not been presented previously to the best of our knowledge. Finally, based on those analyses, we discuss the relation between those homogeneous models and perturbations of open Friedmann-Lemaitre-Robertson-Walker universes. We argue that the electro-vacuum plane-wave modes correspond to a certain long-wavelength limit of electromagnetic perturbations.

El Niño suppresses Antarctic warming

NASA Astrophysics Data System (ADS)

Bertler, Nancy A. N.; Barrett, Peter J.; Mayewski, Paul A.; Fogt, Ryan L.; Kreutz, Karl J.; Shulmeister, James

2004-08-01

Here we present new isotope records derived from snow samples from the McMurdo Dry Valleys, Antarctica and re-analysis data of the European Centre for Medium-Range Weather Forecasts (ERA-40) to explain the connection between the warming of the Pacific sector of the Southern Ocean [Jacka and Budd, 1998; Jacobs et al., 2002] and the current cooling of the terrestrial Ross Sea region [Doran et al., 2002a]. Our analysis confirms previous findings that the warming is linked to the El Niño Southern Oscillation (ENSO) [Kwok and Comiso, 2002a, 2002b; Carleton, 2003; Ribera and Mann, 2003; Turner, 2004], and provides new evidence that the terrestrial cooling is caused by a simultaneous ENSO driven change in atmospheric circulation, sourced in the Amundsen Sea and West Antarctica.

A strategy for evaluating pathway analysis methods.

PubMed

Yu, Chenggang; Woo, Hyung Jun; Yu, Xueping; Oyama, Tatsuya; Wallqvist, Anders; Reifman, Jaques

2017-10-13

Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biological interpretation of high-throughput data. Before practically applying such pathway analysis (PA) methods, we must first evaluate their performance and reliability, using datasets where the pathways perturbed by the conditions of interest have been well characterized in advance. However, such 'ground truths' (or gold standards) are often unavailable. Furthermore, previous evaluation strategies that have focused on defining 'true answers' are unable to systematically and objectively assess PA methods under a wide range of conditions. In this work, we propose a novel strategy for evaluating PA methods independently of any gold standard, either established or assumed. The strategy involves the use of two mutually complementary metrics, recall and discrimination. Recall measures the consistency of the perturbed pathways identified by applying a particular analysis method to an original large dataset and those identified by the same method to a sub-dataset of the original dataset. In contrast, discrimination measures specificity-the degree to which the perturbed pathways identified by a particular method to a dataset from one experiment differ from those identifying by the same method to a dataset from a different experiment. We used these metrics and 24 datasets to evaluate six widely used PA methods. The results highlighted the common challenge in reliably identifying significant pathways from small datasets. Importantly, we confirmed the effectiveness of our proposed dual-metric strategy by showing that previous comparative studies corroborate the performance evaluations of the six methods obtained by our strategy. Unlike any previously proposed strategy for evaluating the performance of PA methods, our dual-metric strategy does not rely on any ground truth, either established or assumed, of the pathways perturbed by a specific clinical or experimental condition. As such, our strategy allows researchers to systematically and objectively evaluate pathway analysis methods by employing any number of datasets for a variety of conditions.

The fibre-folate debate in colo-rectal cancer.

PubMed

Bingham, Sheila

2006-02-01

Intervention and prospective studies showing no effect of fibre in protection against colo-rectal cancer have challenged consensus recommendations that population intakes of fibre should be increased to reduce the risk of colo-rectal cancer. The European Prospective Investigation of Cancer and Nutrition (EPIC) of 519 978 individuals aged 25-70 years is the largest prospective study of diet and cancer to date worldwide. It incorporates ten different European countries in order to increase heterogeneity in dietary habits and calibration procedures to reduce measurement error. Data for 1065 reported cases of colo-rectal cancer were reported in 2003. There was a 40% reduction in risk for the highest quintile v. lowest quintile of fibre in food after calibration. It has been suggested that these effects were a result of confounding by folate and other factors. Although there are a number of hypotheses to explain why folate should be protective in colo-rectal cancer, a meta-analysis has shown that folate in food may be protective but there is no effect of total folate (i.e. food plus supplements). In a further analysis of 1826 cases in EPIC, identified in the latest follow-up, the inclusion of an additional 761 cases has confirmed the previously published results, with a strong and significant reduction in colo-rectal cancer of approximately 9% reduction in risk for each uncalibrated quintile increase in fibre (P<0.001 for linear trend) compared with an 8% reduction in the previous report, which had not been adjusted for folate. Inclusion of the other covariates (physical activity, alcohol, smoking and red and processed meat) with folate has confirmed this significant inverse association for colon cancer and strengthened the association with left-sided colon cancer (P < 0.001).

Combination Testing Using a Single MSH5 Variant alongside HLA Haplotypes Improves the Sensitivity of Predicting Coeliac Disease Risk in the Polish Population.

PubMed

Paziewska, Agnieszka; Cukrowska, Bozena; Dabrowska, Michalina; Goryca, Krzysztof; Piatkowska, Magdalena; Kluska, Anna; Mikula, Michal; Karczmarski, Jakub; Oralewska, Beata; Rybak, Anna; Socha, Jerzy; Balabas, Aneta; Zeber-Lubecka, Natalia; Ambrozkiewicz, Filip; Konopka, Ewa; Trojanowska, Ilona; Zagroba, Malgorzata; Szperl, Malgorzata; Ostrowski, Jerzy

2015-01-01

Assessment of non-HLA variants alongside standard HLA testing was previously shown to improve the identification of potential coeliac disease (CD) patients. We intended to identify new genetic variants associated with CD in the Polish population that would improve CD risk prediction when used alongside HLA haplotype analysis. DNA samples of 336 CD and 264 unrelated healthy controls were used to create DNA pools for a genome wide association study (GWAS). GWAS findings were validated with individual HLA tag single nucleotide polymorphism (SNP) typing of 473 patients and 714 healthy controls. Association analysis using four HLA-tagging SNPs showed that, as was found in other populations, positive predicting genotypes (HLA-DQ2.5/DQ2.5, HLA-DQ2.5/DQ2.2, and HLA-DQ2.5/DQ8) were found at higher frequencies in CD patients than in healthy control individuals in the Polish population. Both CD-associated SNPs discovered by GWAS were found in the CD susceptibility region, confirming the previously-determined association of the major histocompatibility (MHC) region with CD pathogenesis. The two most significant SNPs from the GWAS were rs9272346 (HLA-dependent; localized within 1 Kb of DQA1) and rs3130484 (HLA-independent; mapped to MSH5). Specificity of CD prediction using the four HLA-tagging SNPs achieved 92.9%, but sensitivity was only 45.5%. However, when a testing combination of the HLA-tagging SNPs and the MSH5 SNP was used, specificity decreased to 80%, and sensitivity increased to 74%. This study confirmed that improvement of CD risk prediction sensitivity could be achieved by including non-HLA SNPs alongside HLA SNPs in genetic testing.

Thorough analysis of unorthodox ABO deletions called by the 1000 Genomes project.

PubMed

Möller, M; Hellberg, Å; Olsson, M L

2018-02-01

ABO remains the clinically most important blood group system, but despite earlier extensive research, significant findings are still being made. The vast majority of catalogued ABO null alleles are based on the c.261delG polymorphism. Apart from c.802G>A, other mechanisms for O alleles are rare. While analysing the data set from the 1000 Genomes (1000G) project, we encountered two previously uncharacterized deletions, which needed further exploration. The Erythrogene database, complemented with bioinformatics software, was used to analyse ABO in 2504 individuals from 1000G. DNA samples from selected 1000G donors and African blood donors were examined by allele-specific PCR and Sanger sequencing to characterize predicted deletions. A 5821-bp deletion encompassing exons 5-7 was called in twenty 1000G individuals, predominantly Africans. This allele was confirmed and its exact deletion point defined by bioinformatic analyses and in vitro experiments. A PCR assay was developed, and screening of African samples revealed three donors heterozygous for this deletion, which was thereby phenotypically established as an O allele. Analysis of upstream genetic markers indicated an ancestral origin from ABO*O.01.02. We estimate this deletion as the 3rd most common mechanism behind O alleles. A 24-bp deletion was called in nine individuals and showed greater diversity regarding ethnic distribution and allelic background. It could neither be confirmed by in silico nor in vitro experiments. A previously uncharacterized ABO deletion among Africans was comprehensively mapped and a genotyping strategy devised. The false prediction of another deletion emphasizes the need for cautious interpretation of NGS data and calls for strict validation routines. © 2017 International Society of Blood Transfusion.

Assessing the oxidation states and structural stability of the Ce analogue of brannerite

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

Aluri, Esther Rani; Bachiu, Lisa M.; Grosvenor, Andrew P.

2017-07-04

The Ce-containing analogue of brannerite (ie, UTi2O6) was previously considered to be stoichiometric (ie, CeTi2O6); however, it has recently been determined that the material is O deficient. This oxygen-deficient material has been suggested to be charged balanced by the presence of a minor concentration of Ce3+ or by the A-site being cation deficient with the Ce oxidation state being 4+. A variety of Ti-containing oxides (including brannerite) have been investigated as potential nuclear wasteforms, and it is necessary to understand the electronic structure of a proposed nuclear wasteform material as well as how the structure responds to radiation from incorporatedmore » waste elements. The radiation resistance of a material can be simulated by ion implantation. The objective of this study was to confirm the Ce oxidation state in the cation- and oxygen-deficient material (ie, Ce0.94Ti2O6 - δ) and to determine how radiation damage affects this material. X-ray photoelectron spectroscopy (XPS) and X-ray absorption near-edge spectroscopy were used to study Ce0.94Ti2O6 - δ before and after being implanted with 2 MeV Au- ions. Analysis of the Ce 3d XPS spectra from the as-synthesized samples by using a previously developed fitting method has unequivocally shown that Ce adopts both 4+ (major) and 3+ (minor) oxidation states, which was confirmed by examination of magnetic susceptibility data. Analysis of XPS and X-ray absorption near-edge spectroscopy spectra from ion-implanted materials showed that both Ce and Ti were reduced because of radiation damage and that the local coordination environments of the cations are greatly affected by radiation damage.« less

Unequivocal Identification of 1-Phenylethyl Acetate in Clove Buds (syzygium aromaticum (L.) Merr. & L.M.Perry) and Clove Essential Oil.

PubMed

Gassenmeier, Klaus; Schwager, Hugo; Houben, Eric; Clery, Robin

2017-06-27

The natural occurrence of 1-phenylethyl acetate (styrallyl acetate) was confirmed in commercially available dried clove buds and also in the hydrodistilled oil from clove buds. This confirms previous reports and other anecdotal evidence for its occurrence in nature.

Solvent Hold Tank Sample Results for MCU-16-934-935-936: June 2016 Monthly Sample

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

Fondeur, F. F.; Jones, D. H.

2016-08-30

Savannah River National Laboratory (SRNL) received one set of Solvent Hold Tank (SHT) samples (MCU-16-934-935-936), pulled on 07/01/2016 for analysis. The samples were combined and analyzed for composition. Analysis of the composite sample MCU-16-934-935-936 indicated the Isopar™L concentration is above its nominal level (101%). The modifier (CS-7SB) and the TiDG concentrations are 8% and 29 % below their nominal concentrations. This analysis confirms the solvent may require the addition of TiDG, and possibly of modifier. Based on the current monthly sample, the levels of TiDG, Isopar™L, MaxCalix, and modifier are sufficient for continuing operation but are expected to decrease withmore » time. Periodic characterization and trimming additions to the solvent are recommended. No impurities above the 1000 ppm level were found in this solvent by the Semi-Volatile Organic Analysis (SVOA). No impurities were observed in the Hydrogen Nuclear Magnetic Resonance (HNMR). However, up to 21.1 ± 4 micrograms of mercury per gram of solvent (or 17.5 μg/mL) was detected in this sample (as determined by the XRF method of undigested sample). The current gamma level (1.41E5 dpm/mL) confirmed that the gamma concentration has returned to previous levels (as observed in the late 2015 samples) where the process operated normally and as expected.« less

Development of a scale to assess cancer stigma in the non-patient population.

PubMed

Marlow, Laura A V; Wardle, Jane

2014-04-23

Illness-related stigma has attracted considerable research interest, but few studies have specifically examined stigmatisation of cancer in the non-patient population. The present study developed and validated a Cancer Stigma Scale (CASS) for use in the general population. An item pool was developed on the basis of previous research into illness-related stigma in the general population and patients with cancer. Two studies were carried out. The first study used Exploratory factor analysis to explore the structure of items in a sample of 462 postgraduate students recruited through a London university. The second study used Confirmatory factor analysis to confirm the structure among 238 adults recruited through an online market research panel. Internal reliability, test-retest reliability and construct validity were also assessed. Exploratory factor analysis suggested six subscales, representing: Awkwardness, Severity, Avoidance, Policy Opposition, Personal Responsibility and Financial Discrimination. Confirmatory factor analysis confirmed this structure with a 25-item scale. All subscales showed adequate to good internal and test-retest reliability in both samples. Construct validity was also good, with mean scores for each subscale varying in the expected directions by age, gender, experience of cancer, awareness of lifestyle risk factors for cancer, and social desirability. Means for the subscales were consistent across the two samples. These findings highlight the complexity of cancer stigma and provide the Cancer Stigma Scale (CASS) which can be used to compare populations, types of cancer and evaluate the effects of interventions designed to reduce cancer stigma in non-patient populations.

A Two-Stage Meta-Analysis Identifies Several New Loci for Parkinson's Disease

PubMed Central

2011-01-01

A previous genome-wide association (GWA) meta-analysis of 12,386 PD cases and 21,026 controls conducted by the International Parkinson's Disease Genomics Consortium (IPDGC) discovered or confirmed 11 Parkinson's disease (PD) loci. This first analysis of the two-stage IPDGC study focused on the set of loci that passed genome-wide significance in the first stage GWA scan. However, the second stage genotyping array, the ImmunoChip, included a larger set of 1,920 SNPs selected on the basis of the GWA analysis. Here, we analyzed this set of 1,920 SNPs, and we identified five additional PD risk loci (combined p<5×10−10, PARK16/1q32, STX1B/16p11, FGF20/8p22, STBD1/4q21, and GPNMB/7p15). Two of these five loci have been suggested by previous association studies (PARK16/1q32, FGF20/8p22), and this study provides further support for these findings. Using a dataset of post-mortem brain samples assayed for gene expression (n = 399) and methylation (n = 292), we identified methylation and expression changes associated with PD risk variants in PARK16/1q32, GPNMB/7p15, and STX1B/16p11 loci, hence suggesting potential molecular mechanisms and candidate genes at these risk loci. PMID:21738488

New insights into the diets of harbor seals in the Salish Sea revealed by quantitative fatty acid signature analysis

USGS Publications Warehouse

Bromaghin, Jeffrey F.; Lance, Monique M.; Elliott, Elizabeth W.; Jeffries, Steven J.; Acevedo-Gutiérrez, Alejandro; Kennish, John M.

2013-01-01

Harbor seals (Phoca vitulina) are an abundant predator along the west coast of North America, and there is considerable interest in their diet composition, especially in regard to predation on valued fish stocks. Available information on harbor seal diets, primarily derived from scat analysis, suggests that adult salmon (Oncorhynchus spp.), Pacific Herring (Clupea pallasii), and gadids predominate. Because diet assessments based on scat analysis may be biased, we investigated diet composition through quantitative analysis of fatty acid signatures. Blubber samples from 49 harbor seals captured in western North America from haul-outs within the area of the San Juan Islands and southern Strait of Georgia in the Salish Sea were analyzed for fatty acid composition, along with 269 fish and squid specimens representing 27 potential prey classes. Diet estimates varied spatially, demographically, and among individual harbor seals. Findings confirmed the prevalence of previously identified prey species in harbor seal diets, but other species also contributed significantly. In particular, Black (Sebastes melanops) and Yellowtail (S. flavidus) Rockfish were estimated to compose up to 50% of some individual seal diets. Specialization and high predation rates on Black and Yellowtail Rockfish by a subset of harbor seals may play a role in the population dynamics of these regional rockfish stocks that is greater than previously realized.

Chromosomal evolution and phylogeny in the Nullicauda group (Chiroptera, Phyllostomidae): evidence from multidirectional chromosome painting.

PubMed

Gomes, Anderson José Baia; Nagamachi, Cleusa Yoshiko; Rodrigues, Luis Reginaldo Ribeiro; Ferguson-Smith, Malcolm Andrew; Yang, Fengtang; O'Brien, Patricia Caroline Mary; Pieczarka, Julio Cesar

2018-04-25

The family Phyllostomidae (Chiroptera) shows wide morphological, molecular and cytogenetic variation; many disagreements regarding its phylogeny and taxonomy remains to be resolved. In this study, we use chromosome painting with whole chromosome probes from the Phyllostomidae Phyllostomus hastatus and Carollia brevicauda to determine the rearrangements among several genera of the Nullicauda group (subfamilies Gliphonycterinae, Carolliinae, Rhinophyllinae and Stenodermatinae). These data, when compared with previously published chromosome homology maps, allow the construction of a phylogeny comparable to those previously obtained by morphological and molecular analysis. Our phylogeny is largely in agreement with that proposed with molecular data, both on relationships between the subfamilies and among genera; it confirms, for instance, that Carollia and Rhinophylla, previously considered as part of the same subfamily are, in fact, distant genera. The occurrence of the karyotype considered ancestral for this family in several different branches suggests that the diversification of Phyllostomidae into many subfamilies has occurred in a short period of time. Finally, the comparison with published maps using human whole chromosome probes allows us to track some syntenic associations prior to the emergence of this family.

Trends in biomedical informatics: automated topic analysis of JAMIA articles

PubMed Central

Wang, Shuang; Jiang, Chao; Jiang, Xiaoqian; Kim, Hyeon-Eui; Sun, Jimeng; Ohno-Machado, Lucila

2015-01-01

Biomedical Informatics is a growing interdisciplinary field in which research topics and citation trends have been evolving rapidly in recent years. To analyze these data in a fast, reproducible manner, automation of certain processes is needed. JAMIA is a “generalist” journal for biomedical informatics. Its articles reflect the wide range of topics in informatics. In this study, we retrieved Medical Subject Headings (MeSH) terms and citations of JAMIA articles published between 2009 and 2014. We use tensors (i.e., multidimensional arrays) to represent the interaction among topics, time and citations, and applied tensor decomposition to automate the analysis. The trends represented by tensors were then carefully interpreted and the results were compared with previous findings based on manual topic analysis. A list of most cited JAMIA articles, their topics, and publication trends over recent years is presented. The analyses confirmed previous studies and showed that, from 2012 to 2014, the number of articles related to MeSH terms Methods, Organization & Administration, and Algorithms increased significantly both in number of publications and citations. Citation trends varied widely by topic, with Natural Language Processing having a large number of citations in particular years, and Medical Record Systems, Computerized remaining a very popular topic in all years. PMID:26555018

Familial 4.3 Mb duplication of 21q22 sheds new light on the Down syndrome critical region

PubMed Central

Ronan, Anne; Fagan, Kerry; Christie, Louise; Conroy, Jeffrey; Nowak, Norma J; Turner, Gillian

2007-01-01

A 4.3 Mb duplication of chromosome 21 bands q22.13–q22.2 was diagnosed by interphase fluorescent in‐situ hybridisation (FISH) in a 31‐week gestational age baby with cystic hygroma and hydrops; the duplication was later found in the mother and in her 8‐year‐old daughter by the same method and confirmed by array comparative genomic hybridisation (aCGH). All had the facial gestalt of Down syndrome (DS). This is the smallest accurately defined duplication of chromosome 21 reported with a DS phenotype. The duplication encompasses the gene DYRK1 but not DSCR1 or DSCAM, all of which have previously been implicated in the causation of DS. Previous karyotype analysis and telomere screening of the mother, and karyotype analysis and metaphase FISH of a chorionic villus sample, had all failed to reveal the duplication. The findings in this family add to the identification and delineation of a “critical region” for the DS phenotype on chromosome 21. Cryptic chromosomal abnormalities can be missed on a routine karyotype for investigation of abnormal prenatal ultrasound findings, lending support to the use of aCGH analysis in this setting. PMID:17237124

Gene Expression Profiling of Multiple Leiomyomata Uteri and Matched Normal Tissue from a Single Patient

PubMed Central

Dimitrova, Irina K.; Richer, Jennifer K.; Rudolph, Michael C.; Spoelstra, Nicole S.; Reno, Elaine M.; Medina, Theresa M.; Bradford, Andrew P.

2009-01-01

Objective To identify differentially expressed genes between fibroid and adjacent normal myometrium in an identical hormonal and genetic background. Design Array analysis of 3 leiomyomata and matched adjacent normal myometrium in a single patient. Setting University of Colorado Hospital. Patient(s) A single female undergoing medically indicated hysterectomy for symptomatic fibroids. Interventions(s) mRNA isolation and microarray analysis, reverse-transcriptase polymerase chain reaction, western blotting and immunohistochemistry. Main Outcome Measure(s) Changes in mRNA and protein levels in leiomyomata and matched normal myometrium. Result(s) Expression of 197 genes was increased and 619 decreased, significantly by at least 2 fold, in leiomyomata relative to normal myometrium. Expression profiles between tumors were similar and normal myometrial samples showed minimal variation. Changes in, and variation of, expression of selected genes were confirmed in additional normal and leiomyoma samples from multiple patients. Conclusion(s) Analysis of multiple tumors from a single patient confirmed changes in expression of genes described in previous, apparently disparate, studies and identified novel targets. Gene expression profiles in leiomyomata are consistent with increased activation of mitogenic pathways and inhibition of apoptosis. Down-regulation of genes implicated in invasion and metastasis, of cancers, was observed in fibroids. This expression pattern may underlie the benign nature of uterine leiomyomata and may aid in the differential diagnosis of leiomyosarcoma. PMID:18672237

Classification of Cowpox Viruses into Several Distinct Clades and Identification of a Novel Lineage

PubMed Central

Franke, Annika; Pfaff, Florian; Jenckel, Maria; Hoffmann, Bernd; Höper, Dirk; Antwerpen, Markus; Meyer, Hermann; Beer, Martin; Hoffmann, Donata

2017-01-01

Cowpox virus (CPXV) was considered as uniform species within the genus Orthopoxvirus (OPV). Previous phylogenetic analysis indicated that CPXV is polyphyletic and isolates may cluster into different clades with two of these clades showing genetic similarities to either variola (VARV) or vaccinia viruses (VACV). Further analyses were initiated to assess both the genetic diversity and the evolutionary background of circulating CPXVs. Here we report the full-length sequences of 20 CPXV strains isolated from different animal species and humans in Germany. A phylogenetic analysis of altogether 83 full-length OPV genomes confirmed the polyphyletic character of the species CPXV and suggested at least four different clades. The German isolates from this study mainly clustered into two CPXV-like clades, and VARV- and VACV-like strains were not observed. A single strain, isolated from a cotton-top tamarin, clustered distantly from all other CPXVs and might represent a novel and unique evolutionary lineage. The classification of CPXV strains into clades roughly followed their geographic origin, with the highest clade diversity so far observed for Germany. Furthermore, we found evidence for recombination between OPV clades without significant disruption of the observed clustering. In conclusion, this analysis markedly expands the number of available CPXV full-length sequences and confirms the co-circulation of several CPXV clades in Germany, and provides the first data about a new evolutionary CPXV lineage. PMID:28604604

Clinical and mutation analysis of 51 probands with anophthalmia and/or severe microphthalmia from a single center

PubMed Central

Gerth-Kahlert, Christina; Williamson, Kathleen; Ansari, Morad; Rainger, Jacqueline K; Hingst, Volker; Zimmermann, Theodor; Tech, Stefani; Guthoff, Rudolf F; van Heyningen, Veronica; FitzPatrick, David R

2013-01-01

Clinical evaluation and mutation analysis was performed in 51 consecutive probands with severe eye malformations – anophthalmia and/or severe microphthalmia – seen in a single specialist ophthalmology center. The mutation analysis consisted of bidirectional sequencing of the coding regions of SOX2, OTX2, PAX6 (paired domain), STRA6, BMP4, SMOC1, FOXE3, and RAX, and genome-wide array-based copy number assessment. Fifteen (29.4%) of the 51 probands had likely causative mutations affecting SOX2 (9/51), OTX2 (5/51), and STRA6 (1/51). Of the cases with bilateral anophthalmia, 9/12 (75%) were found to be mutation positive. Three of these mutations were large genomic deletions encompassing SOX2 (one case) or OTX2 (two cases). Familial inheritance of three intragenic, plausibly pathogenic, and heterozygous mutations was observed. An unaffected carrier parent of an affected child with an identified OTX2 mutation confirmed the previously reported nonpenetrance for this disorder. Two families with SOX2 mutations demonstrated a parent and child both with significant but highly variable eye malformations. Heterozygous loss-of-function mutations in SOX2 and OTX2 are the most common genetic pathology associated with severe eye malformations and bi-allelic loss-of-function in STRA6 is confirmed as an emerging cause of nonsyndromal eye malformations. PMID:24498598

Assessment of DNA Damage and Telomerase Activity in Exfoliated Urinary Cells as Sensitive and Noninvasive Biomarkers for Early Diagnosis of Bladder Cancer in Ex-Workers of a Rubber Tyres Industry

PubMed Central

Pira, Enrico; Romano, Canzio; Fresegna, Anna Maria; Ciervo, Aureliano; Buresti, Giuliana; Zoli, Wainer; Calistri, Daniele

2014-01-01

The aim of the present study was to identify sensitive and noninvasive biomarkers of early carcinogenic effect at target organ to use in biomonitoring studies of workers at risk for previous occupational exposure to potential carcinogens. Standard urine cytology (Papanicolaou staining test), comet assay, and quantitative telomerase repeat amplification protocol (TRAP) assay were performed in 159 ex-rubber workers employed in tyres production and 97 unexposed subjects. In TRAP positive cases, a second level analysis using FISH (Urovysion) was done. Cystoscopy results were available for 11 individuals whose 6 FISH/TRAP/comet positive showed in 3 cases a dysplastic condition confirmed by biopsy, 1 comet positive resulted in infiltrating UBC to the biopsy and with hyperplasia and slight dysplasia to the urinary cytology, 1 comet positive resulted in papillary superficial UBC to the biopsy, 1 FISH/TRAP positive showed a normal condition, and 2 TRAP positive showed in one case a phlogosis condition. The results evidenced good concordance of TRAP, comet, and FISH assays as early biomarkers of procarcinogenic effect confirmed by the dysplastic condition and UBC found by cystoscopy-biopsy analysis. The analysis of these markers in urine cells could be potentially more accurate than conventional cytology in monitoring workers exposed to mixture of bladder potential carcinogens. PMID:24877087

An examination of the identity development of African American undergraduate engineering students attending an HBCU

NASA Astrophysics Data System (ADS)

Taylor, Kenneth J.

This study examined the identity development for a sample of 90 African American undergraduate engineering male and female students attending an HBCU. Using the Student Development Task and Lifestyle Assessment (SDTLA), which is based on Chickering and Reisser's identity development theory, differences in identity development were examined with respect to gender, academic classification, and grade point average. Previous research has shown the need to look beyond academic factors to understand and influence the persistence of African American engineering students. Non-cognitive factors, including identity development have proven to be influential in predicting persistence, especially for African American engineering students. Results from the analysis revealed significant means for academic classification and five of the dependent variables to include career planning peer relations, emotional autonomy, educational involvement, and establishing and clarifying purpose. Post hoc analysis confirmed significant differences for four of those dependent variables. However, the analysis failed to confirm statistical significant differences in peer relations due to academic classification. The significant decline in the mean scores for development in these four areas, as students progressed from sophomore to senior year revealed strong implications for the need to provide programming and guidance for those students. Institutions of higher education should provide more attention to the non-cognitive areas of development as a means of understanding identity development and working toward creating support systems for students.

Assessment of DNA damage and telomerase activity in exfoliated urinary cells as sensitive and noninvasive biomarkers for early diagnosis of bladder cancer in ex-workers of a rubber tyres industry.

PubMed

Cavallo, Delia; Casadio, Valentina; Bravaccini, Sara; Iavicoli, Sergio; Pira, Enrico; Romano, Canzio; Fresegna, Anna Maria; Maiello, Raffaele; Ciervo, Aureliano; Buresti, Giuliana; Zoli, Wainer; Calistri, Daniele

2014-01-01

The aim of the present study was to identify sensitive and noninvasive biomarkers of early carcinogenic effect at target organ to use in biomonitoring studies of workers at risk for previous occupational exposure to potential carcinogens. Standard urine cytology (Papanicolaou staining test), comet assay, and quantitative telomerase repeat amplification protocol (TRAP) assay were performed in 159 ex-rubber workers employed in tyres production and 97 unexposed subjects. In TRAP positive cases, a second level analysis using FISH (Urovysion) was done. Cystoscopy results were available for 11 individuals whose 6 FISH/TRAP/comet positive showed in 3 cases a dysplastic condition confirmed by biopsy, 1 comet positive resulted in infiltrating UBC to the biopsy and with hyperplasia and slight dysplasia to the urinary cytology, 1 comet positive resulted in papillary superficial UBC to the biopsy, 1 FISH/TRAP positive showed a normal condition, and 2 TRAP positive showed in one case a phlogosis condition. The results evidenced good concordance of TRAP, comet, and FISH assays as early biomarkers of procarcinogenic effect confirmed by the dysplastic condition and UBC found by cystoscopy-biopsy analysis. The analysis of these markers in urine cells could be potentially more accurate than conventional cytology in monitoring workers exposed to mixture of bladder potential carcinogens.

Computational analysis of Ebolavirus data: prospects, promises and challenges.

PubMed

Michaelis, Martin; Rossman, Jeremy S; Wass, Mark N

2016-08-15

The ongoing Ebola virus (also known as Zaire ebolavirus, a member of the Ebolavirus family) outbreak in West Africa has so far resulted in >28000 confirmed cases compared with previous Ebolavirus outbreaks that affected a maximum of a few hundred individuals. Hence, Ebolaviruses impose a much greater threat than we may have expected (or hoped). An improved understanding of the virus biology is essential to develop therapeutic and preventive measures and to be better prepared for future outbreaks by members of the Ebolavirus family. Computational investigations can complement wet laboratory research for biosafety level 4 pathogens such as Ebolaviruses for which the wet experimental capacities are limited due to a small number of appropriate containment laboratories. During the current West Africa outbreak, sequence data from many Ebola virus genomes became available providing a rich resource for computational analysis. Here, we consider the studies that have already reported on the computational analysis of these data. A range of properties have been investigated including Ebolavirus evolution and pathogenicity, prediction of micro RNAs and identification of Ebolavirus specific signatures. However, the accuracy of the results remains to be confirmed by wet laboratory experiments. Therefore, communication and exchange between computational and wet laboratory researchers is necessary to make maximum use of computational analyses and to iteratively improve these approaches. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Can we trust intraoperative culture results in nonunions?

PubMed

Palmer, Michael P; Altman, Daniel T; Altman, Gregory T; Sewecke, Jeffrey J; Ehrlich, Garth D; Hu, Fen Z; Nistico, Laura; Melton-Kreft, Rachel; Gause, Trent M; Costerton, John W

2014-07-01

To identify the presence of bacterial biofilms in nonunions comparing molecular techniques (multiplex polymerase chain reaction and mass spectrometry, fluorescent in situ hybridization) with routine intraoperative cultures. Thirty-four patients with nonunions were scheduled for surgery and enrolled in this ongoing prospective study. Intraoperative specimens were collected from removed implants, surrounding tissue membrane, and local soft tissue followed by standard culture analysis, Ibis's second generation molecular diagnostics (Ibis Biosystems), and bacterial 16S rRNA-based fluorescence in situ hybridization (FISH). Confocal microscopy was used to visualize the tissue specimens reacted with the FISH probes, which were chosen based on the Ibis analysis. Thirty-four patient encounters were analyzed. Eight were diagnosed as infected nonunions by positive intraoperative culture results. Ibis confirmed the presence of bacteria in all 8 samples. Ibis identified bacteria in a total of 30 of 34 encounters, and these data were confirmed by FISH. Twenty-two of 30 Ibis-positive samples were culture-negative. Four samples were negative by all methods of analysis. No samples were positive by culture, but negative by molecular techniques. Our preliminary data indicate that molecular diagnostics are more sensitive for identifying bacteria than cultures in cases of bony nonunion. This is likely because of the inability of cultures to detect biofilms and bacteria previously exposed to antibiotic therapy. Diagnostic Level I. See Instructions for Authors for a complete description of levels of evidence.

Identifying mutations in Tunisian families with retinal dystrophy.

PubMed

Habibi, Imen; Chebil, Ahmed; Falfoul, Yosra; Allaman-Pillet, Nathalie; Kort, Fedra; Schorderet, Daniel F; El Matri, Leila

2016-11-22

Retinal dystrophies (RD) are a rare genetic disorder with high genetic heterogeneity. This study aimed at identifying disease-causing variants in fifteen consanguineous Tunisian families. Full ophthalmic examination was performed. Index patients were subjected to IROme analysis or whole exome sequencing followed by homozygosity mapping. All detected variations were confirmed by direct Sanger sequencing. Mutation analysis in our patients revealed two compound heterozygous mutations p.(R91W);(V172D) in RPE65, and five novel homozygous mutations: p.R765C in CNGB1, p.H337R in PDE6B, splice site variant c.1129-2A > G and c.678_681delGAAG in FAM161A and c.1133 + 3_1133 + 6delAAGT in CERKL. The latter mutation impacts pre-mRNA splicing of CERKL. The other changes detected were six previously reported mutations in CNGB3 (p.R203*), ABCA4 (p.W782*), NR2E3 (p.R311Q), RPE65 (p.H182Y), PROM1 (c.1354dupT) and EYS (c.5928-2A > G). Segregation analysis in each family showed that all affected individuals were homozygotes and unaffected individuals were either heterozygote carriers or homozygous wild type allele. These results confirm the involvement of a large number of genes in RD in the Tunisian population.

Acidovorax valerianellae sp. nov., a novel pathogen of lamb's lettuce [Valerianella locusta (L.) Laterr].

PubMed

Gardan, Louis; Stead, David E; Dauga, Catherine; Gillis, Moniek

2003-05-01

Bacterial spot disease of lamb's lettuce [Valerianella locusta (L.) Laterr.] was first observed in fields in 1991. This new bacterial disease is localized in western France in high-technology field production of lamb's lettuce for the preparation of ready-to-use salad. Nineteen strains isolated in 1992 and 1993 from typical black leaf spots of naturally infected lamb's lettuce were characterized and compared with reference strains of Acidovorax and Delftia. The pathogenicity of the 19 strains was confirmed by artificial inoculation. Biochemical and physiological tests, fatty acid profiles, DNA-DNA hybridization and other nucleic acid-based tests were performed. A numerical taxonomic analysis of the 19 lamb's lettuce strains showed a single homogeneous phenon closely related to previously described phytopathogenic taxa of the genus Acidovorax. DNA-DNA hybridization studies showed that the lamb's lettuce strains were 91-100% related to a representative strain, strain CFBP 4730(T), and constituted a discrete DNA hybridization group, indicating that they belong to the same novel species. Results from DNA-rRNA hybridization, 16S rRNA sequence analysis and fatty acid analysis studies confirmed that this novel species belongs to the beta-subclass of the Proteobacteria and, more specifically, to the family Comamonadaceae and the genus Acidovorax. The name Acidovorax valerianellae sp. nov. is proposed for this novel taxon of phytopathogenic bacteria. The type strain is strain CFBP 4730(T) (= NCPPB 4283(T)).

Cannabinoid-like anti-inflammatory compounds from flax fiber.

PubMed

Styrczewska, Monika; Kulma, Anna; Ratajczak, Katarzyna; Amarowicz, Ryszard; Szopa, Jan

2012-09-01

Flax is a valuable source of fibers, linseed and oil. The compounds of the latter two products have already been widely examined and have been proven to possess many health-beneficial properties. In the course of analysis of fibers extract from previously generated transgenic plants overproducing phenylpropanoids a new terpenoid compound was discovered.The UV spectra and the retention time in UPLC analysis of this new compound reveal similarity to a cannabinoid-like compound, probably cannabidiol (CBD). This was confirmed by finding two ions at m/z 174.1 and 231.2 in mass spectra analysis. Further confirmation of the nature of the compound was based on a biological activity assay. It was found that the compound affects the expression of genes involved in inflammatory processes in mouse and human fibroblasts and likely the CBD from Cannabis sativa activates the specific peripheral cannabinoid receptor 2 (CB2) gene expression. Besides fibers, the compound was also found in all other flax tissues. It should be pointed out that the industrial process of fabric production does not affect CBD activity.The presented data suggest for the first time that flax products can be a source of biologically active cannabinoid-like compounds that are able to influence the cell immunological response. These findings might open up many new applications for medical flax products, especially for the fabric as a material for wound dressing with anti-inflammatory properties.

Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV).

PubMed

Snow, M; Bain, N; Black, J; Taupin, V; Cunningham, C O; King, J A; Skall, H F; Raynard, R S

2004-10-21

The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders this the most comprehensive molecular epidemiological study of marine VHSV conducted to date. Phylogenetic analysis of nucleoprotein gene sequences confirmed the existence of the 4 major genotypes previously identified based on N- and subsequent G-gene based analyses. The range of Genotype I included subgroups of isolates associated with rainbow trout aquaculture (Genotype Ia) and those from the Baltic marine environment (Genotype Ib) to emphasise the relatively close genetic relationship between these isolates. The existence of an additional genotype circulating within the Baltic Sea (Genotype II) was also confirmed. Genotype III included marine isolates from around the British Isles in addition to those associated with turbot mariculture, highlighting a continued risk to the development of this industry. Genotype IV consisted of isolates from the marine environment in North America. Taken together, these findings suggest a marine origin of VHSV in rainbow trout aquaculture. The implications of these findings with respect to the future control of VHSV are discussed. The capacity for molecular phylogenetic analysis to resolve complex epidemiological problems is also demonstrated and its likely future importance to disease management issues highlighted.

Transcriptome Analysis of Mycobacteria-Specific CD4+ T Cells Identified by Activation-Induced Expression of CD154.

PubMed

Kunnath-Velayudhan, Shajo; Goldberg, Michael F; Saini, Neeraj K; Johndrow, Christopher T; Ng, Tony W; Johnson, Alison J; Xu, Jiayong; Chan, John; Jacobs, William R; Porcelli, Steven A

2017-10-01

Analysis of Ag-specific CD4 + T cells in mycobacterial infections at the transcriptome level is informative but technically challenging. Although several methods exist for identifying Ag-specific T cells, including intracellular cytokine staining, cell surface cytokine-capture assays, and staining with peptide:MHC class II multimers, all of these have significant technical constraints that limit their usefulness. Measurement of activation-induced expression of CD154 has been reported to detect live Ag-specific CD4 + T cells, but this approach remains underexplored and, to our knowledge, has not previously been applied in mycobacteria-infected animals. In this article, we show that CD154 expression identifies adoptively transferred or endogenous Ag-specific CD4 + T cells induced by Mycobacterium bovis bacillus Calmette-Guérin vaccination. We confirmed that Ag-specific cytokine production was positively correlated with CD154 expression by CD4 + T cells from bacillus Calmette-Guérin-vaccinated mice and show that high-quality microarrays can be performed from RNA isolated from CD154 + cells purified by cell sorting. Analysis of microarray data demonstrated that the transcriptome of CD4 + CD154 + cells was distinct from that of CD154 - cells and showed major enrichment of transcripts encoding multiple cytokines and pathways of cellular activation. One notable finding was the identification of a previously unrecognized subset of mycobacteria-specific CD4 + T cells that is characterized by the production of IL-3. Our results support the use of CD154 expression as a practical and reliable method to isolate live Ag-specific CD4 + T cells for transcriptomic analysis and potentially for a range of other studies in infected or previously immunized hosts. Copyright © 2017 by The American Association of Immunologists, Inc.

Kindler syndrome in native Americans from Panama: report of 26 cases.

PubMed

Penagos, Homero; Jaen, Marta; Sancho, Mario T; Saborio, Manuel R; Fallas, Victor G; Siegel, Dawn H; Frieden, Ilona J

2004-08-01

To investigate the clinical, genetic, and laboratory features of 26 patients with Kindler syndrome. Case series of patients recruited when they were seen at outpatient consultations in the Department of Dermatology at the Changuinola Hospital in Bocas del Toro, Panama, between May 1986 and December 1990. Clinical history, physical examination, and laboratory studies were done at a community hospital in Panama. Twelve of the patients had further studies performed at a children's hospital in Costa Rica. A total of 26 patients were entered into the study. They were members of the Ngöbe-Buglé tribe and resided in isolated villages in rural Panama. The major findings were skin fragility with blistering (100%), poikiloderma (96%), photosensitivity (92%), severe cutaneous atrophy (89%), hyperkeratosis of the palms and soles (81%), congenital acral blisters (81%), severe periodontal disease (81%), and phimosis (80% of male subjects). In 1 large family with 10 patients, inheritance of Kindler syndrome followed that of an autosomal recessive disease. Karyotypes in 3 patients and 1 unaffected father were normal. Findings from ultrastructural studies showed replication of lamina densa in 10 patients. To our knowledge, this study represents the largest series to date of patients with Kindler syndrome. The clinical features confirm previously reported cases, and segregation analysis confirms its autosomal recessive inheritance. We also report severe phimosis as a complication, which has not been previously described in this syndrome.

Migratory Whooper Swans Cygnus cygnus Transmit H5N1 Virus between China and Mongolia: Combination Evidence from Satellite Tracking and Phylogenetics Analysis.

PubMed

Li, Shuhong; Meng, Weiyue; Liu, Dongping; Yang, Qiqi; Chen, Lixia; Dai, Qiang; Ma, Tian; Gao, Ruyi; Ru, Wendong; Li, Yunfeng; Yu, Pengbo; Lu, Jun; Zhang, Guogang; Tian, Huaiyu; Chai, Hongliang; Li, Yanbing

2018-05-04

In late 2014, a highly pathogenic avian influenza (hereafter HPAI) H5N1 outbreak infected whooper swans Cygnus cygnus wintering at the Sanmenxia Reservoir area, China, and raised concerns about migratory linkages between wintering and breeding grounds of whooper swans. In this study, 61 swans were satellite tracked from 2013 to 2016 to determine the spatial association of their migration routes and H5N1 outbreaks, and 3596 fecal samples were collected along the migration routes for virology testing. Swans departed the wintering grounds and migrated along the Yellow River, and flew over the Yin Mountains in China. The Brownian bridge movement model showed there was a high degree of spatiotemporal overlap between the core use area along the spring migration pathway and historical H5N1 events in China and Mongolia from 2005 to 2015. The H5N1 strain was isolated and phylogenetic analyses confirmed that the HA gene sequence generated is genetically similar to that of the epidemic strain at a previous wintering site (the Sanmenxia Reservoir area) along its flyway. Our results identified a previously unknown migratory link of whooper swans in central China with Mongolia and confirmed that the swans could carry the HPAI H5N1 virus during migration, resulting in long-distance transmission.

Correlation of ABO blood groups with spontaneous recanalization in acute myocardial infarction.

PubMed

Lin, Xian-Liang; Zhou, Bing-Yang; Li, Sha; Li, Xiao-Lin; Luo, Zhu-Rong; Li, Jian-Jun

2017-08-01

Although previous studies have demonstrated the relationship between ABO blood groups and cardiovascular disease, the association of ABO blood type with spontaneous recanalization (SR) in patients with acute myocardial infarction (AMI) has not been previously investigated. We performed an initial exploratory study on the association of ABO blood groups with the presence of SR in 1209 patients with AMI. They were divided into two groups according to the thrombolysis in myocardial infarction (TIMI) grades: no-SR group (TIMI 0-1, n = 442) and SR group (TIMI 2-3, n = 767). To confirm our primary findings, data from a second AMI population (n = 200) was analyzed. In the initial data, SR group had a significantly higher percentage of blood type O and a lower percentage of blood type A compared to the no-SR group. Multivariate logistic regression analysis showed that blood type O was positively associated with SR (odds ratio: 1.40, 95% confidence interval: 1.05-1.87, p = .02), and this finding was confirmed in our second population. The present study demonstrates that blood type O was independently and positively associated with an open culprit artery in patients with AMI, suggesting that the ABO blood type is not only associated with the susceptibility to coronary artery disease but also to spontaneous reperfusion in AMI patients.

Isolation and initial characterisation of complement components C3 and C4 of the nurse shark and the channel catfish.

PubMed

Dodds, A W; Smith, S L; Levine, R P; Willis, A C

1998-01-01

Complement components C3 and C4 have been isolated from the serum of the nurse shark (Ginglymostoma cirratum) and of the channel catfish (Ictalurus punctatus). As in the higher vertebrates, the fish C4 proteins have three-chain structures while the C3 proteins have two-chain structures. All four proteins have intra-chain thioesters located within their highest molecular mass polypeptides. N-terminal sequence analysis of the polypeptides has confirmed the identity of the proteins. In all cases except the catfish C3 alpha-chain, which appears to have a blocked N-terminus, sequence similarities are apparent in comparisons with the chains of C3 and C4 from higher vertebrates. We have confirmed that the activity/protein previously designated C2n is the nurse shark analogue of mammalian C4. This is the first report of structural evidence for C4 in both the bony and cartilaginous fish.

Primary iris leiomyoma.

PubMed

Yeaney, Gabrielle A; Platt, Sean; Singh, Arun D

Intraocular leiomyomas are uncommon and usually occur in the ciliary body. Primary leiomyoma of the iris is both rare and a difficult diagnosis to make, given melanocytic tumors are more common and may be amelanotic. The somewhat controversial diagnosis of iris leiomyoma requires further confirmation by immunohistochemistry and electron microscopy. Herein, we describe a 58-year-old man with a 2-mm round translucent pink lesion of the iris. The tumor was excised by sector iridectomy. Immunohistochemistry showed positivity for both smooth muscle actin and desmin and negativity for S-100, HMB45, SOX10, MelanA, CD31, CD34, and h-caldesmon. Epstein-Barr virus-associated smooth muscle tumor was excluded by chromogenic in situ hybridization-Epstein-Barr virus-encoded RNA. Ultrastructural analysis showed cytoplasmic myofilaments with focal fusiform densities and micropinocytotic vesicles. Our review of previous literature confirmed the unusual nature of this tumor. Primary iris leiomyoma should be considered in the differential of an amelanotic S-100-immunonegative iris tumor. Copyright © 2016 Elsevier Inc. All rights reserved.

An Automatic Quality Control Pipeline for High-Throughput Screening Hit Identification.

PubMed

Zhai, Yufeng; Chen, Kaisheng; Zhong, Yang; Zhou, Bin; Ainscow, Edward; Wu, Ying-Ta; Zhou, Yingyao

2016-09-01

The correction or removal of signal errors in high-throughput screening (HTS) data is critical to the identification of high-quality lead candidates. Although a number of strategies have been previously developed to correct systematic errors and to remove screening artifacts, they are not universally effective and still require fair amount of human intervention. We introduce a fully automated quality control (QC) pipeline that can correct generic interplate systematic errors and remove intraplate random artifacts. The new pipeline was first applied to ~100 large-scale historical HTS assays; in silico analysis showed auto-QC led to a noticeably stronger structure-activity relationship. The method was further tested in several independent HTS runs, where QC results were sampled for experimental validation. Significantly increased hit confirmation rates were obtained after the QC steps, confirming that the proposed method was effective in enriching true-positive hits. An implementation of the algorithm is available to the screening community. © 2016 Society for Laboratory Automation and Screening.

Alagille syndrome with deletion 20p12.2-p12.3 and hypoplastic left heart.

PubMed

Robert, Marie Leema P; Lopez, Tony; Crolla, John; Huang, Shuwen; Owen, Carol; Burvill-Holmes, Lisa; Stumper, Oliver; Turnpenny, Peter D

2007-10-01

We report a male patient born at 37-weeks gestation, weighing 1.885 kg (<0.4th centile). Shortly after birth, he was diagnosed with hypoplastic left heart syndrome for which he underwent a Norwood procedure. Subsequently, he developed problems with failure to thrive and developmental delay. At the age of 4 years his delay in growth and development led to further investigations, which revealed a small de-novo interstitial deletion of chromosome 20p12.2. JAGGED1 haploinsufficiency was confirmed by fluorescence in situ hybridization. Array-comparative genomic hybridization analysis confirmed and quantified an approximate 5.4 Mb interstitial deletion involving the chromosomal region 20p12.2-p12.3. This precise interstitial deletion has not been previously reported. Further clinical evaluation revealed posterior embryotoxon and butterfly vertebrae. He has normal liver function tests, facial features consistent with Alagille syndrome, and mild learning difficulties. To our knowledge this is the first report of Alagille syndrome associated with hypoplastic left heart syndrome.

Epidemiological, clinical and laboratory profile of scrub typhus cases detected by serology and RT-PCR in Kumaon, Uttarakhand: a hospital-based study.

PubMed

Rawat, Vinita; Singh, Rajesh Kumar; Kumar, Ashok; Saxena, Sandip R; Varshney, Umesh; Kumar, Mukesh

2018-04-01

We analysed the epidemiology, clinical and laboratory data of the 168 scrub typhus cases confirmed by a combination of any one of the following: real time polymerase chain reaction (RT-PCR) and/or immunofluorescence assay (IFA) (IgM and/or IgG). The peak season for scrub typhus was from July to October. By multivariate binary logistic regression analysis, the risk of scrub typhus was about four times in those working in occupation related to forest work. Major clinical manifestations were fever (100%), myalgia (65%), cough (51%) and vomiting (46%); major complications were meningitis/meningoencephatilitis (12.5%) and multi-organ failure (MOF) and pneumonia (5.3% each). Laboratory investigations revealed raised aminotranferase levels and thrombocytopenia in most confirmed cases. We conclude that scrub typhus is an important cause of febrile illness in the Kumaon hills of Uttarakhand where this disease had not previously been considered to exist.

Desulfuromonas thiophila sp. nov., a new obligately sulfur-reducing bacterium from anoxic freshwater sediment.

PubMed

Finster, K; Coates, J D; Liesack, W; Pfennig, N

1997-07-01

A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27T, was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27T is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27T belongs to the Desulfuromonas cluster in the recently proposed family "Geobacteracea" in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27T represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publication, is the name proposed for strain NZ27T in this paper.

Desulfuromonas thiophila sp. nov., a new obligately sulfur-reducing bacterium from anoxic freshwater sediment

USGS Publications Warehouse

Finster, K.; Coates, J.D.; Liesack, W.; Pfennig, N.

1997-01-01

A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27(T), was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27(T) is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27(T) belongs to the Desulfuromonas cluster in the recently proposed family 'Geobacteraceae' in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27(T) represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publications, is the name proposed for strain NZ27(T) in this paper.

Whole-genome analyses resolve early branches in the tree of life of modern birds

PubMed Central

Jarvis, Erich D.; Mirarab, Siavash; Aberer, Andre J.; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y. W.; Faircloth, Brant C.; Nabholz, Benoit; Howard, Jason T.; Suh, Alexander; Weber, Claudia C.; da Fonseca, Rute R.; Li, Jianwen; Zhang, Fang; Li, Hui; Zhou, Long; Narula, Nitish; Liu, Liang; Ganapathy, Ganesh; Boussau, Bastien; Bayzid, Md. Shamsuzzoha; Zavidovych, Volodymyr; Subramanian, Sankar; Gabaldón, Toni; Capella-Gutiérrez, Salvador; Huerta-Cepas, Jaime; Rekepalli, Bhanu; Munch, Kasper; Schierup, Mikkel; Lindow, Bent; Warren, Wesley C.; Ray, David; Green, Richard E.; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Li, Shengbin; Li, Ning; Huang, Yinhua; Derryberry, Elizabeth P.; Bertelsen, Mads Frost; Sheldon, Frederick H.; Brumfield, Robb T.; Mello, Claudio V.; Lovell, Peter V.; Wirthlin, Morgan; Schneider, Maria Paula Cruz; Prosdocimi, Francisco; Samaniego, José Alfredo; Velazquez, Amhed Missael Vargas; Alfaro-Núñez, Alonzo; Campos, Paula F.; Petersen, Bent; Sicheritz-Ponten, Thomas; Pas, An; Bailey, Tom; Scofield, Paul; Bunce, Michael; Lambert, David M.; Zhou, Qi; Perelman, Polina; Driskell, Amy C.; Shapiro, Beth; Xiong, Zijun; Zeng, Yongli; Liu, Shiping; Li, Zhenyu; Liu, Binghang; Wu, Kui; Xiao, Jin; Yinqi, Xiong; Zheng, Qiuemei; Zhang, Yong; Yang, Huanming; Wang, Jian; Smeds, Linnea; Rheindt, Frank E.; Braun, Michael; Fjeldsa, Jon; Orlando, Ludovic; Barker, F. Keith; Jønsson, Knud Andreas; Johnson, Warren; Koepfli, Klaus-Peter; O’Brien, Stephen; Haussler, David; Ryder, Oliver A.; Rahbek, Carsten; Willerslev, Eske; Graves, Gary R.; Glenn, Travis C.; McCormack, John; Burt, Dave; Ellegren, Hans; Alström, Per; Edwards, Scott V.; Stamatakis, Alexandros; Mindell, David P.; Cracraft, Joel; Braun, Edward L.; Warnow, Tandy; Jun, Wang; Gilbert, M. Thomas P.; Zhang, Guojie

2015-01-01

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago. PMID:25504713

Whole-genome analyses resolve early branches in the tree of life of modern birds.

PubMed

Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y W; Faircloth, Brant C; Nabholz, Benoit; Howard, Jason T; Suh, Alexander; Weber, Claudia C; da Fonseca, Rute R; Li, Jianwen; Zhang, Fang; Li, Hui; Zhou, Long; Narula, Nitish; Liu, Liang; Ganapathy, Ganesh; Boussau, Bastien; Bayzid, Md Shamsuzzoha; Zavidovych, Volodymyr; Subramanian, Sankar; Gabaldón, Toni; Capella-Gutiérrez, Salvador; Huerta-Cepas, Jaime; Rekepalli, Bhanu; Munch, Kasper; Schierup, Mikkel; Lindow, Bent; Warren, Wesley C; Ray, David; Green, Richard E; Bruford, Michael W; Zhan, Xiangjiang; Dixon, Andrew; Li, Shengbin; Li, Ning; Huang, Yinhua; Derryberry, Elizabeth P; Bertelsen, Mads Frost; Sheldon, Frederick H; Brumfield, Robb T; Mello, Claudio V; Lovell, Peter V; Wirthlin, Morgan; Schneider, Maria Paula Cruz; Prosdocimi, Francisco; Samaniego, José Alfredo; Vargas Velazquez, Amhed Missael; Alfaro-Núñez, Alonzo; Campos, Paula F; Petersen, Bent; Sicheritz-Ponten, Thomas; Pas, An; Bailey, Tom; Scofield, Paul; Bunce, Michael; Lambert, David M; Zhou, Qi; Perelman, Polina; Driskell, Amy C; Shapiro, Beth; Xiong, Zijun; Zeng, Yongli; Liu, Shiping; Li, Zhenyu; Liu, Binghang; Wu, Kui; Xiao, Jin; Yinqi, Xiong; Zheng, Qiuemei; Zhang, Yong; Yang, Huanming; Wang, Jian; Smeds, Linnea; Rheindt, Frank E; Braun, Michael; Fjeldsa, Jon; Orlando, Ludovic; Barker, F Keith; Jønsson, Knud Andreas; Johnson, Warren; Koepfli, Klaus-Peter; O'Brien, Stephen; Haussler, David; Ryder, Oliver A; Rahbek, Carsten; Willerslev, Eske; Graves, Gary R; Glenn, Travis C; McCormack, John; Burt, Dave; Ellegren, Hans; Alström, Per; Edwards, Scott V; Stamatakis, Alexandros; Mindell, David P; Cracraft, Joel; Braun, Edward L; Warnow, Tandy; Jun, Wang; Gilbert, M Thomas P; Zhang, Guojie

2014-12-12

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago. Copyright © 2014, American Association for the Advancement of Science.

Bacterial anoxygenic photosynthesis on plant leaf surfaces.

PubMed

Atamna-Ismaeel, Nof; Finkel, Omri; Glaser, Fabian; von Mering, Christian; Vorholt, Julia A; Koblížek, Michal; Belkin, Shimshon; Béjà, Oded

2012-04-01

The aerial surface of plants, the phyllosphere, is colonized by numerous bacteria displaying diverse metabolic properties that enable their survival in this specific habitat. Recently, we reported on the presence of microbial rhodopsin harbouring bacteria on the top of leaf surfaces. Here, we report on the presence of additional bacterial populations capable of harvesting light as a means of supplementing their metabolic requirements. An analysis of six phyllosphere metagenomes revealed the presence of a diverse community of anoxygenic phototrophic bacteria, including the previously reported methylobacteria, as well as other known and unknown phototrophs. The presence of anoxygenic phototrophic bacteria was also confirmed in situ by infrared epifluorescence microscopy. The microscopic enumeration correlated with estimates based on metagenomic analyses, confirming both the presence and high abundance of these microorganisms in the phyllosphere. Our data suggest that the phyllosphere contains a phylogenetically diverse assemblage of phototrophic species, including some yet undescribed bacterial clades that appear to be phyllosphere-unique. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

A Novel Vaccine against Crimean-Congo Haemorrhagic Fever Protects 100% of Animals against Lethal Challenge in a Mouse Model

PubMed Central

Buttigieg, Karen R.; Dowall, Stuart D.; Findlay-Wilson, Stephen; Miloszewska, Aleksandra; Rayner, Emma; Hewson, Roger; Carroll, Miles W.

2014-01-01

Crimean-Congo Haemorrhagic Fever (CCHF) is a severe tick-borne disease, endemic in many countries in Africa, the Middle East, Eastern Europe and Asia. Between 15–70% of reported cases are fatal. There is no approved vaccine available, and preclinical protection in vivo by an experimental vaccine has not been demonstrated previously. In the present study, the attenuated poxvirus vector, Modified Vaccinia virus Ankara, was used to develop a recombinant candidate vaccine expressing the CCHF virus glycoproteins. Cellular and humoral immunogenicity was confirmed in two mouse strains, including type I interferon receptor knockout mice, which are susceptible to CCHF disease. This vaccine protected all recipient animals from lethal disease in a challenge model adapted to represent infection via a tick bite. Histopathology and viral load analysis of protected animals confirmed that they had been exposed to challenge virus, even though they did not exhibit clinical signs. This is the first demonstration of efficacy of a CCHF vaccine. PMID:24621656

A novel vaccine against Crimean-Congo Haemorrhagic Fever protects 100% of animals against lethal challenge in a mouse model.

PubMed

Buttigieg, Karen R; Dowall, Stuart D; Findlay-Wilson, Stephen; Miloszewska, Aleksandra; Rayner, Emma; Hewson, Roger; Carroll, Miles W

2014-01-01

Crimean-Congo Haemorrhagic Fever (CCHF) is a severe tick-borne disease, endemic in many countries in Africa, the Middle East, Eastern Europe and Asia. Between 15-70% of reported cases are fatal. There is no approved vaccine available, and preclinical protection in vivo by an experimental vaccine has not been demonstrated previously. In the present study, the attenuated poxvirus vector, Modified Vaccinia virus Ankara, was used to develop a recombinant candidate vaccine expressing the CCHF virus glycoproteins. Cellular and humoral immunogenicity was confirmed in two mouse strains, including type I interferon receptor knockout mice, which are susceptible to CCHF disease. This vaccine protected all recipient animals from lethal disease in a challenge model adapted to represent infection via a tick bite. Histopathology and viral load analysis of protected animals confirmed that they had been exposed to challenge virus, even though they did not exhibit clinical signs. This is the first demonstration of efficacy of a CCHF vaccine.

Er Effect of Low Molecular Liquid Crystal on One-Sided Patterned Electrodes

NASA Astrophysics Data System (ADS)

Kikuchi, Takehito; Inoue, Akio; Furusho, Junji; Kawamuki, Ryohei

Several kinds of ER fluids (ERF) have been developed and have been applied to some mechatronics devices and processing technologies. In many conventional applications of ERFs, these devices consist of bilateral electrodes to apply electric field in ERF. However, the electric field of several kV/mm may be necessary to generate an ER effect sufficiently for practical purposes. The gap between a pair of electrodes should be, therefore, maintained narrowly and exactly for fears of short-circuit. At the same time, this electrode system also requires an interconnection on driving parts. To improve these disadvantages, we proposed "one-sided patterned electrode" (OSPE) systems in previous works. In this report, we confirmed the flow characteristics of low molecular liquid crystal (LMLC) on OSPE. Next, we also confirmed the different characteristics depending on the pattern type. Depending on results of electro-static analysis, we conclude that such a difference may results from the directors of LC molecules derived by electric field.

Ataxia telangiectasia presenting as dopa-responsive cervical dystonia

PubMed Central

Mohire, Mahavir D.; Schneider, Susanne A.; Stamelou, Maria; Wood, Nicholas W.; Bhatia, Kailash P.

2013-01-01

Objective: To identify the cause of cervical dopa-responsive dystonia (DRD) in a Muslim Indian family inherited in an apparently autosomal recessive fashion, as previously described in this journal. Methods: Previous testing for mutations in the genes known to cause DRD (GCH1, TH, and SPR) had been negative. Whole exome sequencing was performed on all 3 affected individuals for whom DNA was available to identify potentially pathogenic shared variants. Genotyping data obtained for all 3 affected individuals using the OmniExpress single nucleotide polymorphism chip (Illumina, San Diego, CA) were used to perform linkage analysis, autozygosity mapping, and copy number variation analysis. Sanger sequencing was used to confirm all variants. Results: After filtering of the variants, exome sequencing revealed 2 genes harboring potentially pathogenic compound heterozygous variants (ATM and LRRC16A). Of these, the variants in ATM segregated perfectly with the cervical DRD. Both mutations detected in ATM have been shown to be pathogenic, and α-fetoprotein, a marker of ataxia telangiectasia, was increased in all affected individuals. Conclusion: Biallelic mutations in ATM can cause DRD, and mutations in this gene should be considered in the differential diagnosis of unexplained DRD, particularly if the dystonia is cervical and if there is a recessive family history. ATM has previously been reported to cause isolated cervical dystonia, but never, to our knowledge, DRD. Individuals with dystonia related to ataxia telangiectasia may benefit from a trial of levodopa. PMID:23946315

Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs

PubMed Central

Oduru, Sreedhar; Campbell, Janee L; Karri, SriTulasi; Hendry, William J; Khan, Shafiq A; Williams, Simon C

2003-01-01

Background Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes. We have utilized a comparative genomics approach involving the sequencing of randomly selected hamster testis cDNAs to begin to identify genes not previously annotated on the human, mouse, rat and Fugu (pufferfish) genomes. Results 735 distinct sequences were analyzed for their relatedness to known sequences in public databases. Eight of these sequences were derived from previously unidentified genes and expression of these genes in testis was confirmed by Northern blotting. The genomic locations of each sequence were mapped in human, mouse, rat and pufferfish, where applicable, and the structure of their cognate genes was derived using computer-based predictions, genomic comparisons and analysis of uncharacterized cDNA sequences from human and macaque. Conclusion The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome. The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted. Each gene was expressed primarily in testis, suggesting that they may play roles in the development and/or function of testicular cells. PMID:12783626

MMASS: an optimized array-based method for assessing CpG island methylation.

PubMed

Ibrahim, Ashraf E K; Thorne, Natalie P; Baird, Katie; Barbosa-Morais, Nuno L; Tavaré, Simon; Collins, V Peter; Wyllie, Andrew H; Arends, Mark J; Brenton, James D

2006-01-01

We describe an optimized microarray method for identifying genome-wide CpG island methylation called microarray-based methylation assessment of single samples (MMASS) which directly compares methylated to unmethylated sequences within a single sample. To improve previous methods we used bioinformatic analysis to predict an optimized combination of methylation-sensitive enzymes that had the highest utility for CpG-island probes and different methods to produce unmethylated representations of test DNA for more sensitive detection of differential methylation by hybridization. Subtraction or methylation-dependent digestion with McrBC was used with optimized (MMASS-v2) or previously described (MMASS-v1, MMASS-sub) methylation-sensitive enzyme combinations and compared with a published McrBC method. Comparison was performed using DNA from the cell line HCT116. We show that the distribution of methylation microarray data is inherently skewed and requires exogenous spiked controls for normalization and that analysis of digestion of methylated and unmethylated control sequences together with linear fit models of replicate data showed superior statistical power for the MMASS-v2 method. Comparison with previous methylation data for HCT116 and validation of CpG islands from PXMP4, SFRP2, DCC, RARB and TSEN2 confirmed the accuracy of MMASS-v2 results. The MMASS-v2 method offers improved sensitivity and statistical power for high-throughput microarray identification of differential methylation.

Clinical presentation of acute coronary syndrome in patients previously treated with nitrates.

PubMed

Latour-Pérez, Jaime; Gómez-Tello, Vicente; Fuset-Cabanes, María Paz; Balsa, Eva de Miguel; Sáez, Frutos Del Nogal; Orts, Francisco Javier Coves; Rodríguez, Carmen Martín; Pino-Izquierdo, Karel; Pesquera, María de la Concepción Pavía; Rodríguez, Antonio José Montón

2013-11-01

Several reports have suggested that nitrates limit acute ischaemic damage by a mechanism similar to preconditioning. This study aims to evaluate the effect of chronic oral nitrates on the clinical presentation and short-term outcomes of patients admitted with acute coronary syndrome (ACS). A retrospective cohort study was conducted in patients with ACS admitted to 62 acute care units from 2010 to 2011. A propensity score-matched samples analysis was performed. We analysed 3171 consecutive patients, of whom 298 (9.4%) were chronically treated with nitrates. Patients previously treated with nitrates had higher comorbidity and disease severity at admission, lower prevalence of ACS with ST elevation, lower troponin elevation, higher prevalence of initial Killip class 2-4 and higher hospital mortality. The propensity score-matched analysis confirmed that previous use of nitrates is independently associated with a lower prevalence of ST-elevation ACS [odds ratio (OR) 0.53, 95% confidence interval (CI) 0.36-0.78; P = 0.0014] and a lower troponin elevation (OR 0.61, 95% CI 0.41-0.92) but not with Killip class on admission (OR 1.18, 95% CI 0.83-1.67, P = 0.3697) or mortality (OR 0.71, 95% CI 0.37-1.38, P = 0.3196). The results support the hypothesis that nitrates have a protective effect on acute ischaemic injury.

Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach.

PubMed

Algama, Manjula; Tasker, Edward; Williams, Caitlin; Parslow, Adam C; Bryson-Richardson, Robert J; Keith, Jonathan M

2017-03-27

Computational identification of non-coding RNAs (ncRNAs) is a challenging problem. We describe a genome-wide analysis using Bayesian segmentation to identify intronic elements highly conserved between three evolutionarily distant vertebrate species: human, mouse and zebrafish. We investigate the extent to which these elements include ncRNAs (or conserved domains of ncRNAs) and regulatory sequences. We identified 655 deeply conserved intronic sequences in a genome-wide analysis. We also performed a pathway-focussed analysis on genes involved in muscle development, detecting 27 intronic elements, of which 22 were not detected in the genome-wide analysis. At least 87% of the genome-wide and 70% of the pathway-focussed elements have existing annotations indicative of conserved RNA secondary structure. The expression of 26 of the pathway-focused elements was examined using RT-PCR, providing confirmation that they include expressed ncRNAs. Consistent with previous studies, these elements are significantly over-represented in the introns of transcription factors. This study demonstrates a novel, highly effective, Bayesian approach to identifying conserved non-coding sequences. Our results complement previous findings that these sequences are enriched in transcription factors. However, in contrast to previous studies which suggest the majority of conserved sequences are regulatory factor binding sites, the majority of conserved sequences identified using our approach contain evidence of conserved RNA secondary structures, and our laboratory results suggest most are expressed. Functional roles at DNA and RNA levels are not mutually exclusive, and many of our elements possess evidence of both. Moreover, ncRNAs play roles in transcriptional and post-transcriptional regulation, and this may contribute to the over-representation of these elements in introns of transcription factors. We attribute the higher sensitivity of the pathway-focussed analysis compared to the genome-wide analysis to improved alignment quality, suggesting that enhanced genomic alignments may reveal many more conserved intronic sequences.

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains.

PubMed

Miller, Martin L; Reznik, Ed; Gauthier, Nicholas P; Aksoy, Bülent Arman; Korkut, Anil; Gao, Jianjiong; Ciriello, Giovanni; Schultz, Nikolaus; Sander, Chris

2015-09-23

In cancer genomics, recurrence of mutations in independent tumor samples is a strong indicator of functional impact. However, rare functional mutations can escape detection by recurrence analysis owing to lack of statistical power. We enhance statistical power by extending the notion of recurrence of mutations from single genes to gene families that share homologous protein domains. Domain mutation analysis also sharpens the functional interpretation of the impact of mutations, as domains more succinctly embody function than entire genes. By mapping mutations in 22 different tumor types to equivalent positions in multiple sequence alignments of domains, we confirm well-known functional mutation hotspots, identify uncharacterized rare variants in one gene that are equivalent to well-characterized mutations in another gene, detect previously unknown mutation hotspots, and provide hypotheses about molecular mechanisms and downstream effects of domain mutations. With the rapid expansion of cancer genomics projects, protein domain hotspot analysis will likely provide many more leads linking mutations in proteins to the cancer phenotype. Copyright © 2015 Elsevier Inc. All rights reserved.

Identification of Potential Anticancer Activities of Novel Ganoderma lucidum Extracts Using Gene Expression and Pathway Network Analysis

PubMed Central

Kao, Chi H.J.; Bishop, Karen S.; Xu, Yuanye; Han, Dug Yeo; Murray, Pamela M.; Marlow, Gareth J.; Ferguson, Lynnette R.

2016-01-01

Ganoderma lucidum (lingzhi) has been used for the general promotion of health in Asia for many centuries. The common method of consumption is to boil lingzhi in water and then drink the liquid. In this study, we examined the potential anticancer activities of G. lucidum submerged in two commonly consumed forms of alcohol in East Asia: malt whiskey and rice wine. The anticancer effect of G. lucidum, using whiskey and rice wine-based extraction methods, has not been previously reported. The growth inhibition of G. lucidum whiskey and rice wine extracts on the prostate cancer cell lines, PC3 and DU145, was determined. Using Affymetrix gene expression assays, several biologically active pathways associated with the anticancer activities of G. lucidum extracts were identified. Using gene expression analysis (real-time polymerase chain reaction [RT-PCR]) and protein analysis (Western blotting), we confirmed the expression of key genes and their associated proteins that were initially identified with Affymetrix gene expression analysis. PMID:27006591

Molecular characterization and phylogenetic study of African swine fever virus isolates from recent outbreaks in Uganda (2010–2013)

PubMed Central

2013-01-01

Background African swine fever (ASF) is a highly lethal and economically significant disease of domestic pigs in Eastern Africa particularly in Uganda where outbreaks regularly occur. Sequence analysis of variable genome regions have been extensively used for molecular epidemiological studies of African swine fever virus (ASFV) isolates. By combining p72, P54 and pB602L (CVR), a high level resolution approach is achieved for viral discrimination. The major aim of this study therefore, was to investigate the genetic relatedness of ASF outbreaks that occurred between 2010 and 2013 in Uganda to contribute to the clarification of the epidemiological situation over a four year period. Methods Tissue samples from infected domestic pigs associated with an ASF outbreak from 15 districts in Uganda were confirmed as being infected with ASFV using a p72 gene-based polymerase chain reaction amplification (PCR) assay recommended by OIE. The analysis was conducted by genotyping based on sequence data from three single copy ASFV genes. The E183L gene encoding the structural protein P54 and part of the gene encoding the p72 protein was used to delineate genotypes. Intra-genotypic resolution of viral relationships was achieved by analysis of tetramer amino acid repeats within the hypervariable CVR of the B602L gene. Results Twenty one (21) ASF outbreaks were confirmed by the p72 ASF diagnostic PCR, however; only 17 isolates were successfully aligned after sequencing. Our entire isolates cluster with previous ASF viruses in genotype IX isolated in Uganda and Kenya using p72 and P54 genes. Analysis of the CVR gene generated three sub-groups one with 23 tetrameric amino acid repeats (TRS) with an additional CAST sequence, the second with 22 TRS while one isolate Ug13. Kampala1 had 13 TRS. Conclusion We identified two new CVR subgroups different from previous studies. This study constitutes the first detailed assessment of the molecular epidemiology of ASFV in domestic pigs in the different regions of Uganda. PMID:23914918

Occupational Decision-Related Processes for Amotivated Adolescents: Confirmation of a Model

ERIC Educational Resources Information Center

Jung, Jae Yup; McCormick, John

2011-01-01

This study developed and (statistically) confirmed a new model of the occupational decision-related processes of adolescents, in terms of the extent to which they may be amotivated about choosing a future occupation. A theoretical framework guided the study. A questionnaire that had previously been administered to an Australian adolescent sample…

Unequivocal Identification of 1-Phenylethyl Acetate in Clove Buds (syzygium aromaticum (L.) Merr. & L.M.Perry) and Clove Essential Oil

PubMed Central

Gassenmeier, Klaus; Schwager, Hugo; Houben, Eric; Clery, Robin

2017-01-01

The natural occurrence of 1-phenylethyl acetate (styrallyl acetate) was confirmed in commercially available dried clove buds and also in the hydrodistilled oil from clove buds. This confirms previous reports and other anecdotal evidence for its occurrence in nature. PMID:28653988

Association analysis of nine candidate gene polymorphisms in Indian patients with type 2 diabetic retinopathy.

PubMed

Balasubbu, Suganthalakshmi; Sundaresan, Periasamy; Rajendran, Anand; Ramasamy, Kim; Govindarajan, Gowthaman; Perumalsamy, Namperumalsamy; Hejtmancik, J Fielding

2010-11-10

Diabetic retinopathy (DR) is classically defined as a microvasculopathy that primarily affects the small blood vessels of the inner retina as a complication of diabetes mellitus (DM).It is a multifactorial disease with a strong genetic component. The aim of this study is to investigate the association of a set of nine candidate genes with the development of diabetic retinopathy in a South Indian cohort who have type 2 diabetes mellitus (T2DM). Seven candidate genes (RAGE, PEDF, AKR1B1, EPO, HTRA1, ICAM and HFE) were chosen based on reported association with DR in the literature. Two more, CFH and ARMS2, were chosen based on their roles in biological pathways previously implicated in DR. Fourteen single nucleotide polymorphisms (SNPs) and one dinucleotide repeat polymorphism, previously reported to show association with DR or other related diseases, were genotyped in 345 DR and 356 diabetic patients without retinopathy (DNR). The genes which showed positive association in this screening set were tested further in additional sets of 100 DR and 90 DNR additional patients from the Aravind Eye Hospital. Those which showed association in the secondary screen were subjected to a combined analysis with the 100 DR and 100 DNR subjects previously recruited and genotyped through the Sankara Nethralaya Hospital, India. Genotypes were evaluated using a combination of direct sequencing, TaqMan SNP genotyping, RFLP analysis, and SNaPshot PCR assays. Chi-square and Fisher exact tests were used to analyze the genotype and allele frequencies. Among the nine loci (15 polymorphisms) screened, SNP rs2070600 (G82S) in the RAGE gene, showed significant association with DR (allelic P = 0.016, dominant model P = 0.012), compared to DNR. SNP rs2070600 further showed significant association with DR in the confirmation cohort (P = 0.035, dominant model P = 0.032). Combining the two cohorts gave an allelic P < 0.003 and dominant P = 0.0013). Combined analysis with the Sankara Nethralaya cohort gave an allelic P = 0.0003 and dominant P = 0.00011 with an OR = 0.49 (0.34 - 0.70) for the minor allele. In HTRA1, rs11200638 (G>A), showed marginal significance with DR (P = 0.055) while rs10490924 in LOC387715 gave a P = 0.07. No statistical significance was observed for SNPs in the other 7 genes studied. This study confirms significant association of one polymorphism only (rs2070600 in RAGE) with DR in an Indian population which had T2DM.

Loci influencing blood pressure identified using a cardiovascular gene-centric array.

PubMed

Ganesh, Santhi K; Tragante, Vinicius; Guo, Wei; Guo, Yiran; Lanktree, Matthew B; Smith, Erin N; Johnson, Toby; Castillo, Berta Almoguera; Barnard, John; Baumert, Jens; Chang, Yen-Pei Christy; Elbers, Clara C; Farrall, Martin; Fischer, Mary E; Franceschini, Nora; Gaunt, Tom R; Gho, Johannes M I H; Gieger, Christian; Gong, Yan; Isaacs, Aaron; Kleber, Marcus E; Mateo Leach, Irene; McDonough, Caitrin W; Meijs, Matthijs F L; Mellander, Olle; Molony, Cliona M; Nolte, Ilja M; Padmanabhan, Sandosh; Price, Tom S; Rajagopalan, Ramakrishnan; Shaffer, Jonathan; Shah, Sonia; Shen, Haiqing; Soranzo, Nicole; van der Most, Peter J; Van Iperen, Erik P A; Van Setten, Jessica; Van Setten, Jessic A; Vonk, Judith M; Zhang, Li; Beitelshees, Amber L; Berenson, Gerald S; Bhatt, Deepak L; Boer, Jolanda M A; Boerwinkle, Eric; Burkley, Ben; Burt, Amber; Chakravarti, Aravinda; Chen, Wei; Cooper-Dehoff, Rhonda M; Curtis, Sean P; Dreisbach, Albert; Duggan, David; Ehret, Georg B; Fabsitz, Richard R; Fornage, Myriam; Fox, Ervin; Furlong, Clement E; Gansevoort, Ron T; Hofker, Marten H; Hovingh, G Kees; Kirkland, Susan A; Kottke-Marchant, Kandice; Kutlar, Abdullah; Lacroix, Andrea Z; Langaee, Taimour Y; Li, Yun R; Lin, Honghuang; Liu, Kiang; Maiwald, Steffi; Malik, Rainer; Murugesan, Gurunathan; Newton-Cheh, Christopher; O'Connell, Jeffery R; Onland-Moret, N Charlotte; Ouwehand, Willem H; Palmas, Walter; Penninx, Brenda W; Pepine, Carl J; Pettinger, Mary; Polak, Joseph F; Ramachandran, Vasan S; Ranchalis, Jane; Redline, Susan; Ridker, Paul M; Rose, Lynda M; Scharnag, Hubert; Schork, Nicholas J; Shimbo, Daichi; Shuldiner, Alan R; Srinivasan, Sathanur R; Stolk, Ronald P; Taylor, Herman A; Thorand, Barbara; Trip, Mieke D; van Duijn, Cornelia M; Verschuren, W Monique; Wijmenga, Cisca; Winkelmann, Bernhard R; Wyatt, Sharon; Young, J Hunter; Boehm, Bernhard O; Caulfield, Mark J; Chasman, Daniel I; Davidson, Karina W; Doevendans, Pieter A; Fitzgerald, Garret A; Gums, John G; Hakonarson, Hakon; Hillege, Hans L; Illig, Thomas; Jarvik, Gail P; Johnson, Julie A; Kastelein, John J P; Koenig, Wolfgang; März, Winfried; Mitchell, Braxton D; Murray, Sarah S; Oldehinkel, Albertine J; Rader, Daniel J; Reilly, Muredach P; Reiner, Alex P; Schadt, Eric E; Silverstein, Roy L; Snieder, Harold; Stanton, Alice V; Uitterlinden, André G; van der Harst, Pim; van der Schouw, Yvonne T; Samani, Nilesh J; Johnson, Andrew D; Munroe, Patricia B; de Bakker, Paul I W; Zhu, Xiaofeng; Levy, Daniel; Keating, Brendan J; Asselbergs, Folkert W

2013-04-15

Blood pressure (BP) is a heritable determinant of risk for cardiovascular disease (CVD). To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP) and pulse pressure (PP), we genotyped ∼50 000 single-nucleotide polymorphisms (SNPs) that capture variation in ∼2100 candidate genes for cardiovascular phenotypes in 61 619 individuals of European ancestry from cohort studies in the USA and Europe. We identified novel associations between rs347591 and SBP (chromosome 3p25.3, in an intron of HRH1) and between rs2169137 and DBP (chromosome1q32.1 in an intron of MDM4) and between rs2014408 and SBP (chromosome 11p15 in an intron of SOX6), previously reported to be associated with MAP. We also confirmed 10 previously known loci associated with SBP, DBP, MAP or PP (ADRB1, ATP2B1, SH2B3/ATXN2, CSK, CYP17A1, FURIN, HFE, LSP1, MTHFR, SOX6) at array-wide significance (P < 2.4 × 10(-6)). We then replicated these associations in an independent set of 65 886 individuals of European ancestry. The findings from expression QTL (eQTL) analysis showed associations of SNPs in the MDM4 region with MDM4 expression. We did not find any evidence of association of the two novel SNPs in MDM4 and HRH1 with sequelae of high BP including coronary artery disease (CAD), left ventricular hypertrophy (LVH) or stroke. In summary, we identified two novel loci associated with BP and confirmed multiple previously reported associations. Our findings extend our understanding of genes involved in BP regulation, some of which may eventually provide new targets for therapeutic intervention.

Genome-wide association analysis and replication of coronary artery disease in South Korea suggests a causal variant common to diverse populations

PubMed Central

Cho, Eun Young; Jang, Yangsoo; Shin, Eun Soon; Jang, Hye Yoon; Yoo, Yeon-Kyeong; Kim, Sook; Jang, Ji Hyun; Lee, Ji Yeon; Yun, Min Hye; Park, Min Young; Chae, Jey Sook; Lim, Jin Woo; Shin, Dong Jik; Park, Sungha; Lee, Jong Ho; Han, Bok Ghee; Rae, Kim Hyung; Cardon, Lon R; Morris, Andrew P; Lee, Jong Eun; Clarke, Geraldine M

2010-01-01

Background Recent genome-wide association (GWA) studies have identified and replicated several genetic loci associated with the risk of development of coronary artery disease (CAD) in samples from populations of Caucasian and Asian descent. However, only chromosome 9p21 has been confirmed as a major susceptibility locus conferring risk for development of CAD across multiple ethnic groups. The authors aimed to find evidence of further similarities and differences in genetic risk of CAD between Korean and other populations. Methods The authors performed a GWA study comprising 230 cases and 290 controls from a Korean population typed on 490 032 single nucleotide polymorphisms (SNPs). A total of 3148 SNPs were taken forward for genotyping in a subsequent replication study using an independent sample of 1172 cases and 1087 controls from the same population. Results The association previously observed on chromosome 9p21 was independently replicated (p=3.08e–07). Within this region, the same risk haplotype was observed in samples from both Korea and of Western European descent, suggesting that the causal mutation carried on this background occurred on a single ancestral allele. Other than 9p21, the authors were unable to replicate any of the previously reported signals for association with CAD. Furthermore, no evidence of association was found at chromosome 1q41 for risk of myocardial infarction, previously identified as conferring risk in a Japanese population. Conclusion A common causal variant is likely to be responsible for risk of CAD in Korean and Western European populations at chromosome 9p21.3. Further investigations are required to confirm non-replication of any other cross-race genetic risk factors. PMID:27325954

Early Miocene hippopotamids (Cetartiodactyla) constrain the phylogenetic and spatiotemporal settings of hippopotamid origin

PubMed Central

Orliac, Maeva; Boisserie, Jean-Renaud; MacLatchy, Laura; Lihoreau, Fabrice

2010-01-01

The affinities of the Hippopotamidae are at the core of the phylogeny of Cetartiodactyla (even-toed mammals: cetaceans, ruminants, camels, suoids, and hippos). Molecular phylogenies support Cetacea as sister group of the Hippopotamidae, implying a long ghost lineage between the earliest cetaceans (∼53 Ma) and the earliest hippopotamids (∼16 Ma). Morphological studies have proposed two different sister taxa for hippopotamids: suoids (notably palaeochoerids) or anthracotheriids. Evaluating these phylogenetic hypotheses requires substantiating the poorly known early history of the Hippopotamidae. Here, we undertake an original morphological phylogenetic analysis including several “suiform” families and previously unexamined early Miocene taxa to test previous conflicting hypotheses. According to our results, Morotochoerus ugandensis and Kulutherium rusingensis, until now regarded as the sole African palaeochoerid and the sole African bunodont anthracotheriid, respectively, are unambiguously included within the Hippopotamidae. They are the earliest known hippopotamids and set the family fossil record back to the early Miocene (∼21 Ma). The analysis reveals that hippopotamids displayed an unsuspected taxonomic and body size diversity and remained restricted to Africa during most of their history, until the latest Miocene. Our results also confirm the deep nesting of Hippopotamidae within the paraphyletic Anthracotheriidae; this finding allows us to reconstruct the sequence of dental innovations that links advanced selenodont anthracotheriids to hippopotamids, previously a source of major disagreements on hippopotamid origins. The analysis demonstrates a close relationship between Eocene choeropotamids and anthracotheriids, a relationship that potentially fills the evolutionary gap between earliest hippopotamids and cetaceans implied by molecular analyses. PMID:20547829

Biology is more theoretical than physics.

PubMed

Gunawardena, Jeremy

2013-06-01

The word "theory" is used in at least two senses--to denote a body of widely accepted laws or principles, as in "Darwinian theory" or "quantum theory," and to suggest a speculative hypothesis, often relying on mathematical analysis, that has not been experimentally confirmed. It is often said that there is no place for the second kind of theory in biology and that biology is not theoretical but based on interpretation of data. Here, ideas from a previous essay are expanded upon to suggest, to the contrary, that the second kind of theory has always played a critical role and that biology, therefore, is a good deal more theoretical than physics.

From the Field: Carbofuran detected on weathered raptor carcass feet

USGS Publications Warehouse

Vyas, N.B.; Spann, J.W.; Hulse, C.S.; Bauer, W.; Olson, S.

2005-01-01

The cause of death for raptors poisoned at illegal carbofuran-Iaced predator baits is often not confirmed because the carcass matrices that are conventionally analyzed are not available due to decomposition and scavenging. However, many such carcasses retain intact feet that may have come into contact with carbofuran. Eastern screech owls (Otus asio) were exposed to carbofuran via simulated predator baits. Detection of carbofuran from owl feet weathered for 28 days demonstrated the temporal reliability of using feet during a forensic investigation. Raptor carcasses previously not submitted for residue analysis because of a lack of the conventional matrices may now be salvaged for their feet.

Comment on high resolution simulations of cosmic strings. 1: Network evoloution

NASA Technical Reports Server (NTRS)

Turok, Neil; Albrecht, Andreas

1990-01-01

Comments are made on recent claims (Albrecht and Turok, 1989) regarding simulations of cosmic string evolution. Specially, it was claimed that results were dominated by a numerical artifact which rounds out kinks on a scale of the order of the correlation length on the network. This claim was based on an approximate analysis of an interpolation equation which is solved herein. The typical rounding scale is actually less than one fifth of the correlation length, and comparable with other numerical cutoffs. Results confirm previous estimates of numerical uncertainties, and show that the approximations poorly represent the real solutions to the interpolation equation.

The use of fatty acid methyl esters as biomarkers to determine aerobic, facultatively aerobic and anaerobic communities in wastewater treatment systems.

PubMed

Quezada, Maribel; Buitrón, Germán; Moreno-Andrade, Iván; Moreno, Gloria; López-Marín, Luz M

2007-01-01

The use of fatty acid methyl esters (FAME) as biomarkers to identify groups of microorganisms was studied. A database was constructed using previously published results that identify FAME biomarkers for aerobic, anaerobic and facultatively aerobic bacteria. FAME profiles obtained from pure cultures were utilized to confirm the predicted presence of biomarkers. Principal component analysis demonstrated that the FAME profiles can be used to determine the incidence of these bacterial groups. The presence of aerobic, anaerobic and facultatively aerobic bacteria in the communities, in four bioreactors being used to treat different wastewaters, was investigated by applying FAME biomarkers.

Identification of Point Mutations in Clinical Staphylococcus aureus Strains That Produce Small-Colony Variants Auxotrophic for Menadione

PubMed Central

Dean, Melissa A.; Olsen, Randall J.; Long, S. Wesley; Rosato, Adriana E.

2014-01-01

Staphylococcus aureus small-colony variants (SCVs) are implicated in chronic and relapsing infections that are difficult to diagnose and treat. Despite many years of study, the underlying molecular mechanisms and virulence effect of the small-colony phenotype remain incompletely understood. We sequenced the genomes of five S. aureus SCV strains recovered from human patients and discovered previously unidentified nonsynonymous point mutations in three genes encoding proteins in the menadione biosynthesis pathway. Analysis of genetic revertants and complementation with wild-type alleles confirmed that these mutations caused the SCV phenotype and decreased virulence for mice. PMID:24452687

Microtropins Q-W, ent-Labdane Glucosides: Microtropiosides G-I, Ursane-Type Triterpene Diglucoside and Flavonol Glycoside from the Leaves of Microtropis japonica.

PubMed

Terazawa, Saori; Uemura, Yuka; Koyama, Yuka; Kawakami, Susumu; Sugimoto, Sachiko; Matsunami, Katsuyoshi; Otsuka, Hideaki; Shinzato, Takakazu; Kawahata, Masatoshi; Yamaguchi, Kentaro

2017-01-01

Microtropins Q-W, (2S,3R)-2-ethyl-2,3-dihydroxybutyrate of various glucosides and glucose, as well as three ent-labdane diterpenoid glucosides, named microtropiosides G, H and I, an ursane-type triterpene diglucoside and a flavonoid glycoside were isolated from the MeOH extract of the leaves of Microtropis japonica. The structure of microtropioside A, also isolated from the branches of M. japonica, was elucidated spectroscopically in a previous experiment and was found to possess a rare seven-membered oxyrane ring. Its structure was confirmed by X-ray crystallographic analysis of its pentaacetate.

Venus gravity - Analysis of Beta Regio

NASA Technical Reports Server (NTRS)

Esposito, P. B.; Sjogren, W. L.; Mottinger, N. A.; Bills, B. G.; Abbott, E.

1982-01-01

Radio tracking data acquired over Beta Regio were analyzed to obtain a surface mass distribution from which a detailed vertical gravity field was derived. In addition, a corresponding vertical gravity field was evaluated solely from the topography of the Beta region. A comparison of these two maps confirms the strong correlation between gravity and topography which was previously seen in line-of-sight gravity maps. It also demonstrates that the observed gravity is a significant fraction of that predicted from the topography alone. The effective depth of complete isostatic compensation for the Beta region is estimated to be 330 km, which is somewhat deeper than that found for other areas of Venus.

Muon-catalyzed D-T fusion at low temperature

NASA Astrophysics Data System (ADS)

Breunlich, W. H.; Cargnelli, M.; Kammel, P.; Marton, J.; Naegele, N.; Pawlek, P.; Scrinzi, A.; Werner, J.; Zmeskal, J.; Bistirlich, J.; Crowe, K. M.; Justice, M.; Kurck, J.; Petitjean, C.; Sherman, R. H.; Bossy, H.; Daniel, H.; Hartmann, F. J.; Neumann, W.; Schmidt, G.

1987-01-01

Muon-catalyzed deuterium-tritium fusion was investigated within a wide range of mixtures in liquid and gas (23-35 K) by detection of fusion neutrons. Our improved analysis includes hyperfine effects and allows a clear separation of intrinsic dt sticking ωs from kinetic effects. Strongly density-dependent cycle rates with values up to 1.45×108 s-1, yields of 113 fusions per muon, and ωs=(0.45+/-0.05)% are found. In comparison with previous experiments we confirm that ωs in liquid is lower than theoretically predicted, but do not find a strong dependence on either ct or density.

Phylogenetic and Epidemiologic Evidence of Multiyear Incubation in Human Rabies

PubMed Central

Boland, Torrey A.; McGuone, Declan; Jindal, Jenelle; Rocha, Marcelo; Cumming, Melissa; Rupprecht, Charles E.; Barbosa, Taciana Fernandes Souza; de Novaes Oliveira, Rafael; Chu, Catherine J.; Cole, Andrew J.; Kotait, Ivanete; Kuzmina, Natalia A.; Yager, Pamela A.; Kuzmin, Ivan V.; Hedley-Whyte, E. Tessa; Brown, Catherine M.; Rosenthal, Eric S.

2014-01-01

Eight years after emigrating from Brazil, an otherwise healthy man developed rabies. An exposure prior to immigration was reported. Genetic analysis revealed a canine rabies virus variant found only in the patient’s home country, and the patient had not traveled internationally since immigrating to the United States. We describe how epidemiological, phylogenetic, and viral sequencing data provided confirmation that rabies encephalomyelitis may present after a long, multiyear incubation period, a consideration that previously has been hypothesized without the ability to exclude a more recent exposure. Accordingly, rabies should be considered in the diagnosis of any acute encephalitis, myelitis, or encephalomyelitis. PMID:24038455

An Improved 360 Degree and Order Model of Venus Topography

NASA Technical Reports Server (NTRS)

Rappaport, Nicole J.; Konopliv, Alex S.; Kucinskas, Algis B.; Ford, Peter G.

1999-01-01

We present an improved 360 degree and order spherical harmonic solution for Venus' topography. The new model uses the most recent set of Venus altimetry data with spacecraft positions derived from a recent high resolution gravity model. Geometric analysis indicates that the offset between the center of mass and center of figure of Venus is about 10 times smaller than that for the Earth, the Moon, or Mars. Statistical analyses confirm that the RMS topography follows a power law over the central part of the spectrum. Compared to the previous topography model, the new model is more highly correlated with Venus' harmonic gravity field.

Analysis of a Near Field MIMO Wireless Channel Using 5.6 GHz Dipole Antennas

NASA Astrophysics Data System (ADS)

Maricar, Mohamed Ismaeel; Gradoni, Gabriele; Greedy, Steve; Ivrlac, Michel T.; Nossek, Josef A.; Phang, Sendy; Creagh, Stephen C.; Tanner, Gregor; Thomas, David W. P.

2016-05-01

Understanding the impact of interference upon the performance of a multiple input multiple output (MIMO) based device is of paramount importance in ensuring a design is both resilient and robust. In this work the effect of element-element interference in the creation of multiple channels of a wireless link approaching the near-field regime is studied. The elements of the 2-antenna transmit- and receive-arrays are chosen to be identical folded dipole antennas operating at 5.6 GHz. We find that two equally strong channels can be created even if the antennas interact at sub-wavelength distances, thus confirming previous theoretical predictions.

Climate change and economic growth: a heterogeneous panel data approach.

PubMed

Sequeira, Tiago Neves; Santos, Marcelo Serra; Magalhães, Manuela

2018-05-31

Climate change is a global phenomenon. Its impact on economic growth must therefore be analyzed in accordance with its (time-varying) common effects. We present an econometric analysis that evaluates this effect taking into account its global nature. Contrary to previous evidence that ignores the global effects, we obtain that the rising temperature has not decreased growth in real GDP per capita in the second half of the twentieth century for the world countries. However, we obtain a negative effect of rising temperatures and a positive effect of rising precipitation in poor countries. This positive effect of rising precipitation is also confirmed for hot and temperate countries.

ECS: Efficient Communication Scheduling for Underwater Sensor Networks

PubMed Central

Hong, Lu; Hong, Feng; Guo, Zhongwen; Li, Zhengbao

2011-01-01

TDMA protocols have attracted a lot of attention for underwater acoustic sensor networks (UWSNs), because of the unique characteristics of acoustic signal propagation such as great energy consumption in transmission, long propagation delay and long communication range. Previous TDMA protocols all allocated transmission time to nodes based on discrete time slots. This paper proposes an efficient continuous time scheduling TDMA protocol (ECS) for UWSNs, including the continuous time based and sender oriented conflict analysis model, the transmission moment allocation algorithm and the distributed topology maintenance algorithm. Simulation results confirm that ECS improves network throughput by 20% on average, compared to existing MAC protocols. PMID:22163775

Mixtures of GAMs for habitat suitability analysis with overdispersed presence / absence data

PubMed Central

Pleydell, David R.J.; Chrétien, Stéphane

2009-01-01

A new approach to species distribution modelling based on unsupervised classification via a finite mixture of GAMs incorporating habitat suitability curves is proposed. A tailored EM algorithm is outlined for computing maximum likelihood estimates. Several submodels incorporating various parameter constraints are explored. Simulation studies confirm, that under certain constraints, the habitat suitability curves are recovered with good precision. The method is also applied to a set of real data concerning presence/absence of observable small mammal indices collected on the Tibetan plateau. The resulting classification was found to correspond to species-level differences in habitat preference described in previous ecological work. PMID:20401331

[Basic results of an experiment with mammals on the Kosmos-782 biosatellite].

PubMed

Gazenko, O G; Genin, A M; Il'in, E A; Portugalov, V V; Serova, L V

1978-01-01

The rat experiments carried out onboard the biosatellite Cosmos-782 contributed to our understanding of mechanisms of animal adaption to prolonged weightlessness. Postflight analysis helped to study nonspecific changes related to the stress-reaction accompanying space flight and return to the Earth gravity as well as specific changes associated with functional unloading of the musculoskeletal system in weightlessness. The flight results confirmed the previously made conclusions concerning possible adaptation of mammals to prolonged weightlessness and lack of pathological changes in vital weightlessness. They included: metabolic and hormonal changes, muscle atrophy, osteoporosis and delayed bone growth, decrease of ATPase activity of myocardial myosin, inhibition of erythropoiesis.

Rethinking childhood adversity in chronic fatigue syndrome.

PubMed

Clark, James E; Davidson, Sean L; Maclachlan, Laura; Newton, Julia L; Watson, Stuart

2018-01-01

Background: Previous studies have consistently shown increased rates of childhood adversity in chronic fatigue syndrome (CFS). However, such aetiopathogenic studies of CFS are potentially confounded by co-morbidity and misdiagnosis particularly with depression. Purpose: We examined the relationship between rates of childhood adversity using two complimentary approaches (1) a sample of CFS patients who had no lifetime history of depression and (2) a modelling approach. Methods: Childhood trauma questionnaire (CTQ) administered to a sample of 52 participants with chronic fatigue syndrome and 19 controls who did not meet criteria for a psychiatric disorder (confirmed using the Structured Clinical Interview for DSM-IV). Subsequently, Mediation Analysis (Baye's Rules) was used to establish the risk childhood adversity poses for CFS with and without depression. Results: In a cohort of CFS patients with depression comprehensively excluded, CTQ scores were markedly lower than in all previous studies and, in contrast to these previous studies, not increased compared with healthy controls. Post-hoc analysis showed that CTQ scores correlated with the number of depressive symptoms during the lifetime worst period of low mood. The probability of developing CFS given a history of childhood trauma is 4%, a two-fold increased risk compared to the general population. However, much of this risk is mediated by the concomitant development of major depression. Conclusions: The data suggests that previous studies showing a relationship between childhood adversity and CFS may be attributable to the confounding effects of co-morbid or misdiagnosed depressive disorder. Abbreviations: CFS: Chronic fatigue syndrome; CTQ: Childhood trauma questionnaire; MDD: Major depressive disorder; CA: Childhood adversity; P : Probability.

Oxidative phosphorylation flexibility in the liver of mice resistant to high-fat diet-induced hepatic steatosis.

PubMed

Poussin, Carinne; Ibberson, Mark; Hall, Diana; Ding, Jun; Soto, Jamie; Abel, E Dale; Thorens, Bernard

2011-09-01

To identify metabolic pathways that may underlie susceptibility or resistance to high-fat diet-induced hepatic steatosis. We performed comparative transcriptomic analysis of the livers of A/J and C57Bl/6 mice, which are, respectively, resistant and susceptible to high-fat diet-induced hepatosteatosis and obesity. Mice from both strains were fed a normal chow or a high-fat diet for 2, 10, and 30 days, and transcriptomic data were analyzed by time-dependent gene set enrichment analysis. Biochemical analysis of mitochondrial respiration was performed to confirm the transcriptomic analysis. Time-dependent gene set enrichment analysis revealed a rapid, transient, and coordinate upregulation of 13 oxidative phosphorylation genes after initiation of high-fat diet feeding in the A/J, but not in the C57Bl/6, mouse livers. Biochemical analysis using liver mitochondria from both strains of mice confirmed a rapid increase by high-fat diet feeding of the respiration rate in A/J but not C57Bl/6 mice. Importantly, ATP production was the same in both types of mitochondria, indicating increased uncoupling of the A/J mitochondria. Together with previous data showing increased expression of mitochondrial β-oxidation genes in C57Bl/6 but not A/J mouse livers, our present study suggests that an important aspect of the adaptation of livers to high-fat diet feeding is to increase the activity of the oxidative phosphorylation chain and its uncoupling to dissipate the excess of incoming metabolic energy and to reduce the production of reactive oxygen species. The flexibility in oxidative phosphorylation activity may thus participate in the protection of A/J mouse livers against the initial damages induced by high-fat diet feeding that may lead to hepatosteatosis.

Spectroscopic orbits of symbiotic stars - Preliminary results

NASA Technical Reports Server (NTRS)

Garcia, M. R.

1986-01-01

The present search for radial velocity variations due to orbital motions in symbiotic stars involved observations of 17 such stars at approximately 1-month intervals, as well as of radial velocity variations in the M-giant primary in nine stars. The observed radial velocity curves are commensurate with those expected from a group of binaries having random sin i and about 20 km/sec orbital velocities. Four of the orbital periods thus suggested for seven stars confirm previously known photometric periods, while one confirms a previously known orbital period and two are completely new. Knowledge of the orbits allows identification of those symbiotics that are close to filling their Roche lobes.

Self-concept clarity and compulsive Internet use: The role of preference for virtual interactions and employment status in British and North-American samples.

PubMed

Quinones, Cristina; Kakabadse, Nada Korak

2015-12-01

Compulsive Internet Use (CIU) describes a maladaptive relationship with the Internet characterised by loss of control and conflict. Although also affecting adults, most studies use teenage samples, and theoretical development on risk factors is scarce. According to Davis (2001), the social connectivity function of the Internet is key in identifying traits associated with CIU. Since Self-Concept Clarity (SCC) is strongly related to social anxiety, and virtual interactions allow "self-edition", we hypothesized that individuals low in SCC could choose virtual interactions as safer alternative to satisfy their social needs. This could in turn increase the risk of CIU. Building on a previous study, we also expected CIU to be more harmful in the unemployed. We collected samples from the U.K. (N = 532) and U.S. (N = 502) with equal distribution of employed and unemployed individuals. We ran Measurement Invariance tests to confirm that the constructs were equivalent across countries. Subsequently, we conducted mediation and moderation analysis to test our hypothesis with Multigroup Confirmatory Factor Analysis. Measurement Invariance was confirmed. The relationship between SCC and CIU was partially mediated by preference of virtual interactions in both countries. This preference was significantly related to lower social support. Short term unemployment seemed to accentuate the negative impact of CIU on life satisfaction in both countries, although only marginally significantly in the U.S. The unemployed reported significantly lower levels of life satisfaction. We demonstrated that SCC is a key vulnerability factor to CIU in adults, and confirmed the additional risks for the unemployed.

Identification of cis-elements for ethylene and circadian regulation of the Solanum melongena gene encoding cysteine proteinase.

PubMed

Rawat, Reetika; Xu, Zeng-Fu; Yao, Kwok-Ming; Chye, Mee-Len

2005-03-01

We have previously shown that the expression of SmCP which encodes Solanum melongena cysteine proteinase is ethylene-inducible and is under circadian control. To understand the regulation of SmCP, a 1.34-kb SmCP 5'-flanking region and its deletion derivatives were analyzed for cis-elements using GUS and luc fusions and by in vitro binding assays. Analysis of transgenic tobacco transformed with SmCP promoter-GUS constructs confirmed that the promoter region -415/+54 containing Ethylene Responsive Element ERE(-355/-348) conferred threefold ethylene-induction of GUS expression, while -827/+54 which also contains ERE(-683/-676), produced fivefold induction. Using gel mobility shift assays, we demonstrated that each ERE binds nuclear proteins from both ethephon-treated and untreated 5-week-old seedlings, suggesting that different transcriptions factors bind each ERE under varying physiological conditions. Binding was also observed in extracts from senescent, but not young, fruits. The variation in binding at the EREs in fruits and seedlings imply that organ-specific factors may participate in binding. Analysis of transgenic tobacco expressing various SmCP promoter-luc constructs containing wild-type or mutant Evening Elements (EEs) confirmed that both conserved EEs at -795/-787 and -785/-777 are important in circadian control. We confirmed the binding of total nuclear proteins to EEs in gel mobility shift assays and in DNase I footprinting. Our results suggest that multiple proteins bind the EEs which are conserved in plants other than Arabidopsis and that functional EEs and EREs are present in the 5'-flanking region of a gene encoding cysteine proteinase.

Changes in coral-associated microbial communities during a bleaching event.

PubMed

Bourne, David; Iida, Yuki; Uthicke, Sven; Smith-Keune, Carolyn

2008-04-01

Environmental stressors such as increased sea surface temperatures are well-known for contributing to coral bleaching; however, the effect of increased temperatures and subsequent bleaching on coral-associated microbial communities is poorly understood. Colonies of the hard coral Acropora millepora were tagged on a reef flat off Magnetic Island (Great Barrier Reef) and surveyed over 2.5 years, which included a severe bleaching event in January/February 2002. Daily average water temperatures exceeded the previous 10-year average by more than 1 degrees C for extended periods with field-based visual surveys recording all tagged colonies displaying signs of bleaching. During the bleaching period, direct counts of coral zooxanthellae densities decreased by approximately 64%, before recovery to pre-bleaching levels after the thermal stress event. A subset of three tagged coral colonies were sampled through the bleaching event and changes in the microbial community elucidated. Denaturing gradient gel electrophoresis (DGGE) analysis demonstrated conserved bacterial banding profiles between the three coral colonies, confirming previous studies highlighting specific microbial associations. As coral colonies bleached, the microbial community shifted and redundancy analysis (RDA) of DGGE banding patterns revealed a correlation of increasing temperature with the appearance of Vibrio-affiliated sequences. Interestingly, this shift to a Vibrio-dominated community commenced prior to visual signs of bleaching. Clone libraries hybridized with Vibrio-specific oligonucleotide probes confirmed an increase in the fraction of Vibrio-affiliated clones during the bleaching period. Post bleaching, the coral microbial associations again shifted, returning to a profile similar to the fingerprints prior to bleaching. This provided further evidence for corals selecting and shaping their microbial partners. For non-bleached samples, a close association with Spongiobacter-related sequences were revealed by both clone libraries and DGGE profiling. Despite Vibrio species being previously implicated in bleaching of specific coral species, it is unsure if the relative increase in retrieved Vibrio sequences is due to bacterial infection or an opportunistic response to compromised health and changing environmental parameters of the coral host. This study provides the first molecular-based study demonstrating changes in coral-associated bacterial assemblages during a bleaching event on a natural reef system.

Modeling of Highly Instrumented Honeywell Turbofan Engine Tested with Ice Crystal Ingestion in the NASA Propulsion System Laboratory

NASA Technical Reports Server (NTRS)

Veres, Joseph P.; Jorgenson, Philip C. E.; Jones, Scott M.

2016-01-01

The Propulsion Systems Laboratory (PSL), an altitude test facility at NASA Glenn Research Center, has been used to test a highly instrumented turbine engine at simulated altitude operating conditions. This is a continuation of the PSL testing that successfully duplicated the icing events that were experienced in a previous engine (serial LF01) during flight through ice crystal clouds, which was the first turbofan engine tested in PSL. This second model of the ALF502R-5A serial number LF11 is a highly instrumented version of the previous engine. The PSL facility provides a continuous cloud of ice crystals with controlled characteristics of size and concentration, which are ingested by the engine during operation at simulated altitudes. Several of the previous operating points tested in the LF01 engine were duplicated to confirm repeatability in LF11. The instrumentation included video cameras to visually illustrate the accretion of ice in the low pressure compressor (LPC) exit guide vane region in order to confirm the ice accretion, which was suspected during the testing of the LF01. Traditional instrumentation included static pressure taps in the low pressure compressor inner and outer flow path walls, as well as total pressure and temperature rakes in the low pressure compressor region. The test data was utilized to determine the losses and blockages due to accretion in the exit guide vane region of the LPC. Multiple data points were analyzed with the Honeywell Customer Deck. A full engine roll back point was modeled with the Numerical Propulsion System Simulation (NPSS) code. The mean line compressor flow analysis code with ice crystal modeling was utilized to estimate the parameters that indicate the risk of accretion, as well as to estimate the degree of blockage and losses caused by accretion during a full engine roll back point. The analysis provided additional validation of the icing risk parameters within the LPC, as well as the creation of models for estimating the rates of blockage growth and losses.

CpG Sites Associated with Cigarette Smoking: Analysis of Epigenome-Wide Data from the Sister Study

PubMed Central

Harlid, Sophia; Xu, Zongli; Panduri, Vijayalakshmi; Sandler, Dale P.

2014-01-01

Background: Smoking increases the risk of many diseases, and it is also linked to blood DNA methylation changes that may be important in disease etiology. Objectives: We sought to identify novel CpG sites associated with cigarette smoking. Methods: We used two epigenome-wide data sets from the Sister Study to identify and confirm CpG sites associated with smoking. One included 908 women with methylation measurements at 27,578 CpG sites using the HumanMethylation27 BeadChip; the other included 200 women with methylation measurements for 473,844 CpG sites using the HumanMethylation450 BeadChip. Significant CpGs from the second data set that were not included in the 27K assay were validated by pyrosequencing in a subset of 476 samples from the first data set. Results: Our study successfully confirmed smoking associations for 9 previously established CpGs and identified 2 potentially novel CpGs: cg26764244 in GNG12 (p = 9.0 × 10–10) and cg22335340 in PTPN6 (p = 2.9 × 10–05). We also found strong evidence of an association between smoking status and cg02657160 in CPOX (p = 7.3 × 10–7), which has not been previously reported. All 12 CpGs were undermethylated in current smokers and showed an increasing percentage of methylation in former and never-smokers. Conclusions: We identified 2 potentially novel smoking related CpG sites, and provided independent replication of 10 previously reported CpGs sites related to smoking, one of which is situated in the gene CPOX. The corresponding enzyme is involved in heme biosynthesis, and smoking is known to increase heme production. Our study extends the evidence base for smoking-related changes in DNA methylation. Citation: Harlid S, Xu Z, Panduri V, Sandler DP, Taylor JA. 2014. CpG sites associated with cigarette smoking: analysis of epigenome-wide data from the Sister Study. Environ Health Perspect 122:673–678; http://dx.doi.org/10.1289/ehp.1307480 PMID:24704585

Phylogenetic sequence analysis, recombinant expression, and tissue distribution of a channel catfish estrogen receptor beta

USGS Publications Warehouse

Xia, Zhenfang; Gale, William L.; Chang, Xiaotian; Langenau, David; Patino, Reynaldo; Maule, Alec G.; Densmore, Llewellyn D.

2000-01-01

An estrogen receptor β (ERβ) cDNA fragment was amplified by RT-PCR of total RNAextracted from liver and ovary of immature channel catfish. This cDNA fragment was used to screen an ovarian cDNA library made from an immature female fish. A clone was obtained that contained an open reading frame encoding a 575-amino-acid protein with a deduced molecular weight of 63.9 kDa. Maximum parsimony and Neighbor Joining analyses were used to generate a phylogenetic classification of channel catfish ERβ on the basis of 25 full-length teleost and tetrapod ER sequences. The consensus tree obtained indicated the existence of two major vertebrate ER subtypes, α and β. Within each subtype, and in accordance with established phylogenetic relationships, teleost and tetrapod ER were monophyletic confirming the results of a previous analysis (Z. Xiaet al., 1999, Gen. Comp. Endocrinol. 113, 360–368). Extracts of COS-7 cells transfectedwith channel catfish ERβ cDNA bound estrogen with high affinity (Kd = 0.21 nM) and specificity. The affinity of channel catfish ERβ for estrogen was higher than previously reported for channel catfish ERα. As determined by qualitative RT-PCR, the tissue distributions of ERα and ERβ were similar but not identical. Both ER subtypes were present in ovary and testis. ERα was found in all other tissues examined from juvenile and mature fish of both sexes. ERβ was also found in most tissues except, in most cases, whole blood and head kidney. Interestingly, the pattern of expression of ER subtypes in head kidney always corresponded to the pattern in whole blood. In conclusion, we isolated a channel catfish ERβ with ligand-binding affinity and tissue expression patterns different from ERα. Also, we confirmed the validity of our previously proposed general classification scheme for vertebrate ER into α and β subtypes and within each subtype, into teleost and tetrapod clades.

Alteration of lipid profile in subclinical hypothyroidism: a meta-analysis.

PubMed

Liu, Xiao-Li; He, Shan; Zhang, Shao-Fang; Wang, Jun; Sun, Xiu-Fa; Gong, Chun-Mei; Zheng, Shi-Jie; Zhou, Ji-Chang; Xu, Jian

2014-08-14

Previous studies yielded controversial results about the alteration of lipid profiles in patients with subclinical hypothyroidism. We performed a meta-analysis to investigate the association between subclinical hypothyroidism and lipid profiles. We searched PubMed, Cochrane Library, and China National Knowledge Infrastructure articles published January 1990 through January 2014. Dissertation databases (PQDT and CDMD) were searched for additional unpublished articles. We included articles reporting the relationship between subclinical hypothyroidism and at least 1 parameter of lipid profiles, and calculated the overall weighted mean difference (WMD) with a random effects model. Meta-regression was used to explore the source of heterogeneity among studies, and the Egger test, Begg test, and the trim and fill method were used to assess potential publication bias. Sixteen observational studies were included in our analysis. Meta-analysis suggested that the serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and total triglyceride levels were significantly increased in patients with subclinical hypothyroidism compared with euthyroidism individuals; the WMD were 12.17 mg/dl, 7.01 mg/dl, and 13.19 mg/dl, respectively (P<0.001 for all). No significant difference was observed for serum high-density lipoprotein cholesterol (HDL-C). Match strategy was the main source of heterogeneity among studies in TC and LDL-C analysis. Potential publication bias was found in TC and LDL-C analysis by the Egger test or Begg test and was not confirmed by the trim and fill method. Subclinical hypothyroidism may correlate with altered lipid profile. Previous studies had limitations in the control of potential confounding factors and further studies should consider those factors.

[The investigation of attitudes toward health behaviour among high school and university students].

PubMed

Nagy, Beáta Erika; Kovács, Karolina Eszter

2017-11-01

Health awareness plays an important role in our life, which contains attitudes as well behavioural components. Social factors influencing health awareness were the basis of many previous investigations, measuring the effect of demographical and psychological factors. However, investigation of these factors usually happened with separated questions. The aim of the present study is to test a new questionnaire, which measures health behaviour and attitudes related to health awareness. In present study, the attention was drawn to the introduction of a new questionnaire related to health behaviour, attitudes toward health awareness and factors influencing those and measured on population in Debrecen (SHTE 2017; n = 256). the new measurement proved to be reliable based on Cronbach α analysis. This was created on the basis of focus content analysis of group conversations with 10 subscales and 35 items. It can be stated that gender, father's educational level, objective and subjective financial status has a significantly negative effect; while sport, subjective health and fitness as well as subjective religiosity have a significantly positive effect which reflects previous findings and confirm the reliability of our questionnaire. Orv Hetil. 2017; 158(44): 1754-1760.

A Rigorous Attempt to Verify Interstellar Glycine

NASA Technical Reports Server (NTRS)

Snyder, L. E.; Lovas, F. J.; Hollis, J. M.; Friedel, D. N.; Jewell, P. R.; Remijan, A.; Ilyushin, V. V.; Alekseev, E. A.; Dyubko, S. F.

2004-01-01

In 2003, Kuan, Charnley, and co-workers reported the detection of interstellar glycine (NH2CH2COOH) based on observations of 27 lines in 19 different spectral bands in one or more of the sources Sgr BP(N-LMH), Orion KL, and W51 e1/e2. They supported their detection report with rotational temperature diagrams for all three sources. In this paper, we present essential criteria which can be used in a straightforward analysis technique to confirm the identity of an interstellar asymmetric rotor such as glycine. We use new laboratory measurements of glycine as a basis for applying this analysis technique, both to our previously unpublished 12 m telescope data and to the previously published SEST data of Nummelin and colleagues. We conclude that key lines necessary for an interstellar glycine identification have not yet been found. We identify several common molecular candidates that should be examined further as more likely carriers of the lines reported as glycine. Finally, we illustrate that rotational temperature diagrams used without the support of correct spectroscopic assignments are not a reliable tool for the identification of interstellar molecules. Subject headings: ISM: abundances - ISM: clouds - ISM: individual (Sagittarius B2[N-

Photometric study of the W UMa eclipsing binaries VW LMi and BX Dra

NASA Astrophysics Data System (ADS)

Sánchez-Bajo, F.; García-Melendo, E.; Gómez-Forrellad, J. M.

2007-12-01

New ephemeris and the absolute parameters—masses, radii and luminosities—of the contact systems VW LMi and BX Dra have been obtained, by means of the analysis of the minima data available in the literature (for the determination of the ephemeris) and combining the previously published spectroscopic information and the results of the Wilson-Devinney method using photometric data (for the determination of the absolute parameters). The VW LMi O- C analysis confirms the multiplicity of the system detected previously from the spectroscopic data. Masses of the VW LMi contact system primary and secondary components are 1.67 ± 0.02 M ⊙ and 0.70 ± 0.02 M ⊙, respectively. The corresponding radii are 1.709 ± 0.007 R ⊙ and 1.208 ± 0.006 R ⊙, respectively. For the BX Dra contact system the masses are 2.19 ± 0.13 M ⊙ and 0.63 ± 0.06 M ⊙, and the radii, 2.13 ± 0.04 R ⊙ and 1.26 ± 0.03 R ⊙, for the primary and secondary, respectively. In both cases, the estimated luminosities seem to be slightly greater that the values derived from the Hipparcos distances.

The influence of personality and perceived stress on the development of breast cancer: 20-year follow-up of 29,098 Japanese women.

PubMed

Sawada, Takayuki; Nishiyama, Takeshi; Kikuchi, Norimasa; Wang, Chaochen; Lin, Yingsong; Mori, Mitsuru; Tanno, Kozo; Tamakoshi, Akiko; Kikuchi, Shogo

2016-09-02

Breast cancer is the most common cancer in women. However, it remains unproven whether psychological factors have an influence on breast cancer incidence. In our earlier study, subjects possessing two personality traits, decisiveness and "ikigai" (a Japanese word meaning something that makes one's life worth living), showed a significantly lower risk of developing breast cancer, although no psychological factors have been convincingly demonstrated to have an influence on breast cancer development in other studies. Therefore, we conducted this follow-up analysis to confirm the association between breast cancer incidence and psychological traits, using the final dataset of a large-scale prospective cohort study in Japan. We identified 209 cases of incident breast cancer out of a maximum 21-year follow-up of 29,098 Japanese women. Cox proportional hazard regression analysis, adjusted for the same potential confounders used in our previous study, did not reveal any significant relationships between breast cancer incidence and four psychological traits: having "ikigai", decisiveness, ease of anger arousal, and perceived stress. Our finding is consistent with previous studies, and suggests that the psychological traits are unlikely to be an important risk factor for breast cancer.

Performance comparison of six independent components analysis algorithms for fetal signal extraction from real fMCG data

NASA Astrophysics Data System (ADS)

Hild, Kenneth E.; Alleva, Giovanna; Nagarajan, Srikantan; Comani, Silvia

2007-01-01

In this study we compare the performance of six independent components analysis (ICA) algorithms on 16 real fetal magnetocardiographic (fMCG) datasets for the application of extracting the fetal cardiac signal. We also compare the extraction results for real data with the results previously obtained for synthetic data. The six ICA algorithms are FastICA, CubICA, JADE, Infomax, MRMI-SIG and TDSEP. The results obtained using real fMCG data indicate that the FastICA method consistently outperforms the others in regard to separation quality and that the performance of an ICA method that uses temporal information suffers in the presence of noise. These two results confirm the previous results obtained using synthetic fMCG data. There were also two notable differences between the studies based on real and synthetic data. The differences are that all six ICA algorithms are independent of gestational age and sensor dimensionality for synthetic data, but depend on gestational age and sensor dimensionality for real data. It is possible to explain these differences by assuming that the number of point sources needed to completely explain the data is larger than the dimensionality used in the ICA extraction.

Vaginal delivery after Misgav-Ladach cesarean section--is the risk of uterine rupture acceptable?

PubMed

Hudić, Igor; Fatusić, Zlatan; Kamerić, Lejla; Misić, Mladen; Serak, Indira; Latifagić, Anela

2010-10-01

To evaluate whether the single-layer closure as is a routine by the Misgav-Ladach method compared to the double-layer closure as used by the Dörfler cesarean method is associated with an increased risk of uterine rupture in the subsequent pregnancy and delivery. The analysis is retrospective and is based on medical documentation of the Clinic for Gynecology and Obstetrics, University Clinical Centre, Tuzla, Bosnia and Herzegovina. All patients with one previous cesarean section who attempted vaginal birth following cesarean section were managed from 1 January 2002 to 31 December 2008. Exclusion criteria included multiple gestation, greater than one previous cesarean section, previous incision other than low transverse, gestational age at delivery less than 37 weeks and induction of delivery. We identified 448 patients who met inclusion criteria. We found that 303 patients had a single-layer closure (Misgav-Ladach) and 145 had a double-layer closure (Dörffler) of the previous uterine incision. There were 35 cases of uterine rupture. Of those patients with previous single-layer closure, 5.28% (16/303) had a uterine rupture compared to 13.11% (19/145) in the double-layer closure group (p<0.05). We have not found that a Misgav-Ladach cesarean section method (single-layer uterine closure) might be more likely to result in uterine rupture in women who attempted a vaginal birth after a previous cesarean delivery. This cesarean section method should find its confirmation in everyday clinical practice.

The efficacy of hydroxychloroquine for obstetrical outcome in anti-phospholipid syndrome: Data from a European multicenter retrospective study.

PubMed

Mekinian, Arsène; Lazzaroni, Maria Grazia; Kuzenko, Anna; Alijotas-Reig, Jaume; Ruffatti, Amelia; Levy, Pierre; Canti, Valentina; Bremme, Katarina; Bezanahary, Holy; Bertero, Tiziana; Dhote, Robin; Maurier, Francois; Andreoli, Laura; Benbara, Amélie; Tigazin, Ahmed; Carbillon, Lionel; Nicaise-Roland, Pascale; Tincani, Angela; Fain, Olivier

2015-06-01

In European multicenter study, we aimed to describe the real-life hydroxychloroquine use in APS patients during pregnancy and determine its benefit in refractory obstetrical APS. We analyzed the outcome of pregnancies treated by hydroxychloroquine in patients with APS or asymptomatic antiphospholipid (aPL) antibodies carriers. Thirty patients with APS with 35 pregnancies treated by hydroxychloroquine were analyzed. Comparing the outcome of pregnancies treated by the addition of hydroxychloroquine to previous pregnancies under the conventional treatment, pregnancy losses decreased from 81% to 19% (p<0.05), without differences in the associated treatments. The univariate analysis showed that the previous intrauterine deaths and higher hydroxychloroquine amount (400mg per day) were the factors associated with pregnancy outcome. Considering 14 patients with previous refractory obstetrical APS (n=5 with obstetrical and thrombotic primary APS and n=9 with purely obstetrical APS), all with previous pregnancy losses under treatment (aspirin with LMWH in 11 cases and LMWH in 3 cases), the addition of hydroxychloroquine resulted in live born babies in 11/14 (78%) cases (p<0.05). Our study shows the benefit of hydroxychloroquine addition in patients with refractory obstetrical APS and raises the need of prospective studies to confirm our preliminary study. Copyright © 2015 Elsevier B.V. All rights reserved.

Jamming and percolation in random sequential adsorption of straight rigid rods on a two-dimensional triangular lattice

NASA Astrophysics Data System (ADS)

Perino, E. J.; Matoz-Fernandez, D. A.; Pasinetti, P. M.; Ramirez-Pastor, A. J.

2017-07-01

Monte Carlo simulations and finite-size scaling analysis have been performed to study the jamming and percolation behavior of linear k-mers (also known as rods or needles) on a two-dimensional triangular lattice of linear dimension L, considering an isotropic RSA process and periodic boundary conditions. Extensive numerical work has been done to extend previous studies to larger system sizes and longer k-mers, which enables the confirmation of a nonmonotonic size dependence of the percolation threshold and the estimation of a maximum value of k from which percolation would no longer occur. Finally, a complete analysis of critical exponents and universality has been done, showing that the percolation phase transition involved in the system is not affected, having the same universality class of the ordinary random percolation.

Novel splice mutation in microthalmia-associated transcription factor in Waardenburg Syndrome.

PubMed

Brenner, Laura; Burke, Kelly; Leduc, Charles A; Guha, Saurav; Guo, Jiancheng; Chung, Wendy K

2011-01-01

Waardenburg Syndrome (WS) is a syndromic form of hearing loss associated with mutations in six different genes. We identified a large family with WS that had previously undergone clinical testing, with no reported pathogenic mutation. Using linkage analysis, a region on 3p14.1 with an LOD score of 6.6 was identified. Microthalmia-Associated Transcription Factor, a gene known to cause WS, is located within this region of linkage. Sequencing of Microthalmia-Associated Transcription Factor demonstrated a c.1212 G>A synonymous variant that segregated with the WS in the family and was predicted to cause a novel splicing site that was confirmed with expression analysis of the mRNA. This case illustrates the need to computationally analyze novel synonymous sequence variants for possible effects on splicing to maximize the clinical sensitivity of sequence-based genetic testing.

Clinical utility and validity of minoxidil response testing in androgenetic alopecia.

PubMed

Goren, Andy; Shapiro, Jerry; Roberts, Janet; McCoy, John; Desai, Nisha; Zarrab, Zoulikha; Pietrzak, Aldona; Lotti, Torello

2015-01-01

Clinical response to 5% topical minoxidil for the treatment of androgenetic alopecia (AGA) is typically observed after 3-6 months. Approximately 40% of patients will regrow hair. Given the prolonged treatment time required to elicit a response, a diagnostic test for ruling out nonresponders would have significant clinical utility. Two studies have previously reported that sulfotransferase enzyme activity in plucked hair follicles predicts a patient's response to topical minoxidil therapy. The aim of this study was to assess the clinical utility and validity of minoxidil response testing. In this communication, the present authors conducted an analysis of completed and ongoing studies of minoxidil response testing. The analysis confirmed the clinical utility of a sulfotransferase enzyme test in successfully ruling out 95.9% of nonresponders to topical minoxidil for the treatment of AGA. © 2014 Wiley Periodicals, Inc.

Steroid hormone and epidermal growth factor receptors in meningiomas.

PubMed

Horsfall, D J; Goldsmith, K G; Ricciardelli, C; Skinner, J M; Tilley, W D; Marshall, V R

1989-11-01

A prospective study of steroid hormone and epidermal growth factor receptor expression in 57 meningiomas is presented. Scatchard analysis of radioligand binding identified 20% of meningiomas as expressing classical oestrogen receptors (ER) at levels below that normally accepted for positivity, the remainder being negative. ER could not be visualized in any meningioma using immunocytochemistry. Alternatively, 74% of meningiomas demonstrated the presence of progesterone receptors (PR) by Scatchard analysis, the specificity of which could not be attributed to glucocorticoid or androgen receptors. Confirmation of classical PR presence was determined by immunocytochemical staining. The presence of epidermal growth factor receptor (EGFR) was demonstrated in 100% of meningiomas using immunocytochemical staining. These data are reviewed in the context of previously reported results and are discussed in relation to the potential for medical therapy as an adjunct to surgery.

Interval sampling methods and measurement error: a computer simulation.

PubMed

Wirth, Oliver; Slaven, James; Taylor, Matthew A

2014-01-01

A simulation study was conducted to provide a more thorough account of measurement error associated with interval sampling methods. A computer program simulated the application of momentary time sampling, partial-interval recording, and whole-interval recording methods on target events randomly distributed across an observation period. The simulation yielded measures of error for multiple combinations of observation period, interval duration, event duration, and cumulative event duration. The simulations were conducted up to 100 times to yield measures of error variability. Although the present simulation confirmed some previously reported characteristics of interval sampling methods, it also revealed many new findings that pertain to each method's inherent strengths and weaknesses. The analysis and resulting error tables can help guide the selection of the most appropriate sampling method for observation-based behavioral assessments. © Society for the Experimental Analysis of Behavior.

Analysis of carbohydrate deficient transferrin by capillary zone electrophoresis.

PubMed

Prasad, R; Stout, R L; Coffin, D; Smith, J

1997-09-01

We report a capillary zone electrophoresis method to separate the various sialylated isoforms of transferrin. The separation is carried out under nondenaturing conditions and at basic pH. Under these conditions, transferrin exhibits two major and three minor peaks. Plasma samples from a population consuming varying amounts of alcohol at different intervals were studied. A cut-off value of 3% carbohydrate deficient transferrin (CDT: disialo, monosialo, and asialo transferrin), results in a clinical sensitivity of 88% in a population consuming at least 70 g/day alcohol for a minimum of two weeks. The sensitivity dropped significantly in a population consuming less than 70 g/day. This confirms previous reports of CDT as a specific marker for significant and chronic use of alcohol. Capillary electrophoresis offers an alternative method with respect to analysis time and throughput in the clinical laboratory.

Wood degradation under UV irradiation: A lignin characterization.

PubMed

Cogulet, Antoine; Blanchet, Pierre; Landry, Véronic

2016-05-01

The photodegradation of white spruce by artificial ageing was studied by several techniques: colourimetry, FTIR-ATR and FT-Raman spectroscopy. Samples were exposed at a xenon lamp for 2000h. Two distinct colour changes were found by colourimetric analysis, yellowing and silvering. These colour modifications indicate the formation of chromophoric structures which supports previous FTIR-ATR experiments. The degradation of lignin to generate the first chromophoric group for yellowing and then the appearance of surface layer cellulose. New carbonyl compounds conjugated with double bond at 1615cm(-1) are probably the second chromophoric group. The crystallinity index was also calculated and showed an increase of cellulose crystallinity by prior degradation of amorphous cellulose. The FT-Raman analysis confirms the wood sensitivity to photodegradation but the most remarkable results is the increase of fluorescence as a function of time. In softwood lignin, the compound able to produce fluorescence is a free rotating 5-5' linkage of one biphenyl structure. At native state these linkages are not free rotating, this phenomenon means the release of 5-5' linkage of lignin structure by cleavage of both α carbon linkages (Norrish type I reaction). These data confirm also the photosensitivity of α and β carbon in lignin and the resistance of 5-5' linkages. Copyright © 2016 Elsevier B.V. All rights reserved.

A fundamental study on the [(μ-Cl) 3 Mg 2 (THF) 6 ] + dimer electrolytes for rechargeable Mg batteries

DOE PAGES

Liu, Tianbiao; Cox, Jonathan T.; Hu, Dehong; ...

2015-01-05

We present a fundamental study on [(μ-Cl) 3 Mg 2 (THF) 6 ] + dimer electrolytes using various physical methods including Subambient Pressure Ionization with Nanoelectrospray Mass spectrometry (SPIN-MS), Raman spectroscopy, 25Mg{ 1H} NMR, 27Al{ 1H} NMR and electrochemical analysis. For the first time, long time sought THF solvated [MgCl] + species was experimentally characterized by SPIN mass spectrometry in the solution of the Mgdimer containing electrolyte, confirming the mono-Cl- abstraction reaction between MgCl 2 and an Al Lewis acid. Solvated MgCl 2 in the electrolyte was confirmed by Raman spectroscopy. The experimental results establish the previously proposed dimerization equilibriummore » of solvated [MgCl] + and MgCl2 with [(μ-Cl) 3Mg 2(THF)6] +. 25Mg{ 1H} NMR, 27Al{ 1H} NMR and electrochemical analysis on chloration reaction of [(μ-Cl) 3Mg 2(THF) 6]AlPh 3Cl with external Cl- led to further insights on the coordination chemistry of the dimer electrolyte. Finally, a comprehensive mechanism is proposed for the reversible electrochemical Mg deposition and stripping and Mg 2+ and Cl- ion transports of the Mg dimer electrolytes in rechargeable Mg batteries.« less

First Report of Colonies of Sylvatic Triatoma infestans (Hemiptera: Reduviidae) in the Paraguayan Chaco, Using a Trained Dog

PubMed Central

Rolón, Miriam; Vega, María Celeste; Román, Fabiola; Gómez, Ana; Rojas de Arias, Antonieta

2011-01-01

In the Gran Chaco region, control of Triatoma infestans has been limited by persistent domestic infestations despite the efforts of the Vector Control Services. In Paraguay, this region is the highest endemic area in the country, showing high levels of indoor and outdoor infestation. Although sylvatic T. infestans have been found in the Bolivian and Argentine Chaco, similar searches for sylvatic populations of this species in Paraguay had been unsuccessful over the last 20 years. Here we present a new approach to detecting sylvatic Triatominae, using a trained dog, which has successfully confirmed sylvatic populations of T. infestans and other triatomine species in Paraguay. A total of 22 specimens corresponding to dark morph forms of T. infestans were collected, and 14 were confirmed as T. infestans by the mitochondrial cytochrome B gene analysis. Through this analysis, one of which were previously reported and a second that was a new haplotype. Triatomines were captured from amongst vegetation such as dry branches and hollows trees of different species such Aspidosperma quebracho-blanco, Bulnesia sarmientoi and Stetsonia coryne. The colonies found have been small and without apparent infection with Trypanosoma cruzi. During the study, Triatoma sordida and Triatoma guasayana have also been found in ecotopes close to those of T. infestans. PMID:21572522

Study of 23 day periodicity of Blazar Mkn501 in 1997

NASA Astrophysics Data System (ADS)

Osone, S.

2006-10-01

We confirm a 23 day periodicity during a large flare in 1997 for X-ray data of X-ray satellite RXTE all sky monitor (ASM), 2 TeV gamma ray data from Utah Seven Telescope and HEGRA, with a Fourier analysis. We found the three results to be the same with a newly estimated error. We confirm the presence of a frequency dependent power (1/ f noise) in a frequency-power diagram. Further, we calculated a chance probability of the occurrence of the 23 day periodicity by considering the 1/ f noise and obtained a chance probability 4.88 × 10 -3 for the HEGRA data: this is more significant than the previous result by an order. We also obtained an indentical periodicity with another kind of timing analysis-epoch folding method for the ASM data and HEGRA data. We strongly suggest an existence of the periodicity. We divided the HEGRA data into two data sets, analyzed them with a Fourier method, and found an unstableness of the periodicity with a 3.4 sigma significance. We also analyzed an energy spectra of the X-ray data of a RXTE proportional counter array and we found that a combination of three physical parameters—a magnetic field, a Lorentz factor, and a beaming factor—is related to the periodicity.

General unknown screening procedure for the characterization of human drug metabolites in forensic toxicology: applications and constraints.

PubMed

Sauvage, François-Ludovic; Picard, Nicolas; Saint-Marcoux, Franck; Gaulier, Jean-Michel; Lachâtre, Gérard; Marquet, Pierre

2009-09-01

LC coupled to single (LC-MS) and tandem (LC-MS/MS) mass spectrometry is recognized as the most powerful analytical tools for metabolic studies in drug discovery. In this article, we describe five cases illustrating the utility of screening xenobiotic metabolites in routine analysis of forensic samples using LC-MS/MS. Analyses were performed using a previously published LC-MS/MS general unknown screening (GUS) procedure developed using a hybrid linear IT-tandem mass spectrometer. In each of the cases presented, the presence of metabolites of xenobiotics was suspected after analyzing urine samples. In two cases, the parent drug was also detected and the metabolites were merely useful to confirm drug intake, but in three other cases, metabolite detection was of actual forensic interest. The presented results indicate that: (i) the GUS procedure developed is useful to detect a large variety of drug metabolites, which would have been hardly detected using targeted methods in the context of clinical or forensic toxicology; (ii) metabolite structure can generally be inferred from their "enhanced" product ion scan spectra; and (iii) structure confirmation can be achieved through in vitro metabolic experiments or through the analysis of urine samples from individuals taking the parent drug.

A Simple PCR Method for Rapid Genotype Analysis of Mycobacterium ulcerans

PubMed Central

Stinear, Timothy; Davies, John K.; Jenkin, Grant A.; Portaels, Françoise; Ross, Bruce C.; OppEdIsano, Frances; Purcell, Maria; Hayman, John A.; Johnson, Paul D. R.

2000-01-01

Two high-copy-number insertion sequences, IS2404 and IS2606, were recently identified in Mycobacterium ulcerans and were shown by Southern hybridization to possess restriction fragment length polymorphism between strains from different geographic origins. We have designed a simple genotyping method that captures these differences by PCR amplification of the region between adjacent copies of IS2404 and IS2606. We have called this system 2426 PCR. The method is rapid, reproducible, sensitive, and specific for M. ulcerans, and it has confirmed previous studies suggesting a clonal population structure of M. ulcerans within a geographic region. M. ulcerans isolates from Australia, Papua New Guinea, Malaysia, Surinam, Mexico, Japan, China, and several countries in Africa were easily differentiated based on an array of 4 to 14 PCR products ranging in size from 200 to 900 bp. Numerical analysis of the banding patterns suggested a close evolutionary link between M. ulcerans isolates from Africa and southeast Asia. The application of 2426 PCR to total DNA, extracted directly from M. ulcerans-infected tissue specimens without culture, demonstrated the sensitivity and specificity of this method and confirmed for the first time that both animal and human isolates from areas of endemicity in southeast Australia have the same genotype. PMID:10747130

An ultrastructural analysis of the epithelial-fiber interface (EFI) in primate lenses.

PubMed

Kuszak, J R; Novak, L A; Brown, H G

1995-11-01

The purpose of this study was to conduct a comprehensive ultrastructural analysis of the epithelial-fiber interface (EFI) in normal adult primate (Macaque nemestrina and fascicularis; 6-9 years old, n = 10) lenses. Scanning electron microscopy (SEM) was used to initially characterize the gross size, shape and three-dimensional organization of central zone (cz) epithelial cells and the anterior ends of elongating fibers beneath these cells. This fiducial information was essential to properly orient lens pieces in freeze fracture specimen carriers for the production of replicas with unambiguously identifiable EFI. Transmission electron microscopy (TEM) of replicas and thin-sectioned material were used to ultrastructurally analyse the cz EFI. TEM thin-sectioned material was also used to ultrastructurally analyse the pregerminative (pgz), germinative (gz) and transitional zone (tz) EFI. Correlative SEM and TEM of cz EFI components revealed that the apical membrane of both epithelial and elongating fiber cells were irregularly polygonal in shape, and aligned in parallel as smooth, concave-convex surfaces. However, whereas epithelial cell apical surfaces had minimal size variation, elongating fibers were larger and considerably variable in size. Quantitative analysis of > 10000 micron2 cz elongating fiber apical surfaces failed to detect any gap junctions defined in freeze fracture replicas as complementary aggregates of transmembrane proteins (connexons) conjoined across a narrowed extracellular space. However, a comparable frequency of vesicular events was noted in this region as quantified previously in adult and embryonic chick lens. Correlative TEM analysis > 1500 linear micrometers of thin-sectioned EFI from this region confirmed the presence of epithelial-epithelial gap junctions, elongating fiber-elongating fiber gap junctions, and an extreme paucity of epithelial-elongating fiber gap junctions. In contrast, TEM analysis of > 1000 linear micrometers of thin-sectioned pgz, gz and tz EFI, confirmed the presence of epithelial-epithelial gap junctions, elongating fiber-elongating fiber gap junctions, numerous epithelial-elongating fiber adherens junctions and a few epithelial-elongating fiber gap junctions. Thus, the results of this and previous quantitative morphological and physiological studies (electronic and dye coupling) demonstrate that there is limited coupling between cz epithelial cells and underlying elongating fibers. Furthermore, the absence of gap junctional plaques in cz EFI freeze-fracture replicas and either pentalaminar or septalaminar profiles in correlative thin-sections, suggests that this limited coupling could be mediated via isolated gap junction channels. However, the results of this and previous quantitative studies further show that a greater degree of coupling exists across the pgz, gz and tz regions of the EFI and that this coupling is likely to be mediated by gap junction plaques. Finally, this and other studies continue to demonstrate that transcytotic processes play a role in lens physiology at the EFI.

Inactivation of nuclear factor κB by MIP-based drug combinations augments cell death of breast cancer cells.

PubMed

Subramaniam, Menaga; Liew, Su Ki; In, Lionel LA; Awang, Khalijah; Ahmed, Niyaz; Nagoor, Noor Hasima

2018-01-01

Drug combination therapy to treat cancer is a strategic approach to increase successful treatment rate. Optimizing combination regimens is vital to increase therapeutic efficacy with minimal side effects. In the present study, we evaluated the in vitro cytotoxicity of double and triple combinations consisting of 1'S-1'-acetoxychavicol acetate (ACA), Mycobacterium indicus pranii (MIP) and cisplatin (CDDP) against 14 various human cancer cell lines to address the need for more effective therapy. Our data show synergistic effects in MCF-7 cells treated with MIP:ACA, MIP:CDDP and MIP:ACA:CDDP combinations. The type of interaction between MIP, ACA and CDDP was evaluated based on combination index being <0.8 for synergistic effect. Identifying the mechanism of cell death based on previous studies involved intrinsic apoptosis and nuclear factor kappa B (NF-κB) and tested in Western blot analysis. Inactivation of NF-κB was confirmed by p65 and IκBα, while intrinsic apoptosis pathway activation was confirmed by caspase-9 and Apaf-1 expression. All combinations confirmed intrinsic apoptosis activation and NF-κB inactivation. Double and triple combination regimens that target induction of the same death mechanism with reduced dosage of each drug could potentially be clinically beneficial in reducing dose-related toxicities.

Measles outbreak response decision-making under uncertainty: a retrospective analysis.

PubMed

Fonnesbeck, Christopher J; Shea, Katriona; Carran, Spencer; Cassio de Moraes, Jose; Gregory, Christopher; Goodson, James L; Ferrari, Matthew J

2018-03-01

Resurgent outbreaks of vaccine-preventable diseases that have previously been controlled or eliminated have been observed in many settings. Reactive vaccination campaigns may successfully control outbreaks but must necessarily be implemented in the face of considerable uncertainty. Real-time surveillance may provide critical information about at-risk population and optimal vaccination targets, but may itself be limited by the specificity of disease confirmation. We propose an integrated modelling approach that synthesizes historical demographic and vaccination data with real-time outbreak surveillance via a dynamic transmission model and an age-specific disease confirmation model. We apply this framework to data from the 1996-1997 measles outbreak in São Paulo, Brazil. To simulate the information available to decision-makers, we truncated the surveillance data to what would have been available at 1 or 2 months prior to the realized interventions. We use the model, fitted to real-time observations, to evaluate the likelihood that candidate age-targeted interventions could control the outbreak. Using only data available prior to the interventions, we estimate that a significant excess of susceptible adults would prevent child-targeted campaigns from controlling the outbreak and that failing to account for age-specific confirmation rates would underestimate the importance of adult-targeted vaccination. © 2018 The Author(s).

Utilization of Exocellular Mannan from Rhodotorula glutinis as an Immunoreactive Antigen in Diagnosis of Leptospirosis

PubMed Central

Matsuo, Kouki; Isogai, Emiko; Araki, Yoshio

2000-01-01

Previously, Rhodotorula glutinis was reported to produce a large amount of exocellular mannan, having a repeating unit of →3)-d-Manp-(1→4)-d-Manp-(1→. Recently, we found that antigenic polysaccharides of Leptospira biflexa serovar patoc strain Patoc I have the same repeating unit and cross-react with antisera raised against extended strains of other leptospires (K. Matsuo, E. Isogai, and Y. Araki, Carbohydr. Res., in press). This structural identity and the difficulty of producing and isolating antigens led us to confirm the usefulness of Rhodotorula mannan as an immunoreactive antigen in a serological diagnosis of leptospirosis. In the present investigation, we confirmed the structural identity of an exocellular mannan isolated from R. glutinis AHU 3479 and tried to use it as an immunoreactive antigen in a serological diagnosis of leptospirosis. From its chemical analysis and 1H- and 13C-labeled nuclear magnetic resonance spectrometry, the Rhodotorula mannan was confirmed to consist of the same disaccharide units. Furthermore, such a preparation was shown to immunoreact to various sera from patients suffering with leptospirosis as well as to most rabbit antiserum preparations obtained from immunization with various strains of pathogenic leptospires. Therefore, the Rhodotorula mannan preparation is useful as an immunoreactive antigen in the serological diagnosis for leptospirosis. PMID:11015396

Real-time, non-invasive microscopic confirmation of clinical diagnosis of bullous pemphigoid using in vivo reflectance confocal microscopy.

PubMed

Ardigò, M; Agozzino, M; Amorosi, B; Moscarella, E; Cota, C; de Abreu, L; Berardesca, E

2014-05-01

Bullous pemphigoid is an autoimmune disease affecting prevalently the elder. In vivo reflectance confocal microscopy is a non-invasive technique for real-time imaging of the skin with cellular-level resolution. No previous data has been reported about confocal microscopy of bullous pemphigoid. Aim of this preliminary study is the evaluation of the potential of in vivo reflectance confocal microscopy for real-time, microscopical confirmation of clinical bullous pemphigoid diagnosis. A total of nine lesions from patients affected by pemphigoid underwent in vivo reflectance confocal microscopy before histological examination. In our preliminary study, confocal microscopy showed high grade of correspondence to histopathology. In particular, presence of sub-epidermal cleft and variable amount of oedema of the upper dermis associated with inflammatory cells infiltration were seen as prevalent confocal features in the bullous lesions considered. Differently, in urticarial lesions, no specific features could be appreciated at confocal analysis beside the presence of signs of spongiosis and perivascular inflammation. Confocal microscopy seems to be useful for in vivo, microscopical confirmation of the clinical suspect of bullous pemphigoid and for biopsy site selection in urticarial lesions to obtain a more significant specimen for histopathological examination. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Bos Taurus Breeds and Basal Diets

PubMed Central

Auffret, Marc D.; Stewart, Robert; Dewhurst, Richard J.; Duthie, Carol-Anne; Rooke, John A.; Wallace, Robert J.; Freeman, Tom C.; Snelling, Timothy J.; Watson, Mick; Roehe, Rainer

2018-01-01

Previous shotgun metagenomic analyses of ruminal digesta identified some microbial information that might be useful as biomarkers to select cattle that emit less methane (CH4), which is a potent greenhouse gas. It is known that methane production (g/kgDMI) and to an extent the microbial community is heritable and therefore biomarkers can offer a method of selecting cattle for low methane emitting phenotypes. In this study a wider range of Bos Taurus cattle, varying in breed and diet, was investigated to determine microbial communities and genetic markers associated with high/low CH4 emissions. Digesta samples were taken from 50 beef cattle, comprising four cattle breeds, receiving two basal diets containing different proportions of concentrate and also including feed additives (nitrate or lipid), that may influence methane emissions. A combination of partial least square analysis and network analysis enabled the identification of the most significant and robust biomarkers of CH4 emissions (VIP > 0.8) across diets and breeds when comparing all potential biomarkers together. Genes associated with the hydrogenotrophic methanogenesis pathway converting carbon dioxide to methane, provided the dominant biomarkers of CH4 emissions and methanogens were the microbial populations most closely correlated with CH4 emissions and identified by metagenomics. Moreover, these genes grouped together as confirmed by network analysis for each independent experiment and when combined. Finally, the genes involved in the methane synthesis pathway explained a higher proportion of variation in CH4 emissions by PLS analysis compared to phylogenetic parameters or functional genes. These results confirmed the reproducibility of the analysis and the advantage to use these genes as robust biomarkers of CH4 emissions. Volatile fatty acid concentrations and ratios were significantly correlated with CH4, but these factors were not identified as robust enough for predictive purposes. Moreover, the methanotrophic Methylomonas genus was found to be negatively correlated with CH4. Finally, this study confirmed the importance of using robust and applicable biomarkers from the microbiome as a proxy of CH4 emissions across diverse production systems and environments. PMID:29375511

Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Bos Taurus Breeds and Basal Diets.

PubMed

Auffret, Marc D; Stewart, Robert; Dewhurst, Richard J; Duthie, Carol-Anne; Rooke, John A; Wallace, Robert J; Freeman, Tom C; Snelling, Timothy J; Watson, Mick; Roehe, Rainer

2017-01-01

Previous shotgun metagenomic analyses of ruminal digesta identified some microbial information that might be useful as biomarkers to select cattle that emit less methane (CH 4 ), which is a potent greenhouse gas. It is known that methane production (g/kgDMI) and to an extent the microbial community is heritable and therefore biomarkers can offer a method of selecting cattle for low methane emitting phenotypes. In this study a wider range of Bos Taurus cattle, varying in breed and diet, was investigated to determine microbial communities and genetic markers associated with high/low CH 4 emissions. Digesta samples were taken from 50 beef cattle, comprising four cattle breeds, receiving two basal diets containing different proportions of concentrate and also including feed additives (nitrate or lipid), that may influence methane emissions. A combination of partial least square analysis and network analysis enabled the identification of the most significant and robust biomarkers of CH 4 emissions (VIP > 0.8) across diets and breeds when comparing all potential biomarkers together. Genes associated with the hydrogenotrophic methanogenesis pathway converting carbon dioxide to methane, provided the dominant biomarkers of CH 4 emissions and methanogens were the microbial populations most closely correlated with CH 4 emissions and identified by metagenomics. Moreover, these genes grouped together as confirmed by network analysis for each independent experiment and when combined. Finally, the genes involved in the methane synthesis pathway explained a higher proportion of variation in CH 4 emissions by PLS analysis compared to phylogenetic parameters or functional genes. These results confirmed the reproducibility of the analysis and the advantage to use these genes as robust biomarkers of CH 4 emissions. Volatile fatty acid concentrations and ratios were significantly correlated with CH 4 , but these factors were not identified as robust enough for predictive purposes. Moreover, the methanotrophic Methylomonas genus was found to be negatively correlated with CH 4 . Finally, this study confirmed the importance of using robust and applicable biomarkers from the microbiome as a proxy of CH 4 emissions across diverse production systems and environments.

The function of oxytocin: a potential biomarker for prostate cancer diagnosis and promoter of prostate cancer.

PubMed

Xu, Huan; Fu, Shi; Chen, Qi; Gu, Meng; Zhou, Juan; Liu, Chong; Chen, Yanbo; Wang, Zhong

2017-05-09

To measure the level of oxytocin in serum and prostate cancer (PCa) tissue and study its effect on the proliferation of PCa cells. Oxytocin level in serum was significantly increased in PCa patients compared with the no-carcinoma individuals. Additionally, the levels of oxytocin and its receptor were also elevated in the PCa tissue. However, no significant difference existed among the PCa of various Gleason grades. Western blot analysis confirmed the previous results and revealed an increased expression level of APPL1. The level of oxytocin in serum was measured by ELISA analysis. The expression of oxytocin and its receptor in prostate was analyzed by immunohistochemistry. The proliferation and apoptosis of PCa cells were assessed by the Cell Counting Kit 8 (CCK8) assay, cell cycle analysis and caspase3 activity analysis, respectively. Western blot analysis was used for the detection of PCNA, Caspase3 and APPL1 protein levels. Serum and prostatic oxytocin levels are increased in the PCa subjects. Serum oxytocin level may be a biomarker for PCa in the future. Oxytocin increases PCa growth and APPL1 expression.

Genetic Variation in the Free-Living Amoeba Naegleria fowleri

PubMed Central

Pélandakis, Michel; De Jonckheere, Johan F.; Pernin, Pierre

1998-01-01

In this study, 30 strains of the pathogenic free-living amoeba Naegleria fowleri were investigated by using the randomly amplified polymorphic DNA (RAPD) method. The present study confirmed our previous finding that RAPD variation is not correlated with geographical origin. In particular, Mexican strains belong to the variant previously detected in Asia, Europe, and the United States. In France, surprisingly, strains from Cattenom gave RAPD patterns identical to those of the Japanese strains. In addition, all of these strains, together with an additional French strain from Chooz, exhibited similarities to South Pacific strains. The results also confirmed the presence of numerous variants in Europe, whereas only two variants were detected in the United States. The two variants found in the United States were different from the South Pacific variants. These findings do not support the previous hypothesis concerning the origin and modes of dispersal of N. fowleri. PMID:9687460

Development of a scale to assess cancer stigma in the non-patient population

PubMed Central

2014-01-01

Background Illness-related stigma has attracted considerable research interest, but few studies have specifically examined stigmatisation of cancer in the non-patient population. The present study developed and validated a Cancer Stigma Scale (CASS) for use in the general population. Methods An item pool was developed on the basis of previous research into illness-related stigma in the general population and patients with cancer. Two studies were carried out. The first study used Exploratory factor analysis to explore the structure of items in a sample of 462 postgraduate students recruited through a London university. The second study used Confirmatory factor analysis to confirm the structure among 238 adults recruited through an online market research panel. Internal reliability, test-retest reliability and construct validity were also assessed. Results Exploratory factor analysis suggested six subscales, representing: Awkwardness, Severity, Avoidance, Policy Opposition, Personal Responsibility and Financial Discrimination. Confirmatory factor analysis confirmed this structure with a 25-item scale. All subscales showed adequate to good internal and test-retest reliability in both samples. Construct validity was also good, with mean scores for each subscale varying in the expected directions by age, gender, experience of cancer, awareness of lifestyle risk factors for cancer, and social desirability. Means for the subscales were consistent across the two samples. Conclusions These findings highlight the complexity of cancer stigma and provide the Cancer Stigma Scale (CASS) which can be used to compare populations, types of cancer and evaluate the effects of interventions designed to reduce cancer stigma in non-patient populations. PMID:24758482

Lower rates of hypoglycemia during maintenance treatment with insulin degludec/insulin aspart versus biphasic insulin aspart 30: a combined analysis of two Phase 3a studies in type 2 diabetes.

PubMed

Christiansen, Jens Sandahl; Niskanen, Leo; Rasmussen, Søren; Johansen, Thue; Fulcher, Greg

2016-09-01

Insulin degludec/insulin aspart (IDegAsp) is a soluble coformulation of the basal analog insulin degludec and the rapid-acting prandial insulin aspart in a single injection. The present combined analysis of two Phase 3a trials compared the incidence of hypoglycemia in participants treated twice daily with IDegAsp or biphasic insulin aspart 30 (BIAsp 30). Hypoglycemia data were analyzed from two similarly designed randomized controlled open-label treat-to-target Phase 3a clinical trials of adults with type 2 diabetes (T2D). Participants were treated twice daily with IDegAsp or BIAsp 30, with breakfast and their main evening meal. Over 26 weeks, the rates of overall confirmed, nocturnal confirmed and severe hypoglycemic events were 19%, 57%, and 39% lower, respectively, with IDegAsp (n = 504) than BIAsp 30 (n = 364); estimated rate ratios were 0.81 (95% confidence interval [CI] 0.67, 0.98; P = 0.0341), 0.43 (95% CI 0.31, 0.59; P = 0.0001), and 0.61 (95% CI 0.26, 1.45; P = NS). The between-treatment differences were more pronounced during the maintenance period (≥16 weeks); compared with BIAsp 30, rates of overall confirmed, nocturnal confirmed and severe hypoglycemic events with IDegAsp were 0.69 (95% CI 0.55, 0.87; -31%; P = 0.0015); 0.38 (95% CI 0.25, 0.58; -62%; P < 0.0001), and 0.16 (95% CI 0.04, 0.59; -84%; P = 0.0061), respectively. Compared with BIAsp 30 twice daily, IDegAsp twice daily provided similar improvements in glycemic control with a lower risk of hypoglycemia, particularly nocturnal hypoglycemia, in subjects with T2D previously treated with insulin. © 2016 The Authors. Journal of Diabetes published by John Wiley & Sons Australia, Ltd and Ruijin Hospital, Shanghai Jiaotong University School of Medicine.

THE SWIFT AGN AND CLUSTER SURVEY. II. CLUSTER CONFIRMATION WITH SDSS DATA

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

Griffin, Rhiannon D.; Dai, Xinyu; Kochanek, Christopher S.

2016-01-15

We study 203 (of 442) Swift AGN and Cluster Survey extended X-ray sources located in the SDSS DR8 footprint to search for galaxy over-densities in three-dimensional space using SDSS galaxy photometric redshifts and positions near the Swift cluster candidates. We find 104 Swift clusters with a >3σ galaxy over-density. The remaining targets are potentially located at higher redshifts and require deeper optical follow-up observations for confirmation as galaxy clusters. We present a series of cluster properties including the redshift, brightest cluster galaxy (BCG) magnitude, BCG-to-X-ray center offset, optical richness, and X-ray luminosity. We also detect red sequences in ∼85% ofmore » the 104 confirmed clusters. The X-ray luminosity and optical richness for the SDSS confirmed Swift clusters are correlated and follow previously established relations. The distribution of the separations between the X-ray centroids and the most likely BCG is also consistent with expectation. We compare the observed redshift distribution of the sample with a theoretical model, and find that our sample is complete for z ≲ 0.3 and is still 80% complete up to z ≃ 0.4, consistent with the SDSS survey depth. These analysis results suggest that our Swift cluster selection algorithm has yielded a statistically well-defined cluster sample for further study of cluster evolution and cosmology. We also match our SDSS confirmed Swift clusters to existing cluster catalogs, and find 42, 23, and 1 matches in optical, X-ray, and Sunyaev–Zel’dovich catalogs, respectively, and so the majority of these clusters are new detections.« less

Developing and validating a nutrition knowledge questionnaire: key methods and considerations.

PubMed

Trakman, Gina Louise; Forsyth, Adrienne; Hoye, Russell; Belski, Regina

2017-10-01

To outline key statistical considerations and detailed methodologies for the development and evaluation of a valid and reliable nutrition knowledge questionnaire. Literature on questionnaire development in a range of fields was reviewed and a set of evidence-based guidelines specific to the creation of a nutrition knowledge questionnaire have been developed. The recommendations describe key qualitative methods and statistical considerations, and include relevant examples from previous papers and existing nutrition knowledge questionnaires. Where details have been omitted for the sake of brevity, the reader has been directed to suitable references. We recommend an eight-step methodology for nutrition knowledge questionnaire development as follows: (i) definition of the construct and development of a test plan; (ii) generation of the item pool; (iii) choice of the scoring system and response format; (iv) assessment of content validity; (v) assessment of face validity; (vi) purification of the scale using item analysis, including item characteristics, difficulty and discrimination; (vii) evaluation of the scale including its factor structure and internal reliability, or Rasch analysis, including assessment of dimensionality and internal reliability; and (viii) gathering of data to re-examine the questionnaire's properties, assess temporal stability and confirm construct validity. Several of these methods have previously been overlooked. The measurement of nutrition knowledge is an important consideration for individuals working in the nutrition field. Improved methods in the development of nutrition knowledge questionnaires, such as the use of factor analysis or Rasch analysis, will enable more confidence in reported measures of nutrition knowledge.

Structural analysis of the outermost hair surface using TOF-SIMS with gas cluster ion beam sputtering.

PubMed

Lshikawa, Kazutaka; Okamoto, Masayuki; Aoyagi, Satoka

2016-06-28

A hair cuticle, which consists of flat overlapping scales that surround the hair fiber, protects inner tissues against external stimuli. The outermost surface of the cuticle is covered with a thin membrane containing proteins and lipids called the epicuticle. In a previous study, the authors conducted a depth profile analysis of a hair cuticle's amino acid composition to characterize its multilayer structure. Time-of-flight secondary ion mass spectrometry with a bismuth primary ion source was used in combination with the C60 sputtering technique for the analysis. It was confirmed that the lipids and cysteine-rich layer exist on the outermost cuticle surface, which is considered to be the epicuticle, though the detailed structure of the epicuticle has not been clarified. In this study, depth profile analysis of the cuticle surface was conducted using the argon gas cluster ion beam (Ar-GCIB) sputtering technique, in order to characterize the structure of the epicuticle. The shallow depth profile of the cuticle surface was investigated using an Ar-GCIB impact energy of 5 keV. Compared to the other amino acid peaks rich in the epicuticle, the decay of 18-methyleicosanic acid (18-MEA) thiolate peak was the fastest. This result suggests that the outermost surface of the hair is rich in 18-MEA. In conclusion, our results indicate that the outermost surfaces of cuticles have a multilayer (lipid and protein layers), which is consistent with the previously proposed structure.

US Atlantic Margin Methane Plumes Identified From Water Column Backscatter Data Acquired by NOAA Ship Okeanos Explorer

NASA Astrophysics Data System (ADS)

Kodis, M.; Skarke, A. D.; Ruppel, C. D.; Weber, T.; Lobecker, E.; Malik, M.

2013-12-01

The NOAA Office of Ocean Exploration and Research routinely uses NOAA Ship Okeanos Explorer to collect EM302 (30 kHz) multibeam bathymetric data and water column backscatter imagery. These backscatter data have been used to identify gas plumes associated with seafloor methane seeps as part of previous investigations in the Gulf of Mexico and at Blake Ridge. Here, we use QPS Fledermaus Midwater software to analyze over 200,000 km2 of multibeam data acquired on the continental slope and outer shelf of the US Atlantic margin in 2011, 2012, and 2013. Preliminary application of this analytical methodology in late 2012 revealed the first deepwater (> 1000 m water depth) cold seeps found on the US Atlantic margin north of Cape Hatteras as well as 47 new upper slope seeps (http://www.noaanews.noaa.gov/stories2012/20121219_gas_seeps.html). In this new analysis, we identify over 500 water column backscatter anomalies (WCA) originating at the seafloor and extending to various heights in the water column between Cape Hatteras and the Nantucket margin. Data set quality control was achieved through secondary independent analysis of all WCA backscatter records by a highly experienced researcher who assigned a quality factor to each anomaly. Additionally, a subset of the data was analyzed using a Matlab code designed to automatically detect WCA in backscatter data. These quality-control and WCA comparison procedures provide confidence that several hundred of the WCA are robust picks. The observed WCA are structurally consistent with previously confirmed gas bubble plumes, being vertically elongate, rooted at the seafloor, and deflected by currents. They are not structurally consistent with other common WCA such as schooling or swarming organisms. Additionally, the bases of selected WCA that were identified in this analysis have recently been visually and acoustically confirmed to be associated with emission of gas bubbles from the seafloor by the NOAA remotely operated vehicle Deep Discoverer. The physical characteristics and location of the WCA suggest that they are likely methane plumes, although this has yet to be confirmed by direct gas sampling. The WCA occur both in isolation and in clusters, and repeated observation of select seep fields indicated intermittent WCA identifications that could not be explained by uncertainties in the spatial resolution of the data. Thus, some of the WCA appear to exhibit ephemerality on time scales of hours to days. This research was undertaken while the lead author was a NOAA Hollings Scholar intern with the NOAA Office of Ocean Exploration and Research.

Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf.

PubMed

Magella, Bliss; Adam, Mike; Potter, Andrew S; Venkatasubramanian, Meenakshi; Chetal, Kashish; Hay, Stuart B; Salomonis, Nathan; Potter, S Steven

2018-02-01

The developing kidney provides a useful model for study of the principles of organogenesis. In this report we use three independent platforms, Drop-Seq, Chromium 10x Genomics and Fluidigm C1, to carry out single cell RNA-Seq (scRNA-Seq) analysis of the E14.5 mouse kidney. Using the software AltAnalyze, in conjunction with the unsupervised approach ICGS, we were unable to identify and confirm the presence of 16 distinct cell populations during this stage of active nephrogenesis. Using a novel integrative supervised computational strategy, we were able to successfully harmonize and compare the cell profiles across all three technological platforms. Analysis of possible cross compartment receptor/ligand interactions identified the nephrogenic zone stroma as a source of GDNF. This was unexpected because the cap mesenchyme nephron progenitors had been thought to be the sole source of GDNF, which is a key driver of branching morphogenesis of the collecting duct system. The expression of Gdnf by stromal cells was validated in several ways, including Gdnf in situ hybridization combined with immunohistochemistry for SIX2, and marker of nephron progenitors, and MEIS1, a marker of stromal cells. Finally, the single cell gene expression profiles generated in this study confirmed and extended previous work showing the presence of multilineage priming during kidney development. Nephron progenitors showed stochastic expression of genes associated with multiple potential differentiation lineages. Copyright © 2017 Elsevier Inc. All rights reserved.

Achieving surface chemical and morphologic alterations on tantalum by plasma electrolytic oxidation.

PubMed

Goularte, Marcelo Augusto Pinto Cardoso; Barbosa, Gustavo Frainer; da Cruz, Nilson Cristino; Hirakata, Luciana Mayumi

2016-12-01

Search for materials that may either replace titanium dental implants or constitute an alternative as a new dental implant material has been widely studied. As well, the search for optimum biocompatible metal surfaces remains crucial. So, the aim of this work is to develop an oxidized surface layer on tantalum using plasma electrolytic oxidation (PEO) similar to those existing on oral implants been marketed today. Cleaned tantalum samples were divided into group 1 (control) and groups 2, 3, and 4 (treated by PEO for 1, 3, and 5 min, respectively). An electrolytic solution diluted in 1-L deionized water was used for the anodizing process. Then, samples were washed with anhydrous ethyl alcohol and dried in the open air. For complete anodic treatment disposal, the samples were immersed in acetone altogether, taken to the ultrasonic tank for 10 min, washed again in distilled water, and finally air-dried. For the scanning electron microscopy (SEM) analysis, all samples were previously coated with gold; the salt deposition analysis was conducted with an energy-dispersive X-ray spectroscopy (EDS) system integrated with the SEM unit. SEM images confirmed the changes on tantalum strips surface according to different exposure times while EDS analysis confirmed increased salt deposition as exposure time to the anodizing process also increased. PEO was able to produce both surface alteration and salt deposition on tantalum strips similar to those existing on oral implants been marketed today.

High-Resolution Melting-Curve Analysis of Ligation-Mediated Real-Time PCR for Rapid Evaluation of an Epidemiological Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli ▿

PubMed Central

Woksepp, Hanna; Jernberg, Cecilia; Tärnberg, Maria; Ryberg, Anna; Brolund, Alma; Nordvall, Michaela; Olsson-Liljequist, Barbro; Wisell, Karin Tegmark; Monstein, Hans-Jürg; Nilsson, Lennart E.; Schön, Thomas

2011-01-01

Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described. Our objective was to further develop this method for real-time PCR and high-resolution melting analysis (HRM) in a single-tube system optimized in order to achieve results within 1 day. Following the optimization of LM/PCR for real-time PCR and HRM (LM/HRM), the method was applied for a nosocomial outbreak of extended-spectrum-beta-lactamase (ESBL)-producing and ST131-associated Escherichia coli isolates (n = 15) and control isolates (n = 29), including four previous clusters. The results from LM/HRM were compared to results from pulsed-field gel electrophoresis (PFGE), which served as the gold standard. All isolates from the nosocomial outbreak clustered by LM/HRM, which was confirmed by gel electrophoresis of the LM/PCR products and PFGE. Control isolates that clustered by LM/PCR (n = 4) but not by PFGE were resolved by confirmatory gel electrophoresis. We conclude that LM/HRM is a rapid method for the detection of nosocomial outbreaks of bacterial infections caused by ESBL-producing E. coli strains. It allows the analysis of isolates in a single-tube system within a day, and the discriminatory power is comparable to that of PFGE. PMID:21956981

High-resolution melting-curve analysis of ligation-mediated real-time PCR for rapid evaluation of an epidemiological outbreak of extended-spectrum-beta-lactamase-producing Escherichia coli.

PubMed

Woksepp, Hanna; Jernberg, Cecilia; Tärnberg, Maria; Ryberg, Anna; Brolund, Alma; Nordvall, Michaela; Olsson-Liljequist, Barbro; Wisell, Karin Tegmark; Monstein, Hans-Jürg; Nilsson, Lennart E; Schön, Thomas

2011-12-01

Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described. Our objective was to further develop this method for real-time PCR and high-resolution melting analysis (HRM) in a single-tube system optimized in order to achieve results within 1 day. Following the optimization of LM/PCR for real-time PCR and HRM (LM/HRM), the method was applied for a nosocomial outbreak of extended-spectrum-beta-lactamase (ESBL)-producing and ST131-associated Escherichia coli isolates (n = 15) and control isolates (n = 29), including four previous clusters. The results from LM/HRM were compared to results from pulsed-field gel electrophoresis (PFGE), which served as the gold standard. All isolates from the nosocomial outbreak clustered by LM/HRM, which was confirmed by gel electrophoresis of the LM/PCR products and PFGE. Control isolates that clustered by LM/PCR (n = 4) but not by PFGE were resolved by confirmatory gel electrophoresis. We conclude that LM/HRM is a rapid method for the detection of nosocomial outbreaks of bacterial infections caused by ESBL-producing E. coli strains. It allows the analysis of isolates in a single-tube system within a day, and the discriminatory power is comparable to that of PFGE.

Identifying training needs of logging truck drivers using a skill inventory.

PubMed

Carnahan, B J

2004-11-01

The purpose of this research was to determine if the Driver Skill Inventory (DSI) could be used to characterize the self-assessed driving performance of commercial logging truck drivers. The DSI requires respondents to subjectively evaluate their own ability in regard to 15 different driving skills. The DSI responses of 1000 logging truck drivers were collected across three southeastern states. The underlying hypothesis in the current study was that DSI responses of these drivers would have similar reliability and factor structure as those DSI responses collected from non-commercial drivers in previous studies. Factor analysis of the data confirmed this hypothesis. Statistical analysis revealed that low self-ratings on various safety skill items within the DSI inventory were associated with: (1) inconsistency in using seat belts, (2) inconsistency in performing pre-trip inspections on logging trucks, and (3) committing moving violations. Conversely, high self-ratings ratings on various perceptual-motor skill items were associated with these same at-risk behaviors. The perceptual-motor skill items were also positively associated with negative attitudes toward driving regulations and the number of moving violations incurred over a three-year period. Non-parametric statistical analysis revealed that self-assessments were lowest for DSI skills pertaining to controlling one's anger while driving and managing the truck through a skid or slide. Results of the study confirmed that the DSI can be successfully applied to commercial logging truck drivers as part of an overall comprehensive training needs assessment.

The Effective Dynamic Ranges for Glaucomatous Visual Field Progression With Standard Automated Perimetry and Stimulus Sizes III and V.

PubMed

Wall, Michael; Zamba, Gideon K D; Artes, Paul H

2018-01-01

It has been shown that threshold estimates below approximately 20 dB have little effect on the ability to detect visual field progression in glaucoma. We aimed to compare stimulus size V to stimulus size III, in areas of visual damage, to confirm these findings by using (1) a different dataset, (2) different techniques of progression analysis, and (3) an analysis to evaluate the effect of censoring on mean deviation (MD). In the Iowa Variability in Perimetry Study, 120 glaucoma subjects were tested every 6 months for 4 years with size III SITA Standard and size V Full Threshold. Progression was determined with three complementary techniques: pointwise linear regression (PLR), permutation of PLR, and linear regression of the MD index. All analyses were repeated on "censored'' datasets in which threshold estimates below a given criterion value were set to equal the criterion value. Our analyses confirmed previous observations that threshold estimates below 20 dB contribute much less to visual field progression than estimates above this range. These findings were broadly similar with stimulus sizes III and V. Censoring of threshold values < 20 dB has relatively little impact on the rates of visual field progression in patients with mild to moderate glaucoma. Size V, which has lower retest variability, performs at least as well as size III for longitudinal glaucoma progression analysis and appears to have a larger useful dynamic range owing to the upper sensitivity limit being higher.

In Silico Pattern-Based Analysis of the Human Cytomegalovirus Genome

PubMed Central

Rigoutsos, Isidore; Novotny, Jiri; Huynh, Tien; Chin-Bow, Stephen T.; Parida, Laxmi; Platt, Daniel; Coleman, David; Shenk, Thomas

2003-01-01

More than 200 open reading frames (ORFs) from the human cytomegalovirus genome have been reported as potentially coding for proteins. We have used two pattern-based in silico approaches to analyze this set of putative viral genes. With the help of an objective annotation method that is based on the Bio-Dictionary, a comprehensive collection of amino acid patterns that describes the currently known natural sequence space of proteins, we have reannotated all of the previously reported putative genes of the human cytomegalovirus. Also, with the help of MUSCA, a pattern-based multiple sequence alignment algorithm, we have reexamined the original human cytomegalovirus gene family definitions. Our analysis of the genome shows that many of the coded proteins comprise amino acid combinations that are unique to either the human cytomegalovirus or the larger group of herpesviruses. We have confirmed that a surprisingly large portion of the analyzed ORFs encode membrane proteins, and we have discovered a significant number of previously uncharacterized proteins that are predicted to be G-protein-coupled receptor homologues. The analysis also indicates that many of the encoded proteins undergo posttranslational modifications such as hydroxylation, phosphorylation, and glycosylation. ORFs encoding proteins with similar functional behavior appear in neighboring regions of the human cytomegalovirus genome. All of the results of the present study can be found and interactively explored online (http://cbcsrv.watson.ibm.com/virus/). PMID:12634390

Examination of fungi in domestic interiors by using factor analysis: Correlations and associations with home factors. [Cladosporium, Alternaria, Epicoccum, Aureobasidium, Aspergillus; Penicillium

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

Su, H.J.; Rotnitzky, A.; Spengler, J.D.

1992-01-01

Factor analysis was utilized to investigate correlations among airborne microorganisms collected with Andersen samplers from homes in Topeka, Kans., during the winter of 1987 to 1988. The factors derived were used to relate microbial concentrations with categorical, questionnaire-derived descriptions of housing conditions. This approach successfully identified groups of common aboveground decay fungi including Cladosporium, Alternaria, Epicoccum, and Aureobasidium spp. The common soil fungi Aspergillus and Penicillium spp. were also separated as a group. These previously known ecological groupings were confirmed with air sampling data by a quantitative evaluation technique. The above ground decay fungi sampled indoors in winter were presentmore » at relatively high concentrations in homes with gas stoves for cooking, suggesting a possible association between these fungi and increased humidity from the combustion process. Elevated concentrations of the soil fungi were significantly associated with the dirt floor, crawl-space type of basement. Elevated concentrations of water-requiring fungi, such as Fusarium spp., were shown to be associated with water collection in domestic interiors. Also, elevated mean concentrations for the group of fungi including Cladosporium, Epicoccum, Aureobasidium, and yeast spp. were found to be associated with symptoms reported on a health questionnaire. This finding was consistent with the authors previous study of associations between respiratory health and airborne microorganisms by univariate logistic regression analysis.« less

In silico pattern-based analysis of the human cytomegalovirus genome.

PubMed

Rigoutsos, Isidore; Novotny, Jiri; Huynh, Tien; Chin-Bow, Stephen T; Parida, Laxmi; Platt, Daniel; Coleman, David; Shenk, Thomas

2003-04-01

More than 200 open reading frames (ORFs) from the human cytomegalovirus genome have been reported as potentially coding for proteins. We have used two pattern-based in silico approaches to analyze this set of putative viral genes. With the help of an objective annotation method that is based on the Bio-Dictionary, a comprehensive collection of amino acid patterns that describes the currently known natural sequence space of proteins, we have reannotated all of the previously reported putative genes of the human cytomegalovirus. Also, with the help of MUSCA, a pattern-based multiple sequence alignment algorithm, we have reexamined the original human cytomegalovirus gene family definitions. Our analysis of the genome shows that many of the coded proteins comprise amino acid combinations that are unique to either the human cytomegalovirus or the larger group of herpesviruses. We have confirmed that a surprisingly large portion of the analyzed ORFs encode membrane proteins, and we have discovered a significant number of previously uncharacterized proteins that are predicted to be G-protein-coupled receptor homologues. The analysis also indicates that many of the encoded proteins undergo posttranslational modifications such as hydroxylation, phosphorylation, and glycosylation. ORFs encoding proteins with similar functional behavior appear in neighboring regions of the human cytomegalovirus genome. All of the results of the present study can be found and interactively explored online (http://cbcsrv.watson.ibm.com/virus/).

Cost analysis of hospitalized Clostridium difficile-associated diarrhea (CDAD)

PubMed Central

Hübner, Claudia; Hübner, Nils-Olaf; Muhr, Michaela; Claus, Franziska; Leesch, Henning; Kramer, Axel; Flessa, Steffen

2015-01-01

Aim: Clostridium difficile-associated diarrhea (CDAD) causes heavy financial burden on healthcare systems worldwide. As with all hospital-acquired infections, prolonged hospital stays are the main cost driver. Previous cost studies only include hospital billing data and compare the length of stay in contrast to non-infected patients. To date, a survey of actual cost has not yet been conducted. Method: A retrospective analysis of data for patients with nosocomial CDAD was carried out over a 1-year period at the University Hospital of Greifswald. Based on identification of CDAD related treatment processes, cost of hygienic measures, antibiotics and laboratory as well as revenue losses due to bed blockage and increased length of stay were calculated. Results: 19 patients were included in the analysis. On average, a CDAD patient causes additional costs of € 5,262.96. Revenue losses due to extended length of stay take the highest proportion with € 2,555.59 per case, followed by loss in revenue due to bed blockage during isolation with € 2,413.08 per case. Overall, these opportunity costs accounted for 94.41% of total costs. In contrast, costs for hygienic measures (€ 253.98), pharmaceuticals (€ 22.88) and laboratory (€ 17.44) are quite low. Conclusion: CDAD results in significant additional costs for the hospital. This survey of actual costs confirms previous study results. PMID:26550553

Trends in biomedical informatics: automated topic analysis of JAMIA articles.

PubMed

Han, Dong; Wang, Shuang; Jiang, Chao; Jiang, Xiaoqian; Kim, Hyeon-Eui; Sun, Jimeng; Ohno-Machado, Lucila

2015-11-01

Biomedical Informatics is a growing interdisciplinary field in which research topics and citation trends have been evolving rapidly in recent years. To analyze these data in a fast, reproducible manner, automation of certain processes is needed. JAMIA is a "generalist" journal for biomedical informatics. Its articles reflect the wide range of topics in informatics. In this study, we retrieved Medical Subject Headings (MeSH) terms and citations of JAMIA articles published between 2009 and 2014. We use tensors (i.e., multidimensional arrays) to represent the interaction among topics, time and citations, and applied tensor decomposition to automate the analysis. The trends represented by tensors were then carefully interpreted and the results were compared with previous findings based on manual topic analysis. A list of most cited JAMIA articles, their topics, and publication trends over recent years is presented. The analyses confirmed previous studies and showed that, from 2012 to 2014, the number of articles related to MeSH terms Methods, Organization & Administration, and Algorithms increased significantly both in number of publications and citations. Citation trends varied widely by topic, with Natural Language Processing having a large number of citations in particular years, and Medical Record Systems, Computerized remaining a very popular topic in all years. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Solid-phase extraction and GC-MS analysis of THC-COOH method optimized for a high-throughput forensic drug-testing laboratory.

PubMed

Stout, P R; Horn, C K; Klette, K L

2001-10-01

In order to facilitate the confirmation analysis of large numbers of urine samples previously screened positive for delta9-tetrahydrocannabinol (THC), an extraction, derivitization, and GC-MS analysis method was developed. This method utilized a positive pressure manifold anion-exchange polymer-based solid-phase extraction followed by elution directly into the automated liquid sampling (ALS) vials. Rapid derivitization was accomplished using pentafluoropropionic anhydride/pentafluoropropanol (PFPA/PFPOH). Recoveries averaged 95% with a limit of detection of 0.875 ng/mL with a 3-mL sample volume. Performance of 11-nor-delta9-tetrahydrocannabinol-9-carboxylic acid (THC-COOH)-d3 and THC-COOH-d9 internal standards were evaluated. The method was linear to 900 ng/mL THC-COOH using THC-COOH-d9 with negligible contribution from the internal standard to very weak samples. Excellent agreement was seen with previous quantitations of human urine samples. More than 1000 human urine samples were analyzed using the method with 300 samples analyzed using an alternate qualifier ion (m/z 622) after some interference was observed with a qualifier ion (m/z 489). The 622 ion did not exhibit any interference even in samples with interfering peaks present in the 489 ion. The method resulted in dramatic reductions in processing time, waste production, and exposure hazards to laboratory personnel.

A Pilot Genome-Wide Association Study in Postmenopausal Mexican-Mestizo Women Implicates the RMND1/CCDC170 Locus Is Associated with Bone Mineral Density

PubMed Central

Villalobos-Comparán, Marisela; Estrada, Karol; Parra-Torres, Alma Y.; González-Mercado, Anahí; Patiño, Nelly; Castillejos-López, Manuel; Quiterio, Manuel; Fernandez-López, Juan Carlos; Ibarra, Bertha; Romero-Hidalgo, Sandra; Salmerón, Jorge

2017-01-01

To identify genetic variants influencing bone mineral density (BMD) in the Mexican-Mestizo population, we performed a GWAS for femoral neck (FN) and lumbar spine (LS) in Mexican-Mestizo postmenopausal women. In the discovery sample, 300,000 SNPs were genotyped in a cohort of 411 postmenopausal women and seven SNPs were analyzed in the replication cohort (n = 420). The combined results of a meta-analysis from the discovery and replication samples identified two loci, RMND1 (rs6904364, P = 2.77 × 10−4) and CCDC170 (rs17081341, P = 1.62 × 10−5), associated with FN BMD. We also compared our results with those of the Genetic Factors for Osteoporosis (GEFOS) Consortium meta-analysis. The comparison revealed two loci previously reported in the GEFOS meta-analysis: SOX6 (rs7128738) and PKDCC (rs11887431) associated with FN and LS BMD, respectively, in our study population. Interestingly, rs17081341 rare in Caucasians (minor allele frequency < 0.03) was found in high frequency in our population, which suggests that this association could be specific to non-Caucasian populations. In conclusion, the first pilot Mexican GWA study of BMD confirmed previously identified loci and also demonstrated the importance of studying variability in diverse populations and/or specific populations. PMID:28840121

Systematic analysis of gene expression pattern in has-miR-197 over-expressed human uterine leiomyoma cells.

PubMed

Ling, Jing; Wu, Xiaoli; Fu, Ziyi; Tan, Jie; Xu, Qing

2015-10-01

Our previous study showed that the expression of miR-197 in leiomyoma was down-regulated compared with myometrium. Further, miR-197 has been identified to affect uterine leiomyoma cell proliferation, apoptosis, and metastasis ability, though the responsible molecular mechanism has not been well elucidated. In this study, we sought to determine the expression patterns of miR-197 targeted genes and to explore their potential functions, participating Pathways and the networks that are involved in the biological behavior of human uterine leiomyoma. After transfection of human uterine leiomyoma cells with miR-197, we confirmed the expression level of miR-197 using quantitative real-time PCR (qRT-PCR), and we detected the gene expression profiles after miR-197 over-expression through DNA microarray analysis. Further, we performed GO and Pathway analysis. The dominantly dys-regulated genes, which were up- or down-regulated by more than 10-fold, compared with parental cells, were confirmed using qRT-PCR technology. Compared with the control group, miR-197 was up-regulated by 30-fold after miR-197 lentiviral transfection. The microarray data showed that 872 genes were dys-regulated by more than 2-fold in human uterine leiomyoma cells after miR-197 overexpression, including 537 up-regulated and 335 down-regulated genes. The GO analysis indicated that the dys-regulated genes were primarily involved in response to stimuli, multicellular organ processes, and the signaling of biological progression. Further, Pathway analysis data showed that these genes participated in regulating several signaling Pathways, including the JAK/STAT signaling Pathway, the Toll-like receptor signaling Pathway, and cytokine-cytokine receptor interaction. The qRT-PCR results confirmed that 17 of the 66 selected genes, which were up- or down-regulated more than 10-fold by miR-197, were consistent with the microarray results, including tumorigenesis-related genes, such as DRT7, SLC549, SFMBT2, FLJ37956, FBLN2, C10orf35, HOXD12, CACNG7, and LOC100134279. Our study explored gene expression patterns after miR-197 overexpression and confirmed 17 dominantly dys-regulated genes, which could expand the insights into the function of miR-197 and the molecular mechanisms during the development and progression of uterine leiomyomas. This study might afford new clues for understanding the pathogenesis of uterine leiomyomas, and it could likely provide a unique method for diagnosing or predicting prognosis in the clinical treatment of leiomyoma. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea.

PubMed

Desgroux, Aurore; L'Anthoëne, Virginie; Roux-Duparque, Martine; Rivière, Jean-Philippe; Aubert, Grégoire; Tayeh, Nadim; Moussart, Anne; Mangin, Pierre; Vetel, Pierrick; Piriou, Christophe; McGee, Rebecca J; Coyne, Clarice J; Burstin, Judith; Baranger, Alain; Manzanares-Dauleux, Maria; Bourion, Virginie; Pilet-Nayel, Marie-Laure

2016-02-20

Genome-wide association (GWA) mapping has recently emerged as a valuable approach for refining the genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil-borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. Linkage mapping studies reported quantitative trait loci (QTL) controlling resistance to A. euteiches in pea. However the confidence intervals (CIs) of these QTL remained large and were often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to use a GWA approach to validate and refine CIs of the previously reported Aphanomyces resistance QTL, as well as identify new resistance loci. A pea-Aphanomyces collection of 175 pea lines, enriched in germplasm derived from previously studied resistant sources, was evaluated for resistance to A. euteiches in field infested nurseries in nine environments and with two strains in climatic chambers. The collection was genotyped using 13,204 SNPs from the recently developed GenoPea Infinium® BeadChip. GWA analysis detected a total of 52 QTL of small size-intervals associated with resistance to A. euteiches, using the recently developed Multi-Locus Mixed Model. The analysis validated six of the seven previously reported main Aphanomyces resistance QTL and detected novel resistance loci. It also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of favourable haplotypes in the most resistant lines. Previous linkages between resistance alleles and undesired late-flowering alleles for dry pea breeding were mostly confirmed, but the linkage between loci controlling resistance and coloured flowers was broken due to the high resolution of the analysis. A high proportion of the putative candidate genes underlying resistance loci encoded stress-related proteins and others suggested that the QTL are involved in diverse functions. This study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding.

Phylogenetic Interrelationships of Ginglymodian Fishes (Actinopterygii: Neopterygii)

PubMed Central

López-Arbarello, Adriana

2012-01-01

The Ginglymodi is one of the most common, though poorly understood groups of neopterygians, which includes gars, macrosemiiforms, and “semionotiforms.” In particular, the phylogenetic relationships between the widely distributed “semionotiforms,” and between them and other ginglymodians have been enigmatic. Here, the phylogenetic relationships between eight of the 11 “semionotiform” genera, five genera of living and fossil gars and three macrosemiid genera, are analysed through cladistic analysis, based on 90 morphological characters and 37 taxa, including 7 out-group taxa. The results of the analysis show that the Ginglymodi includes two main lineages: Lepisosteiformes and †Semionotiformes. The genera †Pliodetes, †Araripelepidotes, †Lepidotes, †Scheenstia, and †Isanichthys are lepisosteiforms, and not semionotiforms, as previously thought, and these taxa extend the stratigraphic range of the lineage leading to gars back up to the Early Jurassic. A monophyletic †Lepidotes is restricted to the Early Jurassic species, whereas the strongly tritoral species previously referred to †Lepidotes are referred to †Scheenstia. Other species previously referred to †Lepidotes represent other genera or new taxa. The macrosemiids are well nested within semionotiforms, together with †Semionotidae, here restricted to †Semionotus, and a new family including †Callipurbeckia n. gen. minor (previously referred to †Lepidotes), †Macrosemimimus, †Tlayuamichin, †Paralepidotus, and †Semiolepis. Due to the numerous taxonomic changes needed according to the phylogenetic analysis, this article also includes formal taxonomic definitions and diagnoses for all generic and higher taxa, which are new or modified. The study of Mesozoic ginglymodians led to confirm Patterson’s observation that these fishes show morphological affinities with both halecomorphs and teleosts. Therefore, the compilation of large data sets including the Mesozoic ginglymodians and the re-evaluation of several hypotheses of homology are essential to test the hypotheses of the Halecostomi vs. the Holostei, which is one of the major topics in the evolution of Mesozoic vertebrates and the origin of modern fish faunas. PMID:22808031

Phylogenetic interrelationships of ginglymodian fishes (Actinopterygii: Neopterygii).

PubMed

López-Arbarello, Adriana

2012-01-01

The Ginglymodi is one of the most common, though poorly understood groups of neopterygians, which includes gars, macrosemiiforms, and "semionotiforms." In particular, the phylogenetic relationships between the widely distributed "semionotiforms," and between them and other ginglymodians have been enigmatic. Here, the phylogenetic relationships between eight of the 11 "semionotiform" genera, five genera of living and fossil gars and three macrosemiid genera, are analysed through cladistic analysis, based on 90 morphological characters and 37 taxa, including 7 out-group taxa. The results of the analysis show that the Ginglymodi includes two main lineages: Lepisosteiformes and †Semionotiformes. The genera †Pliodetes, †Araripelepidotes, †Lepidotes, †Scheenstia, and †Isanichthys are lepisosteiforms, and not semionotiforms, as previously thought, and these taxa extend the stratigraphic range of the lineage leading to gars back up to the Early Jurassic. A monophyletic †Lepidotes is restricted to the Early Jurassic species, whereas the strongly tritoral species previously referred to †Lepidotes are referred to †Scheenstia. Other species previously referred to †Lepidotes represent other genera or new taxa. The macrosemiids are well nested within semionotiforms, together with †Semionotidae, here restricted to †Semionotus, and a new family including †Callipurbeckia n. gen. minor (previously referred to †Lepidotes), †Macrosemimimus, †Tlayuamichin, †Paralepidotus, and †Semiolepis. Due to the numerous taxonomic changes needed according to the phylogenetic analysis, this article also includes formal taxonomic definitions and diagnoses for all generic and higher taxa, which are new or modified. The study of Mesozoic ginglymodians led to confirm Patterson's observation that these fishes show morphological affinities with both halecomorphs and teleosts. Therefore, the compilation of large data sets including the Mesozoic ginglymodians and the re-evaluation of several hypotheses of homology are essential to test the hypotheses of the Halecostomi vs. the Holostei, which is one of the major topics in the evolution of Mesozoic vertebrates and the origin of modern fish faunas.

Age differences in the effect of framing on risky choice: A meta-analysis

PubMed Central

Best, Ryan; Charness, Neil

2015-01-01

The framing of decision scenarios in terms of potential gains versus losses has been shown to influence choice preferences between sure and risky options. Normative cognitive changes associated with aging have been known to affect decision-making, which has led to a number of studies investigating the influence of aging on the effect of framing. Mata, Josef, Samanez-Larkin, and Hertwig (2011) systematically reviewed the available literature using a meta-analytic approach, but did not include tests of homogeneity nor subsequent moderator variable analyses. The current review serves to extend the previous analysis to include such tests as well as update the pool of studies available for analysis. Results for both positively and negatively framed conditions were reviewed using two meta-analyses encompassing data collected from 3,232 subjects across 18 studies. Deviating from the previous results, the current analysis finds a tendency for younger adults to choose the risky option more often than older adults for positively framed items. Moderator variable analyses find this effect to likely be driven by the specific decision scenario, showing a significant effect with younger adults choosing the risky option more often in small-amount financial and large-amount mortality-based scenarios. For negatively framed items, the current review found no overall age difference in risky decision making, confirming the results from the prior meta-analysis. Moderator variable analyses conducted to address heterogeneity found younger adults to be more likely than older adults to choose the risky option for negatively framed high-amount mortality-based decision scenarios. Practical implications for older adults are discussed. PMID:26098168

Age differences in the effect of framing on risky choice: A meta-analysis.

PubMed

Best, Ryan; Charness, Neil

2015-09-01

The framing of decision scenarios in terms of potential gains versus losses has been shown to influence choice preferences between sure and risky options. Normative cognitive changes associated with aging have been known to affect decision making, which has led to a number of studies investigating the influence of aging on the effect of framing. Mata, Josef, Samanez-Larkin, and Hertwig (2011) systematically reviewed the available literature using a meta-analytic approach, but did not include tests of homogeneity or subsequent moderator variable analyses. The current review serves to extend the previous analysis to include such tests as well as update the pool of studies available for analysis. Results for both positively and negatively framed conditions were reviewed using 2 meta-analyses encompassing data collected from 3,232 subjects across 18 studies. Deviating from the previous results, the current analysis found a tendency for younger adults to choose the risky option more often than older adults for positively framed items. Moderator variable analyses found this effect likely to be driven by the specific decision scenario, showing a significant effect, with younger adults choosing the risky option more often in small-amount financial and large-amount mortality-based scenarios. For negatively framed items, the current review found no overall age difference in risky decision making, confirming the results from the prior meta-analysis. Moderator variable analyses conducted to address heterogeneity found younger adults to be more likely than older adults to choose the risky option for negatively framed high-amount mortality-based decision scenarios. Practical implications for older adults are discussed. (c) 2015 APA, all rights reserved).

Usher syndrome associated with Fuchs' heterochromic uveitis.

PubMed

Lichtinger, Alejandro; Chowers, Itay; Amer, Radgonde

2010-10-01

The purpose of this study is to report two new cases of Usher syndrome associated with Fuchs' heterochromic uveitis (FHU), to confirm our previous observation of the association between FHU and retinitis pigmentosa (RP), and to evaluate if FHU is particularly associated with Usher syndrome. Retrospective medical record review of all new RP cases at Hadassah Medical Center between the years 2000 and 2007, review of our previously published data, and a meta-analysis of published relevant articles in peer reviewed journals. During the time frame of the study we diagnosed 58 new cases of RP, of whom one male and one female had the typical findings of FHU, and both had Usher syndrome type II. The difference in the occurrence of FHU between the 616 controls and the patients with RP was significant (p = 0.0073, Fisher's exact test). In our combined data, FHU occurred only in two types of RP; RP simplex with an incidence of 0.57%, and Usher syndrome with an incidence of 13.5%. This difference between the incidence of FHU in patients with Usher syndrome and other types of RP was significant (p < 0.0001, Fisher's exact test). Adding up these two cases with what is already published in the literature makes up a total of 17 RP patients with coexisting FHU. This study confirms the association between FHU and RP; and a particularly stronger association with Usher syndrome type II. Although infectious agents seem to play a role, the cause for this significant correlation is still unclear.

Investigating biogeographic boundaries of the Sunda shelf: A phylogenetic analysis of two island populations of Macaca fascicularis.

PubMed

Klegarth, A R; Sanders, S A; Gloss, A D; Lane-deGraaf, K E; Jones-Engel, L; Fuentes, A; Hollocher, H

2017-08-01

Cyclical submergence and re-emergence of the Sunda Shelf throughout the Pleistocene served as a dynamic biogeographic landscape, across which long-tailed macaques (Macaca fascicularis) have migrated and evolved. Here, we tested the integrity of the previously reported continental-insular haplotype divide reported among Y and mitochondrial DNA lineages across multiple studies. The continental-insular haplotype divide was tested by heavily sampling wild macaques from two important biogeographic regions within Sundaland: (1) Singapore, the southernmost tip of continental Asia and (2) Bali, Indonesia, the southeastern edge of the Indonesian archipelago, immediately west of Wallace's line. Y DNA was haplotyped for samples from Bali, deep within the Indonesian archipelago. Mitochondrial D-loop from both islands was analyzed against existing data using Maximum Likelihood and Bayesian approaches. We uncovered both "continental" and "insular" Y DNA haplotypes in Bali. Between Singapore and Bali we found 52 unique mitochondrial haplotypes, none of which had been previously described. Phylogenetic analyses confirmed a major haplogroup division within Singapore and identified five new Singapore subclades and two primary subclades in Bali. While we confirmed the continental-insular divide among mtDNA haplotypes, maintenance of both Y DNA haplotypes on Bali, deep within the Indonesian archipelago calls into question the mechanism by which Y DNA diversity has been maintained. It also suggests the continental-insular designation is less appropriate for Y DNA, leading us to propose geographically neutral Y haplotype designations. © 2017 Wiley Periodicals, Inc.

Workplace bullying and common mental disorders: a follow-up study.

PubMed

Lahelma, Eero; Lallukka, Tea; Laaksonen, Mikko; Saastamoinen, Peppiina; Rahkonen, Ossi

2012-06-01

Workplace bullying has been associated with mental health, but longitudinal studies confirming the association are lacking. This study examined the associations of workplace bullying with subsequent common mental disorders 5-7 years later, taking account of baseline common mental disorders and several covariates. Baseline questionnaire survey data were collected in 2000-2002 among municipal employees, aged 40-60 years (n=8960; 80% women; response rate 67%). Follow-up data were collected in 2007 (response rate 83%). The final data amounted to 6830 respondents. Workplace bullying was measured at baseline using an instructed question about being bullied currently, previously or never. Common mental disorders were measured at baseline and at follow-up using the 12-item version of the General Health Questionnaire. Those scoring 3-12 were classified as having common mental disorders. Covariates included bullying in childhood, occupational and employment position, work stress, obesity and limiting longstanding illness. Logistic regression analysis was used. After adjusting for age, being currently bullied at baseline was associated with common mental disorders at follow-up among women (OR 2.34, CI 1.81 to 3.02) and men (OR 3.64, CI 2.13 to 6.24). The association for the previously bullied was weaker. Adjusting for baseline common mental disorders, the association attenuated but remained. Adjusting for further covariates did not substantially alter the studied association. CONCLUSION The study confirms that workplace bullying is likely to contribute to subsequent common mental disorders. Measures against bullying are needed at workplaces to prevent mental disorders.

Genetic characterization of Echinostoma revolutum and Echinoparyphium recurvatum (Trematoda: Echinostomatidae) in Thailand and phylogenetic relationships with other isolates inferred by ITS1 sequence.

PubMed

Saijuntha, Weerachai; Tantrawatpan, Chairat; Sithithaworn, Paiboon; Andrews, Ross H; Petney, Trevor N

2011-03-01

Echinostomatidae are common, widely distributed intestinal parasites causing significant disease in both animals and humans worldwide. In spite of their importance, the taxonomy of these echinostomes is still controversial. The taxonomic status of two species, Echinostoma revolutum and Echinoparyphium recurvatum, which commonly infect poultry and other birds, as well as human, is problematical. Previous phylogenetic analyses of Southeast Asian strains indicate that these species cluster as sister taxa. In the present study, the first internal transcribed spacer (ITS1) sequence was used for genetic characterization and to examine the phylogenetic relationships between an isolate from Thailand with other isolates available from GenBank database. Interspecies differences in ITS1 sequence between E. revolutum and E. recurvatum were detected at 6 (3%) of the 203 alignment positions. Of these, nucleotide deletion at positions 25, 26, and 27, pyrimidine transition at 50, 189, and pyrimidine transversion at 118 were observed. Phylogenetic analysis revealed that E. recurvatum from Thailand clustered as a sister taxa with E. revolutum and not with other members of the genus Echinoparyphium. Interestingly, this result confirms a previous report based on allozyme electrophoresis and mitochondrial DNA that E. revolutum and E. recurvatum in Southeast Asia are sister species. Hence, the taxonomic status of E. recurvatum in Thailand, as well as in Southeast Asian countries needs to be confirmed and revised using more comprehensive analyses based on morphology and other molecular techniques.

Truncating SLC5A7 mutations underlie a spectrum of dominant hereditary motor neuropathies.

PubMed

Salter, Claire G; Beijer, Danique; Hardy, Holly; Barwick, Katy E S; Bower, Matthew; Mademan, Ines; De Jonghe, Peter; Deconinck, Tine; Russell, Mark A; McEntagart, Meriel M; Chioza, Barry A; Blakely, Randy D; Chilton, John K; De Bleecker, Jan; Baets, Jonathan; Baple, Emma L; Walk, David; Crosby, Andrew H

2018-04-01

To identify the genetic cause of disease in 2 previously unreported families with forms of distal hereditary motor neuropathies (dHMNs). The first family comprises individuals affected by dHMN type V, which lacks the cardinal clinical feature of vocal cord paralysis characteristic of dHMN-VII observed in the second family. Next-generation sequencing was performed on the proband of each family. Variants were annotated and filtered, initially focusing on genes associated with neuropathy. Candidate variants were further investigated and confirmed by dideoxy sequence analysis and cosegregation studies. Thorough patient phenotyping was completed, comprising clinical history, examination, and neurologic investigation. dHMNs are a heterogeneous group of peripheral motor neuron disorders characterized by length-dependent neuropathy and progressive distal limb muscle weakness and wasting. We previously reported a dominant-negative frameshift mutation located in the concluding exon of the SLC5A7 gene encoding the choline transporter (CHT), leading to protein truncation, as the likely cause of dominantly-inherited dHMN-VII in an extended UK family. In this study, our genetic studies identified distinct heterozygous frameshift mutations located in the last coding exon of SLC5A7 , predicted to result in the truncation of the CHT C-terminus, as the likely cause of the condition in each family. This study corroborates C-terminal CHT truncation as a cause of autosomal dominant dHMN, confirming upper limb predominating over lower limb involvement, and broadening the clinical spectrum arising from CHT malfunction.

Cognitive correlates of verbal memory and verbal fluency in schizophrenia, and differential effects of various clinical symptoms between male and female patients.

PubMed

Brébion, Gildas; Villalta-Gil, Victoria; Autonell, Jaume; Cervilla, Jorge; Dolz, Montserrat; Foix, Alexandrina; Haro, Josep Maria; Usall, Judith; Vilaplana, Miriam; Ochoa, Susana

2013-06-01

Impairment of higher cognitive functions in patients with schizophrenia might stem from perturbation of more basic functions, such as processing speed. Various clinical symptoms might affect cognitive efficiency as well. Notably, previous research has revealed the role of affective symptoms on memory performance in this population, and suggested sex-specific effects. We conducted a post-hoc analysis of an extensive neuropsychological study of 88 patients with schizophrenia. Regression analyses were conducted on verbal memory and verbal fluency data to investigate the contribution of semantic organisation and processing speed to performance. The role of negative and affective symptoms and of attention disorders in verbal memory and verbal fluency was investigated separately in male and female patients. Semantic clustering contributed to verbal recall, and a measure of reading speed contributed to verbal recall as well as to phonological and semantic fluency. Negative symptoms affected verbal recall and verbal fluency in the male patients, whereas attention disorders affected these abilities in the female patients. Furthermore, depression affected verbal recall in women, whereas anxiety affected it in men. These results confirm the association of processing speed with cognitive efficiency in patients with schizophrenia. They also confirm the previously observed sex-specific associations of depression and anxiety with memory performance in these patients, and suggest that negative symptoms and attention disorders likewise are related to cognitive efficiency differently in men and women. Copyright © 2013 Elsevier B.V. All rights reserved.

Analysis of stimulant drugs in the wastewater of five Nordic capitals.

PubMed

Löve, Arndís Sue Ching; Baz-Lomba, Jose Antonio; Reid, Malcolm J; Kankaanpää, Aino; Gunnar, Teemu; Dam, Maria; Ólafsdóttir, Kristín; Thomas, Kevin V

2018-06-15

Wastewater-based epidemiology is an efficient way to assess illicit drug use, complementing currently used methods retrieved from different data sources. The aim of this study is to compare stimulant drug use in five Nordic capital cities that include for the first time wastewater samples from Torshavn in the Faroe Islands. Currently there are no published reports that compare stimulant drug use in these Nordic capitals. All wastewater samples were analyzed using solid phase extraction and ultra-high performance liquid chromatography coupled to tandem mass spectrometry. The results were compared with data published by the European Monitoring Centre for Drugs and Drug Addiction based on illicit drugs in wastewater from over 50 European cities. Confirming previous reports, the results showed high amphetamine loads compared with other European countries. Very little apparent abuse of stimulant drugs was detected in Torshavn. Methamphetamine loads were the highest from Helsinki of the Nordic countries, indicating substantial fluctuations in the availability of the drug compared with previous studies. Methamphetamine loads from Oslo confirmed that the use continues to be high. Estimated cocaine use was found to be in the lower range compared with other cities in the southern and western part of Europe. Ecstasy and cocaine showed clear variations between weekdays and weekends, indicating recreational use. This study further demonstrates geographical trends in the stimulant drug market in five Nordic capitals, which enables a better comparison with other areas of the continent. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Biophysics and clinical practice for regenerative processes in cirrhosis of the liver/of liver cirrhosis assisted by Delta-S Entropy Variation Systems.

PubMed

Marineo, G; Fesce, E

2006-12-01

The therapy in question uses an innovative bioengineering device denoted as ''Delta-S DVD Entropy Variation System''. Previous research indicated regression of cirrhosis as evaluated in its morphofunctional and symptomatological aspects. The aim of the study is to confirm and extend previous experimental observations by enhancing hemodynamic evaluation techniques. In order to clarify scar regression, it was decided to include in the endpoints a quantitative evaluation of portal hypertension called HVPG, which is sensitive to the breakdown of hepatic architecture and the influence of regeneration nodules and therefore the advance of cirrhosis. The experimental design consists of a self-controlled study carried out on Child A-B cirrhosis patients with portal hypertension (hepatic venous pressure gradient, HVPG > or = 10 mmHg). Five patients were enrolled, 4 HCV positive, one with autoimmune cirrhosis, all showing extensive symptoms. At the end of the treatment all patients showed a reduction in portal hypertension (mean reduction HVPG = 40.2%, P<0.011), together with an improved ultrasound flowmeter pattern and a sharp decrease or disappearance of the symptoms. No adverse effects were reported. Efficacy on autoimmune cirrhosis was unaffected. By means of a quantitative analysis of portal hypertension and of functional aspects, this study confirms that the Delta-S DVD system can lead to the regression of the scar component of cirrhosis, promote the regeneration of functioning liver tissue with positive effects on hepatic functionality and prevent symptoms and the risk of varicose vein rupture.

The newt (Cynops pyrrhogaster) RPE65 promoter: molecular cloning, characterization and functional analysis.

PubMed

Casco-Robles, Martin Miguel; Miura, Tomoya; Chiba, Chikafumi

2015-06-01

The adult newt has the ability to regenerate the neural retina following injury, a process achieved primarily by the retinal pigment epithelium (RPE). To deliver exogenous genes to the RPE for genetic manipulation of regenerative events, we isolated the newt RPE65 promoter region by genome walking. First, we cloned the 2.8 kb RPE65 promoter from the newt, Cynops pyrrhogaster. Sequence analysis revealed several conserved regulatory elements described previously in mouse and human RPE65 promoters. Second, having previously established an I-SceI-mediated transgenic protocol for the newt, we used it here to examine the -657 bp proximal promoter of RPE65. The promoter assay used with F0 transgenic newts confirmed transgene expression of mCherry fluorescent protein in the RPE. Using bioinformatic tools and the TRANSFAC database, we identified a 340 bp CpG island located between -635 and -296 bp in the promoter; this region contains response elements for the microphthalmia-associated transcription factor known as MITF (CACGTG, CATGTG), and E-boxes (CANNTG). Sex-determining region box 9 (or SOX9) response element previously reported in the regulation of RPE genes (including RPE65) was also identified in the newt RPE65 promoter. Third, we identified DNA motif boxes in the newt RPE65 promoter that are conserved among other vertebrates. The newt RPE65 promoter is an invaluable tool for site-specific delivery of exogenous genes or genetic manipulation systems for the study of retinal regeneration in this animal.

Single Nucleotide Polymorphism Analysis of European Archaeological M. leprae DNA

PubMed Central

Watson, Claire L.; Lockwood, Diana N. J.

2009-01-01

Background Leprosy was common in Europe eight to twelve centuries ago but molecular confirmation of this has been lacking. We have extracted M. leprae ancient DNA (aDNA) from medieval bones and single nucleotide polymorphism (SNP) typed the DNA, this provides insight into the pattern of leprosy transmission in Europe and may assist in the understanding of M. leprae evolution. Methods and Findings Skeletons have been exhumed from 3 European countries (the United Kingdom, Denmark and Croatia) and are dated around the medieval period (476 to 1350 A.D.). we tested for the presence of 3 previously identified single nucleotide polymorphisms (SNPs) in 10 aDNA extractions. M. leprae aDNA was extracted from 6 of the 10 bone samples. SNP analysis of these 6 extractions were compared to previously analysed European SNP data using the same PCR assays and were found to be the same. Testing for the presence of SNPs in M. leprae DNA extracted from ancient bone samples is a novel approach to analysing European M. leprae DNA and the findings concur with the previously published data that European M. leprae strains fall in to one group (SNP group 3). Conclusions These findings support the suggestion that the M. leprae genome is extremely stable and show that archaeological M. leprae DNA can be analysed to gain detailed information about the genotypic make-up of European leprosy, which may assist in the understanding of leprosy transmission worldwide. PMID:19847306

A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese.

PubMed

Qin, Pengfei; Li, Zhiqiang; Jin, Wenfei; Lu, Dongsheng; Lou, Haiyi; Shen, Jiawei; Jin, Li; Shi, Yongyong; Xu, Shuhua

2014-02-01

Population stratification acts as a confounding factor in genetic association studies and may lead to false-positive or false-negative results. Previous studies have analyzed the genetic substructures in Han Chinese population, the largest ethnic group in the world comprising ∼20% of the global human population. In this study, we examined 5540 Han Chinese individuals with about 1 million single-nucleotide polymorphisms (SNPs) and screened a panel of ancestry informative markers (AIMs) to facilitate the discerning and controlling of population structure in future association studies on Han Chinese. Based on genome-wide data, we first confirmed our previous observation of the north-south differentiation in Han Chinese population. Second, we developed a panel of 150 validated SNP AIMs to determine the northern or southern origin of each Han Chinese individual. We further evaluated the performance of our AIMs panel in association studies in simulation analysis. Our results showed that this AIMs panel had sufficient power to discern and control population stratification in Han Chinese, which could significantly reduce false-positive rates in both genome-wide association studies (GWAS) and candidate gene association studies (CGAS). We suggest this AIMs panel be genotyped and used to control and correct population stratification in the study design or data analysis of future association studies, especially in CGAS which is the most popular approach to validate previous reports on genetic associations of diseases in post-GWAS era.

Renormalization group analysis of the 2000-2002 anti-bubble in the US S&P500 index: explanation of the hierarchy of five crashes and prediction

NASA Astrophysics Data System (ADS)

Zhou, Wei-Xing; Sornette, Didier

2003-12-01

We propose a straightforward extension of our previously proposed log-periodic power-law model of the “anti-bubble” regime of the USA stock market since the summer of 2000, in terms of the renormalization group framework to model critical points. Using a previous work by Gluzman and Sornette (Phys. Rev. E 65 (2003) 036142) on the classification of the class of Weierstrass-like functions, we show that the five crashes that occurred since August 2000 can be accurately modeled by this approach, in a fully consistent way with no additional parameters. Our theory suggests an overall consistent organization of the investors forming a collective network which interact to form the pessimistic bearish “anti-bubble” regime with intermittent acceleration of the positive feedbacks of pessimistic sentiment leading to these crashes. We develop retrospective predictions, that confirm the existence of significant arbitrage opportunities for a trader using our model. Finally, we offer a prediction for the unknown future of the US S&P500 index extending over 2003 and 2004, that refines the previous prediction of Sornette and Zhou (Quant. Finance 2 (2002) 468).

Masticatory jaw movement of Exaeretodon argentinus (Therapsida: Cynodontia) inferred from its dental microwear

PubMed Central

Yamada, Eisuke; Kubo, Mugino O.

2017-01-01

Dental microwear of four postcanine teeth of Exaeretodon argentinus was analyzed using both two dimensional (2D) and three dimensional (3D) methods to infer their masticatory jaw movements. Results of both methods were congruent, showing that linear microwear features (scratches) were well aligned and mostly directed to the antero-posterior direction in all four teeth examined. These findings support the palinal masticatory jaw movement, which was inferred in previous studies based on the observation of gross morphology of wear facets. In contrast, the lack of detection of lateral scratches confirmed the absence of the lateral jaw movement that was also proposed by a previous study. Considering previous microwear studies on cynodonts, palinal jaw movements observed in Exaeretodon evolved within cynognathian cynodonts from the fully orthal jaw movement of its basal member. Although there are currently only three studies of dental microwear of non-mammalian cynodonts including the present study, microwear analysis is a useful tool for the reconstruction of masticatory jaw movement and its future application to various cynodonts will shed light on the evolutionary process of jaw movement towards the mammalian condition in more detail. PMID:29186178

Superconducting cosmic string: Equation of state for spacelike and timelike current in the neutral limit

NASA Astrophysics Data System (ADS)

Peter, Patrick

1992-02-01

The equation of state relating the tension T and the energy per unit length U of a cosmic string is investigated in the simplest nontrivial case, namely, that of a field theory with U(1)local×U(1)global invariance, in four dimensions, which is interpretable as the zero-charge-coupling-constant limit of the more general superconducting string models that have been previously investigated. This limit has the advantage of giving vacuum vortex defects that are strictly local so that the quantities such as U and T that are relevant for the macroscopic description can be computed without ambiguity. In the case of ``electric'' states (with timelike current) for which no comparable previous calculations exist, it is shown there is a critical frequency wc beyond which the vortex becomes unstable due to ``charge'' carrier emission. In the case of ``magnetic'' states (with spacelike current), the present analysis provides more precise results than those of previous investigations, whose predictions are broadly confirmed for typical moderate models in which the tension T remains comparable to the energy density U though not for extreme models, in which serious discrepancies are revealed.

Antitrypanosomal lead discovery: Identification of a ligand-efficient inhibitor of Trypanosoma cruzi CYP51 and parasite growth

PubMed Central

Andriani, Grasiella; Amata, Emanuele; Beatty, Joel; Clements, Zeke; Coffey, Brian J.; Courtemanche, Gilles; Devine, William; Erath, Jessey; Juda, Cristin E.; Wawrzak, Zdzislaw; Wood, JodiAnne T.; Lepesheva, Galina I.; Rodriguez, Ana; Pollastri, Michael P.

2013-01-01

Chagas disease is caused by the intracellular protozoan parasite Trypanosomal cruzi, and current drugs are lacking in terms of desired safety and efficacy profiles. Following on a recently reported high-throughput screening campaign, we have explored initial structure-activity relationships around a class of imidazole-based compounds. This profiling has uncovered compounds 4c (NEU321) and 4j (NEU704), which are potent against in vitro cultures of T. cruzi and are greater than 160-fold selective over host cells. We report in vitro drug metabolism and properties profiling of 4c and show that this chemotype inhibits the T cruzi CYP51 enzyme, an observation confirmed by X-ray crystallographic analysis. We compare the binding orientation of 4c to that of other, previously reported inhibitors. We show that 4c displays a significantly better ligand efficiency and a shorter synthetic route over previously disclosed CYP51 inhibitors, and should therefore be considered a promising lead compound for further optimization. PMID:23448316

Molecular Taxonomy Provides New Insights into Anopheles Species of the Neotropical Arribalzagia Series

PubMed Central

Gómez, Giovan F.; Bickersmith, Sara A.; González, Ranulfo; Conn, Jan E.; Correa, Margarita M.

2015-01-01

Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I (COI) and nuclear internal transcribed spacer 2 (ITS2) sequences were used to evaluate initial identification and to investigate phylogenetic relationships of seven Anopheles morphospecies of the Arribalzagia Series from Colombia. Phylogenetic trees recovered highly supported clades for An. punctimaculas.s., An. calderoni, An. malefactor s.l., An. neomaculipalpus, An. apicimacula s.l., An. mattogrossensis and An. peryassui. This study provides the first molecular confirmation of An. malefactorfrom Colombia and discovered conflicting patterns of divergence for the molecular markers among specimens from northeast and northern Colombia suggesting the presence of two previously unrecognized Molecular Operational Taxonomic Units (MOTUs). Furthermore, two highly differentiated An. apicimacula MOTUs previously found in Panama were detected. Overall, the combined molecular dataset facilitated the detection of known and new Colombian evolutionary lineages, and constitutes the baseline for future research on their bionomics, ecology and potential role as malaria vectors. PMID:25774795

Initial sequence characterization of the rhabdoviruses of squamate reptiles, including a novel rhabdovirus from a caiman lizard (Dracaena guianensis).

PubMed

Wellehan, James F X; Pessier, Allan P; Archer, Linda L; Childress, April L; Jacobson, Elliott R; Tesh, Robert B

2012-08-17

Rhabdoviruses infect a variety of hosts, including non-avian reptiles. Consensus PCR techniques were used to obtain partial RNA-dependent RNA polymerase gene sequence from five rhabdoviruses of South American lizards; Marco, Chaco, Timbo, Sena Madureira, and a rhabdovirus from a caiman lizard (Dracaena guianensis). The caiman lizard rhabdovirus formed inclusions in erythrocytes, which may be a route for infecting hematophagous insects. This is the first information on behavior of a rhabdovirus in squamates. We also obtained sequence from two rhabdoviruses of Australian lizards, confirming previous Charleville virus sequence and finding that, unlike a previous sequence report but in agreement with serologic reports, Almpiwar virus is clearly distinct from Charleville virus. Bayesian and maximum likelihood phylogenetic analysis revealed that most known rhabdoviruses of squamates cluster in the Almpiwar subgroup. The exception is Marco virus, which is found in the Hart Park group. Copyright © 2012 Elsevier B.V. All rights reserved.

High flexibility of DNA on short length scales probed by atomic force microscopy.

PubMed

Wiggins, Paul A; van der Heijden, Thijn; Moreno-Herrero, Fernando; Spakowitz, Andrew; Phillips, Rob; Widom, Jonathan; Dekker, Cees; Nelson, Philip C

2006-11-01

The mechanics of DNA bending on intermediate length scales (5-100 nm) plays a key role in many cellular processes, and is also important in the fabrication of artificial DNA structures, but previous experimental studies of DNA mechanics have focused on longer length scales than these. We use high-resolution atomic force microscopy on individual DNA molecules to obtain a direct measurement of the bending energy function appropriate for scales down to 5 nm. Our measurements imply that the elastic energy of highly bent DNA conformations is lower than predicted by classical elasticity models such as the worm-like chain (WLC) model. For example, we found that on short length scales, spontaneous large-angle bends are many times more prevalent than predicted by the WLC model. We test our data and model with an interlocking set of consistency checks. Our analysis also shows how our model is compatible with previous experiments, which have sometimes been viewed as confirming the WLC.

Immune biosensors based on the SPR and TIRE: efficiency of their application for bacteria determination

NASA Astrophysics Data System (ADS)

Starodub, N. F.; Ogorodniichuk, J.; Lebedeva, T.; Shpylovyy, P.

2013-11-01

In this work we have designed high-specific biosensors for Salmonella typhimurium detection based on the surface plasmon resonance (SPR) and total internal reflection ellipsometry (TIRE). It has been demonstrated high selectivity and sensitivity of analysis. As a registering part for our experiments the Spreeta (USA) and "Plasmonotest" (Ukraine) with flowing cell have been applied among of SPR device. Previous researches confirmed an efficiency of SPR biosensors using for detecting of specific antigen-antibody interactions therefore this type of reactions with some previous preparations of surface binding layer was used as reactive part. It has been defined that in case with Spreeta sensitivity was on the level 103 - 107 cells/ml. Another biosensor based on the SPR has shown the sensitivity within 101 - 106 cells/ml. Maximal sensitivity was on the level of several cells in 10 ml (up to the fact that less than 5 cells) which has been obtained using the biosensor based on TIRE.

The KASCADE-Grande energy spectrum of cosmic rays and the role of hadronic interaction models

NASA Astrophysics Data System (ADS)

Apel, W. D.; Arteaga-Velázquez, J. C.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Finger, M.; Fuchs, B.; Fuhrmann, D.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Kampert, K.-H.; Kang, D.; Klages, H. O.; Link, K.; Łuczak, P.; Ludwig, M.; Mathes, H. J.; Mayer, H. J.; Melissas, M.; Milke, J.; Mitrica, B.; Morello, C.; Oehlschläger, J.; Ostapchenko, S.; Palmieri, N.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schoo, S.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Wommer, M.; Zabierowski, J.

2014-05-01

Previous results obtained by KASCADE-Grande using the QGSjetII-02 hadronic interaction model have shown that the energy spectrum of cosmic rays between 1016 eV and 1018 eV exhibits a significant hardening at approximately 2×1016 eV and a slight but statistically significant steepening close to 1017 eV. Moreover, the analysis with QGSjetII-02 suggests that the break observed around 1017 eV is caused by the heavy component of primary cosmic rays. In this paper, we report on the results of similar analyses performed using the SIBYLL 2.1 and EPOS 1.99 hadronic interaction models to interpret the data. The present results confirm qualitatively the previous findings. However, the intensity of the all-particle spectrum, the positions of the hardening and steepening of the spectrum, as well as the relative abundance of the heavy and light mass groups depend on the hadronic interaction model used to interpret the data.

Detection, breakpoint identification and detailed characterisation of a CNV at the FRA16D site using SNP assays.

PubMed

Winchester, L; Newbury, D F; Monaco, A P; Ragoussis, J

2008-01-01

Copy Number Variants (CNV) and other submicroscopic structural changes are now recognised to be widespread across the human genome. We show that SNP data generated for association study can be utilised for the identification of deletion CNVs. During analysis of data for an SNP association study for Specific Language Impairment (SLI) a deletion was identified. SLI adversely affects the language development of children in the absence of any obvious cause. Previous studies have found linkage to a region on chromosome 16. The deletion was located in a known fragile site FRA16D in intron 5-6 of the WWOX gene (also known as FOR). Changes in the FRA16D site have been previously linked to cancer and are often characterised in cell lines. A long-range PCR assay was used to confirm the existence of the deletion. We also show the breakpoint identification and large-scale characterisation of this CNV in a normal human sample set. Copyright 2009 S. Karger AG, Basel.

Investigation of Buckling Phenomenon Induced by Growth of Vertebral Bodies Using a Mechanical Spine Model

NASA Astrophysics Data System (ADS)

Sasaoka, Ryu; Azegami, Hideyuki; Murachi, Shunji; Kitoh, Junzoh; Ishida, Yoshito; Kawakami, Noriaki; Makino, Mitsunori; Matsuyama, Yukihiro

A hypothesis that idiopathic scoliosis is a buckling phenomenon of the fourth or sixth mode, which is the second or third lateral bending mode, induced by the growth of vertebral bodies was presented in a previous paper by the authors using numerical simulations with a finite-element model of the spine. This paper presents experimental proof of the buckling phenomenon using mechanical spine models constructed with the geometrical data of the finite-element model used in a previous work. Using three spine mechanical models with different materials at intervertebral joints, the change in the natural vibration eigenvalue of the second lateral bending mode with the growth of vertebral bodies was measured by experimental modal analysis. From the result, it was observed that natural vibration eigenvalue decreased with the growth of vertebral bodies. Since the increase in primary factor inducing the buckling phenomenon decreases natural vibration eigenvalue, the obtained result confirms the buckling hypothesis.

Computer-delivered screening and brief intervention (e-SBI) for postpartum drug use: a randomized trial.

PubMed

Ondersma, Steven J; Svikis, Dace S; Thacker, Leroy R; Beatty, Jessica R; Lockhart, Nancy

2014-01-01

Electronic screening and brief intervention (e-SBI) approaches for substance use have shown early promise. This trial was designed to replicate previous findings from a single 20-minute e-SBI for drug use among postpartum women. A total of 143 postpartum, primarily low-income African-American women meeting criteria for drug use, were randomly assigned to either a tailored e-SBI or a time-matched control condition. Blinded follow-up evaluation 3- and 6-months following childbirth revealed strong effects for confirmed illicit drug use abstinence at the 3-month observation (OR=3.3, p=.01), as did hair analysis at 6months (OR=4.8, p=.018). Additional primary outcomes suggested small to moderate effect sizes in favor of the e-SBI, but did not reach significance. This result replicates previous findings but fails to show durable effects. Assessment reactivity, e-SBI design, and possible extension of e-SBI via tailored messaging all merit careful consideration. © 2013 Elsevier Inc. All rights reserved.

Construction of an integrated gene regulatory network link to stress-related immune system in cattle.

PubMed

Behdani, Elham; Bakhtiarizadeh, Mohammad Reza

2017-10-01

The immune system is an important biological system that is negatively impacted by stress. This study constructed an integrated regulatory network to enhance our understanding of the regulatory gene network used in the stress-related immune system. Module inference was used to construct modules of co-expressed genes with bovine leukocyte RNA-Seq data. Transcription factors (TFs) were then assigned to these modules using Lemon-Tree algorithms. In addition, the TFs assigned to each module were confirmed using the promoter analysis and protein-protein interactions data. Therefore, our integrated method identified three TFs which include one TF that is previously known to be involved in immune response (MYBL2) and two TFs (E2F8 and FOXS1) that had not been recognized previously and were identified for the first time in this study as novel regulatory candidates in immune response. This study provides valuable insights on the regulatory programs of genes involved in the stress-related immune system.

Rabies neutralizing antibody response to different schedules of serum and vaccine inoculations in non-exposed persons

PubMed Central

Atanasiu, P.; Cannon, D. A.; Dean, D. J.; Fox, J. P.; Habel, K.; Kaplan, M. M.; Kissling, R. E.; Koprowski, H.; Lépine, P.; Gallardo, F. Pérez

1961-01-01

This study is the third in a series on virus-neutralizing antibody response to different schedules of antirabies serum and vaccines in previously non-exposed persons. Three types of vaccine were studied—phenolized (Semple), duck embryo and high-egg-passage (HEP) chicken embryo. Reduced schedules of vaccine, consisting of 2-7 inoculations given at various intervals, did not give results comparable in efficacy (time of appearance, level and persistence of antibody) with schedules comprising at least 14 daily inoculations of vaccine as determined in previous trials. The effectiveness of a booster dose in previously sensitized individuals was confirmed with a demonstration that a rise in serum antibody appears between 4 and 8 days after the booster inoculation. Effective sensitization appears to be as much a function of spacing of inoculations as of total dosage of vaccine antigen. Interference by immune serum with the antigenicity of subsequently administered vaccine, noted previously by the present authors and by other workers, was again confirmed. This interference could be overcome by the administration of a sufficient amount of vaccine. PMID:13863061

Love withdrawal predicts electrocortical responses to emotional faces with performance feedback: a follow-up and extension.

PubMed

Huffmeijer, Renske; Bakermans-Kranenburg, Marian J; Alink, Lenneke R A; van IJzendoorn, Marinus H

2014-06-02

Parental use of love withdrawal is thought to affect children's later psychological functioning because it creates a link between children's performance and relational consequences. In addition, recent studies have begun to show that experiences of love withdrawal also relate to the neural processing of socio-emotional information relevant to a performance-relational consequence link, and can moderate effects of oxytocin on social information processing and behavior. The current study follows-up on our previous results by attempting to confirm and extend previous findings indicating that experiences of maternal love withdrawal are related to electrocortical responses to emotional faces presented with performance feedback. More maternal love withdrawal was related to enhanced early processing of facial feedback stimuli (reflected in more positive VPP amplitudes, and confirming previous findings). However, attentional engagement with and processing of the stimuli at a later stage were diminished in those reporting higher maternal love withdrawal (reflected in less positive LPP amplitudes, and diverging from previous findings). Maternal love withdrawal affects the processing of emotional faces presented with performance feedback differently in different stages of neural processing.

Minimally-invasive Laser Ablation Inductively Coupled Plasma Mass Spectrometry analysis of model ancient copper alloys

NASA Astrophysics Data System (ADS)

Walaszek, Damian; Senn, Marianne; Wichser, Adrian; Faller, Markus; Wagner, Barbara; Bulska, Ewa; Ulrich, Andrea

2014-09-01

This work describes an evaluation of a strategy for multi-elemental analysis of typical ancient bronzes (copper, lead bronze and tin bronze) by means of laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS).The samples originating from archeological experiments on ancient metal smelting processes using direct reduction in a ‘bloomery’ furnace as well as historical casting techniques were investigated with the use of the previously proposed analytical procedure, including metallurgical observation and preliminary visual estimation of the homogeneity of the samples. The results of LA-ICPMS analysis were compared to the results of bulk composition obtained by X-ray fluorescence spectrometry (XRF) and by inductively coupled plasma mass spectrometry (ICPMS) after acid digestion. These results were coherent for most of the elements confirming the usefulness of the proposed analytical procedure, however the reliability of the quantitative information about the content of the most heterogeneously distributed elements was also discussed in more detail.

Partial wave analysis of the reaction γ p → p ω and the search for nucleon resonances

DOE PAGES

Williams, M.; Applegate, D.; Bellis, M.; ...

2009-12-30

We performed an event-based partial wave analysis (PWA) of the reaction γ p -> p ω on a high-statistics dataset obtained using the CLAS at Jefferson Lab for center-of-mass energies from threshold up to 2.4 GeV. This analysis benefits from access to the world's first high precision spin density matrix element measurements, available to the event-based PWA through the decay distribution of omega-> π + π - π 0. The data confirm the dominance of the t-channel π 0 exchange amplitude in the forward direction. The dominant resonance contributions are consistent with the previously identified states F[15](1680) and D[13](1700)more » near threshold, as well as the G[17](2190) at higher energies. Suggestive evidence for the presence of a J(P)=5/2 + state around 2 GeV, a "missing" state, has also been found. Evidence for other states is inconclusive.« less

Population structure of Streptococcus oralis

PubMed Central

Do, Thuy; Jolley, Keith A.; Maiden, Martin C. J.; Gilbert, Steven C.; Clark, Douglas; Wade, William G.; Beighton, David

2009-01-01

Streptococcus oralis is a member of the normal human oral microbiota, capable of opportunistic pathogenicity; like related oral streptococci, it exhibits appreciable phenotypic and genetic variation. A multilocus sequence typing (MLST) scheme for S. oralis was developed and the resultant data analysed to examine the population structure of the species. Analysis of 113 isolates, confirmed as belonging to the S. oralis/mitis group by 16S rRNA gene sequencing, characterized the population as highly diverse and undergoing inter- and intra-species recombination with a probable clonal complex structure. ClonalFrame analysis of these S. oralis isolates along with examples of Streptococcus pneumoniae, Streptococcus mitis and Streptococcus pseudopneumoniae grouped the named species into distinct, coherent populations and did not support the clustering of S. pseudopneumoniae with S. mitis as reported previously using distance-based methods. Analysis of the individual loci suggested that this discrepancy was due to the possible hybrid nature of S. pseudopneumoniae. The data are available on the public MLST website (http://pubmlst.org/soralis/). PMID:19423627

Implication of the C terminus of the Prunus necrotic ringspot virus movement protein in cell-to-cell transport and in its interaction with the coat protein.

PubMed

Aparicio, Frederic; Pallás, Vicente; Sánchez-Navarro, Jesús

2010-07-01

The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for viral transport. Previous analysis with MPs of other members of the family Bromoviridae has shown that the C-terminal part of these MPs plays a critical role in the interaction with the cognate coat protein (CP) and in cell-to-cell transport. Bimolecular fluorescence complementation and overlay analysis confirm an interaction between the C-terminal 38 aa of PNRSV MP and its cognate CP. Mutational analysis of the C-terminal region of the PNRSV MP revealed that its C-terminal 38 aa are dispensable for virus transport, however, the 4 aa preceding the dispensable C terminus are necessary to target the MP to the plasmodesmata and for the functionality of the protein. The capacity of the PNRSV MP to use either a CP-dependent or a CP-independent cell-to-cell transport is discussed.

Diabetes mellitus, admission glucose, and outcomes after stroke thrombolysis: a registry and systematic review.

PubMed

Desilles, Jean-Philippe; Meseguer, Elena; Labreuche, Julien; Lapergue, Bertrand; Sirimarco, Gaia; Gonzalez-Valcarcel, Jaime; Lavallée, Philippa; Cabrejo, Lucie; Guidoux, Celine; Klein, Isabelle; Amarenco, Pierre; Mazighi, Mikael

2013-07-01

The potential detrimental effect of diabetes mellitus and admission glucose level (AGL) on outcomes after stroke thrombolysis is unclear. We evaluated outcomes of patients treated by intravenous and/or intra-arterial therapy, according to diabetes mellitus and AGL. We analyzed data from a patient registry (n=704) and conducted a systematic review of previous observational studies. The primary study outcome was the percentage of patients who achieved a favorable outcome (modified Rankin score ≤2 at 3 months). We identified 54 previous reports that evaluated the effect of diabetes mellitus or AGL on outcomes after thrombolysis. In an unadjusted meta-analysis that included our registry data and previous available observational data, diabetes mellitus was associated with less favorable outcome (odds ratio [OR], 0.76; 95% confidence interval [CI], 0.73-0.79) and more symptomatic intracranial hemorrhage (OR, 1.38; 95% CI, 1.21-1.56). However, in multivariable analysis, diabetes mellitus remained associated with less favorable outcome (OR, 0.77; 95% CI, 0.69-0.87) but not with symptomatic intracranial hemorrhage (OR, 1.11; 95% CI, 0.83-1.48). In unadjusted and in adjusted meta-analysis, higher AGL was associated with less favorable outcome and more symptomatic intracranial hemorrhage; the adjusted OR (95% CI) per 1 mmol/L increase in AGL was 0.92 (0.90-0.94) for favorable outcome, and 1.09 (1.04-1.14) for symptomatic intracranial hemorrhage. These results confirm that AGL and history of diabetes mellitus are associated with poor clinical outcome after thrombolysis. AGL may be a surrogate marker of brain infarction severity rather than a causal factor. However, randomized controlled evidences are needed to address the significance of a tight glucose control during thrombolysis on clinical outcome.

Sunyaev-Zel'dovich Effect and X-ray Scaling Relations from Weak-Lensing Mass Calibration of 32 SPT Selected Galaxy Clusters

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

Dietrich, J.P.; et al.

Uncertainty in the mass-observable scaling relations is currently the limiting factor for galaxy cluster based cosmology. Weak gravitational lensing can provide a direct mass calibration and reduce the mass uncertainty. We present new ground-based weak lensing observations of 19 South Pole Telescope (SPT) selected clusters and combine them with previously reported space-based observations of 13 galaxy clusters to constrain the cluster mass scaling relations with the Sunyaev-Zel'dovich effect (SZE), the cluster gas massmore » $$M_\\mathrm{gas}$$, and $$Y_\\mathrm{X}$$, the product of $$M_\\mathrm{gas}$$ and X-ray temperature. We extend a previously used framework for the analysis of scaling relations and cosmological constraints obtained from SPT-selected clusters to make use of weak lensing information. We introduce a new approach to estimate the effective average redshift distribution of background galaxies and quantify a number of systematic errors affecting the weak lensing modelling. These errors include a calibration of the bias incurred by fitting a Navarro-Frenk-White profile to the reduced shear using $N$-body simulations. We blind the analysis to avoid confirmation bias. We are able to limit the systematic uncertainties to 6.4% in cluster mass (68% confidence). Our constraints on the mass-X-ray observable scaling relations parameters are consistent with those obtained by earlier studies, and our constraints for the mass-SZE scaling relation are consistent with the the simulation-based prior used in the most recent SPT-SZ cosmology analysis. We can now replace the external mass calibration priors used in previous SPT-SZ cosmology studies with a direct, internal calibration obtained on the same clusters.« less

Association analysis of 9,560 prostate cancer cases from the International Consortium of Prostate Cancer Genetics confirms the role of reported prostate-cancer associated SNPs for familial disease

PubMed Central

Teerlink, Craig C.; Thibodeau, Stephen N.; McDonnell, Shannon K.; Schaid, Daniel J.; Rinckleb, Antje; Maier, Christiane; Vogel, Walther; Cancel-Tassin, Geraldine; Egrot, Christophe; Cussenot, Olivier; Foulkes, William D.; Giles, Graham G.; Hopper, John L.; Severi, Gianluca; Eeles, Ros; Easton, Douglas; Kote-Jarai, Zsofia; Guy, Michelle; Cooney, Kathleen A.; Ray, Anna M.; Zuhlke, Kimberly A.; Lange, Ethan M.; FitzGerald, Liesel M.; Stanford, Janet L.; Ostrander, Elaine A.; Wiley, Kathleen E.; Isaacs, Sarah D.; Walsh, Patrick C.; Isaacs, William B.; Wahlfors, Tiina; Tammela, Teuvo; Schleutker, Johanna; Wiklund, Fredrik; Grönberg, Henrik; Emanuelsson, Monica; Carpten, John; Bailey-Wilson, Joan; Whittemore, Alice S.; Oakley-Girvan, Ingrid; Hsieh, Chih-Lin; Catalona, William J.; Zheng, S. Lilly; Jin, Guangfu; Lu, Lingyi; Xu, Jianfeng; Camp, Nicola J.; Cannon-Albright, Lisa A.

2013-01-01

Previous GWAS studies have reported significant associations between various common SNPs and prostate cancer risk using cases unselected for family history. How these variants influence risk in familial prostate cancer is not well studied. Here, we analyzed 25 previously reported SNPs across 14 loci from prior prostate cancer GWAS. The International Consortium for Prostate Cancer Genetics (ICPCG) previously validated some of these using a family-based association method (FBAT). However, this approach suffered reduced power due to the conditional statistics implemented in FBAT. Here, we use a case-control design with an empirical analysis strategy to analyze the ICPCG resource for association between these 25 SNPs and familial prostate cancer risk. Fourteen sites contributed 12,506 samples (9,560 prostate cancer cases, 3,368 with aggressive disease, and 2,946 controls from 2,283 pedigrees). We performed association analysis with Genie software which accounts for relationships. We analyzed all familial prostate cancer cases and the subset of aggressive cases. For the familial prostate cancer phenotype, 20 of the 25 SNPs were at least nominally associated with prostate cancer and 16 remained significant after multiple testing correction (p≤1E−3) occurring on chromosomal bands 6q25, 7p15, 8q24, 10q11, 11q13, 17q12, 17q24, and Xp11. For aggressive disease, 16 of the SNPs had at least nominal evidence and 8 were statistically significant including 2p15. The results indicate that the majority of common, low-risk alleles identified in GWAS studies for all prostate cancer also contribute risk for familial prostate cancer, and that some may be contribute risk to aggressive disease. PMID:24162621

Extending Theory-Based Quantitative Predictions to New Health Behaviors.

PubMed

Brick, Leslie Ann D; Velicer, Wayne F; Redding, Colleen A; Rossi, Joseph S; Prochaska, James O

2016-04-01

Traditional null hypothesis significance testing suffers many limitations and is poorly adapted to theory testing. A proposed alternative approach, called Testing Theory-based Quantitative Predictions, uses effect size estimates and confidence intervals to directly test predictions based on theory. This paper replicates findings from previous smoking studies and extends the approach to diet and sun protection behaviors using baseline data from a Transtheoretical Model behavioral intervention (N = 5407). Effect size predictions were developed using two methods: (1) applying refined effect size estimates from previous smoking research or (2) using predictions developed by an expert panel. Thirteen of 15 predictions were confirmed for smoking. For diet, 7 of 14 predictions were confirmed using smoking predictions and 6 of 16 using expert panel predictions. For sun protection, 3 of 11 predictions were confirmed using smoking predictions and 5 of 19 using expert panel predictions. Expert panel predictions and smoking-based predictions poorly predicted effect sizes for diet and sun protection constructs. Future studies should aim to use previous empirical data to generate predictions whenever possible. The best results occur when there have been several iterations of predictions for a behavior, such as with smoking, demonstrating that expected values begin to converge on the population effect size. Overall, the study supports necessity in strengthening and revising theory with empirical data.

Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks.

PubMed

Demenais, Florence; Margaritte-Jeannin, Patricia; Barnes, Kathleen C; Cookson, William O C; Altmüller, Janine; Ang, Wei; Barr, R Graham; Beaty, Terri H; Becker, Allan B; Beilby, John; Bisgaard, Hans; Bjornsdottir, Unnur Steina; Bleecker, Eugene; Bønnelykke, Klaus; Boomsma, Dorret I; Bouzigon, Emmanuelle; Brightling, Christopher E; Brossard, Myriam; Brusselle, Guy G; Burchard, Esteban; Burkart, Kristin M; Bush, Andrew; Chan-Yeung, Moira; Chung, Kian Fan; Couto Alves, Alexessander; Curtin, John A; Custovic, Adnan; Daley, Denise; de Jongste, Johan C; Del-Rio-Navarro, Blanca E; Donohue, Kathleen M; Duijts, Liesbeth; Eng, Celeste; Eriksson, Johan G; Farrall, Martin; Fedorova, Yuliya; Feenstra, Bjarke; Ferreira, Manuel A; Freidin, Maxim B; Gajdos, Zofia; Gauderman, Jim; Gehring, Ulrike; Geller, Frank; Genuneit, Jon; Gharib, Sina A; Gilliland, Frank; Granell, Raquel; Graves, Penelope E; Gudbjartsson, Daniel F; Haahtela, Tari; Heckbert, Susan R; Heederik, Dick; Heinrich, Joachim; Heliövaara, Markku; Henderson, John; Himes, Blanca E; Hirose, Hiroshi; Hirschhorn, Joel N; Hofman, Albert; Holt, Patrick; Hottenga, Jouke; Hudson, Thomas J; Hui, Jennie; Imboden, Medea; Ivanov, Vladimir; Jaddoe, Vincent W V; James, Alan; Janson, Christer; Jarvelin, Marjo-Riitta; Jarvis, Deborah; Jones, Graham; Jonsdottir, Ingileif; Jousilahti, Pekka; Kabesch, Michael; Kähönen, Mika; Kantor, David B; Karunas, Alexandra S; Khusnutdinova, Elza; Koppelman, Gerard H; Kozyrskyj, Anita L; Kreiner, Eskil; Kubo, Michiaki; Kumar, Rajesh; Kumar, Ashish; Kuokkanen, Mikko; Lahousse, Lies; Laitinen, Tarja; Laprise, Catherine; Lathrop, Mark; Lau, Susanne; Lee, Young-Ae; Lehtimäki, Terho; Letort, Sébastien; Levin, Albert M; Li, Guo; Liang, Liming; Loehr, Laura R; London, Stephanie J; Loth, Daan W; Manichaikul, Ani; Marenholz, Ingo; Martinez, Fernando J; Matheson, Melanie C; Mathias, Rasika A; Matsumoto, Kenji; Mbarek, Hamdi; McArdle, Wendy L; Melbye, Mads; Melén, Erik; Meyers, Deborah; Michel, Sven; Mohamdi, Hamida; Musk, Arthur W; Myers, Rachel A; Nieuwenhuis, Maartje A E; Noguchi, Emiko; O'Connor, George T; Ogorodova, Ludmila M; Palmer, Cameron D; Palotie, Aarno; Park, Julie E; Pennell, Craig E; Pershagen, Göran; Polonikov, Alexey; Postma, Dirkje S; Probst-Hensch, Nicole; Puzyrev, Valery P; Raby, Benjamin A; Raitakari, Olli T; Ramasamy, Adaikalavan; Rich, Stephen S; Robertson, Colin F; Romieu, Isabelle; Salam, Muhammad T; Salomaa, Veikko; Schlünssen, Vivi; Scott, Robert; Selivanova, Polina A; Sigsgaard, Torben; Simpson, Angela; Siroux, Valérie; Smith, Lewis J; Solodilova, Maria; Standl, Marie; Stefansson, Kari; Strachan, David P; Stricker, Bruno H; Takahashi, Atsushi; Thompson, Philip J; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Tiesler, Carla M T; Torgerson, Dara G; Tsunoda, Tatsuhiko; Uitterlinden, André G; van der Valk, Ralf J P; Vaysse, Amaury; Vedantam, Sailaja; von Berg, Andrea; von Mutius, Erika; Vonk, Judith M; Waage, Johannes; Wareham, Nick J; Weiss, Scott T; White, Wendy B; Wickman, Magnus; Widén, Elisabeth; Willemsen, Gonneke; Williams, L Keoki; Wouters, Inge M; Yang, James J; Zhao, Jing Hua; Moffatt, Miriam F; Ober, Carole; Nicolae, Dan L

2018-01-01

We examined common variation in asthma risk by conducting a meta-analysis of worldwide asthma genome-wide association studies (23,948 asthma cases, 118,538 controls) of individuals from ethnically diverse populations. We identified five new asthma loci, found two new associations at two known asthma loci, established asthma associations at two loci previously implicated in the comorbidity of asthma plus hay fever, and confirmed nine known loci. Investigation of pleiotropy showed large overlaps in genetic variants with autoimmune and inflammatory diseases. The enrichment in enhancer marks at asthma risk loci, especially in immune cells, suggested a major role of these loci in the regulation of immunologically related mechanisms.

Comparative analysis of rabbit hemorrhagic disease virus (RHDV) and new RHDV2 virus antigenicity, using specific virus-like particles.

PubMed

Bárcena, Juan; Guerra, Beatriz; Angulo, Iván; González, Julia; Valcárcel, Félix; Mata, Carlos P; Castón, José R; Blanco, Esther; Alejo, Alí

2015-09-24

In 2010 a new Lagovirus related to rabbit haemorrhagic disease virus (RHDV) emerged in France and has since rapidly spread throughout domestic and wild rabbit populations of several European countries. The new virus, termed RHDV2, exhibits distinctive genetic, antigenic and pathogenic features. Notably, RHDV2 kills rabbits previously vaccinated with RHDV vaccines. Here we report for the first time the generation and characterization of RHDV2-specific virus-like particles (VLPs). Our results further confirmed the differential antigenic properties exhibited by RHDV and RHDV2, highlighting the need of using RHDV2-specific diagnostic assays to monitor the spread of this new virus.

Tetraploidy acute myeloid leukaemia after chromosome 16 inversion.

PubMed

Vilches, Alba Sara; Díaz de Bustamante, Aranzazu; Sanchez-Calero, Jorge; Darnaude, María Teresa

2017-03-22

Our patient is a 36-year-old man referred by his general physician to the Department of Hematology because of mild neutropenia in a routine analysis at work. There was no history of previous diseases, and examination was normal. Blood investigations confirmed the neutropenia and showed elongation of prothrombin time. A bone marrow examination was performed revealing about 10% of myeloblasts on the aspirate smears. A cytogenetic study showed chromosome 16 inversion in all of these cells and tetraploidy only in some of them, which were extremely large in size. According to the revised WHO classification of tumours (2008), the patient was diagnosed as a case of acute myeloid leukaemia with chromosome 16 inversion. 2017 BMJ Publishing Group Ltd.

[Study on transformation of P-dissolving Penicillium oxalicum P8 with double-marker vector expressing green fluorescent protein and hygromycin B resistance].

PubMed

Zhang, Lei; Fan, Bing-Quan; Huang, Wei-Yi

2005-12-01

P-dissolving Penicillium oxalicum P8 was isolated previously in this lab which has a considerable ability to dissolve many kinds of inorganic phosphorus and improve crop growth. In order to study rhizosphere colonization of plants by Penicillium oxalicum P8, protoplasts were transformed with a double-marker expression vector of green fluorescent protein and hygromycin B resistance. Some transformants were selected which expressed both the GFP and hygromycin B phosphotransferase and did not show significant morphological or physiological differences as compared to wild-type strain. Southern blot analysis confirmed the heterogeneous genomic integration of the vector DNA into the transformants.

Rodentolepis straminea (Cestoda: Hymenolepididae) in an urban population of Apodemus sylvaticus in the UK.

PubMed

Rushworth, R L; Boufana, B; Hall, J L; Brannan, V; Mastin, A; Birtles, R J; Craig, P S; Rogan, M T

2016-07-01

The presence of the cyclophyllidean cestode Rodentolepis straminea (Cestoda: Hymenolepididae), was confirmed by molecular DNA analysis from a wood mouse (Apodemus sylvaticus) population inhabiting urban woodland in Salford, Greater Manchester (UK) with a prevalence of 27.8%. It would appear that the only previously published record of this species in A. sylvaticus in the British Isles is that from south-west Ireland, where 24% of the wood mice examined were infected with R. straminea. This species has been recorded in studies on A. sylvaticus in continental Europe. The current report represents a new record for R. straminea on mainland Britain and a first study of helminth parasites in an urban wood mouse population.

Smoking in inflammatory bowel diseases: good, bad or ugly?

PubMed

Lakatos, Peter Laszlo; Szamosi, Tamas; Lakatos, Laszlo

2007-12-14

Smoking is an important environmental factor in inflammatory bowel disease (IBD), having different effects in ulcerative colitis (UC) and Crohn's disease (CD). A recent meta-analysis partially confirmed previous findings that smoking was found to be protective against ulcerative colitis and, after onset of the disease, might improve its course, decreasing the need for colectomy. However, smoking increases the risk of developing CD and worsens its course, increasing the need for steroids, immunosuppressants and re-operations. Smoking cessation aggravates ulcerative colitis and improves CD. Data are however, largely conflictive as well as the potential mechanisms involved in this dual relationship are still unknown. In this review article, the authors review the role of smoking in inflammatory bowel diseases.

Semantic Drift in Espresso-style Bootstrapping: Graph-theoretic Analysis and Evaluation in Word Sense Disambiguation

NASA Astrophysics Data System (ADS)

Komachi, Mamoru; Kudo, Taku; Shimbo, Masashi; Matsumoto, Yuji

Bootstrapping has a tendency, called semantic drift, to select instances unrelated to the seed instances as the iteration proceeds. We demonstrate the semantic drift of Espresso-style bootstrapping has the same root as the topic drift of Kleinberg's HITS, using a simplified graph-based reformulation of bootstrapping. We confirm that two graph-based algorithms, the von Neumann kernels and the regularized Laplacian, can reduce the effect of semantic drift in the task of word sense disambiguation (WSD) on Senseval-3 English Lexical Sample Task. Proposed algorithms achieve superior performance to Espresso and previous graph-based WSD methods, even though the proposed algorithms have less parameters and are easy to calibrate.

Observations and simulations of specularly reflected He++ at Earth's quasiperpendicular bow shock

NASA Astrophysics Data System (ADS)

Broll, J. M.; Fuselier, S. A.; Trattner, K. J.; Anderson, B. J.; Burch, J. L.; Giles, B. L.

2016-12-01

Specular reflection of protons at Earth's quasiperpendicular bow shock is an important process for supercritical shock dissipation. Previous studies have found evidence of He++ specular reflection from reduced particle distributions downstream from the shock, but confirmation of the process for heavier ions in the shock foot was not possible due to time resolution constraints. We present He++ distributions, observed by MMS in a quasiperpendicular bow shock crossing, that are consistent with specularly reflected He++. We also investigate the He++ dynamics with test-particle simulations in a simulated shock based on this crossing and we conduct wave analysis to determine what processes lead to separate gyrotropization timescales for the transmitted and reflected populations.

Pharmaceutical identifier confirmation via DART-TOF.

PubMed

Easter, Jacob L; Steiner, Robert R

2014-07-01

Pharmaceutical analysis comprises a large amount of the casework in forensic controlled substances laboratories. In order to reduce the time of analysis for pharmaceuticals, a Direct Analysis in Real Time ion source coupled with an accurate mass time-of-flight (DART-TOF) mass spectrometer was used to confirm identity. DART-TOF spectral data for pharmaceutical samples were analyzed and evaluated by comparison to standard spectra. Identical mass pharmaceuticals were differentiated using collision induced dissociation fragmentation, present/absent ions, and abundance comparison box plots; principal component analysis (PCA) and linear discriminant analysis (LDA) were used for differentiation of identical mass mixed drug spectra. Mass assignment reproducibility and robustness tests were performed on the DART-TOF spectra. Impacts on the forensic science community include a decrease in analysis time over the traditional gas chromatograph/mass spectrometry (GC/MS) confirmations, better laboratory efficiency, and simpler sample preparation. Using physical identifiers and the DART-TOF to confirm pharmaceutical identity will eliminate the use of GC/MS and effectively reduce analysis time while still complying with accepted analysis protocols. This will prove helpful in laboratories with large backlogs and will simplify the confirmation process. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Prospective relationships between body weight and physical activity: an observational analysis from the NAVIGATOR study.

PubMed

Preiss, David; Thomas, Laine E; Wojdyla, Daniel M; Haffner, Steven M; Gill, Jason M R; Yates, Thomas; Davies, Melanie J; Holman, Rury R; McMurray, John J; Califf, Robert M; Kraus, William E

2015-08-14

While bidirectional relationships exist between body weight and physical activity, direction of causality remains uncertain and previous studies have been limited by self-reported activity or weight and small sample size. We investigated the prospective relationships between weight and physical activity. Observational analysis of data from the Nateglinide And Valsartan in Impaired Glucose Tolerance Outcomes Research (NAVIGATOR) study, a double-blinded randomised clinical trial of nateglinide and valsartan, respectively. Multinational study of 9306 participants. Participants with biochemically confirmed impaired glucose tolerance had annual measurements of both weight and step count using research grade pedometers, worn for 7 days consecutively. Along with randomisation to valsartan or placebo plus nateglinide or placebo, participants took part in a lifestyle modification programme. Longitudinal regression using weight as response value and physical activity as predictor value was conducted, adjusted for baseline covariates. Analysis was then repeated with physical activity as response value and weight as predictor value. Only participants with a response value preceded by at least three annual response values were included. Adequate data were available for 2811 (30%) of NAVIGATOR participants. Previous weight (χ(2)=16.8; p<0.0001), but not change in weight (χ(2)=0.1; p=0.71) was inversely associated with subsequent step count, indicating lower subsequent levels of physical activity in heavier individuals. Change in step count (χ(2)=5.9; p=0.02) but not previous step count (χ(2)=0.9; p=0.34) was inversely associated with subsequent weight. However, in the context of trajectories already established for weight (χ(2) for previous weight measurements 747.3; p<0.0001) and physical activity (χ(2) for previous step count 432.6; p<0.0001), these effects were of limited clinical importance. While a prospective bidirectional relationship was observed between weight and physical activity, the magnitude of any effect was very small in the context of natural trajectories already established for these variables. NCT00097786. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Reproductive function in relation to duty assignments among military personnel.

PubMed

Schrader, S M; Langford, R E; Turner, T W; Breitenstein, M J; Clark, J C; Jenkins, B L; Lundy, D O; Simon, S D; Weyandt, T B

1998-01-01

As a follow-up to the pilot study of semen quality of soldiers with various military assignments a larger, more complete study was conducted. Soldiers were recruited at Fort Hood, Texas. Thirty-three men were exposed to radar as part of their duty assignment in the Signal Corps, 57 men were involved with firing the 155 mm howitzer (potential lead exposure), and 103 soldiers had neither lead nor radar exposure and served as the comparison control group. Both serum and urinary follicle-stimulating hormone and luteinizing hormone and serum, salivary, and urine testosterone levels were determined in all men. A complete semen analysis was conducted on each soldier. For statistical analysis, the primary study variables were: sperm concentration, sperm/ejaculate, semen volume, percent normal morphology, percent motile, percent viable (both vital stain and hypoosmotic swelling), curvilinear velocity, straight-line velocity, linearity, sperm head length, width, area, and perimeter. Variables were adjusted for significant confounders (e.g., abstinence, sample age, race). No statistical differences (P < 0.05) were observed in any measurement. While these results are in agreement with two previous studies assessing soldiers firing the 155-mm howitzer, they contradict our previous report indicating that radar exposure caused a significant decrease in sperm numbers. A possible explanation is that the radar exposure in this study was that used in Signal Corps operations while the men in the previous study were using different radar as part of military intelligence operations. The data presented here in men firing the 155-mm howitzer combined with the results from the previous studies confirms that there are no deficits in semen quality in these men. The contradiction between the results of the radar exposure studies indicates that more data are needed to evaluate the relationship of military radar and male reproductive health.

Risk of venous thromboembolism following influenza vaccination in adults aged 50years and older in the Vaccine Safety Datalink.

PubMed

Vickers, Elizabeth R; McClure, David L; Naleway, Allison L; Jacobsen, Steven J; Klein, Nicola P; Glanz, Jason M; Weintraub, Eric S; Belongia, Edward A

2017-10-13

Influenza-like illness and inflammation are known risk factors for venous thromboembolism (VTE), which includes deep vein thrombosis (DVT) and pulmonary embolism (PE). However, few studies have characterized the risk of VTE following influenza vaccination. We examined VTE risk after vaccination in adults 50years old and older within the Vaccine Safety Datalink (VSD). We used the self-controlled case series method to determine the risk of VTE among age-eligible adults who received influenza vaccine (with or without pandemic H1N1) and experienced a VTE during the months of September through December in 2007 through 2012. Presumptive VTE cases were identified among VSD participants using diagnostic codes, diagnostic tests, and oral anticoagulant prescription. Potential cases were validated by medical record review. The VTE incidence rate ratio was calculated among confirmed cases for the risk window 1 to 10days after vaccination relative to all other person-time from September through December. Of the 1,488 presumptive cases identified, 508 were reviewed, of which 492 (97%) were confirmed cases of VTE. The analysis included 396 incident, confirmed cases. Overall, there was no increased risk of VTE in the 1 to 10days after influenza vaccination (IRR=0.89, 95% CI 0.69-1.17) compared to the control period. Results were similar when all person-time was censored before vaccination. A post hoc analysis showed an increased risk among current tobacco smokers (IRR=2.57, 95% CI 1.06-6.23). No clustering of VTE was observed in the 1-42days after vaccination. Overall, there was no evidence that inactivated influenza vaccine was associated with VTE in adults ≥50years old. An increased risk was found among current smokers in a post hoc analysis. These findings are consistent with previous research and support the safety of annual vaccination in this population. Copyright © 2017 Elsevier Ltd. All rights reserved.