Evaluation of a portable test system for assessing endotoxin activity in raw milk

PubMed Central

SUZUKI, Yohko; SUZUKI, Kazuyuki; SHIMAMORI, Toshio; TSUCHIYA, Masakazu; NIEHAUS, Andrew; LAKRITZ, Jeffrey

2015-01-01

The aim of the present study was to compare endotoxin activities detected in raw milk samples obtained from cattle by a commercially available portable test system (PTS) and traditional microplate limulus amebocyte lysate (LAL)-based assay, which determined activities using a kinetic turbidimetric (KT) assay. Raw milk samples were obtained from 53 and 12 dairy cattle without and with clinical mastitis, respectively. Comparison between the KT and PTS was performed by the Friedman test. The Pearson product moment correlation coefficients were calculated to evaluate associations between any two continuous variables. Linear regression model analysis was also performed to obtain the equation describing the relationship between PTS and KT assay. The endotoxin activities detected in 200- or 400-fold diluted milk samples were similar between PTS and KT assay, whereas a significant difference was observed in 100-fold diluted milk (P<0.001). The results obtained from 200- (r2=0.778, P<0.001) and 400-fold diluted milk samples (r2=0.945, P<0.001) using PTS correlated with those using KT assay. The median milk endotoxin activities in Gram-positive and Gram-negative clinical mastitis cows were 0.655 and 11,523.5 EU/ml, respectively. The results of the present study suggest that PTS as a simple and easy test to assess endotoxin activity in raw milk is efficient, simple and reproducible. PMID:26279135

Negative refractive index, perfect lenses and checkerboards: Trapping and imaging effects in folded optical spaces

NASA Astrophysics Data System (ADS)

Guenneau, Sébastien; Ramakrishna, S. Anantha

2009-06-01

Newly discovered metamaterials have opened new vistas for better control of light via negative refraction, whereby light refracts in the "wrong" manner. These are dielectric and metallic composite materials structured at subwavelength lengthscales. Their building blocks consist of local resonators such as conducting thin bars and split rings driving the material parameters such as the dielectric permittivity and magnetic permeability to negative (complex) values. Combined together, these structural elements can bring about a (complex valued) negative effective refractive index for the Snell-Descartes law and result in negative refraction of radiation. Negative refractive index materials can support a host of surface plasmon states for both polarizations of light. This makes possible unique effects such as imaging with subwavelength image resolution through the Pendry-Veselago slab lens. Other geometries have also been investigated, such as cylindrical or spherical lenses that enable a magnification of images with subwavelength resolution. Superlenses of three-fold (equilateral triangle), four-fold (square) and six-fold (hexagonal) geometry allow for multiple images, respectively two, three, and five. Generalization to rectangular and triangular checkerboards consisting of alternating cells of positive and negative refractive index represents a very singular situation in which the density of modes diverges at the corners, with an infinity of images. Sine-cosecant anisotropic heterogeneous square and triangular checkerboards can be respectively mapped onto three-dimensional cubic and icosahedral corner lenses consisting of alternating positive and negative refractive regions. All such systems with corners between negative and positive refractive media display very singular behavior with the local density of states becoming infinitely large at the corner, in the limit of no dissipation. We investigate all of these, using the unifying viewpoint of transformation optics. To cite this article: S. Guenneau, S.A. Ramakrishna, C. R. Physique 10 (2009).

Morning glory resin glycosides as modulators of antibiotic activity in multidrug-resistant gram-negative bacteria.

PubMed

Corona-Castañeda, Berenice; Pereda-Miranda, Rogelio

2012-01-01

Twenty-six microbiologically inactive (MIC > 512 µg/mL) convolvulaceous resin glycosides ( 1- 26) were tested for resistance modulatory activity in vitro against Escherichia coli Rosetta-gami and two nosocomial pathogens, Salmonella typhi and Shigella flexneri. These compounds exerted a potentiation effect of the clinically useful antibiotics tetracycline, kanamycin, and chloramphenicol against the tested gram-negative bacteria by increasing antibiotic susceptibility up to 32-fold at concentrations of 25 µg/mL. Therefore, the oligosaccharides from the morning glory family (Convolvulaceae) represent metabolites that reverse microbial resistance mechanisms, favoring an increase in the strength and effectiveness of current antibiotics that are not effective in the treatment of refractive infections caused by multidrug-resistant strains. © Georg Thieme Verlag KG Stuttgart · New York.

Effects of biotic feedback and harvest management on boreal forest fire activity under climate change.

PubMed

Krawchuk, Meg A; Cumming, Steve G

2011-01-01

Predictions of future fire activity over Canada's boreal forests have primarily been generated from climate data following assumptions that direct effects of weather will stand alone in contributing to changes in burning. However, this assumption needs explicit testing. First, areas recently burned can be less likely to burn again in the near term, and this endogenous regulation suggests the potential for self-limiting, negative biotic feedback to regional climate-driven increases in fire. Second, forest harvest is ongoing, and resulting changes in vegetation structure have been shown to affect fire activity. Consequently, we tested the assumption that fire activity will be driven by changes in fire weather without regulation by biotic feedback or regional harvest-driven changes in vegetation structure in the mixedwood boreal forest of Alberta, Canada, using a simulation experiment that includes the interaction of fire, stand dynamics, climate change, and clear cut harvest management. We found that climate change projected with fire weather indices calculated from the Canadian Regional Climate Model increased fire activity, as expected, and our simulations established evidence that the magnitude of regional increase in fire was sufficient to generate negative feedback to subsequent fire activity. We illustrate a 39% (1.39-fold) increase in fire initiation and 47% (1.47-fold) increase in area burned when climate and stand dynamics were included in simulations, yet 48% (1.48-fold) and 61% (1.61-fold) increases, respectively, when climate was considered alone. Thus, although biotic feedbacks reduced burned area estimates in important ways, they were secondary to the direct effect of climate on fire. We then show that ongoing harvest management in this region changed landscape composition in a way that led to reduced fire activity, even in the context of climate change. Although forest harvesting resulted in decreased regional fire activity when compared to unharvested conditions, forest composition and age structure was shifted substantially, illustrating a trade-off between management goals to minimize fire and conservation goals to emulate natural disturbance.

Cytokine profile in severe gram-positive and gram-negative abdominal sepsis

PubMed Central

Surbatovic, Maja; Popovic, Nada; Vojvodic, Danilo; Milosevic, Ivan; Acimovic, Gordana; Stojicic, Milan; Veljovic, Milic; Jevdjic, Jasna; Djordjevic, Dragan; Radakovic, Sonja

2015-01-01

Sepsis is a principal cause of death in critical care units worldwide and consumes considerable healthcare resources. The aim of our study was to determine whether the early cytokine profile can discriminate between Gram-positive and Gram-negative bacteraemia (GPB and GNB, respectively) and to assess the prognostic value regarding outcome in critically ill patients with severe abdominal sepsis. The outcome measure was hospital mortality. Blood samples were obtained from 165 adult patients with confirmed severe abdominal sepsis. Levels of the proinflammatory mediators TNF-α, IL-8, IL-12 and IFN-γ and the anti-inflammatory mediators IL-1ra, IL-4, IL-10 and TGF-β1 were determined and correlated with the nature of the bacteria isolated from the blood culture and outcome. The cytokine profile in our study indicated that the TNF-α levels were 2-fold, IL-8 were 3.3-fold, IFN-γ were 13-fold, IL-1ra were 1.05-fold, IL-4 were 1.4-fold and IL-10 were 1.83-fold higher in the GNB group compared with the GPB group. The TNF-α levels were 4.7-fold, IL-8 were 4.6-fold, IL-1ra were 1.5-fold and IL-10 were 3.3-fold higher in the non-survivors compared with the survivors. PMID:26079127

The Putative PAX8/PPARγ Fusion Oncoprotein Exhibits Partial Tumor Suppressor Activity through Up-Regulation of Micro-RNA-122 and Dominant-Negative PPARγ Activity.

PubMed

Reddi, Honey V; Madde, Pranathi; Milosevic, Dragana; Hackbarth, Jennifer S; Algeciras-Schimnich, Alicia; McIver, Bryan; Grebe, Stefan K G; Eberhardt, Norman L

2011-01-01

In vitro studies have demonstrated that the PAX8/PPARγ fusion protein (PPFP), which occurs frequently in follicular thyroid carcinomas (FTC), exhibits oncogenic activity. However, paradoxically, a meta-analysis of extant tumor outcome studies indicates that 68% of FTC-expressing PPFP are minimally invasive compared to only 32% of those lacking PPFP (χ(2) = 6.86, P = 0.008), suggesting that PPFP favorably impacts FTC outcomes. In studies designed to distinguish benign thyroid neoplasms from thyroid carcinomas, the previously identified tumor suppressor miR-122, a major liver micro-RNA (miR) that is decreased in hepatocellular carcinoma, was increased 8.9-fold (P < 0.05) in all FTC versus normal, 9.2-fold in FTC versus FA (P < 0.05), and 16.8-fold (P < 0.001) in FTC + PPFP versus FTC - PPFP. Constitutive expression of PPFP in the FTC-derived cell line WRO (WRO-PPFP) caused a 5-fold increase of miR-122 expression (P < 0.05) and a striking 5.1-fold reduction (P < 0.0001) in tumor progression compared to WRO-vector cells in a mouse xenograft model. Constitutive expression of either miR-122 or a dominant-negative PPARγ mutant in WRO cells was less effective than PPFP at inhibiting xenograft tumor progression (1.8-fold [P < 0.001] and 1.7-fold [P < 0.03], respectively). PPFP-induced up-regulation of miR-122 expression was independent of its known dominant-negative PPARγ activity. Up-regulation of miR-122 negatively regulates ADAM-17, a known downstream target, in thyroid cells, suggesting an antiangiogenic mechanism in thyroid carcinoma. This latter inference is directly supported by reduced CD-31 expression in WRO xenografts expressing PPFP, miR-122, and DN-PPARγ. We conclude that, in addition to its apparent oncogenic potential in vitro, PPFP exhibits paradoxical tumor suppressor activity in vivo, mediated by multiple mechanisms including up-regulation of miR-122 and dominant-negative inhibition of PPARγ activity.

Spiral Salmonella assay: validation against the standard pour-plate assay.

PubMed

Diehl, M; Fort, F

1996-01-01

The spiral Ames assay, an automated approach to bacterial mutagenicity testing which simplifies the test procedure and reduces the amount of drug required to generate mutagenic dose-response information, has been evaluated and validated for routine screening. The spiral plater delivers the Salmonella bacteria, exogenous metabolic activation system and drug to the surface of a rotating agar plate one on top of another in such a way that a uniform density of bacteria is exposed to a logarithmically decreasing volume of drug. Following an incubation of 48 hr at 37 degrees C, the plates are scanned by a laser counter, and the data are subjected to a computerized analysis. Petri plates of 15 cm diameter were used to provide a concentration range of about 250-fold per plate. The Salmonella were concentrated 20-fold to increase sensitivity. Thirty-eight compounds from a variety of chemical classes, including both pharmaceuticals and known mutagens of moderate to strong potency, were tested in both the spiral and the standard pour-plate assays. There was overall test agreement on positive or negative results for 82% of the compounds tested. When only the results from strains TA98 plus TA100 were considered, the agreement was 87%. When positive results were obtained, the fold increase over vehicle control was on average twice as great for the spiral assay compared to the pour-plate assay. It was concluded that the two assay procedures generally provided comparable results, with the spiral assay being somewhat more sensitive in terms of dose-response than the pour-plate assay.

Systematic bias of correlation coefficient may explain negative accuracy of genomic prediction.

PubMed

Zhou, Yao; Vales, M Isabel; Wang, Aoxue; Zhang, Zhiwu

2017-09-01

Accuracy of genomic prediction is commonly calculated as the Pearson correlation coefficient between the predicted and observed phenotypes in the inference population by using cross-validation analysis. More frequently than expected, significant negative accuracies of genomic prediction have been reported in genomic selection studies. These negative values are surprising, given that the minimum value for prediction accuracy should hover around zero when randomly permuted data sets are analyzed. We reviewed the two common approaches for calculating the Pearson correlation and hypothesized that these negative accuracy values reflect potential bias owing to artifacts caused by the mathematical formulas used to calculate prediction accuracy. The first approach, Instant accuracy, calculates correlations for each fold and reports prediction accuracy as the mean of correlations across fold. The other approach, Hold accuracy, predicts all phenotypes in all fold and calculates correlation between the observed and predicted phenotypes at the end of the cross-validation process. Using simulated and real data, we demonstrated that our hypothesis is true. Both approaches are biased downward under certain conditions. The biases become larger when more fold are employed and when the expected accuracy is low. The bias of Instant accuracy can be corrected using a modified formula. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A tailored approach to BRAF and MLH1 methylation testing in a universal screening program for Lynch syndrome.

PubMed

Adar, Tomer; Rodgers, Linda H; Shannon, Kristen M; Yoshida, Makoto; Ma, Tianle; Mattia, Anthony; Lauwers, Gregory Y; Iafrate, Anthony J; Chung, Daniel C

2017-03-01

To determine the correlation between BRAF genotype and MLH1 promoter methylation in a screening program for Lynch syndrome (LS), a universal screening program for LS was established in two medical centers. Tumors with abnormal MLH1 staining were evaluated for both BRAF V600E genotype and MLH1 promoter methylation. Tumors positive for both were considered sporadic, and genetic testing was recommended for all others. A total 1011 colorectal cancer cases were screened for Lynch syndrome, and 148 (14.6%) exhibited absent MLH1 immunostaining. Both BRAF and MLH1 methylation testing were completed in 126 cases. Concordant results (both positive or both negative) were obtained in 86 (68.3%) and 16 (12.7%) cases, respectively, with 81% concordance overall. The positive and negative predictive values for a BRAF mutation in predicting MLH1 promoter methylation were 98.9% and 41%, respectively, and the negative predictive value fell to 15% in patients ≥70 years old. Using BRAF genotyping as a sole test to evaluate cases with absent MLH1 staining would have increased referral rates for genetic testing by 2.3-fold compared with MLH1 methylation testing alone (31% vs 13.5%, respectively, P<0.01). However, a hybrid approach that reserves MLH1 methylation testing for BRAF wild-type cases only would significantly decrease the number of methylation assays performed and reduce the referral rate for genetic testing to 12.7%. A BRAF mutation has an excellent positive predictive value but poor negative predictive value in predicting MLH1 promoter methylation. A hybrid use of these tests may reduce the number of low-risk patients referred to genetic counseling and facilitate wider implementation of Lynch syndrome screening programs.

In vitro antibacterial activity and beta-lactamase stability of CP-70,429 a new penem antibiotic.

PubMed

Minamimura, M; Taniyama, Y; Inoue, E; Mitsuhashi, S

1993-07-01

In in vitro susceptibility tests, the new penem CP-70,429 showed potent antibacterial activity against gram-positive and gram-negative bacteria except Pseudomonas aeruginosa and Xanthomonas maltophilia. CP-70,429 was stable to various types of beta-lactamases except for the enzyme from X. maltophilia and was 16- to 128-fold more active than the other compounds against beta-lactamase-producing strains of Enterobacter cloacae and Citrobacter freundii.

In vitro antibacterial activity and beta-lactamase stability of CP-70,429 a new penem antibiotic.

PubMed Central

Minamimura, M; Taniyama, Y; Inoue, E; Mitsuhashi, S

1993-01-01

In in vitro susceptibility tests, the new penem CP-70,429 showed potent antibacterial activity against gram-positive and gram-negative bacteria except Pseudomonas aeruginosa and Xanthomonas maltophilia. CP-70,429 was stable to various types of beta-lactamases except for the enzyme from X. maltophilia and was 16- to 128-fold more active than the other compounds against beta-lactamase-producing strains of Enterobacter cloacae and Citrobacter freundii. PMID:8363389

Flow fields and acoustics in a unilateral scarred vocal fold model.

PubMed

Murugappan, Shanmugam; Khosla, Sid; Casper, Keith; Oren, Liran; Gutmark, Ephraim

2009-01-01

From prior work in an excised canine larynx model, it has been shown that intraglottal vortices form between the vocal folds during the latter part of closing. It has also been shown that the vortices generate a negative pressure between the folds, producing a suction force that causes sudden, rapid closing of the folds. This rapid closing will produce increased loudness and increased higher harmonics. We used a unilateral scarred excised canine larynx model to determine whether the intraglottal vortices and resulting acoustics were changed, compared to those of normal larynges. Acoustic, flow field, and high-speed imaging measurements from 5 normal and 5 unilaterally scarred canine larynges are presented in this report. Scarring was produced by complete resection of the vocal fold mucosa and superficial layer of the lamina propria on the right vocal fold only. Two months later, these dogs were painlessly sacrificed, and testing was done on the excised larynges during phonation. High-speed video imaging was then used to measure vocal fold displacement during different phases. Particle image velocimetry and acoustic measurements were used to describe possible acoustic effects of the vortices. A higher phonation threshold was required to excite the motion of the vocal fold in scarred larynges. As the subglottal pressure increased, the strength of the vortices and the higher harmonics both consistently increased. However, it was seen that increasing the maximum displacement of the scarred fold did not consistently increase the higher harmonics. The improvements that result from increasing subglottal pressure may be due to a combination of increasing the strength of the intraglottal vortices and increasing the maximum displacement of the vocal fold; however, the data in this study suggest that the vortices play a much more important role. The current study indicates that higher subglottal pressures may excite higher harmonics and improve loudness for patients with unilateral vocal fold scarring. This finding implies that therapies that raise the subglottal pressure may be helpful in improving voice quality.

Multicenter evaluation of the performance characteristics of the bayer VERSANT HCV RNA 3.0 assay (bDNA).

PubMed

Elbeik, Tarek; Surtihadi, Johan; Destree, Mark; Gorlin, Jed; Holodniy, Mark; Jortani, Saeed A; Kuramoto, Ken; Ng, Valerie; Valdes, Roland; Valsamakis, Alexandra; Terrault, Norah A

2004-02-01

In this multicenter evaluation, the VERSANT HCV RNA 3.0 Assay (bDNA) (Bayer Diagnostics, Tarrytown, N.Y.) was shown to have excellent reproducibility, linearity, and analytical sensitivity across specimen collection matrices (serum, EDTA, ACD-A), and hepatitis C virus (HCV) genotypes 1 to 6. The VERSANT HCV bDNA Assay has a reportable range of 615 to 7690000 (7.69 x 10(6)) IU/ml. The total coefficient of variation (CV) ranged from 32.4% at 615 IU/ml to 17% at 6.8 x 10(6) IU/ml. The assay was linear across the reportable range. Analytical specificity of 98.8% was determined by testing 999 specimens from volunteer blood donors. Evaluation of HCV genotypes using RNA transcripts of representative clones of 1a, 1b, 2a, 2b, 2c, 3a, 4a, 5a, and 6a and patient specimens showed that the largest difference between genotype 1, upon which the assay is standardized, and non-1 genotypes was within 1.5-fold. Testing of potentially interfering endogenous substances and exogenous substances and conditions found no interference in HCV-positive or HCV-negative specimens except for unconjugated bilirubin at concentrations of >or=20 mg/dl and protein at concentrations of >or=9 g/dl. Biological variability was estimated from 29 clinically stable individuals not on HCV therapy who were tested weekly over an 8-week period. The combined estimate of total (biologic plus assay) variability was 0.15 log(10) standard deviation (CV, 36.1%), a fold change of 2.6. Thus, the observed fold change between any two consecutive HCV RNA measures is expected to be less than 2.6-fold (equivalent to 0.41 log(10) IU/ml) 95% of the time in clinically stable individuals.

Analysis of negative historical control group data from the in vitro micronucleus assay using TK6 cells.

PubMed

Lovell, David P; Fellows, Mick; Marchetti, Francesco; Christiansen, Joan; Elhajouji, Azeddine; Hashimoto, Kiyohiro; Kasamoto, Sawako; Li, Yan; Masayasu, Ozaki; Moore, Martha M; Schuler, Maik; Smith, Robert; Stankowski, Leon F; Tanaka, Jin; Tanir, Jennifer Y; Thybaud, Veronique; Van Goethem, Freddy; Whitwell, James

2018-01-01

The recent revisions of the Organisation for Economic Co-operation and Development (OECD) genetic toxicology test guidelines emphasize the importance of historical negative controls both for data quality and interpretation. The goal of a HESI Genetic Toxicology Technical Committee (GTTC) workgroup was to collect data from participating laboratories and to conduct a statistical analysis to understand and publish the range of values that are normally seen in experienced laboratories using TK6 cells to conduct the in vitro micronucleus assay. Data from negative control samples from in vitro micronucleus assays using TK6 cells from 13 laboratories were collected using a standard collection form. Although in some cases statistically significant differences can be seen within laboratories for different test conditions, they were very small. The mean incidence of micronucleated cells/1000 cells ranged from 3.2/1000 to 13.8/1000. These almost four-fold differences in micronucleus levels cannot be explained by differences in scoring method, presence or absence of exogenous metabolic activation (S9), length of treatment, presence or absence of cytochalasin B or different solvents used as vehicles. The range of means from the four laboratories using flow cytometry methods (3.7-fold: 3.5-12.9 micronucleated cells/1000 cells) was similar to that from the nine laboratories using other scoring methods (4.3-fold: 3.2-13.8 micronucleated cells/1000 cells). No laboratory could be identified as an outlier or as showing unacceptably high variability. Quality Control (QC) methods applied to analyse the intra-laboratory variability showed that there was evidence of inter-experimental variability greater than would be expected by chance (i.e. over-dispersion). However, in general, this was low. This study demonstrates the value of QC methods in helping to analyse the reproducibility of results, building up a 'normal' range of values, and as an aid to identify variability within a laboratory in order to implement processes to maintain and improve uniformity. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Functional assessment of the ex vivo vocal folds through biomechanical testing: A review

PubMed Central

Dion, Gregory R.; Jeswani, Seema; Roof, Scott; Fritz, Mark; Coelho, Paulo; Sobieraj, Michael; Amin, Milan R.; Branski, Ryan C.

2016-01-01

The human vocal folds are complex structures made up of distinct layers that vary in cellular and extracellular composition. The mechanical properties of vocal fold tissue are fundamental to the study of both the acoustics and biomechanics of voice production. To date, quantitative methods have been applied to characterize the vocal fold tissue in both normal and pathologic conditions. This review describes, summarizes, and discusses the most commonly employed methods for vocal fold biomechanical testing. Force-elongation, torsional parallel plate rheometry, simple-shear parallel plate rheometry, linear skin rheometry, and indentation are the most frequently employed biomechanical tests for vocal fold tissues and each provide material properties data that can be used to compare native tissue verses diseased for treated tissue. Force-elongation testing is clinically useful, as it allows for functional unit testing, while rheometry provides physiologically relevant shear data, and nanoindentation permits micrometer scale testing across different areas of the vocal fold as well as whole organ testing. Thoughtful selection of the testing technique during experimental design to evaluate a hypothesis is important to optimizing biomechanical testing of vocal fold tissues. PMID:27127075

Glucose Metabolism Disorders, HIV and Antiretroviral Therapy among Tanzanian Adults

PubMed Central

Maganga, Emmanuel; Smart, Luke R.; Kalluvya, Samuel; Kataraihya, Johannes B.; Saleh, Ahmed M.; Obeid, Lama; Downs, Jennifer A.; Fitzgerald, Daniel W.; Peck, Robert N.

2015-01-01

Introduction Millions of HIV-infected Africans are living longer due to long-term antiretroviral therapy (ART), yet little is known about glucose metabolism disorders in this group. We aimed to compare the prevalence of glucose metabolism disorders among HIV-infected adults on long-term ART to ART-naïve adults and HIV-negative controls, hypothesizing that the odds of glucose metabolism disorders would be 2-fold greater even after adjusting for possible confounders. Methods In this cross-sectional study conducted between October 2012 and April 2013, consecutive adults (>18 years) attending an HIV clinic in Tanzania were enrolled in 3 groups: 153 HIV-negative controls, 151 HIV-infected, ART-naïve, and 150 HIV-infected on ART for ≥ 2 years. The primary outcome was the prevalence of glucose metabolism disorders as determined by oral glucose tolerance testing. We compared glucose metabolism disorder prevalence between each HIV group vs. the control group by Fisher’s exact test and used multivariable logistic regression to determine factors associated with glucose metabolism disorders. Results HIV-infected adults on ART had a higher prevalence of glucose metabolism disorders (49/150 (32.7%) vs.11/153 (7.2%), p<0.001) and frank diabetes mellitus (27/150 (18.0%) vs. 8/153 (5.2%), p = 0.001) than HIV-negative adults, which remained highly significant even after adjusting for age, gender, adiposity and socioeconomic status (OR = 5.72 (2.78–11.77), p<0.001). Glucose metabolism disorders were significantly associated with higher CD4+ T-cell counts. Awareness of diabetes mellitus was <25%. Conclusions HIV-infected adults on long-term ART had 5-fold greater odds of glucose metabolism disorders than HIV-negative controls but were rarely aware of their diagnosis. Intensive glucose metabolism disorder screening and education are needed in HIV clinics in sub-Saharan Africa. Further research should determine how glucose metabolism disorders might be related to immune reconstitution. PMID:26287742

Meta-structure correlation in protein space unveils different selection rules for folded and intrinsically disordered proteins.

PubMed

Naranjo, Yandi; Pons, Miquel; Konrat, Robert

2012-01-01

The number of existing protein sequences spans a very small fraction of sequence space. Natural proteins have overcome a strong negative selective pressure to avoid the formation of insoluble aggregates. Stably folded globular proteins and intrinsically disordered proteins (IDPs) use alternative solutions to the aggregation problem. While in globular proteins folding minimizes the access to aggregation prone regions, IDPs on average display large exposed contact areas. Here, we introduce the concept of average meta-structure correlation maps to analyze sequence space. Using this novel conceptual view we show that representative ensembles of folded and ID proteins show distinct characteristics and respond differently to sequence randomization. By studying the way evolutionary constraints act on IDPs to disable a negative function (aggregation) we might gain insight into the mechanisms by which function-enabling information is encoded in IDPs.

Reproducibility of risk figures in 2nd-trimester maternal serum screening for down syndrome: comparison of 2 laboratories.

PubMed

Benn, Peter A; Makowski, Gregory S; Egan, James F X; Wright, Dave

2006-11-01

Analytical error affects 2nd-trimester maternal serum screening for Down syndrome risk estimation. We analyzed the between-laboratory reproducibility of risk estimates from 2 laboratories. Laboratory 1 used Bayer ACS180 immunoassays for alpha-fetoprotein (AFP) and human chorionic gonadotropin (hCG), Diagnostic Systems Laboratories (DSL) RIA for unconjugated estriol (uE3), and DSL enzyme immunoassay for inhibin-A (INH-A). Laboratory 2 used Beckman immunoassays for AFP, hCG, and uE3, and DSL enzyme immunoassay for INH-A. Analyte medians were separately established for each laboratory. We used the same computational algorithm for all risk calculations, and we used Monte Carlo methods for computer modeling. For 462 samples tested, risk figures from the 2 laboratories differed >2-fold for 44.7%, >5-fold for 7.1%, and >10-fold for 1.7%. Between-laboratory differences in analytes were greatest for uE3 and INH-A. The screen-positive rates were 9.3% for laboratory 1 and 11.5% for laboratory 2, with a significant difference in the patients identified as screen-positive vs screen-negative (McNemar test, P<0.001). Computer modeling confirmed the large between-laboratory risk differences. Differences in performance of assays and laboratory procedures can have a large effect on patient-specific risks. Screening laboratories should minimize test imprecision and ensure that each assay performs in a manner similar to that assumed in the risk computational algorithm.

Impact of the Mycobaterium africanum West Africa 2 Lineage on TB Diagnostics in West Africa: Decreased Sensitivity of Rapid Identification Tests in The Gambia.

PubMed

Ofori-Anyinam, Boatema; Kanuteh, Fatoumatta; Agbla, Schadrac C; Adetifa, Ifedayo; Okoi, Catherine; Dolganov, Gregory; Schoolnik, Gary; Secka, Ousman; Antonio, Martin; de Jong, Bouke C; Gehre, Florian

2016-07-01

MPT64 rapid speciation tests are increasingly being used in diagnosis of tuberculosis (TB). Mycobacterium africanum West Africa 2 (Maf 2) remains an important cause of TB in West Africa and causes one third of disease in The Gambia. Since the introduction of MPT64 antigen tests, a higher than expected rate of suspected non-tuberculous mycobacteria (NTM) was seen among AFB smear positive TB suspects, which led us to prospectively assess sensitivity of the MPT64 antigen test in our setting. We compared the abundance of mRNA encoded by the mpt64 gene in sputa of patients with untreated pulmonary TB caused by Maf 2 and Mycobacterium tuberculosis (Mtb). Subsequently, prospectively collected sputum samples from presumptive TB patients were inoculated in the BACTEC MGIT 960 System. One hundred and seventy-three acid fast bacilli (AFB)-positive and blood agar negative MGIT cultures were included in the study. Cultures were tested on the day of MGIT positivity with the BD MGIT TBc Identification Test. A random set of positives and all negatives were additionally tested with the SD Bioline Ag MPT64 Rapid. MPT64 negative cultures were further incubated at 37°C and retested until positive. Bacteria were spoligotyped and assigned to different lineages. Maf 2 isolates were 2.52-fold less likely to produce a positive test result and sensitivity ranged from 78.4% to 84.3% at the beginning and end of the recommended 10 day testing window, respectively. There was no significant difference between the tests. We further showed that the decreased rapid test sensitivity was attributable to variations in mycobacterial growth behavior and the smear grades of the patient. In areas where Maf 2 is endemic MPT64 tests should be cautiously used and MPT64 negative results confirmed by a second technique, such as nucleic acid amplification tests, to avoid their misclassification as NTMs.

The evolution of a Late Cretaceous-Cenozoic intraplate basin (Duaringa Basin), eastern Australia: evidence for the negative inversion of a pre-existing fold-thrust belt

NASA Astrophysics Data System (ADS)

Babaahmadi, Abbas; Sliwa, Renate; Esterle, Joan; Rosenbaum, Gideon

2017-12-01

The Duaringa Basin in eastern Australia is a Late Cretaceous?-early Cenozoic sedimentary basin that developed simultaneously with the opening of the Tasman and Coral Seas. The basin occurs on the top of an earlier (Permian-Triassic) fold-thrust belt, but the negative inversion of this fold-thrust belt, and its contribution to the development of the Duaringa Basin, are not well understood. Here, we present geophysical datasets, including recently surveyed 2D seismic reflection lines, aeromagnetic and Bouguer gravity data. These data provide new insights into the structural style in the Duaringa Basin, showing that the NNW-striking, NE-dipping, deep-seated Duaringa Fault is the main boundary fault that controlled sedimentation in the Duaringa Basin. The major activity of the Duaringa Fault is observed in the southern part of the basin, where it has undergone the highest amount of displacement, resulting in the deepest and oldest depocentre. The results reveal that the Duaringa Basin developed in response to the partial negative inversion of the pre-existing Permian-Triassic fold-thrust belt, which has similar orientation to the extensional faults. The Duaringa Fault is the negative inverted part of a single Triassic thrust, known as the Banana Thrust. Furthermore, small syn-depositional normal faults at the base of the basin likely developed due to the reactivation of pre-existing foliations, accommodation faults, and joints associated with Permian-Triassic folds. In contrast to equivalent offshore basins, the Duaringa Basin lacks a complex structural style and thick syn-rift sediments, possibly because of the weakening of extensional stresses away from the developing Tasman Sea.

Negative Coulomb damping, limit cycles, and self-oscillation of the vocal folds

NASA Astrophysics Data System (ADS)

Fulcher, Lewis P.; Scherer, Ronald C.; Melnykov, Artem; Gateva, Vesela; Limes, Mark E.

2006-05-01

An effective one-mass model of phonation is developed. It borrows the salient features of the classic two-mass model of human speech developed by Ishizaka, Matsudaira, and Flanagan. Their model is based on the idea that the oscillating vocal folds maintain their motion by deriving energy from the flow of air through the glottis. We argue that the essence of the action of the aerodynamic forces on the vocal folds is captured by negative Coulomb damping, which acts on the oscillator to energize it. A viscous force is added to include the effects of tissue damping. The solutions to this single oscillator model show that when it is excited by negative Coulomb damping, it will reach a limit cycle. Displacements, phase portraits, and energy histories are presented for two underdamped linear oscillators. A nonlinear force is added so that the variations of the fundamental frequency and the open quotient with lung pressure are comparable to the behavior of the two-mass model.

Predicting drug-induced liver injury in human with Naïve Bayes classifier approach.

PubMed

Zhang, Hui; Ding, Lan; Zou, Yi; Hu, Shui-Qing; Huang, Hai-Guo; Kong, Wei-Bao; Zhang, Ji

2016-10-01

Drug-induced liver injury (DILI) is one of the major safety concerns in drug development. Although various toxicological studies assessing DILI risk have been developed, these methods were not sufficient in predicting DILI in humans. Thus, developing new tools and approaches to better predict DILI risk in humans has become an important and urgent task. In this study, we aimed to develop a computational model for assessment of the DILI risk with using a larger scale human dataset and Naïve Bayes classifier. The established Naïve Bayes prediction model was evaluated by 5-fold cross validation and an external test set. For the training set, the overall prediction accuracy of the 5-fold cross validation was 94.0 %. The sensitivity, specificity, positive predictive value and negative predictive value were 97.1, 89.2, 93.5 and 95.1 %, respectively. The test set with the concordance of 72.6 %, sensitivity of 72.5 %, specificity of 72.7 %, positive predictive value of 80.4 %, negative predictive value of 63.2 %. Furthermore, some important molecular descriptors related to DILI risk and some toxic/non-toxic fragments were identified. Thus, we hope the prediction model established here would be employed for the assessment of human DILI risk, and the obtained molecular descriptors and substructures should be taken into consideration in the design of new candidate compounds to help medicinal chemists rationally select the chemicals with the best prospects to be effective and safe.

Comparative Dietary Therapy Effectiveness in Remission of Pediatric Eosinophilic Esophagitis

PubMed Central

Henderson, Carol J.; Abonia, J. Pablo; King, Eileen C.; Putnam, Philip E.; Collins, Margaret H.; Franciosi, James P.; Rothenberg, Marc E.

2012-01-01

Background Eosinophilic esophagitis is a chronic, immune-mediated inflammatory disorder that responds to dietary therapy; however, data evaluating the effectiveness of dietary therapeutic strategies is limited. Objective This study compared the effectiveness of three frequently prescribed dietary therapies [elemental, six-food elimination, and skin prick and atopy patch-directed elimination] and assessed the remission predictability of skin tests and their utility in directing dietary planning. Methods A retrospective cohort of proton-pump inhibitor-unresponsive, non-glucocorticoid-treated eosinophilic esophagitis patients who had two consecutive endoscopic biopsies associated with dietary intervention was identified. Biopsy histology and remissions (< 15 eosinophils/high-power field) following dietary therapy and food reintroductions were evaluated. Results Ninety-eight of 513 patients met eligibility criteria. Of these 98, 50% (49), 27% (26), and 23% (23) received elemental, six-food elimination, and directed diets, respectively. Remission occurred in 96%, 81%, and 65% of patients on elemental, six-food elimination, and directed diets, respectively. The odds of post-diet remission vs. non-remission were 5.6-fold higher (P=0.05) on elemental vs. six-food elimination, 12.5-fold higher (P=0.003) on elemental vs. directed, and were not significantly different (P=0.22) on six-food elimination vs. directed diets. Following 116 single-food reintroductions, the negative predictive value of skin testing for remission was 40%–67% (milk 40%, egg 56%, soy 64%, and wheat 67%). Conclusion All three dietary therapies are effective; however, an elemental diet is superior at inducing histologic remission compared with six-food elimination and skin test-directed diets. Notably, an empiric six-food elimination diet is as effective as a skin test-directed diet. The negative predictive values of foods most commonly reintroduced in single-food challenges are not sufficient to support the development of dietary advancement plans solely based on skin tests. PMID:22541246

Paleomagnetic and Anisotropy of Magnetic Susceptibility (AMS) Documentation of the Formation of Large-Scale Rheomorphic Structures in the 2.06 Ma Huckleberry Ridge Tuff, Eastern Idaho

NASA Astrophysics Data System (ADS)

Geissman, J. W.; Holm, D.; Harlan, S. S.

2006-12-01

In the Teton River Valley, east of Rexburg, Idaho, the ca. 2.06 Ma Huckleberry Ridge Tuff is about 130 m thick, exceedingly well-exposed, and displays large-scale (100-150 m+ amplitude) rheomorphic folds, with eutaxitic fabrics that are parallel to inferred primary internal zonation (e.g. boundary between basal vitrophyre and overlying devitrified part of the pyroclastic deposit) as well as the basal contact with older deposits defining the fold geometries. One 150 m amplitude fold , is well-exposed on the north side of the valley about 2.5 km east of Teton Dam, has a NW trending fold axis and has a southwest limb that is overturned by about 45o. Samples were collected from 16 sites in this fold, on both limbs and the hinge area, to test the hypothesis that folding took place above maximum TRM blocking temperatures (about 580C). Progressive AF and thermal demagnetization both yield characteristic magnetizations of southwest to south-southwest declination and shallow inclination removed over a range of peak fields (typically between 20 and 80 mT) and laboratory unblocking temperatures (typically between 350 and 580C). The preliminary determination of an in situ mean based on the 16 sites is about D = 215°, I = -5°, a95= 5°, N = 16 site means). The direction of this ChRM is statistically indistinguishable from that reported by previous studies of the tuff (e.g. Reynolds, 1977, JGR; Byrd et al., 1994, JGR). The trend of the fold axis is orthogonal to this declination; the paleomagnetic fold test applied to these data is negative, with k values continuously decreasing upon unfolding, thus indicating that the entire structure in the tuff formed after the well-developed compaction fabric was acquired, at a temperature above maximum blocking temperatures of the ChRM. Post-compaction, high temperature deformation is consistent with field evidence indicating plastic secondary deformation of much of the tuff prior to devitrification. Rapid strain rates probably contributed to the formation of brittle features in the uppermost parts of the tuff (joints and fissures). AMS fabrics, at the site level, are typically very well-defined, with AMS foliations roughly parallel to compaction fabric, with K1 (maximum principal susceptibility) axes typically directed in a southwest-northeast orientation.

Effects of positive results for Mycobacterium avium subsp paratuberculosis as determined by microbial culture of feces or antibody ELISA on results of caudal fold tuberculin test and interferon-gamma assay for tuberculosis in cattle.

PubMed

Dunn, John R; Kaneene, John B; Grooms, Daniel L; Bolin, Steven R; Bolin, Carole A; Bruning-Fann, Colleen S

2005-02-01

To determine whether cattle testing positive for Mycobacterium avium subsp paratuberculosis as determined by microbial culture of feces or antibody ELISA were more likely to have false-positive responses on the caudal fold tuberculin (CFT) test or interferon-gamma (IFN-gamma) assay for Mycobacterium bovis than cattle testing negative for M paratuberculosis. 1043 cattle from 10 herds in Michigan. Feces and blood samples for plasma were collected from cattle > or =24 months old on the day the CFT test was read. Fecal samples were submitted for microbial culture for M paratuberculosis. Plasma samples were tested for antibody against M paratuberculosis, and IFN-gamma after stimulation with purified protein derivative tuberculin from M bovis or M avium. Of 1043 cattle, 180 (17.3%) had positive CFT test results (suspects) and 8 (0.8%) had positive IFN-gamma assay results after stimulation with purified protein derivative tuberculin from M bovis. Forty-five (4.3%) and 115 (11.0%) cattle tested positive for M paratuberculosis as determined by microbial culture of feces and antibody ELISA, respectively. Cattle with positive responses for M paratuberculosis appeared to have an increased likelihood of false-positive results on the CFT test, although this association was not significant. No significant association was detected among cattle testing positive for M paratuberculosis as determined by microbial culture of feces and antibody ELISA and positive CFT test and IFN-gamma assay results for M bovis.

Fhit-deficient normal and cancer cells are mitomycin C and UVC resistant

PubMed Central

Ottey, M; Han, S-Y; Druck, T; Barnoski, B L; McCorkell, K A; Croce, C M; Raventos-Suarez, C; Fairchild, C R; Wang, Y; Huebner, K

2004-01-01

To identify functions of the fragile tumour suppressor gene, FHIT, matched pairs of Fhit-negative and -positive human cancer cell clones, and normal cell lines established from Fhit −/− and +/+ mice, were stressed and examined for differences in cell cycle kinetics and survival. A larger fraction of Fhit-negative human cancer cells and murine kidney cells survived treatment with mitomycin C or UVC light compared to matched Fhit-positive cells; ∼10-fold more colonies of Fhit-deficient cells survived high UVC doses in clonigenic assays. The human cancer cells were synchronised in G1, released into S and treated with UVC or mitomycin C. At 18 h post mitomycin C treatment ∼6-fold more Fhit-positive than -negative cells had died, and 18 h post UVC treatment 3.5-fold more Fhit-positive cells were dead. Similar results were obtained for the murine −/− cells. After low UVC doses, the rate of DNA synthesis in −/− cells decreased more rapidly and steeply than in +/+ cells, although the Atr–Chk1 pathway appeared intact in both cell types. UVC surviving Fhit −/− cells appear transformed and exhibit >5-fold increased mutation frequency. This increased mutation burden could explain the susceptibility of Fhit-deficient cells in vivo to malignant transformation. PMID:15494723

Recoverable and Programmable Collapse from Folding Pressurized Origami Cellular Solids.

PubMed

Li, S; Fang, H; Wang, K W

2016-09-09

We report a unique collapse mechanism by exploiting the negative stiffness observed in the folding of an origami solid, which consists of pressurized cells made by stacking origami sheets. Such a collapse mechanism is recoverable, since it only involves rigid folding of the origami sheets and it is programmable by pressure control and the custom design of the crease pattern. The collapse mechanism features many attractive characteristics for applications such as energy absorption. The reported results also suggest a new branch of origami study focused on its nonlinear mechanics associated with folding.

Predicting protein-binding regions in RNA using nucleotide profiles and compositions.

PubMed

Choi, Daesik; Park, Byungkyu; Chae, Hanju; Lee, Wook; Han, Kyungsook

2017-03-14

Motivated by the increased amount of data on protein-RNA interactions and the availability of complete genome sequences of several organisms, many computational methods have been proposed to predict binding sites in protein-RNA interactions. However, most computational methods are limited to finding RNA-binding sites in proteins instead of protein-binding sites in RNAs. Predicting protein-binding sites in RNA is more challenging than predicting RNA-binding sites in proteins. Recent computational methods for finding protein-binding sites in RNAs have several drawbacks for practical use. We developed a new support vector machine (SVM) model for predicting protein-binding regions in mRNA sequences. The model uses sequence profiles constructed from log-odds scores of mono- and di-nucleotides and nucleotide compositions. The model was evaluated by standard 10-fold cross validation, leave-one-protein-out (LOPO) cross validation and independent testing. Since actual mRNA sequences have more non-binding regions than protein-binding regions, we tested the model on several datasets with different ratios of protein-binding regions to non-binding regions. The best performance of the model was obtained in a balanced dataset of positive and negative instances. 10-fold cross validation with a balanced dataset achieved a sensitivity of 91.6%, a specificity of 92.4%, an accuracy of 92.0%, a positive predictive value (PPV) of 91.7%, a negative predictive value (NPV) of 92.3% and a Matthews correlation coefficient (MCC) of 0.840. LOPO cross validation showed a lower performance than the 10-fold cross validation, but the performance remains high (87.6% accuracy and 0.752 MCC). In testing the model on independent datasets, it achieved an accuracy of 82.2% and an MCC of 0.656. Testing of our model and other state-of-the-art methods on a same dataset showed that our model is better than the others. Sequence profiles of log-odds scores of mono- and di-nucleotides were much more powerful features than nucleotide compositions in finding protein-binding regions in RNA sequences. But, a slight performance gain was obtained when using the sequence profiles along with nucleotide compositions. These are preliminary results of ongoing research, but demonstrate the potential of our approach as a powerful predictor of protein-binding regions in RNA. The program and supporting data are available at http://bclab.inha.ac.kr/RBPbinding .

Improved antimicrobial activities of synthetic-hybrid bacteriocins designed from enterocin E50-52 and pediocin PA-1.

PubMed

Tiwari, Santosh Kumar; Sutyak Noll, Katia; Cavera, Veronica L; Chikindas, Michael L

2015-03-01

Two hybrid bacteriocins, enterocin E50-52/pediocin PA-1 (EP) and pediocin PA-1/enterocin E50-52 (PE), were designed by combining the N terminus of enterocin E50-52 and the C terminus of pediocin PA-1 and by combining the C terminus of pediocin PA-1 and the N terminus of enterocin E50-52, respectively. Both hybrid bacteriocins showed reduced MICs compared to those of their natural counterparts. The MICs of hybrid PE and EP were 64- and 32-fold lower, respectively, than the MIC of pediocin PA-1 and 8- and 4-fold lower, respectively, than the MIC of enterocin E50-52. In this study, the effect of hybrid as well as wild-type (WT) bacteriocins on the transmembrane electrical potential (ΔΨ) and their ability to induce the efflux of intracellular ATP were investigated. Enterocin E50-52, pediocin PA-1, and hybrid bacteriocin PE were able to dissipate ΔΨ, but EP was unable to deplete this component. Both hybrid bacteriocins caused a loss of the intracellular concentration of ATP. EP, however, caused a faster efflux than PE and enterocin E50-52. Enterocin E50-52 and hybrids PE and EP were active against the Gram-positive and Gram-negative bacteria tested, such as Micrococcus luteus, Salmonella enterica serovar Enteritidis 20E1090, and Escherichia coli O157:H7. The hybrid bacteriocins designed and described herein are antimicrobial peptides with MICs lower those of their natural counterparts. Both hybrid peptides induce the loss of intracellular ATP and are capable of inhibiting Gram-negative bacteria, and PE dissipates the electrical potential. In this study, the MIC of hybrid bacteriocin PE decreased 64-fold compared to the MIC of its natural peptide counterpart, pediocin PA-1. Inhibition of Gram-negative pathogens confers an additional advantage for the application of these peptides in therapeutics. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Improved Antimicrobial Activities of Synthetic-Hybrid Bacteriocins Designed from Enterocin E50-52 and Pediocin PA-1

PubMed Central

Tiwari, Santosh Kumar; Sutyak Noll, Katia; Cavera, Veronica L.

2014-01-01

Two hybrid bacteriocins, enterocin E50-52/pediocin PA-1 (EP) and pediocin PA-1/enterocin E50-52 (PE), were designed by combining the N terminus of enterocin E50-52 and the C terminus of pediocin PA-1 and by combining the C terminus of pediocin PA-1 and the N terminus of enterocin E50-52, respectively. Both hybrid bacteriocins showed reduced MICs compared to those of their natural counterparts. The MICs of hybrid PE and EP were 64- and 32-fold lower, respectively, than the MIC of pediocin PA-1 and 8- and 4-fold lower, respectively, than the MIC of enterocin E50-52. In this study, the effect of hybrid as well as wild-type (WT) bacteriocins on the transmembrane electrical potential (ΔΨ) and their ability to induce the efflux of intracellular ATP were investigated. Enterocin E50-52, pediocin PA-1, and hybrid bacteriocin PE were able to dissipate ΔΨ, but EP was unable to deplete this component. Both hybrid bacteriocins caused a loss of the intracellular concentration of ATP. EP, however, caused a faster efflux than PE and enterocin E50-52. Enterocin E50-52 and hybrids PE and EP were active against the Gram-positive and Gram-negative bacteria tested, such as Micrococcus luteus, Salmonella enterica serovar Enteritidis 20E1090, and Escherichia coli O157:H7. The hybrid bacteriocins designed and described herein are antimicrobial peptides with MICs lower those of their natural counterparts. Both hybrid peptides induce the loss of intracellular ATP and are capable of inhibiting Gram-negative bacteria, and PE dissipates the electrical potential. In this study, the MIC of hybrid bacteriocin PE decreased 64-fold compared to the MIC of its natural peptide counterpart, pediocin PA-1. Inhibition of Gram-negative pathogens confers an additional advantage for the application of these peptides in therapeutics. PMID:25527560

Counting the ions surrounding nucleic acids

PubMed Central

2017-01-01

Abstract Nucleic acids are strongly negatively charged, and thus electrostatic interactions—screened by ions in solution—play an important role in governing their ability to fold and participate in biomolecular interactions. The negative charge creates a region, known as the ion atmosphere, in which cation and anion concentrations are perturbed from their bulk values. Ion counting experiments quantify the ion atmosphere by measuring the preferential ion interaction coefficient: the net total number of excess ions above, or below, the number expected due to the bulk concentration. The results of such studies provide important constraints on theories, which typically predict the full three-dimensional distribution of the screening cloud. This article reviews the state of nucleic acid ion counting measurements and critically analyzes their ability to test both analytical and simulation-based models. PMID:28034959

Multicenter Evaluation of the Performance Characteristics of the Bayer VERSANT HCV RNA 3.0 Assay (bDNA)

PubMed Central

Elbeik, Tarek; Surtihadi, Johan; Destree, Mark; Gorlin, Jed; Holodniy, Mark; Jortani, Saeed A.; Kuramoto, Ken; Ng, Valerie; Valdes, Roland; Valsamakis, Alexandra; Terrault, Norah A.

2004-01-01

In this multicenter evaluation, the VERSANT HCV RNA 3.0 Assay (bDNA) (Bayer Diagnostics, Tarrytown, N.Y.) was shown to have excellent reproducibility, linearity, and analytical sensitivity across specimen collection matrices (serum, EDTA, ACD-A), and hepatitis C virus (HCV) genotypes 1 to 6. The VERSANT HCV bDNA Assay has a reportable range of 615 to 7,690,000 (7.69 × 106) IU/ml. The total coefficient of variation (CV) ranged from 32.4% at 615 IU/ml to 17% at 6.8 × 106 IU/ml. The assay was linear across the reportable range. Analytical specificity of 98.8% was determined by testing 999 specimens from volunteer blood donors. Evaluation of HCV genotypes using RNA transcripts of representative clones of 1a, 1b, 2a, 2b, 2c, 3a, 4a, 5a, and 6a and patient specimens showed that the largest difference between genotype 1, upon which the assay is standardized, and non-1 genotypes was within 1.5-fold. Testing of potentially interfering endogenous substances and exogenous substances and conditions found no interference in HCV-positive or HCV-negative specimens except for unconjugated bilirubin at concentrations of ≥20 mg/dl and protein at concentrations of ≥9 g/dl. Biological variability was estimated from 29 clinically stable individuals not on HCV therapy who were tested weekly over an 8-week period. The combined estimate of total (biologic plus assay) variability was 0.15 log10 standard deviation (CV, 36.1%), a fold change of 2.6. Thus, the observed fold change between any two consecutive HCV RNA measures is expected to be less than 2.6-fold (equivalent to 0.41 log10 IU/ml) 95% of the time in clinically stable individuals. PMID:14766817

High-dose HOOK effect in urinary DcR2 assay in patients with chronic kidney disease.

PubMed

Chen, Jia; Chen, Ke-Hong; Wang, Li-Ming; Zhang, Wei-Wei; Feng, Lei; Dai, Huan-Zi; He, Ya-Ni

2018-06-05

Urinary DcR2 (uDcR2) is a biomarker for the early detection the tubulointerstitial injury (TII) in patients with chronic kidney disease (CKD), but the high-dose hook effect may lead to falsely low or even negative results when using an enzyme-linked immunosorbent assay (ELISA). This study aimed to investigate if the high-dose hook effect exists with ELISA testing, and to uncover a potential approach for reducing this effect. 72 CKD patients were recruited and categorized into four groups based on TII scores. uDcR2 was measured in undiluted and serially diluted (two-, four-, eight- and 16-fold dilutions) urine using an ELISA kit. The results from the assay were normalized to urinary creatinine. We evaluated the correlation between uDcR2/cre levels at different dilutions and renal histological parameters. Receiver operating characteristic (ROC) curves were generated to examine the value of uDcR2/cre for predicting TII. uDcR2/cre levels in the undiluted urine were significantly higher in patients with CKD than those in the control. However, higher TII scores did not yield higher levels of uDcR2/cre in the undiluted urine. After serial dilution, uDcR2/cre levels were highest with the four-fold dilution. A positive correlation was found between uDcR2/cre levels at different dilutions and TII scores, with the highest correlation coefficient and the largest AUC being observed at the four-fold dilution. The high-dose hook effect was apparent during ELISA testing of uDcR2 in CKD patients, yet dilution of the urine samples neutralized this effect. However, the use of a four-fold dilution of urine for uDcR2/cre testing may eliminate the high-dose hook effect and make it possible to effectively monitor the severity of TII in CKD patients. Copyright © 2018. Published by Elsevier Inc.

Role of protein surface charge in monellin sweetness.

PubMed

Xue, Wei-Feng; Szczepankiewicz, Olga; Thulin, Eva; Linse, Sara; Carey, Jannette

2009-03-01

A small number of proteins have the unusual property of tasting intensely sweet. Despite many studies aimed at identifying their sweet taste determinants, the molecular basis of protein sweetness is not fully understood. Recent mutational studies of monellin have implicated positively charged residues in sweetness. In the present work, the effect of overall net charge was investigated using the complementary approach of negative charge alterations. Multiple substitutions of Asp/Asn and Glu/Gln residues radically altered the surface charge of single-chain monellin by removing six negative charges or adding four negative charges. Biophysical characterization using circular dichroism, fluorescence, and two-dimensional NMR demonstrates that the native fold of monellin is preserved in the variant proteins under physiological solution conditions although their stability toward chemical denaturation is altered. A human taste test was employed to determine the sweetness detection threshold of the variants. Removal of negative charges preserves monellin sweetness, whereas added negative charge has a large negative impact on sweetness. Meta-analysis of published charge variants of monellin and other sweet proteins reveals a general trend toward increasing sweetness with increasing positive net charge. Structural mapping of monellin variants identifies a hydrophobic surface predicted to face the receptor where introduced positive or negative charge reduces sweetness, and a polar surface where charges modulate long-range electrostatic complementarity.

A negative feedback signal that is triggered by peril curbs honey bee recruitment.

PubMed

Nieh, James C

2010-02-23

Decision making in superorganisms such as honey bee colonies often uses self-organizing behaviors, feedback loops that allow the colony to gather information from multiple individuals and achieve reliable and agile solutions. Honey bees use positive feedback from the waggle dance to allocate colony foraging effort. However, the use of negative feedback signals by superorganisms is poorly understood. I show that conspecific attacks at a food source lead to the production of stop signals, communication that was known to reduce waggle dancing and recruitment but lacked a clear natural trigger. Signalers preferentially targeted nestmates visiting the same food source, on the basis of its odor. During aggressive food competition, attack victims increased signal production by 43 fold. Foragers that attacked competitors or experienced no aggression did not alter signal production. Biting ambush predators also attack foragers at flowers. Simulated biting of foragers or exposure to bee alarm pheromone also elicited signaling (88-fold and 14-fold increases, respectively). This provides the first clear evidence of a negative feedback signal elicited by foraging peril to counteract the positive feedback of the waggle dance. As in intra- and intercellular communication, negative feedback may play an important, though currently underappreciated, role in self-organizing behaviors within superorganisms. Copyright 2010 Elsevier Ltd. All rights reserved.

All complete intersection Calabi-Yau four-folds

NASA Astrophysics Data System (ADS)

Gray, James; Haupt, Alexander S.; Lukas, Andre

2013-07-01

We present an exhaustive, constructive, classification of the Calabi-Yau four-folds which can be described as complete intersections in products of projective spaces. A comprehensive list of 921,497 configuration matrices which represent all topologically distinct types of complete intersection Calabi-Yau four-folds is provided and can be downloaded from http://www-thphys.physics.ox.ac.uk/projects/CalabiYau/Cicy4folds/index.html. The manifolds have non-negative Euler characteristics in the range 0 ≤ χ ≤ 2610. This data set will be of use in a wide range of physical and mathematical applications. Nearly all of these four-folds are elliptically fibered and are thus of interest for F-theory model building.

Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution

PubMed Central

Bastolla, Ugo

2014-01-01

The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change. PMID:24970217

The application of visible wavelength reflectance hyperspectral imaging for the detection and identification of blood stains.

PubMed

Li, Bo; Beveridge, Peter; O'Hare, William T; Islam, Meez

2014-12-01

Current methods of detection and identification of blood stains rely largely on visual examination followed by presumptive tests such as Kastle-Meyer, Leuco-malachite green or luminol. Although these tests are useful, they can produce false positives and can also have a negative impact on subsequent DNA tests. A novel application of visible wavelength reflectance hyperspectral imaging has been used for the detection and positive identification of blood stains in a non contact and non destructive manner on a range of coloured substrates. The identification of blood staining was based on the unique visible absorption spectrum of haemoglobin between 400 and 500 nm. Images illustrating successful discrimination of blood stains from nine red substances are included. It has also been possible to distinguish between blood and approximately 40 other reddish stains. The technique was also successfully used to detect latent blood stains deposited on white filter paper at dilutions of up to 1 in 512 folds and on red tissue at dilutions of up to 1 in 32 folds. Finally, in a blind trial, the method successfully detected and identified a total of 9 blood stains on a red T-shirt. Copyright © 2014 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

Exploring the cause of initially reactive bovine brains on rapid tests for BSE

PubMed Central

Dudas, Sandor; James, Jace; Anderson, Renee; Czub, Stefanie

2015-01-01

ABSTRACT Bovine spongiform encephalopathy (BSE) is an invariably fatal prion disease of cattle. The identification of the zoonotic potential of BSE prompted safety officials to initiate surveillance testing for this disease. In Canada, BSE surveillance is primarily focused on high risk cattle including animals which are dead, down and unable to rise, diseased or distressed. This targeted surveillance results in the submission of brain samples with a wide range of tissue autolysis and associated contaminants. These contaminants have the potential to interfere with important steps of surveillance tests resulting in initially positive test results requiring additional testing to confirm the disease status of the animal. The current tests used for BSE screening in Canada utilize the relative protease resistance of the prion protein gained when it misfolds from PrPC to PrPSc as part of the disease process. Proteinase K completely digests PrPC in normal brains, but leaves most of the PrPSc in BSE positive brains intact which is detected using anti-prion antibodies. These tests are highly reliable but occasionally give rise to initially reactive/false positive results. Test results for these reactive samples were close to the positive/negative cut-off on a sub set of test platforms. This is in contrast to all of the previous Canadian positive samples whose numeric values on these same test platforms were 10 to 100 fold greater than the test positive/negative cut-off. Here we explore the potential reason why a sample is repeatedly positive on a sub-set of rapid surveillance tests, but negative on other test platforms. In order to better understand and identify what might cause these initial reactions, we have conducted a variety of rapid and confirmatory assays as well as bacterial isolation and identification on BSE positive, negative and initially reactive samples. We observed high levels of viable bacterial contamination in initially reactive samples suggesting that the reactivity may be related to bacterial factors. Several bacteria isolated from the initially reactive samples have characteristics of biofilm forming bacteria and this extracellular matrix might play a role in preventing complete digestion of PrPC in these samples. PMID:26689488

Removing the effects of metamorphism from the Neoproterozoic carbon isotope record: a case study on Islay, western Scotland

NASA Astrophysics Data System (ADS)

Skelton, Alasdair

2016-04-01

The Port Askaig Formation on Islay, western Scotland is the first discovered tillite (glacial sediment) of Neoproterozoic age. This formation is sandwiched between carbonate rocks which preserve an extreme negative carbon isotope excursion. This so called "Islay anomaly" has been correlated with other such anomalies worldwide and together with the tillites has been cited as evidence of major (worldwide) glaciation events. During subsequent mountain building, this carbonate-tillite- carbonate sequence has been folded, producing a major en-echelon anticlinal fold system. Folding was accompanied by metamorphism at greenschist facies conditions which was, in turn, accompanied by metamorphic fluid flow. Mapping of the δ18O and δ13C values of these carbonate rocks reveals that metamorphic fluids were channelled through the axial region of the anticlinal fold. The metamorphic fluid was found to have a highly negative δ13C value, which was found to be in equilibrium with metamorphosed graphitic mudstones beneath the carbonate-tillite-carbonate sequence. Devolatilisation of these mudstones is therefore a likely source of this metamorphic fluid. Removal of the effects of metamorphic fluid flow on δ13C values recorded by metamorphosed carbonate rocks on Islay allows us to re-evaluate the isotopic evidence used to reconstruct Neoproterozoic climate. We are able to show that extreme negative δ13C values can partly be attributed to metamorphic fluid flow.

Administration of different Lactobacillus strains in fermented oatmeal soup: in vivo colonization of human intestinal mucosa and effect on the indigenous flora.

PubMed Central

Johansson, M L; Molin, G; Jeppsson, B; Nobaek, S; Ahrné, S; Bengmark, S

1993-01-01

In vivo colonization by different Lactobacillus strains on human intestinal mucosa of healthy volunteers was studied together with the effect of Lactobacillus administration on different groups of indigenous bacteria. A total of 19 test strains were administered in fermented oatmeal soup containing 5 x 10(6) CFU of each strain per ml by using a dose of 100 ml of soup per day for 10 days. Biopsies were taken from both the upper jejunum and the rectum 1 day before administration was started and 1 and 11 days after administration was terminated. The administration significantly increased the Lactobacillus counts on the jejunum mucosa, and high levels remained 11 days after administration was terminated. The levels of streptococci increased by 10- to 100-fold in two persons, and the levels of sulfite-reducing clostridia in the jejunum decreased by 10- to 100-fold in three of the volunteers 1 day after administration was terminated. In recta, the anaerobic bacterium counts and the gram-negative anaerobic bacterium counts decreased significantly by the end of administration. Furthermore, a decrease in the number of members of the Enterobacteriaceae by 1,000-fold was observed on the rectal mucosa of two persons. Randomly picked Lactobacillus isolates were identified phenotypically by API 50CH tests and genotypically by the plasmid profiles of strains and by restriction endonuclease analysis of chromosomal DNAs.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:8439146

Inhibition of Fosfomycin Resistance Protein FosA by Phosphonoformate (Foscarnet) in Multidrug-Resistant Gram-Negative Pathogens

PubMed Central

Ito, Ryota; Tomich, Adam D.; McElheny, Christi L.; Mettus, Roberta T.; Sluis-Cremer, Nicolas

2017-01-01

ABSTRACT FosA proteins confer fosfomycin resistance to Gram-negative pathogens via glutathione-mediated modification of the antibiotic. In this study, we assessed whether inhibition of FosA by sodium phosphonoformate (PPF) (foscarnet), a clinically approved antiviral agent, would reverse fosfomycin resistance in representative Gram-negative pathogens. The inhibitory activity of PPF against purified recombinant FosA from Escherichia coli (FosA3), Klebsiella pneumoniae (FosAKP), Enterobacter cloacae (FosAEC), and Pseudomonas aeruginosa (FosAPA) was determined by steady-state kinetic measurements. The antibacterial activity of PPF against FosA in clinical strains of these species was evaluated by susceptibility testing and time-kill assays. PPF increased the Michaelis constant (Km) for fosfomycin in a dose-dependent manner, without affecting the maximum rate (Vmax) of the reaction, for all four FosA enzymes tested, indicating a competitive mechanism of inhibition. Inhibitory constant (Ki) values were 22.6, 35.8, 24.4, and 56.3 μM for FosAKP, FosAEC, FosAPA, and FosA3, respectively. Addition of clinically achievable concentrations of PPF (∼667 μM) reduced the fosfomycin MICs by ≥4-fold among 52% of the K. pneumoniae, E. cloacae, and P. aeruginosa clinical strains tested and led to a bacteriostatic or bactericidal effect in time-kill assays among representative strains. PPF inhibits FosA activity across Gram-negative species and can potentiate fosfomycin activity against the majority of strains with chromosomally encoded fosA. These data suggest that PPF may be repurposed as an adjuvant for fosfomycin to treat infections caused by some FosA-producing, multidrug-resistant, Gram-negative pathogens. PMID:28993329

Alteration of swing leg work and power during human accelerated sprinting

PubMed Central

Matsubayashi, Takeo; Matsuo, Akifumi; Zushi, Koji

2017-01-01

ABSTRACT This study investigated changes in lower-extremity joint work and power during the swing phase in a maximal accelerated sprinting. Twelve male sprinters performed 60 m maximal sprints while motion data was recorded. Lower-extremity joint work and power during the swing phase of each stride for both legs were calculated. Positive hip and negative knee work (≈4.3 and ≈−2.9 J kg−1) and mean power (≈13.4 and ≈−8.7 W kg−1) during the entire swing phase stabilized or decreased after the 26.2±1.1 (9.69±0.25 m s−1) or 34.3±1.5 m mark (9.97±0.26 m s−1) during the acceleration phase. In contrast, the hip negative work and mean power during the early swing phase (≈7-fold and ≈3.7-fold increase in total), as well as the knee negative work and power during the terminal swing phase (≈1.85-fold and ≈2-fold increase in total), increased until maximal speed. Moreover, only the magnitudes of increases in negative work and mean power at hip and knee joints during the swing phase were positively associated with the increment of running speed from the middle of acceleration phase. These findings indicate that the roles of energy generation and absorption at the hip and knee joints shift around the middle of the acceleration phase as energy generation and absorption at the hip during the late swing phase and at the knee during early swing phase are generally maintained or decreased, and negative work and power at hip during the early swing phase and at knee during the terminal swing phase may be responsible for increasing running speed when approaching maximal speed. PMID:28396485

Laryngeal Electromyography for Prognosis of Vocal Fold Paralysis.

PubMed

Pardo-Maza, Adriana; García-Lopez, Isabel; Santiago-Pérez, Susana; Gavilán, Javier

2017-01-01

This study aimed to determine the value of laryngeal electromyography in the prognosis of vocal fold paralysis. This is a retrospective descriptive study. This study included 80 patients diagnosed with unilateral or bilateral vocal fold paralysis on flexible laryngoscopy between 2002 and 2014 in a tertiary medical center. Laryngeal electromyography using a standardized protocol was performed; the outcome measures were classified and analyzed into two groups according to the degree of injury. Group 1 included patients with mild to moderate injury, and group 2 included patients with severe to complete injury. Prognosis was correlated with vocal fold motion recovery status with a minimum of 6 months of follow-up since the symptoms onset using positive and negative predictive values. Sixty patients showed acute or chronic recurrent laryngeal neuropathy in laryngeal electromyography. Twelve of 41 patients included in group 1 recovered motion, and 30 of 35 patients included in group 2 did not recover, resulting in 88.2% of positive predictive value and 35.7% of negative predictive value. Our data confirm that laryngeal electromyography is a useful clinical tool in predicting poor recovery in patients with vocal fold paralysis. It allows identification of candidates for early intervention. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops

PubMed Central

Paslawski, Wojciech; Lillelund, Ove K.; Kristensen, Julie Veje; Schafer, Nicholas P.; Baker, Rosanna P.; Urban, Sinisa; Otzen, Daniel E.

2015-01-01

Despite the ubiquity of helical membrane proteins in nature and their pharmacological importance, the mechanisms guiding their folding remain unclear. We performed kinetic folding and unfolding experiments on 69 mutants (engineered every 2–3 residues throughout the 178-residue transmembrane domain) of GlpG, a membrane-embedded rhomboid protease from Escherichia coli. The only clustering of significantly positive ϕ-values occurs at the cytosolic termini of transmembrane helices 1 and 2, which we identify as a compact nucleus. The three loops flanking these helices show a preponderance of negative ϕ-values, which are sometimes taken to be indicative of nonnative interactions in the transition state. Mutations in transmembrane helices 3–6 yielded predominantly ϕ-values near zero, indicating that this part of the protein has denatured-state–level structure in the transition state. We propose that loops 1–3 undergo conformational rearrangements to position the folding nucleus correctly, which then drives folding of the rest of the domain. A compact N-terminal nucleus is consistent with the vectorial nature of cotranslational membrane insertion found in vivo. The origin of the interactions in the transition state that lead to a large number of negative ϕ-values remains to be elucidated. PMID:26056273

Age-related changes in the gut microbiota influence systemic inflammation and stroke outcome.

PubMed

Spychala, Monica S; Venna, Venugopal Reddy; Jandzinski, Michal; Doran, Sarah J; Durgan, David J; Ganesh, Bhanu Priya; Ajami, Nadim J; Putluri, Nagireddy; Graf, Joerg; Bryan, Robert M; McCullough, Louise D

2018-05-07

Objective Chronic systemic inflammation contributes to the pathogenesis of many age-related diseases. Although not well understood, alterations in the gut microbiota, or dysbiosis, may be responsible for age-related inflammation. Methods Using stroke as a disease model, we tested the hypothesis that a youthful microbiota, when established in aged mice, produces positive outcomes following ischemic stroke. Conversely, an aged microbiota, when established in young mice, produces negative outcomes after stroke. Young and aged male mice had either a young or an aged microbiota established by fecal transplant gavage (FTG). Mice were subjected to ischemic stroke (MCAO) or sham surgery. During the subsequent weeks, mice underwent behavioral testing and fecal samples were collected for 16S rRNA analysis of bacterial content. Results We found that the microbiota is altered after experimental stroke in young mice, and resembles the biome of uninjured aged mice. In aged mice, the ratio of Firmicutes to Bacteroidetes (F:B), two main bacterial phyla in gut microbiota, increased ∼9-fold (P<0.001) compared to young. This increased F:B ratio in aged mice is indicative of dysbiosis. Altering the microbiota in young by fecal gavage to resemble that of aged mice (∼6-fold increase in F:B ratio, P<0.001) increased mortality following MCAO, decreased performance in behavioral testing, and increased cytokine levels. Conversely, altering the microbiota in aged to resemble that of young (∼9-fold decrease in F:B ratio, P<0.001) increased survival and improved recovery following MCAO. Interpretation Aged biome increased the levels of systemic pro-inflammatory cytokines. We conclude that the gut microbiota can be modified to positively impact outcomes from age-related diseases. This article is protected by copyright. All rights reserved. © 2018 American Neurological Association.

Potentiating the Activity of Nisin against Escherichia coli

PubMed Central

Zhou, Liang; van Heel, Auke J.; Montalban-Lopez, Manuel; Kuipers, Oscar P.

2016-01-01

Lantibiotics are antimicrobial (methyl)lanthionine-containing peptides produced by various Gram-positive bacteria. The model lantibiotic, nisin, binds lipid II in the cell membrane. Additionally, after binding it can insert into the membrane creating a pore. Nisin can efficiently inhibit the growth of Gram-positive bacteria and resistance is rarely observed. However, the activity of lantibiotics is at least 100-fold lower against certain Gram-negative bacteria. This is caused by the fact that Gram-negative bacteria have an outer membrane that hinders the peptides to reach lipid II, which is located in the inner membrane. Improving the activity of lantibiotics against Gram-negative bacteria could be achieved if the outer membrane traversing efficiency is increased. Here, several anti-Gram-negative peptides (e.g., apidaecin 1b, oncocin), or parts thereof, were fused to the C-terminus of either a truncated version of nisin containing the first three/five rings or full length nisin. The activities of these fusion peptides were tested against Gram-negative pathogens. Our results showed that when an eight amino acids (PRPPHPRL) tail from apidaecin 1b was attached to nisin, the activity of nisin against Escherichia coli CECT101 was increased more than two times. This research presents a new and promising method to increase the anti-Gram-negative activity of lantibiotics. PMID:26904542

Dry eye in vitamin D deficiency: more than an incidental association.

PubMed

Yildirim, Pelin; Garip, Yeşim; Karci, Ayse Aslihan; Guler, Tuba

2016-01-01

The aim of this article is two-fold: (i) to demonstrate the relation between vitamin D deficiency and dry eye and impaired tear function; and (ii) to investigate the possible associations among clinical parameters of hypovitaminosis D with dry eye parameters. Fifty premenopausal women with vitamin D deficiency (serum vitamin D levels < 20 ng/mL) and 48 controls were included. Participants were assessed by Schirmer's test, tear break-up time test (TBUT), ocular surface disease index (OSDI), Stanford Health Assessment Questionnaire (HAQ), fatigue severity scale (FSS), and visual analogue scale-pain (VAS-pain). Lower scores in Schirmer's test and TBUT, and higher in OSDI were detected in patients with vitamin D deficiency than in controls (P < 0.05). FSS was negatively correlated with Schirmer's test (r = -0,29; P = 0.038) and TBUT scores (r = -0,43; P = 0.002); VAS-pain was negatively correlated with TBUT scores (r = -0.32; P = 0.023). HAQ scores showed no significant correlation with dry eye parameters (P > 0.05). Vitamin D level was negatively correlated with OSDI (r = -0.49; P < 0.001), and positively with Schirmer's test (r = 0.45; P = 0.001) and TBUT scores (r = 0.30; P = 0.029). Dry eye and impaired tear function in patients with vitamin D deficiency may indicate a protective role of vitamin D in the development of dry eye, probably by enhancing tear film parameters and reducing ocular surface inflammation. Patients with vitamin D deficiency should be evaluated for dry eye syndromes. © 2015 Asia Pacific League of Associations for Rheumatology and Wiley Publishing Asia Pty Ltd.

A DsbA-Deficient Periplasm Enables Functional Display of a Protein with Redox-Sensitive Folding on M13 Phage.

PubMed

Chen, Minyong; Samuelson, James C

2016-06-14

The requirements for target protein folding in M13 phage display are largely underappreciated. Here we chose Fbs1, a carbohydrate binding protein, as a model to address this issue. Importantly, folding of Fbs1 is impaired in an oxidative environment. Fbs1 can be displayed on M13 phage using the SRP or Sec pathway. However, the displayed Fbs1 protein is properly folded only when Fbs1 is translocated via the SRP pathway and displayed using Escherichia coli cells with a DsbA-negative periplasm. This study indicates M13 phage display may be improved using a system specifically designed according to the folding requirements of each target protein.

Selective immunoglobulin A deficiency and celiac disease: let's give serology a chance.

PubMed

Valletta, E; Fornaro, M; Pecori, S; Zanoni, G

2011-01-01

Patients with selective immunoglobulin (Ig) A deficiency have a 10- to 20-fold increased risk of celiac disease. In these patients, serological diagnosis of celiac disease can be difficult, since specific IgA-based assays are usually negative and IgG-specific antibody tests are insufficiently reliable. We describe a girl with selective IgA deficiency who had a troublesome diagnosis of celiac disease that was established only after an unexpected positive test result for antitransglutaminase IgA and antiendomysium IgA. Our observation indicates that IgA-based serology should not be forgotten in patients with selective IgA deficiency, since positive results for antitransglutaminase IgA, antiendomysium IgA, or both can be observed at any time during diagnostic investigations.

Improving Docking Performance Using Negative Image-Based Rescoring.

PubMed

Kurkinen, Sami T; Niinivehmas, Sanna; Ahinko, Mira; Lätti, Sakari; Pentikäinen, Olli T; Postila, Pekka A

2018-01-01

Despite the large computational costs of molecular docking, the default scoring functions are often unable to recognize the active hits from the inactive molecules in large-scale virtual screening experiments. Thus, even though a correct binding pose might be sampled during the docking, the active compound or its biologically relevant pose is not necessarily given high enough score to arouse the attention. Various rescoring and post-processing approaches have emerged for improving the docking performance. Here, it is shown that the very early enrichment (number of actives scored higher than 1% of the highest ranked decoys) can be improved on average 2.5-fold or even 8.7-fold by comparing the docking-based ligand conformers directly against the target protein's cavity shape and electrostatics. The similarity comparison of the conformers is performed without geometry optimization against the negative image of the target protein's ligand-binding cavity using the negative image-based (NIB) screening protocol. The viability of the NIB rescoring or the R-NiB, pioneered in this study, was tested with 11 target proteins using benchmark libraries. By focusing on the shape/electrostatics complementarity of the ligand-receptor association, the R-NiB is able to improve the early enrichment of docking essentially without adding to the computing cost. By implementing consensus scoring, in which the R-NiB and the original docking scoring are weighted for optimal outcome, the early enrichment is improved to a level that facilitates effective drug discovery. Moreover, the use of equal weight from the original docking scoring and the R-NiB scoring improves the yield in most cases.

In vitro gastrointestinal digestion increases the translocation of polystyrene nanoparticles in an in vitro intestinal co-culture model.

PubMed

Walczak, Agata P; Kramer, Evelien; Hendriksen, Peter J M; Helsdingen, Richard; van der Zande, Meike; Rietjens, Ivonne M C M; Bouwmeester, Hans

2015-01-01

The conditions of the gastrointestinal tract may change the physicochemical properties of nanoparticles (NPs) and therewith the bioavailability of orally taken NPs. Therefore, we assessed the impact of in vitro gastrointestinal digestion on the protein corona of polystyrene NPs (PS-NPs) and their subsequent translocation across an in vitro intestinal barrier. A co-culture of intestinal Caco-2 and HT29-MTX cells was exposed to 50 nm PS-NPs of different charges (positive and negative) in two forms: pristine and digested in an in vitro gastrointestinal digestion model. In vitro digestion significantly increased the translocation of all, except the "neutral", PS-NPs. Upon in vitro digestion, translocation was 4-fold higher for positively charged NPs and 80- and 1.7-fold higher for two types of negatively charged NPs. Digestion significantly reduced the amount of protein in the corona of three out of four types of NPs. This reduction of proteins was 4.8-fold for "neutral", 3.5-fold for positively charged and 1.8-fold for one type of negatively charged PS-NPs. In vitro digestion also affected the composition of the protein corona of PS-NPs by decreasing the presence of higher molecular weight proteins and shifting the protein content of the corona to low molecular weight proteins. These findings are the first to report that in vitro gastrointestinal digestion significantly affects the protein corona and significantly increases the in vitro translocation of differently charged PS-NPs. These findings stress the importance of including the in vitro digestion in future in vitro intestinal translocation screening studies for risk assessment of orally taken NPs.

Induction of DREB2A pathway with repression of E2F, jasmonic acid biosynthetic and photosynthesis pathways in cold acclimation-specific freeze-resistant wheat crown.

PubMed

Karki, Amrit; Horvath, David P; Sutton, Fedora

2013-03-01

Winter wheat lines can achieve cold acclimation (development of tolerance to freezing temperatures) and vernalization (delay in transition from vegetative to reproductive phase) in response to low non-freezing temperatures. To describe cold-acclimation-specific processes and pathways, we utilized cold acclimation transcriptomic data from two lines varying in freeze survival but not vernalization. These lines, designated freeze-resistant (FR) and freeze-susceptible (FS), were the source of crown tissue RNA. Well-annotated differentially expressed genes (p ≤ 0.005 and fold change ≥ 2 in response to 4 weeks cold acclimation) were used for gene ontology and pathway analysis. "Abiotic stimuli" was identified as the most enriched and unique for FR. Unique to FS was "cytoplasmic components." Pathway analysis revealed the "triacylglycerol degradation" pathway as significantly downregulated and common to both FR and FS. The most enriched of FR pathways was "neighbors of DREB2A," with the highest positive median fold change. The "13-LOX and 13-HPL" and the "E2F" pathways were enriched in FR only with a negative median fold change. The "jasmonic acid biosynthesis" pathway and four "photosynthetic-associated" pathways were enriched in both FR and FS but with a more negative median fold change in FR than in FS. A pathway unique to FS was "binding partners of LHCA1," which was enriched only in FS with a significant negative median fold change. We propose that the DREB2A, E2F, jasmonic acid biosynthesis, and photosynthetic pathways are critical for discrimination between cold-acclimated lines varying in freeze survival.

Exact folded-band chaotic oscillator.

PubMed

Corron, Ned J; Blakely, Jonathan N

2012-06-01

An exactly solvable chaotic oscillator with folded-band dynamics is shown. The oscillator is a hybrid dynamical system containing a linear ordinary differential equation and a nonlinear switching condition. Bounded oscillations are provably chaotic, and successive waveform maxima yield a one-dimensional piecewise-linear return map with segments of both positive and negative slopes. Continuous-time dynamics exhibit a folded-band topology similar to Rössler's oscillator. An exact solution is written as a linear convolution of a fixed basis pulse and a discrete binary sequence, from which an equivalent symbolic dynamics is obtained. The folded-band topology is shown to be dependent on the symbol grammar.

Academic Procrastination among College Students with Learning Disabilities: The Role of Positive and Negative Self-Oriented Perfectionism in Terms of Gender, Specialty and Grade

ERIC Educational Resources Information Center

Mohammed, Adel Abdulla; Sherit, Asharaf Mohammed A.; Eissa, Mourad Ali; Mostafa, Amaal Ahmed

2013-01-01

The purpose of this study was three folds: to explore whether there were relationship between academic procrastination and positive and negative self-oriented perfectionism of college students with learning disabilities, the extent to which positive and negative self-oriented perfectionism of college students with learning disabilities predicts…

Post-exposure temperature influence on the toxicity of conventional and new chemistry insecticides to green lacewing Chrysoperla carnea (Stephens) (Neuroptera: Chrysopidae)

PubMed Central

Mansoor, Muhammad Mudassir; Afzal, Muhammad; Raza, Abu Bakar M.; Akram, Zeeshan; Waqar, Adil; Afzal, Muhammad Babar Shahzad

2014-01-01

Chrysoperla carnea (Stephens) is an important biological control agent currently being used in many integrated pest management (IPM) programs to control insect pests. The effect of post-treatment temperature on insecticide toxicity of a spinosyn (spinosad), pyrethroid (lambda cyhalothrin), organophosphate (chlorpyrifos) and new chemistry (acetamiprid) to C. carnea larvae was investigated under laboratory conditions. Temperature coefficients of each insecticide tested were evaluated. From 20 to 40 °C, toxicity of lambda cyhalothrin and spinosad decreased by 2.15- and 1.87-fold while toxicity of acetamiprid and chlorpyrifos increased by 2.00 and 1.79-fold, respectively. The study demonstrates that pesticide effectiveness may vary according to environmental conditions. In cropping systems where multiple insecticide products are used, attention should be given to temperature variation as a key factor in making pest management strategies safer for biological control agents. Insecticides with a negative temperature coefficient may play a constructive role to conserve C. carnea populations. PMID:25972753

Post-exposure temperature influence on the toxicity of conventional and new chemistry insecticides to green lacewing Chrysoperla carnea (Stephens) (Neuroptera: Chrysopidae).

PubMed

Mansoor, Muhammad Mudassir; Afzal, Muhammad; Raza, Abu Bakar M; Akram, Zeeshan; Waqar, Adil; Afzal, Muhammad Babar Shahzad

2015-05-01

Chrysoperla carnea (Stephens) is an important biological control agent currently being used in many integrated pest management (IPM) programs to control insect pests. The effect of post-treatment temperature on insecticide toxicity of a spinosyn (spinosad), pyrethroid (lambda cyhalothrin), organophosphate (chlorpyrifos) and new chemistry (acetamiprid) to C. carnea larvae was investigated under laboratory conditions. Temperature coefficients of each insecticide tested were evaluated. From 20 to 40 °C, toxicity of lambda cyhalothrin and spinosad decreased by 2.15- and 1.87-fold while toxicity of acetamiprid and chlorpyrifos increased by 2.00 and 1.79-fold, respectively. The study demonstrates that pesticide effectiveness may vary according to environmental conditions. In cropping systems where multiple insecticide products are used, attention should be given to temperature variation as a key factor in making pest management strategies safer for biological control agents. Insecticides with a negative temperature coefficient may play a constructive role to conserve C. carnea populations.

Comparative activity of ceftobiprole against Gram-positive and Gram-negative isolates from Europe and the Middle East: the CLASS study.

PubMed

Rossolini, Gian M; Dryden, Matthew S; Kozlov, Roman S; Quintana, Alvaro; Flamm, Robert K; Läuffer, Jörg M; Lee, Emma; Morrissey, Ian; CLASS Study Group

2011-01-01

to assess the in vitro activity of ceftobiprole and comparators against a recent collection of Gram-positive and Gram-negative pathogens, in order to detect potential changes in susceptibility patterns, and to evaluate the Etest assay for ceftobiprole susceptibility testing. contemporary Gram-positive and Gram-negative isolates (excluding extended-spectrum β-lactamase-producing isolates) from across Europe and the Middle East were collected, and their susceptibility to ceftobiprole, vancomycin, teicoplanin, linezolid, ceftazidime and cefepime was assessed using the Etest method. Quality testing [using Etest and broth microdilution (BMD)] was conducted at a central reference laboratory. some 5041 Gram-positive and 4026 Gram-negative isolates were included. Against Gram-positive isolates overall, ceftobiprole had the lowest MIC50 (0.5 mg/L), compared with 1 mg/L for its comparators (vancomycin, teicoplanin and linezolid). Against methicillin-resistant Staphylococcus aureus, all four agents had a similar MIC90 (2 mg/L), but ceftobiprole had a 4-fold better MIC90 (0.5 mg/L) against methicillin-susceptible strains. Only 38 Gram-positive isolates were confirmed as ceftobiprole resistant. Among Gram-negative strains, 86.9%, 91.7% and 95.2% were susceptible to ceftobiprole, ceftazidime and cefepime, respectively. Pseudomonas aeruginosa was less susceptible to all three antimicrobials than any other Gram-negative pathogen. There was generally good agreement between local Etest results and those obtained at the reference laboratory (for ceftobiprole: 86.8% with Gram-negatives; and 94.7% with Gram-positives), as well as between results obtained by BMD and Etest methods (for ceftobiprole: 98.2% with Gram-negatives; and 98.4% with Gram-positives). ceftobiprole exhibits in vitro activity against a wide range of Gram-positive and Gram-negative pathogens, including multidrug-resistant strains. No changes in its known susceptibility profile were identified.

Pressure-jump small-angle x-ray scattering detected kinetics of staphylococcal nuclease folding.

PubMed Central

Woenckhaus, J; Köhling, R; Thiyagarajan, P; Littrell, K C; Seifert, S; Royer, C A; Winter, R

2001-01-01

The kinetics of chain disruption and collapse of staphylococcal nuclease after positive or negative pressure jumps was monitored by real-time small-angle x-ray scattering under pressure. We used this method to probe the overall conformation of the protein by measuring its radius of gyration and pair-distance-distribution function p(r) which are sensitive to the spatial extent and shape of the particle. At all pressures and temperatures tested, the relaxation profiles were well described by a single exponential function. No fast collapse was observed, indicating that the rate limiting step for chain collapse is the same as that for secondary and tertiary structure formation. Whereas refolding at low pressures occurred in a few seconds, at high pressures the relaxation was quite slow, approximately 1 h, due to a large positive activation volume for the rate-limiting step for chain collapse. A large increase in the system volume upon folding implies significant dehydration of the transition state and a high degree of similarity in terms of the packing density between the native and transition states in this system. This study of the time-dependence of the tertiary structure in pressure-induced folding/unfolding reactions demonstrates that novel information about the nature of protein folding transitions and transition states can be obtained from a combination of small-angle x-ray scattering using high intensity synchrotron radiation with the high pressure perturbation technique. PMID:11222312

Ground Deployment Demonstration and Material Testing for Solar Sail

NASA Astrophysics Data System (ADS)

Huang, Xiaoqi; Cheng, Zhengai; Liu, Yufei; Wang, Li

2016-07-01

Solar Sail is a kind of spacecraft that can achieve extremely high velocity by light pressure instead of chemical fuel. The great accelerate rely on its high area-to-mass ratio. So solar sail is always designed in huge size and it use ultra thin and light weight materials. For 100-meter class solar sail, two key points must be considered in the design process. They are fold-deployment method, and material property change in space environment. To test and verify the fold-deployment technology, a 8*8m principle prototype was developed. Sail membrane folding in method of IKAROS, Nanosail-D , and new proposed L-shape folding pattern were tested on this prototype. Their deployment properties were investigated in detail, and comparisons were made between them. Also, the space environment suitability of ultra thin polyimide films as candidate solar sail material was analyzed. The preliminary test results showed that membrane by all the folding method could deploy well. Moreover, sail membrane folding by L-shape pattern deployed more rapidly and more organized among the three folding pattern tested. The mechanical properties of the polyimide had no significant change after electron irradiation. As the preliminary research on the key technology of solar sail spacecraft, in this paper, the results of the study would provide important basis on large-scale solar sail membrane select and fold-deploying method design.

Elimination of sucrose transport and hydrolysis in Saccharomyces cerevisiae: a platform strain for engineering sucrose metabolism

PubMed Central

Marques, Wesley Leoricy; Mans, Robert; Marella, Eko Roy; Cordeiro, Rosa Lorizolla; van den Broek, Marcel; Daran, Jean-Marc G.; Pronk, Jack T.; Gombert, Andreas K.; van Maris, Antonius J.A.

2017-01-01

Abstract Many relevant options to improve efficacy and kinetics of sucrose metabolism in Saccharomyces cerevisiae and, thereby, the economics of sucrose-based processes remain to be investigated. An essential first step is to identify all native sucrose-hydrolysing enzymes and sucrose transporters in this yeast, including those that can be activated by suppressor mutations in sucrose-negative strains. A strain in which all known sucrose-transporter genes (MAL11, MAL21, MAL31, MPH2, MPH3) were deleted did not grow on sucrose after 2 months of incubation. In contrast, a strain with deletions in genes encoding sucrose-hydrolysing enzymes (SUC2, MAL12, MAL22, MAL32) still grew on sucrose. Its specific growth rate increased from 0.08 to 0.25 h−1 after sequential batch cultivation. This increase was accompanied by a 3-fold increase of in vitro sucrose-hydrolysis and isomaltase activities, as well as by a 3- to 5-fold upregulation of the isomaltase-encoding genes IMA1 and IMA5. One-step Cas9-mediated deletion of all isomaltase-encoding genes (IMA1-5) completely abolished sucrose hydrolysis. Even after 2 months of incubation, the resulting strain did not grow on sucrose. This sucrose-negative strain can be used as a platform to test metabolic engineering strategies and for fundamental studies into sucrose hydrolysis or transport. PMID:28087672

Rat testicular impairment induced by electromagnetic radiation from a conventional cellular telephone and the protective effects of the antioxidants vitamins C and E

PubMed Central

Al-Damegh, Mona Abdullah

2012-01-01

OBJECTIVE: The aim of this study was to investigate the possible effects of electromagnetic radiation from conventional cellular phone use on the oxidant and antioxidant status in rat blood and testicular tissue and determine the possible protective role of vitamins C and E in preventing the detrimental effects of electromagnetic radiation on the testes. MATERIALS AND METHODS: The treatment groups were exposed to an electromagnetic field, electromagnetic field plus vitamin C (40 mg/kg/day) or electromagnetic field plus vitamin E (2.7 mg/kg/day). All groups were exposed to the same electromagnetic frequency for 15, 30, and 60 min daily for two weeks. RESULTS: There was a significant increase in the diameter of the seminiferous tubules with a disorganized seminiferous tubule sperm cycle interruption in the electromagnetism-exposed group. The serum and testicular tissue conjugated diene, lipid hydroperoxide, and catalase activities increased 3-fold, whereas the total serum and testicular tissue glutathione and glutathione peroxidase levels decreased 3-5 fold in the electromagnetism-exposed animals. CONCLUSION: Our results indicate that the adverse effect of the generated electromagnetic frequency had a negative impact on testicular architecture and enzymatic activity. This finding also indicated the possible role of vitamins C and E in mitigating the oxidative stress imposed on the testes and restoring normality to the testes. PMID:22892924

Rat testicular impairment induced by electromagnetic radiation from a conventional cellular telephone and the protective effects of the antioxidants vitamins C and E.

PubMed

Al-Damegh, Mona Abdullah

2012-07-01

The aim of this study was to investigate the possible effects of electromagnetic radiation from conventional cellular phone use on the oxidant and antioxidant status in rat blood and testicular tissue and determine the possible protective role of vitamins C and E in preventing the detrimental effects of electromagnetic radiation on the testes. The treatment groups were exposed to an electromagnetic field, electromagnetic field plus vitamin C (40 mg/kg/day) or electromagnetic field plus vitamin E (2.7 mg/kg/day). All groups were exposed to the same electromagnetic frequency for 15, 30, and 60 min daily for two weeks. There was a significant increase in the diameter of the seminiferous tubules with a disorganized seminiferous tubule sperm cycle interruption in the electromagnetism-exposed group. The serum and testicular tissue conjugated diene, lipid hydroperoxide, and catalase activities increased 3-fold, whereas the total serum and testicular tissue glutathione and glutathione peroxidase levels decreased 3-5 fold in the electromagnetism-exposed animals. Our results indicate that the adverse effect of the generated electromagnetic frequency had a negative impact on testicular architecture and enzymatic activity. This finding also indicated the possible role of vitamins C and E in mitigating the oxidative stress imposed on the testes and restoring normality to the testes.

High Phenotypic Variability among Representative Strains of Common Salmonella enterica Serovars with Possible Implications for Food Safety.

PubMed

Abdullah, Wan Zawiah Wan; Mackey, Bernard M; Karatzas, Kimon Andreas G

2018-01-01

Salmonella is an important foodborne pathogen, whose ability to resist stress and survive can vary among strains. This variability is normally not taken into account when predictions are made about survival in foods with negative consequences. Therefore, we examined the contribution of variable phenotypic properties to survival under stress in 10 Salmonella serovars. One strain (Typhimurium 10) was intentionally RpoS-negative; however, another strain (Heidelberg) showed an rpoS mutation, rendering it inactive. We assessed an array of characteristics (motility, biofilm formation, bile resistance, acid resistance, and colony morphology) that show major variability among strains associated with a 10- to 19-fold difference between the highest and the lowest strain for most characteristics. The RpoS status of isolates did not affect variability in the characteristics, with the exception of resistance to NaCl, acetic acid, lactic acid, and the combination of acetic acid and salt, where the variability between the highest and the lowest strain was reduced to 3.1-fold, 1.7-fold, 2-fold, and 1.7-fold, respectively, showing that variability was significant among RpoS-positive strains. Furthermore, we also found a good correlation between acid resistance and lysine decarboxylase activity, showing its importance for acid resistance, and demonstrated a possible role of RpoS in the lysine decarboxylase activity in Salmonella.

Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption

PubMed Central

Morris, Megan M.; Brown, Matt; Doane, Michael; Edwards, Matthew S.; Michael, Todd P.; Dinsdale, Elizabeth A.

2018-01-01

Global climate change includes rising temperatures and increased pCO2 concentrations in the ocean, with potential deleterious impacts on marine organisms. In this case study we conducted a four-week climate change incubation experiment, and tested the independent and combined effects of increased temperature and partial pressure of carbon dioxide (pCO2), on the microbiomes of a foundation species, the giant kelp Macrocystis pyrifera, and the surrounding water column. The water and kelp microbiome responded differently to each of the climate stressors. In the water microbiome, each condition caused an increase in a distinct microbial order, whereas the kelp microbiome exhibited a reduction in the dominant kelp-associated order, Alteromondales. The water column microbiomes were most disrupted by elevated pCO2, with a 7.3 fold increase in Rhizobiales. The kelp microbiome was most influenced by elevated temperature and elevated temperature in combination with elevated pCO2. Kelp growth was negatively associated with elevated temperature, and the kelp microbiome showed a 5.3 fold increase Flavobacteriales and a 2.2 fold increase alginate degrading enzymes and sulfated polysaccharides. In contrast, kelp growth was positively associated with the combination of high temperature and high pCO2 ‘future conditions’, with a 12.5 fold increase in Planctomycetales and 4.8 fold increase in Rhodobacteriales. Therefore, the water and kelp microbiomes acted as distinct communities, where the kelp was stabilizing the microbiome under changing pCO2 conditions, but lost control at high temperature. Under future conditions, a new equilibrium between the kelp and the microbiome was potentially reached, where the kelp grew rapidly and the commensal microbes responded to an increase in mucus production. PMID:29474389

Comparative effectiveness study on human papillomavirus detection methods used in the cervical cancer screening programme

PubMed Central

Nygård, Mari; Røysland, Kjetil; Campbell, Suzanne; Dillner, Joakim

2014-01-01

Objectives To compare the short-term and long-term effectiveness of human papillomavirus (HPV) tests in Norwegian Cervical Cancer Screening Programme (NCCSP). Design Nationwide register-based prospective follow-up study. Setting In 2005, the NCCSP implemented HPV testing in follow-up of unsatisfactory, atypical squamous cells of undetermined significance (ASC-US) and low-grade squamous intraepithelial lesion (LSIL) cytology. Participants 19 065 women with repeat cytology and HPV test after unsatisfactory ASC-US or LSIL screening result in 2005–2009. Interventions Through individual registry linkages we observed how women were treated in the regular medical care. Main outcome measures We estimated cumulative incidence of cervical intraepithelial neoplasia grade 2 or worse (CIN2+) in 6 months and 3 years after repeat cytology and HPV test. Patients diagnosed with CIN2+ in 6 months and 3 years were assessed for initial HPV positivity. Results 5392 had ASC-US/LSIL and 13 673 had normal/unsatisfactory repeat cytology; for HPV detection 4715 used AMPLICOR HPV Test (Roche Diagnostics, Basel, Switzerland), 9162 Hybrid Capture 2 (HC2) High-Risk HPV DNA Test (QIAGEN, Gaithersburg, Maryland, USA) and 5188 PreTect HPV-Proofer (NorChip, Klokkarstua, Norway). Among those with ASC-US/LSIL repeat cytology, 3-year risk of CIN2+ was 15-fold in Amplicor/HC2-positives compared with Amplicor/HC2-negatives and sevenfold in Proofer-positives compared with Proofer-negatives; a 3-year risk of CIN2+ was 2.1% (95% CI 0.7% to 3.4%) in Amplicor-negatives and 7.2% (95% CI 5.4% to 8.9%) in Proofer-negatives. Close to 100% of patients with CIN2+ diagnosed within 6 months tested positive to HPV (all methods). Considering all patients diagnosed with CIN2+ in 3-year follow-up, 97% were initially positive in the Amplicor group and more than 94% in the HC2 group, compared with less than 80% in the Proofer group. Conclusions While the long-term evaluation of new screening routines showed a good overall performance of triage-HPV DNA testing, the management of HPV-negative women with persistent ASC-US/LSIL was suboptimal. PMID:24401720

Administration of antibiotic agents before intraoperative sampling in orthopedic infections alters culture results.

PubMed

Al-Mayahi, Mohamed; Cian, Anais; Lipsky, Benjamin A; Suvà, Domizio; Müller, Camillo; Landelle, Caroline; Miozzari, Hermès H; Uçkay, Ilker

2015-11-01

Many physicians and surgeons think that prescribing antibiotics before intraoperative sampling does not alter the microbiological results. Case-control study of adult patients hospitalized with orthopedic infections. Among 2740 episodes of orthopedic infections, 1167 (43%) had received antibiotic therapy before surgical sampling. Among these, 220 (19%) grew no pathogens while the proportion of culture-negative results in the 2573 who had no preoperative antibiotic therapy was only 6%. By multivariate analyses, pre-operative antibiotic exposure was associated with significantly more culture-negative results (odds ratio 2.8, 95% confidence interval 2.1-3.7), more non-fermenting rods and skin commensals (odds ratio 2.8 and 3.0, respectively). Even a single pre-operative dose of antibiotic was significantly associated with subsequent culture-negative results (19/93 vs. 297/2350; χ²-test, p = 0.01) and skin commensals (17/74 vs. 274/2350; p = 0.01) compared to episodes without preceding prophylaxis. Prior antibiotic use, including single-dose prophylactic administrations, is three-fold associated with culture-negative results, non-fermenting rods and resistant skin commensals. Copyright © 2015 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Evaluating 6 ricin field detection assays.

PubMed

Slotved, Hans-Christian; Sparding, Nadja; Tanassi, Julia Tanas; Steenhard, Nina R; Heegaard, Niels H H

2014-01-01

This study presents data showing the performance of 6 commercial detection assays against ricin around concentrations specified as detection limits by the producers. A 2-fold dilution series of 20 ng/ml ricin was prepared and used for testing the lateral-flow kits: BADD, Pro Strips™, ENVI, RAID DX, Ricin BioThreat Alert, and IMASS™ device. Three of the 6 tested field assays (IMASS™ device, ENVI assay, and the BioThreat Alert assay) were able to detect ricin, although differences in the measured detection limits compared to the official detection limits and false-negative results were observed. We were not able to get the BADD, Pro Strips™, and RAID assays to function in our laboratory. We conclude that when purchasing a field responder assay, there is large variation in the specificity of the assays, and a number of in-house tests must be performed to ensure functionality.

T-lymphoid, megakaryocyte, and granulocyte development are sensitive to decreases in CBFβ dosage.

PubMed Central

Talebian, Laleh; Li, Zhe; Guo, Yalin; Gaudet, Justin; Speck, Maren E.; Sugiyama, Daisuke; Kaur, Prabhjot; Pear, Warren S.; Maillard, Ivan; Speck, Nancy A.

2007-01-01

The family of core-binding factors includes the DNA-binding subunits Runx1-3 and their common non–DNA-binding partner CBFβ. We examined the collective role of core-binding factors in hematopoiesis with a hypomorphic Cbfb allelic series. Reducing CBFβ levels by 3- or 6-fold caused abnormalities in bone development, megakaryocytes, granulocytes, and T cells. T-cell development was very sensitive to an incremental reduction of CBFβ levels: mature thymocytes were decreased in number upon a 3-fold reduction in CBFβ levels, and were virtually absent when CBFβ levels were 6-fold lower. Partially penetrant consecutive differentiation blocks were found among early T-lineage progenitors within the CD4−CD8− double-negative 1 and downstream double-negative 2 thymocyte subsets. Our data define a critical CBFβ threshold for normal T-cell development, and situate an essential role for core-binding factors during the earliest stages of T-cell development. PMID:16940420

A case of pheochromocytoma with negative MIBG scintigraphy, PET-CT and genetic tests (VHL included) and a rare case of post-operative erectile dysfunction.

PubMed

Defeudis, Giuseppe; Fioriti, Elvira; Palermo, Andrea; Tuccinardi, Dario; Minucci, Angelo; Capoluongo, Ettore; Pozzilli, Paolo; Manfrini, Silvia

2018-06-02

Pheochromocytoma (Ph) is a rare catecholamine-secreting neuroendocrine tumour that arises from the chromaffin cells of the adrenal medulla. Ph usually presents with symptoms including paroxysmal headache, sweating, palpitations, and hypertension. During a computed tomography (CT) scan in a normotensive 49-year-old man, an incidentaloma of 4.5 cm was detected. Hypercortisolism was excluded after the dexamethasone suppression test, levels of DHEAS all falling within the normal range. After a 24-h urine collection, normal urinary metanephrines and a 4-fold higher level compared to the normal range of urinary normetanephrines were observed. Cortisoluria levels were within the normal range. Multiple endocrine neoplasia type 2 (MEN 2) was also excluded. Before the adrenalectomy, 123 I meta-iodobenzylguanidine scintigraphy (MIBG) and 18F-fluoro-2-deoxy-D-glucose-positron emission tomography (FDG PET)/CT were performed and were both negative. Histological examination confirmed the laboratory diagnosis of Ph. Genetic screening to evaluate the SDHB, SDHD, RET, CDKN1B, and VHL genes was requested in order to test for Von Hippel Lindau disease, but unexpectedly all of these were negative. On follow-up after surgery, the patient presented normal urinary catecholamines. However, after Ph removal, he reported frequent episodes of erectile dysfunction (ED) despite non-use of any antihypertensive medications and in the absence of any other precipitating factors, such as hormonal imbalance. This is a case report in which, in a normotensive patient with Ph, both MIBG and FDG PET-CT were negative, as were also genetic exams, including VHL, this underlining the difficulties in diagnosing this condition; furthermore, a rare case of ED occurred after surgery.

Studies on the antibacterial activity of two new acylureidopenicillins, mezlocillin and azlocillin.

PubMed

Soares, L A; Trabulsi, L R

1979-01-01

The antimicrobial activity of 6-[(R)-2[3-methylsulfonyl-2-oxo-imidazolidine-1-carboxamido]-2-phenylacetamido]-penicillanic acid sodium salt (mezlocillin, Baypen) and 6-[(R)-2-(2-oxo-imidazolidine-1-carboxamido)-2-phenylacetamido-a1-penicillanic acid sodium salt (azlocillin, Securopen) was measured against 545 clinical isolates, including gram-negative rods, gram-positive cocci and Bacteroides. Mezlocillin was more effective than azlocillin against the majority of the strains studied, but azlocillin was more effective against Pseudomonas strains. The minimal bactericidal concentration was equal to the minimal inhibitory concentration for the strains tested, but it was twice or four-fold as high for Staphylococcus.

Audit of the autoantibody test, EarlyCDT®-lung, in 1600 patients: an evaluation of its performance in routine clinical practice.

PubMed

Jett, James R; Peek, Laura J; Fredericks, Lynn; Jewell, William; Pingleton, William W; Robertson, John F R

2014-01-01

EarlyCDT(®)-Lung may enhance detection of early stage lung cancer by aiding physicians in assessing high-risk patients through measurement of biological markers (i.e., autoantibodies). The test's performance characteristics in routine clinical practice were evaluated by auditing clinical outcomes of 1613 US patients deemed at high risk for lung cancer by their physician, who ordered the EarlyCDT-Lung test for their patient. Clinical outcomes for all 1613 patients who provided HIPAA authorization are reported. Clinical data were collected from each patient's treating physician. Pathology reports when available were reviewed for diagnostic classification. Staging was assessed on histology, otherwise on imaging. Six month follow-up for the positives/negatives was 99%/93%. Sixty-one patients (4%) were identified with lung cancer, 25 of whom tested positive by EarlyCDT-Lung (sensitivity=41%). A positive EarlyCDT-Lung test on the current panel was associated with a 5.4-fold increase in lung cancer incidence versus a negative. Importantly, 57% (8/14) of non-small cell lung cancers detected as positive (where stage was known) were stage I or II. EarlyCDT-Lung has been extensively tested and validated in case-control settings and has now been shown in this audit to perform in routine clinical practice as predicted. EarlyCDT-Lung may be a complementary tool to CT for detection of early lung cancer. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Plasmid-determined resistance to tellurium compounds.

PubMed Central

Summers, A O; Jacoby, G A

1977-01-01

Transferable plasmids in gram-negative bacteria that confer resistance to potassium tellurite or tellurate were found. This re-istance was distinct from resistance to mercury, silver, or arsenic compounds and was unrelated to antibiotic resistance. In Escherichia coli, plasmids determine a 100-fold increase in the minimal inhibitory concentration for tellurite and a 10-fold increase in tellurate resistance. Many, but not all, of the plasmids belong to incompatibility group S. In Pseudomonas aeruginosa, tellurium resistance is specifically associated with incompatibility group P-2 and involves a 5- to 10-fold increase in tellurite or tellurate resistance. Images PMID:401494

Three dimensional Origami-based metamaterial

NASA Astrophysics Data System (ADS)

Kamrava, Soroush; Mousanezhad, Davood; Ebrahimi, Hamid; Ghosh, Ranajay; Vaziri, Ashkan; High Performance Materials; Structures Labratory Team

We present a novel cellular metamaterial constructed from Origami building blocks based on Miura-ori fold. The proposed cellular metamaterial exhibits unusual properties some of which stemming from the inherent properties of its Origami building blocks, and others manifesting due to its unique geometrical construction and architecture. These properties include foldability with two fully-folded configurations, auxeticity (i.e., negative Poisson's ratio), bistability, and self-locking of Origami building blocks to construct load-bearing cellular metamaterials. The kinematics and force response of the cellular metamaterial during folding were studied to investigate the underlying mechanisms resulting in its unique properties using analytical modeling and experiments.

Shedding and serological patterns of dairy cows following abortions associated with Coxiella burnetii DNA detection.

PubMed

Guatteo, R; Joly, A; Beaudeau, F

2012-03-23

To describe both shedding and serological patterns following abortions detected as being associated with Coxiella burnetii (Cb), 24 cows experiencing an abortion due to Cb were followed over a one month period. Samples taken on the day of abortion (D0) were followed 3-fold by weekly samplings from day 14 (D14) to D28 after the abortion. Milk and vaginal mucus were collected at each weekly sampling and tested using real-time PCR while blood samples were collected 2-fold on D21 and D28 and tested using ELISA. We found a very short duration of C. burnetii shedding in vaginal mucus after abortion, highlighting the need to collect samples as rapidly as possible following an abortion to avoid false negative results. In contrast with previous results, concomitancy of vaginal and mucus shedding was frequent, especially for cows shedding a high bacterial load on DO leading to the hypothesis that the clinical onset of the infection influences the modalities of Cb shedding. Lastly, serological results indicating a lack of sensitivity to detect Cb shedder cows (especially for cows for which Ct values were high) suggest that ELISA is not a useful tool to diagnose abortions at the individual level. Copyright © 2011 Elsevier B.V. All rights reserved.

IL-8 expression and its possible relationship with estrogen-receptor-negative status of breast cancer cells

PubMed Central

Freund, Ariane; Chauveau, Corine; Brouillet, Jean-Paul; Lucas, Annick; Lacroix, Matthieu; Licznar, Anne; Vignon, Françoise; Lazennec, Gwendal

2003-01-01

Estrogen receptor (ER) status is an important parameter in breast cancer management as ER-positive breast cancers have a better prognosis than ER-negative tumors. This difference comes essentially from the lower aggressiveness and invasiveness of ER-positive tumors. Here, we demonstrate, that IL-8 was clearly overexpressed in most ER-negative breast, ovary cell lines and breast tumor samples tested, whereas no significant IL-8 level could be detected in ER-positive breast or ovarian cell lines. We have also cloned human IL-8 from ER-negative MDA-MB-231 cells and we show that IL-8 produced by breast cancer cells is identical to monocyte-derived IL-8. Interestingly, the invasion potential of ER-negative breast cancer cells is associated at least in part with expression of interleukin-8 (IL-8), but not with IL-8 receptors levels. Moreover, IL-8 increases the invasiveness of ER-positive breast cancer cells by 2 fold, thus confirming the invasion-promoting role of IL-8. On the other hand, exogenous expression of estrogen receptors in ER-negative cells led to a decrease of IL-8 levels. In summary, our data show that IL-8 expression is negatively linked to ER-status of breast and ovarian cancer cells. We also support the idea that IL-8 expression is associated with a higher invasiveness potential of cancer cells in vitro, which suggests that IL-8 could be a novel marker of tumor aggressiveness. PMID:12527894

HIV Testing and Awareness of Partner's HIV Status Among Chinese Men Who Have Sex with Men in Main Partnerships.

PubMed

Wei, Chongyi; Yan, Hongjing; Raymond, H Fisher; Shi, Ling-En; Li, Jianjun; Yang, Haitao; McFarland, Willi

2016-04-01

Many men who have sex with men (MSM) do not use condoms with their main partners, especially if both parties are of the same HIV status. However, significant proportions of MSM have never tested or recently tested and are unaware of their main partners' HIV status. A cross-sectional survey was conducted among 524 MSM in Jiangsu, China in 2013-2014. Time-location sampling and online convenience sampling were used to recruit participants. We compared awareness of HIV status and recent HIV testing between participants who had main partners versus those who did not, and identified factors associated with recent HIV testing among men in main partnerships. Participants in main partnerships were significantly more likely to report recent HIV testing and being HIV-negative instead of HIV-unknown compared to participants in casual partnerships only. Overall, 74.5 % of participants were aware of their main partners' HIV status. Among participants in main partnerships, those who had 2-5 male anal sex partners in the past 6 months and those who reported that their partners were HIV-negative had 2.36 (95 % CI 1.12, 4.97) and 4.20 (95 % CI 2.03, 8.70) fold greater odds of being tested in the past year compared to those who had main partners only and those whose partners were HIV-positive/unknown, respectively. Chinese MSM in main partnerships might be practicing serosorting and may be at lower risk for HIV infection due to increased awareness of main partners' HIV status and higher uptake of recent testing.

Enhancing nZVI mobility in porous media using humate

NASA Astrophysics Data System (ADS)

Schmid, Doris; Micic Batka, Vesna; Gondikas, Andreas; Velimirovic, Milica; von der Kammer, Frank; Hofmann, Thilo

2016-04-01

The limited transport of nanoscale zero-valent iron (nZVI) particles in porous media is a major drawback for its use in groundwater remediation. Among other factors, transport of nZVI particles might be negatively affected by mineralogical and physical heterogeneities of the aquifer matrix. Carbonate minerals and iron oxides, for instance, provide positively charged patches which would further increase particle attachment to the sand grains. This study does assess the potential of sodium humate, a salt of humic acids, to enhance the mobility of nZVI particles. Humate is a non-toxic, inexpensive material extracted from natural oxidized lignite and obtained in commercial grade, which makes it advantageous for field applications. Humate is expected to shield the positively charged patches of the sand grains and consequently enhance nZVI mobility in porous media. In this study the humate was injected into an aquifer prior to injection of the nZVI particles. The potential of humate for enhancing the mobility of nZVI particles was tested in an array of columns packed with heterogeneous natural porous media of different mineralogical composition and sediment texture. The results demonstrated that without pre-injection of humates only limited mobility of nZVI particles can be obtained in all tested porous media. After the pre-injection of low concentration of humate (10 mg/L) the mobility of nZVI particles (1 g/L) was enhanced in all tested porous media. The magnitude of this enhancement was depended on the properties of the porous media. The largest improvement of nZVI mobility was observed for homogeneous quartz. This material had also the highest porosity (~ 40%), good sorting, and therefore a higher permeability compared to the other porous media tested. It is assumed that the higher permeability of this porous medium allowed an optimal distribution of humate, resulting in an approximately 6-fold enhancement of nZVI mobility. In carbonate-rich porous medium with a lower permeability a 1.5-fold enhancement of the nZVI mobility was observed. Enhanced nZVI mobility (up to 1.2-folds) was also observed for the porous media containing high quartz content and lower porosity. This might be attributed to the iron oxides minerals present in this porous medium. The results of this study showed that the pre-injection of humate can enhance the mobility of nZVI in various natural porous media. Enhancement of nZVI mobility was more pronounced in porous media with the highest permeability and porous media with higher carbonate or iron oxide content. The humates shield the positively charged patches and therefore make the overall charge of the porous media more negatively charged. Consequently, the mobility of the negatively charged nZVI particles due to electrosteric and electrostatic repulsion was promoted. Future work will focus on understanding the mechanisms leading to the different attachment of humates onto the porous media. This research receives funding from the European Union's Seventh Framework Programme FP7/2007-2013 under grant agreement n°309517.

Evolving role of mitomycin-C laryngology

NASA Astrophysics Data System (ADS)

Richards, Steven V.; Garrett, C. Gaelyn

2001-05-01

Topical mitomycin-C, a chemotherapeutic agent and a fibroblast inhibitor, has been successfully used in larynx, primarily to treat stenosis. Subglottic, tracheal, and anterior glottic stenosis have all shown promising results in a canine model. Less favorable results have been obtained when topical mitomycin-C is used on the vocal folds following surgical excision of mucosa. In the vocal fold studies, laryngeal videostroboscopy revealed diminished mucosal wave vibration in the vocal folds treated with mitomycin-C as well as a more atrophic appearance to the vibratory surface. The tissue treated with mitomycin-C showed fewer fibroblasts and less collagen. However, inflammatory infiltrate was not significantly different between the treated and untreated tissue. These results are consistent with the known suppression of fibroblast proliferation by mitomycin-C. In contrast to the positive effects of mitomycin-C on stenosis, the observed decrease in the healing response in the vocal fold had negative consequences on vocal fold vibratory pattern.

American cutaneous leishmaniasis: use of a skin test as a predictor of relapse after treatment.

PubMed Central

Passos, V. M.; Barreto, S. M.; Romanha, A. J.; Krettli, A. U.; Volpini, A. C.; Lima e Costa, M. F.

2000-01-01

While relapses following clinical cure of American cutaneous leishmaniasis are frequent, no test has been described until now to predict such relapses. A cohort of 318 American cutaneous leishmaniasis patients was followed up for two years after treatment with meglumine antimoniate, during which time 32 relapses occurred, 30 in the first year and two in the second (accumulated risk: 10.5%). No association was found between these relapses and the parasite-specific antibody response before and after treatment, or between the relapses and stratification by sociodemographic and clinical characteristics. However when Leishmania was used as antigen, patients with a negative skin test at the time of diagnosis presented a 3.4-fold higher risk (hazard risk = 3.4; 95% confidence interval, 1.7-7.0) of American cutaneous leishmaniasis relapse, compared with patients with a positive response. This result shows that the skin test can be a predictor of American cutaneous leishmaniasis relapse after treatment. PMID:10994280

Regulation of Msx genes by a Bmp gradient is essential for neural crest specification.

PubMed

Tribulo, Celeste; Aybar, Manuel J; Nguyen, Vu H; Mullins, Mary C; Mayor, Roberto

2003-12-01

There is evidence in Xenopus and zebrafish embryos that the neural crest/neural folds are specified at the border of the neural plate by a precise threshold concentration of a Bmp gradient. In order to understand the molecular mechanism by which a gradient of Bmp is able to specify the neural crest, we analyzed how the expression of Bmp targets, the Msx genes, is regulated and the role that Msx genes has in neural crest specification. As Msx genes are directly downstream of Bmp, we analyzed Msx gene expression after experimental modification in the level of Bmp activity by grafting a bead soaked with noggin into Xenopus embryos, by expressing in the ectoderm a dominant-negative Bmp4 or Bmp receptor in Xenopus and zebrafish embryos, and also through Bmp pathway component mutants in the zebrafish. All the results show that a reduction in the level of Bmp activity leads to an increase in the expression of Msx genes in the neural plate border. Interestingly, by reaching different levels of Bmp activity in animal cap ectoderm, we show that a specific concentration of Bmp induces msx1 expression to a level similar to that required to induce neural crest. Our results indicate that an intermediate level of Bmp activity specifies the expression of Msx genes in the neural fold region. In addition, we have analyzed the role that msx1 plays on neural crest specification. As msx1 has a role in dorsoventral pattering, we have carried out conditional gain- and loss-of-function experiments using different msx1 constructs fused to a glucocorticoid receptor element to avoid an early effect of this factor. We show that msx1 expression is able to induce all other early neural crest markers tested (snail, slug, foxd3) at the time of neural crest specification. Furthermore, the expression of a dominant negative of Msx genes leads to the inhibition of all the neural crest markers analyzed. It has been previously shown that snail is one of the earliest genes acting in the neural crest genetic cascade. In order to study the hierarchical relationship between msx1 and snail/slug we performed several rescue experiments using dominant negatives for these genes. The rescuing activity by snail and slug on neural crest development of the msx1 dominant negative, together with the inability of msx1 to rescue the dominant negatives of slug and snail strongly argue that msx1 is upstream of snail and slug in the genetic cascade that specifies the neural crest in the ectoderm. We propose a model where a gradient of Bmp activity specifies the expression of Msx genes in the neural folds, and that this expression is essential for the early specification of the neural crest.

Unraveling metamaterial properties in zigzag-base folded sheets.

PubMed

Eidini, Maryam; Paulino, Glaucio H

2015-09-01

Creating complex spatial objects from a flat sheet of material using origami folding techniques has attracted attention in science and engineering. In the present work, we use the geometric properties of partially folded zigzag strips to better describe the kinematics of known zigzag/herringbone-base folded sheet metamaterials such as Miura-ori. Inspired by the kinematics of a one-degree of freedom zigzag strip, we introduce a class of cellular folded mechanical metamaterials comprising different scales of zigzag strips. This class of patterns combines origami folding techniques with kirigami. Using analytical and numerical models, we study the key mechanical properties of the folded materials. We show that our class of patterns, by expanding on the design space of Miura-ori, is appropriate for a wide range of applications from mechanical metamaterials to deployable structures at small and large scales. We further show that, depending on the geometry, these materials exhibit either negative or positive in-plane Poisson's ratios. By introducing a class of zigzag-base materials in the current study, we unify the concept of in-plane Poisson's ratio for similar materials in the literature and extend it to the class of zigzag-base folded sheet materials.

Pharmacokinetics and absorption of the anticancer agents dasatinib and GDC-0941 under various gastric conditions in dogs--reversing the effect of elevated gastric pH with betaine HCl.

PubMed

Pang, Jodie; Dalziel, Gena; Dean, Brian; Ware, Joseph A; Salphati, Laurent

2013-11-04

Changes in gastric pH can impact the dissolution and absorption of compounds presenting pH-dependent solubility. We assessed, in dogs, the effects of gastric pH-modifying agents on the oral absorption of two weakly basic anticancer drugs, dasatinib and GDC-0941. We also tested whether drug-induced hypochlorhydria could be temporarily mitigated using betaine HCl. Pretreatments with pentagastrin, famotidine, betaine HCl, or combinations of famotidine and betaine HCl were administered orally to dogs prior to drug dosing. The gastric pH was measured under each condition for up to 7 h, and the exposure of the compounds tested was calculated. The average gastric pH in fasted dogs ranged from 1.45 to 3.03. Pentagastrin or betaine HCl treatments lowered the pH and reduced its variability between dogs compared to control animals. In contrast, famotidine treatment maintained gastric pH at values close to 7 for up to 5 h, while betaine HCl transiently reduced the pH to approximately 2 in the famotidine-treated dogs. Famotidine pretreatment lowered GDC-0941 exposure by 5-fold, and decreased dasatinib measurable concentrations 30-fold, compared to the pentagastrin-treated dogs. Betaine HCl restored GDC-0941 AUC in famotidine-treated dogs to levels achieved in control animals, and increased dasatinib AUC to 1.5-fold that measured in control dogs. The results confirmed the negative impact of acid-reducing agents on the absorption of weakly basic drugs. They also suggested that betaine HCl coadministration may be a viable strategy in humans treated with acid-reducing agents in order to temporarily reduce gastric pH and restore drug exposure.

High-throughput quantification for a drug mixture in rat plasma-a comparison of Ultra Performance liquid chromatography/tandem mass spectrometry with high-performance liquid chromatography/tandem mass spectrometry.

PubMed

Yu, Kate; Little, David; Plumb, Rob; Smith, Brian

2006-01-01

A quantitative Ultra Performance liquid chromatography/tandem mass spectrometry (UPL/MS/MS) protocol was developed for a five-compound mixture in rat plasma. A similar high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) quantification protocol was developed for comparison purposes. Among the five test compounds, three preferred positive electrospray ionization (ESI) and two preferred negative ESI. As a result, both UPLC/MS/MS and HPLC/MS/MS analyses were performed by having the mass spectrometer collecting ESI multiple reaction monitoring (MRM) data in both positive and negative ion modes during a single injection. Peak widths for most standards were 4.8 s for the HPLC analysis and 2.4 s for the UPLC analysis. There were 17 to 20 data points obtained for each of the LC peaks. Compared with the HPLC/MS/MS method, the UPLC/MS/MS method offered 3-fold decrease in retention time, up to 10-fold increase in detected peak height, with 2-fold decrease in peak width. Limits of quantification (LOQs) for both HPLC and UPLC methods were evaluated. For UPLC/MS/MS analysis, a linear range up to four orders of magnitude was obtained with r2 values ranging from 0.991 to 0.998. The LOQs for the five analytes ranged from 0.08 to 9.85 ng/mL. Three levels of quality control (QC) samples were analyzed. For the UPLC/MS/MS protocol, the percent relative standard deviation (RSD%) for low QC (2 ng/mL) ranged from 3.42 to 8.67% (N = 18). The carryover of the UPLC/MS/MS protocol was negligible and the robustness of the UPLC/MS/MS system was evaluated with up to 963 QC injections. Copyright 2006 John Wiley & Sons, Ltd.

Novel FR-900493 Analogues That Inhibit the Outgrowth of Clostridium difficile Spores

PubMed Central

2018-01-01

The spectrum of antibacterial activity for the nucleoside antibiotic FR-900493 (1) can be extended by chemical modifications. We have generated a small focused library based on the structure of 1 and identified UT-17415 (9), UT-17455 (10), UT-17460 (11), and UT-17465 (12), which exhibit anti-Clostridium difficile growth inhibitory activity. These analogues also inhibit the outgrowth of C. difficile spores at 2× minimum inhibitory concentration. One of these analogues, 11, relative to 1 exhibits over 180-fold and 15-fold greater activity against the enzymes, phospho-MurNAc-pentapeptide translocase (MraY) and polyprenyl phosphate-GlcNAc-1-phosphate transferase (WecA), respectively. The phosphotransferase inhibitor 11 displays antimicrobial activity against several tested bacteria including Bacillus subtilis, Clostridium spp., and Mycobacterium smegmatis, but no growth inhibitory activity is observed against the other Gram-positive and Gram-negative bacteria. The selectivity index (Vero cell cytotoxicity/C. difficileantimicrobial activity) of 11 is approximately 17, and 11 does not induce hemolysis even at a 100 μM concentration. PMID:29503973

Origami-based cellular metamaterial with auxetic, bistable, and self-locking properties

NASA Astrophysics Data System (ADS)

Kamrava, Soroush; Mousanezhad, Davood; Ebrahimi, Hamid; Ghosh, Ranajay; Vaziri, Ashkan

2017-04-01

We present a novel cellular metamaterial constructed from Origami building blocks based on Miura-ori fold. The proposed cellular metamaterial exhibits unusual properties some of which stemming from the inherent properties of its Origami building blocks, and others manifesting due to its unique geometrical construction and architecture. These properties include foldability with two fully-folded configurations, auxeticity (i.e., negative Poisson’s ratio), bistability, and self-locking of Origami building blocks to construct load-bearing cellular metamaterials. The kinematics and force response of the cellular metamaterial during folding were studied to investigate the underlying mechanisms resulting in its unique properties using analytical modeling and experiments.

Origami-based cellular metamaterial with auxetic, bistable, and self-locking properties

PubMed Central

Kamrava, Soroush; Mousanezhad, Davood; Ebrahimi, Hamid; Ghosh, Ranajay; Vaziri, Ashkan

2017-01-01

We present a novel cellular metamaterial constructed from Origami building blocks based on Miura-ori fold. The proposed cellular metamaterial exhibits unusual properties some of which stemming from the inherent properties of its Origami building blocks, and others manifesting due to its unique geometrical construction and architecture. These properties include foldability with two fully-folded configurations, auxeticity (i.e., negative Poisson’s ratio), bistability, and self-locking of Origami building blocks to construct load-bearing cellular metamaterials. The kinematics and force response of the cellular metamaterial during folding were studied to investigate the underlying mechanisms resulting in its unique properties using analytical modeling and experiments. PMID:28387345

Synthesis, Crystal Study, and Anti-Proliferative Activity of Some 2-Benzimidazolylthioacetophenones towards Triple-Negative Breast Cancer MDA-MB-468 Cells as Apoptosis-Inducing Agents.

PubMed

Abdel-Aziz, Hatem A; Eldehna, Wagdy M; Ghabbour, Hazem; Al-Ansary, Ghada H; Assaf, Areej M; Al-Dhfyan, Abdullah

2016-07-29

On account of its poor prognosis and deficiency of therapeutic stratifications, triple negative breast cancer continues to form the causative platform of an incommensurate number of breast cancer deaths. Aiming at the development of potent anticancer agents as a continuum of our previous efforts, a novel series of 2-((benzimidazol-2-yl)thio)-1-arylethan-1-ones 5a-w was synthesized and evaluated for its anti-proliferative activity towards triple negative breast cancer (TNBC) MDA-MB-468 cells. Compound 5k was the most active analog against MDA-MB-468 (IC50 = 19.90 ± 1.37 µM), with 2.1-fold increased activity compared to 5-fluorouracil (IC50 = 41.26 ± 3.77 µM). Compound 5k was able to induce apoptosis in MDA-MB-468, as evidenced by the marked boosting in the percentage of florecsein isothiocyanate annexin V (Annexin V-FITC)-positive apoptotic cells (upper right (UR) + lower right (LR)) by 2.8-fold in comparison to control accompanied by significant increase in the proportion of cells at pre-G1 (the first gap phase) by 8.13-fold in the cell-cycle analysis. Moreover, a quantitative structure activity relationship (QSAR) model was established to investigate the structural requirements orchestrating the anti-proliferative activity. Finally, we established a theoretical kinetic study.

Large scale wind tunnel investigation of a folding tilt rotor

NASA Technical Reports Server (NTRS)

1972-01-01

A twenty-five foot diameter folding tilt rotor was tested in a large scale wind tunnel to determine its aerodynamic characteristics in unfolded, partially folded, and fully folded configurations. During the tests, the rotor completed over forty start/stop sequences. After completing the sequences in a stepwise manner, smooth start/stop transitions were made in approximately two seconds. Wind tunnel speeds up through seventy-five knots were used, at which point the rotor mast angle was increased to four degrees, corresponding to a maneuver condition of one and one-half g.

A Synthetic Influenza Virus Vaccine Induces a Cellular Immune Response That Correlates with Reduction in Symptomatology and Virus Shedding in a Randomized Phase Ib Live-Virus Challenge in Humans

PubMed Central

Pleguezuelos, Olga; Robinson, Stuart; Fernández, Ana; Stoloff, Gregory A.; Mann, Alex; Gilbert, Anthony; Balaratnam, Ganesh; Wilkinson, Tom; Lambkin-Williams, Rob; Oxford, John

2015-01-01

Current influenza vaccines elicit primarily antibody-based immunity. They require yearly revaccination and cannot be manufactured until the identification of the circulating viral strain(s). These issues remain to be addressed. Here we report a phase Ib trial of a vaccine candidate (FLU-v) eliciting cellular immunity. Thirty-two males seronegative for the challenge virus by hemagglutination inhibition assay participated in this single-center, randomized, double-blind study. Volunteers received one dose of either the adjuvant alone (placebo, n = 16) or FLU-v (500 μg) and the adjuvant (n = 16), both in saline. Twenty-one days later, FLU-v (n = 15) and placebo (n = 13) volunteers were challenged with influenza virus A/Wisconsin/67/2005 (H3N2) and monitored for 7 days. Safety, tolerability, and cellular responses were assessed pre- and postvaccination. Virus shedding and clinical signs were assessed postchallenge. FLU-v was safe and well tolerated. No difference in the prevaccination FLU-v-specific gamma interferon (IFN-γ) response was seen between groups (average ± the standard error of the mean [SEM] for the placebo and FLU-v, respectively, 1.4-fold ± 0.2-fold and 1.6-fold ± 0.5-fold higher than the negative-control value). Nineteen days postvaccination, the FLU-v group, but not the placebo group, developed FLU-v-specific IFN-γ responses (8.2-fold ± 3.9-fold versus 1.3-fold ± 0.1-fold higher than the negative-control value [average ± SEM] for FLU-v versus the placebo [P = 0.0005]). FLU-v-specific cellular responses also correlated with reductions in both viral titers (P = 0.01) and symptom scores (P = 0.02) postchallenge. Increased cellular immunity specific to FLU-v correlates with reductions in both symptom scores and virus loads. (This study has been registered at ClinicalTrials.gov under registration no. NCT01226758 and at hra.nhs.uk under EudraCT no. 2009-014716-35.) PMID:25994549

A Synthetic Influenza Virus Vaccine Induces a Cellular Immune Response That Correlates with Reduction in Symptomatology and Virus Shedding in a Randomized Phase Ib Live-Virus Challenge in Humans.

PubMed

Pleguezuelos, Olga; Robinson, Stuart; Fernández, Ana; Stoloff, Gregory A; Mann, Alex; Gilbert, Anthony; Balaratnam, Ganesh; Wilkinson, Tom; Lambkin-Williams, Rob; Oxford, John; Caparrós-Wanderley, Wilson

2015-07-01

Current influenza vaccines elicit primarily antibody-based immunity. They require yearly revaccination and cannot be manufactured until the identification of the circulating viral strain(s). These issues remain to be addressed. Here we report a phase Ib trial of a vaccine candidate (FLU-v) eliciting cellular immunity. Thirty-two males seronegative for the challenge virus by hemagglutination inhibition assay participated in this single-center, randomized, double-blind study. Volunteers received one dose of either the adjuvant alone (placebo, n = 16) or FLU-v (500 μg) and the adjuvant (n = 16), both in saline. Twenty-one days later, FLU-v (n = 15) and placebo (n = 13) volunteers were challenged with influenza virus A/Wisconsin/67/2005 (H3N2) and monitored for 7 days. Safety, tolerability, and cellular responses were assessed pre- and postvaccination. Virus shedding and clinical signs were assessed postchallenge. FLU-v was safe and well tolerated. No difference in the prevaccination FLU-v-specific gamma interferon (IFN-γ) response was seen between groups (average ± the standard error of the mean [SEM] for the placebo and FLU-v, respectively, 1.4-fold ± 0.2-fold and 1.6-fold ± 0.5-fold higher than the negative-control value). Nineteen days postvaccination, the FLU-v group, but not the placebo group, developed FLU-v-specific IFN-γ responses (8.2-fold ± 3.9-fold versus 1.3-fold ± 0.1-fold higher than the negative-control value [average ± SEM] for FLU-v versus the placebo [P = 0.0005]). FLU-v-specific cellular responses also correlated with reductions in both viral titers (P = 0.01) and symptom scores (P = 0.02) postchallenge. Increased cellular immunity specific to FLU-v correlates with reductions in both symptom scores and virus loads. (This study has been registered at ClinicalTrials.gov under registration no. NCT01226758 and at hra.nhs.uk under EudraCT no. 2009-014716-35.). Copyright © 2015, American Society for Microbiology. All Rights Reserved.

76 FR 35832 - Folding Metal Tables and Chairs From the People's Republic of China: Preliminary Results of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-20

... incurred negative profit. Meco, subsequently, argues that the Department should resort to using Indonesian... statements for the year ending March 31, 2009.\\13\\ We agree with Meco that a negative profit would preclude... control.\\21\\ \\19\\ See, e.g., Certain Coated Paper Suitable for High-Quality Print Graphics Using Sheet-Fed...

In vitro activity of doripenem and other carbapenems against contemporary Gram-negative pathogens isolated from hospitalised patients in the Asia-Pacific region: results of the COMPACT Asia-Pacific Study.

PubMed

Christiansen, K J; Ip, M; Ker, H B; Mendoza, M; Hsu, L; Kiratisin, P; Chongthaleong, A; Redjeki, I S; Quintana, A; Flamm, R; Garcia, J; Cassettari, M; Cooper, D; Okolo, P; Morrissey, I

2010-12-01

The Comparative Activity of Carbapenems Testing (COMPACT) Study was designed to determine the in vitro potency of doripenem compared with imipenem and meropenem against a large number of contemporary Gram-negative pathogens from more than 100 centres across Europe and the Asia-Pacific region and to assess the reliability of Etest methodology for doripenem minimum inhibitory concentration (MIC) determination against these pathogens. Data from eight countries within the Asia-Pacific region, which collected 1612 bacterial isolates, are presented here. Etest methodology was found to be a reliable method for MIC determination. Doripenem showed in vitro activity similar to or better than meropenem and at least four-fold better than imipenem against Enterobacteriaceae. Against Pseudomonas aeruginosa, doripenem was also the most active of the three carbapenems in vitro. However, in vitro results do not necessarily correlate with clinical outcome. Copyright © 2010 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

The sensitivity and reproducibility of the zebrafish (Danio rerio) embryo test for the screening of waste water quality and for testing the toxicity of chemicals.

PubMed

Lahnsteiner, Franz

2008-07-01

The sensitivity of the zebrafish embryo test, a test proposed for routine waste water control, was compared with the acute fish toxicity test, in the determination of six types of waste water and ten different chemicals. The waste water was sampled from the following industrial processes: paper and cardboard production, hide tanning, metal galvanisation, carcass treatment and utilisation, and sewage treatment. The chemicals tested were: dimethylacetamide, dimethylsulphoxide, cadmium chloride, cyclohexane, hydroquinone, mercuric chloride, nickel chloride, nonylphenol, resmethrin and sodium nitrite. For many of the test substances, the zebrafish embryo test and the acute fish toxicity test results showed high correlations. However, there were certain environmentally-relevant substances for which the results of the zebrafish embryo test and the acute fish toxicity test differed significantly, up to 10,000-fold (Hg(2+) > 150-fold difference; NO(2)(-) > 300-fold; Cd(2+) > 200-fold; resmethrin > 10,000-fold). For the investigated waste water samples and chemicals, the survival rate of the zebrafish embryos showed high variations between different egg samples, within the range of the EC50 concentration. Subsequently, 5-6 parallel assays were deemed to be the appropriate number necessary for the precise evaluation of the toxicity of the test substances. Also, it was found that the sensitivities of different ontogenetic stages to chemical exposure differed greatly. During the first 12 hours after fertilisation (4-cell stage to the 5-somite stage), the embryos reacted most sensitively to test substance exposure, whereas the later ontogenetic stages showed only slight or no response, indicating that the test is most sensitive during the first 24 hours post-fertilisation.

Mechanisms of protein-folding diseases at a glance.

PubMed

Valastyan, Julie S; Lindquist, Susan

2014-01-01

For a protein to function appropriately, it must first achieve its proper conformation and location within the crowded environment inside the cell. Multiple chaperone systems are required to fold proteins correctly. In addition, degradation pathways participate by destroying improperly folded proteins. The intricacy of this multisystem process provides many opportunities for error. Furthermore, mutations cause misfolded, nonfunctional forms of proteins to accumulate. As a result, many pathological conditions are fundamentally rooted in the protein-folding problem that all cells must solve to maintain their function and integrity. Here, to illustrate the breadth of this phenomenon, we describe five examples of protein-misfolding events that can lead to disease: improper degradation, mislocalization, dominant-negative mutations, structural alterations that establish novel toxic functions, and amyloid accumulation. In each case, we will highlight current therapeutic options for battling such diseases.

Latex agglutination test (LAT) for the diagnosis of typhoid fever.

PubMed

Sahni, Gopal Shankar

2013-06-01

The efficacy of latex agglutination test in the rapid diagnosis of typhoid fever was studied and the result compared with that of blood culture. This study included 80 children suffering from typhoid fever, among which 40 were confirmed by blood culture isolation and 40 had possible typhoid fever based on high Widal's titre (a four-fold rise in the titre of antibody to typhi "O" and "H" antigen was considered as a positive Widal's test result). Eighty children, 40 with febrile illness confirmed to be other than typhoid and 40 normal healthy children were used as negative controls. The various groups were: (i) Study group ie, group I had 40 children confirmed by culture isolation of Salmonella typhi(confirmed typhoid cases). (ii) Control groups ie, (a) group II with 40 febrile controls selected from paediatrics ward where cause other than S typhi has been established, (b) group III with 40 afebrile healthy controls that were siblings of the children admitted in paediatric ward for any reason with no history of fever and TAB vaccination in the last one year, and (c) group IV with 40 children with high Widal's titre in paired sera sample. Widal's test with paired sera with a one week interval between collections were done in all 40 patients. Latex aggtutination test which could detect 900 ng/ml of antigen as observed in checker board titration, was positive in all 40 children from group I who had positive blood culture and in 30 children from group IV who had culture negative and had high Widal's titre positive. Latex agglutination test was positive in 4 children in group II and none in group III. Using blood culture positive cases as true positive and children in groups II and III as true negative, the test had a sensitivity of 100% and specificity of 96%. Latex agglutination test was found to be significantly sensitive (100%) and specific (96%) and could detect 75% more cases in group IV (possible typhoid cases). Thus latex agglutination test can be used for rapid diagnosis of typhoid fever though it cannot replace conventional blood culture required for isolation of organism to report the antibiotic sensitivity.

How pH, Temperature, and Time of Incubation Affect False-Positive Responses and Uncertainty of the LAL Gel-Clot Test.

PubMed

Lourenço, Felipe Rebello; Botelho, Túlia De Souza; Pinto, Terezinha De Jesus Andreoli

2012-01-01

The limulus amebocyte lysate (LAL) test is the simplest and most widely used procedure for detection of endotoxin in parenteral drugs. The LAL test demands optimal pH, ionic strength, temperature, and time of incubation. Slight changes in these parameters may increase the frequency of false-positive responses and the estimated uncertainty of the LAL test. The aim of this paper is to evaluate how changes in the pH, temperature, and time of incubation affect the occurrence of false-positive responses in the LAL test. LAL tests were performed in nominal conditions (37 °C, 60 min, and pH 7) and in different conditions of temperature (36 °C and 38 °C), time of incubation (58 and 62 min), and pH (6 and 8). Slight differences in pH increase the frequency of false-positive responses 5-fold (relative risk 5.0), resulting in an estimated of uncertainty 7.6%. Temperature and time of incubation affect the LAL test less, showing relative risks of 1.5 and 1.0, respectively. Estimated uncertainties in 36 °C or 38 °C temperatures and 58 or 62 min of incubation were found to be 2.0% and 1.0%, respectively. Simultaneous differences in these parameters significantly increase the frequency of false-positive responses. The limulus amebocyte lysate (LAL) gel-clot test is a simple test for detection of endotoxin from Gram-negative bacteria. The test is based on a gel formation when a certain amount of endotoxin is present; it is a pass/fail test. The LAL test requires optimal pH, ionic strength, temperature, and time of incubation. Slight difference in these parameters may increase the frequency of false-positive responses. The aim of this paper is to evaluate how changes in the pH, temperature, and time of incubation affect the occurrence of false-positive responses in the LAL test. We find that slight differences in pH increase the frequency of false-positive responses 5-fold. Temperature and time of incubation affect the LAL test less. Simultaneous differences in these parameters significantly increase the frequency of false-positive responses.

Orogenic remagnetizations and paleomagnetic analysis of fault propagation folds in Lower Carboniferous carbonates, Northern Rockies, NW Montana and SW Alberta

NASA Astrophysics Data System (ADS)

Zechmeister, M. S.; O'Brien, V. J.; Elmore, R. D.; Evans, M. A.

2006-12-01

Results from paleomagnetic analysis of Lower Carboniferous carbonates in the Sawtooth Range, northwestern Montana and the Livingstone range in Southwestern Alberta are presented. Paleomagnetic cores were collected from both limbs of four fault propagation folds, one at Swift Dam in MT as well as one along Green Creek and two along Oldman River in Alberta. The Swift Dam Fold is in the Madison Group and contains a widespread characteristic remanent magnetization (ChRM) that resides in magnetite with southerly declinations and moderately steep up inclinations. A tilt test reveals a synfolding ChRM, and the paleopole suggests remanence acquisition in the Cretaceous to Early Tertiary. This result contrasts with results from another fold in MT, the Teton anticline, which is a buckle fold where a similar ChRM is pretilting. The reason for the differences in the fold test results are under investigation. The ChRM is not thermoviscous in origin based on a comparison of unblocking temperature with the low burial temperatures and is interpreted as a chemical remanent magnetization (CRM). Preliminary data from the folds in Livingstone Range suggest a similar ChRM in the organic rich lithologies of the Livingstone, Banff and Mount Head formations. Tilt test results for the fault propagation folds in Alberta will be presented as well as a discussion on the origin of orogenic remagnetizations.

Paleomagnetic age and tectonic constraints on the genesis of the giant Jinding Zn-Pb deposit, Yunnan, China

NASA Astrophysics Data System (ADS)

Yalikun, Yaxiaer; Xue, Chunji; Symons, D. T. A.

2018-02-01

The Jinding Zn-Pb deposit is located in the Lanping-Simao basin, Yunnan, China. Paleomagnetic results are reported from the Beichang, Jiayashan, and Nanchang mineralization zones that are hosted in the Lower Cretaceous Jinxing and Upper Paleocene Yunlong Formations. The timing of formation of the Zn-Pb mineralization has not been previously defined but is geologically constrained to be younger than Upper Paleocene. Paleomagnetic analyses of 645 specimens from 42 sites using mostly thermal and then alternating field step demagnetization isolated a stable characteristic remanent magnetization (ChRM) for 29 mineralized sites. Step demagnetization and rock magnetic analyses of Zn and Pb concentrates and tailings show that the main remanence carriers are pyrrhotite and magnetite or low Ti titanomagnetite inclusions in sphalerite and galena. Randomly oriented ChRM directions for 18 clast specimens collected from site 40 provide a conglomerate test that shows that the clasts have not been remagnetized by a metamorphic event. A paleomagnetic fold test on the mineralized specimens is negative, showing that the mineralization is epigenetic because its ChRM substantially postdates the major thrust folding event that formed the dome structure of the Jinding deposit. Using extensive regional geologic and paleomagnetic data from other studies with the Jinding paleomagnetic data yields a mean age of 23 ± 3 Ma for the mineralization.

Correlation of final evoked potential amplitudes on intraoperative electromyography of the recurrent laryngeal nerve with immediate postoperative vocal fold function after thyroid and parathyroid surgery.

PubMed

Genther, Dane J; Kandil, Emad H; Noureldine, Salem I; Tufano, Ralph P

2014-02-01

Thyroid and parathyroid surgery are among the most common operations in the United States. Recurrent laryngeal nerve (RLN) injury is an infrequent but potentially detrimental complication. To correlate the final evoked potential amplitudes on intraoperative electromyography (EMG) after stimulation of the RLN with immediate postoperative vocal fold function after thyroid and parathyroid surgery. Retrospective observational study at a tertiary academic medical center. We included 674 patients (with 1000 nerves at risk) undergoing thyroid or parathyroid surgery from July 1, 2008, through June 30, 2012. Thyroid and parathyroid surgery. The association of final evoked potential amplitudes on EMG after thyroid and parathyroid surgery with vocal fold function as determined by postoperative fiberoptic laryngoscopy. Three patients experienced permanent vocal fold paresis (VFP) secondary to intraoperative RLN transection. Of the remaining 997 RLNs at risk, 22 (2.2%) in 20 patients exhibited temporary VFP on fiberoptic laryngoscopy after extubation. Eighteen patients experienced unilateral temporary VFP, and 2 experienced bilateral VFP without the need for tracheostomy or reintubation. Of the 22 RLNs, postdissection EMG amplitudes were less than 200 µV (true-positive findings) in 21 and at least 200 µV (false-negative finding) in 1. Of the 975 RLNs (97.5%) with normal function, postdissection EMG amplitudes were at least 200 µV (true-negative findings) in 967 and less than 200 µV (false-positive findings) in 8. In regard to immediate postoperative VFP, sensitivity, specificity, positive and negative predictive values, and accuracy of postdissection EMG amplitudes of less than 200 µV were 95.5%, 99.2%, 72.4%, 99.9%, and 99.1%, respectively. Intraoperative nerve monitoring of the RLN with EMG provides real-time information regarding neurophysiologic function of the RLN and can predict immediate postoperative VFP reliably when a cutoff of 200 µV is used. The high negative predictive value means that the surgeon can presume with confidence that the RLN has not been injured in the presence of a potential of at least 200 µV. This information would be useful in patients for whom bilateral thyroid surgery is being considered.

Drought-Stressed Tomato Plants Trigger Bottom–Up Effects on the Invasive Tetranychus evansi

PubMed Central

Ximénez-Embún, Miguel G.; Ortego, Félix; Castañera, Pedro

2016-01-01

Climate change will bring more drought periods that will have an impact on the irrigation practices of some crops like tomato, from standard water regime to deficit irrigation. This will promote changes in plant metabolism and alter their interactions with biotic stressors. We have tested if mild or moderate drought-stressed tomato plants (simulating deficit irrigation) have an effect on the biological traits of the invasive tomato red spider mite, Tetranychus evansi. Our data reveal that T evansi caused more leaf damage to drought-stressed tomato plants (≥1.5 fold for both drought scenarios). Mite performance was also enhanced, as revealed by significant increases of eggs laid (≥2 fold) at 4 days post infestation (dpi), and of mobile forms (≥2 fold and 1.5 fold for moderate and mild drought, respectively) at 10 dpi. The levels of several essential amino acids (histidine, isoleucine, leucine, tyrosine, valine) and free sugars in tomato leaves were significantly induced by drought in combination with mites. The non-essential amino acid proline was also strongly induced, stimulating mite feeding and egg laying when added to tomato leaf disks at levels equivalent to that estimated on drought-infested tomato plants at 10 dpi. Tomato plant defense proteins were also affected by drought and/or mite infestation, but T. evansi was capable of circumventing their potential adverse effects. Altogether, our data indicate that significant increases of available free sugars and essential amino acids, jointly with their phagostimulant effect, created a favorable environment for a better T. evansi performance on drought-stressed tomato leaves. Thus, drought-stressed tomato plants, even at mild levels, may be more prone to T evansi outbreaks in a climate change scenario, which might negatively affect tomato production on area-wide scales. PMID:26735490

Internally folded expanded metal electrode for battery construction

NASA Technical Reports Server (NTRS)

Pierce, Doug C. (Inventor); Korinek, Paul D. (Inventor); Morgan, Maurice C. (Inventor)

1993-01-01

A battery system is disclosed which includes folded grids of expanded metal inserted through non-conductive substrates and pasted with electrochemically active materials. In the most preferred embodiment, a frame is provided with a plastic insert, and slots are provided in the latter to receive the expanded metal grid. After suitable coinage of the grid and insertion through the plastic film, the grid is sealed and pasted on opposite sides with positive and negative active material. A battery is assembled using one or a plurality of the resulting electrode elements, with separators, to produce a high-power, lead-acid battery. The folded grid provides many of the design benefits of standard bipolar construction.

Microbial detection method based on sensing molecular hydrogen

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Stoner, G. E.; Boykin, E. H.

1974-01-01

A simple method for detecting bacteria, based on the time of hydrogen evolution, was developed and tested against various members of the Enterobacteriaceae group. The test system consisted of (1) two electrodes, platinum and a reference electrode, (2) a buffer amplifier, and (3) a strip-chart recorder. Hydrogen evolution was measured by an increase in voltage in the negative (cathodic) direction. A linear relationship was established between inoculum size and the time hydrogen was detected (lag period). Lag times ranged from 1 h for 1 million cells/ml to 7 h for 1 cell/ml. For each 10-fold decrease in inoculum, length of the lag period increased 60 to 70 min. Based on the linear relationship between inoculum and lag period, these results indicate the potential application of the hydrogen-sensing method for rapidly detecting coliforms and other gas-producing microorganisms in a variety of clinical, food, and other samples.

Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study.

PubMed

Chikenji, George; Fujitsuka, Yoshimi; Takada, Shoji

2006-02-28

Predicting protein tertiary structure by folding-like simulations is one of the most stringent tests of how much we understand the principle of protein folding. Currently, the most successful method for folding-based structure prediction is the fragment assembly (FA) method. Here, we address why the FA method is so successful and its lesson for the folding problem. To do so, using the FA method, we designed a structure prediction test of "chimera proteins." In the chimera proteins, local structural preference is specific to the target sequences, whereas nonlocal interactions are only sequence-independent compaction forces. We find that these chimera proteins can find the native folds of the intact sequences with high probability indicating dominant roles of the local interactions. We further explore roles of local structural preference by exact calculation of the HP lattice model of proteins. From these results, we suggest principles of protein folding: For small proteins, compact structures that are fully compatible with local structural preference are few, one of which is the native fold. These local biases shape up the funnel-like energy landscape.

Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study

PubMed Central

Chikenji, George; Fujitsuka, Yoshimi; Takada, Shoji

2006-01-01

Predicting protein tertiary structure by folding-like simulations is one of the most stringent tests of how much we understand the principle of protein folding. Currently, the most successful method for folding-based structure prediction is the fragment assembly (FA) method. Here, we address why the FA method is so successful and its lesson for the folding problem. To do so, using the FA method, we designed a structure prediction test of “chimera proteins.” In the chimera proteins, local structural preference is specific to the target sequences, whereas nonlocal interactions are only sequence-independent compaction forces. We find that these chimera proteins can find the native folds of the intact sequences with high probability indicating dominant roles of the local interactions. We further explore roles of local structural preference by exact calculation of the HP lattice model of proteins. From these results, we suggest principles of protein folding: For small proteins, compact structures that are fully compatible with local structural preference are few, one of which is the native fold. These local biases shape up the funnel-like energy landscape. PMID:16488978

Laboratory Evaluation of Vocal Fold Paralysis and Paresis.

PubMed

White, Michelle; Meenan, Kirsten; Patel, Tirth; Jaworek, Aaron; Sataloff, Robert T

2017-03-01

This study aimed to assess the value of comprehensive laboratory evaluation in patients with vocal fold paralysis or paresis. This is a retrospective chart review. Records of 231 patients with vocal fold paralysis or paresis were reviewed to determine whether there is a significant increase in the number of abnormal test results compared with rates of abnormal results for these tests in the general population and whether testing resulted in clinically important diagnosis. Laboratory data were collected from charts from initial visits from 2010 to 2014 and compared with national data. When controlled for age and sex, white blood cell count was found to have a significantly higher rate of abnormal test results (P < 0.001) in patients with vocal fold paralysis or paresis than the general population. Although hemoglobin, thyroid-stimulating hormone, and thyroid antibody tests were more likely to be abnormal in our patient population, the trend was not statistically significant. Further, the prevalence of syphilis and myasthenia gravis was found to be higher in these subjects than their respective national prevalences, and the incidence of Lyme disease was found to be higher than the national prevalence of Lyme disease. Several patients were diagnosed with medically important conditions such as diabetes, thyroid dysfunction, syphilis, myasthenia gravis, and Lyme disease based on these tests. This study suggests that comprehensive testing of patients with vocal fold movement disorders results in diagnoses that would be missed without a comprehensive evaluation, some of which are important medically, although their causal relationship to vocal fold paralysis or paresis was not investigated or established. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

In vitro activity of the siderophore monosulfactam BAL30072 against contemporary Gram-negative pathogens from New York City, including multidrug-resistant isolates.

PubMed

Landman, David; Singh, Manisha; El-Imad, Badiaa; Miller, Ezra; Win, Thida; Quale, John

2014-06-01

The in vitro activity of BAL30072 was assessed against clinical isolates from NYC hospitals, including isolates from a citywide surveillance study and a collection of isolates with well-characterised resistance mechanisms. BAL30072 was the most active β-lactam against Pseudomonas aeruginosa (MIC50/90, 0.25/1 μg/mL), Acinetobacter baumannii (MIC50/90, 4/>64 μg/mL) and KPC-possessing Klebsiella pneumoniae (MIC50/90, 4/>64 μg/mL). Combining BAL30072 with meropenem resulted in a ≥ 4-fold decrease in the BAL30072 MIC90 both for A. baumannii and K. pneumoniae. For isolates with a BAL30072 MIC>4 μg/mL, addition of a sub-MIC concentration of colistin resulted in a four-fold decrease in the BAL30072 MIC in 44% of P. aeruginosa, 82% of A. baumannii and 23% of K. pneumoniae. Using sub-MIC concentrations, BAL30072 plus colistin was bactericidal against 4 of 11 isolates in time-kill studies. BAL30072 MICs were frequently lower for P. aeruginosa and K. pneumoniae when tested using Mueller-Hinton agar versus Iso-Sensitest agar or Mueller-Hinton broth. Against the well-characterised isolates, reduced susceptibility to BAL30072 correlated with mexA and mexX expression (P. aeruginosa), adeB expression (A. baumannii) and presence of SHV-type ESBLs (A. baumannii and K. pneumoniae). BAL30072 shows promising activity against contemporary Gram-negatives, including MDR P. aeruginosa, A. baumannii and K. pneumoniae. Enhanced activity was often present when BAL30072 was combined with meropenem or colistin. BAL30072 MICs were influenced by the testing method, particularly for P. aeruginosa and K. pneumoniae. Further in vivo studies are warranted to determine the potential clinical utility of BAL30072 alone and combined with other agents. Copyright © 2014 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Incidence of carbapenem-resistant gram negatives in Italian transplant recipients: a nationwide surveillance study.

PubMed

Lanini, Simone; Costa, Alessandro Nanni; Puro, Vincenzo; Procaccio, Francesco; Grossi, Paolo Antonio; Vespasiano, Francesca; Ricci, Andrea; Vesconi, Sergio; Ison, Michael G; Carmeli, Yehuda; Ippolito, Giuseppe

2015-01-01

Bacterial infections remain a challenge to solid organ transplantation. Due to the alarming spread of carbapenem-resistant gram negative bacteria, these organisms have been frequently recognized as cause of severe infections in solid organ transplant recipients. Between 15 May and 30 September 2012 we enrolled 887 solid organ transplant recipients in Italy with the aim to describe the epidemiology of gram negative bacteria spreading, to explore potential risk factors and to assess the effect of early isolation of gram negative bacteria on recipients' mortality during the first 90 days after transplantation. During the study period 185 clinical isolates of gram negative bacteria were reported, for an incidence of 2.39 per 1000 recipient-days. Positive cultures for gram negative bacteria occurred early after transplantation (median time 26 days; incidence rate 4.33, 1.67 and 1.14 per 1,000 recipient-days in the first, second and third month after SOT, respectively). Forty-nine of these clinical isolates were due to carbapenem-resistant gram negative bacteria (26.5%; incidence 0.63 per 1000 recipient-days). Carbapenems resistance was particularly frequent among Klebsiella spp. isolates (49.1%). Recipients with longer hospital stay and those who received either heart or lung graft were at the highest risk of testing positive for any gram negative bacteria. Moreover recipients with longer hospital stay, lung recipients and those admitted to hospital for more than 48h before transplantation had the highest probability to have culture(s) positive for carbapenem-resistant gram negative bacteria. Forty-four organ recipients died (0.57 per 1000 recipient-days) during the study period. Recipients with at least one positive culture for carbapenem-resistant gram negative bacteria had a 10.23-fold higher mortality rate than those who did not. The isolation of gram-negative bacteria is most frequent among recipient with hospital stays >48 hours prior to transplant and in those receiving either heart or lung transplants. Carbapenem-resistant gram negative isolates are associated with significant mortality.

A new class of compact high sensitive tiltmeter based on the UNISA folded pendulum mechanical architecture

NASA Astrophysics Data System (ADS)

Barone, Fabrizio; Giordano, Gerardo

2018-02-01

We present the Extended Folded Pendulum Model (EFPM), a model developed for a quantitative description of the dynamical behavior of a folded pendulum generically oriented in space. This model, based on the Tait-Bryan angular reference system, highlights the relationship between the folded pendulum orientation in the gravitational field and its natural resonance frequency. Tis model validated by tests performed with a monolithic UNISA Folded Pendulum, highlights a new technique of implementation of folded pendulum based tiltmeters.

Evaluation of cellular effects of fine particulate matter from combustion of solid fuels used for indoor heating on the Navajo Nation using a stratified oxidative stress response model

NASA Astrophysics Data System (ADS)

Li, Ning; Champion, Wyatt M.; Imam, Jemal; Sidhu, Damansher; Salazar, Joseph R.; Majestic, Brian J.; Montoya, Lupita D.

2018-06-01

Communities in the Navajo Nation face public health burdens caused in part by the combustion of wood and coal for indoor heating using stoves that are old or in disrepair. Wood and coal combustion emits particulate matter (PM) with aerodynamic diameter < 2.5 μm (PM2.5), which can reach deep in the lung and cause injuries. Currently, there is little information about the health effects of wood and coal combustion-derived PM2.5 on Navajo Nation residents. This study tested the hypothesis that PM2.5 generated from solid fuel combustion in stoves commonly used by Navajo residents would induce stratified oxidative stress responses ranging from activation of antioxidant defense to inflammation and cell death in mouse macrophages (RAW 264.7). PM2.5 emitted from burning Ponderosa Pine (PP) and Utah Juniper (UJ) wood and Black Mesa (BM) and Fruitland (FR) coal in a stove representative of those widely used by Navajo residents were collected, and their aqueous suspensions used for cellular exposure. PM from combustion of wood had significantly more elemental carbon (EC) (15%) and soluble Ni (0.0029%) than the samples from coal combustion (EC: 3%; Ni: 0.0019%) and was also a stronger activator of antioxidant enzyme heme oxygenase-1 (11-fold increase vs. control) than that from coal (5-fold increase). Only PM from PP-wood (12-fold) and BM-coal (3-fold) increased the release of inflammatory cytokine tumor necrosis factor alpha. Among all samples, PP-wood consistently had the strongest oxidative stress and inflammatory effects. PM components, i.e. low-volatility organic carbon, EC, Cu, Ni and K were positively correlated with the cellular responses. Results showed that, at the concentrations tested, emissions from all fuels did not have significant cytotoxicity. These findings suggest that PM2.5 emitted from combustion of wood and coal commonly used by Navajo residents may negatively impact the health of this community.

Low-Magnitude, High-Frequency Vibration Fails to Accelerate Ligament Healing but Stimulates Collagen Synthesis in the Achilles Tendon.

PubMed

Thompson, William R; Keller, Benjamin V; Davis, Matthew L; Dahners, Laurence E; Weinhold, Paul S

2015-05-01

Low-magnitude, high-frequency vibration accelerates fracture and wound healing and prevents disuse atrophy in musculoskeletal tissues. To investigate the role of low-magnitude, high-frequency vibration as a treatment to accelerate healing of an acute ligament injury and to examine gene expression in the intact Achilles tendon of the injured limb after low-magnitude, high-frequency vibration. Controlled laboratory study. Complete surgical transection of the medial collateral ligament (MCL) was performed in 32 Sprague-Dawley rats, divided into control and low-magnitude, high-frequency vibration groups. Low-magnitude, high-frequency vibration started on postoperative day 2, and rats received vibration for 30 minutes a day for 12 days. All rats were sacrificed 2 weeks after the operation, and their intact and injured MCLs were biomechanically tested or used for histological analysis. Intact Achilles tendons from the injured limb were evaluated for differences in gene expression. Mechanical testing revealed no differences in the ultimate tensile load or the structural stiffness between the control and vibration groups for either the injured or intact MCL. Vibration exposure increased gene expression of collagen 1 alpha (3-fold), interleukin 6 (7-fold), cyclooxygenase 2 (5-fold), and bone morphogenetic protein 12 (4-fold) in the intact Achilles tendon when compared with control tendons ( P < .05). While no differences were observed in the mechanical or histological properties of the fully transected MCL after low-magnitude, high-frequency vibration treatment, significant enhancements in gene expression were observed in the intact Achilles tendon. These included collagen, several inflammatory cytokines, and growth factors critical for tendons. As low-magnitude, high-frequency vibration had no negative effects on ligament healing, vibration therapy may be a useful tool to accelerate healing of other tissues (bone) in multitrauma injuries without inhibiting ligament healing. Additionally, the enhanced gene expression in response to low-magnitude, high-frequency vibration in the intact Achilles tendon suggests the need to further study its potential to accelerate tendon healing in partial injury or repair models.

US incidence of breast cancer subtypes defined by joint hormone receptor and HER2 status.

PubMed

Howlader, Nadia; Altekruse, Sean F; Li, Christopher I; Chen, Vivien W; Clarke, Christina A; Ries, Lynn A G; Cronin, Kathleen A

2014-04-28

In 2010, Surveillance, Epidemiology, and End Results (SEER) registries began collecting human epidermal growth factor 2 (HER2) receptor status for breast cancer cases. Breast cancer subtypes defined by joint hormone receptor (HR; estrogen receptor [ER] and progesterone receptor [PR]) and HER2 status were assessed across the 28% of the US population that is covered by SEER registries. Age-specific incidence rates by subtype were calculated for non-Hispanic (NH) white, NH black, NH Asian Pacific Islander (API), and Hispanic women. Joint HR/HER2 status distributions by age, race/ethnicity, county-level poverty, registry, stage, Bloom-Richardson grade, tumor size, and nodal status were evaluated using multivariable adjusted polytomous logistic regression. All statistical tests were two-sided. Among case patients with known HR/HER2 status, 36810 (72.7%) were found to be HR(+)/HER2(-), 6193 (12.2%) were triple-negative (HR(-)/HER2(-)), 5240 (10.3%) were HR(+)/HER2(+), and 2328 (4.6%) were HR(-)/HER2(+); 6912 (12%) had unknown HR/HER2 status. NH white women had the highest incidence rate of the HR(+)/HER2(-) subtype, and NH black women had the highest rate of the triple-negative subtype. Compared with women with the HR(+)/HER2(-) subtype, triple-negative patients were more likely to be NH black and Hispanic; HR(+)/HER2(+) patients were more likely to be NH API; and HR(-)/HER2(+) patients were more likely to be NH black, NH API, and Hispanic. Patients with triple-negative, HR(+)/HER2(+), and HR(-)/HER2(+) breast cancer were 10% to 30% less likely to be diagnosed at older ages compared with HR(+)/HER2(-) patients and 6.4-fold to 20.0-fold more likely to present with high-grade disease. In the future, SEER data can be used to monitor clinical outcomes in women diagnosed with different molecular subtypes of breast cancer for a large portion (approximately 28%) of the US population. Published by Oxford University Press 2014.

Enhanced HTS hit selection via a local hit rate analysis.

PubMed

Posner, Bruce A; Xi, Hualin; Mills, James E J

2009-10-01

The postprocessing of high-throughput screening (HTS) results is complicated by the occurrence of false positives (inactive compounds misidentified as active by the primary screen) and false negatives (active compounds misidentified as inactive by the primary screen). An activity cutoff is frequently used to select "active" compounds from HTS data; however, this approach is insensitive to both false positives and false negatives. An alternative method that can minimize the occurrence of these artifacts will increase the efficiency of hit selection and therefore lead discovery. In this work, rather than merely using the activity of a given compound, we look at the presence and absence of activity among all compounds in its "chemical space neighborhood" to give a degree of confidence in its activity. We demonstrate that this local hit rate (LHR) analysis method outperforms hit selection based on ranking by primary screen activity values across ten diverse high throughput screens, spanning both cell-based and biochemical assay formats of varying biology and robustness. On average, the local hit rate analysis method was approximately 2.3-fold and approximately 1.3-fold more effective in identifying active compounds and active chemical series, respectively, than selection based on primary activity alone. Moreover, when applied to finding false negatives, this method was 2.3-fold better than ranking by primary activity alone. In most cases, novel hit series were identified that would have otherwise been missed. Additional uses of and observations regarding this HTS analysis approach are also discussed.

Quantitative skin prick and bronchial provocation tests with platinum salt.

PubMed Central

Merget, R; Schultze-Werninghaus, G; Bode, F; Bergmann, E M; Zachgo, W; Meier-Sydow, J

1991-01-01

Occupational asthma due to platinum salts is a frequent disease in platinum refineries. The diagnosis is based upon a history of work related symptoms and a positive skin prick test with platinum salts. Bronchial provocation tests have not been performed in epidemiological studies because the skin test is believed to be highly specific and sensitive. As no reliable data about this issue currently exist, this study assesses the use of skin prick and bronchial provocation tests with methacholine and platinum salt in platinum refinery workers. Twenty seven of 35 workers, who were referred to our clinic with work related symptoms and nine control subjects with bronchial hyperreactivity underwent a skin prick test and bronchial provocation with methacholine and platinum salt. For skin prick and bronchial provocation tests with platinum salt a 10(-2)-10(-8) mol/l hexachloroplatinic acid solution, in 10-fold dilutions was used. Four of the 27 subjects and all controls showed neither a bronchial reaction nor a skin reaction. Twenty three subjects were considered allergic to platinum salt; 22 of these showed a fall of 50% or more in specific airway conductance after inhalation of the platinum salt solution. Four workers experienced a positive bronchial reaction despite a negative skin prick test. No correlation of responsiveness to methacholine with responsiveness to platinum salt was found, but the skin prick test correlated with the bronchial reaction to platinum salt (rs = 0.50, p less than 0.023, n = 22). One dual reaction was seen in bronchial provocation tests. Side effects of both skin tests and bronchial provocation tests with platinum salt were rare and were not encountered in workers without a skin reaction to platinum salt. It is concluded that bronchial provocation tests with platinum salts should be performed on workers with work related symptoms but negative skin tests with platinum salts. PMID:1772797

Equilibrium folding of pro-HlyA from Escherichia coli reveals a stable calcium ion dependent folding intermediate.

PubMed

Thomas, Sabrina; Bakkes, Patrick J; Smits, Sander H J; Schmitt, Lutz

2014-09-01

HlyA from Escherichia coli is a member of the repeats in toxin (RTX) protein family, produced by a wide range of Gram-negative bacteria and secreted by a dedicated Type 1 Secretion System (T1SS). RTX proteins are thought to be secreted in an unfolded conformation and to fold upon secretion by Ca(2+) binding. However, the exact mechanism of secretion, ion binding and folding to the correct native state remains largely unknown. In this study we provide an easy protocol for high-level pro-HlyA purification from E. coli. Equilibrium folding studies, using intrinsic tryptophan fluorescence, revealed the well-known fact that Ca(2+) is essential for stability as well as correct folding of the whole protein. In the absence of Ca(2+), pro-HlyA adopts a non-native conformation. Such molecules could however be rescued by Ca(2+) addition, indicating that these are not dead-end species and that Ca(2+) drives pro-HlyA folding. More importantly, pro-HlyA unfolded via a two-state mechanism, whereas folding was a three-state process. The latter is indicative of the presence of a stable folding intermediate. Analysis of deletion and Trp mutants revealed that the first folding transition, at 6-7M urea, relates to Ca(2+) dependent structural changes at the extreme C-terminus of pro-HlyA, sensed exclusively by Trp914. Since all Trp residues of HlyA are located outside the RTX domain, our results demonstrate that Ca(2+) induced folding is not restricted to the RTX domain. Taken together, Ca(2+) binding to the pro-HlyA RTX domain is required to drive the folding of the entire protein to its native conformation. Copyright © 2014 Elsevier B.V. All rights reserved.

[Focal cerebral ischemia in rats with estrogen deficiency and endothelial dysfunction].

PubMed

Litvinov, A A; Volotova, E V; Kurkin, D V; Logvinova, E O; Darmanyan, A P; Tyurenkov, I N

2017-01-01

To assess an effect of ovariectomy (OE) on the cerebral blood flow, endothelium-dependent vasodilation, neurological, cognitive and locomotor deficit as markers of brain damage after focal ischemia in rats. The study was conducted in 48 female Wistar rats. Ovariectomy was performed with ovaries and uterine body extirpation, cerebral ischemia was performed by middle cerebral artery occlusion (MCAO) in rats. To assess brain damage, Combs and Garcia scores, 'open field' test (OFT), 'extrapolatory escape test' (EET), 'passive avoidance test' (PAT), 'beam-walking test' were used. Cerebral blood flow was measured using ultrasonic flowmetry. After 7 days of MCAO, the cerebral blood flow in ovarioectomized animals was reduced by 20% compared to sham-ovariectomized animals. Ovariectomized animals with MCAO showed a three-fold endothelium-dependent vasodilation reduction (the reaction of cerebral vessels to the introduction of acetylcholine and N-L-arginine), indicating the presence of severe endothelial dysfunction. In ovarioectomized animals, the cerebral blood flow was reduced by 34% compared to sham-operated animals. MCAO and OE taken together resulted in more than 2-fold increase in neurological, motor disturbances, 3-fold decrease in motor activity of the animals in the OP test. Focal ischemia in ovarioectomized animals with endothelial dysfunction led to memory decrease by 1/5 fold in PAT and by 2-fold in EET.

Comparison of sodium hydroxide and calcium hydroxide pretreatments of giant reed for enhanced enzymatic digestibility and methane production.

PubMed

Jiang, Danping; Ge, Xumeng; Zhang, Quanguo; Zhou, Xuehua; Chen, Zhou; Keener, Harold; Li, Yebo

2017-11-01

NaOH pretreatment with leachate reuse and Ca(OH) 2 pretreatment were compared for improved enzymatic digestibility and biogas production from giant reed, a promising energy crop. The NaOH pretreatment with leachate reuse increased glucose yields during enzymatic hydrolysis by 2.6-fold, and methane yields during anaerobic digestion by 1.4- to 1.6-fold. However, NaOH pretreatment had a negative net benefit (i.e., revenue from increased energy production minus chemical cost). Pretreatment with 7-20% Ca(OH) 2 not only improved glucose yield and methane yield by up to 2.3-fold and 1.4-fold, respectively, but also obtained a net benefit of $1.1-5.8/tonne dry biomass. Thus, Ca(OH) 2 pretreatment was shown to be more feasible than NaOH pretreatment for biogas production from giant reed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Free-energy landscape of a hyperstable RNA tetraloop.

PubMed

Miner, Jacob C; Chen, Alan A; García, Angel E

2016-06-14

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

21-Gene recurrence score and locoregional recurrence in lymph node-negative, estrogen receptor-positive breast cancer

PubMed Central

Turashvili, Gulisa; Chou, Joanne F.; Brogi, Edi; Morrow, Monica; Dickler, Maura; Norton, Larry; Hudis, Clifford; Wen, Hannah Y

2017-01-01

Background/purpose The 21-gene recurrence score (RS) assay evaluates the likelihood of distant recurrence and benefit of chemotherapy in lymph node-negative, estrogen receptor (ER)-positive, HER2-negative breast cancer patients. The RS categories are associated with the risk of locoregional recurrence (LRR) in some, but not all studies. Methods We reviewed the institutional database to identify consecutive female patients with node-negative, ER+/HER2− breast carcinoma tested for the 21-gene RS assay and treated at our center from 2008 to 2013. We collected data on clinicopathologic features, treatment, and outcome. Statistical analysis was performed using SAS version 9.4 or R version 3.3.2. Results Of 2326 patients, 60% (1394) were in the low RS group, 33.4% (777) in the intermediate RS group, and 6.6% (155) in the high RS group. Median follow-up was 53 months. A total of 44 LRRs were observed, with a cumulative incidence of 0.17% at 12 months and 1.6% at 48 months. The cumulative incidence of LRR at 48 months was 0.84%, 2.72% and 2.80% for low, intermediate, and high RS groups, respectively (p<0.01). Univariate analysis showed that the risk of LRR was associated with the RS categories (p<0.01), T stage (p<0.01) and lymphovascular invasion (LVI) (p=0.009). There was no difference in LRR rates by initial local treatment (total mastectomy vs. breast-conserving surgery plus radiation therapy). The RS remained significantly associated with LRR after adjusting for LVI and T stage. Compared to patients with low RS, the risk of LRR was increased more than 4-fold (hazard ratio: 4.61, 95% CI 1.90–11.19, p<0.01), and 3-fold (hazard ratio: 2.81, 95% CI 1.41–5.56, p<0.01) for high and intermediate risk categories, respectively. Conclusions Our study confirms that RS is significantly associated with the risk of LRR in node-negative, ER+/HER2− breast cancer patients. Our findings suggest that in addition to its value for prognostic stage grouping and decision-making regarding adjuvant systemic therapy, the role of the RS in identifying patients not requiring radiotherapy should be studied. PMID:28702894

A longitudinal test of the predictions of the interpersonal-psychological theory of suicidal behaviour for passive and active suicidal ideation in a large community-based cohort.

PubMed

Batterham, Philip J; Walker, Jennie; Leach, Liana S; Ma, Jennifer; Calear, Alison L; Christensen, Helen

2018-02-01

The Interpersonal-Psychological Theory of Suicide (IPTS) aims to elucidate the key antecedents of suicide deaths. Limited research has tested the IPTS in a community setting, and very little longitudinal research has been conducted. The current study longitudinally tested the predictions of the IPTS for suicidal ideation in a large population-based sample. The PATH through Life study assesses three age cohorts (20's, 40's, 60's) every four years. Two interpersonal factors were estimated at the third wave of assessment: thwarted belongingness (TB) and perceived burdensomeness (PB). The roles of these factors in suicide ideation (active and passive) four years later were estimated using logistic regression models (n = 4545). A one SD increase in TB was associated with increased odds of 37% for passive ideation and 24% for active ideation. For PB, odds were increased 2.5-fold for passive ideation and 2.4-fold for active ideation. A significant negative PB × TB interaction was found for passive but not active ideation. Effects were not consistent by age group or gender. Proxy measures were used to assess the constructs. The extended timeframe and low prevalence of suicidal ideation limited power to find effects within subgroups. Although TB and PB were individually associated with suicidal thoughts, little evidence was found for the key predictions of the IPTS longitudinally. Further investigation of the dynamic interplay between interpersonal factors over time is needed. Copyright © 2017 Elsevier B.V. All rights reserved.

Exosome Adherence and Internalization by Hepatic Stellate Cells Triggers Sphingosine 1-Phosphate-dependent Migration*

PubMed Central

Wang, Ruisi; Ding, Qian; Yaqoob, Usman; de Assuncao, Thiago M.; Verma, Vikas K.; Hirsova, Petra; Cao, Sheng; Mukhopadhyay, Debabrata; Huebert, Robert C.; Shah, Vijay H.

2015-01-01

Exosomes are cell-derived extracellular vesicles thought to promote intercellular communication by delivering specific content to target cells. The aim of this study was to determine whether endothelial cell (EC)-derived exosomes could regulate the phenotype of hepatic stellate cells (HSCs). Initial microarray studies showed that fibroblast growth factor 2 induced a 2.4-fold increase in mRNA levels of sphingosine kinase 1 (SK1). Exosomes derived from an SK1-overexpressing EC line increased HSC migration 3.2-fold. Migration was not conferred by the dominant negative SK1 exosome. Incubation of HSCs with exosomes was also associated with an 8.3-fold increase in phosphorylation of AKT and 2.5-fold increase in migration. Exosomes were found to express the matrix protein and integrin ligand fibronectin (FN) by Western blot analysis and transmission electron microscopy. Blockade of the FN-integrin interaction with a CD29 neutralizing antibody or the RGD peptide attenuated exosome-induced HSC AKT phosphorylation and migration. Inhibition of endocytosis with transfection of dynamin siRNA, the dominant negative dynamin GTPase construct Dyn2K44A, or the pharmacological inhibitor Dynasore significantly attenuated exosome-induced AKT phosphorylation. SK1 levels were increased in serum exosomes derived from mice with experimental liver fibrosis, and SK1 mRNA levels were up-regulated 2.5-fold in human liver cirrhosis patient samples. Finally, S1PR2 inhibition protected mice from CCl4-induced liver fibrosis. Therefore, EC-derived SK1-containing exosomes regulate HSC signaling and migration through FN-integrin-dependent exosome adherence and dynamin-dependent exosome internalization. These findings advance our understanding of EC/HSC cross-talk and identify exosomes as a potential target to attenuate pathobiology signals. PMID:26534962

Exosome Adherence and Internalization by Hepatic Stellate Cells Triggers Sphingosine 1-Phosphate-dependent Migration.

PubMed

Wang, Ruisi; Ding, Qian; Yaqoob, Usman; de Assuncao, Thiago M; Verma, Vikas K; Hirsova, Petra; Cao, Sheng; Mukhopadhyay, Debabrata; Huebert, Robert C; Shah, Vijay H

2015-12-25

Exosomes are cell-derived extracellular vesicles thought to promote intercellular communication by delivering specific content to target cells. The aim of this study was to determine whether endothelial cell (EC)-derived exosomes could regulate the phenotype of hepatic stellate cells (HSCs). Initial microarray studies showed that fibroblast growth factor 2 induced a 2.4-fold increase in mRNA levels of sphingosine kinase 1 (SK1). Exosomes derived from an SK1-overexpressing EC line increased HSC migration 3.2-fold. Migration was not conferred by the dominant negative SK1 exosome. Incubation of HSCs with exosomes was also associated with an 8.3-fold increase in phosphorylation of AKT and 2.5-fold increase in migration. Exosomes were found to express the matrix protein and integrin ligand fibronectin (FN) by Western blot analysis and transmission electron microscopy. Blockade of the FN-integrin interaction with a CD29 neutralizing antibody or the RGD peptide attenuated exosome-induced HSC AKT phosphorylation and migration. Inhibition of endocytosis with transfection of dynamin siRNA, the dominant negative dynamin GTPase construct Dyn2K44A, or the pharmacological inhibitor Dynasore significantly attenuated exosome-induced AKT phosphorylation. SK1 levels were increased in serum exosomes derived from mice with experimental liver fibrosis, and SK1 mRNA levels were up-regulated 2.5-fold in human liver cirrhosis patient samples. Finally, S1PR2 inhibition protected mice from CCl4-induced liver fibrosis. Therefore, EC-derived SK1-containing exosomes regulate HSC signaling and migration through FN-integrin-dependent exosome adherence and dynamin-dependent exosome internalization. These findings advance our understanding of EC/HSC cross-talk and identify exosomes as a potential target to attenuate pathobiology signals. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Sexual violence and associated factors among women in HIV discordant and concordant relationships in Uganda.

PubMed

Shuaib, Faisal M B; Ehiri, John E; Jolly, Pauline; Zhang, Qionghui; Emusu, Donath; Ngu, Julius; Foushee, Herman; Katongole, Drake; Kirby, Russell; Wabwire-Mangen, Fred

2012-01-01

HIV serodiscordance is a sexual partnership in which one partner is infected with HIV while the other is not. Managing emotional and sexual intimacy in HIV serodiscordant unions can be difficult due to concerns about HIV transmission and the challenge of initiating and maintaining safe sex. In situations where couples are jointly aware of their HIV status, women in serodiscordant unions may face increased risk of partner violence. We conducted an investigation to assess risk factors for HIV serodiscordance and determine if HIV serodiscordance is associated with incident sexual violence among a cohort of women attending HIV post-test club services at three AIDS Information Centers (AICs) in Uganda. Using a prospective study of 250 women, we elicited information about sexual violence using structured face-to-face interviews. Sexual violence and risk factors were assessed and compared among HIV positive women in HIV discordant unions, HIV negative women in discordant unions, and HIV negative women in negative concordant unions. Multivariable logistic regression was used to assess the association between participants' serostatus and sexual violence. HIV negative women in serodiscordant relationships (36.1±11.1 years, range: 19-65 years) were significantly older than either HIV positive women in serodiscordant relationships (32.2±9.0 years, range: 18-56 years), or HIV negative women in concordant relationships (32.3±11.0 years, range: 18-62), (p=0.033). Early age at sexual debut was associated with a 2.4-fold increased risk of experiencing sexual violence (OR 2.4, 95% CI 1.27-4.65). Based on unadjusted analysis, HIV positive women in discordant relationship were at highest risk for sexual violence compared to HIV negative women in discordant unions, and HIV negative women in negative concordant unions. HIV negative women in discordant relationships and those in concordant negative relationships showed no increased risk for sexual violence. However, couples' HIV serostatus was not significant related to incident sexual violence after controlling for potential confounding covariates. Nevertheless, the results were able to elucidate the sexual violence risk factor profile of participants based on couples' HIV serostatus. Couple counseling protocols at HIV voluntary counseling and testing centers in Uganda should identify those at risk for sexual violence and develop interventions to reduce its incidence.

A carcinogenic potency database of the standardized results of animal bioassays

PubMed Central

Gold, Lois Swirsky; Sawyer, Charles B.; Magaw, Renae; Backman, Georganne M.; De Veciana, Margarita; Levinson, Robert; Hooper, N. Kim; Havender, William R.; Bernstein, Leslie; Peto, Richard; Pike, Malcolm C.; Ames, Bruce N.

1984-01-01

The preceding paper described our numerical index of carcinogenic potency, the TD50 and the statistical procedures adopted for estimating it from experimental data. This paper presents the Carcinogenic Potency Database, which includes results of about 3000 long-term, chronic experiments of 770 test compounds. Part II is a discussion of the sources of our data, the rationale for the inclusion of particular experiments and particular target sites, and the conventions adopted in summarizing the literature. Part III is a guide to the plot of results presented in Part IV. A number of appendices are provided to facilitate use of the database. The plot includes information about chronic cancer tests in mammals, such as dose and other aspects of experimental protocol, histopathology and tumor incidence, TD50 and its statistical significance, dose response, author's opinion and literature reference. The plot readily permits comparisons of carcinogenic potency and many other aspects of cancer tests; it also provides quantitative information about negative tests. The range of carcinogenic potency is over 10 million-fold. PMID:6525996

Individual-based model of young-of-the-year striped bass population dynamics. II. Factors affecting recruitment in the Potomac River, Maryland

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

Cowan, J.H.; Rose, K.A.; Rutherford, E.S.

1993-05-01

An individual-based model of the population dynamics of young-of-the-year striped bass Morone saxatilis in the Potomac River, Maryland, was used to test the hypothesis that historically high recruitment variability can be explained by changes in environmental and biological factors that result in relatively small changes in growth and mortality rates of striped bass larvae. The four factors examined were (1) size distribution of female parents, (2) zooplankton prey density during the development of striped bass larvae, (3) density of completing larval white perch M. americana, and (4) temperature during larval development. Simulation results suggest that variations in female size andmore » in prey for larvae alone could cause 10-fold variability in recruitment. But no single factor alone caused changes in vital rates of age-0 fish that could account for the 145-fold variability in the Potomac River index of juvenile recruitment. However, combined positive or negative effects of two or more factors resulted in more than a 150-fold simulated recruitment variability, suggesting that combinations of factors can account for the high observed annual variability in striped bass recruitment success. Higher cumulative mortality of feeding larvae and younger life stages than of juveniles was common to all simulations. supporting the contention that striped bass year-class strength is determined prior to metamorphosis. 76 refs., 7 figs., 4 tabs.« less

Design of a hydraulically-driven bionic folding wing.

PubMed

Zhang, Zhijun; Sun, Xuwei; Du, Pengyu; Sun, Jiyu; Wu, Yongfeng

2018-06-01

Membranous hind wings of the beetles can be folded under the elytra when they are at rest, and rotate and lift the elytra up only when they need to fly. This characteristic provides excellent flying capability and good environment adaptability. Inspired by the beetles, the new type of the bionic folding wing for the flapping wing Micro Air Vehicle (MAV) was designed. This flapping wing can be unfolded to get a sufficient lift in flight, and can be folded off flight to reduce the wing area and risk of the wing damage. The relationship between the internal pressures of the hydraulic system for the bionic wing folding varies and temperature was analyzed, the results show that the pressure within the system tends to increase with temperature, which proves the feasibility of the schematic design in theory. Stress analysis of the bionic wing was conducted, it was shown that stress distributions and deformation of the bionic wing under the positive and negative side loading are basically the same, which demonstrates that the strength of the bionic folding wing meets the requirements and further proves the feasibility of the schematic design. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Deceleration of arginine kinase refolding by induced helical structures.

PubMed

Li, Hai-Long; Zhou, Sheng-Mei; Park, Daeui; Jeong, Hyoung Oh; Chung, Hae Young; Yang, Jun-Mo; Meng, Fan-Guo; Hu, Wei-Jiang

2012-04-01

Arginine kinase (AK) is a key metabolic enzyme for keeping energy balance in invertebrates. Therefore, regulation of the enzymatic activity and the folding studies of AK from the various invertebrates have been the focus of investigation. We studied the effects of helical structures by using hexafluoroisopropanol (HFIP) on AK folding. Folding kinetic studies showed that the folding rates of the urea-denatured AKs were significantly decelerated after being induced in various concentrations of HFIP. AK lost its activity completely at concentrations greater than 60%. The results indicated that the HFIP-induced helical structures in the denatured state play a negative role in protein folding, and the helical structures induced in 5% (v/v) HFIP act as the most effective barrier against AK taking its native structure. The computational docking simulations (binding energies for -2.19 kcal/mol for AutoDock4.2 and -20.47 kcal/mol for Dock6.3) suggested that HFIP interacts with the several important residues that are predicted by both programs. The excessively pre-organized helical structures not only hampered the folding process, but also ultimately brought about changes in the three-dimensional conformation and biological function of AK.

Early onset primary pulmonary cryptococcosis in a renal transplant patient.

PubMed

Tarai, B; Kher, V; Kotru, P; Sabhikhi, A; Barman, P; Rattan, A

2010-01-01

We report a case of primary pulmonary cryptococcosis in a post-renal transplant patient. A 65-year-old male renal transplant patient was admitted to the hospital with a low grade fever of 1 month, radiologically mimicking tuberculosis (TB). Broncho-alveolar fluid (BAL) shows capsulated yeast, and Cryptococcus neoformans was grown on culture supported by cytology and histopathological examination. Cryptococcal antigen was positive (32-fold) in serum and was negative in cerebrospinal fluid (CSF). The patient was given amphotericin B and 5-flucytosine and clinical improvement was seen on a weekly follow up. The serum cryptococcal antigen test might contribute to the early detection and treatment of pulmonary cryptococcosis. The results of antifungal susceptibility were aid in selecting the drug of choice for treatment.

From Folding to Function: Design of a New Switchable Biosurfactant Protein.

PubMed

Zhao, Chun-Xia; Dwyer, Mirjana Dimitrijev; Yu, Lei; Middelberg, Anton P J

2017-03-03

A new anionic biosurfactant protein (SP16) capable of tuning foaming behaviour by pH or salt has been designed. This biosurfactant exhibits unique foaming behaviour with high sensitivity to pH. A good level of foaming was observed at pH 2 but not at pH 3. A further increase by one pH unit to pH 4 restored good foaming. At pH 5-8, SP16 again showed low foaming propensity, whereas the presence of salt (NaCl) was able to restore foaming again. Interfacial tension and circular dichroism investigations revealed the foaming control mechanism. The high negative charge (-16.6) at pH 6 and above restricted the ability of SP16 to fold into an α-helical conformation and also restricted surface activity. For pH 5 (-13.6), even though SP16 folds in bulk to give α-helical structure, the high charge inhibited adsorption at the air-water interface, resulting in a significant lag time of about 150-200 sec to achieve a decrease in interfacial tension. In contrast to its low foaming behaviour at pH 5-8, the presence of salt (NaCl) was found to effectively screen negative charge, thus leading to its folding and a decrease of interfacial tension. This new design offers a new strategy to control foaming behaviour, and elaborates a clear link between charge, structure and interfacial activity for biosurfactants. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exaggerated Health Benefits of Physical Fitness and Activity dueto Self-selection.

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

Williams, Paul T.

Background: The predicted health benefits of becomingphysically active or fit will be exaggerated if health outcomes causefitness and activity rather than the converse in prospective andcross-sectional epidemiological studies. Objective: Assess whether therelationships of adiposity to fitness and activity are explained byadiposity prior to exercising. Design: Cross-sectional study of physicalfitness (running speed during 10km foot race) and physical activity(weekly running distance) to current BMI (BMIcurrent) and BMI at thestart of running (BMIstarting) in 44,370 male and 25,252 femaleparticipants of the National Runners' Health Study. Results: BMIstartingexplained all of the association between fitness and BMIcurrent in bothsexes, but less than a thirdmore » of the association between physical activityand BMIcurrent in men. In women, BMIstarting accounted for 58 percent ofthe association between BMIcurrent and activity levels. The 95thpercentile of BMIcurrent showed substantially greater declines withfitness and activity levels than the 5th percentile of BMIcurrent in men(i.e., the negative slope for 95th percentile was 2.6-fold greater thanthe 5th percentile for fitness and 3-fold greater for activity) and women(6-fold and 3.4-fold greater, respectively). At all percentiles, theregression slopes relating BMIstarting to fitness were comparable orgreater (more negative) than the slopes relating BMIcurrent to fitness,whereas the converse was true for activity. Conclusion: Self-selectionbias accounts for all of the association between fitness and adiposityand probably a portion of other health outcomes, but has less affect onassociations involving physical activity« less

Iron translocation into and out of Listeria innocua Dps and size distribution of the protein-enclosed nanomineral are modulated by the electrostatic gradient at the 3-fold "ferritin-like" pores.

PubMed

Bellapadrona, Giuliano; Stefanini, Simonetta; Zamparelli, Carlotta; Theil, Elizabeth C; Chiancone, Emilia

2009-07-10

Elucidating pore function at the 3-fold channels of 12-subunit, microbial Dps proteins is important in understanding their role in the management of iron/hydrogen peroxide. The Dps pores are called "ferritin-like" because of the structural resemblance to the 3-fold channels of 24-subunit ferritins used for iron entry and exit to and from the protein cage. In ferritins, negatively charged residues lining the pores generate a negative electrostatic gradient that guides iron ions toward the ferroxidase centers for catalysis with oxidant and destined for the mineralization cavity. To establish whether the set of three aspartate residues that line the pores in Listeria innocua Dps act in a similar fashion, D121N, D126N, D130N, and D121N/D126N/D130N proteins were produced; kinetics of iron uptake/release and the size distribution of the iron mineral in the protein cavity were compared. The results, discussed in the framework of crystal growth in a confined space, indicate that iron uses the hydrophilic 3-fold pores to traverse the protein shell. For the first time, the strength of the electrostatic potential is observed to modulate kinetic cooperativity in the iron uptake/release processes and accordingly the size distribution of the microcrystalline iron minerals in the Dps protein population.

Investigation of land-use spectral signatures. Ph.D. Thesis. Final Report

NASA Technical Reports Server (NTRS)

Hagewood, J. F.

1975-01-01

A technique was developed to obtain bidirectional reflectance data from natural surfaces by using a folding mirror to transfer the reflected energy from the test surface to a spectroradiometer. The folding mirror was a first surface reflector made by stretching Mylar vacuum coated with aluminum over a light weight frame. The optically folding mirror was positioned over the test surfaces with a moveable platform for both laboratory and field tests. Field tests were conducted using a tethered balloon system to position the folding mirror. A spectroradiometer was designed and built specifically for this investigation. The spectroradiometer had an angular field of view of twenty-four minutes in one axis and ten minutes in the other axis. The radiometer was capable of detecting energies in small bandwidths throughout the electromagnetic spectrum from 0.3 microns to 3.0 microns. Bidirectional reflectance data and variations in the data with source angles were obtained for Saint Augustine grass, Bermuda grass, and a black alluvium soil from the Mississippi River delta.

The sensor kinase PhoQ mediates virulence in Pseudomonas aeruginosa.

PubMed

Gooderham, W James; Gellatly, Shaan L; Sanschagrin, François; McPhee, Joseph B; Bains, Manjeet; Cosseau, Celine; Levesque, Roger C; Hancock, Robert E W

2009-03-01

Pseudomonas aeruginosa is a ubiquitous environmental Gram-negative bacterium that is also a major opportunistic human pathogen in nosocomial infections and cystic fibrosis chronic lung infections. PhoP-PhoQ is a two-component regulatory system that has been identified as essential for virulence and cationic antimicrobial peptide resistance in several other Gram-negative bacteria. This study demonstrated that mutation of phoQ caused reduced twitching motility, biofilm formation and rapid attachment to surfaces, 2.2-fold reduced cytotoxicity to human lung epithelial cells, substantially reduced lettuce leaf virulence, and a major, 10 000-fold reduction in competitiveness in chronic rat lung infections. Microarray analysis revealed that PhoQ controlled the expression of many genes consistent with these phenotypes and with its known role in polymyxin B resistance. It was also demonstrated that PhoQ controls the expression of many genes outside the known PhoP regulon.

Potential strategies for the eradication of multidrug-resistant Gram-negative bacterial infections.

PubMed

Huwaitat, Rawan; McCloskey, Alice P; Gilmore, Brendan F; Laverty, Garry

2016-07-01

Antimicrobial resistance is one of the leading threats to society. The increasing burden of multidrug-resistant Gram-negative infection is particularly concerning as such bacteria are demonstrating resistance to nearly all currently licensed therapies. Various strategies have been hypothesized to treat multidrug-resistant Gram-negative infections including: targeting the Gram-negative outer membrane; neutralization of lipopolysaccharide; inhibition of bacterial efflux pumps and prevention of protein folding. Silver and silver nanoparticles, fusogenic liposomes and nanotubes are potential strategies for extending the activity of licensed, Gram-positive selective, antibiotics to Gram-negatives. This may serve as a strategy to fill the current void in pharmaceutical development in the short term. This review outlines the most promising strategies that could be implemented to solve the threat of multidrug-resistant Gram-negative infections.

The prominent antihelix and helix--the myth of the 'overcorrected' ear in otoplasty.

PubMed

Shokrollahi, Kayvan; Manning, Steven; Sadri, Amir; Molajo, Adeyinka; Lineaweaver, William

2015-06-01

Classic teaching of ear anatomy in the context of otoplasty states that if the antihelical fold is more prominent than the helical fold after surgery then the ear is "overcorrected." We set out to explore the role of the antihelix in normal ear anatomy, its relevance to aesthetic perceptions of the ear, and a snapshot of its incidence in nonoperated ears. To readily identify junior staff in our department, their color photographs, names, and contact details are posted on every ward. Using digital methods, we cropped the left ear out of the source images, making them unidentifiable. Clinical and nonclinical staff in our unit were asked to choose their favorite and their least favorite ears based on their aesthetic appeal. Responses were tabulated and the 2 most popular ears were compared. The preferred ear did not conform to the traditional dogma because it had a prominent antihelix and was statistically significant when compared to other choices. We also noted that a prominent antihelix is common among the general population and among colleagues within the department, and hence "normal." Also interesting was that the helix of the ear chosen as the most aesthetic was also the ear where the helix was almost touching the side of the head. We found that when judging the aesthetic nature of the "virgin" ear, antihelical fold prominence did not appear to be a negative attribute. Indeed, we noted that a prominent antihelix was a common attribute, and we conclude that this was a normal variant without undue negative aesthetic stigma. A surgically corrected ear should not necessarily be regarded as a poor outcome simply on the basis of antihelical prominence. Furthermore, we postulate that patients who have a prominent antihelix might be part of a spectrum of individuals who might have had the subtype of prominent ears featuring a deep conchal bowl. Finally, although not tested directly, it appears that we do not have an idea of our own ear shape, as none of the participants was able to recognize their own ear from the photographs.

Fold assessment for comparative protein structure modeling.

PubMed

Melo, Francisco; Sali, Andrej

2007-11-01

Accurate and automated assessment of both geometrical errors and incompleteness of comparative protein structure models is necessary for an adequate use of the models. Here, we describe a composite score for discriminating between models with the correct and incorrect fold. To find an accurate composite score, we designed and applied a genetic algorithm method that searched for a most informative subset of 21 input model features as well as their optimized nonlinear transformation into the composite score. The 21 input features included various statistical potential scores, stereochemistry quality descriptors, sequence alignment scores, geometrical descriptors, and measures of protein packing. The optimized composite score was found to depend on (1) a statistical potential z-score for residue accessibilities and distances, (2) model compactness, and (3) percentage sequence identity of the alignment used to build the model. The accuracy of the composite score was compared with the accuracy of assessment by single and combined features as well as by other commonly used assessment methods. The testing set was representative of models produced by automated comparative modeling on a genomic scale. The composite score performed better than any other tested score in terms of the maximum correct classification rate (i.e., 3.3% false positives and 2.5% false negatives) as well as the sensitivity and specificity across the whole range of thresholds. The composite score was implemented in our program MODELLER-8 and was used to assess models in the MODBASE database that contains comparative models for domains in approximately 1.3 million protein sequences.

A rabbit vocal fold laser scarring model for testing lamina propria tissue engineering therapies

PubMed Central

Mau, Ted; Du, Mindy; Xu, Chet C.

2015-01-01

Objectives/Hypothesis To develop a vocal fold scarring model using an ablative laser in the rabbit as a platform for testing bioengineered therapies for missing or damaged lamina propria. Study Design Prospective controlled animal study. Methods An optimal laser energy level was first determined by assessing the depths of vocal fold injury created by a Holmium:YAG laser at various energy levels on fresh cadaveric rabbit larynges. The selected energy level was then used to create controlled unilateral injuries in vocal folds of New Zealand white rabbits, with the contralateral folds serving as uninjured controls. After 4 weeks, the larynges were harvested and subjected to excised-larynx phonation with high-speed imaging and immunohistochemical staining for collagen types I and III, elastin, and hyaluronic acid (HA) with quantitative histological analysis. Results 1.8 joules produced full-thickness injury of the lamina propria without extensive muscle injury. After 4 weeks, the injured vocal folds vibrated with reduced amplitude (P = 0.036) in excised-larynx phonation compared to normal vocal folds. The injured vocal folds contained a higher relative density of collagen type I (P = 0.004), higher elastin (P = 0.022), and lower HA (P = 0.030) compared to normal controls. Collagen type III was unchanged. Conclusions With its potential for higher precision of injury, this laser vocal fold scarring model may serve as an alternative to scarring produced by cold instruments for studying the effects of vocal fold lamina propria bioengineered therapies. Level of Evidence N/A. PMID:24715695

The Pacific White Shrimp β-actin Promoter: Functional Properties and the Potential Application for Transduction System Using Recombinant Baculovirus.

PubMed

Shi, Yingli; Xiang, Jianhai; Zhou, Guangzhou; Ron, Tetsuzan Benny; Tong, Hsin-I; Kang, Wen; Sun, Si; Lu, Yuanan

2016-06-01

A newly isolated Pacific white shrimp (Litopenaeus vannamei) beta-actin promoter SbaP and its derivative compact construct SbaP (ENX) have recently been demonstrated to promote ectopic gene expression in vitro and in vivo. To further explore the potential transduction application, this newly isolated shrimp promoter SbaP was comparatively tested with cytomegalovirus (CMV), simian virus 40 (SV40), polyhedrin (Polh), and white spot syndrome virus immediate early gene 1 (WSSV ie1) four constitutive promoters and a beta-actin promoter (TbaP) from tilapia fish to characterize its promoting function in eight different cell lines. Luciferase quantitation assays revealed that SbaP can drive luciferase gene expression in all eight cell lines including sf21 (insect), PAC2 (zebrafish), EPC (carp), CHSE-214 (chinook salmon), GSTEF (green sea turtle), MS-1 (monk seal), 293T (human), and HeLa (human), but at different levels. Comparative analysis revealed that the promoting activity of SbaP was lower (≤10-fold) than CMV but higher (2-20 folds) than Polh in most of these cell lines tested. Whereas, SbaP mediated luciferase expression in sf21 cells was over 20-fold higher than CMV, SV40, Polh, and TbaP promoter. Compared to the SbaP, SbaP (ENX), which was constructed on the basis of SbaP by deletion of two "negative" regulatory elements, exhibited no significant change of promoting activity in EPC and PAC2 cells, but a 5 and 16 % lower promoting effect in 293T and HeLa cells, respectively. Additionally, a recombinant baculovirus was constructed under the control of SbaP (ENX), and efficient promoter activity of newly generated baculoviral vector was detected both in vitro of infected sf21 cells and in vivo of injected indicator shrimp. These results warrant the potential application of SbaP, particularly SbaP (ENX) in ectopic gene expression in future.

Role of the Pepino mosaic virus 3'-untranslated region elements in negative-strand RNA synthesis in vitro.

PubMed

Osman, Toba A M; Olsthoorn, René C L; Livieratos, Ioannis C

2014-09-22

Pepino mosaic virus (PepMV) is a mechanically-transmitted positive-strand RNA potexvirus, with a 6410 nt long single-stranded (ss) RNA genome flanked by a 5'-methylguanosine cap and a 3' poly-A tail. Computer-assisted folding of the 64 nt long PepMV 3'-untranslated region (UTR) resulted in the prediction of three stem-loop structures (hp1, hp2, and hp3 in the 3'-5' direction). The importance of these structures and/or sequences for promotion of negative-strand RNA synthesis and binding to the RNA dependent RNA polymerase (RdRp) was tested in vitro using a specific RdRp assay. Hp1, which is highly variable among different PepMV isolates, appeared dispensable for negative-strand synthesis. Hp2, which is characterized by a large U-rich loop, tolerated base-pair changes in its stem as long as they maintained the stem integrity but was very sensitive to changes in the U-rich loop. Hp3, which harbours the conserved potexvirus ACUUAA hexamer motif, was essential for template activity. Template-RNA polymerase binding competition experiments showed that the ACUUAA sequence represents a high-affinity RdRp binding element. Copyright © 2014 Elsevier B.V. All rights reserved.

Conductive choline transport by alveolar epithelial plasma membrane vesicles.

PubMed

Oelberg, D G; Xu, F

1998-11-01

Choline is an important substrate in alveolar epithelia for both surfactant production and cellular maintenance. The underlying mechanisms of uptake and sites of membrane transport remain uncertain. To test the hypothesis that choline transport occurs at the basolateral side of alveolar epithelia by both Na+-independent and -dependent mechanisms, plasma membrane vesicles were prepared from the apical and basolateral membranes of mature porcine type II pneumocytes. Choline+ transport was assayed by uptake of [3H]choline+ by enriched apical or basolateral vesicles. In the presence of imposed, inside-negative charge gradients, basolateral vesicles exhibited early overshoot of [3H]choline+ uptake unaffected by the presence or absence of external Na+ (541 +/- 53 vs 564 +/- 79 pmol/mg protein (NS)). High sensitivity to hemicholinium-3 was observed in the presence or absence of Na+. In the absence of inside-negative charge gradients, uptake was reduced 12-fold in the presence or absence of Na+, and external choline+ induced internal alkalization of acidified basolateral vesicles. Accumulative [3H]choline+ uptakes by apical vesicles in the presence or absence of inside-negative charge gradients and Na+ were insignificant. We conclude that predominant choline+ uptake by type II pneumocytes occurs at the basolateral membrane by Na+-independent, electrogenic choline+ conductance. The presence of electroneutral choline+/H+ exchange is suggested. Copyright 1998 Academic Press.

Inhibition of growth hormone receptor by Somavert reduces expression of GPER and prevents growth stimulation of triple-negative breast cancer by 17β-estradiol

PubMed Central

Girgert, Rainer; Emons, Günter; Gründker, Carsten

2018-01-01

Currently, conventional chemotherapy is the only treatment option for triple-negative breast cancers (TNBC) due to a lack of a unique target. In TNBC, a high expression of the membrane bound G protein-coupled estrogen receptor (GPER), correlates with a worse outcome. There is a potential for an association between growth hormone receptor (GHR) and GPER expression. To confirm this hypothesis, GHR was inhibited in TNBC cells with Somavert, and GPER expression levels, and the effect on signal transduction and proliferation induction in TNBC cells were analyzed. Proliferation of TNBC cells was measured using an Alamar-blue assay. Expression of GPER and activation of c-src and epidermal growth factor receptor (EGFR) by 17β-estradiol was analyzed by western blotting. Induction of c-fos, cyclin D1 and aromatase expression was determined by reverse transcription-semi-quantitative polymerase chain reaction. The expression of GPER was concentration- and time-dependently reduced by Somavert down to 46±7% (P<0.01) of the control. Furthermore, 17β-estradiol significantly increased the cell number of HCC1806 cells to 128±14% (P<0.05), and that of MDA-MB-453 cells to 115±3%. This increase in cell number was reduced to 103±11% in HCC1806 cells in which GPER expression was downregulated by Somavert, and to 102±3% in MDA-MB-453 cells. In addition, 17β-estradiol increased the activation of c-src in HCC1806 cells by 1.8-fold, and Somavert reduced p-src to 63% of control. In MDA-MB-453 cells src phosphorylation increased by 7-fold upon stimulation with estradiol, but after treatment with Somavert only a 4-fold increase was observed. Phosphorylation of EGFR was increased by 2.2-fold of control in HCC1806 cells by 17β-estradiol, and by 1.4-fold in MDA-MD-453 cells. Somavert completely prevented this activation. Induction of cyclin D1 and aromatase expression by 17β-estradiol was also prevented by Somavert. Somavert reduces GPER expression in triple negative breast cancer cells. Treatment with Somavert prevents induction of genes regulating proliferation by 17β-estradiol. Inhibition of GPER expression is a promising therapeutic intervention for TNBC. PMID:29805678

Inhibition of growth hormone receptor by Somavert reduces expression of GPER and prevents growth stimulation of triple-negative breast cancer by 17β-estradiol.

PubMed

Girgert, Rainer; Emons, Günter; Gründker, Carsten

2018-06-01

Currently, conventional chemotherapy is the only treatment option for triple-negative breast cancers (TNBC) due to a lack of a unique target. In TNBC, a high expression of the membrane bound G protein-coupled estrogen receptor (GPER), correlates with a worse outcome. There is a potential for an association between growth hormone receptor (GHR) and GPER expression. To confirm this hypothesis, GHR was inhibited in TNBC cells with Somavert, and GPER expression levels, and the effect on signal transduction and proliferation induction in TNBC cells were analyzed. Proliferation of TNBC cells was measured using an Alamar-blue assay. Expression of GPER and activation of c-src and epidermal growth factor receptor (EGFR) by 17β-estradiol was analyzed by western blotting. Induction of c-fos, cyclin D1 and aromatase expression was determined by reverse transcription-semi-quantitative polymerase chain reaction. The expression of GPER was concentration- and time-dependently reduced by Somavert down to 46±7% (P<0.01) of the control. Furthermore, 17β-estradiol significantly increased the cell number of HCC1806 cells to 128±14% (P<0.05), and that of MDA-MB-453 cells to 115±3%. This increase in cell number was reduced to 103±11% in HCC1806 cells in which GPER expression was downregulated by Somavert, and to 102±3% in MDA-MB-453 cells. In addition, 17β-estradiol increased the activation of c-src in HCC1806 cells by 1.8-fold, and Somavert reduced p-src to 63% of control. In MDA-MB-453 cells src phosphorylation increased by 7-fold upon stimulation with estradiol, but after treatment with Somavert only a 4-fold increase was observed. Phosphorylation of EGFR was increased by 2.2-fold of control in HCC1806 cells by 17β-estradiol, and by 1.4-fold in MDA-MD-453 cells. Somavert completely prevented this activation. Induction of cyclin D1 and aromatase expression by 17β-estradiol was also prevented by Somavert. Somavert reduces GPER expression in triple negative breast cancer cells. Treatment with Somavert prevents induction of genes regulating proliferation by 17β-estradiol. Inhibition of GPER expression is a promising therapeutic intervention for TNBC.

Cognitive deficits in Korean women treated with chemotherapy for breast cancer.

PubMed

Jung, Mi Sook; Cimprich, Bernadine

2014-01-01

Cognitive deficits have been reported as detrimental side effects in chemotherapy-treated breast cancer patients and survivors. Korean women treated for breast cancer may experience unrecognized cognitive deficits related to their treatment. However, no research has examined cognitive test performance in chemotherapy-treated Korean breast cancer survivors. The objectives of this study were 2-fold: (1) to examine differences in occurrence and severity of cognitive deficits in Korean women treated with adjuvant chemotherapy for breast cancer as compared with a control group of women without breast cancer and (2) to examine the relationship of selected demographic and cultural factors with cognitive test performance. Sixty-four Korean women, 32 women treated for localized breast cancer and 32 healthy controls, were enrolled. Breast cancer participants were assessed with established cognitive measures within 4 months after chemotherapy, and healthy controls, within 6 months after negative screening mammography. The breast cancer group showed a significantly higher occurrence and greater severity of cognitive deficits than controls did. Importantly, older age, less education, greater collectivist tendency, and greater childrearing burden were reliably associated with poorer attention and working memory test performance. Cognitive deficits were found in chemotherapy-treated Korean women with moderate to large effect sizes compared with controls. Cultural characteristics contributed to worse cognitive performance. Healthcare providers should recognize that Korean women may be highly vulnerable to cognitive deficits. Cultural factors also need to be considered when assessing cognitive function and designing therapeutic interventions to counteract negative cognitive outcomes.

Co-evolutionary constraints of globular proteins correlate with their folding rates.

PubMed

Mallik, Saurav; Kundu, Sudip

2015-08-04

Folding rates (lnkf) of globular proteins correlate with their biophysical properties, but relationship between lnkf and patterns of sequence evolution remains elusive. We introduce 'relative co-evolution order' (rCEO) as length-normalized average primary chain separation of co-evolving pairs (CEPs), which negatively correlates with lnkf. In addition to pairs in native 3D contact, indirectly connected and structurally remote CEPs probably also play critical roles in protein folding. Correlation between rCEO and lnkf is stronger in multi-state proteins than two-state proteins, contrasting the case of contact order (co), where stronger correlation is found in two-state proteins. Finally, rCEO, co and lnkf are fitted into a 3D linear correlation. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Clostridium difficile Testing in the Clinical Laboratory by Use of Multiple Testing Algorithms ▿

PubMed Central

Novak-Weekley, Susan M.; Marlowe, Elizabeth M.; Miller, John M.; Cumpio, Joven; Nomura, Jim H.; Vance, Paula H.; Weissfeld, Alice

2010-01-01

The incidence of Clostridium difficile infection (CDI) has risen almost 3-fold in the United States over the past decade, emphasizing the need for rapid and accurate tests for CDI. The Cepheid Xpert C. difficile assay is an integrated, closed, nucleic acid amplification system that automates sample preparation and real-time PCR detection of the toxin B gene (tcdB). A total of 432 stool specimens from symptomatic patients were tested by a glutamate dehydrogenase (GDH) assay, a toxin A and B enzyme immunoassay (EIA), the Xpert C. difficile assay, and a cell culture cytotoxicity neutralization assay (CCCN). The results of these methods, used individually and in combination, were compared to those of toxigenic culture. Results for the Xpert C. difficile assay alone showed a sensitivity, specificity, positive predictive value, and negative predictive value (NPV) of 94.4, 96.3, 84.0, and 98.8%, while the EIA alone gave corresponding values of 58.3, 94.7, 68.9, and 91.9%, respectively. An algorithm using the GDH assay and the EIA (plus the CCCN if the EIA was negative) showed corresponding values of 83.1, 96.7, 83.1, and 96.1%. The Xpert C. difficile assay was statistically superior to the EIA (P, <0.001 by Fisher's exact test) and to the GDH-EIA-CCCN algorithm (P, 0.0363). Combining the GDH and Xpert C. difficile assays lowered both the sensitivity and the NPV of the Xpert assay. The GDH-EIA-CCCN procedure required, on average, 2 days to complete testing on GDH-positive results, while testing by the Xpert C. difficile assay was completed, on average, in less than 1 h. Xpert C. difficile testing yielded the highest sensitivity and NPV, in the least amount of time, of the individual- and multiple-test algorithms evaluated in this study. PMID:20071552

Prediction of hypotension during spinal anesthesia for elective cesarean section by altered heart rate variability induced by postural change.

PubMed

Sakata, K; Yoshimura, N; Tanabe, K; Kito, K; Nagase, K; Iida, H

2017-02-01

Maternal hypotension is a common complication during cesarean section performed under spinal anesthesia. Changes in maternal heart rate with postural changes or values of heart rate variability have been reported to predict hypotension. Therefore, we hypothesized that changes in heart rate variability due to postural changes can predict hypotension. A total of 45 women scheduled to undergo cesarean section under spinal anesthesia were enrolled. A postural change test was performed the day before cesarean section. The ratio of the power of low and high frequency components contributing to heart rate variability was assessed in the order of supine, left lateral, and supine. Patients who exhibited a ⩾two-fold increase in the low-to-high frequency ratio when moving to supine from the lateral position were assigned to the postural change test-positive group. According to the findings of the postural change test, patients were assigned to the positive (n=22) and negative (n=23) groups, respectively. Hypotension occurred in 35/45 patients, of whom 21 (60%) were in the positive group and 14 (40%) were in the negative group. The incidence of hypotension was greater in the positive group (P<0.01). The total dose of ephedrine was greater in the positive group (15±11 vs. 7±7mg, P=0.005). The area under the receiver operating characteristic curve was 0.76 for the postural change test as a predictor of hypotension. The postural change test with heart rate variability analysis may be used to predict the risk of hypotension during spinal anesthesia for cesarean section. Copyright © 2016 Elsevier Ltd. All rights reserved.

The X-38 V-201 Fin Fold Actuation Mechanism

NASA Technical Reports Server (NTRS)

Lupo, Christian; Robertson, Brandan; Gafka, George

2004-01-01

The X-38 Vehicle 201 (V-201) is a space flight prototype lifting body vehicle that was designed to launch to orbit in the Space Shuttle orbiter payload bay. Although the project was cancelled in May 2003, many of the systems were nearly complete. This paper will describe the fin folding actuation mechanism flight subsystems and development units as well as lessons learned in the design, assembly, development testing, and qualification testing. The two vertical tail fins must be stowed (folded inboard) to allow the orbiter payload bay doors to close. The fin folding actuation mechanism is a remotely or extravehicular activity (EVA) actuated single fault tolerant system consisting of seven subsystems capable of repeatedly deploying or stowing the fins.

Engineered fluorescent proteins illuminate the bacterial periplasm

PubMed Central

Dammeyer, Thorben; Tinnefeld, Philip

2012-01-01

The bacterial periplasm is of special interest whenever cell factories are designed and engineered. Recombinantely produced proteins are targeted to the periplasmic space of Gram negative bacteria to take advantage of the authentic N-termini, disulfide bridge formation and easy accessibility for purification with less contaminating cellular proteins. The oxidizing environment of the periplasm promotes disulfide bridge formation - a prerequisite for proper folding of many proteins into their active conformation. In contrast, the most popular reporter protein in all of cell biology, Green Fluorescent Protein (GFP), remains inactive if translocated to the periplasmic space prior to folding. Here, the self-catalyzed chromophore maturation is blocked by formation of covalent oligomers via interchain disulfide bonds in the oxidizing environment. However, different protein engineering approaches addressing folding and stability of GFP resulted in improved proteins with enhanced folding properties. Recent studies describe GFP variants that are not only active if translocated in their folded form via the twin-arginine translocation (Tat) pathway, but actively fold in the periplasm following general secretory pathway (Sec) and signal recognition particle (SRP) mediated secretion. This mini-review highlights the progress that enables new insights into bacterial export and periplasmic protein organization, as well as new biotechnological applications combining the advantages of the periplasmic production and the Aequorea-based fluorescent reporter proteins. PMID:24688673

Last stand of single small field inflation

NASA Astrophysics Data System (ADS)

Bramante, Joseph; Lehman, Landon; Martin, Adam; Downes, Sean

2014-07-01

By incorporating both the tensor-to-scalar ratio and the measured value of the spectral index, we set a bound on solo small field inflation of Δϕ/mPl≥1.00√r/0.1 . Unlike previous bounds which require monotonic ɛV, |ηV|<1, and 60 e-folds of inflation, the bound remains valid for nonmonotonic ɛV, |ηV|≳1, and for inflation which occurs only over the eight e-folds which have been observed on the cosmic microwave background. The negative value of the spectral index over the observed eight e-folds is what makes the bound strong; we illustrate this by surveying single field models and finding that for r ≳0.1 and eight e-folds of inflation, there is no simple potential which reproduces observed cosmic microwave background perturbations and remains sub-Planckian. Models that are sub-Planckian after eight e-folds must be patched together with a second epoch of inflation that fills out the remaining ˜50 e-folds. This second, post-cosmic microwave background epoch is characterized by extremely small ɛV and therefore an increasing scalar power spectrum. Using the fact that large power can overabundantly produce primordial black holes, we bound the maximum energy level of the second phase of inflation.

Common diagnoses and treatments in professional voice users.

PubMed

Franco, Ramon A; Andrus, Jennifer G

2007-10-01

Common problems among all patients seen by the laryngologist are also common among professional voice users. These include laryngopharyngeal reflux, muscle tension dysphonia, fibrovascular vocal fold lesions (eg, nodules and polyps), cysts, vocal fold scarring, changes in vocal fold mobility, and age-related changes. Microvascular lesions and their associated sequelae of vocal fold hemorrhage and laryngitis due to voice overuse are more common among professional voice users. Much more common among professional voice users is the negative impact that voice problems have on their ability to work, on their overall sense of well-being, and sometimes on their very sense of self. This article reviews the diagnosis and treatment options for these and other problems among professional voice users, describing the relevant roles of medical treatment, voice therapy, and surgery. The common scenario of multiple concomitant entities contributing to a symptom complex is underscored. Emphasis is placed on gaining insight into the "whole" patient so that individualized management plans can be developed. Videos of select diagnoses accompany this content online.

Free-energy landscape of a hyperstable RNA tetraloop

PubMed Central

Miner, Jacob C.; Chen, Alan A.; García, Angel E.

2016-01-01

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif. PMID:27233937

Automation of the in vitro micronucleus and chromosome aberration assay for the assessment of the genotoxicity of the particulate and gas-vapor phase of cigarette smoke.

PubMed

Roemer, Ewald; Zenzen, Volker; Conroy, Lynda L; Luedemann, Kathrin; Dempsey, Ruth; Schunck, Christian; Sticken, Edgar Trelles

2015-01-01

Total particulate matter (TPM) and the gas-vapor phase (GVP) of mainstream smoke from the Reference Cigarette 3R4F were assayed in the cytokinesis-block in vitro micronucleus (MN) assay and the in vitro chromosome aberration (CA) assay, both using V79-4 Chinese hamster lung fibroblasts exposed for up to 24 h. The Metafer image analysis platform was adapted resulting in a fully automated evaluation system of the MN assay for the detection, identification and reporting of cells with micronuclei together with the determination of the cytokinesis-block proliferation index (CBPI) to quantify the treatment-related cytotoxicity. In the CA assay, the same platform was used to identify, map and retrieve metaphases for a subsequent CA evaluation by a trained evaluator. In both the assays, TPM and GVP provoked a significant genotoxic effect: up to 6-fold more micronucleated target cells than in the negative control and up to 10-fold increases in aberrant metaphases. Data variability was lower in the automated version of the MN assay than in the non-automated. It can be estimated that two test substances that differ in their genotoxicity by approximately 30% can statistically be distinguished in the automated MN and CA assays. Time savings, based on man hours, due to the automation were approximately 70% in the MN and 25% in the CA assays. The turn-around time of the evaluation phase could be shortened by 35 and 50%, respectively. Although only cigarette smoke-derived test material has been applied, the technical improvements should be of value for other test substances.

Electrodynamic pressure modulation of protein stability in cosolvents.

PubMed

Damodaran, Srinivasan

2013-11-19

Cosolvents affect structural stability of proteins in aqueous solutions. A clear understanding of the mechanism by which cosolvents impact protein stability is critical to understanding protein folding in a biological milieu. In this study, we investigated the Lifshitz-van der Waals dispersion interaction of seven different solutes with nine globular proteins and report that in an aqueous medium the structure-stabilizing solutes exert a positive electrodynamic pressure, whereas the structure-destabilizing solutes exert a negative electrodynamic pressure on the proteins. The net increase in the thermal denaturation temperature (ΔTd) of a protein in 1 M solution of various solutes was linearly related to the electrodynamic pressure (PvdW) between the solutes and the protein. The slope of the PvdW versus ΔTd plots was protein-dependent. However, we find a positive linear relationship (r(2) = 0.79) between the slope (i.e., d(ΔTd)/dPvdW) and the adiabatic compressibility (βs) of the proteins. Together, these results clearly indicate that the Lifshitz's dispersion forces are inextricably involved in solute-induced stabilization/destabilization of globular proteins. The positive and/or negative electrodynamic pressure generated by the solute-protein interaction across the water medium seems to be the fundamental mechanism by which solutes affect protein stability. This is at variance with the existing preferential hydration concept. The implication of these results is significant in the sense that, in addition to the hydrophobic effect that drives protein folding, the electrodynamic forces between the proteins and solutes in the biological milieu also might play a role in the folding process as well as in the stability of the folded state.

Differential cytokine expression in skin graft healing in inducible nitric oxide synthase knockout mice.

PubMed

Most, D; Efron, D T; Shi, H P; Tantry, U S; Barbul, A

2001-10-01

Inducible nitric oxide synthase (iNOS) and its product, nitric oxide, have been shown to play important roles in wound biology. The present study was performed to investigate the role of iNOS in modulating the cytokine cascade during the complex process of skin graft wound healing.Fifteen iNOS-knockout mice and 15 wild-type C57BL/6J mice were subjected to autogenous 1-cm2 intrascapular full-thickness skin grafts. Three animals in each group were killed on postoperative days 3, 5, 7, 10, and 14. Specimens were then analyzed using nonisotopic in situ hybridization versus mRNA of tumor growth factor-beta1, vascular endothelial growth factor, iNOS, endothelial nitric oxide synthase (eNOS), tumor necrosis factor-alpha, and basic fibroblast growth factor, as well as positive and negative control probes. Positive cells in both grafts and wound beds were counted using a Leica microgrid. Scar thickness was measured with a Leica micrometer. Data were analyzed using the unpaired Student's t test. Expression of iNOS was 2- to 4-fold higher in knockout mice than in wild-type mice on postoperative days 5, 7, and 14. Expression of eNOS was 2- to 2.5-fold higher in knockout mice than in wild-type mice on postoperative days 5 and 7. Tumor necrosis factor-alpha expression was 2- to 7-fold higher in knockout mice than in wild-type mice on all postoperative days. In contrast, expression levels of angiogenic/fibrogenic cytokines (vascular endothelial growth factor, basis fibroblast growth factor, and tumor growth factor-beta1) were 2.5- to 4-fold higher in wild-type mice than in knockout mice. Scars were 1.5- to 2.5-fold thicker in knockout mice than in wild-type mice at all time points. All of the above results represent statistically significant differences (p < 0.05). Significantly different patterns of cytokine expression were seen in knockout and wild-type mice. Although the scar layer was thicker in knockout mice, it showed much greater infiltration with inflammatory cells. These data further delineate the modulatory effect of iNOS and nitric oxide in healing skin grafts.

Insertional inactivation of oprD in carbapenem-resistant Pseudomonas aeruginosa strains isolated from burn patients in Tehran, Iran.

PubMed

Shariati, A; Azimi, T; Ardebili, A; Chirani, A S; Bahramian, A; Pormohammad, A; Sadredinamin, M; Erfanimanesh, S; Bostanghadiri, N; Shams, S; Hashemi, A

2018-01-01

In this study, we report the insertion sequence IS Ppu 21 in the opr D porin gene of carbapenem-resistant Pseudomonas aeruginosa isolates from burn patients in Tehran, Iran. Antibiotic susceptibility tests for P. aeruginosa isolates were determined. Production of metallo-β-lactamases (MBLs) and carbapenemase was evaluated and the β-lactamase-encoding and aminoglycoside-modifying enzyme genes were investigated by PCR and sequencing methods. The mRNA transcription level of oprD and mex efflux pump genes were evaluated by real-time PCR. The outer membrane protein profile was determined by SDS-PAGE. The genetic relationship between the P. aeruginosa isolates was assessed by random amplified polymorphic DNA PCR. In all, 10.52% (10/95) of clinical isolates of P. aeruginosa harboured the IS Ppu 21 insertion element in the opr D gene. The extended-spectrum β-lactamase-encoding gene in IS Ppu 21-carrying isolates was bla TEM . PCR assays targeting MBL and carbapenemase-encoding genes were also negative in all ten isolates. The rmt A, aad A, aad B and arm A genes were positive in all IS Ppu 21 harbouring isolates. The relative expression levels of the mex X, mex B, mex T and mex D genes in ten isolates ranged from 0.1- to 1.4-fold, 1.1- to 3.68-fold, 0.3- to 8.22-fold and 1.7- to 35.17-fold, respectively. The relative expression levels of the oprD in ten isolates ranged from 0.57- to 35.01-fold, which was much higher than those in the control strain P. aeruginosa PAO1. Evaluation of the outer membrane protein by SDS-PAGE suggested that opr D was produced at very low levels by all isolates. Using random amplified polymorphic DNA PCR genotyping, eight of the ten isolates containing IS Ppu 21 were shown to be clonally related. The present study describes a novel molecular mechanism, IS Ppu 21 insertion of the opr D gene, associated with carbapenem resistance in clinical P. aeruginosa isolates.

GroEL actively stimulates folding of the endogenous substrate protein PepQ.

PubMed

Weaver, Jeremy; Jiang, Mengqiu; Roth, Andrew; Puchalla, Jason; Zhang, Junjie; Rye, Hays S

2017-06-30

Many essential proteins cannot fold without help from chaperonins, like the GroELS system of Escherichia coli. How chaperonins accelerate protein folding remains controversial. Here we test key predictions of both passive and active models of GroELS-stimulated folding, using the endogenous E. coli metalloprotease PepQ. While GroELS increases the folding rate of PepQ by over 15-fold, we demonstrate that slow spontaneous folding of PepQ is not caused by aggregation. Fluorescence measurements suggest that, when folding inside the GroEL-GroES cavity, PepQ populates conformations not observed during spontaneous folding in free solution. Using cryo-electron microscopy, we show that the GroEL C-termini make physical contact with the PepQ folding intermediate and help retain it deep within the GroEL cavity, resulting in reduced compactness of the PepQ monomer. Our findings strongly support an active model of chaperonin-mediated protein folding, where partial unfolding of misfolded intermediates plays a key role.

Active chiral control of GHz acoustic whispering-gallery modes

NASA Astrophysics Data System (ADS)

Mezil, Sylvain; Fujita, Kentaro; Otsuka, Paul H.; Tomoda, Motonobu; Clark, Matt; Wright, Oliver B.; Matsuda, Osamu

2017-10-01

We selectively generate chiral surface-acoustic whispering-gallery modes in the gigahertz range on a microscopic disk by means of an ultrafast time-domain technique incorporating a spatial light modulator. Active chiral control is achieved by making use of an optical pump spatial profile in the form of a semicircular arc, positioned on the sample to break the symmetry of clockwise- and counterclockwise-propagating modes. Spatiotemporal Fourier transforms of the interferometrically monitored two-dimensional acoustic fields measured to micron resolution allow individual chiral modes and their azimuthal mode order, both positive and negative, to be distinguished. In particular, for modes with 15-fold rotational symmetry, we demonstrate ultrafast chiral control of surface acoustic waves in a micro-acoustic system with picosecond temporal resolution. Applications include nondestructive testing and surface acoustic wave devices.

Incidence of Carbapenem-Resistant Gram Negatives in Italian Transplant Recipients: A Nationwide Surveillance Study

PubMed Central

Lanini, Simone; Costa, Alessandro Nanni; Puro, Vincenzo; Procaccio, Francesco; Grossi, Paolo Antonio; Vespasiano, Francesca; Ricci, Andrea; Vesconi, Sergio; Ison, Michael G.; Carmeli, Yehuda; Ippolito, Giuseppe

2015-01-01

Background Bacterial infections remain a challenge to solid organ transplantation. Due to the alarming spread of carbapenem-resistant gram negative bacteria, these organisms have been frequently recognized as cause of severe infections in solid organ transplant recipients. Methods and Findings Between 15 May and 30 September 2012 we enrolled 887 solid organ transplant recipients in Italy with the aim to describe the epidemiology of gram negative bacteria spreading, to explore potential risk factors and to assess the effect of early isolation of gram negative bacteria on recipients’ mortality during the first 90 days after transplantation. During the study period 185 clinical isolates of gram negative bacteria were reported, for an incidence of 2.39 per 1000 recipient-days. Positive cultures for gram negative bacteria occurred early after transplantation (median time 26 days; incidence rate 4.33, 1.67 and 1.14 per 1,000 recipient-days in the first, second and third month after SOT, respectively). Forty-nine of these clinical isolates were due to carbapenem-resistant gram negative bacteria (26.5%; incidence 0.63 per 1000 recipient-days). Carbapenems resistance was particularly frequent among Klebsiella spp. isolates (49.1%). Recipients with longer hospital stay and those who received either heart or lung graft were at the highest risk of testing positive for any gram negative bacteria. Moreover recipients with longer hospital stay, lung recipients and those admitted to hospital for more than 48h before transplantation had the highest probability to have culture(s) positive for carbapenem-resistant gram negative bacteria. Forty-four organ recipients died (0.57 per 1000 recipient-days) during the study period. Recipients with at least one positive culture for carbapenem-resistant gram negative bacteria had a 10.23-fold higher mortality rate than those who did not. Conclusion The isolation of gram-negative bacteria is most frequent among recipient with hospital stays >48 hours prior to transplant and in those receiving either heart or lung transplants. Carbapenem-resistant gram negative isolates are associated with significant mortality. PMID:25835018

Appendicectomies in Albanians in Greece: outcomes in a highly mobile immigrant patient population

PubMed Central

2001-01-01

Background Albanian immigrants in Greece comprise a highly mobile population with unknown health care profile. We aimed to assess whether these immigrants were more or less likely to undergo laparotomy for suspected appendicitis with negative findings (negative appendicectomy), by performing a controlled study with individual (1:4) matching. We used data from 6 hospitals in the Greek prefecture of Epirus that is bordering Albania. Results Among a total of 2027 non-incidental appendicectomies for suspected appendicitis performed in 1994-1999, 30 patients with Albanian names were matched (for age, sex, time of operation and hospital) to 120 patients with Greek names. The odds for a negative appendicectomy were 3.4-fold higher (95% confidence interval [CI], 1.24-9.31, p = 0.02) in Albanian immigrants than in matched Greek-name subjects. The difference was most prominent in men (odds ratio 20.0, 95% CI, 1.41-285, p = 0.02) while it was not formally significant in women (odds ratio 1.56, 95% CI, 0.44-5.48). The odds for perforation were 1.25-fold higher in Albanian-name immigrants than in Greek-name patients (95% CI 0.44- 3.57). Conclusions Albanian immigrants in Greece are at high risk for negative appendicectomies. Socioeconomic, cultural and language parameters underlying health care inequalities in highly mobile immigrant populations need better study. PMID:11472640

Expression, purification and in vitro refolding of the recombinant truncated Saposin-like protein 2 antigen for development of diagnosis of human fascioliasis.

PubMed

Mirzadeh, Abolfazl; Valadkhani, Zarrintaj; Yoosefy, Asiyeh; Babaie, Jalal; Golkar, Majid; Esmaeili Rastaghi, Ahmad Reza; Kazemi-Rad, Elham; Ashrafi, Keyhan

2017-07-01

Early diagnosis of fascioliasis is critical in prevention of injury to the liver and bile ducts. Saposin-like protein (FhSAP-2) is probably the most ideal antigen of Fasciola hepatica for development of ELISA kits. SAP-2 has a conserved tertiary structure containing three disulfide bonds and conformational epitopes. Therefore, antigenicity of SAP-2 is greatly depends on disulfide bond formation and proper folding. We produced the recombinant truncated SAP-2 (rtSAP-2) in the SHuffle ® T7 and Rosetta strain of Escherichia coli, in soluble and insoluble forms, respectively and purified by immobilized metal affinity chromatography (IMAC). The refolding process of denatured rtSAP-2 was performed using dialysis and dilution methods in the presence of chemical additives, along with reduced/oxidized glutathione (in vitro). Physicochemical studies, including non-reducing gel electrophoresis, Ellman's assay, Western blotting and ELISA showed the most antigenicity and likely correct folding of rtSAP-2, which was obtained by dialysis method. An IgG ELISA test was developed using rtSAP-2 refolded by dialysis and compared with excretory/secretory products of parasite with 52 positive fascioliasis samples, 79 other parasitic samples and 70 negative controls samples. The results exhibited 100% sensitivity and 98% specificity for rtSAP-2, also, 100% and 95.3% for excretory/secretory (E/S) antigen, respectively. In conclusion, it is suggested that rtSAP-2 with the correct folding could be used as a candidate antigen for detection of human fascioliasis. Copyright © 2017 Elsevier B.V. All rights reserved.

Adapted to Roar: Functional Morphology of Tiger and Lion Vocal Folds

PubMed Central

Klemuk, Sarah A.; Riede, Tobias; Walsh, Edward J.; Titze, Ingo R.

2011-01-01

Vocal production requires active control of the respiratory system, larynx and vocal tract. Vocal sounds in mammals are produced by flow-induced vocal fold oscillation, which requires vocal fold tissue that can sustain the mechanical stress during phonation. Our understanding of the relationship between morphology and vocal function of vocal folds is very limited. Here we tested the hypothesis that vocal fold morphology and viscoelastic properties allow a prediction of fundamental frequency range of sounds that can be produced, and minimal lung pressure necessary to initiate phonation. We tested the hypothesis in lions and tigers who are well-known for producing low frequency and very loud roaring sounds that expose vocal folds to large stresses. In histological sections, we found that the Panthera vocal fold lamina propria consists of a lateral region with adipocytes embedded in a network of collagen and elastin fibers and hyaluronan. There is also a medial region that contains only fibrous proteins and hyaluronan but no fat cells. Young's moduli range between 10 and 2000 kPa for strains up to 60%. Shear moduli ranged between 0.1 and 2 kPa and differed between layers. Biomechanical and morphological data were used to make predictions of fundamental frequency and subglottal pressure ranges. Such predictions agreed well with measurements from natural phonation and phonation of excised larynges, respectively. We assume that fat shapes Panthera vocal folds into an advantageous geometry for phonation and it protects vocal folds. Its primary function is probably not to increase vocal fold mass as suggested previously. The large square-shaped Panthera vocal fold eases phonation onset and thereby extends the dynamic range of the voice. PMID:22073246

Multicenter evaluation of the new Abbott RealTime assays for quantitative detection of human immunodeficiency virus type 1 and hepatitis C virus RNA.

PubMed

Schutten, M; Peters, D; Back, N K T; Beld, M; Beuselinck, K; Foulongne, V; Geretti, A-M; Pandiani, L; Tiemann, C; Niesters, H G M

2007-06-01

The analytical performances of the new Abbott RealTime hepatitis C virus (HCV) and human immunodeficiency virus type 1 viral load assays were compared at nine laboratories with different competitor assays. These included the Abbott LcX, Bayer Versant bDNA, Roche COBAS Amplicor, and Roche COBAS TaqMan assays. Two different protocols used during the testing period with and without a pre-m1000 RNA isolation spin were compared. The difference proved to be nonsignificant. A uracil-N-glycosylase (UNG) contamination control option in the HCV test for previous Roche COBAS Amplicor users was evaluated. It proved to decrease amplicon carryover by 100-fold independent of the amplicon input concentration. The protocol including UNG proved to overcome problems with false-positive negative controls. Comparison with other assays revealed only minor differences. The largest difference was observed between the Abbott HCV RealTime assay and the Roche COBAS Amplicor HCV Monitor version 2.0 assay.

Sulfaguanidine cocrystals: Synthesis, structural characterization and their antibacterial and hemolytic analysis.

PubMed

Abidi, Syed Sibte Asghar; Azim, Yasser; Khan, Shahper Nazeer; Khan, Asad U

2018-02-05

Sulfaguanidine (SG), belongs to the class of sulfonamide drug used as an effective antibiotic. In the present work, using crystal engineering approach two novel cocrystals of SG were synthesized (SG-TBA and SG-PT) with thiobarbutaric acid (TBA) and 1,10-phenanthroline (PT), characterized by solid state techniques viz., powder X-ray diffraction (PXRD), fourier transform infrared spectroscopy (FT-IR), differential scanning calorimetry (DSC) and the crystal structures were determined by single crystal X-ray diffraction studies. A comparative antibacterial activity and hemolytic potential was done on SG drug, coformers and their cocrystals. The tested cocrystals formulations showed almost two fold higher antibacterial activity against the tested strains of bacteria Gram-positive bacteria (S. mutans and E. faecalis) and Gram-negative bacteria (E. coli, K. pneumonia and E. clocae) over SG alone and their coformers. Cocrystal SG-TBA showed better antibacterial activity and reduced hemolysis, thereby, reduced cytotoxicity than SG-PT. Copyright © 2017 Elsevier B.V. All rights reserved.

The behaviour of entrainment defects formed in commercial purity Mg alloy cast under a cover gas of SF6

NASA Astrophysics Data System (ADS)

Li, T.; Griffiths, W. D.

2016-03-01

In the casting of light alloys, the oxidised film on the melt surface can be folded due to surface turbulence, thus forming entrainment defects that have a significant negative effect on the mechanical properties of castings. Previous researchers reported that the surface film of Mg alloys formed in an atmosphere containing SF6 had a complicated structure composed of MgO and MgF2. The work reported here aims to investigate the behaviour of entrainment defects formed in magnesium alloys protected by SF6-containing atmospheres. Tensile test bars of commercial purity Mg were cast in an unsealed environment under a cover gas of pure SF6. 34Scanning electron microscopy (SEM) of the fracture surface of the test bars indicated entrainment defects that consisted of symmetrical films containing MgO, but also sulphur and fluorine. The results of these examinations of the symmetrical films were used to infer the potential formation and development of entrainment defects in commercial purity Mg alloy.

Sex differences in association of race performance, skin-fold thicknesses, and training variables for recreational half-marathon runners.

PubMed

Knechtle, Beat; Knechtle, Patrizia; Rosemann, Thomas; Senn, Oliver

2010-12-01

The purpose of this study was to investigate the association between selected skin-fold thicknesses and training variables with a half-marathon race time, for both male and female recreational runners, using bi- and multivariate analysis. In 52 men, two skin-fold thicknesses (abdominal and calf) were significantly and positively correlated with race time; whereas in 15 women, five (pectoral, mid-axilla, subscapular, abdominal, and suprailiac) showed positive and significant relations with total race time. In men, the mean weekly running distance, minimum distance run per week, maximum distance run per week, mean weekly hours of running, number of running training sessions per week, and mean speed of the training sessions were significantly and negatively related to total race time, but not in women. Interaction analyses suggested that race time was more strongly associated with anthropometry in women than men. Race time for the women was independently associated with the sum of eight skin-folds; but for the men, only the mean speed during training sessions was independently associated. Skin-fold thicknesses and training variables in these groups were differently related to race time according to their sex.

Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and cryoEM modeling

PubMed Central

Rizzo, Alessandro A.; Suhanovsky, Margaret M.; Baker, Matthew L.; Fraser, LaTasha C.R.; Jones, Lisa M.; Rempel, Don L.; Gross, Michael L.; Chiu, Wah; Alexandrescu, Andrei T.; Teschke, Carolyn M.

2014-01-01

SUMMARY Some capsid proteins built on the ubiquitous HK97-fold have accessory domains that impart specific functions. Bacteriophage P22 coat protein has a unique inserted I-domain. Two prior I-domain models from sub-nanometer cryoEM reconstructions differed substantially. Therefore, the NMR structure of the I-domain was determined, which also was used to improve cryoEM models of coat protein. The I-domain has an anti-parallel 6-stranded β-barrel fold, previously not observed in HK97-fold accessory domains. The D-loop, which is dynamic both in the isolated I-domain and intact monomeric coat protein, forms stabilizing salt bridges between adjacent capsomers in procapsids. A newly described S-loop is important for capsid size determination, likely through intra-subunit interactions. Ten of eighteen coat protein temperature-sensitive-folding substitutions are in the I-domain, indicating its importance in folding and stability. Several are found on a positively charged face of the β-barrel that anchors the I-domain to a negatively charged surface of the coat protein HK97-core. PMID:24836025

Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and CryoEM modeling.

PubMed

Rizzo, Alessandro A; Suhanovsky, Margaret M; Baker, Matthew L; Fraser, LaTasha C R; Jones, Lisa M; Rempel, Don L; Gross, Michael L; Chiu, Wah; Alexandrescu, Andrei T; Teschke, Carolyn M

2014-06-10

Some capsid proteins built on the ubiquitous HK97-fold have accessory domains imparting specific functions. Bacteriophage P22 coat protein has a unique insertion domain (I-domain). Two prior I-domain models from subnanometer cryoelectron microscopy (cryoEM) reconstructions differed substantially. Therefore, the I-domain's nuclear magnetic resonance structure was determined and also used to improve cryoEM models of coat protein. The I-domain has an antiparallel six-stranded β-barrel fold, not previously observed in HK97-fold accessory domains. The D-loop, which is dynamic in the isolated I-domain and intact monomeric coat protein, forms stabilizing salt bridges between adjacent capsomers in procapsids. The S-loop is important for capsid size determination, likely through intrasubunit interactions. Ten of 18 coat protein temperature-sensitive-folding substitutions are in the I-domain, indicating its importance in folding and stability. Several are found on a positively charged face of the β-barrel that anchors the I-domain to a negatively charged surface of the coat protein HK97-core. Copyright © 2014 Elsevier Ltd. All rights reserved.

Hydrogen bonds are a primary driving force for de novo protein folding

DOE PAGES

Lee, Schuyler; Wang, Chao; Liu, Haolin; ...

2017-11-10

The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1–153; AID 153 ), an optimized in vitro folding procedure was derived to obtain large amounts of AID 153 , which led to crystals with good quality and to final structural determination. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent. The difference in the distribution of cis and trans configurations of proline residues in the proteinmore » after complete denaturation is a major determining factor of the final yield. A point mutation of one of four proline residues to an asparagine led to a near-doubling of the yield of refolded protein after complete denaturation. It was concluded that the driving force behind protein folding could not overcome the cis -to- trans proline isomerization, or vice versa , during the protein-folding process. Furthermore, it was found that successful refolding of proteins optimally occurs at high pH values, which may mimic protein folding in vivo . It was found that high pH values could induce the polarization of peptide bonds, which may trigger the formation of protein secondary structures through hydrogen bonds. It is proposed that a hydrophobic environment coupled with negative charges is essential for protein folding. Combined with our earlier discoveries on protein-unfolding mechanisms, it is proposed that hydrogen bonds are a primary driving force for de novo protein folding.« less

Hydrogen bonds are a primary driving force for de novo protein folding

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

Lee, Schuyler; Wang, Chao; Liu, Haolin

The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1–153; AID 153 ), an optimized in vitro folding procedure was derived to obtain large amounts of AID 153 , which led to crystals with good quality and to final structural determination. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent. The difference in the distribution of cis and trans configurations of proline residues in the proteinmore » after complete denaturation is a major determining factor of the final yield. A point mutation of one of four proline residues to an asparagine led to a near-doubling of the yield of refolded protein after complete denaturation. It was concluded that the driving force behind protein folding could not overcome the cis -to- trans proline isomerization, or vice versa , during the protein-folding process. Furthermore, it was found that successful refolding of proteins optimally occurs at high pH values, which may mimic protein folding in vivo . It was found that high pH values could induce the polarization of peptide bonds, which may trigger the formation of protein secondary structures through hydrogen bonds. It is proposed that a hydrophobic environment coupled with negative charges is essential for protein folding. Combined with our earlier discoveries on protein-unfolding mechanisms, it is proposed that hydrogen bonds are a primary driving force for de novo protein folding.« less

Dynamics of thin-skinned fold and thrust belts with a tilted detachment

NASA Astrophysics Data System (ADS)

Fernandez, Naiara; Kaus, Boris J. P.; Epard, Jean-Luc

2014-05-01

The formation of the Jura fold and thrust belt is linked to the Alpine orogeny. However, it is still a matter of debate why the Jura was formed tens of kilometres far away from the active deformation front while the Molasse basin that lies in between remained mostly undeformed. Progressive thickening of the Molasse basin due to its infill with sediments, and the existence of a tilted potential detachment level at the Triassic evaporitic units, have been pushed forward as the main causes for the detachment of the Molasse basin and the consequent jump of the deformation front from the Alpine front to the position of the Jura at around 22 Ma or later (e.g Willett and Schlunegger, 2010). In order to better understand the dynamics of a thin-skinned fold and thrust belt with a tilted detachment we have performed systematic forward numerical simulations with the 2D thermo-mechanical finite element code MILAMIN_VEP. The modelled setup consists of a tilted detachment, overlain by a sedimentary cover of constant thickness and a wedge shaped basin infill that makes the initial surface slope of the system to be zero. In this study we have tested the importance of the following factors in the dynamics of such a fold and thrust belt evolution: 1) the applied boundary conditions 2) the angle of a uniformly tilted detachment 3) the end displacement of a curved detachment with a flexural foreland basin profile. The implications of the studied factors are discussed for the case of the Jura-Molasse system. Acknowledgements Funding was provided by the European Research Council under the European Community's Seventh Framework program (FP7/2007-2013) ERC Grant agreement #258830. References Willett, S.D. and Schlunegger, F. 2010, The last phase of deposition in the Swiss Molasse Basin: from foredeep to negative-alpha basin. Basin Research 22, 623-639, doi: 10.1111/j.1365-2117.2009.00435.x

Alteration of Electrostatic Surface Potential Enhances Affinity and Tumor Killing Properties of Anti-ganglioside GD2 Monoclonal Antibody hu3F8.

PubMed

Zhao, Qi; Ahmed, Mahiuddin; Guo, Hong-fen; Cheung, Irene Y; Cheung, Nai-Kong V

2015-05-22

Ganglioside GD2 is highly expressed on neuroectodermal tumors and an attractive therapeutic target for antibodies that have already shown some clinical efficacy. To further improve the current antibodies, which have modest affinity, we sought to improve affinity by using a combined method of random mutagenesis and in silico assisted design to affinity-mature the anti-GD2 monoclonal antibody hu3F8. Using yeast display, mutants in the Fv with enhanced binding over the parental clone were FACS-sorted and cloned. In silico modeling identified the minimal key interacting residues involved in the important charged interactions with the sialic acid groups of GD2. Two mutations, D32H (L-CDR1) and E1K (L-FR1) altered the electrostatic surface potential of the antigen binding site, allowing for an increase in positive charge to enhance the interaction with the negatively charged GD2-pentasaccharide headgroup. Purified scFv and IgG mutant forms were then tested for antigen specificity by ELISA, for tissue specificity by immunohistochemistry, for affinity by BIACORE, for antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-mediated cytotoxicity in vitro, and for anti-tumor efficacy in xenografted humanized mice. The nearly 7-fold improvement in affinity of hu3F8 with a single D32H (L-CDR1) mutation translated into a ∼12-fold improvement in NK92MI-transfected CD16-mediated ADCC, a 6-fold improvement in CD32-mediated ADCC, and a 2.5-fold improvement in complement-mediated cytotoxicity while maintaining restricted normal tissue cross-reactivity and achieving substantial improvement in tumor ablation in vivo. Despite increasing GD2 affinity, the double mutation D32H (L-CDR1) and E1K (L-FR1) did not further improve anti-tumor efficacy. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Seawater-driven forward osmosis for enriching nitrogen and phosphorous in treated municipal wastewater: effect of membrane properties and feed solution chemistry.

PubMed

Xue, Wenchao; Tobino, Tomohiro; Nakajima, Fumiyuki; Yamamoto, Kazuo

2015-02-01

Seawater-driven forward osmosis (FO) is considered to be a novel strategy to concentrate nutrients in treated municipal wastewater for further recovery as well as simultaneous discharge of highly purified wastewater into the sea with low cost. As a preliminary test, the performance of FO membranes in concentrating nutrients was investigated by both batch experiments and model simulation approaches. With synthetic seawater as the draw solution, the dissolved organic carbon, phosphate, and ammonia in the effluent from a membrane bioreactor (MBR) treating municipal wastewater were 2.3-fold, 2.3-fold, and 2.1-fold, respectively, concentrated by the FO process with approximately 57% of water reduction. Most of the dissolved components, including trace metals in the MBR effluent, were highly retained (>80%) in the feed side, indicating high water quality of permeate to be discharged. The effect of membrane properties on the nutrient enrichment performance was investigated by comparing three types of FO membranes. Interestingly, a polyamide membrane possessing a high negative charge demonstrated a poor capability of retaining ammonia, which was hypothesized because of an ion exchange-like mechanism across the membrane prompted by the high ionic concentration of the draw solution. A feed solution pH of 7 was demonstrated to be an optimum condition for improving the overall retention of nutrients, especially for ammonia because of the pH-dependent speciation of ammonia/ammonium forms. The modeling results showed that higher than 10-fold concentrations of ammonia and phosphate are achievable by seawater-driven FO with a draw solution to feed solution volume ratio of 2:1. The enriched municipal wastewater contains nitrogen and phosphorous concentrations comparable with typical animal wastewater and anaerobic digestion effluent, which are used for direct nutrient recovery. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of 31 FDA approved small-molecule kinase inhibitors on isolated rat liver mitochondria.

PubMed

Zhang, Jun; Salminen, Alec; Yang, Xi; Luo, Yong; Wu, Qiangen; White, Matthew; Greenhaw, James; Ren, Lijun; Bryant, Matthew; Salminen, William; Papoian, Thomas; Mattes, William; Shi, Qiang

2017-08-01

The FDA has approved 31 small-molecule kinase inhibitors (KIs) for human use as of November 2016, with six having black box warnings for hepatotoxicity (BBW-H) in product labeling. The precise mechanisms and risk factors for KI-induced hepatotoxicity are poorly understood. Here, the 31 KIs were tested in isolated rat liver mitochondria, an in vitro system recently proposed to be a useful tool to predict drug-induced hepatotoxicity in humans. The KIs were incubated with mitochondria or submitochondrial particles at concentrations ranging from therapeutic maximal blood concentrations (Cmax) levels to 100-fold Cmax levels. Ten endpoints were measured, including oxygen consumption rate, inner membrane potential, cytochrome c release, swelling, reactive oxygen species, and individual respiratory chain complex (I-V) activities. Of the 31 KIs examined only three including sorafenib, regorafenib and pazopanib, all of which are hepatotoxic, caused significant mitochondrial toxicity at concentrations equal to the Cmax, indicating that mitochondrial toxicity likely contributes to the pathogenesis of hepatotoxicity associated with these KIs. At concentrations equal to 100-fold Cmax, 18 KIs were found to be toxic to mitochondria, and among six KIs with BBW-H, mitochondrial injury was induced by regorafenib, lapatinib, idelalisib, and pazopanib, but not ponatinib, or sunitinib. Mitochondrial liability at 100-fold Cmax had a positive predictive power (PPV) of 72% and negative predictive power (NPV) of 33% in predicting human KI hepatotoxicity as defined by product labeling, with the sensitivity and specificity being 62% and 44%, respectively. Similar predictive power was obtained using the criterion of Cmax ≥1.1 µM or daily dose ≥100 mg. Mitochondrial liability at 1-2.5-fold Cmax showed a 100% PPV and specificity, though the NPV and sensitivity were 32% and 14%, respectively. These data provide novel mechanistic insights into KI hepatotoxicity and indicate that mitochondrial toxicity at therapeutic levels can help identify hepatotoxic KIs.

miR-205 and miR-200c: Predictive Micro RNAs for Lymph Node Metastasis in Triple Negative Breast Cancer

PubMed Central

Yilmaz, Ismail; Narli, Gizem; Haholu, Aptullah; Kucukodaci, Zafer; Demirel, Dilaver

2014-01-01

Purpose We examined expression profiles of 16 micro RNAs (miRNAs) in triple negative breast cancers to identify their potential as biomarkers for lymph node metastasis. Methods The expression profiles of miR-9, miR-21, miR-30a, miR-30d, miR-31, miR-34a, miR-34c, miR-100, miR-122, miR-125b, miR-146a, miR-146b, miR-155, miR-181a, miR-200c, and miR-205 were examined by using real-time quantitative reverse transcription polymerase chain reaction in tumor samples and corresponding benign breast tissues. Their associations with histopathological features and prognostic parameters were assessed. Results When compared with the expression in benign breast tissues, seven of the miRNAs (miR-31, miR-205, miR-34a, miR-146a, miR-125b, miR-34c, and miR-181a) were downregulated more than 1.5-fold in tumor tissues, whereas, only miR-21 was found to be upregulated more than 1.5-fold in tumor tissues. Although miR-200c levels were decreased only 1.12-fold in tumor tissues, the reduced expressions of miR-200c and miR-205 were significantly associated with lymph node metastasis (p=0.021 and p=0.016, respectively). Conclusion Our results demonstrate that miR-205 and miR-200c expression levels may be useful in predicting lymph node metastasis in triple negative breast cancer patients. PMID:25013435

Mechanical challenges to freshwater residency in sharks and rays.

PubMed

Gleiss, Adrian C; Potvin, Jean; Keleher, James J; Whitty, Jeff M; Morgan, David L; Goldbogen, Jeremy A

2015-04-01

Major transitions between marine and freshwater habitats are relatively infrequent, primarily as a result of major physiological and ecological challenges. Few species of cartilaginous fish have evolved to occupy freshwater habitats. Current thought suggests that the metabolic physiology of sharks has remained a barrier to the diversification of this taxon in freshwater ecosystems. Here, we demonstrate that the physical properties of water provide an additional constraint for this species-rich group to occupy freshwater systems. Using hydromechanical modeling, we show that occurrence in fresh water results in a two- to three-fold increase in negative buoyancy for sharks and rays. This carries the energetic cost of lift production and results in increased buoyancy-dependent mechanical power requirements for swimming and increased optimal swim speeds. The primary source of buoyancy, the lipid-rich liver, offers only limited compensation for increased negative buoyancy as a result of decreasing water density; maintaining the same submerged weight would involve increasing the liver volume by very large amounts: 3- to 4-fold in scenarios where liver density is also reduced to currently observed minimal levels and 8-fold without any changes in liver density. The first data on body density from two species of elasmobranch occurring in freshwater (the bull shark Carcharhinus leucas, Müller and Henle 1839, and the largetooth sawfish Pristis pristis, Linnaeus 1758) support this hypothesis, showing similar liver sizes as marine forms but lower liver densities, but the greatest negative buoyancies of any elasmobranch studied to date. Our data suggest that the mechanical challenges associated with buoyancy control may have hampered the invasion of freshwater habitats in elasmobranchs, highlighting an additional key factor that may govern the predisposition of marine organisms to successfully establish in freshwater habitats. © 2015. Published by The Company of Biologists Ltd.

Kinetics and risk of de novo hepatitis B infection in HBsAg-negative patients undergoing cytotoxic chemotherapy.

PubMed

Hui, Chee-Kin; Cheung, Winnie W W; Zhang, Hai-Ying; Au, Wing-Yan; Yueng, Yui-Hung; Leung, Anskar Y H; Leung, Nancy; Luk, John M; Lie, Albert K W; Kwong, Yok-Lam; Liang, Raymond; Lau, George K K

2006-07-01

De novo hepatitis B virus (HBV)-related hepatitis after chemotherapy results in high morbidity and mortality. We evaluate the clinical course of de novo HBV-related hepatitis after chemotherapy. Two hundred forty-four consecutive hepatitis B surface antigen (HBsAg)-negative lymphoma patients treated with chemotherapy were followed up for a median of 12.4 (range, 0.1-65.0) months. Serially collected serum samples were analyzed for hepatitis, serum HBV DNA, and HBsAg seroreversion. Eight of the 244 patients (3.3%) developed de novo HBV-related hepatitis. A 100-fold increase in serum HBV DNA preceded de novo HBV-related hepatitis by a median of 18.5 (range, 12-28) weeks. All 8 patients had normal serum alanine aminotransaminase level when the 100-fold increase in serum HBV DNA occurred. Patients with de novo HBV-related hepatitis were more likely to have occult HBV infection before chemotherapy. Direct sequencing results showed that these 8 patients had de novo HBV-related hepatitis from reactivation of occult HBV infection. Three of the 8 patients with de novo HBV-related hepatitis compared with 6 of the 236 patients without de novo HBV-related hepatitis developed fulminant hepatic failure (37.5% vs 2.5%, respectively, P < .001). On multivariate Cox analysis, de novo HBV-related hepatitis was independently associated with a higher risk of fulminant hepatic failure (relative risk, 29.854; 95% confidence interval: 4.844-183.980; P < .001). Close surveillance for a 100-fold increase in HBV DNA is recommended for HBsAg-negative patients treated with chemotherapy so that early commencement of antiviral therapy can be initiated before the occurrence of de novo HBV-related hepatitis.

Evaluation of clinical measures and different criteria for diagnosis of adult-onset Still's disease in a Chinese population.

PubMed

Jiang, Lindi; Wang, Zhen; Dai, Xiaomin; Jin, Xuejuan

2011-04-01

To determine the value of clinical measures in diagnosis of adult-onset Still's disease (AOSD), and to identify the optimal set of proposed classification criteria, in a Chinese population. A total of 70 patients with AOSD and 140 non-AOSD inpatients with fever were retrospectively identified at Zhongshan Hospital, Shanghai, from January 2003 to December 2009. Clinical measures and 4 sets of diagnostic criteria (Yamaguchi, Calabro, Cush, and Reginato) were evaluated by sensitivity, specificity, positive/negative predictive value (PPV, NPV), and positive/negative likelihood ratio (PLR, NLR) for diagnosis of AOSD. In our series, higher sensitivity included hyperpyrexia (temperature ≥ 39°C, 94.29%), arthralgia (80.0%), polymorphonuclear neutrophils (PMN) ≥ 75% (84.29%), serum ferritin ≥ 2-fold the upper normal value (90.0%), negative antinuclear antibodies (85.29%), and rheumatoid factor (84.38%); while higher specificity included transient erythema (98.57%), sore throat (85.0%), leukocytes ≥ 15,000/mm(3) (87.86%), and PMN ≥ 85% (85.0%). Rash, arthralgia, and sore throat were found to have better sensitivity and specificity (PLR 3.29-4.86). Leukocytes ≥ 10,000/mm(3), PMN ≥ 80%, and serum ferritin ≥ 5-fold the upper normal limit were set as critical points. The Reginato criteria set had the highest specificity, 99.29%. The Yamaguchi set had the highest sensitivity, 78.57%, with a better accuracy of 87.14%. The Yamaguchi diagnostic criteria had better accuracy in Chinese patients. Indicators such as rash, arthralgia, sore throat, leukocytes ≥ 10,000/mm(3), PMN ≥ 80%, and serum ferritin ≥ 5-fold the upper normal limit were helpful for diagnosis of AOSD. We recommend using these indicators in combination instead of alone.

Identification of Mur34 as the Novel Negative Regulator Responsible for the Biosynthesis of Muraymycin in Streptomyces sp. NRRL30471

PubMed Central

Xu, Dongmei; Liu, Guang; Cheng, Lin; Lu, Xinhua; Chen, Wenqing; Deng, Zixin

2013-01-01

Background Muraymycin, a potent translocase I (MraY) inhibitor, is produced by Streptomyces sp. NRRL30471. The muraymycin gene cluster (mur) was recently cloned, and bioinformatic analysis of mur34 revealed its encoding product exhibits high homology to a large family of proteins, including KanI and RacI in individual biosynthetic pathway of kanamycin and ribostamycin. However, the precise role of these proteins remains unknown. Principal Findings Here we report the identification of Mur34 as the novel negative regulator involved in muraymycin biosynthesis. Independent disruption of mur34 on chromosome and cosmid directly resulted in significant improvement of muraymycin production by at least 10 folds, thereof confirming the negative function of Mur34 during muraymycin biosynthesis and realizing the engineered production of muraymycin in heterologous host. Gene expression analysis indicated that the transcription level of the mur genes in mur34 mutant (DM-5) was dramatically enhanced by ca. 30 folds. Electrophoretic mobility shift assay (EMSA) showed that Mur34 specifically bound to the promoter region of mur33. Further experiments showed that a 28-bp region downstream of the transcription start point (TSP) was protected by His6Mur34, and the −10 region is essential for the activity of mur33 promoter. Conclusions Mur34 plays an unambiguously negative role in muraymycin biosynthesis via binding to the upstream of mur33. More importantly, Mur34 represents a novel family of regulators acting in negative manner to regulate the secondary metabolites biosynthesis in bacteria. PMID:24143177

[Estimation of quality of voice after removal of neoplasms T1 and T2 of glottis with simultaneous reconstruction of vocal fold with pedunculated sterno-thyroid muscle flap].

PubMed

Ratajczak, Jan; Wójtowicz, Piotr; Krzeski, Antoni

2014-01-01

In recent years there has been an increasing number of cases of cancer, including cancer of the larynx. The choice of treatment should be primarily dictated by the complete elimination of cancer, but from the point of view of the patient, an important factor to keep in mind, is the quality of the voice that will be created at the end of the therapeutic process. The aim of this study was to evaluate the voice quality of patients after partial surgery of the larynx with vocal fold reconstruction pedunculated sterno-thyroid muscle flap. The study included 30 men aged 53-72 years who were treated at the Clinic of Otorhinolaryngology Department of Medical-Dental Medical University of Warsaw on account of cancer of the larynx, qualified according to the TNM classification T1 or T2. The radical removal of cancer was associated with resection of one vocal fold, laryngeal pouches and ventricular fold. In 15 patients, included to the group I at the end of phase oncology surgery, a reconstruction of "vocal fold" pedunculated sterno-thyroid muscle flap were performed simultaneously. The group II consisted of 15 patients who underwent surgery that removed only the cancerous lesions. Impact assessments arising after surgery of voice disorders on quality of life were made using the self-test failure of the voice (Voice Handicap Index in the Pruszewicz modification). The nature of the created voice was studied using GRBAS scale. All patients performed the laryngostroboscope examination. With "IRIS" program, prepared by a team at Wrocław University of Technology, the voice was recorded, and then was subjected to acoustic analysis. In addition, noise level and the maximum phonation time was measured. The results indicate that the patients of group I gained a better voice confirming the values of objective acoustic analysis. The assessment made by the scale GRBAS patients who supplemented the resulting loss after tumour removal, with much less hoarseness of voice, did not have the hyperkinesis and there was no puff character. They had the better flow of voice and phonation time of vowels "a" was much longer. The assessment of quality of life of patients in group I made in a test of the VHI was higher than in group II. The laryngostroboscope examination confirmed a good phonatory occlusion and a nearly regular, healthy vocal fold vibration in patients who had received flap of muscle. Evaluation of the quality of voice after removing the tumor multiplicity in the glottis with simultaneous reconstruction "vocal fold" has confirmed that this is a very good surgical technique, which allows radically curing cancer for the simultaneous preservation of a good voice. The operation has limited indications for radiotherapy because of the desire to preserve the phonatory function of the larynx, and thus avoids the negative effects of radiation. Copyright © 2014 Polish Otorhinolaryngology - Head and Neck Surgery Society. Published by Elsevier Urban & Partner Sp. z.o.o. All rights reserved.

Ligand-promoted protein folding by biased kinetic partitioning.

PubMed

Hingorani, Karan S; Metcalf, Matthew C; Deming, Derrick T; Garman, Scott C; Powers, Evan T; Gierasch, Lila M

2017-04-01

Protein folding in cells occurs in the presence of high concentrations of endogenous binding partners, and exogenous binding partners have been exploited as pharmacological chaperones. A combined mathematical modeling and experimental approach shows that a ligand improves the folding of a destabilized protein by biasing the kinetic partitioning between folding and alternative fates (aggregation or degradation). Computationally predicted inhibition of test protein aggregation and degradation as a function of ligand concentration are validated by experiments in two disparate cellular systems.

Ligand-Promoted Protein Folding by Biased Kinetic Partitioning

PubMed Central

Hingorani, Karan S.; Metcalf, Matthew C.; Deming, Derrick T.; Garman, Scott C.; Powers, Evan T.; Gierasch, Lila M.

2017-01-01

Protein folding in cells occurs in the presence of high concentrations of endogenous binding partners, and exogenous binding partners have been exploited as pharmacological chaperones. A combined mathematical modeling and experimental approach shows that a ligand improves the folding of a destabilized protein by biasing the kinetic partitioning between folding and alternative fates (aggregation or degradation). Computationally predicted inhibition of test protein aggregation and degradation as a function of ligand concentration are validated by experiments in two disparate cellular systems. PMID:28218913

Land use imperils plant and animal community stability through changes in asynchrony rather than diversity

PubMed Central

Blüthgen, Nico; Simons, Nadja K.; Jung, Kirsten; Prati, Daniel; Renner, Swen C.; Boch, Steffen; Fischer, Markus; Hölzel, Norbert; Klaus, Valentin H.; Kleinebecker, Till; Tschapka, Marco; Weisser, Wolfgang W.; Gossner, Martin M.

2016-01-01

Human land use may detrimentally affect biodiversity, yet long-term stability of species communities is vital for maintaining ecosystem functioning. Community stability can be achieved by higher species diversity (portfolio effect), higher asynchrony across species (insurance hypothesis) and higher abundance of populations. However, the relative importance of these stabilizing pathways and whether they interact with land use in real-world ecosystems is unknown. We monitored inter-annual fluctuations of 2,671 plant, arthropod, bird and bat species in 300 sites from three regions. Arthropods show 2.0-fold and birds 3.7-fold higher community fluctuations in grasslands than in forests, suggesting a negative impact of forest conversion. Land-use intensity in forests has a negative net impact on stability of bats and in grasslands on birds. Our findings demonstrate that asynchrony across species—much more than species diversity alone—is the main driver of variation in stability across sites and requires more attention in sustainable management. PMID:26869180

3D reconstruction of the Shigella T3SS transmembrane regions reveals 12-fold symmetry and novel features throughout

PubMed Central

Hodgkinson, Julie L.; Horsley, Ashley; Stabat, David; Simon, Martha; Johnson, Steven; da Fonseca, Paula C. A.; Morris, Edward P.; Wall, Joseph S.; Lea, Susan M.; Blocker, Ariel J.

2009-01-01

Type III secretion systems (T3SSs) mediate bacterial protein translocation into eukaryotic cells, a process essential for virulence of many Gram-negative pathogens. They are composed of a cytoplasmic secretion machinery and a base bridging both bacterial membranes into which a hollow, external needle is embedded. When isolated, the latter two parts are termed ‘needle complex’ (NC). Incomplete understanding of NC structure hampers studies of T3SS function. To estimate the stoichiometry of its components, the mass f its sub-domains was measured by scanning transmission electron microscopy (STEM). Subunit symmetries were determined by analysis of top and side views within negatively stained samples in low dose transmission electron microscopy (TEM). Application of 12-fold symmetry allowed generation of a 21-25Å resolution three-dimensional (3D) reconstruction of the NC base, revealing many new features and permitting tentative docking of the crystal structure of EscJ, an inner membrane component. PMID:19396171

Land use imperils plant and animal community stability through changes in asynchrony rather than diversity.

PubMed

Blüthgen, Nico; Simons, Nadja K; Jung, Kirsten; Prati, Daniel; Renner, Swen C; Boch, Steffen; Fischer, Markus; Hölzel, Norbert; Klaus, Valentin H; Kleinebecker, Till; Tschapka, Marco; Weisser, Wolfgang W; Gossner, Martin M

2016-02-12

Human land use may detrimentally affect biodiversity, yet long-term stability of species communities is vital for maintaining ecosystem functioning. Community stability can be achieved by higher species diversity (portfolio effect), higher asynchrony across species (insurance hypothesis) and higher abundance of populations. However, the relative importance of these stabilizing pathways and whether they interact with land use in real-world ecosystems is unknown. We monitored inter-annual fluctuations of 2,671 plant, arthropod, bird and bat species in 300 sites from three regions. Arthropods show 2.0-fold and birds 3.7-fold higher community fluctuations in grasslands than in forests, suggesting a negative impact of forest conversion. Land-use intensity in forests has a negative net impact on stability of bats and in grasslands on birds. Our findings demonstrate that asynchrony across species--much more than species diversity alone--is the main driver of variation in stability across sites and requires more attention in sustainable management.

Modeling folding related multi-scale deformation of sedimentary rock using ALSM and fracture characterization at Raplee Ridge, UT

NASA Astrophysics Data System (ADS)

Mynatt, I.; Hilley, G. E.; Pollard, D. D.

2006-12-01

Understanding and predicting the characteristics of folding induced fracturing is an important and intriguing structural problem. Folded sequences of sedimentary rock at depth are common traps for hydrocarbons and water and fractures can strongly effect (both positively and negatively) this trapping capability. For these reasons fold-fracture relationships are well studied, but due to the complex interactions between the remote tectonic stress, rheologic properties, underlying fault geometry and slip, and pre-existing fractures, fracture characteristics can vary greatly from fold to fold. Additionally, examination of the relationships between fundamental characteristics such as fold geometry and fracture density are difficult even in thoroughly studied producing fields as measurements of fold shape are hampered by the low resolution of seismic surveying and measurements of fractures are limited to sparse well-bore locations. Due to the complexity of the system, the limitations of available data and small number of detailed case studies, prediction of fracture characteristics, e.g. the distribution of fracture density, are often difficult to make for a particular fold. We suggest a combination of mechanical and numerical modeling and analysis combined with detailed field mapping can lead to important insights into fold-fracture relationships. We develop methods to quantify both fold geometry and fracture characteristics, and summarize their relationships for an exhumed analogue reservoir case study. The field area is Raplee Monocline, a Laramide aged, N-S oriented, ~14-km long fold exposed in the Monument Upwarp of south-eastern Utah and part of the larger Colorado Plateau geologic province. The investigation involves three distinct parts: 1) Field based characterization and mapping of the fractures on and near the fold; 2) Development of accurate models of the fold geometry using high resolution data including ~3.5x107 x, y, z topographic points collected using Airborne Laser Swath Mapping (ALSM); and 3) Analysis of the fold shape and fracture patterns using the concepts of differential geometry and fracture mechanics. Field documentation of fracture characteristics enables the classification of distinct pre- and syn- folding fracture sets and the development of conceptual models of multiple stages of fracture evolution. Numerical algorithms, visual methods and field mapping techniques are used to extract the geometry of specific stratigraphic bedding surfaces and interpolate fold geometry between topographic exposures, thereby creating models of the fold geometry at several stratigraphic levels. Geometric characteristics of the fold models, such as magnitudes and directions of maximum and minimum normal curvature and fold limb dip, are compared to the observed fracture characteristics to identify the following relationships: 1) Initiation of folding related fractures at ten degrees of limb dip and increasing fracture density with increasing dip and 2) No correlation between absolute maximum fold curvature and fracture density.

Tracking of fatness during childhood, adolescence and young adulthood: a 7-year follow-up study in Madeira Island, Portugal.

PubMed

Freitas, Duarte; Beunen, Gaston; Maia, José; Claessens, Albrecht; Thomis, Martine; Marques, António; Gouveia, Elvio; Lefevre, Johan

2012-01-01

Investigating tracking of fatness from childhood to adolescence, early adolescence to young adulthood and late adolescence to young adulthood. Participants from the Madeira Growth Study were followed during an average period of 7.2 years. Height, body mass, skin-folds and circumferences were measured, nine health- and performance-related tests were administered and the Baecke questionnaire was used to assess physical activity. Skeletal maturity was estimated using the TW3 method. The prevalence of overweight plus obesity ranged from 8.2-20.0% at baseline and from 20.4-40.0% at follow-up, in boys. Corresponding percentages for girls were 10.6-12.0% and 13.2-18.0%. Inter-age correlations for fatness indicators ranged from 0.43-0.77. BMI, waist circumference and sum of skin-folds at 8, 12 and 16-years old were the main predictors of these variables at 15, 19 and 23-years old, respectively. Strength, muscular endurance and aerobic fitness were negatively related to body fatness. Physical activity and maturation were independently associated with adolescent (15 years) and young adult (19 years) fatness. Over 7.2 years, tracking was moderate-to-high for fatness. Variance was explained by fatness indicators and to a small extent by physical fitness, physical activity and maturation.

Low-dose endotoxemia and human neuropsychological functions.

PubMed

Krabbe, Karen Suárez; Reichenberg, Abraham; Yirmiya, Raz; Smed, Annelise; Pedersen, Bente Klarlund; Bruunsgaard, Helle

2005-09-01

Epidemiological data demonstrate an association between systemic low-grade inflammation defined as 2- to 3-fold increases in circulating inflammatory mediators and age-related decline in cognitive function. However, it is not known whether small elevations of circulating cytokine levels cause direct effects on human neuropsychological functions. We investigated changes in emotional, cognitive, and inflammatory parameters in an experimental in vivo model of low-grade inflammation. In a double-blind crossover study, 12 healthy young males completed neuropsychological tests before as well as 1.5, 6, and 24 h after an intravenous injection of Escherichia coli endotoxin (0.2 ng/kg) or saline in two experimental sessions. Endotoxin administration had no effect on body temperature, cortisol levels, blood pressure or heart rate, but circulating levels of tumor necrosis factor (TNF) and interleukin (IL)-6 increased 2- and 7-fold, respectively, reaching peak values at 3 h, whereas soluble TNF-receptors and IL-1 receptor antagonist peaked at 4.5 h. The neutrophil count increased and the lymphocyte count declined. In this model, low-dose endotoxemia did not affect cognitive performance significantly but declarative memory performance was inversely correlated with cytokine increases. In conclusion, our findings demonstrate a negative association between circulating IL-6 and memory functions during very low-dose endotoxemia independently of physical stress symptoms, and the hypothalamo-pituitary-adrenal axis.

Biochemical enhancement of transdermal delivery with magainin peptide: modification of electrostatic interactions by changing pH.

PubMed

Kim, Yeu-Chun; Late, Sameer; Banga, Ajay K; Ludovice, Peter J; Prausnitz, Mark R

2008-10-01

Magainin is a naturally occurring, pore-forming peptide that has recently been shown to increase skin permeability. This study tested the hypothesis that electrostatic forces between magainin peptides and drugs mediate drug transport across the skin. Electrostatic interaction between positively charged magainin and a negatively charged model drug, fluorescein, was attractive at pH 7.4 and resulted in a 35-fold increase in delivery across human epidermis in vitro when formulated with 2% N-lauroylsarcosine in 50% ethanol. Increasing to pH 10 or 11 largely neutralized magainin's charge, which eliminated enhancement due to magainin. Shielding electrostatic interactions with 1-2M NaCl solution similarly eliminated enhancement. Showing the opposite dependence on pH, electrostatic interaction between magainin and a positively charged anti-nausea drug, granisetron, was largely neutralized at pH 10 and resulted in a 92-fold increase in transdermal delivery. Decreasing to pH 5 increased magainin's positive charge, which repelled granisetron and progressively decreased transdermal flux. Circular dichroism analysis, multi-photon microscopy, and FTIR spectroscopy showed no significant pH effect on magainin secondary structure, magainin deposition in stratum corneum, or stratum corneum lipid order, respectively. We conclude that magainin increases transdermal delivery by a mechanism involving electrostatic interaction between magainin peptides and drugs.

Biochemical enhancement of transdermal delivery with magainin peptide: Modification of electrostatic interactions by changing pH

PubMed Central

Kim, Yeu-Chun; Late, Sameer; Banga, Ajay K.; Ludovice, Peter J.; Prausnitz, Mark R.

2008-01-01

Magainin is a naturally occurring, pore-forming peptide that has recently been shown to increase skin permeability. This study tested the hypothesis that electrostatic forces between magainin peptides and drugs mediate drug transport across the skin. Electrostatic interaction between positively charged magainin and a negatively charged model drug, fluorescein, was attractive at pH 7.4 and resulted in a 35 fold increase in delivery across human epidermis in vitro when formulated with 2% N-lauroylsarcosine in 50% ethanol. Increasing to pH 10 or 11 largely neutralized magainin’s charge, which eliminated enhancement due to magainin. Shielding electrostatic interactions with 1–2 M NaCl solution similarly eliminated enhancement. Showing the opposite dependence on pH, electrostatic interaction between magainin and a positively charged anti-nausea drug, granisetron, was largely neutralized at pH 10 and resulted in a 59 fold increase in transdermal delivery. Decreasing to pH 5 increased magainin’s positive charge, which repelled granisetron and progressively decreased transdermal flux. Circular dichroism analysis, multi-photon microscopy, and FTIR spectroscopy showed no significant pH effect on magainin secondary structure, magainin deposition in stratum corneum, or stratum corneum lipid order, respectively. We conclude that magainin increases transdermal delivery by a mechanism involving electrostatic interaction between magainin peptides and drugs. PMID:18601987

The non-contact detection and identification of blood stained fingerprints using visible wavelength reflectance hyperspectral imaging: Part 1.

PubMed

Cadd, Samuel; Li, Bo; Beveridge, Peter; O'Hare, William T; Campbell, Andrew; Islam, Meez

2016-05-01

Blood is one of the most commonly encountered types of biological evidence found at scenes of violent crime and one of the most commonly observed fingerprint contaminants. Current visualisation methods rely on presumptive tests or chemical enhancement methods. Although these can successfully visualise ridge detail, they are destructive, do not confirm the presence of blood and can have a negative impact on DNA sampling. A novel application of visible wavelength reflectance hyperspectral imaging (HSI) has been used for the detection and positive identification of blood stained fingerprints in a non-contact and non-destructive manner on white ceramic tiles. The identification of blood was based on the unique visible absorption spectrum of haemoglobin between 400 and 500 nm. HSI has been used to successfully visualise ridge detail in blood stained fingerprints to the ninth depletion. Ridge detail was still detectable with diluted blood to 20-fold dilutions. Latent blood stains were detectable to 15,000-fold dilutions. Ridge detail was detectable for fingerprints up to 6 months old. HSI was also able to conclusively distinguish blood stained fingerprints from fingerprints in six paints and eleven other red/brown media with zero false positives. Copyright © 2016 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

Viscoelastic properties of rabbit vocal folds after augmentation.

PubMed

Hertegård, Stellan; Dahlqvist, Ake; Laurent, Claude; Borzacchiello, Assunta; Ambrosio, Luigi

2003-03-01

Vocal fold function is closely related to tissue viscoelasticity. Augmentation substances may alter the viscoelastic properties of vocal fold tissues and hence their vibratory capacity. We sought to investigate the viscoelastic properties of rabbit vocal folds in vitro after injections of various augmentation substances. Polytetrafluoroethylene (Teflon), cross-linked collagen (Zyplast), and cross-linked hyaluronan, hylan b gel (Hylaform) were injected into the lamina propria and the thyroarytenoid muscle of rabbit vocal folds. Dynamic viscosity of the injected vocal fold as a function of frequency was measured with a Bohlin parallel-plate rheometer during small-amplitude oscillation. All injected vocal folds showed a decreasing dynamic viscosity with increasing frequency. Vocal fold samples injected with hylan b gel showed the lowest dynamic viscosity, quite close to noninjected control samples. Vocal folds injected with polytetrafluoroethylene showed the highest dynamic viscosity followed by the collagen samples. The data indicated that hylan b gel in short-term renders the most natural viscoelastic properties to the vocal fold among the substances tested. This is of importance to restore/preserve the vibratory capacity of the vocal folds when glottal insufficiency is treated with injections.

When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches

PubMed Central

Muñoz, Victor; Cerminara, Michele

2016-01-01

Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico. All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats. PMID:27574021

Antitumor and immunomodulatory effects of weikangfu granule compound in tumor-bearing mice

PubMed Central

Nie, Xiaohua; Shi, Baojun; Ding, Yuting; Tao, Wenyi

2006-01-01

Background: Weikangfu granule compound (WKC) is a drug preparation based on a clinical prescription drug, Weikangfu-tang, which has been found to have therapeutic effects on gastric cancer. WKC comprises 7 components, including polysaccharides, saponin, flavonoids, and essential oil. Objective: The purpose of this study was to assess the antitumor and immunomodulatory effects of WKC in a tumor-bearing rodent model. Methods: Male and female Kuming mice weighing ∼20 g were subcutaneously implanted with sarcoma 180 (S180) tumor cells and randomly assigned to 1 of 5 treatment groups: oral WKC 175, 350, or 525 mg/kg·d, isotonic saline (negative control), or intraperitoneal cyclophosphamide 25 mg/kg·d (positive control). All treatments were administered daily for 10 days. After euthanization on day 11, the mice, tumors, and spleens were weighed. Lymphocyte proliferation and cytotoxic T lymphocyte (CTL) activity were determined using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cellular viability assay method. Macrophage phagocytosis was identified using a yeast test. Results: Fifty mice were included in the study (10 mice were assigned to each group). The tumors of the mice administered WKC 175, 350, and 525 mg/kg·d were significantly regressed, as determined using MICs, compared with those in the negative-control group (P<0.05, P<0.01, and P<0.01, respectively), and the inhibitory rates were 30.43%, 46.72%, and 54.35%, respectively. Compared with those in the negative-control group, CTL activities and lymphocyte proliferations in the presence of concanavalin A were significantly greater in the WKC-treated groups at all doses (CTL activities: P<0.05, P<0.01, and P<0.01, respectively; lymphocyte proliferations: P<0.05, P<0.01, and P<0.01, respectively). In the groups receiving WKC 175, 350, and 525 mg/kg·d, the phagocytic rates were 1.5- to 2.0-fold those in the negative-control group (P<0.05, P<0.01, and P<0.01, respectively). In the groups receiving WKC 175, 350, and 525 mg/kg·d, the phagocytic indexes were 3.7- to 5.0-fold those in the negative-control group (all, P<0.01). In contrast, lymphocyte proliferation in the positive-control group was significantly less compared with that in the negative-control group (P<0.01), but no significant differences were found in CTL activities or macrophage phagocytosis between these 2 groups. Conclusion: The results of this study in a rodent model suggest that WKC exhibited antitumor and immunomodulatory activities in S180-bearing mice, and that WKC improved nonspecific and specific immune functions in mice, such as lymphocyte proliferation, CTL activity, and macrophage phagocytosis. PMID:24678090

Premier pôle paléomagnétique, d'âge Moscovien contraint par un test du pli, obtenu dans le bassin d'Illizi (Craton saharien, Algérie)First palaeomagnetic pole, of Moscovian age constrained by a fold test, in the Illizi Basin (Saharan Craton, Algeria)

NASA Astrophysics Data System (ADS)

Bayou, Boualem; Derder, Mohamed El-Messaoud; Henry, Bernard; Djellit, Hamou; Amenna, Mohamed

Palaeomagnetic study, carried out in the Moscovian (˜305 Ma) formation in the Edjeleh anticline, shows the existence of three magnetisation components. Two of them are probably Cenozoic and Permian remagnetisations. The third component determined by both well defined ChRMs and remagnetisation circles analysis passes the fold test. Because the folding started before or during the Stephano-Autunian, this third component is the primary magnetisation. Its palaeomagnetic pole (28.3°S, 58.9°E), close to other poles from the Saharan platform obtained from neighbouring periods but without palaeomagnetic tests, confirms the age of these last data. To cite this article: B. Bayou et al., C. R. Geoscience 334 (2002) 81-87.

A Computationally Efficient Hypothesis Testing Method for Epistasis Analysis using Multifactor Dimensionality Reduction

PubMed Central

Pattin, Kristine A.; White, Bill C.; Barney, Nate; Gui, Jiang; Nelson, Heather H.; Kelsey, Karl R.; Andrew, Angeline S.; Karagas, Margaret R.; Moore, Jason H.

2008-01-01

Multifactor dimensionality reduction (MDR) was developed as a nonparametric and model-free data mining method for detecting, characterizing, and interpreting epistasis in the absence of significant main effects in genetic and epidemiologic studies of complex traits such as disease susceptibility. The goal of MDR is to change the representation of the data using a constructive induction algorithm to make nonadditive interactions easier to detect using any classification method such as naïve Bayes or logistic regression. Traditionally, MDR constructed variables have been evaluated with a naïve Bayes classifier that is combined with 10-fold cross validation to obtain an estimate of predictive accuracy or generalizability of epistasis models. Traditionally, we have used permutation testing to statistically evaluate the significance of models obtained through MDR. The advantage of permutation testing is that it controls for false-positives due to multiple testing. The disadvantage is that permutation testing is computationally expensive. This is in an important issue that arises in the context of detecting epistasis on a genome-wide scale. The goal of the present study was to develop and evaluate several alternatives to large-scale permutation testing for assessing the statistical significance of MDR models. Using data simulated from 70 different epistasis models, we compared the power and type I error rate of MDR using a 1000-fold permutation test with hypothesis testing using an extreme value distribution (EVD). We find that this new hypothesis testing method provides a reasonable alternative to the computationally expensive 1000-fold permutation test and is 50 times faster. We then demonstrate this new method by applying it to a genetic epidemiology study of bladder cancer susceptibility that was previously analyzed using MDR and assessed using a 1000-fold permutation test. PMID:18671250

Fault-related fold styles and progressions in fold-thrust belts: Insights from sandbox modeling

NASA Astrophysics Data System (ADS)

Yan, Dan-Ping; Xu, Yan-Bo; Dong, Zhou-Bin; Qiu, Liang; Zhang, Sen; Wells, Michael

2016-03-01

Fault-related folds of variable structural styles and assemblages commonly coexist in orogenic belts with competent-incompetent interlayered sequences. Despite their commonality, the kinematic evolution of these structural styles and assemblages are often loosely constrained because multiple solutions exist in their structural progression during tectonic restoration. We use a sandbox modeling instrument with a particle image velocimetry monitor to test four designed sandbox models with multilayer competent-incompetent materials. Test results reveal that decollement folds initiate along selected incompetent layers with decreasing velocity difference and constant vorticity difference between the hanging wall and footwall of the initial fault tips. The decollement folds are progressively converted to fault-propagation folds and fault-bend folds through development of fault ramps breaking across competent layers and are followed by propagation into fault flats within an upper incompetent layer. Thick-skinned thrust is produced by initiating a decollement fault within the metamorphic basement. Progressive thrusting and uplifting of the thick-skinned thrust trigger initiation of the uppermost incompetent decollement with formation of a decollement fold and subsequent converting to fault-propagation and fault-bend folds, which combine together to form imbricate thrust. Breakouts at the base of the early formed fault ramps along the lowest incompetent layers, which may correspond to basement-cover contacts, domes the upmost decollement and imbricate thrusts to form passive roof duplexes and constitute the thin-skinned thrust belt. Structural styles and assemblages in each of tectonic stages are similar to that in the representative orogenic belts in the South China, Southern Appalachians, and Alpine orogenic belts.

Overexpression of the Lactobacillus plantarum peptidoglycan biosynthesis murA2 gene increases the tolerance of Escherichia coli to alcohols and enhances ethanol production.

PubMed

Yuan, Yongbo; Bi, Changhao; Nicolaou, Sergios A; Zingaro, Kyle A; Ralston, Matthew; Papoutsakis, Eleftherios T

2014-10-01

A major challenge in producing chemicals and biofuels is to increase the tolerance of the host organism to toxic products or byproducts. An Escherichia coli strain with superior ethanol and more generally alcohol tolerance was identified by screening a library constructed by randomly integrating Lactobacillus plantarum genomic DNA fragments into the E. coli chromosome via Cre-lox recombination. Sequencing identified the inserted DNA fragment as the murA2 gene and its upstream intergenic 973-bp sequence, both coded on the negative genomic DNA strand. Overexpression of this murA2 gene and its upstream 973-bp sequence significantly enhanced ethanol tolerance in both E. coli EC100 and wild type E. coli MG1655 strains by 4.1-fold and 2.0-fold compared to control strains, respectively. Tolerance to n-butanol and i-butanol in E. coli MG1655 was increased by 1.85-fold and 1.91-fold, respectively. We show that the intergenic 973-bp sequence contains a native promoter for the murA2 gene along with a long 5' UTR (286 nt) on the negative strand, while a noncoding, small RNA, named MurA2S, is expressed off the positive strand. MurA2S is expressed in E. coli and may interact with murA2, but it does not affect murA2's ability to enhance alcohol tolerance in E. coli. Overexpression of murA2 with its upstream region in the ethanologenic E. coli KO11 strain significantly improved ethanol production in cultures that simulate the industrial Melle-Boinot fermentation process.

The effect of sleep duration and quality on academical success of the elementary school children in Kayseri Turkey.

PubMed

Unalan, Demet; Ozturk, Ahmet; Ismailogullari, Sevda; Akgul, Nilgun; Aksu, Murat

2013-05-01

To assess the sleeping habits of primary school children and establish link between sleeping hours and academic achievement. The cross-sectional study was conducted between April and June 2007, involving 2422 students of 6-8th grades in 12 primary schools located in Kayseri, Turkey. A questionnaire was presented to the students on the basis of probability sampling method. Academic performance was evaluated with regard to their school grades. SPSS 20 was used for statistical analysis. Of the total 2422 questionnaires distributed, 1966 (81.2%) were used for further evaluation. The mean sleeping period of the students during school days was 8.86 +/- 1.10 hours. The number of students having difficulty in waking up in the morning was 940 (47.8%), while 910 (46.3%) were confused when they woke up during the night, and the 886 (45.1%) had nightmares, while 609 (31.0%) were sleepy all day long. As the sleeping period increased, the probability of a mediocre achievement in science lessons increased by 1.33 fold and poor achievement increased by 1.57 fold. Besides, the probability of a mediocre achievement in mathematics lessons increased by 1.36 fold, and poor achievement increased by 1.67 fold. For Turkish language lessons, these increases were found to be 1.40 and 1.60 respectively. Correlation analysis showed a significant negative relationship between sleeping time and successful scores in Turkish (r = -0.65, p < 0.025) and science (r = -0.061, p < 0.036) lessons. As the sleeping period increased, the academic achievement of the students was negatively affected. The academic success was low in children who felt sleepy throughout the day.

In vitro and in vivo genotoxicity assessment of the dopamine receptor antagonist molindone hydrochloride.

PubMed

Krishna, Gopala; Gopalakrishnan, Gopa; Goel, Saryu

2016-05-01

Molindone hydrochloride is a dihydroindolone neuroleptic with dopamine D2 and D5 receptor antagonist activity. As an integral component of its preclinical safety evaluation, molindone hydrochloride was evaluated in a series of in vitro and in vivo genetic toxicology assays. In the bacterial reverse gene mutation assays employing four Salmonella tester strains (TA98, TA100, TA1535, and TA1537) and the E. coli tester strain WP2uvrA, molindone hydrochloride was negative in all strains, except TA100, in which it induced a positive response (up to 3-fold) in the presence of rat liver S9. With human S9, a small (2-fold), but nonreproducible, increase in revertants was observed in TA100 at the highest concentration of molindone tested (5,000 µg/plate). The mutagenicity was completely abrogated by the addition of glutathione and UDP-glucuronic acid to rat liver S9, suggesting detoxification of the mutagenic metabolite(s) by Phase II conjugation reactions, pathways commonly operational in humans. Molindone hydrochloride did not induce chromosomal aberrations in human lymphocyte cultures, did not elicit a positive response in a rat bone marrow micronucleus test for clastogencity/aneugenicity, and did not give a positive response in the rat liver comet assay for DNA damage. Collectively, the weight of evidence from these studies, combined with a large margin of safety and efficient detoxification through Phase II conjugation supports the interpretation that molindone hydrochloride does not pose a genotoxic risk to humans at the anticipated clinical dose levels. © 2016 Wiley Periodicals, Inc.

Microbubble signal and trial of org in acute stroke treatment (TOAST) classification in ischemic stroke.

PubMed

Lee, Chan-Hyuk; Kang, Hyun Goo; Lee, Ji Sung; Ryu, Han Uk; Jeong, Seul-Ki

2018-07-15

Right-to-left shunt (RLS) through a patent foramen ovale (PFO) is likely associated with ischemic stroke. Many studies have attempted to demonstrate the association between RLS and ischemic stroke. However, information on the association between the degree of RLS and the subtypes of ischemic stroke categorized by the Trial of ORG 10172 in Acute Stroke Treatment (TOAST) classification is lacking. This was a retrospective study involving 508 patients with ischemic stroke who underwent a transcranial Doppler (TCD) microbubble test between 2013 and 2015. The degree of RLS was divided into 4 grades according to the microbubble signal (MBS) as follows: no MBS, grade 1; MBS < 20, grade 2; MBS > 20, grade 3; curtain sign, grade 4. The degree of RLS and the type of ischemic stroke as classified by TOAST were analyzed and compared with other clinical information and laboratory findings. The higher RLS grade was associated with the cardioembolism (CE) and stroke of undetermined etiology (SUE), and the microbubble signals were inversely related with small vessel disease (SVD). An MBS higher than grade 3 showed a 2.95-fold higher association with SUE than large artery atherosclerosis (LAA), while grade 4 MBS revealed an approximately 8-fold higher association with SUE than LAA. RLS identified by the TCD microbubble test was significantly and independently associated with cryptogenic ischemic stroke (negative evaluation). Subsequent studies are needed to determine the biologic relationship between RLS and ischemic stroke, particularly the cryptogenic subtype of ischemic stroke. Copyright © 2018 Elsevier B.V. All rights reserved.

Positive surgical margins in robot-assisted partial nephrectomy: a multi-institutional analysis of oncologic outcomes (leave no tumor behind).

PubMed

Khalifeh, Ali; Kaouk, Jihad H; Bhayani, Sam; Rogers, Craig; Stifelman, Michael; Tanagho, Youssef S; Kumar, Ramesh; Gorin, Michael A; Sivarajan, Ganesh; Samarasekera, Dinesh; Allaf, Mohamad E

2013-11-01

Expanding indications for robot-assisted partial nephrectomy raise major oncologic concerns for positive surgical margins. Previous reports showed no correlation between positive surgical margins and oncologic outcomes. We report a multi-institutional experience with the oncologic outcomes of positive surgical margins on robot-assisted partial nephrectomy. Pathological and clinical followup data were reviewed from an institutional review board approved, prospectively maintained joint database from 5 institutions. Tumors with malignant pathology were isolated and statistically analyzed for demographics and oncologic followup. The log rank test was used to compare recurrence-free and metastasis-free survival between patients with positive and negative surgical margins. The proportional hazards method was used to assess the influence of multiple factors, including positive surgical margins, on recurrence and metastasis. A total of 943 robot-assisted partial nephrectomies for malignant tumors were successfully completed. Of the patients 21 (2.2%) had positive surgical margins on final pathological assessment, resulting in 2 groups, including the 21 with positive surgical margins and 922 with negative surgical margins. Positive surgical margin cases had higher recurrence and metastasis rates (p<0.001). As projected by the Kaplan-Meier method in the population as a whole at followup out to 63.6 months, 5-year recurrence-free and metastasis-free survival was 94.8% and 97.5%, respectively. There was a statistically significant difference in recurrence-free and metastasis-free survival between patients with positive and negative surgical margins (log rank test<0.001), which favored negative surgical margins. Positive surgical margins showed an 18.4-fold higher HR for recurrence when adjusted for multiple tumors, tumor size, tumor growth pattern and pathological stage. Positive surgical margins on final pathological evaluation increase the HR of recurrence and metastasis. In addition to pathological and molecular tumor characteristics, this should be considered to plan appropriate management. Copyright © 2013 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Design and simulation of origami structures with smooth folds

PubMed Central

Peraza Hernandez, E. A.; Lagoudas, D. C.

2017-01-01

Origami has enabled new approaches to the fabrication and functionality of multiple structures. Current methods for origami design are restricted to the idealization of folds as creases of zeroth-order geometric continuity. Such an idealization is not proper for origami structures of non-negligible fold thickness or maximum curvature at the folds restricted by material limitations. For such structures, folds are not properly represented as creases but rather as bent regions of higher-order geometric continuity. Such fold regions of arbitrary order of continuity are termed as smooth folds. This paper presents a method for solving the following origami design problem: given a goal shape represented as a polygonal mesh (termed as the goal mesh), find the geometry of a single planar sheet, its pattern of smooth folds, and the history of folding motion allowing the sheet to approximate the goal mesh. The parametrization of the planar sheet and the constraints that allow for a valid pattern of smooth folds are presented. The method is tested against various goal meshes having diverse geometries. The results show that every determined sheet approximates its corresponding goal mesh in a known folded configuration having fold angles obtained from the geometry of the goal mesh. PMID:28484322

Design and simulation of origami structures with smooth folds.

PubMed

Peraza Hernandez, E A; Hartl, D J; Lagoudas, D C

2017-04-01

Origami has enabled new approaches to the fabrication and functionality of multiple structures. Current methods for origami design are restricted to the idealization of folds as creases of zeroth-order geometric continuity. Such an idealization is not proper for origami structures of non-negligible fold thickness or maximum curvature at the folds restricted by material limitations. For such structures, folds are not properly represented as creases but rather as bent regions of higher-order geometric continuity. Such fold regions of arbitrary order of continuity are termed as smooth folds . This paper presents a method for solving the following origami design problem: given a goal shape represented as a polygonal mesh (termed as the goal mesh ), find the geometry of a single planar sheet, its pattern of smooth folds, and the history of folding motion allowing the sheet to approximate the goal mesh. The parametrization of the planar sheet and the constraints that allow for a valid pattern of smooth folds are presented. The method is tested against various goal meshes having diverse geometries. The results show that every determined sheet approximates its corresponding goal mesh in a known folded configuration having fold angles obtained from the geometry of the goal mesh.

Ability of circulating human hematopoietic lineage negative cells to support hematopoiesis.

PubMed

Peris, Pilar; Roforth, Matthew M; Nicks, Kristy M; Fraser, Daniel; Fujita, Koji; Jilka, Robert L; Khosla, Sundeep; McGregor, Ulrike

2015-01-01

Hematopoietic stem cell (HSC) self-renewal is regulated by osteoblast and/or endothelial cells within the hematopoietic niche. However, the true identity of the supporting cells and the nature of the secreted factors remain uncertain. We developed a novel mouse model and analyzed whether circulating human peripheral hematopoietic lineage negative/AP+ (lin-/AP+) cells support hematopoiesis in vivo. Thus, immunocompromised (Rag) mice expressing thymidine kinase (Tk) under the control of the 3.6Col1α1 promoter (Tk-Rag) were treated with ganciclovir, resulting in osteoblast progenitor cell ablation and subsequent loss of hematopoiesis (evaluated by measuring mouse Ter119+ erythroid cells). Following hematopoietic cell depletion, human bone marrow-derived marrow stromal cells (MSCs) or lin-/AP+ cells were infused into Tk-Rag mice and compared with saline infusions. Ganciclovir significantly reduced (7.4-fold) Ter119+ cells in the bone marrow of Tk-Rag mice compared to saline injections. Infusion of either MSCs or lin-/AP+ cells into ganciclovir-treated mice resulted in a 3.3-fold and 2.7-fold increase (P < 0.01), respectively, in Ter119+ cells compared to mice receiving saline. Relative to lin-/AP- cells, lin-/AP+ cells expressed high levels of mesenchymal, endothelial, and hematopoiesis supporting genes. Thus, human peripheral blood lin-/AP+ cells represent a novel cell type capable of supporting hematopoiesis in a manner comparable to MSCs. © 2014 Wiley Periodicals, Inc.

Identification of Metabolites in the Normal Ovary and Their Transformation in Primary and Metastatic Ovarian Cancer

PubMed Central

Fong, Miranda Y.; McDunn, Jonathan; Kakar, Sham S.

2011-01-01

In this study, we characterized the metabolome of the human ovary and identified metabolic alternations that coincide with primary epithelial ovarian cancer (EOC) and metastatic tumors resulting from primary ovarian cancer (MOC) using three analytical platforms: gas chromatography mass spectrometry (GC/MS) and liquid chromatography tandem mass spectrometry (LC/MS/MS) using buffer systems and instrument settings to catalog positive or negative ions. The human ovarian metabolome was found to contain 364 biochemicals and upon transformation of the ovary caused changes in energy utilization, altering metabolites associated with glycolysis and β-oxidation of fatty acids—such as carnitine (1.79 fold in EOC, p<0.001; 1.88 fold in MOC, p<0.001), acetylcarnitine (1.75 fold in EOC, p<0.001; 2.39 fold in MOC, p<0.001), and butyrylcarnitine (3.62 fold, p<0.0094 in EOC; 7.88 fold, p<0.001 in MOC). There were also significant changes in phenylalanine catabolism marked by increases in phenylpyruvate (4.21 fold; p = 0.0098) and phenyllactate (195.45 fold; p<0.0023) in EOC. Ovarian cancer also displayed an enhanced oxidative stress response as indicated by increases in 2-aminobutyrate in EOC (1.46 fold, p = 0.0316) and in MOC (2.25 fold, p<0.001) and several isoforms of tocopherols. We have also identified novel metabolites in the ovary, specifically N-acetylasparate and N-acetyl-aspartyl-glutamate, whose role in ovarian physiology has yet to be determined. These data enhance our understanding of the diverse biochemistry of the human ovary and demonstrate metabolic alterations upon transformation. Furthermore, metabolites with significant changes between groups provide insight into biochemical consequences of transformation and are candidate biomarkers of ovarian oncogenesis. Validation studies are warranted to determine whether these compounds have clinical utility in the diagnosis or clinical management of ovarian cancer patients. PMID:21625518

Identification of metabolites in the normal ovary and their transformation in primary and metastatic ovarian cancer.

PubMed

Fong, Miranda Y; McDunn, Jonathan; Kakar, Sham S

2011-01-01

In this study, we characterized the metabolome of the human ovary and identified metabolic alternations that coincide with primary epithelial ovarian cancer (EOC) and metastatic tumors resulting from primary ovarian cancer (MOC) using three analytical platforms: gas chromatography mass spectrometry (GC/MS) and liquid chromatography tandem mass spectrometry (LC/MS/MS) using buffer systems and instrument settings to catalog positive or negative ions. The human ovarian metabolome was found to contain 364 biochemicals and upon transformation of the ovary caused changes in energy utilization, altering metabolites associated with glycolysis and β-oxidation of fatty acids--such as carnitine (1.79 fold in EOC, p<0.001; 1.88 fold in MOC, p<0.001), acetylcarnitine (1.75 fold in EOC, p<0.001; 2.39 fold in MOC, p<0.001), and butyrylcarnitine (3.62 fold, p<0.0094 in EOC; 7.88 fold, p<0.001 in MOC). There were also significant changes in phenylalanine catabolism marked by increases in phenylpyruvate (4.21 fold; p = 0.0098) and phenyllactate (195.45 fold; p<0.0023) in EOC. Ovarian cancer also displayed an enhanced oxidative stress response as indicated by increases in 2-aminobutyrate in EOC (1.46 fold, p = 0.0316) and in MOC (2.25 fold, p<0.001) and several isoforms of tocopherols. We have also identified novel metabolites in the ovary, specifically N-acetylasparate and N-acetyl-aspartyl-glutamate, whose role in ovarian physiology has yet to be determined. These data enhance our understanding of the diverse biochemistry of the human ovary and demonstrate metabolic alterations upon transformation. Furthermore, metabolites with significant changes between groups provide insight into biochemical consequences of transformation and are candidate biomarkers of ovarian oncogenesis. Validation studies are warranted to determine whether these compounds have clinical utility in the diagnosis or clinical management of ovarian cancer patients.

Nasal mucus proteomic changes reflect altered immune responses and epithelial permeability in patients with allergic rhinitis.

PubMed

Tomazic, Peter Valentin; Birner-Gruenberger, Ruth; Leitner, Anita; Obrist, Britta; Spoerk, Stefan; Lang-Loidolt, Doris

2014-03-01

Nasal mucus is the first-line defense barrier against (aero-) allergens. However, its proteome and function have not been clearly investigated. The role of nasal mucus in the pathophysiology of allergic rhinitis was investigated by analyzing its proteome in patients with allergic rhinitis (n = 29) and healthy control subjects (n = 29). Nasal mucus was collected with a suction device, tryptically digested, and analyzed by using liquid chromatography-tandem mass spectrometry. Proteins were identified by searching the SwissProt database and annotated by collecting gene ontology data from databases and existing literature. Gene enrichment analysis was performed by using Cytoscape/BINGO software tools. Proteins were quantified with spectral counting, and selected proteins were confirmed by means of Western blotting. In total, 267 proteins were identified, with 20 (7.5%) found exclusively in patients with allergic rhinitis and 25 (9.5%) found exclusively in healthy control subjects. Five proteins were found to be significantly upregulated in patients with allergic rhinitis (apolipoprotein A-2 [APOA2], 9.7-fold; α2-macroglobulin [A2M], 4.5-fold; apolipoprotein A-1 [APOA1], 3.2-fold; α1-antitrypsin [SERPINA1], 2.5-fold; and complement C3 [C3], 2.3-fold) and 5 were found to be downregulated (antileukoproteinase [SLPI], 0.6-fold; WAP 4-disulfide core domain protein [WFDC2], 0.5-fold; haptoglobin [HP], 0.7-fold; IgJ chain [IGJ], 0.7-fold; and Ig hc V-III region BRO, 0.8-fold) compared with levels seen in healthy control subjects. The allergic rhinitis mucus proteome shows an enhanced immune response in which apolipoproteins might play an important role. Furthermore, an imbalance between cysteine proteases and antiproteases could be seen, which negatively affects epithelial integrity on exposure to pollen protease activity. This reflects the important role of mucus as the first-line defense barrier against allergens. Copyright © 2013 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

Imaging markers for Alzheimer disease

PubMed Central

Bocchetta, Martina; Chételat, Gael; Rabinovici, Gil D.; de Leon, Mony J.; Kaye, Jeffrey; Reiman, Eric M.; Scheltens, Philip; Barkhof, Frederik; Black, Sandra E.; Brooks, David J.; Carrillo, Maria C.; Fox, Nick C.; Herholz, Karl; Nordberg, Agneta; Jack, Clifford R.; Jagust, William J.; Johnson, Keith A.; Rowe, Christopher C.; Sperling, Reisa A.; Thies, William; Wahlund, Lars-Olof; Weiner, Michael W.; Pasqualetti, Patrizio; DeCarli, Charles

2013-01-01

Revised diagnostic criteria for Alzheimer disease (AD) acknowledge a key role of imaging biomarkers for early diagnosis. Diagnostic accuracy depends on which marker (i.e., amyloid imaging, 18F-fluorodeoxyglucose [FDG]-PET, SPECT, MRI) as well as how it is measured (“metric”: visual, manual, semiautomated, or automated segmentation/computation). We evaluated diagnostic accuracy of marker vs metric in separating AD from healthy and prognostic accuracy to predict progression in mild cognitive impairment. The outcome measure was positive (negative) likelihood ratio, LR+ (LR−), defined as the ratio between the probability of positive (negative) test outcome in patients and the probability of positive (negative) test outcome in healthy controls. Diagnostic LR+ of markers was between 4.4 and 9.4 and LR− between 0.25 and 0.08, whereas prognostic LR+ and LR− were between 1.7 and 7.5, and 0.50 and 0.11, respectively. Within metrics, LRs varied up to 100-fold: LR+ from approximately 1 to 100; LR− from approximately 1.00 to 0.01. Markers accounted for 11% and 18% of diagnostic and prognostic variance of LR+ and 16% and 24% of LR−. Across all markers, metrics accounted for an equal or larger amount of variance than markers: 13% and 62% of diagnostic and prognostic variance of LR+, and 29% and 18% of LR−. Within markers, the largest proportion of diagnostic LR+ and LR− variability was within 18F-FDG-PET and MRI metrics, respectively. Diagnostic and prognostic accuracy of imaging AD biomarkers is at least as dependent on how the biomarker is measured as on the biomarker itself. Standard operating procedures are key to biomarker use in the clinical routine and drug trials. PMID:23897875

Epidemiological risk factors for adult dengue in Singapore: an 8-year nested test negative case control study.

PubMed

Yung, Chee Fu; Chan, Siew Pang; Thein, Tun Linn; Chai, Siaw Ching; Leo, Yee Sin

2016-07-08

Understanding changes in the ecology and epidemiology of dengue is important to ensure resource intensive control programmes are targeted effectively as well as to inform future dengue vaccination strategies. We analyzed data from a multicentre longitudinal prospective study of fever in adults using a nested test negative case control approach to identify epidemiological risk factors for dengue disease in Singapore. From April 2005 to February 2013, adult patients presenting with fever within 72 h at selected public primary healthcare clinics and a tertiary hospital in Singapore were recruited. Acute and convalescent blood samples were collected and used to diagnose dengue using both PCR and serology methods. A dengue case was defined as having a positive RT-PCR result for DENV OR evidence of serological conversion between acute and convalescent blood samples. Similarly, controls were chosen from patients in the cohort who tested negative for dengue using the same laboratory methods. The host epidemiological factors which increased the likelihood of dengue disease amongst adults in Singapore were those aged between 21 and 40 years old (2 fold increase) while in contrast, Malay ethnicity was protective (OR 0.57, 95%CI 0.35 to 0.91) against dengue disease. Spatial factors which increased the odds of acquiring dengue was residing at a foreign workers dormitory or hostel (OR 3.25, 95 % CI 1.84 to 5.73) while individuals living in the North-West region of the country were less likely to get dengue (OR 0.50, 95%CI 0.29 to 0.86). Other factors such as gender, whether one primarily works indoors or outdoors, general dwelling type or floor, the type of transportation one uses to work, travel history, as well as self-reported history of mosquito bite or household dengue/fever were not useful in helping to inform a diagnosis of dengue. We have demonstrated a test negative study design to better understand the epidemiological risk factors of adult dengue over multiple seasons. We were able to discount other previously speculated factors such as gender, whether one primarily works indoors or outdoors, dwelling floor in a building and the use of public transportation as having no effect on one's risk of getting dengue.

Relationship of Salmonella infection and inflammatory intestinal response with hematological and serum biochemical values in laying hens.

PubMed

Soria, Mario Alberto; Bonnet, María Agustina; Bueno, Dante Javier

2015-06-15

There are few studies about the blood serum of laying hens infected with Salmonella. The differential leukocyte count and blood chemistry values are an important aid in the diagnosis of human diseases, but blood parameters in the avian species are not well known. On the other hand, invasive forms of bacterial gastroenteritis, like Salmonella, often cause intestinal inflammation so this study was undertaken to find a biomarker of Salmonella infection and inflammatory intestinal response in the hematological or serum biochemical parameters in laying hens. Furthermore, we evaluated the association of some farm characteristics with Salmonella infection and fecal leukocytes (FL). A fecal sample with at least one fecal leukocyte per field was considered positive for inflammatory intestinal response. False positive serum reactions for Salmonella infection, by serum plate agglutination (SPA) test, were reduced by heating the sample to 56°C for 30 min and then diluting it 5-fold. The range of hematological and biochemical parameter values was very wide, in addition, there was a poor agreement between the SPA and FL results. Comparison of the positive and negative samples in SPA and FL showed that 1.3% and 79.8% of the laying hens were positive and negative in both tests, respectively. Hens with a positive SPA result showed a higher percentage of monocytes than those with a negative SPA result. Hens with a positive FL test had a higher percentage of heterophils, ratio of heterophils to lymphocytes and aspartate aminotransferase values, while the percentage of lymphocytes was significantly lower (P < 0.05) than those with a negative FL test. The risk of Salmonella infection increased when the age of laying hens and the number of hens per poultry house was greater than or equal to 18 months old and 10,000 laying hens, compared to less than 18 months old and 10,000 laying hens, respectively. On the other hand, the risk of inflammatory intestinal response was higher in laying hens ≥ 18 months old than in hens < 18 months old. Despite the fact that we did not find any specific biomarker of Salmonella infection, this is the first report about the change of Salmonella infection and inflammatory response in hematological/serum biochemical values for laying hens. Copyright © 2015 Elsevier B.V. All rights reserved.

Orbitofrontal sulcogyral patterns are related to temperamental risk for psychopathology.

PubMed

Whittle, Sarah; Bartholomeusz, Cali; Yücel, Murat; Dennison, Meg; Vijayakumar, Nandita; Allen, Nicholas B

2014-02-01

There are marked individual differences in the pattern of cortical (sulcogyral) folding in the orbitofrontal cortex (OFC), and there is a growing literature suggesting that these individual differences are associated with risk for psychotic disorders. To date, however, no study has investigated whether OFC folding patterns are associated with broader risk factors relevant to a range of psychopathology. This study helps address this knowledge gap by examining whether OFC sulcogyral folding patterns are associated with putative risk factors, specifically affective temperament and psychiatric symptoms, in a large community sample (N = 152) of adolescents. Results showed that the most common pattern of folding ('Type I', marked by discontinuity of the medial orbital sulcus and continuity of the lateral orbital sulcus) was associated with low levels of Surgency, high levels of Negative Affectivity (in girls) and higher depressive symptoms. This pattern was also associated with reduced thickness of OFC gray matter. Overall, the findings, combined with previous work, suggest some specificity of neurodevelopmental risk for different types of psychopathology. Thus, these results have the potential to inform the early identification of at-risk individuals.

Thyroid Function and Premature Delivery in TPO Antibody-Negative Women: The Added Value of hCG.

PubMed

Korevaar, Tim I M; Steegers, Eric A P; Chaker, Layal; Medici, Marco; Jaddoe, Vincent W V; Visser, Theo J; de Rijke, Yolanda B; Peeters, Robin P

2017-09-01

Human chorionic gonadotropin (hCG) stimulates thyroid function during pregnancy. We recently showed that thyroid autoimmunity severely attenuated the thyroidal response to hCG stimulation and that this may underlie the higher risk of premature delivery in thyroperoxidase antibody (TPOAb)-positive women. We hypothesized that a lower thyroidal response to hCG stimulation in TPOAb-negative women is also associated with a higher risk of premature delivery and preterm premature rupture of membranes (pPROM). Thyrotropin (TSH), free thyroxine (FT4), and hCG concentrations were available in 5644 TPOAb-negative women from a prospective cohort. We tested for interaction between TSH or FT4 and hCG in linear regression models for duration of pregnancy and logistic regression models for premature delivery/pPROM. Accordingly, analyses were stratified per TSH percentile (TSH ≥ 85th percentile) and hCG per 10,000 IU/L. Women with high TSH and low hCG concentrations did not have a higher risk of premature delivery or pPROM, with protective effect estimates. In contrast, women with a high TSH concentration despite a high hCG concentration had twofold to 10-fold higher risk of premature delivery (Pdifference = 0.022) and an up to fourfold higher risk of pPROM (Pdifference = 0.079). hCG concentrations were not associated with premature delivery or pPROM. In TPOAb-negative women with high-normal TSH concentrations, only women with high hCG concentrations had a higher risk of premature delivery or pPROM. These results suggest a lower thyroidal response to hCG stimulation is also associated with premature delivery in TPOAb-negative women and that an additional measurement of hCG may improve thyroid-related risk assessments during pregnancy. Copyright © 2017 Endocrine Society

Effects of Three Depression Prevention Interventions on Risk for Depressive Disorder Onset in the Context of Depression Risk Factors

PubMed Central

Rohde, Paul; Stice, Eric; Gau, Jeff M.

2013-01-01

Study aims were to identify subgroups of adolescents with elevated depressive symptoms who had the highest likelihood of developing future major/minor depressive disorder on the basis of depression risk factors and participation in three depression prevention programs, with the goal of evaluating the preventive effect of indicated prevention interventions in the context of known risk factors. Adolescents (N = 341) with elevated depressive symptoms were randomized to one of four prevention intervention conditions (cognitive-behavioral group, supportive-expressive group, cognitive-behavioral bibliotherapy, educational brochure control). By 2-year follow-up, 14% showed onset of major/minor depressive disorders. Classification tree analysis (CTA) revealed that negative attributional style was the most important risk factor: youth with high scores showed a 4-fold increase in depression onset compared to youth who did not endorse this attributional style. For adolescents with negative attributional style, prevention condition emerged as the most important predictor: those receiving bibliotherapy showed a 5-fold reduction in depression disorder onset relative to adolescents in the three other intervention conditions. For adolescents who reported low negative attributional style scores, elevated levels of depressive symptoms at baseline emerged as the most potent predictor. Results implicate two key pathways to depression involving negative attributional style and elevated depressive symptoms in this population, and suggest that bibliotherapy may offset the risk conveyed by the most important depression risk factor in this sample. PMID:22932745

Stabilization of enzymes in ionic liquids via modification of enzyme charge.

PubMed

Nordwald, Erik M; Kaar, Joel L

2013-09-01

Due to the propensity of ionic liquids (ILs) to inactivate enzymes, the development of strategies to improve enzyme utility in these solvents is critical to fully exploit ILs for biocatalysis. We have developed a strategy to broadly improve enzyme utility in ILs based on elucidating the effect of charge modifications on the function of enzymes in IL environments. Results of stability studies in aqueous-IL mixtures indicated a clear connection between the ratio of enzyme-containing positive-to-negative sites and enzyme stability in ILs. Stability studies of the effect of [BMIM][Cl] and [EMIM][EtSO4 ] on chymotrypsin specifically found an optimum ratio of positively-charged amine-to-negatively-charged acid groups (0.39). At this ratio, the half-life of chymotrypsin was increased 1.6- and 4.3-fold relative to wild-type chymotrypsin in [BMIM][Cl] and [EMIM][EtSO4 ], respectively. The half-lives of lipase and papain were similarly increased as much as 4.0 and 2.4-fold, respectively, in [BMIM][Cl] by modifying the ratio of positive-to-negative sites of each enzyme. More generally, the results of stability studies found that modifications that reduce the ratio of enzyme-containing positive-to-negative sites improve enzyme stability in ILs. Understanding the impact of charge modification on enzyme stability in ILs may ultimately be exploited to rationally engineer enzymes for improved function in IL environments. Copyright © 2013 Wiley Periodicals, Inc.

Necrotizing Enterocolitis is associated with Ureaplasma Colonization in Preterm Infants

PubMed Central

Okogbule-Wonodi, Adora C.; Gross, George W.; Sun, Chen-Chih J.; Agthe, Alexander G.; Xiao, Li; Waites, Ken B.; Viscardi, Rose Marie

2014-01-01

The study objective was to determine whether Ureaplasma respiratory tract colonization of preterm infants <33 weeks gestation is associated with an increased risk for necrotizing enterocolitis (NEC). One or more tracheal or nasopharyngeal aspirates for Ureaplasma culture and PCR were obtained during the first week of life from 368 infants <33 weeks gestation enrolled from 1999-2003 or from 2007-2009. NEC Bell stage ≥2 was confirmed by radiological criteria, and pathology, if available. Cord serum samples were analyzed for IL-6 and IL-1β concentrations and placentas were reviewed for histological chorioamnionitis in the first cohort. NEC was confirmed in 29/368 (7.9%) of the combined cohorts. The incidence of NEC was 2.2-fold higher in Ureaplasma-positive (12.3%) than Ureaplasma-negative infants (5.5%) <33 wk (OR 2.43, 95%CI 1.13-5.22, P=0.023) and 3.3-fold higher in Ureaplasma-positive (14.6%) than Ureaplasma-negative (4.4%) infants ≤28 wks (OR 3.67, 95%CI 1.36-9.93, P=0.01). Age of onset, hematologic parameters at onset, and NEC severity were similar between Ureaplasma-positive and negative infants. Cord serum IL-6 and IL-1β concentrations were significantly higher in Ureaplasma-positive than in Ureaplasma-negative NEC-affected infants. Ureaplasma may be a factor in NEC pathogenesis in preterm infants by contributing to intestinal mucosal injury and/or altering systemic or local immune responses. PMID:21258263

Effects of three depression prevention interventions on risk for depressive disorder onset in the context of depression risk factors.

PubMed

Rohde, Paul; Stice, Eric; Gau, Jeff M

2012-12-01

Study aims were to identify subgroups of adolescents with elevated depressive symptoms who had the highest likelihood of developing future major/minor depressive disorder on the basis of depression risk factors and participation in three depression prevention programs, with the goal of evaluating the preventive effect of indicated prevention interventions in the context of known risk factors. Adolescents (N = 341) with elevated depressive symptoms were randomized to one of four prevention intervention conditions (cognitive-behavioral group, supportive-expressive group, cognitive-behavioral bibliotherapy, educational brochure control). By 2-year follow-up, 14% showed onset of major/minor depressive disorders. Classification tree analysis (CTA) revealed that negative attributional style was the most important risk factor: Youth with high scores showed a 4-fold increase in depression onset compared to youth who did not endorse this attributional style. For adolescents with negative attributional style, prevention condition emerged as the most important predictor: Those receiving bibliotherapy showed a 5-fold reduction in depression disorder onset relative to adolescents in the three other intervention conditions. For adolescents who reported low negative attributional style scores, elevated levels of depressive symptoms at baseline emerged as the most potent predictor. Results implicate two key pathways to depression involving negative attributional style and elevated depressive symptoms in this population, and suggest that bibliotherapy may offset the risk conveyed by the most important depression risk factor in this sample.

Altered vocal fold kinematics in synthetic self-oscillating models that employ adipose tissue as a lateral boundary condition.

NASA Astrophysics Data System (ADS)

Saidi, Hiba; Erath, Byron D.

2015-11-01

The vocal folds play a major role in human communication by initiating voiced sound production. During voiced speech, the vocal folds are set into sustained vibrations. Synthetic self-oscillating vocal fold models are regularly employed to gain insight into flow-structure interactions governing the phonation process. Commonly, a fixed boundary condition is applied to the lateral, anterior, and posterior sides of the synthetic vocal fold models. However, physiological observations reveal the presence of adipose tissue on the lateral surface between the thyroid cartilage and the vocal folds. The goal of this study is to investigate the influence of including this substrate layer of adipose tissue on the dynamics of phonation. For a more realistic representation of the human vocal folds, synthetic multi-layer vocal fold models have been fabricated and tested while including a soft lateral layer representative of adipose tissue. Phonation parameters have been collected and are compared to those of the standard vocal fold models. Results show that vocal fold kinematics are affected by adding the adipose tissue layer as a new boundary condition.

When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches.

PubMed

Muñoz, Victor; Cerminara, Michele

2016-09-01

Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats. © 2016 The Author(s).

Tensile failure properties of the perinatal, neonatal, and pediatric cadaveric cervical spine.

PubMed

Luck, Jason F; Nightingale, Roger W; Song, Yin; Kait, Jason R; Loyd, Andre M; Myers, Barry S; Bass, Cameron R Dale

2013-01-01

Biomechanical tensile testing of perinatal, neonatal, and pediatric cadaveric cervical spines to failure. To assess the tensile failure properties of the cervical spine from birth to adulthood. Pediatric cervical spine biomechanical studies have been few due to the limited availability of pediatric cadavers. Therefore, scaled data based on human adult and juvenile animal studies have been used to augment the limited pediatric cadaver data. Despite these efforts, substantial uncertainty remains in our understanding of pediatric cervical spine biomechanics. A total of 24 cadaveric osteoligamentous head-neck complexes, 20 weeks gestation to 18 years, were sectioned into segments (occiput-C2 [O-C2], C4-C5, and C6-C7) and tested in tension to determine axial stiffness, displacement at failure, and load-to-failure. Tensile stiffness-to-failure (N/mm) increased by age (O-C2: 23-fold, neonate: 22 ± 7, 18 yr: 504; C4-C5: 7-fold, neonate: 71 ± 14, 18 yr: 509; C6-C7: 7-fold, neonate: 64 ± 17, 18 yr: 456). Load-to-failure (N) increased by age (O-C2: 13-fold, neonate: 228 ± 40, 18 yr: 2888; C4-C5: 9-fold, neonate: 207 ± 63, 18 yr: 1831; C6-C7: 10-fold, neonate: 174 ± 41, 18 yr: 1720). Normalized displacement at failure (mm/mm) decreased by age (O-C2: 6-fold, neonate: 0.34 ± 0.076, 18 yr: 0.059; C4-C5: 3-fold, neonate: 0.092 ± 0.015, 18 yr: 0.035; C6-C7: 2-fold, neonate: 0.088 ± 0.019, 18 yr: 0.037). Cervical spine tensile stiffness-to-failure and load-to-failure increased nonlinearly, whereas normalized displacement at failure decreased nonlinearly, from birth to adulthood. Pronounced ligamentous laxity observed at younger ages in the O-C2 segment quantitatively supports the prevalence of spinal cord injury without radiographic abnormality in the pediatric population. This study provides important and previously unavailable data for validating pediatric cervical spine models, for evaluating current scaling techniques and animal surrogate models, and for the development of more biofidelic pediatric crash test dummies.

Circular Dichroism studies on the interactions of antimicrobial peptides with bacterial cells

NASA Astrophysics Data System (ADS)

Avitabile, Concetta; D'Andrea, Luca Domenico; Romanelli, Alessandra

2014-03-01

Studying how antimicrobial peptides interact with bacterial cells is pivotal to understand their mechanism of action. In this paper we explored the use of Circular Dichroism to detect the secondary structure of two antimicrobial peptides, magainin 2 and cecropin A, with E. coli bacterial cells. The results of our studies allow us to gain two important information in the context of antimicrobial peptides- bacterial cells interactions: peptides fold mainly due to interaction with LPS, which is the main component of the Gram negative bacteria outer membrane and the time required for the folding on the bacterial cells depends on the peptide analyzed.

Impact of Type of Needle on Incidence of Intravascular Injection During Diagnostic Lumbar Medial Branch Block.

PubMed

Joo, Young; Kim, Yong Chul; Lee, Sang Chul; Kim, Hye Young; Park, Keun Suk; Choi, Eun Joo; Moon, Jee Youn

2016-01-01

Intravascular (IV) injection of local anesthetics is a potential cause of false-negative results after lumbar medial branch nerve blockade (L-MBB) performed to diagnose facetogenic back pain. The aim of the present study was to identify the relationship between the needle type and the incidence of IV injection in patients undergoing L-MBB using fluoroscopy with digital subtraction imaging (DSI). In this prospective randomized study, we compared the incidence of IV uptake of contrast medium using the Quincke needle and Whitacre needle under real-time DSI during L-MBB. Clinical and demographic factors associated with the occurrence of IV uptake were also investigated. In total, 126 patients were randomized into the Quincke needle group (n = 62) and Whitacre needle group (n = 64). Intravascular uptake of contrast medium was observed in 66 (9.8%) of 671 L-MBB procedures under DSI. The incidence of IV uptake was 13.9% (47/338) using the Quincke needle and 5.7% (19/333) using the Whitacre needle. In the multivariate generalized estimating equations analysis, use of a Quincke needle was related to positive IV injection at a 1.898-fold higher rate than was use of a Whitacre needle (95% confidence interval, 1.025-3.516) and a positive aspiration test predicted IV injection at a 21.735-fold higher rate (95% confidence interval, 11.996-52.258). Lumbar medial branch nerve blockade using the Quincke needle was associated with a 1.9-fold higher rate of IV injection than was L-MBB using the Whitacre needle under DSI. Although further study is needed to confirm the clinical efficacy, Whitacre needles can be considered to reduce the risk of IV injection during L-MBB.

Apple Polyphenol Phloretin Inhibits Colorectal Cancer Cell Growth via Inhibition of the Type 2 Glucose Transporter and Activation of p53-Mediated Signaling.

PubMed

Lin, Sheng-Tsai; Tu, Shih-Hsin; Yang, Po-Sheng; Hsu, Sung-Po; Lee, Wei-Hwa; Ho, Chi-Tang; Wu, Chih-Hsiung; Lai, Yu-Hsin; Chen, Ming-Yao; Chen, Li-Ching

2016-09-14

Glucose transporters (GLUTs) are required for glucose uptake in malignant cells, and they can be used as molecular targets for cancer therapy. An RT-PCR analysis was performed to investigate the mRNA levels of 14 subtypes of GLUTs in human colorectal cancer (COLO 205 and HT-29) and normal (FHC) cells. RT-PCR (n = 27) was used to assess the differences in paired tissue samples (tumor vs normal) isolated from colorectal cancer patients. GLUT2 was detected in all tested cells. The average GLUT2 mRNA level in 12 of 27 (44.4%) cases was 2.4-fold higher in tumor compared to normal tissues (*, p = 0.027). Higher GLUT2 mRNA expression was preferentially detected in advanced-stage tumors (stage 0 vs 3 = 16.38-fold, 95% CI = 9.22-26.54-fold; *, p = 0.029). The apple polyphenol phloretin (Ph) and siRNA methods were used to inhibit GLUT2 protein expression. Ph (0-100 μM, for 24 h) induced COLO 205 cell growth cycle arrest in a p53-dependent manner, which was confirmed by pretreatment of the cells with a p53-specific dominant negative expression vector. Hepatocyte nuclear factor 6 (HNF6), which was previously reported to be a transcription factor that activates GLUT2 and p53, was also induced by Ph (0-100 μM, for 24 h). The antitumor effect of Ph (25 mg/kg or DMSO twice a week for 6 weeks) was demonstrated in vivo using BALB/c nude mice bearing COLO 205 tumor xenografts. In conclusion, targeting GLUT2 could potentially suppress colorectal tumor cell invasiveness.

Enterococcus faecalis Gene Transfer under Natural Conditions in Municipal Sewage Water Treatment Plants†

PubMed Central

Marcinek, Herbert; Wirth, Reinhard; Muscholl-Silberhorn, Albrecht; Gauer, Matthias

1998-01-01

The ability of Enterococcus faecalis to transfer various genetic elements under natural conditions was tested in two municipal sewage water treatment plants. Experiments in activated sludge basins of the plants were performed in a microcosm which allowed us to work under sterile conditions; experiments in anoxic sludge digestors were performed in dialysis bags. We used the following naturally occurring genetic elements: pAD1 and pIP1017 (two so-called sex pheromone plasmids with restricted host ranges, which are transferred at high rates under laboratory conditions); pIP501 (a resistance plasmid possessing a broad host range for gram-positive bacteria, which is transferred at low rates under laboratory conditions); and Tn916 (a conjugative transposon which is transferred under laboratory conditions at low rates to gram-positive bacteria and at very low rates to gram-negative bacteria). The transfer rate between different strains of E. faecalis under natural conditions was, compared to that under laboratory conditions, at least 105-fold lower for the sex pheromone plasmids, at least 100-fold lower for pIP501, and at least 10-fold lower for Tn916. In no case was transfer from E. faecalis to another bacterial species detected. By determining the dependence of transfer rates for pIP1017 on bacterial concentration and extrapolating to actual concentrations in the sewage water treatment plant, we calculated that the maximum number of transfer events for the sex pheromone plasmids between different strains of E. faecalis in the municipal sewage water treatment plant of the city of Regensburg ranged from 105 to 108 events per 4 h, indicating that gene transfer should take place under natural conditions. PMID:9464401

Moderately high intake of folic acid has a negative impact on mouse embryonic development

USDA-ARS?s Scientific Manuscript database

The incidence of neural tube defects has diminished considerably since the implementation of food fortification with folic acid (FA). However, the impact of excess FA intake, particularly during pregnancy, requires investigation. In a recent study, we reported that a diet supplemented with 20-fold h...

Shrub-steppe early succession following invasive juniper cutting and prescribed fire

USDA-ARS?s Scientific Manuscript database

Piñon-juniper woodlands of the western United States have expanded in area nearly 10-fold since the late 1800’s. Woodland dominance in sagebrush steppe has several negative consequences including reductions in herbaceous production and diversity, decreased wildlife habitat, higher erosion and runof...

Assessing variability in chemical acute toxicity of unionid mussels: Influence of intra- and inter-laboratory testing, life stage, and species

USGS Publications Warehouse

Raimondo, Sandy; Lilavois, Crystal R.; Lee, Larisa; Augspurger, Tom; Wang, Ning; Ingersoll, Christopher G.; Bauer, Candice R.; Hammer, Edward J.; Barron, Mace G.

2016-01-01

We developed a toxicity database for unionid mussels to examine the extent of intra- and inter-laboratory variability in acute toxicity tests with mussel larvae (glochidia) and juveniles; the extent of differential sensitivity of the two life stages; and the variation in sensitivity among commonly tested mussels (Lampsilis siliquoidea, Utterbackia imbecillis, Villosa iris), commonly tested cladocerans (Daphnia magna, Ceriodaphnia dubia) and fish (Oncorhynchus mykiss, Pimephales promelas, Lepomis macrochirus). The results of these analyses indicate intra-laboratory variability for median effect concentrations (EC50) averaged about 2 fold for both life stages, while inter-laboratory variability averaged 3.6 fold for juvenile mussels and 6.3 fold for glochidia. The EC50s for juveniles and glochidia were within a factor of 2 of each other for 50% of paired records across chemicals, with juveniles more sensitive than glochidia by more than 2 fold for 33% of the comparisons made between life stages. There was a high concurrence of the sensitivity of commonly tested L. siliquoidea, U. imbecillis, and V. iris to that of other mussels. However, this concurrence decreases as the taxonomic distance of the commonly tested cladocerans and fish to mussels increases. The compiled mussel database and determination of data variability will advance risk assessments by including more robust species sensitivity distributions, interspecies correlation estimates, and availability of taxon-specific empirically derived application factors for risk assessment.

Amino Acid Distribution Rules Predict Protein Fold: Protein Grammar for Beta-Strand Sandwich-Like Structures

PubMed Central

Kister, Alexander

2015-01-01

We present an alternative approach to protein 3D folding prediction based on determination of rules that specify distribution of “favorable” residues, that are mainly responsible for a given fold formation, and “unfavorable” residues, that are incompatible with that fold, in polypeptide sequences. The process of determining favorable and unfavorable residues is iterative. The starting assumptions are based on the general principles of protein structure formation as well as structural features peculiar to a protein fold under investigation. The initial assumptions are tested one-by-one for a set of all known proteins with a given structure. The assumption is accepted as a “rule of amino acid distribution” for the protein fold if it holds true for all, or near all, structures. If the assumption is not accepted as a rule, it can be modified to better fit the data and then tested again in the next step of the iterative search algorithm, or rejected. We determined the set of amino acid distribution rules for a large group of beta sandwich-like proteins characterized by a specific arrangement of strands in two beta sheets. It was shown that this set of rules is highly sensitive (~90%) and very specific (~99%) for identifying sequences of proteins with specified beta sandwich fold structure. The advantage of the proposed approach is that it does not require that query proteins have a high degree of homology to proteins with known structure. So long as the query protein satisfies residue distribution rules, it can be confidently assigned to its respective protein fold. Another advantage of our approach is that it allows for a better understanding of which residues play an essential role in protein fold formation. It may, therefore, facilitate rational protein engineering design. PMID:25625198

Greater absolute risk for all subtypes of breast cancer in the US than Malaysia.

PubMed

Horne, Hisani N; Beena Devi, C R; Sung, Hyuna; Tang, Tieng Swee; Rosenberg, Philip S; Hewitt, Stephen M; Sherman, Mark E; Anderson, William F; Yang, Xiaohong R

2015-01-01

Hormone receptor (HR) negative breast cancers are relatively more common in low-risk than high-risk countries and/or populations. However, the absolute variations between these different populations are not well established given the limited number of cancer registries with incidence rate data by breast cancer subtype. We, therefore, used two unique population-based resources with molecular data to compare incidence rates for the 'intrinsic' breast cancer subtypes between a low-risk Asian population in Malaysia and high-risk non-Hispanic white population in the National Cancer Institute's surveillance, epidemiology, and end results 18 registries database (SEER 18). The intrinsic breast cancer subtypes were recapitulated with the joint expression of the HRs (estrogen receptor and progesterone receptor) and human epidermal growth factor receptor-2 (HER2). Invasive breast cancer incidence rates overall were fivefold greater in SEER 18 than in Malaysia. The majority of breast cancers were HR-positive in SEER 18 and HR-negative in Malaysia. Notwithstanding the greater relative distribution for HR-negative cancers in Malaysia, there was a greater absolute risk for all subtypes in SEER 18; incidence rates were nearly 7-fold higher for HR-positive and 2-fold higher for HR-negative cancers in SEER 18. Despite the well-established relative breast cancer differences between low-risk and high-risk countries and/or populations, there was a greater absolute risk for HR-positive and HR-negative subtypes in the US than Malaysia. Additional analytical studies are sorely needed to determine the factors responsible for the elevated risk of all subtypes of breast cancer in high-risk countries like the United States.

Structure of the Rift Valley fever virus nucleocapsid protein reveals another architecture for RNA encapsidation

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

Raymond, Donald D.; Piper, Mary E.; Gerrard, Sonja R.

2010-07-13

Rift Valley fever virus (RVFV) is a negative-sense RNA virus (genus Phlebovirus, family Bunyaviridae) that infects livestock and humans and is endemic to sub-Saharan Africa. Like all negative-sense viruses, the segmented RNA genome of RVFV is encapsidated by a nucleocapsid protein (N). The 1.93-{angstrom} crystal structure of RVFV N and electron micrographs of ribonucleoprotein (RNP) reveal an encapsidated genome of substantially different organization than in other negative-sense RNA virus families. The RNP polymer, viewed in electron micrographs of both virus RNP and RNP reconstituted from purified N with a defined RNA, has an extended structure without helical symmetry. N-RNA speciesmore » of {approx}100-kDa apparent molecular weight and heterogeneous composition were obtained by exhaustive ribonuclease treatment of virus RNP, by recombinant expression of N, and by reconstitution from purified N and an RNA oligomer. RNA-free N, obtained by denaturation and refolding, has a novel all-helical fold that is compact and well ordered at both the N and C termini. Unlike N of other negative-sense RNA viruses, RVFV N has no positively charged surface cleft for RNA binding and no protruding termini or loops to stabilize a defined N-RNA oligomer or RNP helix. A potential protein interaction site was identified in a conserved hydrophobic pocket. The nonhelical appearance of phlebovirus RNP, the heterogeneous {approx}100-kDa N-RNA multimer, and the N fold differ substantially from the RNP and N of other negative-sense RNA virus families and provide valuable insights into the structure of the encapsidated phlebovirus genome.« less

Interactions of microbicide nanoparticles with a simulated vaginal fluid.

PubMed

das Neves, José; Rocha, Cristina M R; Gonçalves, Maria Pilar; Carrier, Rebecca L; Amiji, Mansoor; Bahia, Maria Fernanda; Sarmento, Bruno

2012-11-05

The interaction with cervicovaginal mucus presents the potential to impact the performance of drug nanocarriers. These systems must migrate through this biological fluid in order to deliver their drug payload to the underlying mucosal surface. We studied the ability of dapivirine-loaded polycaprolactone (PCL)-based nanoparticles (NPs) to interact with a simulated vaginal fluid (SVF) incorporating mucin. Different surface modifiers were used to produce NPs with either negative (poloxamer 338 NF and sodium lauryl sulfate) or positive (cetyltrimethylammonium bromide) surface charge. Studies were performed using the mucin particle method, rheological measurements, and real-time multiple particle tracking. Results showed that SVF presented rheological properties similar to those of human cervicovaginal mucus. Analysis of NP transport indicated mild interactions with mucin and low adhesive potential. In general, negatively charged NPs underwent subdiffusive transport in SVF, i.e., hindered as compared to their diffusion in water, but faster than for positively charged NPs. These differences were increased when the pH of SVF was changed from 4.2 to 7.0. Diffusivity was 50- and 172-fold lower in SVF at pH 4.2 than in water for negatively charged and positively charged NPs, respectively. At pH 7.0, this decrease was around 20- and 385-fold, respectively. The estimated times required to cross a layer of SVF were equal to or lower than 1.7 h for negatively charged NPs, while for positively charged NPs these values were equal to or higher than 7 h. Overall, our results suggest that negatively charged PCL NPs may be suitable to be used as carriers in order to deliver dapivirine and potentially other antiretroviral drugs to the cervicovaginal mucosal lining. Also, they further reinforce the importance in characterizing the interactions of nanosystems with mucus fluids or surrogates when considering mucosal drug delivery.

Stress orientation and fracturing during three-dimensional buckling: Numerical simulation and application to chocolate-tablet structures in folded turbidites, SW Portugal

NASA Astrophysics Data System (ADS)

Reber, J. E.; Schmalholz, S. M.; Burg, J.-P.

2010-10-01

Two orthogonal sets of veins, both orthogonal to bedding, form chocolate tablet structures on the limbs of folded quartzwackes of Carboniferous turbidites in SW Portugal. Structural observations suggest that (1) mode 1 fractures transverse to the fold axes formed while fold amplitudes were small and limbs were under layer-subparallel compression and (2) mode 1 fractures parallel to the fold axes formed while fold amplitudes were large and limbs were brought to be under layer-subparallel tension. We performed two- and three-dimensional numerical simulations investigating the evolution of stress orientations during viscous folding to test whether and how these two successive sets of fractures were related to folding. We employed ellipses and ellipsoids for the visualization and quantification of the local stress field. The numerical simulations show a change in the orientation of the local σ1 direction by almost 90° with respect to the bedding plane in the fold limbs. The coeval σ3 direction rotates from parallel to the fold axis at low fold amplitudes to orthogonal to the fold axis at high fold amplitudes. The stress orientation changes faster in multilayers than in single-layers. The numerical simulations are consistent with observation and provide a mechanical interpretation for the formation of the chocolate tablet structures through consecutive sets of fractures on rotating limbs of folded competent layers.

Origin of orogenic remagnetizations in Mississippian carbonates, Sawtooth Range, Montana

NASA Astrophysics Data System (ADS)

O'Brien, V. J.; Moreland, K. M.; Elmore, R. D.; Engel, M. H.; Evans, M. A.

2007-06-01

Paleomagnetic results are presented from Mississippian Madison Group carbonates in the Sawtooth Range, northwestern Montana. Samples were collected from sites along two east-west trending transects perpendicular to the thrust faults in the Sun River Canyon and in the North and South Forks of the Teton River and from three folds. The Madison Group contains a widespread characteristic remanent magnetization (ChRM) that resides in magnetite with southerly declinations and moderately steep up inclinations. Tilt test results suggest that the ChRM is pretilting in the thrust sheets and Teton anticline but syntilting in the Clary Coulee and Swift Dam folds. The ChRMs all have the same characteristics and were probably caused by the same remagnetization event, yet the tilt test results are different. One explanation involves the difference in fold types between the Teton anticline (fault bend fold geometry) and the Clary Coulee and Swift Dam folds (fault propagation fold geometries). The deformation that produced the two geometries could have caused variations in strain/stress, which may have altered an original pretilting into a syntilting ChRM. A mean paleopole for the three pretilting tilt test results (67.2°N, 177.9°E; A95 = 13.1°) suggests remanence acquisition in the late Jurassic-early Tertiary. The ChRM is interpreted as a chemical remanent magnetization (CRM). Geochemical studies indicate that the Mississippian carbonates were altered by evolved fluids with radiogenic 87Sr/86Sr values, and petrographic analysis indicates that hydrocarbons migrated through the carbonates. The CRM is interpreted to be related to alteration by one of these fluids.

Computation of the three-dimensional medial surface dynamics of the vocal folds.

PubMed

Döllinger, Michael; Berry, David A

2006-01-01

To increase our understanding of pathological and healthy voice production, quantitative measurement of the medial surface dynamics of the vocal folds is significant, albeit rarely performed because of the inaccessibility of the vocal folds. Using an excised hemilarynx methodology, a new calibration technique, herein referred to as the linear approximate (LA) method, was introduced to compute the three-dimensional coordinates of fleshpoints along the entire medial surface of the vocal fold. The results were compared with results from the direct linear transform. An associated error estimation was presented, demonstrating the improved accuracy of the new method. A test on real data was reported including computation of quantitative measurements of vocal fold dynamics.

Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

NASA Astrophysics Data System (ADS)

Finkelstein, A. V.

1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

Paleomagnetism of Carbonates and the Synfolding Test in the North American Cordillera

NASA Astrophysics Data System (ADS)

Nemkin, Samantha Reevs

Carbonate remagnetizations are globally widespread and typically the result of secondary magnetite growth, which, prior to the 1980's, were erroneously interpreted as primary magnetization directions. Whereas remagnetizations were eventually recognized, their timing remained mostly dated by qualitative comparison to an apparent polar wander path (APWP) after paleomagnetic field tests. This thesis demonstrates that quantitative ages can be assigned to remagnetizations by correlating synfolding remagnetization directions with ages from 40Ar/39Ar dating of individual folds. Central to the approach in this study is sampling of local-scale carbonate folds in order to produce multiple individual fold tests, instead of one regional fold test application in a field area. Results from the North American Cordillera in Montana, Idaho/Wyoming, the Monterrey Salient in northern Mexico, and central Mexico are reported. Remagnetization ages are determined for each field area by connecting synfolding remagnetizations with fold ages, which span the Late Cretaceous to Eocene. Mississippian limestones from Montana (Chpt. 2) and the Lower Cretaceous carbonates from the Monterrey Salient (Chpt. 3) have remagnetization ages of 54 Ma and 48-52 Ma, respectively. Results from Cretaceous carbonates in central Mexico (Chpt. 4) preserve two regionally distinct remagnetization events at 77 Ma and 44 Ma. A study of folded Mississippian limestones in Idaho and Wyoming similarly indicate the presence of a remagnetization event, but results remain inconclusive for lack of suitable sampling sites (Appendix A). Remagnetization ages coincide with periods of tectonic activity in the North American Cordillera and are interpreted as the result of chemical growth of magnetite. It is proposed that the formation mechanism of secondary remanences is from the interaction of carbonates with an iron-bearing fluid that may also have produced illitization in clay-rich interlayers. Lithology and structural characteristics influence whether or not sufficient magnetite will grow, allowing the acquisition of a permanent secondary remanence. The local-scale fold sampling scheme provides a new, detailed understanding into the development of local paleomagnetic and deformational histories across a field area. Combining synfolding remagnetizations and fold ages provides an important method to date the timing of remagnetization acquisition in rock units, contributing significantly to the global paleopole database. Given that many carbonates worldwide are remagnetized, this coupled approach would permit broader use of the method. Moreover, the spatial distribution of syn-, pre-, and/or postfolding remanences in folds constrains local deformation events in an area and provides novel insights into the connection of remagnetization mechanism(s) and carbonate deformation.

A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories

PubMed Central

2015-01-01

Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics. PMID:25988351

A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories.

PubMed

Ramanathan, Ravishankar; Muñoz, Victor

2015-06-25

Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics.

The Role of Nanoparticle Design in Determining Analytical Performance of Lateral Flow Immunoassays.

PubMed

Zhan, Li; Guo, Shuang-Zhuang; Song, Fayi; Gong, Yan; Xu, Feng; Boulware, David R; McAlpine, Michael C; Chan, Warren C W; Bischof, John C

2017-12-13

Rapid, simple, and cost-effective diagnostics are needed to improve healthcare at the point of care (POC). However, the most widely used POC diagnostic, the lateral flow immunoassay (LFA), is ∼1000-times less sensitive and has a smaller analytical range than laboratory tests, requiring a confirmatory test to establish truly negative results. Here, a rational and systematic strategy is used to design the LFA contrast label (i.e., gold nanoparticles) to improve the analytical sensitivity, analytical detection range, and antigen quantification of LFAs. Specifically, we discovered that the size (30, 60, or 100 nm) of the gold nanoparticles is a main contributor to the LFA analytical performance through both the degree of receptor interaction and the ultimate visual or thermal contrast signals. Using the optimal LFA design, we demonstrated the ability to improve the analytical sensitivity by 256-fold and expand the analytical detection range from 3 log 10 to 6 log 10 for diagnosing patients with inflammatory conditions by measuring C-reactive protein. This work demonstrates that, with appropriate design of the contrast label, a simple and commonly used diagnostic technology can compete with more expensive state-of-the-art laboratory tests.

Protective clothing ensembles and physical employment standards.

PubMed

McLellan, Tom M; Havenith, George

2016-06-01

Physical employment standards (PESs) exist for certain occupational groups that also require the use of protective clothing ensembles (PCEs) during their normal work. This review addresses whether these current PESs appropriately incorporate the physiological burden associated with wearing PCEs during respective tasks. Metabolic heat production increases because of wearing PCE; this increase is greater than that because of simply the weight of the clothing and can vary 2-fold among individuals. This variation negates a simple adjustment to the PES for the effect of the clothing on metabolic rate. As a result, PES testing that only simulates the weight of the clothing and protective equipment does not adequately accommodate this effect. The physiological heat strain associated with the use of PCEs is also not addressed with current PESs. Typically the selection tests of a PES lasts less than 20 min, whereas the requirement for use of PCE in the workplace may approach 1 h before cooling strategies can be employed. One option that might be considered is to construct a heat stress test that requires new recruits and incumbents to work for a predetermined duration while exposed to a warm environmental temperature while wearing the PCE.

Solvent viscosity and friction in protein folding dynamics.

PubMed

Hagen, Stephen J

2010-08-01

The famous Kramers rate theory for diffusion-controlled reactions has been extended in numerous ways and successfully applied to many types of reactions. Its application to protein folding reactions has been of particular interest in recent years, as many researchers have performed experiments and simulations to test whether folding reactions are diffusion-controlled, whether the solvent is the source of the reaction friction, and whether the friction-dependence of folding rates generally can provide insight into folding dynamics. These experiments involve many practical difficulties, however. They have also produced some unexpected results. Here we briefly review the Kramers theory for reactions in the presence of strong friction and summarize some of the subtle problems that arise in the application of the theory to protein folding. We discuss how the results of these experiments ultimately point to a significant role for internal friction in protein folding dynamics. Studies of friction in protein folding, far from revealing any weakness in Kramers theory, may actually lead to new approaches for probing diffusional dynamics and energy landscapes in protein folding.

Atomic interaction networks in the core of protein domains and their native folds.

PubMed

Soundararajan, Venkataramanan; Raman, Rahul; Raguram, S; Sasisekharan, V; Sasisekharan, Ram

2010-02-23

Vastly divergent sequences populate a majority of protein folds. In the quest to identify features that are conserved within protein domains belonging to the same fold, we set out to examine the entire protein universe on a fold-by-fold basis. We report that the atomic interaction network in the solvent-unexposed core of protein domains are fold-conserved, extraordinary sequence divergence notwithstanding. Further, we find that this feature, termed protein core atomic interaction network (or PCAIN) is significantly distinguishable across different folds, thus appearing to be "signature" of a domain's native fold. As part of this study, we computed the PCAINs for 8698 representative protein domains from families across the 1018 known protein folds to construct our seed database and an automated framework was developed for PCAIN-based characterization of the protein fold universe. A test set of randomly selected domains that are not in the seed database was classified with over 97% accuracy, independent of sequence divergence. As an application of this novel fold signature, a PCAIN-based scoring scheme was developed for comparative (homology-based) structure prediction, with 1-2 angstroms (mean 1.61A) C(alpha) RMSD generally observed between computed structures and reference crystal structures. Our results are consistent across the full spectrum of test domains including those from recent CASP experiments and most notably in the 'twilight' and 'midnight' zones wherein <30% and <10% target-template sequence identity prevails (mean twilight RMSD of 1.69A). We further demonstrate the utility of the PCAIN protocol to derive biological insight into protein structure-function relationships, by modeling the structure of the YopM effector novel E3 ligase (NEL) domain from plague-causative bacterium Yersinia Pestis and discussing its implications for host adaptive and innate immune modulation by the pathogen. Considering the several high-throughput, sequence-identity-independent applications demonstrated in this work, we suggest that the PCAIN is a fundamental fold feature that could be a valuable addition to the arsenal of protein modeling and analysis tools.

Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds

PubMed Central

Soundararajan, Venkataramanan; Raman, Rahul; Raguram, S.; Sasisekharan, V.; Sasisekharan, Ram

2010-01-01

Vastly divergent sequences populate a majority of protein folds. In the quest to identify features that are conserved within protein domains belonging to the same fold, we set out to examine the entire protein universe on a fold-by-fold basis. We report that the atomic interaction network in the solvent-unexposed core of protein domains are fold-conserved, extraordinary sequence divergence notwithstanding. Further, we find that this feature, termed protein core atomic interaction network (or PCAIN) is significantly distinguishable across different folds, thus appearing to be “signature” of a domain's native fold. As part of this study, we computed the PCAINs for 8698 representative protein domains from families across the 1018 known protein folds to construct our seed database and an automated framework was developed for PCAIN-based characterization of the protein fold universe. A test set of randomly selected domains that are not in the seed database was classified with over 97% accuracy, independent of sequence divergence. As an application of this novel fold signature, a PCAIN-based scoring scheme was developed for comparative (homology-based) structure prediction, with 1–2 angstroms (mean 1.61A) Cα RMSD generally observed between computed structures and reference crystal structures. Our results are consistent across the full spectrum of test domains including those from recent CASP experiments and most notably in the ‘twilight’ and ‘midnight’ zones wherein <30% and <10% target-template sequence identity prevails (mean twilight RMSD of 1.69A). We further demonstrate the utility of the PCAIN protocol to derive biological insight into protein structure-function relationships, by modeling the structure of the YopM effector novel E3 ligase (NEL) domain from plague-causative bacterium Yersinia Pestis and discussing its implications for host adaptive and innate immune modulation by the pathogen. Considering the several high-throughput, sequence-identity-independent applications demonstrated in this work, we suggest that the PCAIN is a fundamental fold feature that could be a valuable addition to the arsenal of protein modeling and analysis tools. PMID:20186337

How Does Chronic Cigarette Smoke Exposure Affect Human Skin? A Global Proteomics Study in Primary Human Keratinocytes.

PubMed

Rajagopalan, Pavithra; Nanjappa, Vishalakshi; Raja, Remya; Jain, Ankit P; Mangalaparthi, Kiran K; Sathe, Gajanan J; Babu, Niraj; Patel, Krishna; Cavusoglu, Nükhet; Soeur, Jeremie; Pandey, Akhilesh; Roy, Nita; Breton, Lionel; Chatterjee, Aditi; Misra, Namita; Gowda, Harsha

2016-11-01

Cigarette smoking has been associated with multiple negative effects on human skin. Long-term physiological effects of cigarette smoke are through chronic and not acute exposure. Molecular alterations due to chronic exposure to cigarette smoke remain unclear. Primary human skin keratinocytes chronically exposed to cigarette smoke condensate (CSC) showed a decreased wound-healing capacity with an increased expression of NRF2 and MMP9. Using quantitative proteomics, we identified 4728 proteins, of which 105 proteins were overexpressed (≥2-fold) and 41 proteins were downregulated (≤2-fold) in primary skin keratinocytes chronically exposed to CSC. We observed an alteration in the expression of several proteins involved in maintenance of epithelial barrier integrity, including keratin 80 (5.3 fold, p value 2.5 × 10 -7 ), cystatin A (3.6-fold, p value 3.2 × 10 -3 ), and periplakin (2.4-fold, p value 1.2 × 10 -8 ). Increased expression of proteins associated with skin hydration, including caspase 14 (2.2-fold, p value 4.7 × 10 -2 ) and filaggrin (3.6-fold, p value 5.4 × 10 -7 ), was also observed. In addition, we report differential expression of several proteins, including adipogenesis regulatory factor (2.5-fold, p value 1.3 × 10 -3 ) and histone H1.0 (2.5-fold, p value 6.3 × 10 -3 ) that have not been reported earlier. Bioinformatics analyses demonstrated that proteins differentially expressed in response to CSC are largely related to oxidative stress, maintenance of skin integrity, and anti-inflammatory responses. Importantly, treatment with vitamin E, a widely used antioxidant, could partially rescue adverse effects of CSC exposure in primary skin keratinocytes. The utility of antioxidant-based new dermatological formulations in delaying or preventing skin aging and oxidative damages caused by chronic cigarette smoke exposure warrants further clinical investigations and multi-omics research.

Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale.

PubMed

Lin, Meishan; Gessmann, Dennis; Naveed, Hammad; Liang, Jie

2016-03-02

Knowledge of the transfer free energy of amino acids from aqueous solution to a lipid bilayer is essential for understanding membrane protein folding and for predicting membrane protein structure. Here we report a computational approach that can calculate the folding free energy of the transmembrane region of outer membrane β-barrel proteins (OMPs) by combining an empirical energy function with a reduced discrete state space model. We quantitatively analyzed the transfer free energies of 20 amino acid residues at the center of the lipid bilayer of OmpLA. Our results are in excellent agreement with the experimentally derived hydrophobicity scales. We further exhaustively calculated the transfer free energies of 20 amino acids at all positions in the TM region of OmpLA. We found that the asymmetry of the Gram-negative bacterial outer membrane as well as the TM residues of an OMP determine its functional fold in vivo. Our results suggest that the folding process of an OMP is driven by the lipid-facing residues in its hydrophobic core, and its NC-IN topology is determined by the differential stabilities of OMPs in the asymmetrical outer membrane. The folding free energy is further reduced by lipid A and assisted by general depth-dependent cooperativities that exist between polar and ionizable residues. Moreover, context-dependency of transfer free energies at specific positions in OmpLA predict regions important for protein function as well as structural anomalies. Our computational approach is fast, efficient and applicable to any OMP.

HMM-ModE: implementation, benchmarking and validation with HMMER3

PubMed Central

2014-01-01

Background HMM-ModE is a computational method that generates family specific profile HMMs using negative training sequences. The method optimizes the discrimination threshold using 10 fold cross validation and modifies the emission probabilities of profiles to reduce common fold based signals shared with other sub-families. The protocol depends on the program HMMER for HMM profile building and sequence database searching. The recent release of HMMER3 has improved database search speed by several orders of magnitude, allowing for the large scale deployment of the method in sequence annotation projects. We have rewritten our existing scripts both at the level of parsing the HMM profiles and modifying emission probabilities to upgrade HMM-ModE using HMMER3 that takes advantage of its probabilistic inference with high computational speed. The method is benchmarked and tested on GPCR dataset as an accurate and fast method for functional annotation. Results The implementation of this method, which now works with HMMER3, is benchmarked with the earlier version of HMMER, to show that the effect of local-local alignments is marked only in the case of profiles containing a large number of discontinuous match states. The method is tested on a gold standard set of families and we have reported a significant reduction in the number of false positive hits over the default HMM profiles. When implemented on GPCR sequences, the results showed an improvement in the accuracy of classification compared with other methods used to classify the familyat different levels of their classification hierarchy. Conclusions The present findings show that the new version of HMM-ModE is a highly specific method used to differentiate between fold (superfamily) and function (family) specific signals, which helps in the functional annotation of protein sequences. The use of modified profile HMMs of GPCR sequences provides a simple yet highly specific method for classification of the family, being able to predict the sub-family specific sequences with high accuracy even though sequences share common physicochemical characteristics between sub-families. PMID:25073805

Binding site feature description of 2-substituted benzothiazoles as potential AcrAB-TolC efflux pump inhibitors in E. coli.

PubMed

Yilmaz, S; Altinkanat-Gelmez, G; Bolelli, K; Guneser-Merdan, D; Ufuk Over-Hasdemir, M; Aki-Yalcin, E; Yalcin, I

2015-01-01

The resistance-nodulation-division (RND) family efflux pumps are important in the antibiotic resistance of Gram-negative bacteria. However, although a number of bacterial RND efflux pump inhibitors have been developed, there has been no clinically available RND efflux pump inhibitor to date. A set of BSN-coded 2-substituted benzothiazoles were tested alone and in combinations with ciprofloxacin (CIP) against the AcrAB-TolC overexpressor Escherichia coli AG102 clinical strain. The results indicated that the BSN compounds did not show intrinsic antimicrobial activity when tested alone. However, when used in combinations with CIP, a reversal in the antibacterial activity of CIP with up to 10-fold better MIC values was observed. In order to describe the binding site features of these BSN compounds with AcrB, docking studies were performed using the CDocker method. The performed docking poses and the calculated binding energy scores revealed that the tested compounds BSN-006, BSN-023, and BSN-004 showed significant binding interactions with the phenylalanine-rich region in the distal binding site of the AcrB binding monomer. Moreover, the tested compounds BSN-006 and BSN-023 possessed stronger binding energies than CIP, verifying that BSN compounds are acting as the putative substrates of AcrB.

Species differences in the negative inotropic effect of acetylcholine and soman in rat, guinea pig, and rabbit hearts. (Reannouncement with new availability information)

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

Maxwell, D.M.; Thomsen, R.H.; Baskin, S.I.

1991-12-31

Acetylcholine reduced atrial contractions by 82.5% in guinea pig, 50.8% in rat, and 41.5% in rabbit. 2. The EC50, values for the negative inotropic effect of acetylcholine were 3.3 x 10(-7) M in rat and guinea pig atria and 4.1 x 10(-6) M in rabbit atria. 3. There was no correlation between the species differences in the negative inotropic effect of acetylcholine in atria and the density or affinity of acetylcholinesterase or muscarinic receptors. 4. Inhibition of atrial acetylcholinesterase with soman reduced the EC50 of acetylcholine three-fold in all species, but did not change the maximal inotropic effect of acetylcholine.more » 5. Species differences in the negative inotropic effect of acetylcholine may be caused by differences in the coupling between myocardial muscarinic receptors and the ion channels that mediate negative inotropy. Acetylcholine, cardiovascular response, species variation negative inotropic response.« less

Phosphorene/rhenium disulfide heterojunction-based negative differential resistance device for multi-valued logic

NASA Astrophysics Data System (ADS)

Shim, Jaewoo; Oh, Seyong; Kang, Dong-Ho; Jo, Seo-Hyeon; Ali, Muhammad Hasnain; Choi, Woo-Young; Heo, Keun; Jeon, Jaeho; Lee, Sungjoo; Kim, Minwoo; Song, Young Jae; Park, Jin-Hong

2016-11-01

Recently, negative differential resistance devices have attracted considerable attention due to their folded current-voltage characteristic, which presents multiple threshold voltage values. Because of this remarkable property, studies associated with the negative differential resistance devices have been explored for realizing multi-valued logic applications. Here we demonstrate a negative differential resistance device based on a phosphorene/rhenium disulfide (BP/ReS2) heterojunction that is formed by type-III broken-gap band alignment, showing high peak-to-valley current ratio values of 4.2 and 6.9 at room temperature and 180 K, respectively. Also, the carrier transport mechanism of the BP/ReS2 negative differential resistance device is investigated in detail by analysing the tunnelling and diffusion currents at various temperatures with the proposed analytic negative differential resistance device model. Finally, we demonstrate a ternary inverter as a multi-valued logic application. This study of a two-dimensional material heterojunction is a step forward toward future multi-valued logic device research.

Phosphorene/rhenium disulfide heterojunction-based negative differential resistance device for multi-valued logic

PubMed Central

Shim, Jaewoo; Oh, Seyong; Kang, Dong-Ho; Jo, Seo-Hyeon; Ali, Muhammad Hasnain; Choi, Woo-Young; Heo, Keun; Jeon, Jaeho; Lee, Sungjoo; Kim, Minwoo; Song, Young Jae; Park, Jin-Hong

2016-01-01

Recently, negative differential resistance devices have attracted considerable attention due to their folded current–voltage characteristic, which presents multiple threshold voltage values. Because of this remarkable property, studies associated with the negative differential resistance devices have been explored for realizing multi-valued logic applications. Here we demonstrate a negative differential resistance device based on a phosphorene/rhenium disulfide (BP/ReS2) heterojunction that is formed by type-III broken-gap band alignment, showing high peak-to-valley current ratio values of 4.2 and 6.9 at room temperature and 180 K, respectively. Also, the carrier transport mechanism of the BP/ReS2 negative differential resistance device is investigated in detail by analysing the tunnelling and diffusion currents at various temperatures with the proposed analytic negative differential resistance device model. Finally, we demonstrate a ternary inverter as a multi-valued logic application. This study of a two-dimensional material heterojunction is a step forward toward future multi-valued logic device research. PMID:27819264

CASP10-BCL::Fold efficiently samples topologies of large proteins.

PubMed

Heinze, Sten; Putnam, Daniel K; Fischer, Axel W; Kohlmann, Tim; Weiner, Brian E; Meiler, Jens

2015-03-01

During CASP10 in summer 2012, we tested BCL::Fold for prediction of free modeling (FM) and template-based modeling (TBM) targets. BCL::Fold assembles the tertiary structure of a protein from predicted secondary structure elements (SSEs) omitting more flexible loop regions early on. This approach enables the sampling of conformational space for larger proteins with more complex topologies. In preparation of CASP11, we analyzed the quality of CASP10 models throughout the prediction pipeline to understand BCL::Fold's ability to sample the native topology, identify native-like models by scoring and/or clustering approaches, and our ability to add loop regions and side chains to initial SSE-only models. The standout observation is that BCL::Fold sampled topologies with a GDT_TS score > 33% for 12 of 18 and with a topology score > 0.8 for 11 of 18 test cases de novo. Despite the sampling success of BCL::Fold, significant challenges still exist in clustering and loop generation stages of the pipeline. The clustering approach employed for model selection often failed to identify the most native-like assembly of SSEs for further refinement and submission. It was also observed that for some β-strand proteins model refinement failed as β-strands were not properly aligned to form hydrogen bonds removing otherwise accurate models from the pool. Further, BCL::Fold samples frequently non-natural topologies that require loop regions to pass through the center of the protein. © 2015 Wiley Periodicals, Inc.

Transiently disordered tails accelerate folding of globular proteins.

PubMed

Mallik, Saurav; Ray, Tanaya; Kundu, Sudip

2017-07-01

Numerous biological proteins exhibit intrinsic disorder at their termini, which are associated with multifarious functional roles. Here, we show the surprising result that an increased percentage of terminal short transiently disordered regions with enhanced flexibility (TstDREF) is associated with accelerated folding rates of globular proteins. Evolutionary conservation of predicted disorder at TstDREFs and drastic alteration of folding rates upon point-mutations suggest critical regulatory role(s) of TstDREFs in shaping the folding kinetics. TstDREFs are associated with long-range intramolecular interactions and the percentage of native secondary structural elements physically contacted by TstDREFs exhibit another surprising positive correlation with folding kinetics. These results allow us to infer probable molecular mechanisms behind the TstDREF-mediated regulation of folding kinetics that challenge protein biochemists to assess by direct experimental testing. © 2017 Federation of European Biochemical Societies.

Accurately controlled sequential self-folding structures by polystyrene film

NASA Astrophysics Data System (ADS)

Deng, Dongping; Yang, Yang; Chen, Yong; Lan, Xing; Tice, Jesse

2017-08-01

Four-dimensional (4D) printing overcomes the traditional fabrication limitations by designing heterogeneous materials to enable the printed structures evolve over time (the fourth dimension) under external stimuli. Here, we present a simple 4D printing of self-folding structures that can be sequentially and accurately folded. When heated above their glass transition temperature pre-strained polystyrene films shrink along the XY plane. In our process silver ink traces printed on the film are used to provide heat stimuli by conducting current to trigger the self-folding behavior. The parameters affecting the folding process are studied and discussed. Sequential folding and accurately controlled folding angles are achieved by using printed ink traces and angle lock design. Theoretical analyses are done to guide the design of the folding processes. Programmable structures such as a lock and a three-dimensional antenna are achieved to test the feasibility and potential applications of this method. These self-folding structures change their shapes after fabrication under controlled stimuli (electric current) and have potential applications in the fields of electronics, consumer devices, and robotics. Our design and fabrication method provides an easy way by using silver ink printed on polystyrene films to 4D print self-folding structures for electrically induced sequential folding with angular control.

Studies on silane to 70 GPa

NASA Astrophysics Data System (ADS)

Narayana, C.; Greene, R. G.; Ruoff, A. L.

2008-07-01

Raman and x-ray diffraction studies were made on silane in the diamond anvil cell using three different gaskets, stainless steel, tungsten and rhenium. The structure existing between 10 and 27 GPa is well characterized by the monoclinic space group P21c (#14). While the Gibbs free energy of formation of silane is positive at one atmosphere, it is calculated from the equation of state of silane and its reactants that this becomes negative near 4 GPa and remains negative until 13 GPa and then becomes positive again. At about 27 GPa, where quasi-quantum mechanical calculations suggest there should be a transformation from 4-fold to 6-fold (or even higher), the sample turns black. The Raman modes seize to exist beyond 30 GPa after showing softening above 25 GPa. At higher pressures it turns silvery. The gaskets play a different role as will be discussed. The sample brought back from 70 GPa contains amorphous Si (with attached hydrogen) as well as crystalline silicon. The lowest free energy system at high pressure is the decomposed reactants as observed.

Antifungal Activity of Eucalyptus Oil against Rice Blast Fungi and the Possible Mechanism of Gene Expression Pattern.

PubMed

Zhou, Li-Jun; Li, Fu-Rong; Huang, Li-Jie; Yang, Zhi-Rong; Yuan, Shu; Bai, Lin-Han

2016-05-12

Eucalyptus oil possesses a wide spectrum of biological activity, including anti-microbial, fungicidal, herbicidal, acaricidal and nematicidal properties. We studied anti-fungal activities of the leaf oil extracted from Eucalyptus. grandis × E. urophylla. Eleven plant pathogenic fungi were tested based on the mycelium growth rates with negative control. The results showed that Eucalyptus oil has broad-spectrum inhibitory effects toward these fungi. Remarkable morphological and structural alterations of hypha have been observed for Magnaporthe grisea after the treatment. The mRNA genome array of M. grisea was used to detect genes that were differentially expressed in the test strains treated by the Eucalyptus oil than the normal strains. The results showed 1919 genes were significantly affected, among which 1109 were down-regulated and 810 were up-regulated (p < 0.05, absolute fold change >2). According to gene ontology annotation analysis, these differentially expressed genes may cause abnormal structures and physiological function disorders, which may reduce the fungus growth. These results show the oil has potential for use in the biological control of plant disease as a green biopesticide.

Development and accuracy of quantitative real-time polymerase chain reaction assays for detection and quantification of enterotoxigenic Escherichia coli (ETEC) heat labile and heat stable toxin genes in travelers' diarrhea samples.

PubMed

Youmans, Bonnie P; Ajami, Nadim J; Jiang, Zhi-Dong; Petrosino, Joseph F; DuPont, Herbert L; Highlander, Sarah K

2014-01-01

Enterotoxigenic Escherichia coli (ETEC), the leading bacterial pathogen of travelers' diarrhea, is routinely detected by an established DNA hybridization protocol that is neither sensitive nor quantitative. Quantitative real-time polymerase chain reaction (qPCR) assays that detect the ETEC toxin genes eltA, sta1, and sta2 in clinical stool samples were developed and tested using donor stool inoculated with known quantities of ETEC bacteria. The sensitivity of the qPCR assays is 89%, compared with 22% for the DNA hybridization assay, and the limits of detection are 10,000-fold lower than the DNA hybridization assays performed in parallel. Ninety-three clinical stool samples, previously characterized by DNA hybridization, were tested using the new ETEC qPCR assays. Discordant toxin profiles were observed for 22 samples, notably, four samples originally typed as ETEC negative were ETEC positive. The qPCR assays are unique in their sensitivity and ability to quantify the three toxin genes in clinical stool samples.

[Knockdown of dopamine receptor D2 upregulates the expression of adiogenic genes in mouse primary mesencephalic neurons].

PubMed

Ding, Jiaqi; Chen, Xiaoli; Lin, Jiaji; Zhu, Junling; Li, Zhuyi

2018-01-01

Objective To study the effects of dopamine receptor D2 (DRD2) on the adipogenesis genes in mouse primary mesencephalic neurons. Methods The lentiviral vectors which expressed specific shRNA targeting DRD2 were constructed to decrease DRD2 expression in mouse primary mesencephalic neurons. High throughput sequencing (HTS) analysis was used to investigate gene expression changes between the DRD2 knock-down group and the negative control group. Real-time quantitative PCR (qRT-PCR) and Western blot analysis were applied to verify the differently expressed genes. Fatty acids were measured by fatty acid detection kit. Results DRD2 expression was effectively down-regulated in mouse primary mesencephalic neurons by lentiviral vectors. HTS revealed adipogenesis genes were significantly up-regulated after DRD2 down-regulation, mainly including delta(14)-sterol reductase, acetyl-coenzyme A synthetase, insulin-induced gene 1 protein and especially stearoyl-coenzyme A desaturase 1 (SCD1, 4-fold upregulated). The qRT-PCR and Western blot analysis verified that SCD1 was upregulated 2.6 folds and 2 folds respectively by lentiviral DRD2-shRNA vectors. Moreover, the SCD1-related free fatty acids were significantly more increased than the negative control group. Conclusion DRD2 in primary mesencephalic neurons had a significant regulative effect on the adipogenesis genes. The up-regulation of SCD1 can accelerate the conversion of saturated fatty acids to monounsaturated fatty acids and prevent the damage of lipid toxicity to cells.

New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface

NASA Astrophysics Data System (ADS)

Zorgani, Mohamed Amine; Patron, Kevin; Desvaux, Mickaël

2014-07-01

Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface.

PubMed

Zorgani, Mohamed Amine; Patron, Kevin; Desvaux, Mickaël

2014-07-01

Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

Health effects of exposure to herb dust in valerian growing farmers.

PubMed

Skórska, Czesława; Golec, Marcin; Mackiewicz, Barbara; Góra, Anna; Dutkiewicz, Jacek

2005-01-01

The aim of the present study was to determine the health status of farmers cultivating valerian (Valeriana officinalis L.) and occupationally exposed to dust from this plant. A group of 75 valerian growing farmers were examined. As a reference group, 50 urban dwellers, not exposed to any kind of organic dust were examined. All people were interviewed for the presence of work-related symptoms and subjected to physical and spirometric examinations. Skin prick tests were conducted with 4 microbial antigens associated with organic dust and 3 herbal extracts, precipitin tests with 12 microbial antigens and 4 herbal extracts and tests for specific inhibition of leukocyte migration with 4 microbial antigens. 30.7 % of the valerian farmers reported occurrence of work-related symptoms. No significant differences were found between the spirometric values in the group of valerian farmers and the reference group. Valerian farmers showed a low frequency of positive skin reactions to all tested antigens (0-4.0 %), not significantly greater compared to reference group. The frequency of positive precipitin reactions to the antigen of Gram-negative bacterium Pantoea agglomerans was very high in valerian farmers (45.5 %) with 3-fold concentrated sera and significantly greater compared to the reference group (p < 0.001). The positive precipitin response of valerian farmers to other microbial and herbal antigens was much lower or absent and did not show any difference compared to reference group. In the test for specific inhibition of leukocyte migration, the highest frequencies of positive reactions in valerian farmers were noted with Pantoea agglomerans and Saccharopolyspora rectivirgula (15.0 % each), in both cases significantly greater compared to reference group (p < 0.05). In conclusion, the farmers growing valerian showed a moderate frequency of work-related symptoms and low reactivity to most microbial and herbal allergens. They exhibited an increased immunologic response to Gram-negative bacterium Pantoea agglomerans which appears to be the most important risk factor associated with valerian dust.

Use of RDTs to improve malaria diagnosis and fever case management at primary health care facilities in Uganda.

PubMed

Kyabayinze, Daniel J; Asiimwe, Caroline; Nakanjako, Damalie; Nabakooza, Jane; Counihan, Helen; Tibenderana, James K

2010-07-12

Early and accurate diagnosis of malaria followed by prompt treatment reduces the risk of severe disease in malaria endemic regions. Presumptive treatment of malaria is widely practised where microscopy or rapid diagnostic tests (RDTs) are not readily available. With the introduction of artemisinin-based combination therapy (ACT) for treatment of malaria in many low-resource settings, there is need to target treatment to patients with parasitologically confirmed malaria in order to improve quality of care, reduce over consumption of anti-malarials, reduce drug pressure and in turn delay development and spread of drug resistance. This study evaluated the effect of malaria RDTs on health workers' anti-malarial drug (AMD) prescriptions among outpatients at low level health care facilities (LLHCF) within different malaria epidemiological settings in Uganda. All health workers (HWs) in 21 selected intervention (where RDTs were deployed) LLHF were invited for training on the use RDTs. All HWs were trained to use RDTs for parasitological diagnosis of all suspected malaria cases irrespective of age. Five LLHCFs with clinical diagnosis (CD only) were included for comparison. Subsequently AMD prescriptions were compared using both a 'pre-post' and 'intervention-control' analysis designs. In-depth interviews of the HWs were conducted to explore any factors that influence AMD prescription practices. A total of 166,131 out-patient attendances (OPD) were evaluated at 21 intervention LLHCFs. Overall use of RDTs resulted in a 38% point reduction in AMD prescriptions. There was a two-fold reduction (RR 0.62, 95% CI 0.55-0.70) in AMD prescription with the greatest reduction in the hypo-endemic setting (RR 0.46 95% CI 0.51-0.53) but no significant change in the urban setting (RR1.01, p-value=0.820). Over 90% of all eligible OPD patients were offered a test. An average of 30% (range 25%-35%) of the RDT-negative fever patients received AMD prescriptions. When the test result was negative, children under five years of age were two to three times more likely (OR 2.6 p-value<0.001) to receive anti-malarial prescriptions relative to older age group. Of the 63 HWs interviewed 92% believed that a positive RDT result confirmed malaria, while only 49% believed that a negative RDT result excluded malaria infection. Use of RDTs resulted in a 2-fold reduction in anti-malarial drug prescription at LLHCFs. The study demonstrated that RDT use is feasible at LLHCFs, and can lead to better targetting of malaria treatment. Nationwide deployment of RDTs in a systematic manner should be prioritised in order to improve fever case management. The process should include plans to educate HWs about the utility of RDTs in order to maximize acceptance and uptake of the diagnostic tools and thereby leading to the benefits of parasitological diagnosis of malaria.

Characterization of orogenic remagnetizations within various fold geometries in Carboniferous carbonates from thin skinned fold and thrust belts, SW Alberta and NW Montana

NASA Astrophysics Data System (ADS)

Zechmeister, M. S.; Elmore, R. D.; Ferre, E. C.; Pannalal, S. J.; Hamilton, E. M.

2007-12-01

Paleomagnetic and rock magnetic analysis was conducted on a complex fault propagation fold train in Kananaskis Country, Alberta to compliment an ongoing study of orogenic remagnetiztions in the thin-skinned, fold and thrust belt (NW Montana and SW Alberta). The complex structure is composed of an asymmetrical anticline to the west and chevron syncline to the east, with both folds plunging ~15° to the south. The fold train contains a magnetization with two stable ancient components. The characteristic remanent magnetization (ChRM) with northerly declinations and steep down inclinations is removed between ~350°C and the maximum unblocking temperature of 540°C. Tilt tests on the preliminary data reveal that the ChRM is early syntilting in the anticline and syntilting in the syncline. These results from this fold train are similar to a previous study in the Sawtooths (NW MT) which reported that fault propagation folds have a syntilting ChRM whereas fault bend folds contain a pretilting ChRM. An intermediate temperature reversed component is unblocked by 340°C and is late syntilting to post-tilting. Preliminary high-field rock magnetic data from folds in Montana and Alberta show that saturation is reached before 0.3T and the majority of the samples have wasp-waisted hysteresis loops. On a log plot of Mrs/Ms versus Hcr/Hc, the data has a power law distribution that is similar to trends reported by other authors. Interestingly though, samples from a fault bend fold have higher Mrs/Ms ratios than those measured in fault propagation folds, suggesting that strain induced by the various folding styles may influence the rock magnetic properties. Additional studies are underway to test these preliminary results and determine if the differences in the hysteresis ratios are significant. Petrographic analysis shows magnetite replacing pyrite in some samples suggesting an authigenic origin for the ChRM. The intensity of the ChRM as well as the strongest rock magnetic signal is most common in dark gray carbonates that are hydrocarbon reservoirs in the subsurface, suggesting the possibility that the origin of the ChRM may be related to hydrocarbon migration.

Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, Infectious hematopoietic necrosis virus

USGS Publications Warehouse

Purcell, Maureen K.; Hart, S. Alexandra; Kurath, Gael; Winton, James R.

2006-01-01

The fish rhabdovirus, Infectious hematopoietic necrosis virus (IHNV), is an important pathogen of salmonids. Cell culture assays have traditionally been used to quantify levels of IHNV in samples; however, real-time or quantitative RT-PCR assays have been proposed as a rapid alternative. For viruses having a single-stranded, negative-sense RNA genome, standard qRT-PCR assays do not distinguish between the negative-sense genome and positive-sense RNA species including mRNA and anti-genome. Thus, these methods do not determine viral genome copy number. This study reports development of strand-specific, qRT-PCR assays that use tagged primers for enhancing strand specificity during cDNA synthesis and quantitative PCR. Protocols were developed for positive-strand specific (pss-qRT-PCR) and negative-strand specific (nss-qRT-PCR) assays for IHNV glycoprotein (G) gene sequences. Validation with synthetic RNA transcripts demonstrated the assays could discriminate the correct strand with greater than 1000-fold fidelity. The number of genome copies in livers of IHNV-infected fish determined by nss-qRT-PCR was, on average, 8000-fold greater than the number of infectious units as determined by plaque assay. We also compared the number of genome copies with the quantity of positive-sense RNA and determined that the ratio of positive-sense molecules to negative-sense genome copies was, on average, 2.7:1. Potential future applications of these IHNV strand-specific qRT-PCR assays are discussed.

Cytoplasmic Electric Fields and Electroosmosis: Possible Solution for the Paradoxes of the Intracellular Transport of Biomolecules

PubMed Central

Andreev, Victor P.

2013-01-01

The objective of the paper is to show that electroosmotic flow might play an important role in the intracellular transport of biomolecules. The paper presents two mathematical models describing the role of electroosmosis in the transport of the negatively charged messenger proteins to the negatively charged nucleus and in the recovery of the fluorescence after photobleaching. The parameters of the models were derived from the extensive review of the literature data. Computer simulations were performed within the COMSOL 4.2a software environment. The first model demonstrated that the presence of electroosmosis might intensify the flux of messenger proteins to the nucleus and allow the efficient transport of the negatively charged phosphorylated messenger proteins against the electrostatic repulsion of the negatively charged nucleus. The second model revealed that the presence of the electroosmotic flow made the time of fluorescence recovery dependent on the position of the bleaching spot relative to cellular membrane. The magnitude of the electroosmotic flow effect was shown to be quite substantial, i.e. increasing the flux of the messengers onto the nucleus up to 4-fold relative to pure diffusion and resulting in the up to 3-fold change in the values of fluorescence recovery time, and therefore the apparent diffusion coefficient determined from the fluorescence recovery after photobleaching experiments. Based on the results of the modeling and on the universal nature of the electroosmotic flow, the potential wider implications of electroosmotic flow in the intracellular and extracellular biological processes are discussed. Both models are available for download at ModelDB. PMID:23613967

Cytoplasmic electric fields and electroosmosis: possible solution for the paradoxes of the intracellular transport of biomolecules.

PubMed

Andreev, Victor P

2013-01-01

The objective of the paper is to show that electroosmotic flow might play an important role in the intracellular transport of biomolecules. The paper presents two mathematical models describing the role of electroosmosis in the transport of the negatively charged messenger proteins to the negatively charged nucleus and in the recovery of the fluorescence after photobleaching. The parameters of the models were derived from the extensive review of the literature data. Computer simulations were performed within the COMSOL 4.2a software environment. The first model demonstrated that the presence of electroosmosis might intensify the flux of messenger proteins to the nucleus and allow the efficient transport of the negatively charged phosphorylated messenger proteins against the electrostatic repulsion of the negatively charged nucleus. The second model revealed that the presence of the electroosmotic flow made the time of fluorescence recovery dependent on the position of the bleaching spot relative to cellular membrane. The magnitude of the electroosmotic flow effect was shown to be quite substantial, i.e. increasing the flux of the messengers onto the nucleus up to 4-fold relative to pure diffusion and resulting in the up to 3-fold change in the values of fluorescence recovery time, and therefore the apparent diffusion coefficient determined from the fluorescence recovery after photobleaching experiments. Based on the results of the modeling and on the universal nature of the electroosmotic flow, the potential wider implications of electroosmotic flow in the intracellular and extracellular biological processes are discussed. Both models are available for download at ModelDB.

Variation in practice and resource utilization associated with the diagnosis and management of appendicitis at freestanding children's hospitals: implications for value-based comparative analysis.

PubMed

Rice-Townsend, Samuel; Barnes, Jeff N; Hall, Matthew; Baxter, Jessica L; Rangel, Shawn J

2014-06-01

To characterize the scope and magnitude of practice variation associated with the diagnosis and treatment of appendicitis at freestanding children's hospitals. Variation in care has been associated with poor outcomes and is believed to be a key driver of excess health care spending. Retrospective cohort study of 13,328 patients treated with appendicitis at 34 children's hospitals (9/2010-9/2011). Patients were divided into complicated and uncomplicated cohorts and examined for interhospital variation in the use of diagnostic imaging (computed tomography or ultrasonography), laboratory tests, parenteral nutrition (PN), peripherally inserted central catheters (PICC), and hospital cost. The number and distribution of statistical outliers were calculated for all measures. Significant variation was found for all measures, including a 3.5-fold difference in preoperative imaging (aggregate rate: 49.0%, range across hospitals: 21.2%-73.5%, P < 0.001) and a 5-fold difference in preoperative laboratory utilization (aggregate median: 2 tests/encounter, range: 1-5 tests/encounter, P < 0.001). For patients with complicated appendicitis, we characterized a 12-fold difference in postoperative imaging (aggregate rate: 19.4%, range: 4.9%-61.6%, P < 0.001), a 48-fold difference in PICC lines (aggregate rate: 18.9%, range: 1.7%-81.8%, P < 0.001), and a 100-fold difference in PN utilization (aggregate rate: 9.3%, range: 0.4%-42.0%, P < 0.001). Median hospital cost differed 4-fold for patients with uncomplicated disease (aggregate median: $6804, range: $4200-$16,796, P < 0.001) and 4.6-fold for patients with complicated disease (aggregate median: $13,138, range: $5419-$24,779, P < 0.001). Statistical outliers on the basis of high and low utilization were identified for all measures. Significant variation exists in practice, resource utilization, and treatment-related cost associated with the management of appendicitis at freestanding children's hospitals. Value-based measures are needed for benchmarking and to prioritize collaborative quality improvement efforts.

HPV testing with cytology triage for cervical cancer screening in routine practice.

PubMed

Louvanto, Karolina; Chevarie-Davis, Myriam; Ramanakumar, Agnihotram Venkata; Franco, Eduardo Luis; Ferenczy, Alex

2014-05-01

The purpose of this study was to evaluate the feasibility and effectiveness of Viral Testing Alone with Pap (Papanicolaou) Triage for Screening Cervical Cancer in Routine Practice (VASCAR) in a publicly funded university-affiliated hospital in Montreal, Canada. Women who are 30-65 years old are screened with the Hybrid Capture-2 assay. Women with negative results are retested at 3-year intervals; women with positive results are triaged with conventional cytologic methods. Women with Papanicolaou positive test results (≥atypical squamous cells of undetermined significance) are referred to colposcopy; women with Papanicolaou negative test results are retested with Hybrid Capture-2 assay and a Papanicolaou test in 1 year. Results were compared with a historic era (annual cytology with ≥atypical squamous cells of undetermined significance threshold for colposcopy referral) in the 3 years before VASCAR. VASCAR included 23,739 eligible women, among whom 1646 women (6.9%) tested positive for the human papillomavirus (HPV). Because of the need for subsequent sampling for cytologic testing, follow-up evaluation for cytologic triage was relatively poor; only 46% and 24% of HPV-positive women were Papanicolaou-triaged and underwent biopsy, respectively. Protocol violations occurred mainly in the early phases of implementation (12%). Detection of high-grade cervical intraepithelial neoplasia increased nearly 3-fold (rate ratio, 2.78; 95% confidence interval [CI], 2.1-3.7) during VASCAR, mostly because of a doubling in the rate of high-grade cervical intraepithelial neoplasia (34.0%; 95% CI, 21.2-48.8) compared with the historic cytology-only era (16.3%; 95% CI, 13.2-19.8). VASCAR reduced the median time to colposcopy from a positive screen from 11 months (95% CI, 10.48-11.50) to 3 months (95% CI, 2.64-3.80). VASCAR is feasible; however, it requires cosampling for HPV and cytology and for continuous education of healthcare providers of the HPV-Papanicolaou triage protocol. Efficacy in disease detection and reduction in time to colposcopy referrals compared with the historic cytology era is encouraging but should be considered preliminary because of the small number of patients who were tested. Copyright © 2014 Mosby, Inc. All rights reserved.

Recurrence predictive models for patients with hepatocellular carcinoma after radiofrequency ablation using support vector machines with feature selection methods.

PubMed

Liang, Ja-Der; Ping, Xiao-Ou; Tseng, Yi-Ju; Huang, Guan-Tarn; Lai, Feipei; Yang, Pei-Ming

2014-12-01

Recurrence of hepatocellular carcinoma (HCC) is an important issue despite effective treatments with tumor eradication. Identification of patients who are at high risk for recurrence may provide more efficacious screening and detection of tumor recurrence. The aim of this study was to develop recurrence predictive models for HCC patients who received radiofrequency ablation (RFA) treatment. From January 2007 to December 2009, 83 newly diagnosed HCC patients receiving RFA as their first treatment were enrolled. Five feature selection methods including genetic algorithm (GA), simulated annealing (SA) algorithm, random forests (RF) and hybrid methods (GA+RF and SA+RF) were utilized for selecting an important subset of features from a total of 16 clinical features. These feature selection methods were combined with support vector machine (SVM) for developing predictive models with better performance. Five-fold cross-validation was used to train and test SVM models. The developed SVM-based predictive models with hybrid feature selection methods and 5-fold cross-validation had averages of the sensitivity, specificity, accuracy, positive predictive value, negative predictive value, and area under the ROC curve as 67%, 86%, 82%, 69%, 90%, and 0.69, respectively. The SVM derived predictive model can provide suggestive high-risk recurrent patients, who should be closely followed up after complete RFA treatment. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Effect of O-acylmenthol and salt formation on the skin permeation of diclofenac acid.

PubMed

Zhao, Ligang; Li, Yan; Fang, Liang; Ren, Changshun; Xu, Yongnan; He, Zhonggui

2009-07-01

To enhance the transdermal delivery of diclofenac acid (DA) by using O-acylmenthol as a penetration enhancer and complexing with amines, or by a combination of the two methods. The skin permeability of diclofenac was tested in vitro across rat skin with each of the evaluated permeants in a saturated isopropyl myristate (IPM) donor solution. A 4.5-fold increase in the flux of diclofenac was observed by ion-pair formation with diethylamine; however, the cations with hydroxyl groups had negative effects on the transdermal delivery of diclofenac. 2-isopropyl-5-methylcyclohexyl 2-hydroxypanoate and 2-isopropyl-5-methylcyclohexyl heptanoate produced significant increase in the permeation of diclofenac potassium (D-K); however, both of them were ineffective for the other diclofenac salts, including diclofenac diethylamine (D-DETA), diclofenac ethanolamine (D-EA), diclofenac diethanolamine (D-DEA), diclofenac triethanolamine, and diclofenac N-(hydroxylethyl) piperidine. 2-isopropyl-5-methylcyclohexyl tetradecanoate was effective on the penetration of D-K, D-DETA, D-EA, and D-DEA. Also, it is exciting to note that the combined use of diethylamine with 2-isopropyl-5-methylcyclohexyl tetradecanoate produced a 9.74-fold increase in accumulation amount of diclofenac compared with DA in IPM. The use of ion pair in combination with O-acylmenthol is necessary to further increase the diclofenac flux to provide better compliance for the patients undergoing clinical therapy.

Reproductive toxicity assessment of benzo[a]pyrene in the marine polychaete Perinereis nuntia

NASA Astrophysics Data System (ADS)

Wu, Qingyang; Wang, Shuqi; Chen, Xiaopeng; Li, Ping

2017-07-01

Benzo[a]pyrene (B[a]P) is an increasingly present marine environmental pollutant, yet our understanding of the long-term consequences of reproductive toxicity in marine benthic polychaetes remains limited. To test the reproductive toxicity of B[a]P on polychaetes, Perinereis nuntia was exposed to B[a]P-contaminated artificial seawater and sexual maturation, the sex ratio, number of eggs spawned, fertilization and hatching rated, as well as vitellogenin (VTG) mRNA expression levels were analyzed. A low concentration of B[a]P (2.5 μg/L) had no effects on the rate of sexual maturation, spawning, or fertilization but significantly increased the sex ratio (female: male) from 1.6±0.15:1 to 2.3±0.18:1, inhibited hatching rate by 27%, and significantly increased VTG mRNA expression level by 3.7-fold following a 60-day exposure, compared with those in the solvent controls. A higher concentration of B[a]P (25 μg/L) caused more serious effects; sexual maturation, fertilization success, and hatching decreased by 31%, 17% and 46%, respectively, and the sex ratio (female: male) and VTG mRNA gene expression level increased by 54% and 7.1-fold, respectively. These results demonstrate that sublethal concentrations of B[a]P negatively affect reproductive performance of the sandworm P. nuntia.

An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation.

PubMed

Friedt, Jenna; Leavens, Fern M V; Mercier, Evan; Wieden, Hans-Joachim; Kothe, Ute

2014-04-01

Pseudouridine synthases introduce the most common RNA modification and likely use the same catalytic mechanism. Besides a catalytic aspartate residue, the contributions of other residues for catalysis of pseudouridine formation are poorly understood. Here, we have tested the role of a conserved basic residue in the active site for catalysis using the bacterial pseudouridine synthase TruB targeting U55 in tRNAs. Substitution of arginine 181 with lysine results in a 2500-fold reduction of TruB's catalytic rate without affecting tRNA binding. Furthermore, we analyzed the function of a second-shell aspartate residue (D90) that is conserved in all TruB enzymes and interacts with C56 of tRNA. Site-directed mutagenesis, biochemical and kinetic studies reveal that this residue is not critical for substrate binding but influences catalysis significantly as replacement of D90 with glutamate or asparagine reduces the catalytic rate 30- and 50-fold, respectively. In agreement with molecular dynamics simulations of TruB wild type and TruB D90N, we propose an electrostatic network composed of the catalytic aspartate (D48), R181 and D90 that is important for catalysis by fine-tuning the D48-R181 interaction. Conserved, negatively charged residues similar to D90 are found in a number of pseudouridine synthases, suggesting that this might be a general mechanism.

An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation

PubMed Central

Friedt, Jenna; Leavens, Fern M. V.; Mercier, Evan; Wieden, Hans-Joachim; Kothe, Ute

2014-01-01

Pseudouridine synthases introduce the most common RNA modification and likely use the same catalytic mechanism. Besides a catalytic aspartate residue, the contributions of other residues for catalysis of pseudouridine formation are poorly understood. Here, we have tested the role of a conserved basic residue in the active site for catalysis using the bacterial pseudouridine synthase TruB targeting U55 in tRNAs. Substitution of arginine 181 with lysine results in a 2500-fold reduction of TruB’s catalytic rate without affecting tRNA binding. Furthermore, we analyzed the function of a second-shell aspartate residue (D90) that is conserved in all TruB enzymes and interacts with C56 of tRNA. Site-directed mutagenesis, biochemical and kinetic studies reveal that this residue is not critical for substrate binding but influences catalysis significantly as replacement of D90 with glutamate or asparagine reduces the catalytic rate 30- and 50-fold, respectively. In agreement with molecular dynamics simulations of TruB wild type and TruB D90N, we propose an electrostatic network composed of the catalytic aspartate (D48), R181 and D90 that is important for catalysis by fine-tuning the D48-R181 interaction. Conserved, negatively charged residues similar to D90 are found in a number of pseudouridine synthases, suggesting that this might be a general mechanism. PMID:24371284

Varicocele Negatively Affects Sperm Mitochondrial Respiration.

PubMed

Ferramosca, Alessandra; Albani, Denise; Coppola, Lamberto; Zara, Vincenzo

2015-10-01

To evaluate the effect of varicocele on oxidative stress, sperm mitochondrial respiratory efficiency, sperm morphology, and semen parameters. A total of 20 patients with varicocele and 20 normozoospermic subjects without varicocele (control group) were recruited from a medical center for reproductive biology. The levels of serum reactive oxygen metabolites and seminal lipid peroxides were assessed for both control and varicocele subjects. Sperm deoxyribonucleic acid fragmentation was measured by sperm chromatin dispersion test. Mitochondrial respiratory activity was evaluated with a polarographic assay of oxygen consumption carried out in hypotonically treated sperm cells. In this study, varicocele patients were compared with men without varicoceles. Oxidative stress was observed in the serum and seminal fluid of varicocele patients. These patients showed an increase of 59% (P <.05) in serum reactive oxygen metabolites and a 3-fold increase in the level of sperm lipid peroxides. A parallel and significant increase (a 2-fold increase; P <.05) in the degree of sperm deoxyribonucleic acid fragmentation was also observed. Varicocele patients showed a 27% decrease (P <.05) in mitochondrial respiratory activity in comparison to the control group. A 32% increase (P <.05) in sperm midpiece defects and a 41% decrease (P <.05) in sperm concentration and motility were also observed. Men with varicocele have increased markers of oxidative stress and decreased mitochondrial respiratory activity. These results correlated with abnormalities in semen parameters. For morphology, these correlated with midpiece defects. Copyright © 2015 Elsevier Inc. All rights reserved.

The potential use of novel chitosan-coated deformable liposomes in an ocular drug delivery system.

PubMed

Chen, Hongdan; Pan, Hao; Li, Panpan; Wang, Hui; Wang, Xin; Pan, Weisan; Yuan, Yue

2016-07-01

In this study, novel chitosan-coated deformable liposomes (DL-CS) were proposed as an ocular drug delivery system to prolong pre-corneal retention, and improve transcorneal penetration and absorption. Flurbiprofen-loaded deformable liposomes (FP-DL) were prepared by a modified ethanol injection method and then coated with chitosan. Both DL and DL-CS exhibited a homogeneous particle size distribution, high encapsulation efficiency and good stability. After coating with 0.1% CS, the zeta potential was shifted from negative to positive. The apparent permeability coefficient of FP-DL-0.1% CS evaluated using isolated rabbit corneas was 1.29-, 1.95- and 4.59- fold greater than that of uncoated FP-DL, conventional liposomes and FP solution (P<0.01), respectively. The in vivo pre-corneal retention time and elimination dynamics were assessed using gamma scintigraphy technology. The area under the remaining activity-time of FP-DL-0.1% CS was prolonged 2.84- and 1.53-fold compared with that of the FP solution and FP-DL groups, respectively. Moreover, the ocular irritation test in vivo revealed that DL-0.1% CS produced no ocular damage or abnormal clinical signs. These results indicate that DL-CS appears to be a novel ophthalmic drug delivery strategy with the potential to overcome the limitations of conventional eye drops. Copyright © 2016 Elsevier B.V. All rights reserved.

NASA Examines Technology To Fold Aircraft Wings In Flight

NASA Image and Video Library

2018-01-17

NASA conducts a flight test series to investigate the ability of an innovative technology to fold the outer portions of wings in flight as part of the Spanwise Adaptive Wing project, or SAW. Flight tests took place at NASA Armstrong Flight Research Center in California, using a subscale UAV called Prototype Technology-Evaluation Research Aircraft, or PTERA, provided by Area-I. NASA Glenn Research Center in Cleveland developed the alloy material, and worked with Boeing Research & Technology to integrate the material into an actuator. The alloy is triggered by temperature to move the outer portions of wings up or down in flight. The ability to fold wings to the ideal position of various flight conditions may produce several aerodynamic benefits for both subsonic and supersonic aircraft.

A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides

NASA Astrophysics Data System (ADS)

Gao, Ya; Zhang, Chaomin; Wang, Xianwei; Zhu, Tong

2017-07-01

We tested the ability of some current AMBER force fields, namely, AMBER03, AMBER99SB, AMBER99SB-ildn, AMBER99SB-nmr, AMBER12SB, AMBER14SB, and AMBER14ipq, with implicit solvent model in reproducing the folding behavior of two peptides by REMD simulations. AMBER99SB-nmr force field provides the most reliable performance. After a novel polarized hydrogen bond charge model is considered, the α-helix successfully folded to its native state, while the further folding of the β-hairpin is not observed. This study strongly suggests that polarization effect and correct torsional term are important to investigate dynamic and conformational properties of peptides with different secondary structures.

Cytosolic ppGpp accumulation induces retarded plant growth and development.

PubMed

Ihara, Yuta; Masuda, Shinji

2016-01-01

In bacteria a second messenger, guanosine 5'-diphosphate 3'-diphosphate (ppGpp), synthesized upon nutrient starvation, controls many gene expressions and enzyme activities, which is necessary for growth under changeable environments. Recent studies have shown that ppGpp synthase and hydrolase are also conserved in eukaryotes, although their functions are not well understood. We recently showed that ppGpp-overaccumulation in Arabidopsis chloroplasts results in robust growth under nutrient-limited conditions, demonstrating that the bacterial-like stringent response at least functions in plastids. To test if ppGpp also functions in the cytosol, we constructed the transgenic Arabidopsis expressing Bacillus subtilis ppGpp synthase gene yjbM. Upon induction of the gene, the mutant synthesizes ∼10-20-fold higher levels of ppGpp, and its fresh weight was reduced to ˜80% that of the wild type. These results indicate that cytosolic ppGpp negatively regulates plant growth and development.

Applicability of ERTS-1 to Montana geology

NASA Technical Reports Server (NTRS)

Weidman, R. M. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Geologic maps of four test sites were compiled at 1/250,000. Band 7 prints enlarged to 1/500,000 scale are the best for the purpose, and negative prints provide a valuable supplement. More than 100 mapped lineaments represent most of the major faults of the area and a large number of suspected faults, including many of northeast trend. Under ideal conditions dip slopes may be recognized, laccoliths outlined, and axial traces drawn for narrow, plunging folds. Use of ERTS-1 imagery will greatly facilitate construction of a needed tectonic map of Montana. From ERTS-1 imagery alone, it was possible to identify up-turned undivided Paleozoic and Mesozoic strata and to map the boundaries of mountain glaciation, intermontane basins, a volcanic field, and an area of granitic rocks. It was also possible to outline clay pans associated with bentonite. However, widespread recognition of gross rock types will be difficult.

Exposure of adolescent mice to 3,4-methylenedioxypyrovalerone increases the psychostimulant, rewarding and reinforcing effects of cocaine in adulthood.

PubMed

López-Arnau, R; Luján, M A; Duart-Castells, L; Pubill, D; Camarasa, J; Valverde, O; Escubedo, E

2017-05-01

3,4-Methylenedioxypyrovalerone (MDPV) is a synthetic cathinone with powerful psychostimulant effects. It selectively inhibits the dopamine transporter (DAT) and is 10-50-fold more potent as a DAT blocker than cocaine, suggesting a high abuse liability. The main objective of the present study was to assess the consequences of an early (adolescence) MDPV exposure on the psychostimulant, rewarding and reinforcing effects induced by cocaine in adult mice. Twenty-one days after MDPV pretreatment (1.5 mg·kg -1 , s.c., twice daily for 7 days), adult mice were tested with cocaine, using locomotor activity, conditioned place preference and self-administration (SA) paradigms. In parallel, dopamine D 2 receptor density and the expression of c-Fos and ΔFosB in the striatum were determined. MDPV treatment enhanced the psychostimulant and conditioning effects of cocaine. Acquisition of cocaine SA was unchanged in mice pretreated with MDPV, whereas the breaking point achieved under a progressive ratio programme and reinstatement after extinction were higher in this group of mice. MDPV decreased D 2 receptor density but increased ΔFosB expression three-fold. As expected, acute cocaine increased c-Fos expression, but MDPV pretreatment negatively influenced its expression. ΔFosB accumulation declined during MDPV withdrawal, although it remained elevated in adult mice when tested for cocaine effects. MDPV exposure during adolescence induced long-lasting adaptive changes related to enhanced responsiveness to cocaine in the adult mice that seems to lead to a higher vulnerability to cocaine abuse. This particular behaviour correlated with increased expression of ΔFosB. © 2017 The British Pharmacological Society.

Stanniocalcin 2 is an estrogen-responsive gene coexpressed with the estrogen receptor in human breast cancer.

PubMed

Bouras, Toula; Southey, Melissa C; Chang, Andy C; Reddel, Roger R; Willhite, Dorian; Glynne, Richard; Henderson, Michael A; Armes, Jane E; Venter, Deon J

2002-03-01

Differences in gene expression are likely to explain the phenotypic variation between hormone-responsive and hormone-unresponsive breast cancers. In this study, DNA microarray analysis of approximately 10,000 known genes and 25,000 expressed sequence tag clusters was performed to identify genes induced by estrogen and repressed by the pure antiestrogen ICI 182 780 in vitro that correlated with estrogen receptor (ER) expression in primary breast carcinomas in vivo. Stanniocalcin (STC) 2 was identified as one of the genes that fulfilled these criteria. DNA microarray hybridization showed a 3-fold induction of STC2 mRNA expression in MCF-7 cells in < or = 3 h of estrogen exposure and a 3-fold repression in the presence of antiestrogen (one-way ANOVA, P < 0.0005). In 13 ER-positive and 12 ER-negative breast carcinomas, the microarray-derived mRNA levels observed for STC2 correlated with tumor ER mRNA (Pearson's correlation, r = 0.85; P < 0.0001) and ER protein status (Spearman's rank correlation, r = 0.73; P < 0.0001). The expression profile of STC2 was further confirmed by in situ hybridization and immunohistochemistry on a larger cohort of 236 unselected breast carcinomas using tissue microarrays. STC2 mRNA and protein expression were found to be associated with tumor ER status (Fisher's exact test, P < 0.005). The related gene, STC1, was also examined and shown to be associated with ER status in breast carcinomas (Fisher's exact test, P < 0.05). This study demonstrates the feasibility of using global gene expression data derived from an in vitro model to pinpoint novel estrogen-responsive genes of potential clinical relevance.

Rapid Detection of Candida albicans by Polymerase Spiral Reaction Assay in Clinical Blood Samples

PubMed Central

Jiang, Xiaoqun; Dong, Derong; Bian, Lihong; Zou, Dayang; He, Xiaoming; Ao, Da; Yang, Zhan; Huang, Simo; Liu, Ningwei; Liu, Wei; Huang, Liuyu

2016-01-01

Candida albicans is the most common human yeast pathogen which causes mucosal infections and invasive fungal diseases. Early detection of this pathogen is needed to guide preventative and therapeutic treatment. The aim of this study was to establish a polymerase spiral reaction (PSR) assay that rapidly and accurately detects C. albicans and to assess the clinical applicability of PSR-based diagnostic testing. Internal transcribed spacer 2 (ITS2), a region between 5.8S and 28S fungal ribosomal DNA, was used as the target sequence. Four primers were designed for amplification of ITS2 with the PSR method, which was evaluated using real time turbidity monitoring and visual detection using a pH indicator. Fourteen non-C. albicans yeast strains were negative for detection, which indicated the specificity of PSR assay was 100%. A 10-fold serial dilution of C. albicans genomic DNA was subjected to PSR and conventional polimerase chain reaction (PCR) to compare their sensitivities. The detection limit of PSR was 6.9 pg/μl within 1 h, 10-fold higher than that of PCR (69.0 pg/μl). Blood samples (n = 122) were collected from intensive care unit and hematological patients with proven or suspected C. albicans infection at two hospitals in Beijing, China. Both PSR assay and the culture method were used to analyze the samples. Of the 122 clinical samples, 34 were identified as positive by PSR. The result was consistent with those obtained by the culture method. In conclusion, a novel and effective C. albicans detection assay was developed that has a great potential for clinical screening and point-of-care testing. PMID:27379048

Associations of maternal exposure to triclosan, parabens, and other phenols with prenatal maternal and neonatal thyroid hormone levels.

PubMed

Berger, Kimberly; Gunier, Robert B; Chevrier, Jonathan; Calafat, Antonia M; Ye, Xiaoyun; Eskenazi, Brenda; Harley, Kim G

2018-05-24

Environmental phenols and parabens are commonly used in personal care products and other consumer products and human exposure to these chemicals is widespread. Although human and animal studies suggest an association between exposure to phenols and parabens and thyroid hormone levels, few studies have investigated the association of in utero exposure to these chemicals and thyroid hormones in pregnant women and their neonates. We measured four environmental phenols (triclosan, benzophenone-3, and 2,4- and 2,5-dichlorophenol), and three parabens (methyl-, propyl-, and butyl paraben) in urine collected from mothers at two time points during pregnancy as part of the CHAMACOS (Center for the Health Assessment of Mothers and Children of Salinas) study. We measured free thyroxine (T4), total T4, and thyroid-stimulating hormone (TSH) in serum of the pregnant women (N = 454) and TSH in their neonates (N = 365). We examined potential confounding by a large number of additional chemical exposures and used Bayesian Model Averaging (BMA) to select the most influential chemicals to include in regression models. We observed negative associations of prenatal urinary concentrations of propyl paraben and maternal TSH (β for two-fold increase = -3.26%, 95% CI: -5.55, -0.90) and negative associations of 2,4-dichlorophenol and maternal free T4 (β for two-fold increase = -0.05, 95% CI: -0.08, -0.02), after controlling for other chemical exposures. We observed negative associations of triclosan with maternal total T4 after controlling for demographic variables, but this association became non-significant after controlling for other chemicals (β for two-fold increase = -0.05, 95% CI: -0.11, 0.00). We found evidence that environmental phenols and parabens are associated with lower TSH and free T4 in pregnant women after controlling for related chemical exposures. Copyright © 2018 Elsevier Inc. All rights reserved.

Mechanisms of reduced susceptibility and genotypic prediction of antibiotic resistance in Prevotella isolated from cystic fibrosis (CF) and non-CF patients

PubMed Central

Sherrard, Laura J.; Schaible, Bettina; Graham, Kathryn A.; McGrath, Stef J.; McIlreavey, Leanne; Hatch, Joseph; Wolfgang, Matthew C.; Muhlebach, Marianne S.; Gilpin, Deirdre F.; Schneiders, Thamarai; Elborn, J. Stuart; Tunney, Michael M.

2014-01-01

Objectives To investigate mechanisms of reduced susceptibility to commonly used antibiotics in Prevotella cultured from patients with cystic fibrosis (CF), patients with invasive infection and healthy control subjects and to determine whether genotype can be used to predict phenotypic resistance. Methods The susceptibility of 157 Prevotella isolates to seven antibiotics was compared, with detection of resistance genes (cfxA-type gene, ermF and tetQ), mutations within the CfxA-type β-lactamase and expression of efflux pumps. Results Prevotella isolates positive for a cfxA-type gene had higher MICs of amoxicillin and ceftazidime compared with isolates negative for this gene (P < 0.001). A mutation within the CfxA-type β-lactamase (Y239D) was associated with ceftazidime resistance (P = 0.011). The UK CF isolates were 5.3-fold, 2.7-fold and 5.7-fold more likely to harbour ermF compared with the US CF, UK invasive and UK healthy control isolates, respectively. Higher concentrations of azithromycin (P < 0.001) and clindamycin (P < 0.001) were also required to inhibit the growth of the ermF-positive isolates compared with ermF-negative isolates. Furthermore, tetQ-positive Prevotella isolates had higher MICs of tetracycline (P = 0.001) and doxycycline (P < 0.001) compared with tetQ-negative isolates. Prevotella spp. were also shown, for the first time, to express resistance nodulation division (RND)-type efflux pumps. Conclusions This study has demonstrated that Prevotella isolated from various sources harbour a common pool of resistance genes and possess RND-type efflux pumps, which may contribute to tetracycline resistance. The findings indicate that antibiotic resistance is common in Prevotella spp., but the genotypic traits investigated do not reflect phenotypic antibiotic resistance in every instance. PMID:24917582

INFO-RNA--a fast approach to inverse RNA folding.

PubMed

Busch, Anke; Backofen, Rolf

2006-08-01

The structure of RNA molecules is often crucial for their function. Therefore, secondary structure prediction has gained much interest. Here, we consider the inverse RNA folding problem, which means designing RNA sequences that fold into a given structure. We introduce a new algorithm for the inverse folding problem (INFO-RNA) that consists of two parts; a dynamic programming method for good initial sequences and a following improved stochastic local search that uses an effective neighbor selection method. During the initialization, we design a sequence that among all sequences adopts the given structure with the lowest possible energy. For the selection of neighbors during the search, we use a kind of look-ahead of one selection step applying an additional energy-based criterion. Afterwards, the pre-ordered neighbors are tested using the actual optimization criterion of minimizing the structure distance between the target structure and the mfe structure of the considered neighbor. We compared our algorithm to RNAinverse and RNA-SSD for artificial and biological test sets. Using INFO-RNA, we performed better than RNAinverse and in most cases, we gained better results than RNA-SSD, the probably best inverse RNA folding tool on the market. www.bioinf.uni-freiburg.de?Subpages/software.html.

De novo inference of protein function from coarse-grained dynamics.

PubMed

Bhadra, Pratiti; Pal, Debnath

2014-10-01

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 µs coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. © 2014 Wiley Periodicals, Inc.

Development of Short-Form Versions of the Screener and Opioid Assessment for Patients with Pain-Revised (SOAPP-R): A Proof-of-Principle Study.

PubMed

Finkelman, Matthew D; Smits, Niels; Kulich, Ronald J; Zacharoff, Kevin L; Magnuson, Britta E; Chang, Hong; Dong, Jinghui; Butler, Stephen F

2017-07-01

The Screener and Opioid Assessment for Patients with Pain-Revised (SOAPP-R) is a 24-item questionnaire designed to assess risk of aberrant medication-related behaviors in chronic pain patients. The introduction of short forms of the SOAPP-R may save time and increase utilization by practitioners. To develop and evaluate candidate SOAPP-R short forms. Retrospective study. Pain centers. Four hundred and twenty-eight patients with chronic noncancer pain. Subjects had previously been administered the full-length version of the SOAPP-R and been categorized as positive or negative for aberrant medication-related behaviors via the Aberrant Drug Behavior Index (ADBI). Short forms of the SOAPP-R were developed using lasso logistic regression. Sensitivity, specificity, and area under the curve (AUC) of all forms were calculated with respect to the ADBI using the complete data set, training-test analysis, and 10-fold cross-validation. The coefficient alpha of each form was also calculated. An external set of 12 pain practitioners reviewed the forms for content. In the complete data set analysis, a form of 12 items exhibited sensitivity, specificity, and AUC greater than or equal to those of the full-length SOAPP-R (which were 0.74, 0.67, and 0.76, respectively). The short form had a coefficient alpha of 0.76. In the training-test analysis and 10-fold cross-validation, it exhibited an AUC value within 0.01 of that of the full-length SOAPP-R. The majority of external practitioners reported a preference for this short form. The 12-item version of the SOAPP-R has potential as a short risk screener and should be tested prospectively. © 2016 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Mozart, Mozart Rhythm and Retrograde Mozart Effects: Evidences from Behaviours and Neurobiology Bases

PubMed Central

Xing, Yingshou; Xia, Yang; Kendrick, Keith; Liu, Xiuxiu; Wang, Maosen; Wu, Dan; Yang, Hua; Jing, Wei; Guo, Daqing; Yao, Dezhong

2016-01-01

The phenomenal finding that listening to Mozart K.448 enhances performance on spatial tasks has motivated a continuous surge in promoting music education over the past two decades. But there have been inconsistent reports in previous studies of the Mozart effect. Here conducted was a systematic study, with Mozart and retrograde Mozart music, Mozart music rhythm and pitch, behaviours and neurobiology tests, rats and humans subjects. We show that while the Mozart K.448 has positive cognitive effects, the retrograde version has a negative effect on rats’ performance in the Morris water maze test and on human subjects’ performance in the paper folding and cutting test and the pencil-and-paper maze test. Such findings are further confirmed by subsequent immunohistochemical analyses in rats on the neurogenesis and protein levels of BDNF and its receptor, TrkB. Furthermore, when the rhythm and pitch of the normal and retrograde Mozart music are manipulated independently, the learning performance of the rats in the Morris water maze test indicated that rhythm is a crucial element in producing the behavioural effects. These findings suggest that the nature of Mozart effect is the Mozart rhythm effect, and indicate that different music may have quite different to opposite effects. Further study on rhythm effect may provide clues to understand the common basis over animals from rats to humans. PMID:26795072

Non-detergent sulphobetaines: a new class of molecules that facilitate in vitro protein renaturation.

PubMed

Goldberg, M E; Expert-Bezançon, N; Vuillard, L; Rabilloud, T

1996-01-01

Attempts to renature proteins often yield aggregates rather than native protein. To minimize aggregation, low protein concentrations and/or solubilizing agents are used. Here, we test new solubilizing molecules, non-detergent sulphobetaines, to improve the renaturation of two very different enzymes, hen egg white lysozyme and bacterial beta-D-galactosidase. The renaturation was conducted in the presence of five different sulphobetaines and the yield of active enzyme was measured. The five sulphobetaines improved the yield of native lysozyme up to 12-fold. Some sulphobetaines improved the yield of galactosidase up to 80-fold, but one reduced it 100-fold. Non-detergent sulphobetaines strongly affect the balance between aggregation and folding. Their effect depends on their structure and on their interactions with folding intermediates. These results should serve as a basis for designing more efficient sulphobetaines; for designing improved renaturation protocols using existing sulphobetaines; and for characterizing folding intermediates that interact with sulphobetaines.

Folding and stability of helical bundle proteins from coarse-grained models.

PubMed

Kapoor, Abhijeet; Travesset, Alex

2013-07-01

We develop a coarse-grained model where solvent is considered implicitly, electrostatics are included as short-range interactions, and side-chains are coarse-grained to a single bead. The model depends on three main parameters: hydrophobic, electrostatic, and side-chain hydrogen bond strength. The parameters are determined by considering three level of approximations and characterizing the folding for three selected proteins (training set). Nine additional proteins (containing up to 126 residues) as well as mutated versions (test set) are folded with the given parameters. In all folding simulations, the initial state is a random coil configuration. Besides the native state, some proteins fold into an additional state differing in the topology (structure of the helical bundle). We discuss the stability of the native states, and compare the dynamics of our model to all atom molecular dynamics simulations as well as some general properties on the interactions governing folding dynamics. Copyright © 2013 Wiley Periodicals, Inc.

Influence of IL-3 functional fragment on cord blood stem cell ex vivo expansion and differentiation.

PubMed

Ren, Zhihua; Zhang, Yu; Zhang, Yanxi; Jiang, Wenhong; Dai, Wei; Ding, Xinxin; Jiang, Yongping

2016-01-01

Recombinant human interleukin-3 (rhIL-3) is a multiple hematopoietic growth factor, which enhances stem cell expansion and hematopoiesis regeneration in vitro and in vivo, when administrated in combination with other cytokines. However, the structure-function study of rhIL-3 remains rarely studied, so far. The purpose of this study was to recognize the short peptide with similar function as rhIL-3, and assess the hematopoietic efficacy in umbilical cord blood (UCB) stem cell culture as well. Two novel monoclonal antibodies (mAb) (C1 and E1) were generated against rhIL-3 using hybridoma technique. Eleven short peptides were depicted and synthesized to overlap covering the full length sequence of rhIL-3. ELISA was employed to distinguish the antibody-binding peptide from the negative peptides. In addition, the multi-potential hematopoiesis capabilities of the positive peptides were evaluated by adding 25 ng/mL of each peptide to the culture medium of hematopoietic stem cells (HSCs) derived from UCB. Total nucleated cell number and the CD34(+) cell number from each individual treatment group were calculated on day 7. Correlated antibodies at 0.5 or 2 molar fold to each peptide were also tested in the stem cell expansion experiment, to further confirm the bioactivity of the peptides. Two peptides were recognized by the novel generated antibodies, using ELISA. Peptide 3 and 8 exhibited comparable hematopoiesis potentials, with 25.01±0.14 fold, and 19.89±0.12 fold increase of total nucleated cell number on day 7, respectively, compared with the basal medium control (4.93±0.55 fold). These biological effects were neutralized by adding the corresponding mAb at a dose dependent manner. Our results identified two specific regions of rhIL-3 responsible for HSC proliferation and differentiation, which were located from 28 to 49 amino acids (P3), and 107 to 127 amino acids (P8), respectively. The short peptide 3 and 8 might act synergistically, which could serve as an economic substitute to rhIL-3 in research laboratory.

The contribution of selective dysventilation to attical middle ear pathology.

PubMed

Marchioni, Daniele; Grammatica, Alberto; Alicandri-Ciufelli, Matteo; Aggazzotti-Cavazza, Elisa; Genovese, Elisabetta; Presutti, Livio

2011-07-01

Epitympanic primary cholesteatoma represents a challenge for ENT surgeons. Its exact pathogenesis is still unknown because of the very complex anatomy of this region. Until now, only a few authors have described this region and tried to hypothesize the causes that could lead to cholesteatoma genesis. We hypothesize the existence of a selective dysventilation of the epitympanic region based on the presence of various mucosal folds occluding air ventilation from the middle ear to the epitympanum, through the epitympanic isthmus, causing a negative epitympanic pressure and consequently cholesteatoma formation. All the anatomic findings were obtained with the aid of 0° and 45° angled surgical endoscopes. From our findings, patients affected by an epitympanic cholesteatoma often have a total isthmus blockage that completely isolates the whole epitympanum from the middle ear, causing a deficit of oxygenation of the mucosa that normally should be guaranteed by the Eustachian tube and which always works physiologically in these patients. This is confirmed by the tympanogram test where we observed how the pressure at the level of the tympanic cavity was normal, whereas the epitympanic pressure was selectively negative. In conclusion, selective epitympanic dysventilation syndrome consists of the concomitant presence of a series of complete or incomplete epitympanic diaphragms and ME isthmus blockage causing negative epitympanic pressure, and leading to the formation of a retraction pocket or cholesteatoma associated with normal Eustachian tube function. Copyright © 2011 Elsevier Ltd. All rights reserved.

Information-Theoretic Uncertainty of SCFG-Modeled Folding Space of The Non-coding RNA

PubMed Central

Manzourolajdad, Amirhossein; Wang, Yingfeng; Shaw, Timothy I.; Malmberg, Russell L.

2012-01-01

RNA secondary structure ensembles define probability distributions for alternative equilibrium secondary structures of an RNA sequence. Shannon’s Entropy is a measure for the amount of diversity present in any ensemble. In this work, Shannon’s entropy of the SCFG ensemble on an RNA sequence is derived and implemented in polynomial time for both structurally ambiguous and unambiguous grammars. Micro RNA sequences generally have low folding entropy, as previously discovered. Surprisingly, signs of significantly high folding entropy were observed in certain ncRNA families. More effective models coupled with targeted randomization tests can lead to a better insight into folding features of these families. PMID:23160142

Mechanically and optically reliable folding structure with a hyperelastic material for seamless foldable displays

NASA Astrophysics Data System (ADS)

Kwon, Hyuk-Jun; Shim, HongShik; Kim, Sunkook; Choi, Woong; Chun, Youngtea; Kee, InSeo; Lee, SangYoon

2011-04-01

We report a mechanically and optically robust folding structure to realize a foldable active matrix organic-light-emitting-diode (AMOLED) display without a visible crease at the junction. A nonlinear stress analysis, based on a finite element method, provided an optimized design. The folding-unfolding test on the structure exhibited negligible deterioration of the relative brightness at the junction of the individual panels up to 105 cycles at a folding radius of 1 mm, indicating highly reliable mechanical and optical tolerances. These results demonstrate the feasibility of seamless foldable AMOLED displays, with potentially important technical implications on fabricating large size flexible displays.

RNAiFold2T: Constraint Programming design of thermo-IRES switches.

PubMed

Garcia-Martin, Juan Antonio; Dotu, Ivan; Fernandez-Chamorro, Javier; Lozano, Gloria; Ramajo, Jorge; Martinez-Salas, Encarnacion; Clote, Peter

2016-06-15

RNA thermometers (RNATs) are cis-regulatory elements that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation. Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the first Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allowing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site (thermo-IRES) elements, whose normalized cap-independent translation efficiency is approximately 50% greater at 42 °C than 30 °C, when tested in reticulocyte lysates. Translation efficiency is lower than that of the wild-type IRES element, which on the other hand is fully resistant to temperature shift-up. This appears to be the first purely computational design of functional RNA thermoswitches, and certainly the first purely computational design of functional thermo-IRES elements. RNAiFold2T is publicly available as part of the new release RNAiFold3.0 at https://github.com/clotelab/RNAiFold and http://bioinformatics.bc.edu/clotelab/RNAiFold, which latter has a web server as well. The software is written in C ++ and uses OR-Tools CP search engine. clote@bc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics.

PubMed

Meuzelaar, Heleen; Vreede, Jocelyne; Woutersen, Sander

2016-06-07

Using a combination of ultraviolet circular dichroism, temperature-jump transient-infrared spectroscopy, and molecular dynamics simulations, we investigate the effect of salt bridges between different types of charged amino-acid residue pairs on α-helix folding. We determine the stability and the folding and unfolding rates of 12 alanine-based α-helical peptides, each of which has a nearly identical composition containing three pairs of positively and negatively charged residues (either Glu(-)/Arg(+), Asp(-)/Arg(+), or Glu(-)/Lys(+)). Within each set of peptides, the distance and order of the oppositely charged residues in the peptide sequence differ, such that they have different capabilities of forming salt bridges. Our results indicate that stabilizing salt bridges (in which the interacting residues are spaced and ordered such that they favor helix formation) speed up α-helix formation by up to 50% and slow down the unfolding of the α-helix, whereas salt bridges with an unfavorable geometry have the opposite effect. Comparing the peptides with different types of charge pairs, we observe that salt bridges between side chains of Glu(-) and Arg(+) are most favorable for the speed of folding, probably because of the larger conformational space of the salt-bridging Glu(-)/Arg(+) rotamer pairs compared to Asp(-)/Arg(+) and Glu(-)/Lys(+). We speculate that the observed impact of salt bridges on the folding kinetics might explain why some proteins contain salt bridges that do not stabilize the final, folded conformation. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Muscle cell atrophy induced by HSP gene silencing was counteracted by HSP overexpression

NASA Astrophysics Data System (ADS)

Choi, Inho; Lee, Joo-Hee; Nikawa, Takeshi; Gwag, Taesik; Park, Kyoungsook; Park, Junsoo

Heat shock proteins (HSP), as molecular chaperones, are known to assist protein quality control under various stresses. Although overexpression of HSP70 was found to contribute to muscle size retention under an unloading condition, it remains largely unclarified whether muscle atrophy is induced by active suppression of HSP expression. In this study, we pre-treated Hsp70 siRNA to rat L6 cells for the HSP gene silencing, and determined myotube diameter, HSP72 expression and anabolic and catabolic signaling activities in the absence or presence of triterpene celastrol (CEL), the HSP70 inducer. Relative to a negative control (NC), muscle cell diameter was reduced 0.89-fold in the siRNA-treated group, increased 1.2-fold in the CEL-treated group and retained at the size of NC in the siRNA+CEL group. HSP72 expression was decreased 0.35-fold by siRNA whereas the level was increased 6- to 8-fold in the CEL and siRNA+CEL groups. Expression of FoxO3 and atrogin-1 was increased 1.8- to 4.8-fold by siRNA, which was abolished by CEL treatment. Finally, phosphorylation of Akt1, S6K and ERK1/2 was not affected by siRNA, but was elevated 2- to 6-fold in the CEL and siRNA+CEL groups. Taken together, HSP downregulation by Hsp gene silencing led to muscle cell atrophy principally via increases in catabolic activities and that such anti-atrophic effect was counteracted by HSP overexpression.

Effect of Bee Venom and Its Fractions on the Release of Pro-Inflammatory Cytokines in PMA-Differentiated U937 Cells Co-Stimulated with LPS

PubMed Central

Tusiimire, Jonans; Wallace, Jennifer; Woods, Nicola; Dufton, Mark J.; Parkinson, John A.; Abbott, Grainne; Clements, Carol J.; Young, Louise; Park, Jin Kyu; Jeon, Jong Woon; Ferro, Valerie A.; Watson, David G.

2016-01-01

The venom of Apis mellifera (honey bee) has been reported to play a role in immunotherapy, but existing evidence to support its immuno-modulatory claims is insufficient. Four fractions from whole bee venom (BV) were separated using medium pressure liquid chromatography. Their ability to induce the production of cytokines TNFα, IL-1β and IL-6 in phorbol-12-myristate-13-acetate (PMA)-treated U937 cells was assessed. The levels of the three cytokines produced by stimulation with the four fractions and crude BV without LPS were not significantly different from negative control values. However, co-stimulation of the cells with LPS and Fraction 4 (F-4) induced a 1.6-fold increase in TNF-α level (p < 0.05) compared to LPS alone. Likewise, LPS-induced IL-1β production was significantly synergised in the presence of F-1 (nine-fold), F-2 (six-fold), F-3 (four-fold) and F-4 (two-fold) fractions, but was only slightly enhanced with crude BV (1.5-fold) relative to LPS. Furthermore, the LPS-stimulated production of IL-6 was not significantly increased in cells co-treated with F-2 and F-3, but the organic fraction (F-4) showed an inhibitory effect (p < 0.05) on IL-6 production. The latter was elucidated by NMR spectroscopy and found to contain(Z)-9-eicosen-1-ol. The effects observed with the purified BV fractions were more marked than those obtained with the crude sample. PMID:27104574

Modulating Phonation Through Alteration of Vocal Fold Medial Surface Contour

PubMed Central

Mau, Ted; Muhlestein, Joseph; Callahan, Sean; Chan, Roger W.

2012-01-01

Objectives 1. To test whether alteration of the vocal fold medial surface contour can improve phonation. 2. To demonstrate that implant material properties affect vibration even when implant is deep to the vocal fold lamina propria. Study Design Induced phonation of excised human larynges. Methods Thirteen larynges were harvested within 24 hours post-mortem. Phonation threshold pressure (PTP) and flow (PTF) were measured before and after vocal fold injections using either calcium hydroxylapatite (CaHA) or hyaluronic acid (HA). Small-volume injections (median 0.0625 mL) were targeted to the infero-medial aspect of the thyroarytenoid (TA) muscle. Implant locations were assessed histologically. Results The effect of implantation on PTP was material-dependent. CaHA tended to increase PTP, whereas HA tended to decrease PTP (Wilcoxon test P = 0.00013 for onset). In contrast, the effect of implantation on PTF was similar, with both materials tending to decrease PTF (P = 0.16 for onset). Histology confirmed implant presence in the inferior half of the vocal fold vertical thickness. Conclusions Taken together, these data suggested the implants may have altered the vocal fold medial surface contour, potentially resulting in a less convergent or more rectangular glottal geometry as a means to improve phonation. An implant with a closer viscoelastic match to vocal fold cover is desirable for this purpose, as material properties can affect vibration even when the implant is not placed within the lamina propria. This result is consistent with theoretical predictions and implies greater need for surgical precision in implant placement and care in material selection. PMID:22865592

Effect of smokeless tobacco products on human oral bacteria growth and viability

PubMed Central

Liu, Min; Jin, Jinshan; Pan, Hongmiao; Feng, Jinhui; Cerniglia, Carl E.; Yang, Maocheng; Chen, Huizhong

2017-01-01

To evaluate the toxicity of smokeless tobacco products (STPs) on oral bacteria, seven smokeless tobacco aqueous extracts (STAEs) from major brands of STPs and three tobacco-specific N-nitrosamines (TSNAs) were used in a growth and viability test against 38 oral bacterial species or subspecies. All seven STAEs showed concentration-dependent effects on the growth and viability of tested oral bacteria under anaerobic culture conditions, although there were strain-to-strain variations. In the presence of 1 mg/ml STAEs, the growth of 4 strains decreased over 0.32–2.14 log10 fold, while 14 strains demonstrated enhanced growth of 0.3–1.76 log10 fold, and the growth of 21 strains was not significantly affected. In the presence of 10 mg/ml STAEs, the growth of 17 strains was inhibited 0.3–2.11 log10 fold, 18 strains showed enhanced growth of 0.3–0.97 log10 fold, and 4 strains were not significantly affected. In the presence of 50 mg/ml STAEs, the growth of 32 strains was inhibited 0.3–2.96 log10 fold, 8 strains showed enhanced growth of 0.3–1.0 log10 fold, and 2 strains were not significantly affected. All seven STAEs could promote the growth of 4 bacterial strains, including Eubacterium nodatum, Peptostreptococcus micros, Streptococcus anginosus, and Streptococcus constellatus. Exposure to STAEs modulated the viability of some bacterial strains, with 21.1–66.5% decrease for 4 strains at 1 mg/ml, 20.3–85.7% decrease for 10 strains at 10 mg/ml, 20.0–93.3% decrease for 27 strains at 50 mg/ml, and no significant effect for 11 strains at up to 50 mg/ml. STAEs from snuffs inhibited more tested bacterial strains than those from snus indicating that the snuffs may be more toxic to the oral bacteria than snus. For TSNAs, cell growth and viability of 34 tested strains were not significantly affected at up to 100 μg/ml; while the growth of P. micros was enhanced 0.31–0.54 log10 fold; the growth of Veillonella parvula was repressed 0.33–0.36 log10 fold; and the cell viabilities of 2 strains decreased 56.6–69.9%. The results demonstrate that STAEs affected the growth of some types of oral bacteria, which may affect the healthy ecological balance of oral bacteria in humans. On the other hand, TSNAs did not significantly affect the growth of the oral bacteria. PMID:27756619

Life prediction of expulsion bladders through fatigue test and fold strain analysis

NASA Technical Reports Server (NTRS)

Chu, H. N.; Unterberg, W.

1972-01-01

Cycle life data are presented in terms of true maximum strain for four metals, two plastics, and two elastomers. The Coffin-Manson fatigue theory was applied for metals and plastics, and cut-growth fatigue theory for elastomers. The data are based on measurements made at room and elevated temperatures. It was found that double folds give rise to far severer folding strains than do simple folds. It was also found that, except for the elastomers, all the bladder materials develop surface cracks due to double folds after only one cycle. The findings indicate that metals, which are bets for premeation resistance, are worst for fatigue resistance, and vice versa for elastomers. The intermediate plastics were found to be unsatisfactory for both permeation and fatigue resistance for missions of extended duration.

EGR-1 and DUSP-1 are important negative regulators of pro-allergic responses in airway epithelium.

PubMed

Golebski, Korneliusz; van Egmond, Danielle; de Groot, Esther J; Roschmann, Kristina I L; Fokkens, Wytske J; van Drunen, Cornelis M

2015-05-01

Primary nasal epithelium of house dust mite allergic individuals is in a permanently activated inflammatory transcriptional state. To investigate whether a deregulated expression of EGR-1 and/or DUSP-1, two potential negative regulators of pro-inflammatory responses, could contribute to the activation of the inflammatory state. We silenced the expression of EGR-1 or DUSP-1 in the airway epithelial cell line NCI-H292. The cell lines were stimulated in a 24-h time course with the house dust mite allergen or poly(I:C). RNA expression profiles of cytokines were established using q-PCR and protein levels were determined in supernatants with ELISA. The shRNA-mediated gene silencing reduced expression levels of EGR-1 by 92% (p<0.0001) and of DUSP-1 by 76% (p<0.0001). Both mutant cells lines showed an increased and prolonged response to the HDM allergen. The mRNA induction of IL-6 was 4.6 fold (p=0.02) and 2.4 fold higher (p=0.01) in the EGR-1 and DUSP-1 knock-down, respectively when compared to the induced levels in the control cell line. For IL-8, the induction levels were 4.6 fold (p=0.01) and 13.0 (p=0.001) fold higher. The outcome was largely similar, yet not identical at the secreted protein levels. Furthermore, steroids were able to suppress the poly(I:C) induced cytokine levels by 70-95%. Deregulation of EGR-1 and/or DUSP-1 in nasal epithelium could be responsible for the prolonged activated transcriptional state observed in vivo in allergic disease. This could have clinical consequences as cytokine levels after the steroid treatment in EGR-1 or DUSP-1 knock-down remained higher than in the control cell line. Copyright © 2015 Elsevier Ltd. All rights reserved.

Automation and validation of micronucleus detection in the 3D EpiDerm™ human reconstructed skin assay and correlation with 2D dose responses.

PubMed

Chapman, K E; Thomas, A D; Wills, J W; Pfuhler, S; Doak, S H; Jenkins, G J S

2014-05-01

Recent restrictions on the testing of cosmetic ingredients in animals have resulted in the need to test the genotoxic potential of chemicals exclusively in vitro prior to licensing. However, as current in vitro tests produce some misleading positive results, sole reliance on such tests could prevent some chemicals with safe or beneficial exposure levels from being marketed. The 3D human reconstructed skin micronucleus (RSMN) assay is a promising new in vitro approach designed to assess genotoxicity of dermally applied compounds. The assay utilises a highly differentiated in vitro model of the human epidermis. For the first time, we have applied automated micronucleus detection to this assay using MetaSystems Metafer Slide Scanning Platform (Metafer), demonstrating concordance with manual scoring. The RSMN assay's fixation protocol was found to be compatible with the Metafer, providing a considerably shorter alternative to the recommended Metafer protocol. Lowest observed genotoxic effect levels (LOGELs) were observed for mitomycin-C at 4.8 µg/ml and methyl methanesulfonate (MMS) at 1750 µg/ml when applied topically to the skin surface. In-medium dosing with MMS produced a LOGEL of 20 µg/ml, which was very similar to the topical LOGEL when considering the total mass of MMS added. Comparisons between 3D medium and 2D LOGELs resulted in a 7-fold difference in total mass of MMS applied to each system, suggesting a protective function of the 3D microarchitecture. Interestingly, hydrogen peroxide (H2O2), a positive clastogen in 2D systems, tested negative in this assay. A non-genotoxic carcinogen, methyl carbamate, produced negative results, as expected. We also demonstrated expression of the DNA repair protein N-methylpurine-DNA glycosylase in EpiDerm™. Our preliminary validation here demonstrates that the RSMN assay may be a valuable follow-up to the current in vitro test battery, and together with its automation, could contribute to minimising unnecessary in vivo tests by reducing in vitro misleading positives.

Collagen Content Limits Optical Coherence Tomography Image Depth in Porcine Vocal Fold Tissue.

PubMed

Garcia, Jordan A; Benboujja, Fouzi; Beaudette, Kathy; Rogers, Derek; Maurer, Rie; Boudoux, Caroline; Hartnick, Christopher J

2016-11-01

Vocal fold scarring, a condition defined by increased collagen content, is challenging to treat without a method of noninvasively assessing vocal fold structure in vivo. The goal of this study was to observe the effects of vocal fold collagen content on optical coherence tomography imaging to develop a quantifiable marker of disease. Excised specimen study. Massachusetts Eye and Ear Infirmary. Porcine vocal folds were injected with collagenase to remove collagen from the lamina propria. Optical coherence tomography imaging was performed preinjection and at 0, 45, 90, and 180 minutes postinjection. Mean pixel intensity (or image brightness) was extracted from images of collagenase- and control-treated hemilarynges. Texture analysis of the lamina propria at each injection site was performed to extract image contrast. Two-factor repeated measure analysis of variance and t tests were used to determine statistical significance. Picrosirius red staining was performed to confirm collagenase activity. Mean pixel intensity was higher at injection sites of collagenase-treated vocal folds than control vocal folds (P < .0001). Fold change in image contrast was significantly increased in collagenase-treated vocal folds than control vocal folds (P = .002). Picrosirius red staining in control specimens revealed collagen fibrils most prominent in the subepithelium and above the thyroarytenoid muscle. Specimens treated with collagenase exhibited a loss of these structures. Collagen removal from vocal fold tissue increases image brightness of underlying structures. This inverse relationship may be useful in treating vocal fold scarring in patients. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2016.

Deep crustal deformation by sheath folding in the Adirondack Mountains, USA

NASA Technical Reports Server (NTRS)

Mclelland, J. M.

1988-01-01

As described by McLelland and Isachsen, the southern half of the Adirondacks are underlain by major isoclinal (F sub 1) and open-upright (F sub 2) folds whose axes are parallel, trend approximately E-W, and plunge gently about the horizontal. These large structures are themselves folded by open upright folds trending NNE (F sub 3). It is pointed out that elongation lineations in these rocks are parallel to X of the finite strain ellipsoid developed during progressive rotational strain. The parallelism between F sub 1 and F sub 2 fold axes and elongation lineations led to the hypothesis that progressive rotational strain, with a west-directed tectonic transport, rotated earlier F sub 1-folds into parallelism with the evolving elongation lineation. Rotation is accomplished by ductile, passive flow of F sub 1-axes into extremely arcuate, E-W hinges. In order to test these hypotheses a number of large folds were mapped in the eastern Adirondacks. Other evidence supporting the existence of sheath folds in the Adirondacks is the presence, on a map scale, of synforms whose limbs pass through the vertical and into antiforms. This type of outcrop pattern is best explained by intersecting a horizontal plane with the double curvature of sheath folds. It is proposed that sheath folding is a common response of hot, ductile rocks to rotational strain at deep crustal levels. The recognition of sheath folds in the Adirondacks reconciles the E-W orientation of fold axes with an E-W elongation lineation.

[Potentialities of the vegetative resonance test for diagnostics of hyperplastic processes in vocal folds].

PubMed

Ukhankova, N I; Sotskaia, T Iu

2010-01-01

The objective of the present study was to evaluate potentialities of the vegetative resonance test (VRT) for the elucidation of metabolic aspects of the inflammatory process in different forms of chronic vocal fold hyperplasty. The proposed diagnostic criteria characterize the inflammatory process in the larynx, specific features of metabolism in patients presenting with catarrhal and oedematopolypous laryngitis, characteristic changes in oedematofibrous and fibrous polyps. The use of VRT allowed diagnostic criteria for precarcinogenic conditions in the larynx to be developed.

Altering calcium influx for selective destruction of breast tumor.

PubMed

Yu, Han-Gang; McLaughlin, Sarah; Newman, Mackenzie; Brundage, Kathleen; Ammer, Amanda; Martin, Karen; Coad, James

2017-03-04

Human triple-negative breast cancer has limited therapeutic choices. Breast tumor cells have depolarized plasma membrane potential. Using this unique electrical property, we aim to develop an effective selective killing of triple-negative breast cancer. We used an engineered L-type voltage-gated calcium channel (Cec), activated by membrane depolarization without inactivation, to induce excessive calcium influx in breast tumor cells. Patch clamp and flow cytometry were used in testing the killing selectivity and efficiency of human breast tumor cells in vitro. Bioluminescence and ultrasound imaging were used in studies of human triple-negative breast cancer cell MDA-MB-231 xenograft in mice. Histological staining, immunoblotting and immunohistochemistry were used to investigate mechanism that mediates Cec-induced cell death. Activating Cec channels expressed in human breast cancer MCF7 cells produced enormous calcium influx at depolarized membrane. Activating the wild-type Cav1.2 channels expressed in MCF7 cells also produced a large calcium influx at depolarized membrane, but this calcium influx was diminished at the sustained membrane depolarization due to channel inactivation. MCF7 cells expressing Cec died when the membrane potential was held at -10 mV for 1 hr, while non-Cec-expressing MCF7 cells were alive. MCF7 cell death was 8-fold higher in Cec-expressing cells than in non-Cec-expressing cells. Direct injection of lentivirus containing Cec into MDA-MB-231 xenograft in mice inhibited tumor growth. Activated caspase-3 protein was detected only in MDA-MB-231 cells expressing Cec, along with a significantly increased expression of activated caspase-3 in xenograft tumor treated with Cec. We demonstrated a novel strategy to induce constant calcium influx that selectively kills human triple-negative breast tumor cells.

Endotoxin hitchhiking on polymer nanoparticles

NASA Astrophysics Data System (ADS)

Donnell, Mason L.; Lyon, Andrew J.; Mormile, Melanie R.; Barua, Sutapa

2016-07-01

The control of microbial infections is critical for the preparation of biological media including water to prevent lethal septic shock. Sepsis is one of the leading causes of death in the United States. More than half a million patients suffer from sepsis every year. Both gram-positive and gram-negative bacteria are responsible for septic infection by the most common organisms i.e., Escherichia coli and Pseuodomonas aeruginosa. The bacterial cell membrane releases negatively charged endotoxins upon death and enzymatic destruction, which stimulate antigenic response in humans to gram-negative infections. Several methods including distillation, ethylene oxide treatment, filtration and irradiation have been employed to remove endotoxins from contaminated samples, however, the reduction efficiency remains low, and presents a challenge. Polymer nanoparticles can be used to overcome the current inability to effectively sequester endotoxins from water. This process is termed endotoxin hitchhiking. The binding of endotoxin on polymer nanoparticles via electrostatic and hydrophobic interactions offers efficient removal from water. However, the effect of polymer nanoparticles and its surface areas has not been investigated for removal of endotoxins. Poly(ε-caprolactone) (PCL) polymer was tested for its ability to effectively bind and remove endotoxins from water. By employing a simple one-step phase separation technique, we were able to synthesize PCL nanoparticles of 398.3 ± 95.13 nm size and a polydispersity index of 0.2. PCL nanoparticles showed ∼78.8% endotoxin removal efficiency, the equivalent of 3.9 × 105 endotoxin units (EU) per ml. This is 8.34-fold more effective than that reported for commercially available membranes. Transmission electron microscopic images confirmed binding of multiple endotoxins to the nanoparticle surface. The concept of using nanoparticles may be applicable not only to eliminate gram-negative bacteria, but also for any gram-positive bacteria, fungi and parasites.

A close examination of double filtering with fold change and t test in microarray analysis

PubMed Central

2009-01-01

Background Many researchers use the double filtering procedure with fold change and t test to identify differentially expressed genes, in the hope that the double filtering will provide extra confidence in the results. Due to its simplicity, the double filtering procedure has been popular with applied researchers despite the development of more sophisticated methods. Results This paper, for the first time to our knowledge, provides theoretical insight on the drawback of the double filtering procedure. We show that fold change assumes all genes to have a common variance while t statistic assumes gene-specific variances. The two statistics are based on contradicting assumptions. Under the assumption that gene variances arise from a mixture of a common variance and gene-specific variances, we develop the theoretically most powerful likelihood ratio test statistic. We further demonstrate that the posterior inference based on a Bayesian mixture model and the widely used significance analysis of microarrays (SAM) statistic are better approximations to the likelihood ratio test than the double filtering procedure. Conclusion We demonstrate through hypothesis testing theory, simulation studies and real data examples, that well constructed shrinkage testing methods, which can be united under the mixture gene variance assumption, can considerably outperform the double filtering procedure. PMID:19995439

Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.

PubMed

Thoendel, Matthew; Jeraldo, Patricio R; Greenwood-Quaintance, Kerryl E; Yao, Janet Z; Chia, Nicholas; Hanssen, Arlen D; Abdel, Matthew P; Patel, Robin

2016-08-01

Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing. Copyright © 2016 Elsevier B.V. All rights reserved.

The low risk of precancer after a screening result of human papillomavirus-negative/atypical squamous cells of undetermined significance papanicolaou and implications for clinical management.

PubMed

Gage, Julia C; Katki, Hormuzd A; Schiffman, Mark; Castle, Philip E; Fetterman, Barbara; Poitras, Nancy E; Lorey, Thomas; Cheung, Li C; Behrens, Catherine; Sharma, Abha; Zhao, Fang-Hui; Cuzick, Jack; Yang, Zi Hua; Kinney, Walter K

2014-11-01

Different US practice guidelines have conflicting recommendations for when women should return after a screening result of human papillomavirus (HPV)-negative with an equivocal Papanicolaou (Pap) result of atypical squamous cells of undetermined significance (ASC-US) (ie, return in either 3 or 5 years). One way to determine management is to compare the risk of precancer/cancer after an HPV-negative/ASC-US result with the risks after other negative screening results. For example, if the risk after an HPV-negative/ASC-US result was similar to the risk after a negative Pap test, a 3-year return would be preferred because guidelines agree that women with negative Pap test results should return in 3 years. Alternatively, if the risk after an HPV-negative/ASC-US result is similar to that after a cotest-negative result (HPV negative/Pap test negative), a 5-year return would be preferred because guidelines agree that women testing cotest negative should return in 5 years. The authors compared risks of cervical intraepithelial neoplasia of grade 3 or higher (CIN3+) and cervical cancer among women aged 30 years to 64 years at Kaiser Permanente Northern California with the following test results from 2003 through 2012: 17,191 women testing HPV negative/ASC-US; 980,268 women testing Pap test negative (regardless of HPV result); and 892,882 women testing cotest negative. The 5-year CIN3+ and cancer risks after an HPV-negative/ASC-US result were closer to the risks after a negative Pap test result (CIN3+: 0.48% vs 0.31% [P =.0019]; and cancer: 0.043% vs 0.031% [P =.4]) than after a negative cotest (CIN3+: 0.48% vs 0.11% [P<.0001]; and cancer: 0.043% vs 0.014% [P =.016]). Women testing HPV negative/ASC-US were found to have precancer/cancer risks that were more closely aligned with women with negative Pap test results, suggesting that women testing HPV negative/ASC-US should be managed similarly to women testing negative on Pap tests with a 3-year return for screening. © 2014 American Cancer Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Evaluation of twenty-two rapid antigen detection tests in the diagnosis of Equine Influenza caused by viruses of H3N8 subtype.

PubMed

Yamanaka, Takashi; Nemoto, Manabu; Bannai, Hiroshi; Tsujimura, Koji; Kondo, Takashi; Matsumura, Tomio; Gildea, Sarah; Cullinane, Ann

2016-03-01

Equine influenza (EI) is a highly contagious disease caused by viruses of the H3N8 subtype. The rapid diagnosis of EI is essential to reduce the disease spread. Many rapid antigen detection (RAD) tests for diagnosing human influenza are available, but their ability to diagnose EI has not been systematically evaluated. The aim of this study was to compare the performance of 22 RAD tests in the diagnosis of EI. The 22 RAD tests were performed on fivefold serial dilutions of EI virus to determine their detection limits. The four most sensitive RAD tests (ImmunoAce Flu, BD Flu examan, Quick chaser Flu A, B and ESPLINE Influenza A&B-N) were further evaluated using nasopharyngeal samples collected from experimentally infected and naturally infected horses. The results were compared to those obtained using molecular tests. The detection limits of the 22 RAD tests varied hugely. Even the four RAD tests showing the best sensitivity were 125-fold less sensitive than the molecular techniques. The duration of virus detection in the experimentally infected horses was shorter using the RAD tests than using the molecular techniques. The RAD tests detected between 27% and 73% of real-time RT-PCR-positive samples from naturally infected horses. The study demonstrated the importance of choosing the right RAD tests as only three of 22 were fit for diagnosing EI. It was also indicated that even RAD tests with the highest sensitivity serve only as an adjunct to molecular tests because of the potential for false-negative results. © 2015 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

Biomechanical effects of hydration in vocal fold tissues.

PubMed

Chan, Roger W; Tayama, Niro

2002-05-01

It has often been hypothesized, with little empirical support, that vocal fold hydration affects voice production by mediating changes in vocal fold tissue rheology. To test this hypothesis, we attempted in this study to quantify the effects of hydration on the viscoelastic shear properties of vocal fold tissues in vitro. Osmotic changes in hydration (dehydration and rehydration) of 5 excised canine larynges were induced by sequential incubation of the tissues in isotonic, hypertonic, and hypotonic solutions. Elastic shear modulus (G'), dynamic viscosity eta' and the damping ratio zeta of the vocal fold mucosa (lamina propria) were measured as a function of frequency (0.01 to 15 Hz) with a torsional rheometer. Vocal fold tissue stiffness (G') and viscosity (eta) increased significantly (by 4 to 7 times) with the osmotically induced dehydration, whereas they decreased by 22% to 38% on the induced rehydration. Damping ratio (zeta) also increased with dehydration and decreased with rehydration, but the detected differences were not statistically significant at all frequencies. These findings support the long-standing hypothesis that hydration affects vocal fold vibration by altering tissue rheologic (or viscoelastic) properties. Our results demonstrated the biomechanical importance of hydration in vocal fold tissues and suggested that hydration approaches may potentially improve the biomechanics of phonation in vocal fold lesions involving disordered fluid balance.

Interpretation of remagnetization directions by Small Circle methods. Application to various tectonic problems

NASA Astrophysics Data System (ADS)

José Villalaín, Juan; Casas, Antonio; Calvín, Pablo; Soto-Marín, Ruth; Torres, Sara; Moussaid, Bennacer

2017-04-01

Secondary magnetizations have been used to constraint geological models in spite of the difficulties of dating the remanence age and the uncertainty in applying the valid tectonic correction, specially if the remagnetization is syntectonic. The fold test is the main tool used traditionally to identify and interpret remagnetization. In particular, the incremental fold test has been applied to attempt calculating the appropriate tectonic correction in synfolding remanences. However the fold test assumes symmetrical deformation giving erroneous solutions when dealing with asymmetrical folding. This strongly limits the use of the fold test because asymmetric tectonic evolution is very common in different geological processes. Therefore, it is necessary to use alternative techniques for analyzing remagnetization directions. In this sense, the use of small circles (SC) represents a very interesting option because it allows considering asymmetric deformations and degrees of freedom which fold test restricts. A SC is defined by a complete rotation of the in situ site mean paleomagnetic direction about the strike of bedding (i.e. the apical angle of its cone is the angle between the paleomagnetic vector and the strike of beds). In this presentation we analyze the use of SC for analysis of remagnetization directions in two phases: a) determination of the magnetic field direction at the remagnetization acquisition time by calculating the SC intersection (SCI) by methods described by Shipunov (1997) or Waldhör and Appel (2006). This obtained direction can be used to date the remagnetization by comparison with the APWP, but also as reference direction for restoration of the rotated remagnetization directions. And b) calculation of the bedding plane at the moment of the acquisition of the remagnetization (paleodip) by restoring the in situ remagnetization directions using each SC as described Villalaín et al. (2003), Henry et al. (2004) and Villalaín et al. (2015). In this work we discuss about the methodological problems observed when using SC analysis, such as the effect of the degree of coaxiality of different tectonic events on the uncertainty of the SCI solution and tectonic corrections, the presence of vertical axis rotation, etc. In addition we analyze different examples of application of SC techniques to solve different tectonic problems in areas affected by widespread remagnetizations, such as palinspastic reconstructions of inverted sedimentary basins, distinction of overlapped deformation events, identification of intra-Mesozoic stages in alpine chains, etc.

Controlling false-negative errors in microarray differential expression analysis: a PRIM approach.

PubMed

Cole, Steve W; Galic, Zoran; Zack, Jerome A

2003-09-22

Theoretical considerations suggest that current microarray screening algorithms may fail to detect many true differences in gene expression (Type II analytic errors). We assessed 'false negative' error rates in differential expression analyses by conventional linear statistical models (e.g. t-test), microarray-adapted variants (e.g. SAM, Cyber-T), and a novel strategy based on hold-out cross-validation. The latter approach employs the machine-learning algorithm Patient Rule Induction Method (PRIM) to infer minimum thresholds for reliable change in gene expression from Boolean conjunctions of fold-induction and raw fluorescence measurements. Monte Carlo analyses based on four empirical data sets show that conventional statistical models and their microarray-adapted variants overlook more than 50% of genes showing significant up-regulation. Conjoint PRIM prediction rules recover approximately twice as many differentially expressed transcripts while maintaining strong control over false-positive (Type I) errors. As a result, experimental replication rates increase and total analytic error rates decline. RT-PCR studies confirm that gene inductions detected by PRIM but overlooked by other methods represent true changes in mRNA levels. PRIM-based conjoint inference rules thus represent an improved strategy for high-sensitivity screening of DNA microarrays. Freestanding JAVA application at http://microarray.crump.ucla.edu/focus

Redesigned Spider Peptide with Improved Antimicrobial and Anticancer Properties.

PubMed

Troeira Henriques, Sónia; Lawrence, Nicole; Chaousis, Stephanie; Ravipati, Anjaneya S; Cheneval, Olivier; Benfield, Aurélie H; Elliott, Alysha G; Kavanagh, Angela Maria; Cooper, Matthew A; Chan, Lai Yue; Huang, Yen-Hua; Craik, David J

2017-09-15

Gomesin, a disulfide-rich antimicrobial peptide produced by the Brazilian spider Acanthoscurria gomesiana, has been shown to be potent against Gram-negative bacteria and to possess selective anticancer properties against melanoma cells. In a recent study, a backbone cyclized analogue of gomesin was shown to be as active but more stable than its native form. In the current study, we were interested in improving the antimicrobial properties of the cyclic gomesin, understanding its selectivity toward melanoma cells and elucidating its antimicrobial and anticancer mode of action. Rationally designed analogues of cyclic gomesin were examined for their antimicrobial potency, selectivity toward cancer cells, membrane-binding affinity, and ability to disrupt cell and model membranes. We improved the activity of cyclic gomesin by ∼10-fold against tested Gram-negative and Gram-positive bacteria without increasing toxicity to human red blood cells. In addition, we showed that gomesin and its analogues are more toxic toward melanoma and leukemia cells than toward red blood cells and act by selectively targeting and disrupting cancer cell membranes. Preference toward some cancer types is likely dependent on their different cell membrane properties. Our findings highlight the potential of peptides as antimicrobial and anticancer leads and the importance of selectively targeting cancer cell membranes for drug development.

Secreted Proteins Defy the Expression Level–Evolutionary Rate Anticorrelation

PubMed Central

Feyertag, Felix; Berninsone, Patricia M.; Alvarez-Ponce, David

2017-01-01

The rates of evolution of the proteins of any organism vary across orders of magnitude. A primary factor influencing rates of protein evolution is expression. A strong negative correlation between expression levels and evolutionary rates (the so-called E–R anticorrelation) has been observed in virtually all studied organisms. This effect is currently attributed to the abundance-dependent fitness costs of misfolding and unspecific protein–protein interactions, among other factors. Secreted proteins are folded in the endoplasmic reticulum, a compartment where chaperones, folding catalysts, and stringent quality control mechanisms promote their correct folding and may reduce the fitness costs of misfolding. In addition, confinement of secreted proteins to the extracellular space may reduce misinteractions and their deleterious effects. We hypothesize that each of these factors (the secretory pathway quality control and extracellular location) may reduce the strength of the E–R anticorrelation. Indeed, here we show that among human proteins that are secreted to the extracellular space, rates of evolution do not correlate with protein abundances. This trend is robust to controlling for several potentially confounding factors and is also observed when analyzing protein abundance data for 6 human tissues. In addition, analysis of mRNA abundance data for 32 human tissues shows that the E–R correlation is always less negative, and sometimes nonsignificant, in secreted proteins. Similar observations were made in Caenorhabditis elegans and in Escherichia coli, and to a lesser extent in Drosophila melanogaster, Saccharomyces cerevisiae and Arabidopsis thaliana. Our observations contribute to understand the causes of the E–R anticorrelation. PMID:28007979

Probing sequence dependence of folding pathway of α-helix bundle proteins through free energy landscape analysis.

PubMed

Shao, Qiang

2014-06-05

A comparative study on the folding of multiple three-α-helix bundle proteins including α3D, α3W, and the B domain of protein A (BdpA) is presented. The use of integrated-tempering-sampling molecular dynamics simulations achieves reversible folding and unfolding events in individual short trajectories, which thus provides an efficient approach to sufficiently sample the configuration space of protein and delineate the folding pathway of α-helix bundle. The detailed free energy landscape analyses indicate that the folding mechanism of α-helix bundle is not uniform but sequence dependent. A simple model is then proposed to predict folding mechanism of α-helix bundle on the basis of amino acid composition: α-helical proteins containing higher percentage of hydrophobic residues than charged ones fold via nucleation-condensation mechanism (e.g., α3D and BdpA) whereas proteins having opposite tendency in amino acid composition more likely fold via the framework mechanism (e.g., α3W). The model is tested on various α-helix bundle proteins, and the predicted mechanism is similar to the most approved one for each protein. In addition, the common features in the folding pathway of α-helix bundle protein are also deduced. In summary, the present study provides comprehensive, atomic-level picture of the folding of α-helix bundle proteins.

ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models.

PubMed

Maghrabi, Ali H A; McGuffin, Liam J

2017-07-03

Methods that reliably estimate the likely similarity between the predicted and native structures of proteins have become essential for driving the acceptance and adoption of three-dimensional protein models by life scientists. ModFOLD6 is the latest version of our leading resource for Estimates of Model Accuracy (EMA), which uses a pioneering hybrid quasi-single model approach. The ModFOLD6 server integrates scores from three pure-single model methods and three quasi-single model methods using a neural network to estimate local quality scores. Additionally, the server provides three options for producing global score estimates, depending on the requirements of the user: (i) ModFOLD6_rank, which is optimized for ranking/selection, (ii) ModFOLD6_cor, which is optimized for correlations of predicted and observed scores and (iii) ModFOLD6 global for balanced performance. The ModFOLD6 methods rank among the top few for EMA, according to independent blind testing by the CASP12 assessors. The ModFOLD6 server is also continuously automatically evaluated as part of the CAMEO project, where significant performance gains have been observed compared to our previous server and other publicly available servers. The ModFOLD6 server is freely available at: http://www.reading.ac.uk/bioinf/ModFOLD/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Air pulse deformation measurement: a preliminary method for noninvasive vocal fold pliability analysis.

PubMed

Larsson, Hans; Lindestad, P Å; Hertegård, S

2011-01-01

A new method, air pulse pliability measurement, is presented, with which the pliability and elasticity of the vocal folds was measured in vitro and in vivo using air pulses. The size of the mucosal movements induced by air pulse stimulation was measured with a laser-based technique. The air pulses fed via a 2-mm tubing, introduced through the working channel of a flexible endoscope. Both in vitro and in vivo tests were performed. Nine normal, vocally healthy subjects were examined by air pulse stimulations of the vocal folds, of the skin (cheek and dorsum of the hand) and of the inside of the lips. The in vitro tests showed a coefficient of variation of 5% within a range of 1-5 mm from the probe to the surface. The elasticity data showed no differences between vocal folds, lips or cheek. The hand data showed a significantly higher stiffness as compared to the other 3 measuring points (p < 0.001). The coefficient of variation was about 35% for all measuring points, but in ideal conditions on skin it was 9%. The results show that the technique allows automatic, quantitative, noninvasive vocal fold pliability measurements on awake subjects. Copyright © 2010 S. Karger AG, Basel.

Sildenafil citrate improves the delivery and anticancer activity of doxorubicin formulations in a mouse model of breast cancer.

PubMed

Greish, Khaled; Fateel, Maryam; Abdelghany, Sara; Rachel, Nanitha; Alimoradi, Houman; Bakhiet, Moiz; Alsaie, Ahmed

2017-11-21

Sildenafil is an approved drug for the treatment of erectile dysfunction. The drug exerts its action through the relaxation of smooth muscles and the modulation of vascular endothelial permeability. In this work, we tested whether the aforementioned effects of sildenafil on tumour vasculatures could result in an improvement of anticancer drug concentration in tumour tissues and hence improves its anticancer effect. Sildenafil when added to doxorubicin showed synergistic anticancer activity against 4T1 breast cancer cells in vitro. Adding 1, 30 and 100 μM of Viagra to 1 μM of doxorubicin resulted in 1.8-fold, 6.2-fold and 21-fold statistically significant increases in its cytotoxic effect, respectively. As a result, 4T1 tumour-bearing mice showed up to 2.7-fold increase in drug concentrations of the fluorescent Dye DiI and doxorubicin in tumour tissues, as well as their nanoformulations. Animals treated with the combinations of both Sildenafil citrate and doxorubicin showed a statistically significant 4.7-fold reduction in tumour size compared to doxorubicin alone. This work highlights the effect of Sildenafil on tumour vasculatures and provides a rational for further testing the combination on breast cancer patients.

Development and validation of a high-fidelity phonomicrosurgical trainer.

PubMed

Klein, Adam M; Gross, Jennifer

2017-04-01

To validate the use of a high-fidelity phonomicrosurgical trainer. A high-fidelity phonomicrosurgical trainer, based on a previously validated model by Contag et al., 1 was designed with multilayered vocal folds that more closely mimic the consistency of true vocal folds, containing intracordal lesions to practice phonomicrosurgical removal. A training module was developed to simulate the true phonomicrosurgical experience. A validation study with novice and expert surgeons was conducted. Novices and experts were instructed to remove the lesion from the synthetic vocal folds, and novices were given four training trials. Performances were measured by the amount of time spent and tissue injury (microflap, superficial, deep) to the vocal fold. An independent Student t test and Fisher exact tests were used to compare subjects. A matched-paired t test and Wilcoxon signed rank tests were used to compare novice performance on the first and fourth trials and assess for improvement. Experts completed the excision with less total errors than novices (P = .004) and made less injury to the microflap (P = .05) and superficial tissue (P = .003). Novices improved their performance with training, making less total errors (P = .002) and superficial tissue injuries (P = .02) and spending less time for removal (P = .002) after several practice trials. This high-fidelity phonomicrosurgical trainer has been validated for novice surgeons. It can distinguish between experts and novices; and after training, it helped to improve novice performance. N/A. Laryngoscope, 127:888-893, 2017. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

PubMed Central

Xu, Dong; Zhang, Yang

2013-01-01

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. PMID:23719418

Imperfect pathogen detection from non-invasive skin swabs biases disease inference

USGS Publications Warehouse

DiRenzo, Graziella V.; Grant, Evan H. Campbell; Longo, Ana; Che-Castaldo, Christian; Zamudio, Kelly R.; Lips, Karen

2018-01-01

1. Conservation managers rely on accurate estimates of disease parameters, such as pathogen prevalence and infection intensity, to assess disease status of a host population. However, these disease metrics may be biased if low-level infection intensities are missed by sampling methods or laboratory diagnostic tests. These false negatives underestimate pathogen prevalence and overestimate mean infection intensity of infected individuals. 2. Our objectives were two-fold. First, we quantified false negative error rates of Batrachochytrium dendrobatidis on non-invasive skin swabs collected from an amphibian community in El Copé, Panama. We swabbed amphibians twice in sequence, and we used a recently developed hierarchical Bayesian estimator to assess disease status of the population. Second, we developed a novel hierarchical Bayesian model to simultaneously account for imperfect pathogen detection from field sampling and laboratory diagnostic testing. We evaluated the performance of the model using simulations and varying sampling design to quantify the magnitude of bias in estimates of pathogen prevalence and infection intensity. 3. We show that Bd detection probability from skin swabs was related to host infection intensity, where Bd infections < 10 zoospores have < 95% probability of being detected. If imperfect Bd detection was not considered, then Bd prevalence was underestimated by as much as 16%. In the Bd-amphibian system, this indicates a need to correct for imperfect pathogen detection caused by skin swabs in persisting host communities with low-level infections. More generally, our results have implications for study designs in other disease systems, particularly those with similar objectives, biology, and sampling decisions. 4. Uncertainty in pathogen detection is an inherent property of most sampling protocols and diagnostic tests, where the magnitude of bias depends on the study system, type of infection, and false negative error rates. Given that it may be difficult to know this information in advance, we advocate that the most cautious approach is to assume all errors are possible and to accommodate them by adjusting sampling designs. The modeling framework presented here improves the accuracy in estimating pathogen prevalence and infection intensity.

Noninvasive Thermal Evaluation of Ventriculoperitoneal Shunt Patency and Cerebrospinal Fluid Flow Using a Flow Enhancing Device.

PubMed

Hameed, Mustafa Q; Zurakowski, David; Proctor, Mark R; Stone, Scellig S D; Warf, Benjamin C; Smith, Edward R; Goumnerova, Liliana C; Swoboda, Marek; Anor, Tomer; Madsen, Joseph R

2018-06-16

While a noninvasive flow determination would be desirable in the diagnosis of cerebrospinal fluid shunt malfunction, existing studies have not yet defined a role for thermal flow detection. To evaluate a revised test protocol using a micropumper designed to transiently enhance flow during thermal testing to determine whether thermal detection of flow is associated with progression to shunt revision surgery. Eighty-two unique tests were performed in 71 shunts. The primary outcome, need for revision within 7 d of testing, was compared with results of micropumper-augmented thermal flow detection. Statistical analysis was based on blind interpretation of test results and raw temperature data recorded during testing. The test was sensitive (73%) and specific (68%) in predicting need for revision, with 5.6-fold higher probability of revision when flow was not detected. Negative predictive value in our sample was 94.2%. The probability of not requiring revision increased with increasing total temperature drop. Analysis of various possible thresholds showed that the optimal temperature cutoff may be lower than suggested by the manufacturer (0.125°C vs 0.2°C). This is the first study to report a strong association between thermal flow evaluation and a clinical impression that a shunt is not malfunctioning. The current recommended threshold may increase the false positive rate unnecessarily, and as clinicians gain experience with the method, they may find value in examining the temperature curves themselves. Multicenter studies are suggested to further define a role for this diagnostic test.

Homochiral stereochemistry: the missing link of structure to energetics in protein folding.

PubMed

Kumar, Anil; Ramakrishnan, Vibin; Ranbhor, Ranjit; Patel, Kirti; Durani, Susheel

2009-12-24

The notion is tested that homochiral stereochemistry being ubiquitous to protein structure could be critical to protein folding as well, causing it to become frustrated energetically providing the basis for its solvent- and sequence-mediated control. The proof in support of the notion is found in a consensus of experiment and computation according to which suitable oligopeptides are in their folding-unfolding equilibria, at both macrostate and microstate levels, susceptible to dielectric because of the conflict of peptide-chain electrostatics with interpeptide hydrogen bonds when the structure is poly-L but not when it is alternating-L,D. The argument is thus made that homochiral stereochemistry may in protein folding provide the unifying basis for its solvent- and sequence-mediated control based on screening of peptide-chain electrostatics under conflict with folding of the chain due to homochiral stereochemistry. Dielectric is brought into spotlight as the effect comparatively obscure but presumably critical to the folding in protein structure for its control.

Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation

NASA Astrophysics Data System (ADS)

Qin, Sanbo; Mittal, Jeetain; Zhou, Huan-Xiang

2013-08-01

We have developed a ‘postprocessing’ method for modeling biochemical processes such as protein folding under crowded conditions (Qin and Zhou 2009 Biophys. J. 97 12-19). In contrast to the direct simulation approach, in which the protein undergoing folding is simulated along with crowders, the postprocessing method requires only the folding simulation without crowders. The influence of the crowders is then obtained by taking conformations from the crowder-free simulation and calculating the free energies of transferring to the crowders. This postprocessing yields the folding free energy surface of the protein under crowding. Here the postprocessing results for the folding of three small proteins under ‘repulsive’ crowding are validated by those obtained previously by the direct simulation approach (Mittal and Best 2010 Biophys. J. 98 315-20). This validation confirms the accuracy of the postprocessing approach and highlights its distinct advantages in modeling biochemical processes under cell-like crowded conditions, such as enabling an atomistic representation of the test proteins.

Phaeochromocytoma: diagnostic challenges for biochemical screening and diagnosis.

PubMed

Barron, Jeffrey

2010-08-01

The aim of this article is to provide knowledge of the origin of catecholamines and metabolites so that there can be an informed approach to the methods for biochemical screening for a possible phaeochromocytoma; The article includes a review of catecholamine and metadrenaline metabolism, with methods used in biochemical screening. In the adrenal medulla and a phaeochromocytoma, catecholamines continuously leak from chromaffin granules into the cytoplasm and are converted to metadrenalines. For a phaeochromocytoma to become biochemically detectable, metnoradrenaline secretion needs to rise fourfold, whereas noradrenaline secretion needs to rise 15-fold. The prevalence of a sporadic phaeochromocytoma is low; therefore false-positive results exceed true-positive results. Assay sensitivity is high because it is important not to miss a possible phaeochromocytoma. The use of urine or plasma fractionated metadrenalines as the first-line test has been recommended due to improved sensitivity. A negative result excludes a phaeochromocytoma. Only after a sporadic phaeochromocytoma has been diagnosed biochemically is it cost effective to request imaging. Sensitivities and specificities of the assays differ according to pre-test probabilities of the presence of a phaeochromocytoma, with hereditary and incidentalomas having a higher pre-test probability than sporadic phaeochromocytoma. In conclusion, in screening for a possible phaeochromocytoma, biochemical investigations should be completed first to exclude or establish the diagnosis. The preferred biochemical screening test is fractionated metadrenalines, including methoxytyramine so as not to miss dopamine-secreting tumours.

Modeling the Pathophysiology of Phonotraumatic Vocal Hyperfunction with a Triangular Glottal Model of the Vocal Folds

ERIC Educational Resources Information Center

Galindo, Gabriel E.; Peterson, Sean D.; Erath, Byron D.; Castro, Christian; Hillman, Robert E.; Zañartu, Matías

2017-01-01

Purpose: Our goal was to test prevailing assumptions about the underlying biomechanical and aeroacoustic mechanisms associated with phonotraumatic lesions of the vocal folds using a numerical lumped-element model of voice production. Method: A numerical model with a triangular glottis, posterior glottal opening, and arytenoid posturing is…

Individual and collective contributions of chaperoning and degradation to protein homeostasis in E. coli.

PubMed

Cho, Younhee; Zhang, Xin; Pobre, Kristine Faye R; Liu, Yu; Powers, David L; Kelly, Jeffery W; Gierasch, Lila M; Powers, Evan T

2015-04-14

The folding fate of a protein in vivo is determined by the interplay between a protein's folding energy landscape and the actions of the proteostasis network, including molecular chaperones and degradation enzymes. The mechanisms of individual components of the E. coli proteostasis network have been studied extensively, but much less is known about how they function as a system. We used an integrated experimental and computational approach to quantitatively analyze the folding outcomes (native folding versus aggregation versus degradation) of three test proteins biosynthesized in E. coli under a variety of conditions. Overexpression of the entire proteostasis network benefited all three test proteins, but the effect of upregulating individual chaperones or the major degradation enzyme, Lon, varied for proteins with different biophysical properties. In sum, the impact of the E. coli proteostasis network is a consequence of concerted action by the Hsp70 system (DnaK/DnaJ/GrpE), the Hsp60 system (GroEL/GroES), and Lon. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Prediction and Identification of Krüppel-Like Transcription Factors by Machine Learning Method.

PubMed

Liao, Zhijun; Wang, Xinrui; Chen, Xingyong; Zou, Quan

2017-01-01

The Krüppel-like factors (KLFs) are a family of containing Zn finger(ZF) motif transcription factors with 18 members in human genome, among them, KLF18 is predicted by bioinformatics. KLFs possess various physiological function involving in a number of cancers and other diseases. Here we perform a binary-class classification of KLFs and non-KLFs by machine learning methods. The protein sequences of KLFs and non-KLFs were searched from UniProt and randomly separate them into training dataset(containing positive and negative sequences) and test dataset(containing only negative sequences), after extracting the 188-dimensional(188D) feature vectors we carry out category with four classifiers(GBDT, libSVM, RF, and k-NN). On the human KLFs, we further dig into the evolutionary relationship and motif distribution, and finally we analyze the conserved amino acid residue of three zinc fingers. The classifier model from training dataset were well constructed, and the highest specificity(Sp) was 99.83% from a library for support vector machine(libSVM) and all the correctly classified rates were over 70% for 10-fold cross-validation on test dataset. The 18 human KLFs can be further divided into 7 groups and the zinc finger domains were located at the carboxyl terminus, and many conserved amino acid residues including Cysteine and Histidine, and the span and interval between them were consistent in the three ZF domains. Two classification models for KLFs prediction have been built by novel machine learning methods. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

MET-activating Residues in the B-repeat of the Listeria monocytogenes Invasion Protein InlB*

PubMed Central

Bleymüller, Willem M.; Lämmermann, Nina; Ebbes, Maria; Maynard, Daniel; Geerds, Christina; Niemann, Hartmut H.

2016-01-01

The facultative intracellular pathogen Listeria monocytogenes causes listeriosis, a rare but life-threatening disease. Host cell entry begins with activation of the human receptor tyrosine kinase MET through the bacterial invasion protein InlB, which contains an internalin domain, a B-repeat, and three GW domains. The internalin domain is known to bind MET, but no interaction partner is known for the B-repeat. Adding the B-repeat to the internalin domain potentiates MET activation and is required to stimulate Madin-Darby canine kidney (MDCK) cell scatter. Therefore, it has been hypothesized that the B-repeat may bind a co-receptor on host cells. To test this hypothesis, we mutated residues that might be important for binding an interaction partner. We identified two adjacent residues in strand β2 of the β-grasp fold whose mutation abrogated induction of MDCK cell scatter. Biophysical analysis indicated that these mutations do not alter protein structure. We then tested these mutants in human HT-29 cells that, in contrast to the MDCK cells, were responsive to the internalin domain alone. These assays revealed a dominant negative effect, reducing the activity of a construct of the internalin domain and mutated B-repeat below that of the individual internalin domain. Phosphorylation assays of MET and its downstream targets AKT and ERK confirmed the dominant negative effect. Attempts to identify a host cell receptor for the B-repeat were not successful. We conclude that there is limited support for a co-receptor hypothesis and instead suggest that the B-repeat contributes to MET activation through low affinity homodimerization. PMID:27789707

Optimization and Interpretation of Serial QuantiFERON Testing to Measure Acquisition of Mycobacterium tuberculosis Infection.

PubMed

Nemes, Elisa; Rozot, Virginie; Geldenhuys, Hennie; Bilek, Nicole; Mabwe, Simbarashe; Abrahams, Deborah; Makhethe, Lebohang; Erasmus, Mzwandile; Keyser, Alana; Toefy, Asma; Cloete, Yolundi; Ratangee, Frances; Blauenfeldt, Thomas; Ruhwald, Morten; Walzl, Gerhard; Smith, Bronwyn; Loxton, Andre G; Hanekom, Willem A; Andrews, Jason R; Lempicki, Maria D; Ellis, Ruth; Ginsberg, Ann M; Hatherill, Mark; Scriba, Thomas J

2017-09-01

Conversion from a negative to positive QuantiFERON-TB test is indicative of Mycobacterium tuberculosis (Mtb) infection, which predisposes individuals to tuberculosis disease. Interpretation of serial tests is confounded by immunological and technical variability. To improve the consistency of serial QuantiFERON-TB testing algorithms and provide a data-driven definition of conversion. Sources of QuantiFERON-TB variability were assessed, and optimal procedures were identified. Distributions of IFN-γ response levels were analyzed in healthy adolescents, Mtb-unexposed control subjects, and patients with pulmonary tuberculosis. Individuals with no known Mtb exposure had IFN-γ values less than 0.2 IU/ml. Among individuals with IFN-γ values less than 0.2 IU/ml, 0.2-0.34 IU/ml, 0.35-0.7 IU/ml, and greater than 0.7 IU/ml, tuberculin skin test positivity results were 15%, 53%, 66%, and 91% (P < 0.005), respectively. Together, these findings suggest that values less than 0.2 IU/ml were true negatives. In short-term serial testing, "uncertain" conversions, with at least one value within the uncertainty zone (0.2-0.7 IU/ml), were partly explained by technical assay variability. Individuals who had a change in QuantiFERON-TB IFN-γ values from less than 0.2 to greater than 0.7 IU/ml had 10-fold higher tuberculosis incidence rates than those who maintained values less than 0.2 IU/ml over 2 years (P = 0.0003). By contrast, "uncertain" converters were not at higher risk than nonconverters (P = 0.229). Eighty-seven percent of patients with active tuberculosis had IFN-γ values greater than 0.7 IU/ml, suggesting that these values are consistent with established Mtb infection. Implementation of optimized procedures and a more rigorous QuantiFERON-TB conversion definition (an increase from IFN-γ <0.2 to >0.7 IU/ml) would allow more definitive detection of recent Mtb infection and potentially improve identification of those more likely to develop disease.

Designing of self-deploying origami structures using geometrically misaligned crease patterns.

PubMed

Saito, Kazuya; Tsukahara, Akira; Okabe, Yoji

2016-01-01

Usually, origami-based morphing structures are designed on the premise of 'rigid folding', i.e. the facets and fold lines of origami can be replaced with rigid panels and ideal hinges, respectively. From a structural mechanics viewpoint, some rigid-foldable origami models are overconstrained and have negative degrees of freedom (d.f.). In these cases, the singularity in crease patterns guarantees their rigid foldability. This study presents a new method for designing self-deploying origami using the geometrically misaligned creases. In this method, some facets are replaced by 'holes' such that the systems become a 1-d.f. mechanism. These perforated origami models can be folded and unfolded similar to rigid-foldable (without misalignment) models because of their d.f. focusing on the removed facets, the holes will deform according to the motion of the frame of the remaining parts. In the proposed method, these holes are filled with elastic parts and store elastic energy for self-deployment. First, a new extended rigid-folding simulation technique is proposed to estimate the deformation of the holes. Next, the proposed method is applied on arbitrary-size quadrilateral mesh origami. Finally, by using the finite-element method, the authors conduct numerical simulations and confirm the deployment capabilities of the models.

Conformational transition of κ-casein in micellar environment: Insight from the tryptophan fluorescence

NASA Astrophysics Data System (ADS)

Mishra, Smruti; Meher, Geetanjali; Chakraborty, Hirak

2017-11-01

Intrinsically disordered proteins (IDPs) are under intense analysis due to their structural flexibility and importance in biological functions. Minuscule modulation in the microenvironment induces significant conformational changes in IDPs, and these non-native conformations of the IDPs often induce aggregation and cause cell death. Changes in the membrane composition often change the microenvironment, which promote conformational change and aggregation of IDPs. κ-Casein, an important milk protein, belongs to the class of IDPs containing net negative charges. In this present work, we have studied the interaction of κ-casein with cetyltrimethyl ammonium bromide (CTAB), a positively charged surfactant, utilizing various steady state fluorescence, time-resolved fluorescence and circular dichroism spectroscopy. Our results clearly indicate that κ-casein undergoes at least two conformational transitions in presence of various concentrations of CTAB. The intrinsically disordered κ-casein assumes a partially folded conformation at lower concentration of CTAB, which adopts an unstructured conformation at higher concentration of CTAB. The partially folded conformation of κ-casein at a lower CTAB concentration might be induced by the favorable electrostatic interaction between the positively charged surfactant headgroup and net negative charges of the protein, whereas surfactant nature of CTAB is being pronounced at higher concentration of CTAB.

Cell Adhesion Molecule L1 in Folded (Horseshoe) and Extended Conformations

PubMed Central

Schürmann, Gregor; Haspel, Jeffrey; Grumet, Martin; Erickson, Harold P.

2001-01-01

We have investigated the structure of the cell adhesion molecule L1 by electron microscopy. We were particularly interested in the conformation of the four N-terminal immunoglobulin domains, because x-ray diffraction showed that these domains are bent into a horseshoe shape in the related molecules hemolin and axonin-1. Surprisingly, rotary-shadowed specimens showed the molecules to be elongated, with no indication of the horseshoe shape. However, sedimentation data suggested that these domains of L1 were folded into a compact shape in solution; therefore, this prompted us to look at the molecules by an alternative technique, negative stain. The negative stain images showed a compact shape consistent with the expected horseshoe conformation. We speculate that in rotary shadowing the contact with the mica caused a distortion of the protein, weakening the bonds forming the horseshoe and permitting the molecule to extend. We have thus confirmed that the L1 molecule is primarily in the horseshoe conformation in solution, and we have visualized for the first time its opening into an extended conformation. Our study resolves conflicting interpretations from previous electron microscopy studies of L1. PMID:11408583

[Transverse folding and the evolution of hind wings in beetles (Insecta, Coleoptera)].

PubMed

Fedorenko, D N

2013-01-01

Strong intensification of the protective function of the fore wing in Coleoptera has made their flight apparatus a posteromotoric one and invited an apparatus responsible for folding the hindwings beneath the elytra to develop. Folding apparatus could hardly develop without higher deformability of veins or their parts, which diminished strength properties of the wing support. The effect was stressed by folds that intersected veins. Organization of the folds into a system confined this negative influence to a few wing regions and some veinal sections. This having happened, wing support and folding pattern evolved interrelated, the former into being more flexible, with no or minimum loss of rigidity, and the latter towards being less harmful for the supporting elements, especially axial ones. Monofunctionality, together with very simple structure and little specialization of constituent parts, made the folding pattern very labile during evolution. The folding pattern evolved more rapidly than wing venation, thus defining transformations of the latter. Evolutionary conservatism of wing venation stemmed from that many veins were strongly specialized in performing two conflicting functions. An adaptive compromise was necessary for the conflict to be solved, which determined the wing to orthogenetic development. The main evolutionary trends for wing venation and folding pattern were those towards simplification and a higher complexity, respectively. The beetle wing has passed through two main evolutionary stages. Among them, the first resulted in the development of the "Archostemata" wing type, the second started from the "cantharoid" structural plan. The main evolutionary factors were the infancies of wing posteromotorism at the first stage while the wing strongly influenced by size evolution, with the main trend towards miniaturization, at the second. The archostematan and "cantharoid" morphofunctional wing types differ fundamentally. In the wing of the former kind, folding and flight apparatus, because of considerably overlapping supporting systems, constitute a lasting coadaptive ensemble, with only minor deviations from the ground-plan occurring through evolution. The uprise of the "cantharoid" wing type was an upgrade of morpho-functional organization. The region of maximum transverse deformations having been extruded from the remigium basal part, chief supporting axes of the wing increased their rigid properties. The supporting systems of the two wing apparatus became more autonomous, having been separated. This expanded the adaptive zone for the wing strongly, which a great variety of derived wing types have emerged from.

Xenobiotics enhance laccase activity in alkali-tolerant γ-proteobacterium JB.

PubMed

Singh, Gursharan; Batish, Mona; Sharma, Prince; Capalash, Neena

2009-01-01

Various genotoxic textile dyes, xenobiotics, substrates (10 µM) and agrochemicals (100 µg/ml) were tested for enhancement of alkalophilic laccase activity in γ-proteobacterium JB. Neutral Red, Indigo Carmine, Naphthol Base Bordears and Sulphast Ruby dyes increased the activity by 3.7, 2.7, 2.6 and 2.3 fold respectively. Xenobiotics/substrates like p-toluidine, 8-hydroxyquinoline and anthracine increased it by 3.4, 2.8 and 2.3 fold respectively. Atrazine and trycyclozole pesticides enhanced the activity by 1.95 and 1.5 fold respectively.

Xenobiotics enhance laccase activity in alkali-tolerant γ-proteobacterium JB

PubMed Central

Singh, Gursharan; Batish, Mona; Sharma, Prince; Capalash, Neena

2009-01-01

Various genotoxic textile dyes, xenobiotics, substrates (10 µM) and agrochemicals (100 µg/ml) were tested for enhancement of alkalophilic laccase activity in γ-proteobacterium JB. Neutral Red, Indigo Carmine, Naphthol Base Bordears and Sulphast Ruby dyes increased the activity by 3.7, 2.7, 2.6 and 2.3 fold respectively. Xenobiotics/substrates like p-toluidine, 8-hydroxyquinoline and anthracine increased it by 3.4, 2.8 and 2.3 fold respectively. Atrazine and trycyclozole pesticides enhanced the activity by 1.95 and 1.5 fold respectively. PMID:24031313

Gepotidacin (GSK2140944) In Vitro Activity against Gram-Positive and Gram-Negative Bacteria

PubMed Central

Farrell, D. J.; Rhomberg, P. R.; Scangarella-Oman, N. E.; Sader, H. S.

2017-01-01

ABSTRACT Gepotidacin is a first-in-class, novel triazaacenaphthylene antibiotic that inhibits bacterial DNA replication and has in vitro activity against susceptible and drug-resistant pathogens. Reference in vitro methods were used to investigate the MICs and minimum bactericidal concentrations (MBCs) of gepotidacin and comparator agents for Staphylococcus aureus, Streptococcus pneumoniae, and Escherichia coli. Gepotidacin in vitro activity was also evaluated by using time-kill kinetics and broth microdilution checkerboard methods for synergy testing and for postantibiotic and subinhibitory effects. The MIC90 of gepotidacin for 50 S. aureus (including methicillin-resistant S. aureus [MRSA]) and 50 S. pneumoniae (including penicillin-nonsusceptible) isolates was 0.5 μg/ml, and for E. coli (n = 25 isolates), it was 4 μg/ml. Gepotidacin was bactericidal against S. aureus, S. pneumoniae, and E. coli, with MBC/MIC ratios of ≤4 against 98, 98, and 88% of the isolates tested, respectively. Time-kill curves indicated that the bactericidal activity of gepotidacin was observed at 4× or 10× MIC at 24 h for all of the isolates. S. aureus regrowth was observed in the presence of gepotidacin, and the resulting gepotidacin MICs were 2- to 128-fold higher than the baseline gepotidacin MICs. Checkerboard analysis of gepotidacin combined with other antimicrobials demonstrated no occurrences of antagonism with agents from multiple antimicrobial classes. The most common interaction when testing gepotidacin was indifference (fractional inhibitory concentration index of >0.5 to ≤4; 82.7% for Gram-positive isolates and 82.6% for Gram-negative isolates). The postantibiotic effect (PAE) of gepotidacin was short when it was tested against S. aureus (≤0.6 h against MRSA and MSSA), and the PAE–sub-MIC effect (SME) was extended (>8 h; three isolates at 0.5× MIC). The PAE of levofloxacin was modest (0.0 to 2.4 h), and the PAE-SME observed varied from 1.2 to >9 h at 0.5× MIC. These in vitro data indicate that gepotidacin is a bactericidal agent that exhibits a modest PAE and an extended PAE-SME against Gram-positive and -negative bacteria and merits further study for potential use in treating infections caused by these pathogens. PMID:28483959

A germline mutation in the BRCA1 3'UTR predicts Stage IV breast cancer.

PubMed

Dorairaj, Jemima J; Salzman, David W; Wall, Deirdre; Rounds, Tiffany; Preskill, Carina; Sullivan, Catherine A W; Lindner, Robert; Curran, Catherine; Lezon-Geyda, Kim; McVeigh, Terri; Harris, Lyndsay; Newell, John; Kerin, Michael J; Wood, Marie; Miller, Nicola; Weidhaas, Joanne B

2014-06-10

A germline, variant in the BRCA1 3'UTR (rs8176318) was previously shown to predict breast and ovarian cancer risk in women from high-risk families, as well as increased risk of triple negative breast cancer. Here, we tested the hypothesis that this variant predicts tumor biology, like other 3'UTR mutations in cancer. The impact of the BRCA1-3'UTR-variant on BRCA1 gene expression, and altered response to external stimuli was tested in vitro using a luciferase reporter assay. Gene expression was further tested in vivo by immunoflourescence staining on breast tumor tissue, comparing triple negative patient samples with the variant (TG or TT) or non-variant (GG) BRCA1 3'UTR. To determine the significance of the variant on clinically relevant endpoints, a comprehensive collection of West-Irish breast cancer patients were tested for the variant. Finally, an association of the variant with breast screening clinical phenotypes was evaluated using a cohort of women from the High Risk Breast Program at the University of Vermont. Luciferase reporters with the BRCA1-3'UTR-variant (T allele) displayed significantly lower gene expression, as well as altered response to external hormonal stimuli, compared to the non-variant 3'UTR (G allele) in breast cancer cell lines. This was confirmed clinically by the finding of reduced BRCA1 gene expression in triple negative samples from patients carrying the homozygous TT variant, compared to non-variant patients. The BRCA1-3'UTR-variant (TG or TT) also associated with a modest increased risk for developing breast cancer in the West-Irish cohort (OR=1.4, 95% CI 1.1-1.8, p=0.033). More importantly, patients with the BRCA1-3'UTR-variant had a 4-fold increased risk of presenting with Stage IV disease (p=0.018, OR=3.37, 95% CI 1.3-11.0). Supporting that this finding is due to tumor biology, and not difficulty screening, obese women with the BRCA1-3'UTR-variant had significantly less dense breasts (p=0.0398) in the Vermont cohort. A variant in the 3'UTR of BRCA1 is functional, leading to decreased BRCA1 expression, modest increased breast cancer risk, and most importantly, presentation with stage IV breast cancer, likely due to aggressive tumor biology.

MicroRNAfold: pre-microRNA secondary structure prediction based on modified NCM model with thermodynamics-based scoring strategy.

PubMed

Han, Dianwei; Zhang, Jun; Tang, Guiliang

2012-01-01

An accurate prediction of the pre-microRNA secondary structure is important in miRNA informatics. Based on a recently proposed model, nucleotide cyclic motifs (NCM), to predict RNA secondary structure, we propose and implement a Modified NCM (MNCM) model with a physics-based scoring strategy to tackle the problem of pre-microRNA folding. Our microRNAfold is implemented using a global optimal algorithm based on the bottom-up local optimal solutions. Our experimental results show that microRNAfold outperforms the current leading prediction tools in terms of True Negative rate, False Negative rate, Specificity, and Matthews coefficient ratio.

Susceptibility patterns for amoxicillin/clavulanate tests mimicking the licensed formulations and pharmacokinetic relationships: do the MIC obtained with 2:1 ratio testing accurately reflect activity against beta-lactamase-producing strains of Haemophilus influenzae and Moraxella catarrhalis?

PubMed

Pottumarthy, Sudha; Sader, Helio S; Fritsche, Thomas R; Jones, Ronald N

2005-11-01

Amoxicillin/clavulanate has recently undergone formulation changes (XR and ES-600) that represent 14:1 and 16:1 ratios of amoxicillin/clavulanate. These ratios greatly differ from the 2:1 ratio used in initial formulations and in vitro susceptibility testing. The objective of this study was to determine if the reference method using a 2:1 ratio accurately reflects the susceptibility to the various clinically used amoxicillin/clavulanate formulations and their respective serum concentration ratios. A collection of 330 Haemophilus influenzae strains (300 beta-lactamase-positive and 30 beta-lactamase-negative) and 40 Moraxella catarrhalis strains (30 beta-lactamase-positive and 10 beta-lactamase-negative) were tested by the broth microdilution method against eight amoxicillin/clavulanate combinations (4:1, 5:1, 7:1, 9:1, 14:1, and 16:1 ratios; 0.5 and 2 microg/mL fixed clavulanate concentrations) and the minimum inhibitory concentration (MIC) results were compared with those obtained with the reference 2:1 ratio testing. For the beta-lactamase-negative strains of both genera, there was no demonstrable change in the MIC values obtained for all ratios analyzed (2:1 to 16:1). For the beta-lactamase-positive strains of H. influenzae and M. catarrhalis, at ratios >or=4:1 there was a shift in the central tendency of the MIC scatterplot compared with the results of testing 2:1 ratio. As a result, there was a 2-fold dilution increase in the MIC(50) and MIC(90) values, most evident for H. influenzae and BRO-1-producing M. catarrhalis strains. For beta-lactamase-positive strains of H. influenzae, the shift resulted in a change in the interpretive result for 3 isolates (1.0%) from susceptible using the reference method (2:1 ratio) to resistant (8/4 microg/mL; very major error) at the 16:1 ratio. In addition, the number of isolates with MIC values at or 1 dilution lower than the breakpoint (4/2 microg/mL) increased from 5% at 2:1 ratio to 32-33% for ratios 14:1 and 16:1. Our results indicate that, for the beta-lactamase-positive strains of H. influenzae and M. catarrhalis, the results of the amoxicillin/clavulanate reference 2:1 ratio testing do not accurately represent all the currently licensed formulations. Pharmacokinetic/pharmacodynamic (PK/PD) target attainment might be compromised when higher amoxicillin/clavulanate ratios are used clinically. With a better understanding of PK/PD parameters, reevaluation of the amoxicillin/clavulanate in vitro susceptibility testing should be considered by the standardizing authorities to reflect the licensed formulations and accurately predict clinical outcomes.

Reducing WBC background in cancer cell separation products by negative acoustic contrast particle immuno-acoustophoresis.

PubMed

Cushing, Kevin; Undvall, Eva; Ceder, Yvonne; Lilja, Hans; Laurell, Thomas

2018-02-13

Cancer cells display acoustic properties enabling acoustophoretic separation from white blood cells (WBCs) with 2-3 log suppression of the WBC background. However, a subset of WBCs has overlapping acoustic properties with cancer cells, which is why label-free acoustophoretic cancer cell isolation needs additional purification prior to analysis. This paper reports for the first time a proof of concept for continuous flow acoustophoretic negative selection of WBCs from cancer cells using negative acoustic contrast elastomeric particles (EPs) activated with CD45-antibodies that specifically bind to WBCs. The EP/WBC complexes align at the acoustic pressure anti-nodes along the channel walls while unbound cancer cells focus to the pressure node in the channel center, enabling continuous flow based depletion of WBC background in a cancer cell product. The method does not provide a single process solution for the CTC separation challenge, but provides an elegant part to a multi-step process by further reducing the WBC background in cancer cell separation products derived from an initial step of label-free acoustophoresis. We report the recorded performance of the negative selection immuno-acoustophoretic WBC depletion and cancer cell recovery. To eliminate the negative impact of the separation due to the known problems of aggregation of negative acoustic contrast particles along the sidewalls of the acoustophoresis channel and to enable continuous separation of EP/WBC complexes from cancer cells, a new acoustic actuation method has been implemented where the ultrasound frequency is scanned (1.991MHz ± 100 kHz, scan rate 200 kHz ms -1 ). Using this frequency scanning strategy EP/WBC complexes were acoustophoretically separated from mixtures of WBCs spiked with breast and prostate cancer cells (DU145 and MCF-7). An 86-fold (MCF-7) and 52-fold (DU145) reduction of WBCs in the cancer cell fractions were recorded with separation efficiencies of 98.6% (MCF-7) and 99.7% (DU145) and cancer cell recoveries of 89.8% (MCF-7) and 85.0% (DU145). Copyright © 2017 Elsevier B.V. All rights reserved.

The Negative Testing and Negative Generation Effects Are Eliminated by Delay

ERIC Educational Resources Information Center

Mulligan, Neil W.; Peterson, Daniel J.

2015-01-01

Although retrieval often enhances subsequent memory (the testing effect), a negative testing effect has recently been documented in which prior retrieval harms later recall compared with restudying. The negative testing effect was predicated on the negative generation effect and the item-specific-relational framework. The present experiments…

Design and 4D Printing of Cross-Folded Origami Structures: A Preliminary Investigation.

PubMed

Teoh, Joanne Ee Mei; An, Jia; Feng, Xiaofan; Zhao, Yue; Chua, Chee Kai; Liu, Yong

2018-03-03

In 4D printing research, different types of complex structure folding and unfolding have been investigated. However, research on cross-folding of origami structures (defined as a folding structure with at least two overlapping folds) has not been reported. This research focuses on the investigation of cross-folding structures using multi-material components along different axes and different horizontal hinge thickness with single homogeneous material. Tensile tests were conducted to determine the impact of multi-material components and horizontal hinge thickness. In the case of multi-material structures, the hybrid material composition has a significant impact on the overall maximum strain and Young's modulus properties. In the case of single material structures, the shape recovery speed is inversely proportional to the horizontal hinge thickness, while the flexural or bending strength is proportional to the horizontal hinge thickness. A hinge with a thickness of 0.5 mm could be folded three times prior to fracture whilst a hinge with a thickness of 0.3 mm could be folded only once prior to fracture. A hinge with a thickness of 0.1 mm could not even be folded without cracking. The introduction of a physical hole in the center of the folding/unfolding line provided stress relief and prevented fracture. A complex flower petal shape was used to successfully demonstrate the implementation of overlapping and non-overlapping folding lines using both single material segments and multi-material segments. Design guidelines for establishing cross-folding structures using multi-material components along different axes and different horizontal hinge thicknesses with single or homogeneous material were established. These guidelines can be used to design and implement complex origami structures with overlapping and non-overlapping folding lines. Combined overlapping folding structures could be implemented and allocating specific hole locations in the overall designs could be further explored. In addition, creating a more precise prediction by investigating sets of in between hinge thicknesses and comparing the folding times before fracture, will be the subject of future work.

Predicting RNA pseudoknot folding thermodynamics

PubMed Central

Cao, Song; Chen, Shi-Jie

2006-01-01

Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics. The model is validated through extensive experimental tests both for the native structures and for the folding thermodynamics. The model predicts strong sequence-dependent helix-loop competitions in the pseudoknot stability and the resultant conformational switches between different hairpin and pseudoknot structures. For instance, for the pseudoknot domain of human telomerase RNA, a native-like and a misfolded hairpin intermediates are found to coexist on the (equilibrium) folding pathways, and the interplay between the stabilities of these intermediates causes the conformational switch that may underlie a human telomerase disease. PMID:16709732

Only Five of 10 Strictly Conserved Disulfide Bonds Are Essential for Folding and Eight for Function of the HIV-1 Envelope Glycoprotein

PubMed Central

van Anken, Eelco; Sanders, Rogier W.; Liscaljet, I. Marije; Land, Aafke; Bontjer, Ilja; Tillemans, Sonja; Nabatov, Alexey A.; Paxton, William A.; Berkhout, Ben

2008-01-01

Protein folding in the endoplasmic reticulum goes hand in hand with disulfide bond formation, and disulfide bonds are considered key structural elements for a protein's folding and function. We used the HIV-1 Envelope glycoprotein to examine in detail the importance of its 10 completely conserved disulfide bonds. We systematically mutated the cysteines in its ectodomain, assayed the mutants for oxidative folding, transport, and incorporation into the virus, and tested fitness of mutant viruses. We found that the protein was remarkably tolerant toward manipulation of its disulfide-bonded structure. Five of 10 disulfide bonds were dispensable for folding. Two of these were even expendable for viral replication in cell culture, indicating that the relevance of these disulfide bonds becomes manifest only during natural infection. Our findings refine old paradigms on the importance of disulfide bonds for proteins. PMID:18653472

Mechanism of and Threshold Biomechanical Conditions for Falsetto Voice Onset

PubMed Central

Deguchi, Shinji

2011-01-01

The sound source of a voice is produced by the self-excited oscillation of the vocal folds. In modal voice production, a drastic increase in transglottal pressure after vocal fold closure works as a driving force that develops self-excitation. Another type of vocal fold oscillation with less pronounced glottal closure observed in falsetto voice production has been accounted for by the mucosal wave theory. The classical theory assumes a quasi-steady flow, and the expected driving force onto the vocal folds under wavelike motion is derived from the Bernoulli effect. However, wavelike motion is not always observed during falsetto voice production. More importantly, the application of the quasi-steady assumption to a falsetto voice with a fundamental frequency of several hundred hertz is unsupported by experiments. These considerations suggested that the mechanism of falsetto voice onset may be essentially different from that explained by the mucosal wave theory. In this paper, an alternative mechanism is submitted that explains how self-excitation reminiscent of the falsetto voice could be produced independent of the glottal closure and wavelike motion. This new explanation is derived through analytical procedures by employing only general unsteady equations of motion for flow and solids. The analysis demonstrated that a convective acceleration of a flow induced by rapid wall movement functions as a negative damping force, leading to the self-excitation of the vocal folds. The critical subglottal pressure and volume flow are expressed as functions of vocal fold biomechanical properties, geometry, and voice fundamental frequency. The analytically derived conditions are qualitatively and quantitatively reasonable in view of reported measurement data of the thresholds required for falsetto voice onset. Understanding of the voice onset mechanism and the explicit mathematical descriptions of thresholds would be beneficial for the diagnosis and treatment of voice diseases and the development of artificial vocal folds. PMID:21408178

Flat battery

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

Waki, E.; Kobayashi, S.; Hashimoto, Y.

A flat battery is described comprising: an electrically insulative sheathing film including a first film portion and a second film portion on opposite sides of a fold line, the film having an outer surface and an inner surface opposite the outer surface, on both of the first and the second film portions. The fold line divides the inner surface into a first inner surface portion on the first film portion and a second inner surface portion on the second film portion, the film being folded along the fold line so that the first inner surface portion faces the second innermore » surface portion. The first and second film portions are sealed to one another along the entire peripheries thereof except along the fold line, the first film portion having first a first terminal hole and a second terminal hole formed therein; a first collector formed in a plane on the first inner surface portion and having a first terminal portion covering the first terminal hole, the first terminal portion being exposed to the exterior of the battery through the first terminal hole so as to define a first terminal; and a second collector consisting of a first part formed on the first inner surface portion and a second part continuous to the first part formed on the second inner surface portion. The second collector extends across and is folded along the fold line, the second part having a second terminal portion covering the second terminal hole, the second terminal portion being exposed to the exterior of the battery through the second terminal hole so as to define a second terminal. The second part is formed in the plane in spaced non-overlapping relation to the first collector, one of the first and second collectors consisting of a positive collector, the other of the first and second collectors consisting of a negative collector.« less

Fractionation and Concentration of High-Salinity Textile Wastewater using an Ultra-Permeable Sulfonated Thin-film Composite.

PubMed

Li, Meng; Yao, Yujian; Zhang, Wen; Zheng, Junfeng; Zhang, Xuan; Wang, Lianjun

2017-08-15

A sulfonated thin-film composite (TFC) nanofiltration membrane was fabricated using 2,2'-benzidinedisulfonic acid (BDSA) and trimesoyl chloride (TMC) on a polyether sulfone substrate by conventional interfacial polymerization. Due to a nascent barrier layer with a loose architecture, the obtained TFC-BDSA-0.2 membrane showed an ultrahigh pure water permeability of 48.1 ± 2.1 L -1 m -2 h -1 bar -1 , and a considerably low NaCl retention ability of <1.8% over a concentration range of 10-100 g L -1 . The membrane, which possesses a negatively charged surface, displayed an excellent rejection of over 99% toward Congo red (CR) and allowed the fast fractionation of high-salinity textile wastewater. The prepared membrane required only 3-fold water addition to accomplish the separation of multiple components, whereas the commercial NF270 (Dow) membrane required 4-fold water addition and almost double the length of time. Furthermore, the TFC-BDSA-0.2 membrane was subsequently tested for the dye concentration process. It maintained a high flux of 8.2 L -1 m -2 h -1 bar -1 and a negligible dye loss, even when the concentration factor reached ∼10. Finally, by using a 20% alcohol solution as a back-washing medium, a flux recovery ratio (FRR) of 95.6% was achieved with TFC-BDSA-0.2, and the CR rejection ability remained the same. These results prove the outstanding antifouling and solvent-resistant properties of the membrane.

Is children's Body Mass Index associated with their parents' personality? A prospective controlled trial.

PubMed

Erdoğan, Fırat; Eliaçik, Mustafa; Özahi Ipek, İlke; Arici, Neslihan; Kadak, Muhammed T; Ceran, Ömer

2017-08-01

The aim of this study was to elucidate the effect of the personal characteristics and psychological status of parents on their children's Body Mass Index (BMI) by using validated questionnaires. Obese and healthy control group was assessed with The Parental Attitude Research Instrument (PARI) for the evaluation of parental attitudes towards their children. Additionally, Depression Anxiety and Stress Scale (DASS) were used to assess the relationships between parental depression, anxiety, stress and childhood obesity. A total of 105 children and their parents were divided into two groups. The study group consisted of 58 children with a BMI of higher than 85th percentile whereas 47 children with normal BMI (<85th percentile) were included as the control group. In both groups, the BMI of mothers which is between 25-and 30 kg/m2 and >30 kg/m2 had significant impact on the risk of children's obesity status 1.12-fold and 3.68-fold respectively. The PARI results provided that the children who had disciplined, over-protective parents and those in the parental incompatibility group had higher risk of being obese. Analysis of the DASS Test results showed that children having depressed parents had significantly higher risk of obesity than children whose parents were not depressed (P<0.05). Our results provided that, the parent's status such as obesity, depression and strict personal behaviors have negative impact on their children's weight which is resulting with obesity.

Plasma free versus deconjugated metanephrines for diagnosis of phaeochromocytoma

PubMed Central

Pamporaki, Christina; Därr, Roland; Bursztyn, Michael; Stephan, Glöckner; Bornstein, Stefan R.; Lenders, Jacques W.M.; Pacak, Karel; Krinner, Axel; Eisenhofer, Graeme

2013-01-01

Summary Background Diagnosis of phaeochromocytoma is commonly performed by measurements of plasma free normetanephrine and metanephrine. Plasma deconjugated normetanephrine and metanephrine have been proposed as alternative equivalent, but easier to measure biomarkers. Objective The aim of this study was to compare the diagnostic performances of plasma free versus deconjugated normetanephrine and metanephrine in patients tested for phaeochromocytoma. Methods The study population included a reference group of 262 normotensive and hypertensive volunteers, 198 patients with phaeochromocytoma and 528 patients initially suspected of having the tumour, but with negative investigations after at least 2 years of follow up. Measurements were performed using liquid chromatography with electrochemical detection. Results Median plasma concentrations of free normetanephrine were 17-fold higher in patients with phaeochromocytoma than in the reference population, a 72% larger (p<0.001) difference than that for the 10-fold higher levels of plasma deconjugated normetanephrine. In contrast, relative increases of plasma concentrations of free and deconjugated metanephrine were similar. Using upper cut-offs established in the reference population, measurements of plasma free metabolites provided superior diagnostic performance than deconjugated metabolites according to measures of both sensitivity (97% vs 92%, p=0.002) and specificity (93 vs 89%, p=0.012). The area under the receiver operating characteristic curve for the free metabolites was larger than that for the deconjugated metabolites (0.986 vs 0.965, p<0.001). Conclusion Measurements of plasma free normetanephrine and metanephrine are superior to the deconjugated metabolites for diagnosis of phaeochromocytoma. PMID:23461656

The Effects of Hormonal Contraception on the Voice: History of Its Evolution in the Literature.

PubMed

Rodney, Jennifer P; Sataloff, Robert Thayer

2016-11-01

Women of reproductive age commonly use hormonal contraceptives, the vocal effects of which have been studied. Otolaryngologists should be aware of this relationship to make recommendations on hormonal contraception as it relates to each patient's voice requirements. A comprehensive literature review of PubMed was completed. The terms "contraception," "vocal folds," "vocal cords," and "voice" were searched in various combinations. Articles from 1971 to 2015 that addressed the effects of contraception on the vocal folds were included. In total, 24 articles were available for review. Historically, contraception was believed to affect the voice negatively. However, more recent studies using low-dose oral contraceptive pills (OCPs) show that they stabilize the voice. However, stabilization generally occurs only during sustained vowel production; connected speech appears unaffected. Therefore, singers may be the only population that experiences clinically increased vocal stability as a result of taking hormonal contraceptives. Only combined OCPs have been studied; other forms of hormonal contraception have not been evaluated for effects on the voice. Significant variability exists between studies in the physical attributes of patients and parameters tested. Hormonal contraception likely has no clinically perceptible effects on the speaking voice. Singers may experience increased vocal stability with low-dose, combined OCP use. Other available forms of contraception have not been studied. Greater consistency in methodology is needed in future research, and other forms of hormonal contraception require study. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Intradermal testing after negative skin prick testing for patients with high suspicion of allergy.

PubMed

Larrabee, Yuna C; Reisacher, William

2015-06-01

Skin testing is a widely accepted method for identifying inhalant allergies. Intradermal (ID) testing is often performed after negative skin prick testing (SPT) when a practitioner has a high level of clinical suspicion for a particular allergen. A retrospective chart review study was performed over a 5-year period in patients with negative SPT for airborne allergens who also underwent ID testing based on a high level of suspicion for clinical allergy. Eighty-seven patients had negative SPT and went on to receive an average of 7 ID tests per patient. A total of 592 ID tests were performed after negative SPT. Of these, 20.8% (123/592) had a positive ID result with negative SPT. The allergens with the greatest percentage of positive ID results with negative SPTs were dog, cat, D. farinae, and D. pteronyssinus (33.3%, 34.3%, 39.4%, and 39.6%, respectively). The allergens least likely to test positive on ID testing after negative SPT were red maple, Cladosporium, and Alternaria (0%, 6.3%, and 6.5%, respectively). Approximately 20% of all negative results on SPT will have a positive ID test, more likely for indoor allergens. If a high suspicion for allergy exists in a patient with a negative SPT result, it may be useful to proceed with ID testing. However, the clinical significance of a positive ID test after negative SPT still needs to be elucidated. © 2015 ARS-AAOA, LLC.

Laryngeal muscle activity in unilateral vocal fold paralysis patients using electromyography and coronal reconstructed images.

PubMed

Sanuki, Tetsuji; Yumoto, Eiji; Nishimoto, Kohei; Minoda, Ryosei

2014-04-01

To assess laryngeal muscle activity in unilateral vocal fold paralysis (UVFP) patients using laryngeal electromyography (LEMG) and coronal images. Case series with chart review. University hospital. Twenty-one patients diagnosed with UVFP of at least 6 months in duration with paralytic dysphonia, underwent LEMG, phonatory function tests, and coronal imaging. A 4-point scale was used to grade motor unit (MU) recruitment: absent = 4+, greatly decreased = 3+, moderately decreased = 2+, and mildly decreased = 1+. Maximum phonation time (MPT) and mean flow rate (MFR) were employed. Coronal images were assessed for differences in thickness and vertical position of the vocal folds during phonation and inhalation. MU recruitment in thyroarytenoid/lateral cricoarytenoid (TA/LCA) muscle complex results were 1+ for 4 patients, 2+ for 5, 3+ for 6, and 4+ for 6. MPT was positively correlated with MU recruitment. Thinning of the affected fold was evident during phonation in 19 of the 21 subjects. The affected fold was at an equal level with the healthy fold in all 9 subjects with MU recruitment of 1+ and 2+. Eleven of 12 subjects with MU recruitments of 3+ and 4+ showed the affected fold at a higher level than the healthy fold. There was a significant difference between MU recruitment and the vertical position of the affected fold. Synkinetic reinnervation may occur in some cases with UVFP. MU recruitments of TA/LCA muscle complex in UVFP patients may be related to phonatory function and the vertical position of the affected fold.

Testicular distribution and toxicity of a novel LTA4H inhibitor in rats

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

Ward, P.D., E-mail: pward4@its.jnj.com; La, D.

JNJ 40929837, a novel leukotriene A4 hydrolase inhibitor in drug development, was reported to induce testicular toxicity in rats. The mechanism of toxicity was considered to be rodent specific and not relevant to humans. To further investigate this finding in rats, the distribution and toxicokinetics of JNJ 40929837 and its two metabolites, M1 and M2, were investigated. A quantitative whole body autoradiography study showed preferential distribution and retention of JNJ 40929837-derived radioactivity in the testes consistent with the observed site of toxicity. Subsequent studies with unlabeled JNJ 40929837 showed different metabolite profiles between the plasma and testes. Following a singlemore » oral 50 mg/kg dose of JNJ 40929837, M2 was the primary metabolite in plasma whereas M1 was the primary metabolite in testes. The exposure of M1 was 386-fold higher in the testes compared to plasma whereas M2 had limited exposure in testes. Furthermore, the T{sub max} of M1 was 48 h in testes suggesting a large accumulation potential of this metabolite in testes compared to plasma. Following six months of repeated daily oral dosing, M1 accumulated approximately five-fold in the testes whereas the parent did not accumulate. These results indicate that the toxicokinetic profiles of JNJ 40929837 and its two metabolites in testes are markedly different compared to plasma and support the importance of understanding the toxicokinetic profiles of compounds and their metabolites in organs/tissues where toxicity is observed. - Highlights: • JNJ 40929837-derived radioactivity preferentially distributed into testes • Primary metabolite flip-flop in plasma and testes • The primary metabolite in testes accumulated 5-fold but not parent.« less

Distributional fold change test – a statistical approach for detecting differential expression in microarray experiments

PubMed Central

2012-01-01

Background Because of the large volume of data and the intrinsic variation of data intensity observed in microarray experiments, different statistical methods have been used to systematically extract biological information and to quantify the associated uncertainty. The simplest method to identify differentially expressed genes is to evaluate the ratio of average intensities in two different conditions and consider all genes that differ by more than an arbitrary cut-off value to be differentially expressed. This filtering approach is not a statistical test and there is no associated value that can indicate the level of confidence in the designation of genes as differentially expressed or not differentially expressed. At the same time the fold change by itself provide valuable information and it is important to find unambiguous ways of using this information in expression data treatment. Results A new method of finding differentially expressed genes, called distributional fold change (DFC) test is introduced. The method is based on an analysis of the intensity distribution of all microarray probe sets mapped to a three dimensional feature space composed of average expression level, average difference of gene expression and total variance. The proposed method allows one to rank each feature based on the signal-to-noise ratio and to ascertain for each feature the confidence level and power for being differentially expressed. The performance of the new method was evaluated using the total and partial area under receiver operating curves and tested on 11 data sets from Gene Omnibus Database with independently verified differentially expressed genes and compared with the t-test and shrinkage t-test. Overall the DFC test performed the best – on average it had higher sensitivity and partial AUC and its elevation was most prominent in the low range of differentially expressed features, typical for formalin-fixed paraffin-embedded sample sets. Conclusions The distributional fold change test is an effective method for finding and ranking differentially expressed probesets on microarrays. The application of this test is advantageous to data sets using formalin-fixed paraffin-embedded samples or other systems where degradation effects diminish the applicability of correlation adjusted methods to the whole feature set. PMID:23122055

Automatic Brain Tumor Detection in T2-weighted Magnetic Resonance Images

NASA Astrophysics Data System (ADS)

Dvořák, P.; Kropatsch, W. G.; Bartušek, K.

2013-10-01

This work focuses on fully automatic detection of brain tumors. The first aim is to determine, whether the image contains a brain with a tumor, and if it does, localize it. The goal of this work is not the exact segmentation of tumors, but the localization of their approximate position. The test database contains 203 T2-weighted images of which 131 are images of healthy brain and the remaining 72 images contain brain with pathological area. The estimation, whether the image shows an afflicted brain and where a pathological area is, is done by multi resolution symmetry analysis. The first goal was tested by five-fold cross-validation technique with 100 repetitions to avoid the result dependency on sample order. This part of the proposed method reaches the true positive rate of 87.52% and the true negative rate of 93.14% for an afflicted brain detection. The evaluation of the second part of the algorithm was carried out by comparing the estimated location to the true tumor location. The detection of the tumor location reaches the rate of 95.83% of correct anomaly detection and the rate 87.5% of correct tumor location.

Washing with contaminated bar soap is unlikely to transfer bacteria.

PubMed Central

Heinze, J. E.; Yackovich, F.

1988-01-01

Recent reports of the isolation of microorganisms from used soap bars have raised the concern that bacteria may be transferred from contaminated soap bars during handwashing. Since only one study addressing this question has been published, we developed an additional procedure to test this concern. In our new method prewashed and softened commercial deodorant soap bars (0.8% triclocarban) not active against Gram-negative bacteria were inoculated with Escherichia coli and Pseudomonas aeruginosa to give mean total survival levels of 4.4 X 10(5) c.f.u. per bar which was 70-fold higher than those reported on used soap bars. Sixteen panelists were instructed to wash with the inoculated bars using their normal handwashing procedure. After washing, none of the 16 panelists had detectable levels of either test bacterium on their hands. Thus, the results obtained using our new method were in complete agreement with those obtained with the previously published method even though the two methods differ in a number of procedural aspects. These findings, along with other published reports, show that little hazard exists in routine handwashing with previously used soap bars and support the frequent use of soap and water for handwashing to prevent the spread of disease. PMID:3402545

Highly conductive and anticorrosion Ag/CNTs/NDs hybrid films on molecular-grafted PET substrate for flexible electrodes

NASA Astrophysics Data System (ADS)

Zhang, Yang; Kang, Zhixin

2018-01-01

We reported an approach of preparing highly conductive, anticorrosion, flexible Ag hybrid films enhanced by multi-walled carbon nanotubes (CNTs) and nanodaimonds (NDs) on molecular-grafted PET substrate by spin-spray for flexible electronics. we studied in this paper and found that even an outstanding enhancement on conductivity of Ag films, CNTs have a negative effect on anticorrosion property. Meanwhile, NDs decreased the conductivity of Ag/CNTs hybrids, but it remained a relatively high conductivity property and even was affirmed a distinctly boost improvement on anticorrosion, microhardness and tensile strength, which meant a better mechanical chemical stabilization and practicability in real flexible electronics. To obtain the strong adhesive strength of films/substrate, molecular-grafting technology was applied, which was affirmed by XPS and cross-cut test. What's more, we evaluated anticorrosion property by electrochemistry test, including Tafel measurements and electrochemical impedance spectroscopy measurements, proving the positive effect of NDs on Ag/CNTs hybrid films. For practical application, a flexible light-emitting diode (LED) circuit was successfully structured and remained steady under bending, folding and twisting. Besides, after 1000000 cycles inner/outer bending deformation, the hybrid films showed a mechanical compliance, fatigue stability and practicability in real flexible electronics.

Effects of Zinc Gluconate and 2 Other Divalent Cationic Compounds on Olfactory Function in Mice

PubMed Central

Duncan-Lewis, Christopher A; Lukman, Roy L; Banks, Robert K

2011-01-01

Intranasal application of zinc gluconate has commonly been used to treat the common cold. The safety of this treatment, however, has come into question recently. In addition to a United States recall of a homeopathic product that contains zinc gluconate, abundant literature reports cytotoxic effects of zinc on the olfactory epithelium. Additional research suggests that divalent cations (such as zinc) can block ion channels that facilitate the transduction of odors into electrical signals on the olfactory epithelium. The purpose of the current study was 2-fold: to confirm whether zinc gluconate causes anosmia and to reveal whether any other divalent cationic compounds produce a similar effect. Groups of mice underwent a buried food-pellet test to gauge olfactory function and then were nasally irrigated with 1 of 3 divalent cationic compounds. When tested after treatment, mice irrigated with zinc gluconate and copper gluconate experienced a marked increase in food-finding time, indicating that they had lost their ability to smell a hidden food source. Control mice irrigated with saline had a significantly lower increase in times. These results confirm that zinc gluconate can cause anosmia and reveal that multiple divalent cations can negatively affect olfaction. PMID:22330252

Rough energy landscapes in protein folding: dimeric E. coli Trp repressor folds through three parallel channels.

PubMed

Gloss, L M; Simler, B R; Matthews, C R

2001-10-05

The folding mechanism of the dimeric Escherichia coli Trp repressor (TR) is a kinetically complex process that involves three distinguishable stages of development. Following the formation of a partially folded, monomeric ensemble of species, within 5 ms, folding to the native dimer is controlled by three kinetic phases. The rate-limiting step in each phase is either a non-proline isomerization reaction or a dimerization reaction, depending on the final denaturant concentration. Two approaches have been employed to test the previously proposed folding mechanism of TR through three parallel channels: (1) unfolding double-jump experiments demonstrate that all three folding channels lead directly to native dimer; and (2) the differential stabilization of the transition state for the final step in folding and the native dimer, by the addition of salt, shows that all three channels involve isomerization of a dimeric species. A refined model for the folding of Trp repressor is presented, in which all three channels involve a rapid dimerization reaction between partially folded monomers followed by the isomerization of the dimeric intermediates to yield native dimer. The ensemble of partially folded monomers can be captured at equilibrium by low pH; one-dimensional proton NMR spectra at pH 2.5 demonstrate that monomers exist in two distinct, slowly interconverting conformations. These data provide a potential structural explanation for the three-channel folding mechanism of TR: random association of two different monomeric forms, which are distinguished by alternative packing modes of the core dimerization domain and the DNA-binding, helix-turn-helix, domain. One, perhaps both, of these packing modes contains non-native contacts. Copyright 2001 Academic Press.

The "Knife-Cut Sign" Revisited: A Distinctive Presentation of Linear Erosive Herpes Simplex Virus Infection in Immunocompromised Patients.

PubMed

Cohen, Philip R

2015-10-01

The "knife-cut sign" is a distinctive presentation of linear erosive herpes simplex virus infection in immunocompromised patients. To describe a man whose herpes simplex virus infection-related skin lesions demonstrated the "knife-cut sign" and to review the characteristics of reported immunosuppressed individuals with "knife-cut" cutaneous herpes simplex virus lesions. A man with multiple myeloma and post-stem cell transplant cutaneous graft-versus-host disease managed with systemic prednisone and sirolimus developed disseminated cutaneous herpes simplex virus infection with virus-associated linear ulcers of the inguinal folds and the area between his ear and scalp; the lesions at both sites had a distinctive "knife-cut" appearance. Using the PubMed database, an extensive literature search was performed on herpes simplex virus, immunocompromised patient, and "knife-cut sign". Herpes simplex virus infection-associated skin lesions that demonstrate the "knife-cut sign" present in patients who are immunosuppressed secondary to either an underlying medical condition or a systemic therapy or both. The distinctive virus-related cutaneous lesions appear as linear ulcers and fissures in intertriginous areas, such as the folds in the inguinal area, the vulva, and the abdomen; in addition, other sites include beneath the breast, within the gluteal cleft, and the area between the ear and the scalp. Not only herpes simplex virus-2, but also herpes simplex virus-1 has been observed as the causative viral serotype; indeed, herpes simplex virus-1 has been associated with genital and inframammary lesions in addition to those above the neck. Direct fluorescent antibody testing is a rapid method for confirming the clinically suspected viral infection; however, since false-negative direct fluorescent antibody testing occurred in some of the patients, it may be prudent to also perform viral cultures and possibly lesional skin biopsies to establish the diagnosis. The herpes simplex virus infection-related skin lesions clinically improve once systemic antiviral therapy is initiated. In immunosuppressed individuals, the "knife-cut sign" is a distinctive presentation of cutaneous linear erosive herpes simplex virus infection. Recognition of the linear ulcers in intertriginous areas and body folds should prompt the clinician to consider herpes simplex virus infection-associated skin lesions in an immunocompromised patient and to initiate systemic antiviral treatment while awaiting the results of laboratory evaluation to confirm the suspected diagnosis.

Endothelial cells in the oral mucosa of Bufo marinus.

PubMed Central

Loo, S K; Yeo, B C; Kovac, H

1980-01-01

The oral mucosa of the cane toad (Bufo marinus) is lined by a pseudostratified columnar ciliated epithelium containing an intraepithelial network of capillaries, which penetrates it to the bases of the distal layer of cells. The capillaries are lined by fenestrated endothelium lying on a complete basal lamina. A connective tissue sheath, approximately 1 micrometer thick, surrounds the capillaries and separates them from the surrounding epithelial cells. Endothelial cells resemble those in lymphatic capillaries in that they show microvillus-like processes or folds projecting into the lumen and also have extremely attenuated and fenestrated cytoplasm except in the nuclear region. Numerous pinocytotic vesicles, bundles of filaments and many electrondense granules occur in the cytoplasm. These granules are oval or round in shape and approximately 250-400 micrometer in diameter. Histochemical tests on the endothelial cells show that the granules do not contain pigment, as both the Schmorl and argentaffin reactions are negative. Both the Sudan black B and Luxol fast blue reactions are also negative showing the lack of stainable lipids. The formaldehyde-induced fluorescence, the argentaffin reactions and lead haematoxylin reactions are negative, indicating that they do not have the characteristics of endocrine cells. The acid phosphatase reaction gives a positive result, localized to the site of the granules by electron microscopy and suggesting that these granules in amphibian capillaries may have a lysosomal function. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 Fig. 9 Fig. 10 Fig. 11 Fig. 12 Fig. 13 Fig. 14 Fig. 15 Fig. 16 PMID:6773911

Impairment of Novel Object Recognition Memory and Brain Insulin Signaling in Fructose- but Not Glucose-Drinking Female Rats.

PubMed

Sangüesa, Gemma; Cascales, Mar; Griñán, Christian; Sánchez, Rosa María; Roglans, Núria; Pallàs, Mercè; Laguna, Juan Carlos; Alegret, Marta

2018-01-26

Excessive sugar intake has been related to cognitive alterations, but it remains unclear whether these effects are related exclusively to increased energy intake, and the molecular mechanisms involved are not fully understood. We supplemented Sprague-Dawley female rats with 10% w/v fructose in drinking water or with isocaloric glucose solution for 7 months. Cognitive function was assessed through the Morris water maze (MWM) and the novel object recognition (NOR) tests. Plasma parameters and protein/mRNA expression in the frontal cortex and hippocampus were determined. Results showed that only fructose-supplemented rats displayed postprandial and fasting hypertriglyceridemia (1.4 and 1.9-fold, p < 0.05) and a significant reduction in the discrimination index in the NOR test, whereas the results of the MWM test showed no differences between groups. Fructose-drinking rats displayed an abnormal glucose tolerance test and impaired insulin signaling in the frontal cortex, as revealed by significant reductions in insulin receptor substrate-2 protein levels (0.77-fold, p < 0.05) and Akt phosphorylation (0.72-fold, p < 0.05), and increased insulin-degrading enzyme levels (1.86-fold, p < 0.001). Fructose supplementation reduced the expression of antioxidant enzymes and altered the amount of proteins involved in mitochondrial fusion/fission in the frontal cortex. In conclusion, cognitive deficits induced by chronic liquid fructose consumption are not exclusively related to increased caloric intake and are correlated with hypertriglyceridemia, impaired insulin signaling, increased oxidative stress and altered mitochondrial dynamics, especially in the frontal cortex.

Identification of RNA Aptamers that Internalize into HPV-16 E6/E7 Transformed Tonsillar Epithelial Cells

PubMed Central

Gourronc, Francoise A.; Rockey, William M.; Thiel, William H.; Giangrande, Paloma H.; Klingelhutz, Aloysius J.

2013-01-01

Human papillomavirus type 16 (HPV-16) associated oropharyngeal cancers are on a significant increase and better therapeutic strategies are needed. The HPV-16 oncogenes E6 and E7 are expressed in HPV-associated cancers and are able to transform human tonsillar epithelial cells (HTECs). We used cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) to select for RNA aptamers that entered into HPV-16 E6/E7-HTECs. After 12 rounds of cell-SELEX, a pool of aptamers was obtained that had significantly greater internalization capacity (~5-fold) into E6/E7-HTECs as compared to primary HTECs or fibroblasts. Analysis of individual aptamers from the pool indicated variable internalization into E6/E7-HTECs (1 to 8-fold as compared to a negative control). Most of the individual aptamers internalized into E6/E7 and primary HTECs with similar efficiency, while one aptamer exhibited ~3-fold better internalization into E6/E7-HTECs. Aptamers that internalize into cells may be useful for delivering therapeutic agents to HPV-16 associated malignancies. PMID:24074596

Developing a molecular dynamics force field for both folded and disordered protein states.

PubMed

Robustelli, Paul; Piana, Stefano; Shaw, David E

2018-05-07

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB- disp , should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields. Copyright © 2018 the Author(s). Published by PNAS.

Vocal fold tissue failure: preliminary data and constitutive modeling.

PubMed

Chan, Roger W; Siegmund, Thomas

2004-08-01

In human voice production (phonation), linear small-amplitude vocal fold oscillation occurs only under restricted conditions. Physiologically, phonation more often involves large-amplitude oscillation associated with tissue stresses and strains beyond their linear viscoelastic limits, particularly in the lamina propria extracellular matrix (ECM). This study reports some preliminary measurements of tissue deformation and failure response of the vocal fold ECM under large-strain shear The primary goal was to formulate and test a novel constitutive model for vocal fold tissue failure, based on a standard-linear cohesive-zone (SL-CZ) approach. Tissue specimens of the sheep vocal fold mucosa were subjected to torsional deformation in vitro, at constant strain rates corresponding to twist rates of 0.01, 0.1, and 1.0 rad/s. The vocal fold ECM demonstrated nonlinear stress-strain and rate-dependent failure response with a failure strain as low as 0.40 rad. A finite-element implementation of the SL-CZ model was capable of capturing the rate dependence in these preliminary data, demonstrating the model's potential for describing tissue failure. Further studies with additional tissue specimens and model improvements are needed to better understand vocal fold tissue failure.

MicroRNA-15b regulates reversion-inducing cysteine-rich protein with Kazal motifs (RECK) expression in human uterine leiomyoma.

PubMed

Guan, Yichun; Guo, Lankai; Zukerberg, Lawrence; Rueda, Bo R; Styer, Aaron K

2016-08-17

Human uterine leiomyoma (fibroids; LYO) are the most common benign neoplasms in reproductive-aged women. Dysregulated extracellular matrix and irregular LYO reversion-inducing cysteine-rich protein with Kazal motifs (RECK) expression are thought to be mediated by aberrant microRNA (miR) expression. The relationship of miR-15b and RECK expression in LYO has not been studied. The expression levels of miR-15b and RECK were determined by quantitative RT-PCR, Western blot, and immunohistochemistry in cultures derived from commercial primary leiomyoma (cpLYO) and myometrial (cpMYO) cell lines and leiomyoma (pLYO) and myometrium (pMYO) tissue from surgical samples respectively. The relationship between miR-15b and RECK expression in cpLYO and pLYO (compared to their respective myometrial controls) was evaluated following transfection of cell cultures with either miR-15b mimic or inhibitor. Elevated levels of miR-15b were observed in cpLYO (2.82-fold; p = 0.04) and pLYO cell (1.30-fold; p = 0.0001) cultures respectively compared to corresponding MYO cell controls. Following transfection with miR-15b mimic, cpLYO cells (0.62-fold; p < 0.0001) and pLYO cells (0.68-fold; p < 0.0001) demonstrated reduced RECK protein expression. Following transfection with miR-15b inhibitor, cpLYO cells (1.20-fold; p < 0.0001) and pLYO cells (1.31-fold; p = 0.0007) demonstrated elevated RECK protein expression. RECK protein expression was reduced in pLYO tissues (0.73-fold; p < 0.0001) and pLYO (0.47-fold; p = 0.047) cells when compared to the corresponding MYO tissue controls. Our findings suggest that miR-15b negatively regulates RECK expression in LYO, and increased miR-15b and decreased RECK expression may contribute to the pathobiology of LYO. The functional significance of miR-15b and RECK expression warrants further investigation as potential therapeutic targets for the treatment of human LYO.

Rapid detection of semenogelin by one-step immunochromatographic assay for semen identification.

PubMed

Sato, Itaru; Kojima, Koichiro; Yamasaki, Tadashi; Yoshida, Kaoru; Yoshiike, Miki; Takano, Shoichi; Mukai, Toshiji; Iwamoto, Teruaki

2004-04-01

To identify semen in forensic samples, we developed an analytical system for one-step immunoassay that has been constructed using the concept of immunochromatography and can identify semenogelin (Sg), which originates in the seminal vesicles. The system employed monoclonal antibody (mAb) and polyclonal antibody (pAb) against recombinant Sg-II (63 kDa), which has been synthesized in insect cells using baculovirus. The two antibodies bound with the seminal plasma motility inhibitor (SPMI; 14 kDa) as a final fragment peptide of Sg. The test stick is based on the sandwich technique using the above antibodies. When serial dilutions of seminal plasma were analyzed using this test stick, the intensity of a clear immunoreactive signal peaked at 2000-fold dilution. Thereafter, the signals decreased slowly but still persisted up to 400,000-fold dilution. The Sg antigen was undetectable in saliva, urine, breast milk, serum or vaginal secretions. Also, the test stick shown did not react with animal semen samples, such as those from horses, dogs, swine and bulls. When semen samples, diluted 100,000-fold from 100 men were tested, the Sg antigenic activity was detectable in all samples. In addition, the specificity and sensitivity of the test stick for identification of semen were demonstrated by comparative forensic studies. We conclude that this immunoassay method is a useful confirmatory test for the identification of semen. The immunochromatographic system for forensic testing or research use will become available commercially soon.

Vocal fold proteoglycans and their influence on biomechanics.

PubMed

Gray, S D; Titze, I R; Chan, R; Hammond, T H

1999-06-01

To examine the interstitial proteins of the vocal fold and their influence on the biomechanical properties of that tissue. Anatomic study of the lamina propria of human cadaveric vocal folds combined with some viscosity testing. Identification of proteoglycans is performed with histochemical staining. Quantitative analysis is performed using an image analysis system. A rheometer is used for viscosity testing. Three-dimensional rendering program is used for the computer images. Proteoglycans play an important role in tissue biomechanics. Hyaluronic acid is a key molecule that affects viscosity. The proteoglycans of the lamina propria have important biological and biomechanical effects. The role of hyaluronic acid in determining tissue viscosity is emphasized. Viscosity, its effect on phonatory threshold pressure and energy expended due to phonation is discussed. Proteoglycans, particularly hyaluronic acid, play important roles in determining biomechanical properties of tissue oscillation. Future research will likely make these proteins of important therapeutic interest.

Physical and Chemical Processes in Turbulent Flames

DTIC Science & Technology

2015-06-23

positive aerodynamics stretch, into a multitude of wrinkled flamelets possessing either positive or negative stretch, such that the intensified...flame surface, such as the flame surface area ratio, build up this global measure. The turbulent flame surface is typically highly wrinkled and folded...consider a filtered/average location of the flame positions to represent a smooth surface. The information contained in the wrinkled surface if

Blind test of physics-based prediction of protein structures.

PubMed

Shell, M Scott; Ozkan, S Banu; Voelz, Vincent; Wu, Guohong Albert; Dill, Ken A

2009-02-01

We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences.

Blind Test of Physics-Based Prediction of Protein Structures

PubMed Central

Shell, M. Scott; Ozkan, S. Banu; Voelz, Vincent; Wu, Guohong Albert; Dill, Ken A.

2009-01-01

We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences. PMID:19186130

Negative running can prevent eternal inflation

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

Kinney, William H.; Freese, Katherine, E-mail: whkinney@buffalo.edu, E-mail: ktfreese@umich.edu

Current data from the Planck satellite and the BICEP2 telescope favor, at around the 2 σ level, negative running of the spectral index of curvature perturbations from inflation. We show that for negative running α < 0, the curvature perturbation amplitude has a maximum on scales larger than our current horizon size. A condition for the absence of eternal inflation is that the curvature perturbation amplitude always remain below unity on superhorizon scales. For current bounds on n{sub S} from Planck, this corresponds to an upper bound of the running α < −9 × 10{sup −5}, so that even tiny running of the scalar spectral index ismore » sufficient to prevent eternal inflation from occurring, as long as the running remains negative on scales outside the horizon. In single-field inflation models, negative running is associated with a finite duration of inflation: we show that eternal inflation may not occur even in cases where inflation lasts as long as 10{sup 4} e-folds.« less

Blood-brain barrier-penetrating amphiphilic polymer nanoparticles deliver docetaxel for the treatment of brain metastases of triple negative breast cancer.

PubMed

He, Chunsheng; Cai, Ping; Li, Jason; Zhang, Tian; Lin, Lucy; Abbasi, Azhar Z; Henderson, Jeffrey T; Rauth, Andrew Michael; Wu, Xiao Yu

2017-01-28

Brain metastasis is a fatal disease with limited treatment options and very short survival. Although systemic chemotherapy has some effect on peripheral metastases of breast cancer, it is ineffective in treating brain metastasis due largely to the blood-brain barrier (BBB). Here we developed a BBB-penetrating amphiphilic polymer-lipid nanoparticle (NP) system that efficiently delivered anti-mitotic drug docetaxel (DTX) for the treatment of brain metastasis of triple negative breast cancer (TNBC). We evaluated the biodistribution, brain accumulation, pharmacokinetics and efficacy of DTX-NP in a mouse model of brain metastasis of TNBC. Confocal fluorescence microscopy revealed extravasation of dye-loaded NPs from intact brain microvessels in healthy mice. DTX-NP also extravasated from brain microvessels and accumulated in micrometastasis lesions in the brain. Intravenously injected DTX-NPs increased the blood circulation time of DTX by 5.5-fold and the AUC 0-24h in tumor-bearing brain by 5-fold compared to the clinically used DTX formulation Taxotere® . The kinetics of NPs in the brain, determined by ex vivo fluorescence imaging, showed synchronization with DTX kinetics in the brain measured by LC-MS/MS. This result confirmed successful delivery of DTX by the NPs into the brain and suggested that ex vivo fluorescence imaging of NP could be an effective and quick means for probing drug disposition in the brain. Treatment with the DTX-NP formulation delayed tumor growth by 11-fold and prolonged median survival of tumor-bearing mice by 94% compared to an equivalent dose of Taxotere®, without inducing histological changes in the major organs. Copyright © 2016 Elsevier B.V. All rights reserved.

Immunization with a dominant-negative recombinant Herpes Simplex Virus (HSV) type 1 protects against HSV-2 genital disease in guinea pigs

PubMed Central

2010-01-01

Background CJ9-gD is a novel dominant-negative recombinant herpes simplex virus type 1 (HSV-1) that is completely replication-defective, cannot establish detectable latent infection in vivo, and expresses high levels of the major HSV-1 antigen glycoprotein D immediately following infection. In the present study, CJ9-gD was evaluated as a vaccine against HSV-2 genital infection in guinea pigs. Results Animals immunized with CJ9-gD developed at least 700-fold higher titers of HSV-2-specific neutralization antibodies than mock-immunized controls. After challenge with wild-type HSV-2, all 10 control guinea pigs developed multiple genital lesions with an average of 21 lesions per animal. In contrast, only 2 minor lesions were found in 2 of 8 CJ9-gD-immunized animals, representing a 40-fold reduction on the incidence of primary genital lesions in immunized animals (p < 0.0001). Immunization significantly reduced the amount and duration of viral shedding and provided complete protection against neurological symptoms, while 90% of mock-immunized animals succumbed due to the severity of disease. Importantly, immunized animals showed no signs of recurrent disease or viral shedding during a 60-days observation period after recovery from primary infection, and carried 50-fold less latent viral DNA load in their dorsal root ganglia than the surviving mock-vaccinated controls (p < 0.0001). Conclusions Collectively, we demonstrate that vaccination with the HSV-1 recombinant CJ9-gD elicits strong and protective immune responses against primary and recurrent HSV-2 genital disease and significantly reduces the extent of latent infection. PMID:20525279

Secreted Proteins Defy the Expression Level-Evolutionary Rate Anticorrelation.

PubMed

Feyertag, Felix; Berninsone, Patricia M; Alvarez-Ponce, David

2017-03-01

The rates of evolution of the proteins of any organism vary across orders of magnitude. A primary factor influencing rates of protein evolution is expression. A strong negative correlation between expression levels and evolutionary rates (the so-called E-R anticorrelation) has been observed in virtually all studied organisms. This effect is currently attributed to the abundance-dependent fitness costs of misfolding and unspecific protein-protein interactions, among other factors. Secreted proteins are folded in the endoplasmic reticulum, a compartment where chaperones, folding catalysts, and stringent quality control mechanisms promote their correct folding and may reduce the fitness costs of misfolding. In addition, confinement of secreted proteins to the extracellular space may reduce misinteractions and their deleterious effects. We hypothesize that each of these factors (the secretory pathway quality control and extracellular location) may reduce the strength of the E-R anticorrelation. Indeed, here we show that among human proteins that are secreted to the extracellular space, rates of evolution do not correlate with protein abundances. This trend is robust to controlling for several potentially confounding factors and is also observed when analyzing protein abundance data for 6 human tissues. In addition, analysis of mRNA abundance data for 32 human tissues shows that the E-R correlation is always less negative, and sometimes nonsignificant, in secreted proteins. Similar observations were made in Caenorhabditis elegans and in Escherichia coli, and to a lesser extent in Drosophila melanogaster, Saccharomyces cerevisiae and Arabidopsis thaliana. Our observations contribute to understand the causes of the E-R anticorrelation. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effect of topical mitomycin-C on total collagen deposits on the submucosa of intact vocal folds in swine.

PubMed

Pereira, Marcelo Charles; Repka, Carlos Domingues; Camargo, Paulo Antonio Monteiro; Rispoli, Daniel Zeni; Campos, Antônio Carlos Ligocki; Matias, Jorge Eduardo Fouto

2009-07-01

To compare the effects of topical mitomycin-C at different concentrations on submucosal collagen deposition on the vocal folds of swine. The animals were divided into three groups according to the composition of the topical solution to be applied to the vocal folds: 0.9% saline solution (control group); 4 mg/ml mitomycin-C (group 1) and 8 mg/ml mitomycin-C (group 2). Thirty days after the application, all animals were sacrificed, their vocal folds were collected and stained by the picrosirius red technique, and submucosal collagen deposition areas were estimated by the Image Pro Plus 4.5 software. Mann-Whitney test was used to compare differences between parameters of each group. The means of the areas of submucosal collagen deposits on vocal folds were 3110.44 square micrometers (microm(2)), 3115.98 microm(2) and 3105.78 microm(2) for groups control, 1 and 2, respectively. There were no statistical differences across the three groups (p>0.05). Mitomycin-C topically applied to intact vocal folds of swine did not alter submucosal collagen deposition.

Detection and mapping of delays in early cortical folding derived from in utero MRI

NASA Astrophysics Data System (ADS)

Habas, Piotr A.; Rajagopalan, Vidya; Scott, Julia A.; Kim, Kio; Roosta, Ahmad; Rousseau, Francois; Barkovich, A. James; Glenn, Orit A.; Studholme, Colin

2011-03-01

Understanding human brain development in utero and detecting cortical abnormalities related to specific clinical conditions is an important area of research. In this paper, we describe and evaluate methodology for detection and mapping of delays in early cortical folding from population-based studies of fetal brain anatomies imaged in utero. We use a general linear modeling framework to describe spatiotemporal changes in curvature of the developing brain and explore the ability to detect and localize delays in cortical folding in the presence of uncertainty in estimation of the fetal age. We apply permutation testing to examine which regions of the brain surface provide the most statistical power to detect a given folding delay at a given developmental stage. The presented methodology is evaluated using MR scans of fetuses with normal brain development and gestational ages ranging from 20.57 to 27.86 weeks. This period is critical in early cortical folding and the formation of the primary and secondary sulci. Finally, we demonstrate a clinical application of the framework for detection and localization of folding delays in fetuses with isolated mild ventriculomegaly.

Modeling coupled aerodynamics and vocal fold dynamics using immersed boundary methods.

PubMed

Duncan, Comer; Zhai, Guangnian; Scherer, Ronald

2006-11-01

The penalty immersed boundary (PIB) method, originally introduced by Peskin (1972) to model the function of the mammalian heart, is tested as a fluid-structure interaction model of the closely coupled dynamics of the vocal folds and aerodynamics in phonation. Two-dimensional vocal folds are simulated with material properties chosen to result in self-oscillation and volume flows in physiological frequency ranges. Properties of the glottal flow field, including vorticity, are studied in conjunction with the dynamic vocal fold motion. The results of using the PIB method to model self-oscillating vocal folds for the case of 8 cm H20 as the transglottal pressure gradient are described. The volume flow at 8 cm H20, the transglottal pressure, and vortex dynamics associated with the self-oscillating model are shown. Volume flow is also given for 2, 4, and 12 cm H2O, illustrating the robustness of the model to a range of transglottal pressures. The results indicate that the PIB method applied to modeling phonation has good potential for the study of the interdependence of aerodynamics and vocal fold motion.

Dynamic viscosity of implantable autologous materials into the vocal fold.

PubMed

Wiikmann, Christian; da Silva, Marcelo Alves; Arêas, Elizabeth Pinheiro Gomes; Tsuji, Domingos Hiroshi; Sennes, Luiz Ubirajara

2012-07-01

To compare the dynamic viscosity (DV) of superficial layer of temporalis fascia (SLTF) with that of other biological tissues traditionally used for vocal fold implants to treat vocal fold rigidity. Experimental. Measurement of DV of samples of SLTF, deep layer of temporalis fascia (DLTF), and abdominal fat of 12 cadavers. DV values of the different samples were presented in the following increasing order: SLTF, DLTF, and abdominal fat. There was statistical difference between the samples. DV of SLTF is lower than of other tissues tested. Copyright © 2012 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

Negative pressure wound therapy combined with skin grafting improves surgical wound healing in the perianal area.

PubMed

Jia-Zi, Shi; Xiao, Zhai; Jun-Hui, Li; Chun-Yu, Xue; Hong-da, Bi

2016-08-01

Management of large tissue defects resulting from local wide resection of perianal is a clinical challenge for surgeons. The aim of the present study was to investigate the efficacy of negative pressure wound therapy (NPWT) following skin grafting on perianal surgical wound healing.Included in this study were 12 patients with perianal tumors who received skin grafting after perianal tumor resection between December 2012 and December 2014. A self-designed negative pressure drainage device was then applied to maintain a standard negative pressure at -150 mm Hg and removed on day 8 postoperation. The outcome was recorded immediately after NPWT and at 6-month follow-up.All skin grafts survived without infection, hematoma, and necrosis in all 12 patients. No tumor recurrence was detected during 6-month follow-up. Natural folds were observed around the anus. All patients showed normal bowel movements.NPWT following skin grafting was effective for perianal surgical wound healing and infection prevention, thus benefiting anatomical and functional recovery of the anus.

A model of infected burn wounds using Escherichia coli O18:K1:H7 for the study of gram-negative bacteremia and sepsis.

PubMed

Busch, N A; Zanzot, E M; Loiselle, P M; Carter, E A; Allaire, J E; Yarmush, M L; Warren, H S

2000-06-01

A difficulty that has emerged in the development and preclinical evaluation of adjuvant therapies for gram-negative sepsis is the lack of easily studied animal models that closely mimic human infection. An objective of this study was to adapt a previously described model of infection in burned mice to rats with a defined bacterial strain of Escherichia coli. Challenge with two colonies of live E. coli O18:K1:H7 bacteria into an 8% full-thickness burn of the dorsal skin surface of rats produced predictable bacteremia at 24 to 48 h and 80 to 100% mortality at 3 to 4 days. E. coli O18:K1:H7 was approximately 10-million-fold more virulent than several other gram-negative bacterial strains. The model should be a useful tool in studying the pathogenicity of burn wound infections and in evaluating the efficacy of novel adjuvant therapies for gram-negative sepsis.

Thermodynamics of Coupled Folding in the Interaction of Archaeal RNase P Proteins RPP21 and RPP29

PubMed Central

Xu, Yiren; Oruganti, Sri Vidya; Gopalan, Venkat; Foster, Mark P.

2014-01-01

We have used isothermal titration calorimetry (ITC) to identify and describe binding-coupled equilibria in the interaction between two protein subunits of archaeal ribonuclease P (RNase P). In all three domains of life, RNase P is a ribonucleoprotein complex that is primarily responsible for catalyzing the Mg2+-dependent cleavage of the 5′ leader sequence of precursor tRNAs during tRNA maturation. In archaea, RNase P has been shown to be composed of one catalytic RNA and up to five proteins, four of which associate in the absence of RNA as two functional heterodimers, POP5-RPP30 and RPP21-RPP29. NMR studies of the Pyrococcus furiosus RPP21 and RPP29 proteins in their free and complexed states provided evidence for significant protein folding upon binding. ITC experiments were performed over a range of temperatures, ionic strengths, pH values and in buffers with varying ionization potential, and with a folding-deficient RPP21 point mutant. These experiments revealed a negative heat capacity change (ΔCp), nearly twice that predicted from surface accessibility calculations, a strong salt dependence to the interaction and proton release at neutral pH, but a small net contribution from these to the excess ΔCp. We considered potential contributions from protein folding and burial of interfacial water molecules based on structural and spectroscopic data. We conclude that binding-coupled protein folding is likely responsible for a significant portion of the excess ΔCp. These findings provide novel structural-thermodynamic insights into coupled equilibria that enable specificity in macromolecular assemblies. PMID:22243443

Evaluation of the use of a needle-free injection syringe as a cause of non-specific reactions in the intradermal tuberculin test used for the diagnosis of bovine tuberculosis.

PubMed

Díez-Guerrier, A; Roy, A; de la Cruz, M L; Sáez, J L; Sanz, C; Boschiroli, M L; Romero, B; de Juan, L; Domínguez, L; Bezos, J

2018-05-24

The objective of the study was to elucidate whether the use of the needle-free Dermojet syringe, which is based on a high pressure inoculation and is used to inject tuberculin in cattle in several countries, may, in itself, cause skin reactions that can be interpreted as positive reactions to the intradermal tests that are not, in fact, related to the real infection status of the animals. Forty-four cattle from an officially tuberculosis-free (OTF) herd were selected, and four single intradermal tuberculin (SIT) tests were performed on each animal, two on each side of the neck. Three different Dermojet (D1, D2 and D3) and one McLintock (M4) syringes were used to carry out sterile phosphate buffer saline (PBS) with 10% of glycerol and bovine PPD injections. No positive reactions to the SIT test were observed when using the D1-D3 syringes in the case of either bovine PPD or PBS. With regard to M4 (PBS), all the tests were negative when using a standard interpretation but three were positive in the case of the severe interpretation. Significant differences (p < 0.05) in the skin fold thickness measured were found only between certain Dermojet and McLintock syringes at certain inoculation sites. The results showed that the needle-free Dermojet syringe used for PPD intradermal testing in cattle did not cause significant reactions that could be misunderstood as positives. Copyright © 2018 Elsevier Ltd. All rights reserved.

Local Vascularized Flaps for Augmentation of Reinke’s Space

PubMed Central

Dailey, Seth H.; Gunderson, McLean; Chan, Roger; Torrealba, Jose; Kimura, Miwako; Welham, Nathan V.

2011-01-01

Objectives/Hypothesis The purpose of this study is to describe and test a novel surgical strategy for augmentation of Reinke’s space using vascularized flaps: a thyroid ala perichondrium flap (TAP) and a composite thyroid ala perichondrium flap (CTAP) from the anterior larynx. We hypothesized that these specially designed vascularized flaps would remain viable once inset into the lamina propria, and that they would not disrupt rheologic, biomechanical, and histologic properties of the native vocal fold. Study Design Experimental. In vivo canine model. Methods The length and volume of test flaps harvested in six adult human cadaveric larynges were analyzed to determine suitability for use in augmentation in the lamina propria. Also, 12 beagles randomly underwent unilateral placement of either TAP or CTAP, which were designed in accordance with the human adult cadaveric experiments. Flap perfusion was measured before and after harvest with laser Doppler. After 1 month, the beagles were humanely sacrificed and their larynges subjected to aerodynamic and acoustic evaluation using an excised larynx apparatus. The vocal fold lamina propria of four larynges—two TAP and two CTAP—underwent rheologic evaluation using a simple-shear rheometer. The remaining eight larynges underwent quantitative histologic and immunohistochemical evaluation. The survival and complication (swallowing, airway, local wound) rates of all dogs were noted. Results Initial studies with adult human cadaveric larynges established that TAP and CTAP possessed length and volume greater than native lamina propria. In the canine experiments, the perfusion change in the flaps was similar between flap groups. The damping ratio (ζ), dynamic viscosity (η′), elastic shear modulus (G′), and viscous shear modulus (G″) of treated and untreated native vocal folds were not statistically different. The glottic function measures of vocal efficiency, laryngeal resistance, jitter, shimmer, and harmonics-to-noise ratio (HNR) of treated and normal larynges were not statistically different. Similarly, the values for collagen, elastin, and glycosaminoglycans (GAGs) in treated and untreated vocal folds were not statistically different. Also, neither neochrondrogenesis nor neoosteogenesis was detected in any treated vocal fold. The values for vascular and cellular proliferation in treated and untreated vocal folds were not statistically different. All test dogs survived and had no complications related to swallowing, airway distress, or the local wound. Conclusions The test flaps described and tested in this study appear to have conceptually attractive features for augmentation of Reinke’s space. When placed in an in vivo setting TAP and CTAP did not reveal unfavorable vascular, rheologic, aerodynamic, acoustic, or histologic characteristics. There was no unanticipated morbidity or mortality to the test animals. Long-term viability of these flaps is unknown. TAP and CTAP may open novel pathways for correction of glottic defects and may offer crossover opportunities with tissue engineering techniques. Level of Evidence None. PMID:21271606

Local vascularized flaps for augmentation of Reinke's space.

PubMed

Dailey, Seth H; Gunderson, McLean; Chan, Roger; Torrealba, Jose; Kimura, Miwako; Welham, Nathan V

2011-02-01

The purpose of this study is to describe and test a novel surgical strategy for augmentation of Reinke's space using vascularized flaps: a thyroid ala perichondrium flap (TAP) and a composite thyroid ala perichondrium flap (CTAP) from the anterior larynx. We hypothesized that these specially designed vascularized flaps would remain viable once inset into the lamina propria, and that they would not disrupt rheologic, biomechanical, and histologic properties of the native vocal fold. Experimental. In vivo canine model. The length and volume of test flaps harvested in six adult human cadaveric larynges were analyzed to determine suitability for use in augmentation in the lamina propria. Also, 12 beagles randomly underwent unilateral placement of either TAP or CTAP, which were designed in accordance with the human adult cadaveric experiments. Flap perfusion was measured before and after harvest with laser Doppler. After 1 month, the beagles were humanely sacrificed and their larynges subjected to aerodynamic and acoustic evaluation using an excised larynx apparatus. The vocal fold lamina propria of four larynges--two TAP and two CTAP--underwent rheologic evaluation using a simple-shear rheometer. The remaining eight larynges underwent quantitative histologic and immunohistochemical evaluation. The survival and complication (swallowing, airway, local wound) rates of all dogs were noted. Initial studies with adult human cadaveric larynges established that TAP and CTAP possessed length and volume greater than native lamina propria. In the canine experiments, the perfusion change in the flaps was similar between flap groups. The damping ratio (ζ), dynamic viscosity (η'), elastic shear modulus (G'), and viscous shear modulus (G″) of treated and untreated native vocal folds were not statistically different. The glottic function measures of vocal efficiency, laryngeal resistance, jitter, shimmer, and harmonics-to-noise ratio (HNR) of treated and normal larynges were not statistically different. Similarly, the values for collagen, elastin, and glycosaminoglycans (GAGs) in treated and untreated vocal folds were not statistically different. Also, neither neochrondrogenesis nor neoosteogenesis was detected in any treated vocal fold. The values for vascular and cellular proliferation in treated and untreated vocal folds were not statistically different. All test dogs survived and had no complications related to swallowing, airway distress, or the local wound. The test flaps described and tested in this study appear to have conceptually attractive features for augmentation of Reinke's space. When placed in an in vivo setting TAP and CTAP did not reveal unfavorable vascular, rheologic, aerodynamic, acoustic, or histologic characteristics. There was no unanticipated morbidity or mortality to the test animals. Long-term viability of these flaps is unknown. TAP and CTAP may open novel pathways for correction of glottic defects and may offer crossover opportunities with tissue engineering techniques. © 2010 The American Laryngological, Rhinological, and Otological Society, Inc.

On retrodictions of global mantle flow with assimilated surface velocities

NASA Astrophysics Data System (ADS)

Colli, Lorenzo; Bunge, Hans-Peter; Schuberth, Bernhard S. A.

2016-04-01

Modeling past states of Earth's mantle and relating them to geologic observations such as continental-scale uplift and subsidence is an effective method for testing mantle convection models. However, mantle convection is chaotic and two identical mantle models initialized with slightly different temperature fields diverge exponentially in time until they become uncorrelated, thus limiting retrodictions (i.e., reconstructions of past states of Earth's mantle obtained using present information) to the recent past. We show with 3-D spherical mantle convection models that retrodictions of mantle flow can be extended significantly if knowledge of the surface velocity field is available. Assimilating surface velocities produces in some cases negative Lyapunov times (i.e., e-folding times), implying that even a severely perturbed initial condition may evolve toward the reference state. A history of the surface velocity field for Earth can be obtained from past plate motion reconstructions for time periods of a mantle overturn, suggesting that mantle flow can be reconstructed over comparable times.

On retrodictions of global mantle flow with assimilated surface velocities

NASA Astrophysics Data System (ADS)

Colli, Lorenzo; Bunge, Hans-Peter; Schuberth, Bernhard S. A.

2015-10-01

Modeling past states of Earth's mantle and relating them to geologic observations such as continental-scale uplift and subsidence is an effective method for testing mantle convection models. However, mantle convection is chaotic and two identical mantle models initialized with slightly different temperature fields diverge exponentially in time until they become uncorrelated, thus limiting retrodictions (i.e., reconstructions of past states of Earth's mantle obtained using present information) to the recent past. We show with 3-D spherical mantle convection models that retrodictions of mantle flow can be extended significantly if knowledge of the surface velocity field is available. Assimilating surface velocities produces in some cases negative Lyapunov times (i.e., e-folding times), implying that even a severely perturbed initial condition may evolve toward the reference state. A history of the surface velocity field for Earth can be obtained from past plate motion reconstructions for time periods of a mantle overturn, suggesting that mantle flow can be reconstructed over comparable times.

Petroliferous wastewaters treatment with water hyacinths (Raffinerie de Provence, France): Experimental statement

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

Casabianca, M.L. de; Laugier, T.; Posada, F.

1995-12-31

The production and purification abilities of the water hyacinth, Eichhornia crassipes (Mart.) Solms., were tested on petrochemical wastewaters at Raffinerie de Provence, Total (La Mede, France), in controlled and in situ experiments. The mean production obtained was of about 6.1 g (dry weight) day{sup {minus}1} m{sup {minus}2} (10-fold lower than those obtained on paper industry effluent), and can be explained by the high salinity and pH of the effluent, and the negative effect of hydrocarbons. In comparison with the control pond, the water hyacinth system induced a rapid settlement effect. Finally, the removal gains due to the water hyacinths systemmore » were about 26% for the suspended solids (i.e., 40.1 kg day{sup {minus}1}), 28% for the total hydrocarbons (i.e., 17.2 kg day{sup {minus}1}) and 18% for the total organic carbon (i.e., 27 kg day{sup {minus}1}).« less

Determination of quality television programmes based on sentiment analysis on Twitter

NASA Astrophysics Data System (ADS)

Amalia, A.; Oktinas, W.; Aulia, I.; Rahmat, R. F.

2018-03-01

Public sentiment from social media like Twitter can be used as one of the indicators to determine the quality of TV Programmes. In this study, we implemented information extraction on Twitter by using sentiment analysis method to assess the quality of TV Programmes. The first stage of this study is pre-processing which consists of cleansing, case folding, tokenizing, stop-word removal, stemming, and redundancy filtering. The next stage is weighting process for every single word by using TF-IDF method. The last step of this study is the sentiment classification process which is divided into three sentiment category which is positive, negative and neutral. We classify the TV programmes into several categories such as news, children, or films/soap operas. We implemented an improved k-nearest neighbor method in classification 4000 twitter status, for four biggest TV stations in Indonesia, with ratio 70% data for training and 30% of data for the testing process. The result obtained from this research generated the highest accuracy with k=10 as big as 90%.

Real-Time Detection of Telomerase Activity in Cancer Cells using a Label-Free Electrochemical Impedimetric Biosensing Microchip.

PubMed

Cunci, Lisandro; Vargas, Marina Martinez; Cunci, Roman; Gomez-Moreno, Ramon; Perez, Ivan; Baerga-Ortiz, Abel; Gonzalez, Carlos I; Cabrera, Carlos R

2014-10-15

The enzyme telomerase is present in about 85% of human cancers which makes it not only a good target for cancer treatment but also an excellent marker for cancer detection. Using a single stranded DNA probe specific for telomerase binding and reverse transcription tethered to an interdigital gold electrode array surface, the chromosome protection provided by the telomerase was replicated and followed by Electrochemical Impedance Spectroscopy as an unlabeled biosensor. Using this system designed in-house, easy and affordable, impedance measurements were taken while incubating at 37 °C and promoting the probe elongation. This resulted in up to 14-fold increase in the charge transfer resistance when testing a telomerase-positive nuclear extract from Jurkat cells compared to the heat-inactivated telomerase-negative nuclear extract. The electron transfer process at the Au electrodes was studied before the elongation, at different times after the elongation, and after desorption of non-specific binding.

Evidence for Placental HPV Infection in Both HIV Positive and Negative Women

PubMed Central

Chisanga, Chrispin; Eggert, Dawn; Mitchell, Charles D.; Wood, Charles; Angeletti, Peter C.

2016-01-01

Human papillomaviruses (HPVs) have previously been reported to infect epithelial trophoblast cells of the placenta. To investigate this possibility, 200 placental samples from Zambian women were separated into HIV+ and HIV− groups and tested for HPV by redundant primer PCR, using GP5+/GP6+ and CPI/CPII primer sets. Three HPV genotypes (HPV6, 16 and 90) were detected in placental samples. Whereas, 20 different HPV genotypes were detected in vaginal sampling of the same patients, suggesting that compartment specific sub-populations of HPV may exist. The incidence of HPV16 in placental samples was almost 2-fold greater in HIV+ women compared to HIV− (p = 0.0241). HPV16 L1 expression, detected by immunochemistry, was significantly higher in HIV+ than HIV− samples (p = 0.0231). HPV16 DNA was detected in the nuclei of trophoblast cells by in situ hybridization. Overall, these results suggest that HPVs infect the placenta and that HIV significantly influences these infections. PMID:26865986

Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs.

PubMed

Shamim, Mohammad Tabrez Anwar; Anwaruddin, Mohammad; Nagarajaram, H A

2007-12-15

Fold recognition is a key step in the protein structure discovery process, especially when traditional sequence comparison methods fail to yield convincing structural homologies. Although many methods have been developed for protein fold recognition, their accuracies remain low. This can be attributed to insufficient exploitation of fold discriminatory features. We have developed a new method for protein fold recognition using structural information of amino acid residues and amino acid residue pairs. Since protein fold recognition can be treated as a protein fold classification problem, we have developed a Support Vector Machine (SVM) based classifier approach that uses secondary structural state and solvent accessibility state frequencies of amino acids and amino acid pairs as feature vectors. Among the individual properties examined secondary structural state frequencies of amino acids gave an overall accuracy of 65.2% for fold discrimination, which is better than the accuracy by any method reported so far in the literature. Combination of secondary structural state frequencies with solvent accessibility state frequencies of amino acids and amino acid pairs further improved the fold discrimination accuracy to more than 70%, which is approximately 8% higher than the best available method. In this study we have also tested, for the first time, an all-together multi-class method known as Crammer and Singer method for protein fold classification. Our studies reveal that the three multi-class classification methods, namely one versus all, one versus one and Crammer and Singer method, yield similar predictions. Dataset and stand-alone program are available upon request.

Voluntary counselling and testing for HIV in a Zambian mining community: serial interviews with people testing negative.

PubMed

Sikasote, Janet; Grant, Liz; Chinn, David J; Macwang'i, Mubiana; Murray, Scott A

2011-08-01

To understand the influence of voluntary counselling and testing (VCT) and an HIV-negative result on subsequent sexual behaviour; and to identify the specific felt needs of those testing negative. Serial interviews, 6 months apart, with people who had tested negative, and three one-off focus group discussions with counsellors. Interviews were transcribed verbatim and analysed thematically. Paired transcripts were analysed longitudinally. Purposively sampled from first attenders for VCT who had tested negative. Four health-facility affiliated VCT centres in two mining towns in the Copperbelt Province of Zambia. Participants in the 42 initial and 31 follow-up interviews understood VCT as 'testing for HIV'. Most participants reported having adopted safer sexual behaviour months before attending VCT. They had already recognised personal susceptibility to HIV infection and reported engaging both emotionally and cognitively with the issues of testing. Ultimately attendance at testing was to know their status in order to regain control of their lives. Unmet post-test support needs were common and included additional information, supportive networks, life-skills training and access to recreational activities. In this population who tested HIV negative the majority said they had made life changes months before attending VCT. Counselling served to consolidate pre-test decisions about risk behaviour. Those testing HIV negative are underserved compared with those testing positive. We recommend that counselling for HIV should be de-linked from testing to encourage earlier attendance for counselling and that clients testing negative should receive more post-test support to help them remain HIV negative.

Phase 1 testing of detoxified LPS/group B meningococcal outer membrane protein vaccine with and without synthetic CPG 7909 adjuvant for the prevention and treatment of sepsis.

PubMed

Cross, Alan S; Greenberg, Nancy; Billington, Melissa; Zhang, Lei; DeFilippi, Christopher; May, Ryan C; Bajwa, Kanwaldeep K

2015-11-27

Gram-negative bacteria (GNB) are a leading cause of nosocomial infection and sepsis. Increasing multi-antibiotic resistance has left clinicians with fewer therapeutic options. Antibodies to GNB lipopolysaccharide (LPS, or endotoxin) have reduced morbidity and mortality as a result of infection and are not subject to the resistance mechanisms deployed by bacteria against antibiotics. In this phase 1 study, we administered a vaccine that elicits antibodies against a highly conserved portion of LPS with and without a CpG oligodeoxynucleotide (ODN) TLR9 agonist as adjuvant. A vaccine composed of the detoxified LPS (dLPS) from E. coli O111:B4 (J5 mutant) non-covalently complexed to group B meningococcal outer membrane protein (OMP). Twenty healthy adult subjects received three doses at 0, 29 and 59 days of antigen (10 μg dLPS) with or without CPG 7909 (250 or 500 μg). Subjects were evaluated for local and systemic adverse effects and laboratory findings. Anti-J5 LPS IgG and IgM antibody levels were measured by electrochemiluminesence. Due to premature study termination, not all subjects received all three doses. All vaccine formulations were well-tolerated with no local or systemic events of greater than moderate severity. The vaccine alone group achieved a ≥ 4-fold "responder" response in IgG and IgM antibody in only one of 6 subjects. In contrast, the vaccine plus CPG 7909 groups appeared to have earlier and more sustained (to 180 days) responses, greater mean-fold increases, and a higher proportion of "responders" achieving ≥ 4-fold increases over baseline. Although the study was halted before all enrolled subjects received all three doses, the J5dLPS/OMP vaccine, with or without CpG adjuvant, was safe and well-tolerated. The inclusion of CpG increased the number of subjects with a ≥ 4-fold antibody response, evident even after the second of three planned doses. A vaccine comprising J5dLPS/OMP antigen with CpG adjuvant merits further investigation. ClinicalTrials.gov Identifier: NCT01164514. Copyright © 2015 Elsevier Ltd. All rights reserved.

Negative HPV screening test predicts low cervical cancer risk better than negative Pap test

Cancer.gov

Based on a study that included more than 1 million women, investigators at NCI have determined that a negative test for HPV infection compared to a negative Pap test provides greater safety, or assurance, against future risk of cervical cancer.

Cisplatin and Oxaliplatin Toxicity: Importance of Cochlear Kinetics as a Determinant for Ototoxicity

PubMed Central

Wallin, Inger; Eriksson, Sofi; Hernlund, Emma; Jerremalm, Elin; Berndtsson, Maria; Eksborg, Staffan; Arnér, Elias S. J.; Shoshan, Maria; Ehrsson, Hans; Laurell, Göran

2009-01-01

Background Cisplatin is a cornerstone anticancer drug with pronounced ototoxicity, whereas oxaliplatin, a platinum derivative with a different clinical profile, is rarely ototoxic. This difference has not been explained. Methods In HCT116 cells, cisplatin (20 μM)-induced apoptosis was reduced by a calcium chelator from 9.9-fold induction (95% confidence interval [CI] = 8.1- to 11.7-fold), to 3.1-fold induction (95% CI = 2.0- to 4.2-fold) and by superoxide scavenging from 9.3-fold (95% CI = 8.8- to 9.8-fold), to 5.1-fold (95% CI = 4.4- to 5.8-fold). A guinea pig model (n = 23) was used to examine pharmacokinetics. Drug concentrations were determined by liquid chromatography with post-column derivatization. The total platinum concentration in cochlear tissue was determined by inductively coupled plasma mass spectrometry. Drug pharmacokinetics was assessed by determining the area under the concentration–time curve (AUC). Statistical tests were two-sided. Results In HCT116 cells, cisplatin (20 μM)-induced apoptosis was reduced by a calcium chelator from 9.9-fold induction (95% confidence interval [CI] = 8.1- to 11.7-fold to 3.1-fold induction) (95% CI = 2.0- to 4.2-fold) and by superoxide scavenging (from 9.3-fold, 95% CI = 8.8- to 9.8-fold, to 5.1-fold, 95% CI = 4.4- to 5.8-fold). Oxaliplatin (20 μM)-induced apoptosis was unaffected by calcium chelation (from 7.1- to 6.2-fold induction) and by superoxide scavenging (from 5.9- to 5.6-fold induction). In guinea pig cochlea, total platinum concentration (0.12 vs 0.63 μg/kg, respectively, P = .008) and perilymphatic drug concentrations (238 vs 515 μM × minute, respectively, P < .001) were lower after intravenous oxaliplatin treatment (16.6 mg/kg) than after equimolar cisplatin treatment (12.5 mg/kg). However, after a non-ototoxic cisplatin dose (5 mg/kg) or the same oxaliplatin dose (16.6 mg/kg), the AUC for perilymphatic concentrations was similar, indicating that the two drugs have different cochlear pharmacokinetics. Conclusion Cisplatin- but not oxaliplatin-induced apoptosis involved superoxide-related pathways. Lower cochlear uptake of oxaliplatin than cisplatin appears to be a major explanation for its lower ototoxicity. PMID:19116379

TPP1 is a homologue of ciliate TEBP-β and interacts with POT1 to recruit telomerase

NASA Astrophysics Data System (ADS)

Xin, Huawei; Liu, Dan; Wan, Ma; Safari, Amin; Kim, Hyeung; Sun, Wen; O'Connor, Matthew S.; Songyang, Zhou

2007-02-01

Telomere dysfunction may result in chromosomal abnormalities, DNA damage responses, and even cancer. Early studies in lower organisms have helped to establish the crucial role of telomerase and telomeric proteins in maintaining telomere length and protecting telomere ends. In Oxytricha nova, telomere G-overhangs are protected by the TEBP-α/β heterodimer. Human telomeres contain duplex telomeric repeats with 3' single-stranded G-overhangs, and may fold into a t-loop structure that helps to shield them from being recognized as DNA breaks. Additionally, the TEBP-α homologue, POT1, which binds telomeric single-stranded DNA (ssDNA), associates with multiple telomeric proteins (for example, TPP1, TIN2, TRF1, TRF2 and RAP1) to form the six-protein telosome/shelterin and other subcomplexes. These telomeric protein complexes in turn interact with diverse pathways to form the telomere interactome for telomere maintenance. However, the mechanisms by which the POT1-containing telosome communicates with telomerase to regulate telomeres remain to be elucidated. Here we demonstrate that TPP1 is a putative mammalian homologue of TEBP-β and contains a predicted amino-terminal oligonucleotide/oligosaccharide binding (OB) fold. TPP1-POT1 association enhanced POT1 affinity for telomeric ssDNA. In addition, the TPP1 OB fold, as well as POT1-TPP1 binding, seemed critical for POT1-mediated telomere-length control and telomere-end protection in human cells. Disruption of POT1-TPP1 interaction by dominant negative TPP1 expression or RNA interference (RNAi) resulted in telomere-length alteration and DNA damage responses. Furthermore, we offer evidence that TPP1 associates with the telomerase in a TPP1-OB-fold-dependent manner, providing a physical link between telomerase and the telosome/shelterin complex. Our findings highlight the critical role of TPP1 in telomere maintenance, and support a yin-yang model in which TPP1 and POT1 function as a unit to protect human telomeres, by both positively and negatively regulating telomerase access to telomere DNA.

Correlation of transarterial transport of various dextrans with their physicochemical properties.

PubMed

Elmalak, O; Lovich, M A; Edelman, E

2000-11-01

Local vascular drug delivery provides elevated concentrations of drug in the target tissue while minimizing systemic side effects. To better characterize local pharmacokinetics we examined the arterial transport of locally applied dextran and dextran derivatives in vivo. Using a two-compartment pharmacokinetic model to correct the measured transmural flux of these compounds for systemic redistribution and elimination as delivered from a photopolymerizable hydrogel surrounding rat carotid arteries, we found that the diffusivities and the transendothelial permeabilities were strongly dependent on molecular weight and charge. For neutral dextrans, the effective diffusive resistance in the media increased with molecular weight approximately 4.1-fold between the molecular weights of 10 and 282 kDa. Similarly, endothelial resistance increased 28-fold over the same molecular weight range. The effective medial diffusive resistance was unaffected by cationic charge as such molecules moved identically to neutral compounds, but increased approximately 40% when dextrans were negatively charged. Transendothelial resistance was 20-fold lower for the cationic dextrans, and 11-fold higher for the anionic dextrans, when both were compared to neutral counterparts. These results suggest that, while low molecular weight drugs will rapidly traverse the arterial wall with the endothelium posing a minimal barrier, the reverse is true for high molecular weight agents. With these data, the deposition and distribution of locally released vasotherapeutic compounds might be predicted based upon chemical properties, such as molecular weight and charge.

Column-parallel correlated multiple sampling circuits for CMOS image sensors and their noise reduction effects.

PubMed

Suh, Sungho; Itoh, Shinya; Aoyama, Satoshi; Kawahito, Shoji

2010-01-01

For low-noise complementary metal-oxide-semiconductor (CMOS) image sensors, the reduction of pixel source follower noises is becoming very important. Column-parallel high-gain readout circuits are useful for low-noise CMOS image sensors. This paper presents column-parallel high-gain signal readout circuits, correlated multiple sampling (CMS) circuits and their noise reduction effects. In the CMS, the gain of the noise cancelling is controlled by the number of samplings. It has a similar effect to that of an amplified CDS for the thermal noise but is a little more effective for 1/f and RTS noises. Two types of the CMS with simple integration and folding integration are proposed. In the folding integration, the output signal swing is suppressed by a negative feedback using a comparator and one-bit D-to-A converter. The CMS circuit using the folding integration technique allows to realize a very low-noise level while maintaining a wide dynamic range. The noise reduction effects of their circuits have been investigated with a noise analysis and an implementation of a 1Mpixel pinned photodiode CMOS image sensor. Using 16 samplings, dynamic range of 59.4 dB and noise level of 1.9 e(-) for the simple integration CMS and 75 dB and 2.2 e(-) for the folding integration CMS, respectively, are obtained.

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models.

PubMed

Jacquin, Hugo; Gilson, Amy; Shakhnovich, Eugene; Cocco, Simona; Monasson, Rémi

2016-05-01

Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the inferred effective Potts Hamiltonian and real protein structure and energetics remain untested so far. Here we use lattice protein model (LP) to benchmark those inverse statistical approaches. We build MSA of highly stable sequences in target LP structures, and infer the effective pairwise Potts Hamiltonians from those MSA. We find that inferred Potts Hamiltonians reproduce many important aspects of 'true' LP structures and energetics. Careful analysis reveals that effective pairwise couplings in inferred Potts Hamiltonians depend not only on the energetics of the native structure but also on competing folds; in particular, the coupling values reflect both positive design (stabilization of native conformation) and negative design (destabilization of competing folds). In addition to providing detailed structural information, the inferred Potts models used as protein Hamiltonian for design of new sequences are able to generate with high probability completely new sequences with the desired folds, which is not possible using independent-site models. Those are remarkable results as the effective LP Hamiltonians used to generate MSA are not simple pairwise models due to the competition between the folds. Our findings elucidate the reasons for the success of inverse approaches to the modelling of proteins from sequence data, and their limitations.

Role of the tail in the regulated state of myosin 2

PubMed Central

Jung, HyunSuk; Billington, Neil; Thirumurugan, Kavitha; Salzameda, Bridget; Cremo, Christine R.; Chalovich, Joseph M.; Chantler, Peter D.; Knight, Peter J.

2013-01-01

Myosin 2 from vertebrate smooth muscle or non-muscle sources is in equilibrium between compact, inactive monomers and thick filaments under physiological conditions. In the inactive monomer, the two heads pack compactly together and the long tail is folded into three closely-packed segments that are associated chiefly with one of the heads. The molecular basis of the folding of the tail remains unexplained. Using electron microscopy, we show that compact monomers of smooth muscle myosin 2 have the same structure in both the native state and following specific, intramolecular photo-cross-linking between Cys109 of the regulatory light chain (RLC) and segment 3 of the tail. Non-specific cross-linking between lysine residues of the folded monomer by glutaraldehyde also does not perturb the compact conformation, and stabilises it against unfolding at high ionic strength. Sequence comparisons across phyla and myosin 2 isoforms suggest that folding of the tail is stabilised by ionic interactions between the positively-charged N-terminal sequence of the RLC and a negatively-charged region near the start of tail segment 3, and that phosphorylation of the RLC could perturb these interactions. Our results support the view that interactions between the heads and the distal tail perform a critical role in regulating activity of myosin 2 molecules through stabilising the compact monomer conformation. PMID:21419133

The Effect of Hydration on Voice Quality in Adults: A Systematic Review.

PubMed

Alves, Maxine; Krüger, Esedra; Pillay, Bhavani; van Lierde, Kristiane; van der Linde, Jeannie

2017-11-06

We aimed to critically appraise scientific, peer-reviewed articles, published in the past 10 years on the effects of hydration on voice quality in adults. This is a systematic review. Five databases were searched using the key words "vocal fold hydration", "voice quality", "vocal fold dehydration", and "hygienic voice therapy". The Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) guidelines were followed. The included studies were scored based on American Speech-Language-Hearing Association's levels of evidence and quality indicators, as well as the Cochrane Collaboration's risk of bias tool. Systemic dehydration as a result of fasting and not ingesting fluids significantly negatively affected the parameters of noise-to-harmonics ratio (NHR), shimmer, jitter, frequency, and the s/z ratio. Water ingestion led to significant improvements in shimmer, jitter, frequency, and maximum phonation time values. Caffeine intake does not appear to negatively affect voice production. Laryngeal desiccation challenges by oral breathing led to surface dehydration which negatively affected jitter, shimmer, NHR, phonation threshold pressure, and perceived phonatory effort. Steam inhalation significantly improved NHR, shimmer, and jitter. Only nebulization of isotonic solution decreased phonation threshold pressure and showed some indication of a potential positive effect of nebulization substances. Treatments in high humidity environments prove to be effective and adaptations of low humidity environments should be encouraged. Recent literature regarding vocal hydration is high quality evidence. Systemic hydration is the easiest and most cost-effective solution to improve voice quality. Recent evidence therefore supports the inclusion of hydration in a vocal hygiene program. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure

PubMed Central

Suddala, Krishna C.; Rinaldi, Arlie J.; Feng, Jun; Mustoe, Anthony M.; Eichhorn, Catherine D.; Liberman, Joseph A.; Wedekind, Joseph E.; Al-Hashimi, Hashim M.; Brooks, Charles L.; Walter, Nils G.

2013-01-01

Riboswitches are structural elements in the 5′ untranslated regions of many bacterial messenger RNAs that regulate gene expression in response to changing metabolite concentrations by inhibition of either transcription or translation initiation. The preQ1 (7-aminomethyl-7-deazaguanine) riboswitch family comprises some of the smallest metabolite sensing RNAs found in nature. Once ligand-bound, the transcriptional Bacillus subtilis and translational Thermoanaerobacter tengcongensis preQ1 riboswitch aptamers are structurally similar RNA pseudoknots; yet, prior structural studies have characterized their ligand-free conformations as largely unfolded and folded, respectively. In contrast, through single molecule observation, we now show that, at near-physiological Mg2+ concentration and pH, both ligand-free aptamers adopt similar pre-folded state ensembles that differ in their ligand-mediated folding. Structure-based Gō-model simulations of the two aptamers suggest that the ligand binds late (Bacillus subtilis) and early (Thermoanaerobacter tengcongensis) relative to pseudoknot folding, leading to the proposal that the principal distinction between the two riboswitches lies in their relative tendencies to fold via mechanisms of conformational selection and induced fit, respectively. These mechanistic insights are put to the test by rationally designing a single nucleotide swap distal from the ligand binding pocket that we find to predictably control the aptamers′ pre-folded states and their ligand binding affinities. PMID:24003028

Design and 4D Printing of Cross-Folded Origami Structures: A Preliminary Investigation

PubMed Central

Teoh, Joanne Ee Mei; Feng, Xiaofan; Zhao, Yue; Liu, Yong

2018-01-01

In 4D printing research, different types of complex structure folding and unfolding have been investigated. However, research on cross-folding of origami structures (defined as a folding structure with at least two overlapping folds) has not been reported. This research focuses on the investigation of cross-folding structures using multi-material components along different axes and different horizontal hinge thickness with single homogeneous material. Tensile tests were conducted to determine the impact of multi-material components and horizontal hinge thickness. In the case of multi-material structures, the hybrid material composition has a significant impact on the overall maximum strain and Young’s modulus properties. In the case of single material structures, the shape recovery speed is inversely proportional to the horizontal hinge thickness, while the flexural or bending strength is proportional to the horizontal hinge thickness. A hinge with a thickness of 0.5 mm could be folded three times prior to fracture whilst a hinge with a thickness of 0.3 mm could be folded only once prior to fracture. A hinge with a thickness of 0.1 mm could not even be folded without cracking. The introduction of a physical hole in the center of the folding/unfolding line provided stress relief and prevented fracture. A complex flower petal shape was used to successfully demonstrate the implementation of overlapping and non-overlapping folding lines using both single material segments and multi-material segments. Design guidelines for establishing cross-folding structures using multi-material components along different axes and different horizontal hinge thicknesses with single or homogeneous material were established. These guidelines can be used to design and implement complex origami structures with overlapping and non-overlapping folding lines. Combined overlapping folding structures could be implemented and allocating specific hole locations in the overall designs could be further explored. In addition, creating a more precise prediction by investigating sets of in between hinge thicknesses and comparing the folding times before fracture, will be the subject of future work. PMID:29510503

Exercise training, but not resveratrol, improves metabolic and inflammatory status in skeletal muscle of aged men

PubMed Central

Olesen, Jesper; Gliemann, Lasse; Biensø, Rasmus; Schmidt, Jakob; Hellsten, Ylva; Pilegaard, Henriette

2014-01-01

The aim was to investigate the metabolic and anti-inflammatory effects of resveratrol alone and when combined with exercise training in skeletal muscle of aged human subjects. Healthy, physically inactive men (60–72 years old) were randomized to either 8 weeks of daily intake of 250 mg resveratrol or placebo or to 8 weeks of high-intensity exercise training with 250 mg resveratrol or placebo. Before and after the interventions, resting blood samples and muscle biopsies were obtained and a one-legged knee-extensor endurance exercise test was performed. Exercise training increased skeletal muscle peroxisome proliferator-activated receptor-γ co-activator-1α mRNA ∼1.5-fold, cytochrome c protein ∼1.3-fold, cytochrome c oxidase I protein ∼1.5-fold, citrate synthase activity ∼1.3-fold, 3-hydroxyacyl-CoA dehydrogenase activity ∼1.3-fold, inhibitor of κB-α and inhibitor of κB-β protein content ∼1.3-fold and time to exhaustion in the one-legged knee-extensor endurance exercise test by ∼1.2-fold, with no significant additive or adverse effects of resveratrol on these parameters. Despite an overall ∼25% reduction in total acetylation level in skeletal muscle with resveratrol, no exclusive resveratrol-mediated metabolic effects were observed on the investigated parameters. Notably, however, resveratrol blunted an exercise training-induced decrease (∼20%) in protein carbonylation and decrease (∼40%) in tumour necrosis factor α mRNA content in skeletal muscle. In conclusion, resveratrol did not elicit metabolic improvements in healthy aged subjects; in fact, resveratrol even impaired the observed exercise training-induced improvements in markers of oxidative stress and inflammation in skeletal muscle. Collectively, this highlights the metabolic efficacy of exercise training in aged subjects and does not support the contention that resveratrol is a potential exercise mimetic in healthy aged subjects. PMID:24514907

Impact of Perioperative Voice Therapy on Outcomes in the Surgical Management of Vocal Fold Cysts.

PubMed

Tibbetts, Kathleen M; Dominguez, Laura M; Simpson, C Blake

2018-05-01

Vocal fold cysts are benign mid-membranous lesions of the true vocal fold, classified as mucus retention or epidermal inclusion cysts. Treatment is surgical excision with or without postoperative voice therapy. A retrospective review was performed of the demographics, treatment approach, and outcomes of patients treated for vocal fold cysts between 2009 and 2014. Voice Handicap Index (VHI)-10 scores before and after treatment were compared using the Wilcoxon Rank-Sum test and the two-tailed Student's t test. Videostroboscopy examinations were reviewed for posttreatment changes in vibratory characteristics of the vocal folds. Twenty-five patients were identified, and one was excluded for incomplete records. Mean age was 41.9 years (66.7% female), and mean follow-up time was 5.58 months. Microflap excision was pursued by 21/24 (87.5%) patients, with 14 patients (58.3%) undergoing perioperative voice therapy. One cyst recurred. Two patients elected for observation, and their cysts persisted. VHI-10 decreased from 23.8 to 6.6 (P < 0.001) overall. There was a statistically significant reduction in VHI-10 in patients undergoing surgery with and without postoperative voice therapy (P < 0.004 and 0.001), but there was no significant difference between these two groups. Mucosal wave was classified as normal or improved in the majority. Cysts were characterized as mucus retention cysts in 19/21 (90%) and as epidermal inclusion cysts in 2/21 (10%). Vocal fold cysts impact mucosal wave and glottic closure. Surgical excision resulted in low rates of recurrence, and in improvement in the mucosal wave and VHI-10. Perioperative voice therapy did not offer a significant benefit. Mucus retention cysts were the majority, in contrast to other published studies. Copyright © 2018 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

A specific transition state for S-peptide combining with folded S-protein and then refolding

PubMed Central

Goldberg, Jonathan M.; Baldwin, Robert L.

1999-01-01

We measured the folding and unfolding kinetics of mutants for a simple protein folding reaction to characterize the structure of the transition state. Fluorescently labeled S-peptide analogues combine with S-protein to form ribonuclease S analogues: initially, S-peptide is disordered whereas S-protein is folded. The fluorescent probe provides a convenient spectroscopic probe for the reaction. The association rate constant, kon, and the dissociation rate constant, koff, were both determined for two sets of mutants. The dissociation rate constant is measured by adding an excess of unlabeled S-peptide analogue to a labeled complex (RNaseS*). This strategy allows kon and koff to be measured under identical conditions so that microscopic reversibility applies and the transition state is the same for unfolding and refolding. The first set of mutants tests the role of the α-helix in the transition state. Solvent-exposed residues Ala-6 and Gln-11 in the α-helix of native RNaseS were replaced by the helix destabilizing residues glycine or proline. A plot of log kon vs. log Kd for this series of mutants is linear over a very wide range, with a slope of −0.3, indicating that almost all of the molecules fold via a transition state involving the helix. A second set of mutants tests the role of side chains in the transition state. Three side chains were investigated: Phe-8, His-12, and Met-13, which are known to be important for binding S-peptide to S-protein and which also contribute strongly to the stability of RNaseS*. Only the side chain of Phe-8 contributes significantly, however, to the stability of the transition state. The results provide a remarkably clear description of a folding transition state. PMID:10051587

Analysis and Manipulation of Aspartate Pathway Genes for l-Lysine Overproduction from Methanol by Bacillus methanolicus▿

PubMed Central

Nærdal, Ingemar; Netzer, Roman; Ellingsen, Trond E.; Brautaset, Trygve

2011-01-01

We investigated the regulation and roles of six aspartate pathway genes in l-lysine overproduction in Bacillus methanolicus: dapG, encoding aspartokinase I (AKI); lysC, encoding AKII; yclM, encoding AKIII; asd, encoding aspartate semialdehyde dehydrogenase; dapA, encoding dihydrodipicolinate synthase; and lysA, encoding meso-diaminopimelate decarboxylase. Analysis of the wild-type strain revealed that in vivo lysC transcription was repressed 5-fold by l-lysine and induced 2-fold by dl-methionine added to the growth medium. Surprisingly, yclM transcription was repressed 5-fold by dl-methionine, while the dapG, asd, dapA, and lysA genes were not significantly repressed by any of the aspartate pathway amino acids. We show that the l-lysine-overproducing classical B. methanolicus mutant NOA2#13A52-8A66 has—in addition to a hom-1 mutation—chromosomal mutations in the dapG coding region and in the lysA promoter region. No mutations were found in its dapA, lysC, asd, and yclM genes. The mutant dapG gene product had abolished feedback inhibition by meso-diaminopimelate in vitro, and the lysA mutation was accompanied by an elevated (6-fold) lysA transcription level in vivo. Moreover, yclM transcription was increased 16-fold in mutant strain NOA2#13A52-8A66 compared to the wild-type strain. Overexpression of wild-type and mutant aspartate pathway genes demonstrated that all six genes are important for l-lysine overproduction as tested in shake flasks, and the effects were dependent on the genetic background tested. Coupled overexpression of up to three genes resulted in additive (above 80-fold) increased l-lysine production levels. PMID:21724876

Analysis and manipulation of aspartate pathway genes for L-lysine overproduction from methanol by Bacillus methanolicus.

PubMed

Nærdal, Ingemar; Netzer, Roman; Ellingsen, Trond E; Brautaset, Trygve

2011-09-01

We investigated the regulation and roles of six aspartate pathway genes in L-lysine overproduction in Bacillus methanolicus: dapG, encoding aspartokinase I (AKI); lysC, encoding AKII; yclM, encoding AKIII; asd, encoding aspartate semialdehyde dehydrogenase; dapA, encoding dihydrodipicolinate synthase; and lysA, encoding meso-diaminopimelate decarboxylase. Analysis of the wild-type strain revealed that in vivo lysC transcription was repressed 5-fold by L-lysine and induced 2-fold by dl-methionine added to the growth medium. Surprisingly, yclM transcription was repressed 5-fold by dl-methionine, while the dapG, asd, dapA, and lysA genes were not significantly repressed by any of the aspartate pathway amino acids. We show that the L-lysine-overproducing classical B. methanolicus mutant NOA2#13A52-8A66 has-in addition to a hom-1 mutation-chromosomal mutations in the dapG coding region and in the lysA promoter region. No mutations were found in its dapA, lysC, asd, and yclM genes. The mutant dapG gene product had abolished feedback inhibition by meso-diaminopimelate in vitro, and the lysA mutation was accompanied by an elevated (6-fold) lysA transcription level in vivo. Moreover, yclM transcription was increased 16-fold in mutant strain NOA2#13A52-8A66 compared to the wild-type strain. Overexpression of wild-type and mutant aspartate pathway genes demonstrated that all six genes are important for L-lysine overproduction as tested in shake flasks, and the effects were dependent on the genetic background tested. Coupled overexpression of up to three genes resulted in additive (above 80-fold) increased L-lysine production levels.

Prediction of human pharmacokinetics using physiologically based modeling: a retrospective analysis of 26 clinically tested drugs.

PubMed

De Buck, Stefan S; Sinha, Vikash K; Fenu, Luca A; Nijsen, Marjoleen J; Mackie, Claire E; Gilissen, Ron A H J

2007-10-01

The aim of this study was to evaluate different physiologically based modeling strategies for the prediction of human pharmacokinetics. Plasma profiles after intravenous and oral dosing were simulated for 26 clinically tested drugs. Two mechanism-based predictions of human tissue-to-plasma partitioning (P(tp)) from physicochemical input (method Vd1) were evaluated for their ability to describe human volume of distribution at steady state (V(ss)). This method was compared with a strategy that combined predicted and experimentally determined in vivo rat P(tp) data (method Vd2). Best V(ss) predictions were obtained using method Vd2, providing that rat P(tp) input was corrected for interspecies differences in plasma protein binding (84% within 2-fold). V(ss) predictions from physicochemical input alone were poor (32% within 2-fold). Total body clearance (CL) was predicted as the sum of scaled rat renal clearance and hepatic clearance projected from in vitro metabolism data. Best CL predictions were obtained by disregarding both blood and microsomal or hepatocyte binding (method CL2, 74% within 2-fold), whereas strong bias was seen using both blood and microsomal or hepatocyte binding (method CL1, 53% within 2-fold). The physiologically based pharmacokinetics (PBPK) model, which combined methods Vd2 and CL2 yielded the most accurate predictions of in vivo terminal half-life (69% within 2-fold). The Gastroplus advanced compartmental absorption and transit model was used to construct an absorption-disposition model and provided accurate predictions of area under the plasma concentration-time profile, oral apparent volume of distribution, and maximum plasma concentration after oral dosing, with 74%, 70%, and 65% within 2-fold, respectively. This evaluation demonstrates that PBPK models can lead to reasonable predictions of human pharmacokinetics.

Up-regulation of glutathione-related genes, enzyme activities and transport proteins in human cervical cancer cells treated with doxorubicin.

PubMed

Drozd, Ewa; Krzysztoń-Russjan, Jolanta; Marczewska, Jadwiga; Drozd, Janina; Bubko, Irena; Bielak, Magda; Lubelska, Katarzyna; Wiktorska, Katarzyna; Chilmonczyk, Zdzisław; Anuszewska, Elżbieta; Gruber-Bzura, Beata

2016-10-01

Doxorubicin (DOX), one of the most effective anticancer drugs, acts in a variety of ways including DNA damage, enzyme inhibition and generation of reactive oxygen species. Glutathione (GSH) and glutathione-related enzymes including: glutathione peroxidase (GPX), glutathione reductase (GSR) and glutathione S-transferases (GST) may play a role in adaptive detoxification processes in response to the oxidative stress, thus contributing to drug resistance phenotype. In this study, we investigated effects of DOX treatment on expression and activity of GSH-related enzymes and multidrug resistance-associated proteins in cultured human cervical cancer cells displaying different resistance against this drug (HeLa and KB-V1). Determination of expression level of genes encoding GST isoforms and MRP proteins (GCS, GPX, GSR, GSTA1-3, GSTM1, GSTP1, ABCC1-3, MGST1-3) was performed using StellARray™ Technology. Enzymatic activities of GPX and GSR were measured using biochemical methods. Expression of MRP1 was examined by immunofluorescence microscopy. This study showed that native expression levels of GSTM1 and GSTA3 were markedly higher in KB-V1 cells (2000-fold and 200-fold) compared to HeLa cells. Resistant cells have also shown significantly elevated expression of GSTA1 and GSTA2 genes (200-fold and 50-fold) as a result of DOX treatment. In HeLa cells, exposure to DOX increased expression of all genes: GSTM1 (7-fold) and GSTA1-3 (550-fold, 150-fold and 300-fold). Exposure to DOX led to the slight increase of GCS expression as well as GPX activity in KB-V1 cells, while in HeLa cells it did not. Expression of ABCC1 (MRP1) was not increased in any of the tested cell lines. Our results indicate that expression of GSTM1 and GSTA1-3 genes is up-regulated by DOX treatment and suggest that activity of these genes may be associated with drug resistance of the tested cells. At the same time, involvement of MRP1 in DOX resistance in the given experimental conditions is unlikely. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

High prevalence of prior contact sports play and concussion among orthopedic and neurosurgical department chairs.

PubMed

Sone, Je Yeong; Courtney-Kay Lamb, S; Techar, Kristina; Dammavalam, Vikalpa; Uppal, Mohit; Williams, Cedric; Bergman, Thomas; Tupper, David; Ort, Paul; Samadani, Uzma

2018-04-27

OBJECTIVE Increased understanding of the consequences of traumatic brain injury has heightened concerns about youth participation in contact sports. This study investigated the prevalence of high school and collegiate contact sports play and concussion history among surgical department chairs. METHODS A cross-sectional survey was administered to 107 orthopedic and 74 neurosurgery chairs. Responses were compared to published historical population norms for contact sports (high school 27.74%, collegiate 1.44%), football (high school 10.91%, collegiate 0.76%), and concussion prevalence (12%). One-proportion Z-tests, chi-square tests, and binary logistic regression were used to analyze differences. RESULTS High school contact sports participation was 2.35-fold higher (65.3%, p < 0.001) for orthopedic chairs and 1.73-fold higher (47.9%, p = 0.0018) for neurosurgery chairs than for their high school peers. Collegiate contact sports play was 31.0-fold higher (44.7%, p < 0.001) for orthopedic chairs and 15.1-fold higher (21.7%, p < 0.001) for neurosurgery chairs than for their college peers. Orthopedic chairs had a 4.30-fold higher rate of high school football participation (46.9%, p < 0.001) while neurosurgery chairs reported a 3.05-fold higher rate (33.3%, p < 0.001) than their high school peers. Orthopedic chairs reported a 28.1-fold higher rate of collegiate football participation (21.3%, p < 0.001) and neurosurgery chairs reported an 8.58-fold higher rate (6.5%, p < 0.001) compared to their college peers. The rate at which orthopedic (42.6%, p < 0.001) and neurosurgical (42.4%, p < 0.001) chairs reported having at least 1 concussion in their lifetime was significantly higher than the reported prevalence in the general population. After correction for worst possible ascertainment bias, all results except high school contact sports participation remained significant. CONCLUSIONS The high prevalence of youth contact sports play and concussion among surgical specialty chairs affirms that individuals in careers requiring high motor and cognitive function frequently played contact sports. The association highlights the need to further examine the relationships between contact sports and potential long-term benefits as well as risks of sport-related injury.

Sensitive detection of influenza viruses with Europium nanoparticles on an epoxy silica sol-gel functionalized polycarbonate-polydimethylsiloxane hybrid microchip.

PubMed

Liu, Jikun; Zhao, Jiangqin; Petrochenko, Peter; Zheng, Jiwen; Hewlett, Indira

2016-12-15

In an effort to develop new tools for diagnosing influenza in resource-limited settings, we fabricated a polycarbonate (PC)-polydimethylsiloxane (PDMS) hybrid microchip using a simple epoxy silica sol-gel coating/bonding method and employed it in sensitive detection of influenza virus with Europium nanoparticles (EuNPs). The incorporation of sol-gel material in device fabrication provided functionalized channel surfaces ready for covalent immobilization of primary antibodies and a strong bonding between PDMS substrates and PC supports without increasing background fluorescence. In microchip EuNP immunoassay (µENIA) of inactivated influenza viruses, replacing native PDMS microchips with hybrid microchips allowed the achievement of a 6-fold increase in signal-to-background ratio, a 12-fold and a 6-fold decreases in limit-of-detection (LOD) in influenza A and B tests respectively. Using influenza A samples with known titers, the LOD of influenza µENIA on hybrid microchips was determined to be ~10(4) TCID50 titer/mL and 10(3)-10(4) EID50 titer/mL. A comparison test indicated that the sensitivity of influenza µENIA enhanced using the hybrid microchips even surpassed that of a commercial laboratory influenza ELISA test. In addition to the sensitivity improvement, assay variation was clearly reduced when hybrid microchips instead of native PDMS microchips were used in the µENIA tests. Finally, infectious reference viruses and nasopharyngeal swab patient specimens were successfully tested using μENIA on hybrid microchip platforms, demonstrating the potential of this unique microchip nanoparticle assay in clinical diagnosis of influenza. Meanwhile, the tests showed the necessity of using nucleic acid confirmatory tests to clarify ambiguous test results obtained from prototype or developed point-of-care testing devices for influenza diagnosis. Published by Elsevier B.V.

Comparison of fenspiride with beclomethasone as adjunctive anti-inflammatory treatment in patients with chronic obstructive pulmonary disease.

PubMed

Shmelev, E I; Kunicina, Yu L

2006-01-01

This study aimed to compare the clinical efficacy of two anti-inflammatory medications (fenspiride and inhaled beclomethasone [beclomethasone dipropionate]) in patients with stable chronic obstructive pulmonary disease (COPD) over 6 months. DESIGN, METHODS AND PATIENTS: This was a randomised comparison of 58 patients with COPD, divided into five treatment groups: fenspiride (stages 1 and 2), beclomethasone (stage 2), and two control groups (stages 1 and 2). In addition, 64 patients with exacerbations of COPD were evaluated over a 2-week treatment period during which they received either fenspiride or prednisolone. Clinical signs and symptoms of COPD were evaluated every 2 months (aggregated numerical index of signs and symptoms), as were lung function tests (forced vital capacity [FVC], forced expiratory volume in 1 second [FEV1], FEV1/FVC) and a 6-minute walking test. Statistically significant reductions in all evaluated COPD signs and symptoms were achieved with fenspiride in stage 1 COPD. Fenspiride therapy significantly reduced the indices of sputum parameters (8-fold decrease), incidence of dry rales (6-fold decrease), dyspnoea (4-fold decrease) and cough (2.5-fold decrease). In comparison with beclomethasone, fenspiride was superior in stage 2 COPD. In patients with stage 2 COPD, reductions were less marked, but remained significantly superior in the fenspiride group in comparison with the beclomethasone group and the control groups. In patients with exacerbations of COPD, fenspiride had equivalent efficacy to that of systemic corticosteroids. Anti-inflammatory therapy with fenspiride in addition to bronchodilators significantly improved clinical signs and symptoms, external respiratory function tests and physical activity tests in patients with stage 1 COPD. Adjunctive fenspiride therapy was superior to inhaled beclomethasone in stage 2 COPD. Anti-inflammatory therapy in COPD may be more effective at an early stage of this disease.

Brief Report: The Use of Self-Report Measures in Young People with Autism Spectrum Disorder to Access Symptoms of Anxiety, Depression and Negative Thoughts

ERIC Educational Resources Information Center

Ozsivadjian, Ann; Hibberd, Charlotte; Hollocks, Matthew J.

2014-01-01

The aims of this study were two-fold; firstly, to investigate whether self-report measures are useful and reflect parent-reported psychiatric symptoms in children with autism spectrum disorder (ASD), and secondly, to investigate whether children with ASD are able to access and report their cognitions, a prerequisite skill for cognitive behavior…

Targeting MUC1-Mediated Tumor-Stromal Metabolic Interactions in Triple-Negative Breast Cancer

DTIC Science & Technology

2015-09-01

exhibit increased dependence on glycolysis, resulting in abundant export of lactic acid . Lactic acid is mainly transported by two H+/lactate symporters...and ammonia recycling were most significantly altered in MDA-MB468 closely followed by citric acid cycle pathway. Mitochondrial electron transport...chain and citric acid cycle pathways were most significantly altered in BT20. Furthermore, relative comparison of the fold change in individual

Cancellation of the central singularity of the Schwarzschild solution with natural mass inversion process

NASA Astrophysics Data System (ADS)

Petit, Jean-Pierre; D'Agostini, G.

2015-03-01

We reconsider the classical Schwarzschild solution in the context of a Janus cosmological model. We show that the central singularity can be eliminated through a simple coordinate change and that the subsequent transit from one fold to the other is accompanied by mass inversion. In such scenario matter swallowed by black holes could be ejected as invisible negative mass and dispersed in space.

Intracapsular implant rupture: MR findings of incomplete shell collapse.

PubMed

Soo, M S; Kornguth, P J; Walsh, R; Elenberger, C; Georgiade, G S; DeLong, D; Spritzer, C E

1997-01-01

The objective of this study was to determine the frequency and significance of the MR findings of incomplete shell collapse for detecting implant rupture in a series of surgically removed breast prostheses. MR images of 86 breast implants in 44 patients were studied retrospectively and correlated with surgical findings at explantation. MR findings included (a) complete shell collapse (linguine sign), 21 implants; (b) incomplete shell collapse (subcapsular line sign, teardrop sign, and keyhole sign), 33 implants; (c) radial folds, 31 implants; and (d) normal, 1 implant. The subcapsular line sign was seen in 26 implants, the teardrop sign was seen in 27 implants, and the keyhole sign was seen in 23 implants. At surgery, 48 implants were found to be ruptured and 38 were intact. The MR findings of ruptured implants showed signs of incomplete collapse in 52% (n = 25), linguine sign in 44% (n = 21), and radial folds in 4% (n = 2). The linguine sign perfectly predicted implant rupture, but sensitivity was low. Findings of incomplete shell collapse improved sensitivity and negative predictive values, and the subcapsular line sign produced a significant incremental increase in predictive ability. MRI signs of incomplete shell collapse were more common than the linguine sign in ruptured implants and are significant contributors to the high sensitivity and negative predictive values of MRI for evaluating implant integrity.

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.

PubMed

Seligmann, Hervé; Warthi, Ganesh

2017-01-01

A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').

Outcomes of Laryngeal Reinnervation for Unilateral Vocal Fold Paralysis in Children: Associations With Age and Time Since Injury.

PubMed

Smith, Marshall E; Houtz, Daniel R

2016-05-01

Outcomes of laryngeal reinnervation with ansa-cervicalis for unilateral vocal fold paralysis (UVFP) may be influenced by age of the patient and time interval between laryngeal nerve injury and reinnervation, suggesting less favorable outcomes in older patients and greater than 2-year time interval after injury. This study examines these issues in the pediatric population. Review of prospectively collected data set of 35 children and adolescents (1-21 years) that underwent ansa-recurrent laryngeal nerve (RLN) laryngeal reinnervation for UVFP. The time from RLN injury to reinnervation averaged 5.0 years (range, 0.8-15.2 years). No correlation was found between age at reinnervation (r = 0.15) and patient- or parent-reported global percentage voice outcome or perceptual ratings. There was slight negative correlation in duration between RLN injury and reinnervation and voice outcomes (r = -0.31). Postoperative voice self/surrogate global percentage rating average was 80.5% (range, 50%-100%), and perceptual rating GRBAS sum score average was 2.9 (range, 0-7). In pediatric ansa-RLN reinnervation for UVFP, no correlation between age at surgery and postoperative outcome was found. Denervation duration showed slight negative correlation, similar to what has been reported in adults, though voice improvement was seen in all patients. © The Author(s) 2015.

Kinematics, structural mechanics, and design of origami structures with smooth folds

NASA Astrophysics Data System (ADS)

Peraza Hernandez, Edwin Alexander

Origami provides novel approaches to the fabrication, assembly, and functionality of engineering structures in various fields such as aerospace, robotics, etc. With the increase in complexity of the geometry and materials for origami structures that provide engineering utility, computational models and design methods for such structures have become essential. Currently available models and design methods for origami structures are generally limited to the idealization of the folds as creases of zeroth-order geometric continuity. Such an idealization is not proper for origami structures having non-negligible thickness or maximum curvature at the folds restricted by material limitations. Thus, for general structures, creased folds of merely zeroth-order geometric continuity are not appropriate representations of structural response and a new approach is needed. The first contribution of this dissertation is a model for the kinematics of origami structures having realistic folds of non-zero surface area and exhibiting higher-order geometric continuity, here termed smooth folds. The geometry of the smooth folds and the constraints on their associated kinematic variables are presented. A numerical implementation of the model allowing for kinematic simulation of structures having arbitrary fold patterns is also described. Examples illustrating the capability of the model to capture realistic structural folding response are provided. Subsequently, a method for solving the origami design problem of determining the geometry of a single planar sheet and its pattern of smooth folds that morphs into a given three-dimensional goal shape, discretized as a polygonal mesh, is presented. The design parameterization of the planar sheet and the constraints that allow for a valid pattern of smooth folds and approximation of the goal shape in a known folded configuration are presented. Various testing examples considering goal shapes of diverse geometries are provided. Afterwards, a model for the structural mechanics of origami continuum bodies with smooth folds is presented. Such a model entails the integration of the presented kinematic model and existing plate theories in order to obtain a structural representation for folds having non-zero thickness and comprised of arbitrary materials. The model is validated against finite element analysis. The last contribution addresses the design and analysis of active material-based self-folding structures that morph via simultaneous folding towards a given three-dimensional goal shape starting from a planar configuration. Implementation examples including shape memory alloy (SMA)-based self-folding structures are provided.

Major improvement of the reference method of the French drug resistance network for P-glycoprotein detection in human haematological malignancies.

PubMed

Huet, Sylvie; Marie, Jean-Pierre; Laurand, Armelle; Robert, Jacques

2005-09-01

The aim of this study was to improve significantly the sensitivity and specificity of the flow cytometric assay of P-glycoprotein (Pgp) implemented and validated by the laboratories of the French Drug Resistance Network [Huet S, Marie JP, Gualde N, Robert J. Reference method for detection of Pgp mediated multidrug resistance in human hematological malignancies: a method validated by the laboratories of the French Drug Resistance Network. Cytometry 1998;34:248-56] in cells displaying low level of resistance. Fluoresceine-conjugated monoclonal antibodies (Mabs) and propidium iodide were respectively replaced by phycoerythrin-conjugated Mabs and Sytox green. The removal of erythrocytes and granulocytes by density gradient was replaced by the lysis of erythrocytes after Mab incubation. Using these conditions, Pgp could be detected in the K-H30 line, which was negative in former studies, with Mab/Control ratios increasing by 3.7- to 5.9-fold, and Mab/Control ratios in the parental sensitive K562 line still ranging between 0.8 and 1.2. When tested on 16 blood samples from patients presenting haematological malignancies, six samples presented low positivity, which was not detected with the former method, while 10 samples remained negative with the two methods. Pgp was specifically detected in pathological blood cells in the six positive samples.

Chemical modification of capuramycins to enhance antibacterial activity

PubMed Central

Bogatcheva, Elena; Dubuisson, Tia; Protopopova, Marina; Einck, Leo; Nacy, Carol A.; Reddy, Venkata M.

2011-01-01

Objectives To extend capuramycin spectrum of activity beyond mycobacteria and improve intracellular drug activity. Methods Three capuramycin analogues (SQ997, SQ922 and SQ641) were conjugated with different natural and unnatural amino acids or decanoic acid (DEC) through an ester bond at one or more available hydroxyl groups. In vitro activity of the modified compounds was determined against Mycobacterium spp. and representative Gram-positive and Gram-negative bacteria. Intracellular activity was evaluated in J774A.1 mouse macrophages infected with Mycobacterium tuberculosis (H37Rv). Results Acylation of SQ997 and SQ641 with amino undecanoic acid (AUA) improved in vitro activity against most of the bacteria tested. Conjugation of SQ922 with DEC, but not AUA, improved its activity against Gram-positive bacteria. In the presence of efflux pump inhibitor phenylalanine arginine β-naphthyl amide, MICs of SQ997-AUA, SQ641-AUA and SQ922-DEC compounds improved even further against drug-susceptible and drug-resistant Staphylococcus aureus. In Gram-negative bacteria, EDTA-mediated permeabilization caused 4- to 16-fold enhancement of the activity of AUA-conjugated SQ997, SQ922 and SQ641. Conjugation of all three capuramycin analogues with AUA improved intracellular killing of H37Rv in murine macrophages. Conclusions Conjugation of capuramycin analogues with AUA or DEC enhanced in vitro activity, extended the spectrum of activity in Gram-positive bacteria and increased intracellular activity against H37Rv. PMID:21186194

Next-generation sequencing improves treatment efficacy and reduces hospitalization in children with drug-resistant epilepsy.

PubMed

Peng, Jing; Pang, Nan; Wang, Ying; Wang, Xiao-Le; Chen, Jian; Xiong, Juan; Peng, Pan; Zhu, Can-Hui; Kessi, Miriam Barakael; He, Fang; Yin, Fei

2018-06-22

The purposes of this study were three-fold: (i) to determine the contribution of known genes to the causation of a broad-spectrum of pediatric drug-resistant epilepsy (DRE), (ii) to compare the diagnostic yield and cost among different next-generation sequencing (NGS) approaches, and especially (iii) to assess how NGS approaches can benefit patients by improving diagnosis and treatment efficiency. This study enrolled 273 pediatric DRE patients with no obvious acquired etiology. Seventy-four patients underwent whole-exome sequencing (WES), 141 patients had epilepsy-related gene panel testing, and another 58 patients had clinical WES gene panel testing. We obtained these patients' seizure and hospitalization frequency by periodic follow-up phone calls and outpatient visits. Genetic diagnosis was achieved in 86 patients (31.5%) and involved 93 likely disease-causing mutations in 33 genes. In this study, the detection rates of the epilepsy-related gene panel, the clinical WES gene panel, and WES were 32.6% (46/141), 44.8% (26/58), and 17.3% (13/74), respectively. Moreover, 34 patients accepted corrective therapy according to their mutant genes, after which 52.9% (18/34) became seizure-free and 38.2% (13/34) achieved seizure reduction. In the end, patients with either positive or negative genetic results had significantly fewer hospitalization incidents (times/half year) than before (positive genetic results group 0.58 ± 1.14 vs 0.10 ± 0.26; negative genetic results group 0.72 ± 1.65 vs 0.12 ± 0.33). These results offer further proof that NGS approaches represent powerful tools for establishing a definitive diagnosis. Moreover, this study indicated how NGS can improve treatment efficacy and reduce hospitalization in children with DRE. © 2018 John Wiley & Sons Ltd.

Plant surfaces with cuticular folds are slippery for beetles

PubMed Central

Prüm, Bettina; Seidel, Robin; Bohn, Holger Florian; Speck, Thomas

2012-01-01

Plant surfaces covered with three-dimensional (3D) waxes are known to strongly reduce insect adhesion, leading to slippery surfaces. Besides 3D epicuticular waxes, cuticular folds are a common microstructure found on plant surfaces, which have not been quantitatively investigated with regard to their influence on insect adhesion. We performed traction experiments with Colorado potato beetles on five plant surfaces with cuticular folds of different magnitude. For comparison, we also tested (i) smooth plant surfaces and (ii) plant surfaces possessing 3D epicuticular waxes. Traction forces on surfaces with medium cuticular folds, of about 0.5 µm in both height and thickness and a spacing of 0.5–1.5 µm, were reduced by an average of 88 per cent in comparison to smooth plant surfaces. Traction forces were reduced by the same order of magnitude as on plant surfaces covered with 3D epicuticular waxes. For surface characterization, we performed static contact angle measurements, which proved a strong effect of cuticular folds also on surface wettability. Surfaces possessing cuticular folds of greater magnitude showed higher contact angles up to superhydrophobicity. We hypothesize that cuticular folds reduce insect adhesion mainly due to a critical roughness, reducing the real contact area between the surface and the insect's adhesive devices. PMID:21642366

Universality and diversity of folding mechanics for three-helix bundle proteins.

PubMed

Yang, Jae Shick; Wallin, Stefan; Shakhnovich, Eugene I

2008-01-22

In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo folding simulations using a single transferable all-atom potential. Using these trajectories, we examine the relaxation behavior, secondary structure formation, and transition-state ensembles (TSEs) of the two proteins and compare our results with experimental data and previous computational studies. To obtain a detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Moreover, rigorous p(fold) analysis is used to obtain representative samples of the TSEs and a good quantitative agreement between experimental and simulated Phi values is obtained for protein A. Phi values for Villin also are obtained and left as predictions to be tested by future experiments. Our analysis shows that the two-helix hairpin is a common partially stable structural motif that gets formed before entering the TSE in the studied proteins. These results together with our earlier study of Engrailed Homeodomain and recent experimental studies provide a comprehensive, atomic-level picture of folding mechanics of three-helix bundle proteins.

Accommodating Thickness in Origami-Based Deployable Arrays

NASA Technical Reports Server (NTRS)

Zirbel, Shannon A.; Magleby, Spencer P.; Howell, Larry L.; Lang, Robert J.; Thomson, Mark W.; Sigel, Deborah A.; Walkemeyer, Phillip E.; Trease, Brian P.

2013-01-01

The purpose of this work is to create deployment systems with a large ratio of stowed-to-deployed diameter. Deployment from a compact form to a final flat state can be achieved through origami-inspired folding of panels. There are many models capable of this motion when folded in a material with negligible thickness; however, when the application requires the folding of thick, rigid panels, attention must be paid to the effect of material thickness not only on the final folded state, but also during the folding motion (i.e., the panels must not be required to flex to attain the final folded form). The objective is to develop new methods for deployment from a compact folded form to a large circular array (or other final form). This paper describes a mathematical model for modifying the pattern to accommodate material thickness in the context of the design, modeling, and testing of a deployable system inspired by an origami six-sided flasher model. The model is demonstrated in hardware as a 1/20th scale prototype of a deployable solar array for space applications. The resulting prototype has a ratio of stowed-to-deployed diameter of 9.2 (or 1.25 m deployed outer diameter to 0.136 m stowed outer diameter).

ortho- and meta-substituted aromatic thiols are efficient redox buffers that increase the folding rate of a disulfide-containing protein.

PubMed

Gough, Jonathan D; Barrett, Elvis J; Silva, Yenia; Lees, Watson J

2006-08-20

Thiol based redox buffers are used to enhance the folding rates of disulfide-containing proteins in vitro. Traditionally, small molecule aliphatic thiols such as glutathione are employed. Recently, we have demonstrated that aromatic thiols can further enhance protein-folding rates. In the presence of para-substituted aromatic thiols the folding rate of a disulfide-containing protein was increased by 4-23 times over that measured for glutathione. However, several important practical issues remain to be addressed. Aromatic thiols have never been tested in the presence of denaturants such as guanidine hydrochloride. Only two of the para-substituted aromatic thiols previously examined are commercially available. To expand the number of aromatic thiols for protein folding, several commercially available meta- and ortho-substituted aromatic thiols were studied. Furthermore, an ortho-substituted aromatic thiol, easily obtained from inexpensive starting materials, was investigated. Folding rates of scrambled ribonuclease A at pH 6.0, 7.0 and 7.7, with ortho- and meta-substituted aromatic thiols, were up to 10 times greater than those with glutathione. In the presence of the common denaturant guanidine hydrochloride (0.5M) aromatic thiols provided 100% yield of active protein while maintaining equivalent folding rates.

Effect of transverse aortic constriction on cardiac structure, function and gene expression in pregnant rats.

PubMed

Songstad, Nils Thomas; Johansen, David; How, Ole-Jacob; Kaaresen, Per Ivar; Ytrehus, Kirsti; Acharya, Ganesh

2014-01-01

There is an increased risk of heart failure and pulmonary edema in pregnancies complicated by hypertensive disorders. However, in a previous study we found that pregnancy protects against fibrosis and preserves angiogenesis in a rat model of angiotensin II induced cardiac hypertrophy. In this study we test the hypothesis that pregnancy protects against negative effects of increased afterload. Pregnant (gestational day 5.5-8.5) and non-pregnant Wistar rats were randomized to transverse aortic constriction (TAC) or sham surgery. After 14.2 ± 0.14 days echocardiography was performed. Aortic blood pressure and left ventricular (LV) pressure-volume loops were obtained using a conductance catheter. LV collagen content and cardiomyocyte circumference were measured. Myocardial gene expression was assessed by real-time polymerase chain reaction. Heart weight was increased by TAC (p<0.001) but not by pregnancy. Cardiac myocyte circumference was larger in pregnant compared to non-pregnant rats independent of TAC (p = 0.01), however TAC per se did not affect this parameter. Collagen content in LV myocardium was not affected by pregnancy or TAC. TAC increased stroke work more in pregnant rats (34.1 ± 2.4 vs 17.5 ± 2.4 mmHg/mL, p<0.001) than in non-pregnant (28.2 ± 1.7 vs 20.9 ± 1.5 mmHg/mL, p = 0.06). However, it did not lead to overt heart failure in any group. In pregnant rats, α-MHC gene expression was reduced by TAC. Increased in the expression of β-MHC gene was higher in pregnant (5-fold) compared to non-pregnant rats (2-fold) after TAC (p = 0.001). Nine out of the 19 genes related to cardiac remodeling were affected by pregnancy independent of TAC. This study did not support the hypothesis that pregnancy is cardioprotective against the negative effects of increased afterload. Some differences in cardiac structure, function and gene expression between pregnant and non-pregnant rats following TAC indicated that afterload increase is less tolerated in pregnancy.

A Prospective Trial on Initiation Factor 4E (eIF4E) Overexpression and Cancer Recurrence in Node-Positive Breast Cancer

PubMed Central

McClusky, Derek R.; Chu, Quyen; Yu, Herbert; DeBenedetti, Arrigo; Johnson, Lester W.; Meschonat, Carol; Turnage, Richard; McDonald, John C.; Abreo, Fleurette; Li, Benjamin D. L.

2005-01-01

Objective: A previous study of patients with stage I to III breast cancer showed that those patients whose tumors were in the highest tertile of eIF4E overexpression experienced a higher risk for recurrence. This study was designed to determine whether high eIF4E overexpression predicts cancer recurrence independent of nodal status by specifically targeting patients with node-positive disease. Methods: The prospective trial was designed to accrue 168 patients with node-positive breast cancer to detect a 2.5-fold increase in risk for recurrence. eIF4E level was quantified by Western blots as x-fold elevated compared with breast tissues from noncancer patients. End points measured were disease recurrence and cancer-related death. Statistical analyses performed include survival analysis by the Kaplan-Meier method, log-rank test, and Cox proportional hazard model. Results: One hundred seventy-four patients with node-positive breast cancer were accrued. All patients fulfilled study inclusion and exclusion criteria, treatment protocol, and surveillance requirements, with a compliance rate >95%. The mean eIF4E elevation was 11.0 ± 7.0-fold (range, 1.4–34.3-fold). Based on previously published data, tertile distribution was as follow: 1) lowest tertile (<7.5-fold) = 67 patients, 2) intermediate tertile (7.5–14-fold) = 54 patients, and 3) highest tertile (>14-fold) = 53 patients. At a median follow up of 32 months, patients with the highest tertile had a statistically significant higher cancer recurrence rate (log-rank test, P = 0.002) and cancer-related death rate (P = 0.036) than the lowest group. Relative risk calculations demonstrated that high eIF4E patients had a 2.4-fold increase in relative risk increase for cancer recurrence (95% confidence interval, 1.2–4.1; P = 0.01). Conclusions: In this prospective study designed to specifically address risk for recurrence in patients with node-positive breast cancer, the patients whose tumors were in the highest tertile of eIF4E overexpression had a 2.4-fold increase in relative risk for cancer recurrence. Therefore, eIF4E overexpression appears to be an independent predictor of a worse outcome in patients with breast cancer independent of nodal status. PMID:16192819

The effect of simulated microgravity on lumbar spine biomechanics: an in vitro study.

PubMed

Laws, Cory J; Berg-Johansen, Britta; Hargens, Alan R; Lotz, Jeffrey C

2016-09-01

Disc herniation risk is quadrupled following spaceflight. This study tested the hypothesis that swelling-induced disc height increases (comparable to those reported in spaceflight) stiffen the spine and elevate annular strain and nuclear pressure during forward bending. Eight human lumbar motion segments were secured to custom-designed testing jigs and subjected to baseline flexion and compression and pure moment flexibility tests. Discs were then free-swelled in saline to varying supraphysiologic heights consistent with prolonged weightlessness and re-tested to assess biomechanical changes. Swelling-induced disc height changes correlated positively with intradiscal pressure (p < 0.01) and stiffening in flexion (p < 0.01), and negatively with flexion range of motion (p < 0.05). Swelling-induced increases in disc height also led to increased annular surface strain under combined flexion with compression. Disc wedge angle decreased with swelling (p < 0.05); this loss of wedge angle correlated with decreased flexion range of motion (R (2) = 0.94, p < 0.0001) and decreased stiffness fold change in extension (p < 0.05). Swelling-induced increases in disc height decrease flexibility and increase annular strain and nuclear pressure during forward bending. These changes, in combination with the measured loss of lordotic curvature with disc swelling, may contribute toward increased herniation risk. This is consistent with clinical observations of increased disc herniation rates after microgravity exposure and may provide the basis for future countermeasure development.

Pneumocystis PCR: It Is Time to Make PCR the Test of Choice.

PubMed

Doyle, Laura; Vogel, Sherilynn; Procop, Gary W

2017-01-01

The testing strategy for Pneumocystis at the Cleveland Clinic changed from toluidine blue staining to polymerase chain reaction (PCR). We studied the differences in positivity rates for these assays and compared each with the detection of Pneumocystis in companion specimens by cytology and surgical pathology. We reviewed the results of all Pneumocystis test orders 1 year before and 1 year after the implementation of a Pneumocystis -specific PCR. We also reviewed the corresponding cytology and surgical pathology results, if performed. Finally, we reviewed the medical records of patients with rare Pneumocystis detected by PCR in an effort to differentiate colonization vs true disease. Toluidine blue staining and surgical pathology had similar sensitivities and negative predictive values, both of which were superior to cytology. There was a >4-fold increase in the annual detection of Pneumocystis by PCR compared with toluidine blue staining (toluidine blue staining: 11/1583 [0.69%] vs PCR: 44/1457 [3.0%]; chi-square P < .001). PCR detected 1 more case than surgical pathology and was far more sensitive than cytology. Chart review demonstrated that the vast majority of patients with rare Pneumocystis detected were immunosuppressed, had radiologic findings supportive of this infection, had no other pathogens detected, and were treated for pneumocystosis by the clinical team. PCR was the most sensitive method for the detection of Pneumocystis and should be considered the diagnostic test of choice. Correlation with clinical and radiologic findings affords discrimination of early true disease from the far rarer instances of colonization.

The effect of simulated microgravity on lumbar spine biomechanics: an in vitro study

PubMed Central

Laws, Cory J.; Berg-Johansen, Britta; Hargens, Alan R.; Lotz, Jeffrey C.

2015-01-01

Purpose Disc herniation risk is quadrupled following spaceflight. This study tested the hypothesis that swelling-induced disc height increases (comparable to those reported in spaceflight) stiffen the spine and elevate annular strain and nuclear pressure during forward bending. Methods Eight human lumbar motion segments were secured to custom-designed testing jigs and subjected to baseline flexion and compression and pure moment flexibility tests. Discs were then free-swelled in saline to varying supraphysiologic heights consistent with prolonged weightlessness and re-tested to assess biomechanical changes. Results Swelling-induced disc height changes correlated positively with intradiscal pressure (p < 0.01) and stiffening in flexion (p < 0.01), and negatively with flexion range of motion (p < 0.05). Swelling-induced increases in disc height also led to increased annular surface strain under combined flexion with compression. Disc wedge angle decreased with swelling (p < 0.05); this loss of wedge angle correlated with decreased flexion range of motion (R2 = 0.94, p < 0.0001) and decreased stiffness fold change in extension (p < 0.05). Conclusion Swelling-induced increases in disc height decrease flexibility and increase annular strain and nuclear pressure during forward bending. These changes, in combination with the measured loss of lordotic curvature with disc swelling, may contribute toward increased herniation risk. This is consistent with clinical observations of increased disc herniation rates after microgravity exposure and may provide the basis for future countermeasure development. PMID:26403291

Methods to test the interactive effects of drought and plant invasion on ecosystem structure and function using complementary common garden and field experiments.

PubMed

Alba, Christina; NeSmith, Julienne E; Fahey, Catherine; Angelini, Christine; Flory, Stephen Luke

2017-03-01

Abiotic global change drivers affect ecosystem structure and function, but how they interact with biotic factors such as invasive plants is understudied. Such interactions may be additive, synergistic, or offsetting, and difficult to predict. We present methods to test the individual and interactive effects of drought and plant invasion on native ecosystems. We coupled a factorial common garden experiment containing resident communities exposed to drought (imposed with rainout shelters) and invasion with a field experiment where the invader was removed from sites spanning a natural soil moisture gradient. We detail treatments and their effects on abiotic conditions, including soil moisture, light, temperature, and humidity, which shape community and ecosystem responses. Ambient precipitation during the garden experiment exceeded historic norms despite severe drought in prior years. Soil moisture was 48% lower in drought than ambient plots, but the invader largely offset drought effects. Additionally, temperature and light were lower and humidity higher in invaded plots. Field sites spanned up to a 10-fold range in soil moisture and up to a 2.5-fold range in light availability. Invaded and resident vegetation did not differentially mediate soil moisture, unlike in the garden experiment. Herbicide effectively removed invaded and resident vegetation, with removal having site-specific effects on soil moisture and light availability. However, light was generally higher in invader-removal than control plots, whereas resident removal had less effect on light, similar to the garden experiment. Invasion mitigated a constellation of abiotic conditions associated with drought stress in the garden experiment. In the field, where other factors co-varied, these patterns did not emerge. Still, neither experiment suggested that drought and invasion will have synergistic negative effects on ecosystems, although invasion can limit light availability. Coupling factorial garden experiments with field experiments across environmental gradients will be effective for predicting how multiple stressors interact in natural systems.

Formulation of carbapenems loaded gold nanoparticles to combat multi-antibiotic bacterial resistance: In vitro antibacterial study.

PubMed

Shaker, Mohamed A; Shaaban, Mona I

2017-06-15

Despite the fact that carbapenems (powerful β-lactams antibiotics) were able to fight serious infectious diseases, nowadays the spread of carbapenems-resistant bacteria is considered the main challenge in antibacterial therapy. In this study, we focused on evaluating the surface conjugation of carbapenems (imipenem and meropenem) with gold nanoparticles as a delivering strategy to specifically and safely maximize their therapeutic efficacy while destroying the developing resistance of the pathogens. Different particle size formulae (35, 70 and 200nm) were prepared by citrate reduction method. The prepared nanoparticles were functionalized with imipenem (Ipm) or meropenem (Mem) and physico-chemically characterized for loading efficiency, particle size, morphology, and in-vitro release. The antibacterial efficacy was also evaluated against carbapenems resistant Gram-negative bacteria isolated from infected human, through measuring the minimum inhibitory concentration and antibiotic kill test. All the obtained gold nanoparticles showed a distinct nano-size with loading efficiency up to 72% and 74% for Ipm and Mem, respectively. The conjugation and physico-chemical stability of the formulated carbapenems were confirmed by FTIR and X-RPD. Diffusion driven release behavior was observed for both Ipm and Mem from all of the loaded gold nanoparticles. For both Ipm and Mem, formula with 35nm diameter showed the most significant enhancement in antibacterial activity against all the selected isolates including Klebsiella pneumoniae, Proteus mirabilis and Acinteobacter baumanii. Ipm loaded Gold nanoparticles demonstrated decrease in the MIC of Ipm down to four folds, whereas, Mem loaded gold nanoparticles showed decrease in the MIC of Mem down to three folds on the tested bacterial isolates. Based on these results, the formulation of carbapenems-loaded gold nanoparticles demonstrated to be a promising nano-size delivery vehicle for improving the therapeutic activity and destroying the bacterial resistance for carbapenems. Copyright © 2017 Elsevier B.V. All rights reserved.

Paleomagnetism of Neoproterozoic cap carbonates of the Sao Francisco and Amazonian cratons, Brazil

NASA Astrophysics Data System (ADS)

Trindade, R. I. F.; Dagrella-Filho, M. S.; Figueiredo, F. T.; Font, E.; Babinski, M.; Nogueira, A. C. R.; Riccomini, C.

2003-04-01

The low-latitude paleomagnetic record of some Neoproterozoic glacial successions has long been used as an evidence for dramatic changes in Earth climate (Snowball Earth events). But the test for such events demands a global-scale paleomagnetic database in the Neoproterozoic glacial/carbonate successions. In order to better constrain these extreme climatic events, an extensive paleomagnetic survey has been conducted in carbonates that cap the Neoproterozoic glacial rocks of the Sao Francisco (SFC) and Amazonian (AMC) cratons, Brazil. In the SFC, sampling was performed at 104 sites (horizontal beds) distributed at two sectors (north and south), about 1.000 km apart, within the stable area of the craton. In the AMC, sampling included 15 sites in undeformed, sub-horizontal beds, and 25 sites along the limbs of regional folds in the margin of the craton. After paleomagnetic cleaning, most samples from both SFC and AMC yielded similar PGVs (mean SFC: 32°N, 322°E (A95=2.8, K=65.3); mean AMC: 31°N, 336°E (A95=6.8, K=46.2)). Pb-Pb ages around 520 Ma for SFC samples, a negative fold-test for AMC samples, and the coincidence of these poles with 520 Ma Gondwanan reference poles after rotation of South America to Africa, suggest a continental-scale remagnetization by this time. Some sites from both cratons, however, seem to have not been affected by the Cambrian remagnetization. Two mean poles were calculated for SFC and AMC for which consistent reversals could be recorded, suggesting a primary nature for the characteristic magnetization (mean SFC pole: 66°S, 198°E (A95=5.4, K=47.5); mean AMC pole: 77°S, 66°E (A95=8.8, K=47.7)). These results indicate a moderate latitude (51°) for the SFC Bebedouro (Sturtian) glaciation and a low latitude (24°) for the AMC Puga (Varanger) glaciation, and reinforces the hypothesis of Neoproterozoic global-scale ice-ages.

Efficient Killing of Planktonic and Biofilm-Embedded Coagulase-Negative Staphylococci by Bactericidal Protein P128

PubMed Central

Poonacha, Nethravathi; Nair, Sandhya; Desai, Srividya; Tuppad, Darshan; Hiremath, Deepika; Mohan, Thulasi; Vipra, Aradhana

2017-01-01

ABSTRACT Coagulase-negative staphylococci (CoNS) are the major causative agents of foreign-body-related infections, including catheter-related bloodstream infections. Because of the involvement of biofilms, foreign-body-related infections are difficult to treat. P128, a chimeric recombinant phage-derived ectolysin, has been shown to possess bactericidal activity on strains of Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA). We tested the killing potential of P128 on three clinically significant species of CoNS, S. epidermidis, S. haemolyticus, and S. lugdunensis, under a variety of physiological conditions representing growing and nongrowing states. The MIC90 and minimum bactericidal concentration at which 90% of strains tested are killed (MBC90) of P128 on 62 clinical strains of CoNS were found to be 16 and 32 μg/ml (0.58 and 1.16 μM), respectively, demonstrating the bactericidal nature of P128 on CoNS strains. Serum showed a potentiating effect on P128 inhibition, as indicated by 4- to 32-fold lower MIC values observed in serum. P128 caused a rapid loss of viability in all CoNS strains tested. Persisters of CoNS that were enriched in the presence of vancomycin or daptomycin were killed by P128 at 1× the MIC in a rapid manner. Low concentrations of P128 caused a 2- to 5-log reduction in CFU in stationary-phase or poorly metabolizing CoNS cultures. P128 at low concentrations eliminated CoNS biofilms in microtiter plates and on the surface of catheters. Combinations of P128 and standard-of-care (SoC) antibiotics were highly synergistic in inhibiting growth in preformed biofilms. Potent activity on planktonic cells, persisters, and biofilms of CoNS suggests that P128 is a promising candidate for the clinical development of treatments for foreign-body-related and other CoNS infections. PMID:28559263

[Application of transcription mediated amplification and real-time reverse transcription polymerase chain reaction in detection of human immunodeficiency virus RNA].

PubMed

Wu, Daxian; Tao, Shuhui; Liu, Shuiping; Zhou, Jiebin; Tan, Deming; Hou, Zhouhua

2017-07-28

To observe the sensitivity of transcription mediated amplification (TMA), and to compare its performance with real-time reverse transcription polymerase chain reaction (real-time RT-PCR) in detecting human immunodeficiency virus RNA (HIV RNA).
 Methods: TMA system was established with TaqMan probes, specific primers, moloney murine leukemia virus (MMLV) reverse transcriptase, T7 RNA polymerase, and reaction substrates. The sensitivity of TMA was evaluated by amplifying a group of 10-fold diluted HIV RNA standards which were transcribed in vitro. A total of 60 plasma of HIV infected patients were measured by TMA and Cobas Amplicor HIV-1 Monitor test to observe the positive rate. The correlation and concordance of the above two technologies were investigated by linear regression and Bland-Altman analysis.
 Results: TMA system was established successfully and HIV RNA transcribed standards at concentration of equal or more than 10 copies/mL could be detected by TMA technology. Among 60 samples of plasma from HIV infected patients, 46 were positively detected and 12 were negatively amplified by both TMA and Cobas reagents; 2 samples were positively tested by Cobas reagent but negatively tested by TMA system. The concordance rate of the two methods was 97.1% and the difference of positive detection rate between the two methods was not statistically significant (P>0.05). Linear regression was used for 46 samples which were positively detected by both TMA and Cobas reagents and showed an excellent correlation between the two reagents (r=0.997, P<0.001). Bland-Altma analysis revealed that the mean different value of HIV RNA levels for denary logarithm was 0.02. Forty-four samples were included in 95% of credibility interval of concordance.
 Conclusion: TMA system has the potential of high sensitivity. TMA and real-time RT-PCR keep an excellent correlation and consistency in detecting HIV RNA.

Cluster Randomized Test-Negative Design (CR-TND) Trials: A Novel and Efficient Method to Assess the Efficacy of Community Level Dengue Interventions.

PubMed

Anders, Katherine L; Cutcher, Zoe; Kleinschmidt, Immo; Donnelly, Christl A; Ferguson, Neil M; Indriani, Citra; O'Neill, Scott L; Jewell, Nicholas P; Simmons, Cameron P

2018-05-07

Cluster randomized trials are the gold standard for assessing efficacy of community-level interventions, such as vector control strategies against dengue. We describe a novel cluster randomized trial methodology with a test-negative design, which offers advantages over traditional approaches. It utilizes outcome-based sampling of patients presenting with a syndrome consistent with the disease of interest, who are subsequently classified as test-positive cases or test-negative controls on the basis of diagnostic testing. We use simulations of a cluster trial to demonstrate validity of efficacy estimates under the test-negative approach. This demonstrates that, provided study arms are balanced for both test-negative and test-positive illness at baseline and that other test-negative design assumptions are met, the efficacy estimates closely match true efficacy. We also briefly discuss analytical considerations for an odds ratio-based effect estimate arising from clustered data, and outline potential approaches to analysis. We conclude that application of the test-negative design to certain cluster randomized trials could increase their efficiency and ease of implementation.

Sample processing approach for detection of ricin in surface samples.

PubMed

Kane, Staci; Shah, Sanjiv; Erler, Anne Marie; Alfaro, Teneile

2017-12-01

With several ricin contamination incidents reported over the past decade, rapid and accurate methods are needed for environmental sample analysis, especially after decontamination. A sample processing method was developed for common surface sampling devices to improve the limit of detection and avoid false negative/positive results for ricin analysis. Potential assay interferents from the sample matrix (bleach residue, sample material, wetting buffer), including reference dust, were tested using a Time-Resolved Fluorescence (TRF) immunoassay. Test results suggested that the sample matrix did not cause the elevated background fluorescence sometimes observed when analyzing post-bleach decontamination samples from ricin incidents. Furthermore, sample particulates (80mg/mL Arizona Test Dust) did not enhance background fluorescence or interfere with ricin detection by TRF. These results suggested that high background fluorescence in this immunoassay could be due to labeled antibody quality and/or quantity issues. Centrifugal ultrafiltration devices were evaluated for ricin concentration as a part of sample processing. Up to 30-fold concentration of ricin was observed by the devices, which serve to remove soluble interferents and could function as the front-end sample processing step to other ricin analytical methods. The procedure has the potential to be used with a broader range of environmental sample types and with other potential interferences and to be followed by other ricin analytical methods, although additional verification studies would be required. Published by Elsevier B.V.

Diagnosis of aerobic vaginitis by quantitative real-time PCR.

PubMed

Rumyantseva, T A; Bellen, G; Savochkina, Y A; Guschin, A E; Donders, G G G

2016-07-01

To evaluate a real-time PCR-based technique to quantify bacteria associated with aerobic vaginitis (AV) as a potential test. Vaginal samples from 100 women were tested by wet-mount microscopy, gram stain and quantitative real-time PCR targeting Enterobacteriacea, Staphylococcus spp., Streptococcus spp., Enterococcus spp., Escherichia coli, Streptococcus agalactiae, S. aureus; Lactobacillus spp. AV diagnosis obtained by wet-mount microscopy was used as reference. Some level of AV was diagnosed in 23 (23.7 %) cases. Various concentrations of Enterobacteriacea, Staphylococcus spp., Streptococcus spp. were detected an all patients. Enterococcus spp. were detected in 76 (78.3 %) cases. Summarized concentrations of aerobes were tenfold higher in AV-positive compared to AV-negative cases [7.30lg vs 6.06lg (p = 0.02)]. Concentrations of aerobes in severe, moderate and light AV cases did not vary significantly (p = 0.14). Concentration of lactobacilli was 1000-fold lower in AV-positive cases compared to normal cases (5.3lg vs 8.3lg, p < 0.0001). Streptococcus spp. dominated in the majority of AV-positive cases [19/22 (86.4 %) samples]. The relation of high loads of aerobes to the low numbers of Lactobacilli are a reliable marker for the presence of AV and could substitute microscopy as a test. PCR may be a good standardized substitution for AV diagnosis in settings where well-trained microscopists are lacking.

Impact of Experimental Conditions on the Evaluation of Interactions between Multidrug and Toxin Extrusion Proteins and Candidate Drugs.

PubMed

Lechner, Christian; Ishiguro, Naoki; Fukuhara, Ayano; Shimizu, Hidetada; Ohtsu, Naoko; Takatani, Masahito; Nishiyama, Kotaro; Washio, Ikumi; Yamamura, Norio; Kusuhara, Hiroyuki

2016-08-01

Multidrug and toxin extrusion transporters (MATEs) have a determining influence on the pharmacokinetic profiles of many drugs and are involved in several clinical drug-drug interactions (DDIs). Cellular uptake assays with recombinant cells expressing human MATE1 or MATE2-K are widely used to investigate MATE-mediated transport for DDI assessment; however, the experimental conditions and used test substrates vary among laboratories. We therefore initially examined the impact of three assay conditions that have been applied for MATE substrate and inhibitor profiling in the literature. One of the tested conditions resulted in significantly higher uptake rates of the three test substrates, [(14)C]metformin, [(3)H]thiamine, and [(3)H]1-methyl-4-phenylpyridinium (MPP(+)), but IC50 values of four tested MATE inhibitors varied only slightly among the three conditions (<2.5-fold difference). Subsequently, we investigated the uptake characteristics of the five MATE substrates: [(14)C]metformin, [(3)H]thiamine, [(3)H]MPP(+), [(3)H]estrone-3-sulfate (E3S), and rhodamine 123, as well as the impact of the used test substrate on the inhibition profiles of 10 MATE inhibitors at one selected assay condition. [(3)H]E3S showed atypical uptake characteristics compared with those observed with the other four substrates. IC50 values of the tested inhibitors were in a similar range (<4-fold difference) when [(14)C]metformin, [(3)H]thiamine, [(3)H]MPP(+), or [(3)H]E3S were used as substrates but were considerably higher with rhodamine 123 (9.8-fold and 4.1-fold differences compared with [(14)C]metformin with MATE1 and MATE2-K, respectively). This study demonstrated for the first time that the impact of assay conditions on IC50 determination is negligible, that kinetic characteristics differ among used test substrates, and that substrate-dependent inhibition exists for MATE1 and MATE2-K, giving valuable insight into the assessment of clinically relevant MATE-mediated DDIs in vitro. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

Use of genetically modified crops and pesticides in Brazil: growing hazards.

PubMed

Almeida, Vicente Eduardo Soares de; Friedrich, Karen; Tygel, Alan Freihof; Melgarejo, Leonardo; Carneiro, Fernando Ferreira

2017-10-01

Genetically modified (GM) crops were officially authorized in Brazil in 2003. In this documentary study, we aimed to identify possible changes in the patterns of pesticide use after the adoption of this technology over a span of 13 years (2000 to 2012). The following variables were analyzed: Pesticide use (kg), Pesticide use per capita (kg/inhab), Pesticide and herbicide use per area (kg/ha) and productivity (kg/ha). Contrary to the initial expectations of decreasing pesticide use following the adoption of GM crops, overall pesticide use in Brazil increased 1.6-fold between the years 2000 and 2012. During the same period, pesticide use for soybean increased 3-fold. This study shows that the adoption of GM crops in Brazil has led to an increase in pesticide use with possible increases in environmental and human exposure and associated negative impacts.

Hydrogen breath test in schoolchildren.

PubMed Central

Douwes, A C; Schaap, C; van der Klei-van Moorsel, J M

1985-01-01

The frequency of negative hydrogen breath tests due to colonic bacterial flora which are unable to produce hydrogen was determined after oral lactulose challenge in 98 healthy Dutch schoolchildren. There was a negative result in 9.2%. The probability of a false normal lactose breath test (1:77) was calculated from these results together with those from a separate group of children with lactose malabsorption (also determined by hydrogen breath test). A study of siblings and mothers of subjects with a negative breath test did not show familial clustering of this condition. Faecal incubation tests with various sugars showed an increase in breath hydrogen greater than 100 parts per million in those with a positive breath test while subjects with a negative breath test also had a negative faecal incubation test. The frequency of a false negative hydrogen breath test was higher than previously reported, but this does not affect the superiority of this method of testing over the conventional blood glucose determination. PMID:4004310

Comparison of fault-related folding algorithms to restore a fold-and-thrust-belt

NASA Astrophysics Data System (ADS)

Brandes, Christian; Tanner, David

2017-04-01

Fault-related folding means the contemporaneous evolution of folds as a consequence of fault movement. It is a common deformation process in the upper crust that occurs worldwide in accretionary wedges, fold-and-thrust belts, and intra-plate settings, in either strike-slip, compressional, or extensional regimes. Over the last 30 years different algorithms have been developed to simulate the kinematic evolution of fault-related folds. All these models of fault-related folding include similar simplifications and limitations and use the same kinematic behaviour throughout the model (Brandes & Tanner, 2014). We used a natural example of fault-related folding from the Limón fold-and-thrust belt in eastern Costa Rica to test two different algorithms and to compare the resulting geometries. A thrust fault and its hanging-wall anticline were restored using both the trishear method (Allmendinger, 1998; Zehnder & Allmendinger, 2000) and the fault-parallel flow approach (Ziesch et al. 2014); both methods are widely used in academia and industry. The resulting hanging-wall folds above the thrust fault are restored in substantially different fashions. This is largely a function of the propagation-to-slip ratio of the thrust, which controls the geometry of the related anticline. Understanding the controlling factors for anticline evolution is important for the evaluation of potential hydrocarbon reservoirs and the characterization of fault processes. References: Allmendinger, R.W., 1998. Inverse and forward numerical modeling of trishear fault propagation folds. Tectonics, 17, 640-656. Brandes, C., Tanner, D.C. 2014. Fault-related folding: a review of kinematic models and their application. Earth Science Reviews, 138, 352-370. Zehnder, A.T., Allmendinger, R.W., 2000. Velocity field for the trishear model. Journal of Structural Geology, 22, 1009-1014. Ziesch, J., Tanner, D.C., Krawczyk, C.M. 2014. Strain associated with the fault-parallel flow algorithm during kinematic fault displacement. Mathematical Geosciences, 46(1), 59-73.

Plane flame furnace combustion tests on JPL desulfurized coal

NASA Technical Reports Server (NTRS)

Reuther, J. J.; Kim, H. T.; Lima, J. G. H.

1982-01-01

The combustion characteristics of three raw bituminous (PSOC-282 and 276) and subbituminous (PSOC-230) coals, the raw coals partially desulfurized (ca -60%) by JPL chlorinolysis, and the chlorinated coals more completely desulfurized (ca -75%) by JPL hydrodesulfurization were determined. The extent to which the combustion characteristics of the untreated coals were altered upon JPL sulfur removal was examined. Combustion conditions typical of utility boilers were simulated in the plane flame furnace. Upon decreasing the parent coal voltaile matter generically by 80% and the sulfur by 75% via the JPL desulfurization process, ignition time was delayed 70 fold, burning velocity was retarded 1.5 fold, and burnout time was prolonged 1.4 fold. Total flame residence time increased 2.3 fold. The JPL desulfurization process appears to show significant promise for producing technologically combustible and clean burning (low SO3) fuels.

Modulating the folding of P-glycoprotein and cystic fibrosis transmembrane conductance regulator truncation mutants with pharmacological chaperones.

PubMed

Wang, Ying; Loo, Tip W; Bartlett, M Claire; Clarke, David M

2007-03-01

Cystic fibrosis transmembrane conductance regulator (CFTR) and P-glycoprotein (P-gp) are ATP-binding cassette (ABC) transporters that have two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). Defective folding of CFTR lacking phenylalanine 508 (DeltaPhe508) in NBD1 is the most common cause of cystic fibrosis. The Phe508 position seems to be universally important in ABC transporters because deletion of the equivalent residue (Tyr490) in P-gp also inhibits maturation of the protein. The pharmacological chaperone VRT-325 can repair the DeltaPhe508-type folding defects in P-gp or CFTR. VRT-325 may repair the folding defects by promoting dimerization of the two NBDs or by promoting folding of the TMDs. To distinguish between these two mechanisms, we tested the ability of VRT-325 to promote folding of truncation mutants lacking one or both NBDs. Sensitivity to glycosidases was used as an indirect indicator of folding. It was found that VRT-325 could promote maturation of truncation mutants lacking NBD2. Truncation mutants of CFTR or P-gp lacking both NBDs showed deficiencies in core-glycosylation that could be partially reversed by carrying out expression in the presence of VRT-325. The results show that dimerization of the two NBDs to form a "nucleotide-sandwich" structure or NBD interactions with the TMDs are not essential for VRT-325 enhancement of folding. Instead, VRT-325 can promote folding of the TMDs alone. The ability of VRT-325 to promote core-glycosylation of the NBD-less truncation mutants suggests that one mechanism whereby the compound enhances folding is by promoting proper insertion of TM segments attached to the glycosylated loops so that they adopt an orientation favorable for glycosylation.

Impact of intra-tumoral IL17A and IL32 gene expression on T-cell responses and lymph node status in breast cancer patients

PubMed Central

Bhat, Shreyas; Gardi, Nilesh; Hake, Sujata; Kotian, Nirupama; Sawant, Sharada; Kannan, Sadhana; Parmar, Vani; Desai, Sangeeta; Dutt, Amit

2018-01-01

Purpose Pro-inflammatory cytokines such as Interleukin-17A (IL17A) and Interleukin-32 (IL32), known to enhance natural killer and T cell responses, are also elevated in human malignancies and linked to poor clinical outcomes. To address this paradox, we evaluated relation between IL17A and IL32 expression and other inflammation- and T cell response-associated genes in breast tumors. Methods TaqMan-based gene expression analysis was carried out in seventy-eight breast tumors. The association between IL17A and IL32 transcript levels and T cell response genes, ER status as well as lymph node status was also examined in breast tumors from TCGA dataset. Results IL17A expression was detected in 32.7% ER-positive and 84.6% ER-negative tumors, with higher expression in the latter group (26.2 vs 7.1-fold, p < 0.01). ER-negative tumors also showed higher expression of IL32 as opposed to ER-positive tumors (8.7 vs 2.5-fold, p < 0.01). Expression of both IL17A and IL32 genes positively correlated with CCL5, GNLY, TBX21, IL21 and IL23 transcript levels (p < 0.01). Amongst ER-positive tumors, higher IL32 expression significantly correlated with lymph node metastases (p < 0.05). Conversely, in ER-negative subtype, high IL17A and IL32 expression was seen in patients with negative lymph node status (p < 0.05). Tumors with high IL32 and IL17A expression showed higher expression of TH1 response genes studied, an observation validated by similar analysis in the TCGA breast tumors (n=1041). Of note, these tumors were characterized by low expression of a potentially immunosuppressive isoform of IL32 (IL32γ). Conclusion These results suggest that high expression of both IL17A and IL32 leads to enhancement of T cell responses. Our study, thus, provides basis for the emergence of strong T cell responses in an inflammatory milieu that have been shown to be associated with better prognosis in ER-negative breast cancer. PMID:28470472

Effects of Formulation on Microbicide Potency and Mitigation of the Development of Bacterial Insusceptibility

PubMed Central

Cowley, Nicola L.; Forbes, Sarah; Amézquita, Alejandro; McClure, Peter; Humphreys, Gavin J.

2015-01-01

Risk assessments of the potential for microbicides to select for reduced bacterial susceptibility have been based largely on data generated through the exposure of bacteria to microbicides in aqueous solution. Since microbicides are normally formulated with multiple excipients, we have investigated the effect of formulation on antimicrobial activity and the induction of bacterial insusceptibility. We tested 8 species of bacteria (7 genera) before and after repeated exposure (14 passages), using a previously validated gradient plating system, for their susceptibilities to the microbicides benzalkonium chloride, benzisothiozolinone, chlorhexidine, didecyldimethyl ammonium chloride, DMDM-hydantoin, polyhexamethylene biguanide, thymol, and triclosan in aqueous solution (nonformulated) and in formulation with excipients often deployed in consumer products. Susceptibilities were also assessed following an additional 14 passages without microbicide to determine the stability of any susceptibility changes. MICs and minimum bactericidal concentrations (MBC) were on average 11-fold lower for formulated microbicides than for nonformulated microbicides. After exposure to the antimicrobial compounds, of 72 combinations of microbicide and bacterium there were 19 ≥4-fold (mean, 8-fold) increases in MIC for nonformulated and 8 ≥4-fold (mean, 2-fold) increases in MIC for formulated microbicides. Furthermore, there were 20 ≥4-fold increases in MBC (mean, 8-fold) for nonformulated and 10 ≥4-fold (mean, 2-fold) increases in MBC for formulated microbicides. Susceptibility decreases fully or partially reverted back to preexposure values for 49% of MICs and 72% of MBCs after further passage. In summary, formulated microbicides exhibited greater antibacterial potency than unformulated actives and susceptibility decreases after repeated exposure were lower in frequency and extent. PMID:26253662

Detection of swine-origin influenza A (H1N1) viruses using a paired surface plasma waves biosensor

NASA Astrophysics Data System (ADS)

Su, Li-Chen; Chang, Ying-Feng; Li, Ying-Chang; Hsieh, Jo-Ping; Lee, Cheng-Chung; Chou, Chien

2010-08-01

In order to enhance the sensitivity of conventional rapid test technique for the detection of swine-origin influenza A (H1N1) viruses (S-OIVs), we used a paired surface plasma waves biosensor (PSPWB) based on SPR in conjunction with an optical heterodyne technique. Experimentally, PSPWB showed a 125-fold improvement at least in the S-OIV detection as compared to conventional enzyme linked immunosorbent assay. Moreover, the detection limit of the PSPWB for the S-OIV detection was enhanced 250-fold in buffer at least in comparison with that of conventional rapid influenza diagnostic test.

Rover deployment system for lunar landing mission

NASA Astrophysics Data System (ADS)

Sutoh, Masataku; Hoshino, Takeshi; Wakabayashi, Sachiko

2017-09-01

For lunar surface exploration, a deployment system is necessary to allow a rover to leave the lander. The system should be as lightweight as possible and stored retracted when launched. In this paper, two types of retractable deployment systems for lunar landing missions, telescopic- and fold-type ramps, are discussed. In the telescopic-type system, a ramp is stored with the sections overlapping and slides out during deployment. In the fold-type system, it is stored folded and unfolds for the deployment. For the development of these ramps, a design concept study and structural analysis were conducted first. Subsequently, ramp deployment and rover release tests were performed using the developed ramp prototypes. Through these tests, the validity of their design concepts and functions have been confirmed. In the rover release test, it was observed that the developed lightweight ramp was sufficiently strong for a 50-kg rover to descend. This result suggests that this ramp system is suitable for the deployment of a 300-kg-class rover on the Moon, where the gravity is about one-sixth that on Earth. The lightweight and sturdy ramp developed in this study will contribute to both safe rover deployment and increase of lander/rover payload.

Transition Pathway and Its Free-Energy Profile: A Protocol for Protein Folding Simulations

PubMed Central

Lee, In-Ho; Kim, Seung-Yeon; Lee, Jooyoung

2013-01-01

We propose a protocol that provides a systematic definition of reaction coordinate and related free-energy profile as the function of temperature for the protein-folding simulation. First, using action-derived molecular dynamics (ADMD), we investigate the dynamic folding pathway model of a protein between a fixed extended conformation and a compact conformation. We choose the pathway model to be the reaction coordinate, and the folding and unfolding processes are characterized by the ADMD step index, in contrast to the common a priori reaction coordinate as used in conventional studies. Second, we calculate free-energy profile as the function of temperature, by employing the replica-exchange molecular dynamics (REMD) method. The current method provides efficient exploration of conformational space and proper characterization of protein folding/unfolding dynamics from/to an arbitrary extended conformation. We demonstrate that combination of the two simulation methods, ADMD and REMD, provides understanding on molecular conformational changes in proteins. The protocol is tested on a small protein, penta-peptide of met-enkephalin. For the neuropeptide met-enkephalin system, folded, extended, and intermediate sates are well-defined through the free-energy profile over the reaction coordinate. Results are consistent with those in the literature. PMID:23917881

Electrostatic effects on the folding stability of FKBP

NASA Astrophysics Data System (ADS)

Batra, Jyotica; Zhou, Huan-Xiang

2006-11-01

Charged residues play important roles in the folding of proteins and their interactions with biological targets. We have developed computational models for predicting electrostatic contributions to protein folding and binding stability. To rigorously test and further refine these models, we carried out experimental studies on the effects of charge mutations on the folding stability of FKBP. Two close homologues of FKBP, FKBP12 and FKBP12.6, differ in 18 of 107 positions, and 8 of which involve substitutions of charged residues. These 8 substitutions were introduced on FKBP12 and their effects on the folding stability were measured. The changes in unfolding free energy varied from -0.34 to 0.65 kcal/mol. A double and a triple mutation were introduced to accumulate the stabilization effect of individual substitutions, resulting an increase in stability of about 0.84 kcal/mol. On the other hand, neutralizing one or both partners of a conserved salt bridge reduced the stability by as much as 0.64 kcal/mol. These results suggest that charged residues can modulate the folding stability significantly. To further exploit stabilization effects of charged residues, experiments are now underway to introduce charge mutations that are modeled after a thermophilic FKBP.

Effects of triclosan on bacterial community composition and ...

EPA Pesticide Factsheets

Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, Vibrio, a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm) can induce a significant Vibrio growth response (68–1,700 fold increases) in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary), Doctors Arm Canal (Big Pine Key, FL), and Clam Bank Landing (North Inlet Estuary, Georgetown, SC). Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of Vibrionaceae (17-fold), Pseudoalteromonadaceae (65-fold), Alteromonadaceae (108-fold), Colwelliaceae (430-fold), and Oceanospirillaceae (1,494-fold). While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to u

Improving diagnostic recognition of primary hyperparathyroidism with machine learning.

PubMed

Somnay, Yash R; Craven, Mark; McCoy, Kelly L; Carty, Sally E; Wang, Tracy S; Greenberg, Caprice C; Schneider, David F

2017-04-01

Parathyroidectomy offers the only cure for primary hyperparathyroidism, but today only 50% of primary hyperparathyroidism patients are referred for operation, in large part, because the condition is widely under-recognized. The diagnosis of primary hyperparathyroidism can be especially challenging with mild biochemical indices. Machine learning is a collection of methods in which computers build predictive algorithms based on labeled examples. With the aim of facilitating diagnosis, we tested the ability of machine learning to distinguish primary hyperparathyroidism from normal physiology using clinical and laboratory data. This retrospective cohort study used a labeled training set and 10-fold cross-validation to evaluate accuracy of the algorithm. Measures of accuracy included area under the receiver operating characteristic curve, precision (sensitivity), and positive and negative predictive value. Several different algorithms and ensembles of algorithms were tested using the Weka platform. Among 11,830 patients managed operatively at 3 high-volume endocrine surgery programs from March 2001 to August 2013, 6,777 underwent parathyroidectomy for confirmed primary hyperparathyroidism, and 5,053 control patients without primary hyperparathyroidism underwent thyroidectomy. Test-set accuracies for machine learning models were determined using 10-fold cross-validation. Age, sex, and serum levels of preoperative calcium, phosphate, parathyroid hormone, vitamin D, and creatinine were defined as potential predictors of primary hyperparathyroidism. Mild primary hyperparathyroidism was defined as primary hyperparathyroidism with normal preoperative calcium or parathyroid hormone levels. After testing a variety of machine learning algorithms, Bayesian network models proved most accurate, classifying correctly 95.2% of all primary hyperparathyroidism patients (area under receiver operating characteristic = 0.989). Omitting parathyroid hormone from the model did not decrease the accuracy significantly (area under receiver operating characteristic = 0.985). In mild disease cases, however, the Bayesian network model classified correctly 71.1% of patients with normal calcium and 92.1% with normal parathyroid hormone levels preoperatively. Bayesian networking and AdaBoost improved the accuracy of all parathyroid hormone patients to 97.2% cases (area under receiver operating characteristic = 0.994), and 91.9% of primary hyperparathyroidism patients with mild disease. This was significantly improved relative to Bayesian networking alone (P < .0001). Machine learning can diagnose accurately primary hyperparathyroidism without human input even in mild disease. Incorporation of this tool into electronic medical record systems may aid in recognition of this under-diagnosed disorder. Copyright © 2016 Elsevier Inc. All rights reserved.

Androgens and doping tests: genetic variation and pit-falls

PubMed Central

Rane, Anders; Ekström, Lena

2012-01-01

The large variation in disposition known for most drugs is also true for anabolic androgenic steroids. Genetic factors are probably the single most important cause of this variation. Further, there are reasons to believe that there is a corresponding variation in efficacy of doping agents. Doped individuals employ a large variety of doping strategies in respect of choice of substance, dose, dose interval, duration of treatment and use of other drugs for enforcement of effects or correction of side effects. Metabolic steps up-stream and down-stream of testosterone are genetically variable and contribute substantially to the variation in disposition of testosterone, the most common doping agent in sports and in society. Large inter- and intra-ethnic variation in testosterone glucuronidation and excretion is described as well as the pit-falls in evaluation of testosterone doping test results. The hydrolysis and bioactivation of testosterone enanthate is also genetically variable yielding a 2–3 fold variation in excretion rate and serum concentration, thereby implicating a substantial variation in ‘efficacy’ of testosterone. Given this situation it is logical to adopt the new findings in the doping control programme. The population based cut-off level for the testosterone : epitestosterone ratio should be replaced by a Bayesian interpretation of consecutive tests in the same individual. When combined with the above genetic information the sensitivity of the test is considerably improved. The combination of the three approaches should reduce the rate of falsely negative or positive results and the number of expensive follow-up tests, stipulated by the World Anti-Doping Agency. PMID:22506612

Effect of race on biochemical disease-free outcome in patients with prostate cancer treated with definitive radiation therapy in an equal-access health care system: radiation oncology report of the Department of Defense Center for Prostate Disease Research.

PubMed

Johnstone, Peter A S; Kane, Christopher J; Sun, Leon; Wu, Hongyu; Moul, Judd W; McLeod, David G; Martin, Douglas D; Kusuda, Leo; Lance, Raymond; Douglas, Robert; Donahue, Timothy; Beat, Michael G; Foley, John; Baldwin, Dalton; Soderdahl, Douglas; Do, Jason; Amling, Christopher L

2002-11-01

To report on the first collaboration of the Department of Defense Center for Prostate Disease Research concerned with the relationship between African American race and biochemical disease-free outcomes after definitive radiation therapy. Information from the medical records of 1,806 patients (1,349 white, 343 African American, 42 of "other" races, and 72 of "unknown" races) treated with definitive radiation therapy between 1973 and 2000 was reviewed. Patients receiving adjuvant hormonal therapy or postoperative adjuvant or salvage radiation therapy were excluded. Biochemical failure was calculated in over 96% of cases by using ASTRO criteria; patients with fewer than three follow-up visits were considered to have biochemical failure with a prostate-specific antigen (PSA) value more than 10-fold the previous value or with any value greater than 50.0 ng/mL. Median radiation therapy doses were similar. The median follow-up was 58.4 months. Kaplan-Meier tests, Cox proportional hazards regression analysis, and log-rank tests were used for data analysis. There was no statistically significant difference in biochemical disease-free survival according to race when patients were stratified according to T stage. African American race conferred a negative prognosis for patients with lesions of Gleason biopsy score 7 (P =.004) but not for patients with lesions of Gleason score 2-4 (P =.14), 5-6 (P =.79), or 8-10 (P =.86). Similarly, African American race conferred a negative prognosis in patients with PSA values of 20.1-50.0 ng/mL (P =.01) at presentation but not in patients with PSA values less than or equal to 4.0 ng/mL (P =.84), 4.1-10.0 ng/mL (P =.71), 10.1-20.0 ng/mL (P =.75), or above 50.0 ng/mL (P =.15) at presentation. At multivariate analysis, race was not a statistically significant predictor of outcome. In the equal-access health care system of the Department of Defense, African American race is not associated with a consistently negative prognosis in patients treated with definitive radiation therapy for prostate cancer. Race appears to confer a negative prognosis only in patients with advanced disease at presentation.

Comparison between disintegrated and fermented sewage sludge for production of a carbon source suitable for biological nutrient removal.

PubMed

Soares, Ana; Kampas, Pantelis; Maillard, Sarah; Wood, Elizabeth; Brigg, Jon; Tillotson, Martin; Parsons, Simon A; Cartmell, Elise

2010-03-15

There is a need to investigate processes that enable sludge re-use while enhancing sewage treatment efficiency. Mechanically disintegrated thickened surplus activated sludge (SAS) and fermented primary sludge were compared for their capacity to produce a carbon source suitable for BNR by completing nutrient removal predictive tests. Mechanically disintegration of SAS using a deflaker enhanced volatile fatty acids (VFAs) content from 92 to 374 mg l(-1) (4.1-fold increase). In comparison, primary sludge fermentation increased the VFAs content from 3.5 g l(-1) to a final concentration of 8.7 g l(-1) (2.5-fold increase). The carbon source obtained from disintegration and fermentation treatments improved phosphate (PO(4)-P) release and denitrification by up to 0.04 mg NO(3)-Ng(-1)VSS min(-1) and 0.031 mg PO(4)-Pg(-1)VSS min(-1), respectively, in comparison to acetate (0.023 mg NO(3)-Ng(-1)VSS min(-1)and 0.010 mg PO(4)-Pg(-1)VSS min(-1)). Overall, both types of sludge were suitable for BNR but disintegrated SAS displayed lower carbon to nutrient ratios of 8 for SCOD:PO(4)-P and 9 for SCOD:NO(3)-N. On the other hand, SAS increased the concentration of PO(4)-P in the settled sewage by a further 0.97 g PO(4)-P kg(-1)SCOD indicating its potential negative impact towards nutrient recycling in the BNR process. (c) 2009 Elsevier B.V. All rights reserved.

Plasma-free vs deconjugated metanephrines for diagnosis of phaeochromocytoma.

PubMed

Pamporaki, Christina; Därr, Roland; Bursztyn, Michael; Glöckner, Stephan; Bornstein, Stefan R; Lenders, Jacques W M; Pacak, Karel; Krinner, Axel; Eisenhofer, Graeme

2013-10-01

The diagnosis of phaeochromocytoma is commonly performed by the measurements of plasma-free normetanephrine and metanephrine. Plasma-deconjugated normetanephrine and metanephrine have been proposed as alternative, equivalent, but easier to measure biomarkers. The aim of this study was to compare the diagnostic performance of plasma-free vs deconjugated normetanephrine and metanephrine in patients tested for phaeochromocytoma. The study population included a reference group of 262 normotensive and hypertensive volunteers, 198 patients with phaeochromocytoma and 528 patients initially suspected of having the tumour, but with negative investigations after at least 2 years of follow-up. Measurements were performed using liquid chromatography with electrochemical detection. Plasma concentrations of free normetanephrine were 17-fold higher in patients with phaeochromocytoma than in the reference population, a 72% larger (P < 0·001) difference than that for the 10-fold higher levels of plasma-deconjugated normetanephrine. In contrast, relative increases in plasma concentrations of free and deconjugated metanephrine were similar. Using upper cut-offs established in the reference population, measurements of plasma-free metabolites provided superior diagnostic performance than deconjugated metabolites according to measures of both sensitivity (97% vs 92%, P = 0·002) and specificity (93% vs 89%, P = 0·012). The area under the receiver operating characteristic curve for the free metabolites was larger than that for the deconjugated metabolites (0·986 vs 0·965, P < 0·001). Measurements of plasma-free normetanephrine and metanephrine are superior to the deconjugated metabolites for diagnosis of phaeochromocytoma. © 2013 John Wiley & Sons Ltd.

Amino Acid Medical Foods Provide a High Dietary Acid Load and Increase Urinary Excretion of Renal Net Acid, Calcium, and Magnesium Compared with Glycomacropeptide Medical Foods in Phenylketonuria

PubMed Central

Stroup, Bridget M.; Sawin, Emily A.; Murali, Sangita G.; Binkley, Neil; Hansen, Karen E.

2017-01-01

Background. Skeletal fragility is a complication of phenylketonuria (PKU). A diet containing amino acids compared with glycomacropeptide reduces bone size and strength in mice. Objective. We tested the hypothesis that amino acid medical foods (AA-MF) provide a high dietary acid load, subsequently increasing urinary excretion of renal net acid, calcium, and magnesium, compared to glycomacropeptide medical foods (GMP-MF). Design. In a crossover design, 8 participants with PKU (16–35 y) provided food records and 24-hr urine samples after consuming a low-Phe diet in combination with AA-MF and GMP-MF for 1–3 wks. We calculated potential renal acid load (PRAL) of AA-MF and GMP-MF and determined bone mineral density (BMD) measurements using dual X-ray absorptiometry. Results. AA-MF provided 1.5–2.5-fold higher PRAL and resulted in 3-fold greater renal net acid excretion compared to GMP-MF (p = 0.002). Dietary protein, calcium, and magnesium intake were similar. GMP-MF significantly reduced urinary excretion of calcium by 40% (p = 0.012) and magnesium by 30% (p = 0.029). Two participants had low BMD-for-age and trabecular bone scores, indicating microarchitectural degradation. Urinary calcium with AA-MF negatively correlated with L1–L4 BMD. Conclusion. Compared to GMP-MF, AA-MF increase dietary acid load, subsequently increasing urinary calcium and magnesium excretion, and likely contributing to skeletal fragility in PKU. The trial was registered at clinicaltrials.gov as NCT01428258. PMID:28546877

Age-related effects in the neocortical organization of chimpanzees: gray and white matter volume, cortical thickness, and gyrification.

PubMed

Autrey, Michelle M; Reamer, Lisa A; Mareno, Mary Catherine; Sherwood, Chet C; Herndon, James G; Preuss, Todd; Schapiro, Steve J; Hopkins, William D

2014-11-01

Among primates, humans exhibit the most profound degree of age-related brain volumetric decline in particular regions, such as the hippocampus and the frontal lobe. Recent studies have shown that our closest living relatives, the chimpanzees, experience little to no volumetric decline in gray and white matter over the adult lifespan. However, these previous studies were limited with a small sample of chimpanzees of the most advanced ages. In the present study, we sought to further test for potential age-related decline in cortical organization in chimpanzees by expanding the sample size of aged chimpanzees. We used the BrainVisa software to measure total brain volume, gray and white matter volumes, gray matter thickness, and gyrification index in a cross-sectional sample of 219 captive chimpanzees (8-53 years old), with 38 subjects being 40 or more years of age. Mean depth and cortical fold opening of 11 major sulci of the chimpanzee brains were also measured. We found that chimpanzees showed increased gyrification with age and a cubic relationship between age and white matter volume. For the association between age and sulcus depth and width, the results were mostly non-significant with the exception of one negative correlation between age and the fronto-orbital sulcus. In short, results showed that chimpanzees exhibit few age-related changes in global cortical organization, sulcus folding and sulcus width. These findings support previous studies and the theory that the age-related changes in the human brain is due to an extended lifespan. Copyright © 2014 Elsevier Inc. All rights reserved.

GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome

PubMed Central

Zhang, Jian; Yang, Jianyi; Jang, Richard; Zhang, Yang

2015-01-01

SUMMARY Experimental structure determination remains very difficult for G protein-coupled receptors (GPCRs). We propose a new hybrid protocol to construct GPCR structure models that integrates experimental mutagenesis data with ab initio transmembrane (TM) helix assembly simulations. The method was tested on 24 known GPCRs where the ab initio TM-helix assembly procedure constructed the correct fold for 20 cases. When combined with weak-homology and sparse mutagenesis restraints, the method generated correct folds for all the tested cases with an average C-alpha RMSD 2.4 Å in the TM-regions. The new hybrid protocol was applied to model all 1026 GPCRs in the human genome, where 923 have a high confidence score that are expected to have correct folds; these contain many pharmaceutically important families with no previously solved structures, including Trace amine, Prostanoids, Releasing hormones, Melanocortins, Vasopressin and Neuropeptide Y receptors. The results demonstrate new progress on genome-wide structure modeling of transmembrane proteins. PMID:26190572

Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity

NASA Astrophysics Data System (ADS)

Frigori, Rafael B.; Rizzi, Leandro G.; Alves, Nelson A.

2013-01-01

The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid β isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process.

Assessment of biological, psychological and adherence factors in the prediction of step-down treatment for patients with well-controlled asthma.

PubMed

Saito, N; Kamata, A; Itoga, M; Tamaki, M; Kayaba, H; Ritz, T

2017-04-01

Inhaled corticosteroids (ICS) and inhaled corticosteroids combined with long-acting beta2-agonist (ICS/LABA) are standard treatments for asthma. However, factors that might help reduce medication in well-controlled asthma are unknown. We classified problems of asthma patients into biological, psychological and adherence factors, and investigated factors associated with the indication and failure of a medication step-down treatment. Two hundred twenty two well-controlled asthma patients receiving ICS or ICS/LABA were assessed for physical and psychiatric problems and followed up for one year from adjustment of their treatment step. Factor B was defined as a presence of chronic upper airway complications. Factor P was defined as presence of psychiatric complications such as sleep disorder, depression, anxiety and somatoform disorders. Factor A was defined as poor adherence to ICS or ICS/LABA inhaler of 75% or less. Success in step-down treatment was defined as maintenance of well-controlled status for over one year after step-down. Factor B was the most important single negative predictive factor for indication for step-down treatment (Odds ratio; 0.19). Factor A increased the risk of failure to maintain step-down treatment most significantly by 23-fold, and factor B increased it by 11-fold. The combination of factors B and A increased failure by 24-fold, factors P and A by 21-fold, all three factors by 36-fold. Factor P only interacted with the other factors to reduce chances of stepping down, but did not constitute a problem factor when present alone. The evaluation of biological, psychological and adherence problems may lead to a more proactive and targeted approach to step-down treatment for patients with well-controlled asthma. © 2017 John Wiley & Sons Ltd.

Aryl-Aryl Interactions in Designed Peptide Folds: Spectroscopic Characteristics and Placement Issues for Optimal Structure Stabilization

PubMed Central

Anderson, Jordan M.; Kier, Brandon; Jurban, Brice; Byrne, Aimee; Shu, Irene; Eidenschink, Lisa A.; Shcherbakov, Alexander A.; Hudson, Mike; Fesinmeyer, R. M.; Andersen, Niels H.

2017-01-01

We have extended our studies of Trp/Trp to other Aryl/Aryl through-space interactions that stabilize hairpins and other small polypeptide folds. Herein we detail the NMR and CD spectroscopic features of these types of interactions. NMR data remains the best diagnostic for characterizing the common T-shape orientation. Designated as an edge-to-face (EtF or FtE) interaction, large ring current shifts are produced at the edge aryl ring hydrogens and, in most cases, large exciton couplets appear in the far UV circular dichroic (CD) spectrum. The preference for the face aryl in FtE clusters is W≫Y≥F (there are some exceptions in the Y/F order); this sequence corresponds to the order of fold stability enhancement and always predicts the amplitude of the lower energy feature of the exciton couplet in the CD spectrum. The CD spectra for FtE W/W, W/Y, Y/W, and Y/Y pairs all include an intense feature at 225–232 nm. An additional couplet feature seen for W/Y, W/F, Y/Y and F/Y clusters, is a negative feature at 197–200 nm. Tyr/Tyr (as well as F/Y and F/F) interactions produce much smaller exciton couplet amplitudes. The Trp-cage fold was employed to search for the CD effects of other Trp/Trp and Trp/Tyr cluster geometries: several were identified. In this account, we provide additional examples of the application of cross-strand aryl/aryl clusters for the design of stable β-sheet models and a scale of fold stability increments associated with all possible FtE Ar/Ar clusters in several structural contexts. PMID:26850220

Surface Oxide Net Charge of a Titanium Alloy ; Modulation of Fibronectin-Activated Attachment and Spreading of Osteogenic Cells

PubMed Central

Rapuano, Bruce E.; MacDonald, Daniel E.

2010-01-01

In the current study, we have altered the surface oxide properties of a Ti6Al4V alloy using heat treatment or radiofrequency glow discharge (RFGD) in order to evaluate the relationship between the physico-chemical and biological properties of the alloy's surface oxide. The effects of surface pretreatments on the attachment of cells from two osteogenic cell lines (MG63 and MC3T3) and a mesenchymal stem cell line (C3H10T1/2) to fibronectin adsorbed to the alloy were measured. Both heat and RFGD pretreatments produced a several-fold increase in the number of cells that attached to fibronectin adsorbed to the alloy (0.001 and 10 nM FN) for each cell line tested. An antibody (HFN7.1) directed against the central integrin binding domain of fibronectin produced a 65-70% inhibition of cell attachment to fibronectin-coated disks, incdicating that cell attachment to the metal discs was dependent on fibronectin binding to cell integrin receptors. Both treatments also accelerated the cell spreading response manifested by extensive flattening and an increase in mean cellular area. The treatment-induced increases in the cell attachment activity of adsorbed fibronectin were correlated with previously demonstrated increases in Ti6Al4V oxide negative net surface charge at physiological pH produced by both heat and RFGD pretreatments. Since neither treatment increased the adsorption mass of fibronectin, these findings suggest that negatively charged surface oxide functional groups in Ti6Al4V can modulate fibronectin's integrin receptor activity by altering the adsorbed protein's conformation. Our results further suggest that negatively charged functional groups in the surface oxide can play a prominent role in the osseointegration of metallic implant materials. PMID:20884181

Human papillomavirus genotype and oropharynx cancer survival in the United States of America.

PubMed

Goodman, Marc T; Saraiya, Mona; Thompson, Trevor D; Steinau, Martin; Hernandez, Brenda Y; Lynch, Charles F; Lyu, Christopher W; Wilkinson, Edward J; Tucker, Thomas; Copeland, Glenn; Peters, Edward S; Altekruse, Sean; Unger, Elizabeth R

2015-12-01

The presence of human papillomavirus (HPV) DNA in oropharyngeal squamous cell cancer (OPSCC) tissue appears to be a strong predictor of improved prognosis, but this observation has not been explored in a population-based sample with generalisable findings. Follow-up data from a large sample of OPSCC patients identified through six population-based cancer registries in the United States of America (USA) were used to characterise the association of tumour HPV status with survival. HPV DNA was detected in tumour tissue from 71% (378 in 529) of the OPSCC patients. A total of 65% of patients with HPV16-associated tumours survived 5 years compared to 46% of patients with other HPV types and 28% of patients with HPV-negative tumours (p log-rank test <0.0001). The OPSCC patients with detectable HPV16 DNA had a 62% reduced hazard of death at 5 years, and patients with other HPV types had a 42% reduced hazard of death at 5 years compared to HPV-negative patients. Compared to non-Hispanic Whites, Blacks with OPSCC had a 2.6-fold greater risk of death at 5 years after adjustment for HPV status and other prognostic variables. Both surgery and radiation therapy were associated with a reduced 5-year risk of death, but no evidence was found for an interaction between HPV status and radiotherapy or surgery on survival time. Data from this US study suggest that HPV16-positive OPSCC patients survive longer than HPV-negative patients regardless of treatment, highlighting the prognostic importance of HPV status for this malignancy. Optimal treatment regimens for OPSCC could be tailored to each patient's HPV status and prognostic profile. Copyright © 2015 Elsevier Ltd. All rights reserved.

Experimental support for the foldability-function tradeoff hypothesis: segregation of the folding nucleus and functional regions in fibroblast growth factor-1.

PubMed

Longo, Liam; Lee, Jihun; Blaber, Michael

2012-12-01

The acquisition of function is often associated with destabilizing mutations, giving rise to the stability-function tradeoff hypothesis. To test whether function is also accommodated at the expense of foldability, fibroblast growth factor-1 (FGF-1) was subjected to a comprehensive φ-value analysis at each of the 11 turn regions. FGF-1, a β-trefoil fold, represents an excellent model system with which to evaluate the influence of function on foldability: because of its threefold symmetric structure, analysis of FGF-1 allows for direct comparisons between symmetry-related regions of the protein that are associated with function to those that are not; thus, a structural basis for regions of foldability can potentially be identified. The resulting φ-value distribution of FGF-1 is highly polarized, with the majority of positions described as either folded-like or denatured-like in the folding transition state. Regions important for folding are shown to be asymmetrically distributed within the protein architecture; furthermore, regions associated with function (i.e., heparin-binding affinity and receptor-binding affinity) are localized to regions of the protein that fold after barrier crossing (late in the folding pathway). These results provide experimental support for the foldability-function tradeoff hypothesis in the evolution of FGF-1. Notably, the results identify the potential for folding redundancy in symmetric protein architecture with important implications for protein evolution and design. Copyright © 2012 The Protein Society.

Dependence of phonation threshold pressure on vocal tract acoustics and vocal fold tissue mechanics.

PubMed

Chan, Roger W; Titze, Ingo R

2006-04-01

Analytical and computer simulation studies have shown that the acoustic impedance of the vocal tract as well as the viscoelastic properties of vocal fold tissues are critical for determining the dynamics and the energy transfer mechanism of vocal fold oscillation. In the present study, a linear, small-amplitude oscillation theory was revised by taking into account the propagation of a mucosal wave and the inertive reactance (inertance) of the supraglottal vocal tract as the major energy transfer mechanisms for flow-induced self-oscillation of the vocal fold. Specifically, analytical results predicted that phonation threshold pressure (Pth) increases with the viscous shear properties of the vocal fold, but decreases with vocal tract inertance. This theory was empirically tested using a physical model of the larynx, where biological materials (fat, hyaluronic acid, and fibronectin) were implanted into the vocal fold cover to investigate the effect of vocal fold tissue viscoelasticity on Pth. A uniform-tube supraglottal vocal tract was also introduced to examine the effect of vocal tract inertance on Pth. Results showed that Pth decreased with the inertive impedance of the vocal tract and increased with the viscous shear modulus (G") or dynamic viscosity (eta') of the vocal fold cover, consistent with theoretical predictions. These findings supported the potential biomechanical benefits of hyaluronic acid as a surgical bioimplant for repairing voice disorders involving the superficial layer of the lamina propria, such as scarring, sulcus vocalis, atrophy, and Reinke's edema.

Performance of the dipstick screening test as a predictor of negative urine culture

PubMed Central

Marques, Alexandre Gimenes; Doi, André Mario; Pasternak, Jacyr; Damascena, Márcio dos Santos; França, Carolina Nunes; Martino, Marinês Dalla Valle

2017-01-01

ABSTRACT Objective To investigate whether the urine dipstick screening test can be used to predict urine culture results. Methods A retrospective study conducted between January and December 2014 based on data from 8,587 patients with a medical order for urine dipstick test, urine sediment analysis and urine culture. Sensitivity, specificity, positive and negative predictive values were determined and ROC curve analysis was performed. Results The percentage of positive cultures was 17.5%. Nitrite had 28% sensitivity and 99% specificity, with positive and negative predictive values of 89% and 87%, respectively. Leukocyte esterase had 79% sensitivity and 84% specificity, with positive and negative predictive values of 51% and 95%, respectively. The combination of positive nitrite or positive leukocyte esterase tests had 85% sensitivity and 84% specificity, with positive and negative predictive values of 53% and 96%, respectively. Positive urinary sediment (more than ten leukocytes per microliter) had 92% sensitivity and 71% specificity, with positive and negative predictive values of 40% and 98%, respectively. The combination of nitrite positive test and positive urinary sediment had 82% sensitivity and 99% specificity, with positive and negative predictive values of 91% and 98%, respectively. The combination of nitrite or leukocyte esterase positive tests and positive urinary sediment had the highest sensitivity (94%) and specificity (84%), with positive and negative predictive values of 58% and 99%, respectively. Based on ROC curve analysis, the best indicator of positive urine culture was the combination of positives leukocyte esterase or nitrite tests and positive urinary sediment, followed by positives leukocyte and nitrite tests, positive urinary sediment alone, positive leukocyte esterase test alone, positive nitrite test alone and finally association of positives nitrite and urinary sediment (AUC: 0.845, 0.844, 0.817, 0.814, 0.635 and 0.626, respectively). Conclusion A negative urine culture can be predicted by negative dipstick test results. Therefore, this test may be a reliable predictor of negative urine culture. PMID:28444086

Genetic Algorithms and Their Application to the Protein Folding Problem

DTIC Science & Technology

1993-12-01

and symbolic methods, random methods such as Monte Carlo simulation and simulated annealing, distance geometry, and molecular dynamics. Many of these...calculated energies with those obtained using the molecular simulation software package called CHARMm. 10 9) Test both the simple and parallel simpie genetic...homology-based, and simplification techniques. 3.21 Molecular Dynamics. Perhaps the most natural approach is to actually simulate the folding process. This

Dideoxynucleoside resistance emerges with prolonged zidovudine monotherapy. The RV43 Study Group.

PubMed Central

Mayers, D L; Japour, A J; Arduino, J M; Hammer, S M; Reichman, R; Wagner, K F; Chung, R; Lane, J; Crumpacker, C S; McLeod, G X

1994-01-01

Human immunodeficiency virus type 1 (HIV-1) isolates resistant to zidovudine (ZDV) have previously been demonstrated to exhibit in vitro cross-resistance to other similar dideoxynucleoside agents which contain a 3'-azido group. However, cross-resistance to didanosine (ddI) or dideoxycytidine (ddC) has been less well documented. ZDV, ddI, and ddC susceptibility data have been collected from clinical HIV-1 isolates obtained by five clinical centers and their respective retrovirology laboratories. All subjects were treated only with ZDV. Clinical HIV-1 isolates were isolated, amplified, and assayed for drug susceptibility in standardized cultures of phytohemagglutinin-stimulated donor peripheral blood mononuclear cells obtained from healthy seronegative donors. All five cohorts showed a correlation between decreased in vitro susceptibility to ZDV and decreased susceptibility to ddI and ddC. For each 10-fold decrease in ZDV susceptibility, an average corresponding decrease of 2.2-fold in ddI susceptibility was observed (129 isolates studied; P < 0.001, Fisher's test of combined significance). Similarly, susceptibility to ddC decreased 2.0-fold for each 10-fold decrease in ZDV susceptibility (82 isolates studied; P < 0.001, Fisher's test of combined significance). These data indicate that a correlation exists between HIV-1 susceptibilities to ZDV and ddI or ddC for clinical HIV-1 isolates. PMID:8192457

Analysis of molecular chaperones using a Xenopus oocyte protein refolding assay.

PubMed

Heikkila, John J; Kaldis, Angelo; Abdulle, Rashid

2006-01-01

Heat shock proteins (Hsps) are molecular chaperones that aid in the folding and translocation of protein under normal conditions and protect cellular proteins during stressful situations. A family of Hsps, the small Hsps, can maintain denatured target proteins in a folding-competent state such that they can be refolded and regain biological activity in the presence of other molecular chaperones. Previous assays have employed cellular lysates as a source of molecular chaperones involved in folding. In this chapter, we describe the production and purification of a Xenopus laevis recombinant small Hsp, Hsp30C, and an in vivo luciferase (LUC) refolding assay employing microinjected Xenopus oocytes. This assay tests whether LUC can be maintained in a folding-competent state when heat denatured in the presence of a small Hsp or other molecular chaperone. For example, micro-injection of heat-denatured LUC alone into oocytes resulted in minimal reactivation of enzyme activity. However, LUC heat denatured in the presence of Hsp30C resulted in 100% recovery of enzyme activity after microinjection. The in vivo oocyte refolding system is more sensitive and requires less molecular chaperone than in vitro refolding assays. Also, this protocol is not limited to testing Xenopus molecular chaperones because small Hsps from other organisms have been used successfully.

[Vocal cord paralysis after thyroid surgery : Current medicolegal aspects of intraoperative neuromonitoring].

PubMed

Dralle, H; Schneider, R; Lorenz, K; Phuong, N Thanh; Sekulla, C; Machens, A

2015-07-01

Intraoperative neuromonitoring (IONM) has been commercially available for approximately 15 years and is highly predictive in thyroid gland surgery concerning either postoperative vocal fold mobility in the case of an intact signal for muscle action electromyogram (EMG, > 99 % right negative) or vocal fold dysfunction in the case of loss of signal (> 70 % right positive). The use of IONM improves the intraoperative identification of recurrent laryngeal nerve function and due to the high predictive value with respect to the expected vocal cord function the result of IONM has to be integrated into the surgical concept of thyroidectomy. Unilateral loss of function of the recurrent laryngeal nerve cannot be completely avoided despite correct application of IONM; however, bilateral vocal fold palsy can be safely avoided when contralateral surgery is cancelled after a loss of signal occurs during resection of the first side in planned bilateral surgery (alternative strategy). Patients have to be informed preoperatively about the limitations of IONM and potential strategy changes during planned bilateral surgery. Surgeons should apply IONM according to the published current recommendations and by selecting a risk-oriented intraoperative strategy in the case of loss of signal from the recurrent laryngeal nerve.

Expression and crystallization of SeDsbA, SeDsbL and SeSrgA from Salmonella enterica serovar Typhimurium.

PubMed

Jarrott, R; Shouldice, S R; Guncar, G; Totsika, M; Schembri, M A; Heras, B

2010-05-01

Pathogens require protein-folding enzymes to produce functional virulence determinants. These foldases include the Dsb family of proteins, which catalyze oxidative folding in bacteria. Bacterial disulfide catalytic processes have been well characterized in Escherichia coli K-12 and these mechanisms have been extrapolated to other organisms. However, recent research indicates that the K-12 complement of Dsb proteins is not common to all bacteria. Importantly, many pathogenic bacteria have an extended arsenal of Dsb catalysts that is linked to their virulence. To help to elucidate the process of oxidative folding in pathogens containing a wide repertoire of Dsb proteins, Salmonella enterica serovar Typhimurium has been focused on. This Gram-negative bacterium contains three DsbA proteins: SeDsbA, SeDsbL and SeSrgA. Here, the expression, purification, crystallization and preliminary diffraction analysis of these three proteins are reported. SeDsbA, SeDsbL and SeSrgA crystals diffracted to resolution limits of 1.55, 1.57 and 2.6 A and belonged to space groups P2(1), P2(1)2(1)2 and C2, respectively.

Anticancer β-hairpin peptides: membrane-induced folding triggers activity

PubMed Central

Sinthuvanich, Chomdao; Veiga, Ana Salomé; Gupta, Kshitij; Gaspar, Diana; Blumenthal, Robert; Schneider, Joel P.

2012-01-01

Several cationic antimicrobial peptides (AMPs) have recently been shown to display anticancer activity via a mechanism that usually entails the disruption of cancer cell membranes. In this work, we designed an 18-residue anticancer peptide, SVS-1, whose mechanism of action is designed to take advantage of the aberrant lipid composition presented on the outer leaflet of cancer cell membranes, which makes the surface of these cells relatively electronegative relative to non-cancerous cells. SVS-1 is designed to remain unfolded and inactive in aqueous solution but preferentially fold at the surface of cancer cells, adopting an amphiphilic β-hairpin structure capable of membrane disruption. Membrane-induced folding is driven by electrostatic interaction between the peptide and the negatively charge membrane surface of cancer cells. SVS-1 is active against a variety of cancer cell lines such as A549 (lung carcinoma), KB (epidermal carcinoma), MCF-7 (breast carcinoma) and MDA-MB-436 (breast carcinoma). However, the cytotoxicity towards non-cancerous cells having typical membrane compositions, such as HUVEC and erythrocytes, is low. CD spectroscopy, appropriately designed peptide controls, cell-based studies, liposome leakage assays and electron microscopy support the intended mechanism of action, which leads to preferential killing of cancerous cells. PMID:22413859

In vitro kinetics of soybean lipoxygenase with combinatorial fatty substrates and its functional significance in off flavour development.

PubMed

Mandal, Somnath; Dahuja, Anil; Kar, Abhijit; Santha, I M

2014-03-01

Lipoxygenase (Lox) mediated oxidation of polyunsaturated fatty acids (PUFA) in mature soya seeds results in objectionable flavour. In the present study, Lox isozymes were purified to near homogeneity (107-fold). Lox-2 and 3 displayed remarkable kinetic preference (1.7 and 1.5-fold, respectively) for low PUFA ratios (LA/LeA) (PRs) among the selected PUFA combinations. Lox-1 displayed no specific preference. Pure Lox-1 displayed unbiased response towards substrates with marginal preference (1.2-fold) for linoleic acid at its optimum pH. Volatile compounds profiling showed a direct relationship between PRs and hexanal to trans-2-hexenal (1.47, 2.24 and 18.90 for 2, 7 and 15 PRs, respectively) ratio. The off-flavour determining parameters like TBA value, carbonyl value and lipid hydroperoxides (LHPODs) exhibited significant negative correlation (0.76, 0.74, 0.72; p<0.0001) in selected soya genotypes displaying varied PRs and significant positive correlation (0.89, 0.81. 0.89; p<0.0001) with ratio of PI (polyene index) to PRs - suggesting the plausible significance of PUFA ratios in biological lipid peroxidation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Structures of EccB 1 and EccD 1 from the core complex of the mycobacterial ESX-1 type VII secretion system

DOE PAGES

Wagner, Jonathan M.; Chan, Sum; Evans, Timothy J.; ...

2016-02-27

The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system. This study characterizes the structures of the soluble domains of two conserved core ESX-1 components – EccB 1 and EccD 1. The periplasmic domain of EccB 1 consists of 4 repeat domains and a central domain, which together form a quasi 2-fold symmetrical structure. Themore » repeat domains of EccB 1 are structurally similar to a known peptidoglycan binding protein suggesting a role in anchoring the ESX-1 system within the periplasmic space. The cytoplasmic domain of EccD 1 has a ubiquitin-like fold and forms a dimer with a negatively charged groove. In conclusion, these structures represent a major step towards resolving the molecular architecture of the entire ESX-1 assembly and may contribute to ESX-1 targeted tuberculosis intervention strategies.« less