Science.gov

Sample records for multiple endpoint embryonic

  1. Comparing three novel endpoints for developmental osteotoxicity in the embryonic stem cell test

    SciTech Connect

    Nieden, Nicole I. zur; Davis, Lesley A.; Rancourt, Derrick E.

    2010-09-01

    Birth defects belong to the most serious side effects of pharmaceutical compounds or environmental chemicals. In vivo, teratogens most often affect the normal development of bones, causing growth retardation, limb defects or craniofacial malformations. The embryonic stem cell test (EST) is one of the most promising models that allow the in vitro prediction of embryotoxicity, with one of its endpoints being bone tissue development. The present study was designed to describe three novel inexpensive endpoints to assess developmental osteotoxicity using the model compounds penicillin G (non-teratogenic), 5-fluorouracil (strong teratogen) and all-trans retinoic acid (bone teratogen). These three endpoints were: quantification of matrix incorporated calcium by (1) morphometric analysis and (2) measurement of calcium levels as well as (3) activity of alkaline phosphatase, an enzyme involved in matrix calcification. To evaluate our data, we have compared the concentration curves and resulting ID{sub 50}s of the new endpoints with mRNA expression for osteocalcin. Osteocalcin is an exclusive marker found only in mineralized tissues, is regulated upon compound treatment and reliably predicts the potential of a chemical entity acting as a bone teratogen. By comparing the new endpoints to quantitative expression of osteocalcin, which we previously identified as suitable to detect developmental osteotoxicity, we were ultimately able to illustrate IMAGE analysis and Ca{sup 2+} deposition assays as two reliable novel endpoints for the EST. This is of particular importance for routine industrial assessment of novel compounds as these two new endpoints may substitute previously used molecular read-out methods, which are often costly and time-consuming.

  2. Embryotoxicity assessment of developmental neurotoxicants using a neuronal endpoint in the embryonic stem cell test.

    PubMed

    Baek, Dae Hyun; Kim, Tae Gyun; Lim, Hwa Kyung; Kang, Jin Wook; Seong, Su Kyoung; Choi, Seung Eun; Lim, So Yun; Park, Sung Hee; Nam, Bong-hyun; Kim, Eun Hee; Kim, Mun Sin; Park, Kui Lea

    2012-08-01

    The embryonic stem cell test (EST) is a validated in vitro embryotoxicity test; however, as the inhibition of cardiac differentiation alone is used as a differentiation endpoint in the EST, it may not be a useful test to screen embryotoxic chemicals that affect the differentiation of noncardiac tissues. Previously, methylmercury (MeHg), cadmium and arsenic compounds, which are heavy metals that induce developmental neurotoxicity in vivo, were misclassified as nonembryotoxic with the EST. The aim of this study was to improve the EST to correctly screen such developmental neurotoxicants. We developed a neuronal endpoint (Tuj-1 ID₅₀) using flow cytometry analysis of Tuj-1-positive cells to screen developmental neurotoxicants (MeHg, valproic acid, sodium arsenate and sodium arsenite) correctly using an adherent monoculture differentiation method. Using Tuj-1 ID₅₀ in the EST instead of cardiac ID₅₀, all of the tested chemicals were classified as embryotoxic, while the negative controls were correctly classified as nonembryotoxic. To support the validity of Tuj-1 ID₅₀) , we compared the results from two experimenters who independently tested MeHg using our modified EST. An additional neuronal endpoint (MAP2 ID₅₀), obtained by analyzing the relative quantity of MAP2 mRNA, was used to classify the same chemicals. There were no significant differences in the three endpoint values of the two experimenters or in the classification results, except for isoniazid. In conclusion, our results indicate that Tuj-1 ID₅₀ can be used as a surrogate endpoint of the traditional EST to screen developmental neurotoxicants correctly and it can also be applied to other chemicals.

  3. Bayesian meta-analytical methods to incorporate multiple surrogate endpoints in drug development process.

    PubMed

    Bujkiewicz, Sylwia; Thompson, John R; Riley, Richard D; Abrams, Keith R

    2016-03-30

    A number of meta-analytical methods have been proposed that aim to evaluate surrogate endpoints. Bivariate meta-analytical methods can be used to predict the treatment effect for the final outcome from the treatment effect estimate measured on the surrogate endpoint while taking into account the uncertainty around the effect estimate for the surrogate endpoint. In this paper, extensions to multivariate models are developed aiming to include multiple surrogate endpoints with the potential benefit of reducing the uncertainty when making predictions. In this Bayesian multivariate meta-analytic framework, the between-study variability is modelled in a formulation of a product of normal univariate distributions. This formulation is particularly convenient for including multiple surrogate endpoints and flexible for modelling the outcomes which can be surrogate endpoints to the final outcome and potentially to one another. Two models are proposed, first, using an unstructured between-study covariance matrix by assuming the treatment effects on all outcomes are correlated and second, using a structured between-study covariance matrix by assuming treatment effects on some of the outcomes are conditionally independent. While the two models are developed for the summary data on a study level, the individual-level association is taken into account by the use of the Prentice's criteria (obtained from individual patient data) to inform the within study correlations in the models. The modelling techniques are investigated using an example in relapsing remitting multiple sclerosis where the disability worsening is the final outcome, while relapse rate and MRI lesions are potential surrogates to the disability progression.

  4. A Speech Endpoint Detection Algorithm Based on BP Neural Network and Multiple Features

    NASA Astrophysics Data System (ADS)

    Shi, Yong-Qiang; Li, Ru-Wei; Zhang, Shuang; Wang, Shuai; Yi, Xiao-Qun

    Focusing on a sharp decline in the performance of endpoint detection algorithm in a complicated noise environment, a new speech endpoint detection method based on BPNN (back propagation neural network) and multiple features is presented. Firstly, maximum of short-time autocorrelation function and spectrum variance of speech signals are extracted respectively. Secondly, these feature vectors as the input of BP neural network are trained and modeled and then the Genetic Algorithm is used to optimize the BP Neural Network. Finally, the signal's type is determined according to the output of Neural Network. The experiments show that the correct rate of this proposed algorithm is improved, because this method has better robustness and adaptability than algorithm based on maximum of short-time autocorrelation function or spectrum variance.

  5. A convenient formula for sample size calculations in clinical trials with multiple co-primary continuous endpoints.

    PubMed

    Sugimoto, Tomoyuki; Sozu, Takashi; Hamasaki, Toshimitsu

    2012-01-01

    The clinical efficacy of a new treatment may often be better evaluated by two or more co-primary endpoints. Recently, in pharmaceutical drug development, there has been increasing discussion regarding establishing statistically significant favorable results on more than one endpoint in comparisons between treatments, which is referred to as a problem of multiple co-primary endpoints. Several methods have been proposed for calculating the sample size required to design a trial with multiple co-primary correlated endpoints. However, because these methods require users to have considerable mathematical sophistication and knowledge of programming techniques, their application and spread may be restricted in practice. To improve the convenience of these methods, in this paper, we provide a useful formula with accompanying numerical tables for sample size calculations to design clinical trials with two treatments, where the efficacy of a new treatment is demonstrated on continuous co-primary endpoints. In addition, we provide some examples to illustrate the sample size calculations made using the formula. Using the formula and the tables, which can be read according to the patterns of correlations and effect size ratios expected in multiple co-primary endpoints, makes it convenient to evaluate the required sample size promptly.

  6. The Impact of Multiple Endpoint Dependency on "Q" and "I"[superscript 2] in Meta-Analysis

    ERIC Educational Resources Information Center

    Thompson, Christopher Glen; Becker, Betsy Jane

    2014-01-01

    A common assumption in meta-analysis is that effect sizes are independent. When correlated effect sizes are analyzed using traditional univariate techniques, this assumption is violated. This research assesses the impact of dependence arising from treatment-control studies with multiple endpoints on homogeneity measures "Q" and…

  7. Time-dependent endpoints as predictors of overall survival in multiple myeloma

    PubMed Central

    2013-01-01

    Background Supporting health care sector decisions using time-dependent endpoints (TDEs) such as time to progression (TTP), progression-free survival (PFS), and event-free survival (EFS) remains controversial. This study estimated the quantitative relationship between median TDE and median overall survival (OS) in multiple myeloma (MM) patients. Methods Studies (excluding allogeneic transplantation) published from 1970 to 2011 were systematically searched (PubMed). The nonparametric Spearman’s rank correlation coefficient measured the association between median TDE and OS. The quantitative relationship between TDEs and OS was estimated with a two-step approach to a simultaneous Tobit model. Results We identified 153 studies: 230 treatment arms, 22,696 patients and mean study duration of 3.8 years. Mean of median TDEs was 22.5 months and median OS was 39.1 months. Correlation coefficients of median TTP, PFS, and EFS with median OS were 0.51 (P = 0.003), 0.75 (P < 0.0001), and 0.84 (P < 0.0001), respectively. We estimate a 2.5 month (95% confidence interval, 1.7–3.2) increase in median OS for each additional month reported for median TDEs. There was no evidence that this relationship differed by type of surrogate. Conclusion TDEs predict OS in MM patients; this relationship may be valuable in clinical trial design, drug comparisons, and economic evaluation. PMID:23497363

  8. Analyzing multiple endpoints in a confirmatory randomized clinical trial-an approach that addresses stratification, missing values, baseline imbalance and multiplicity for strictly ordinal outcomes.

    PubMed

    Sun, Hengrui; Kawaguchi, Atsushi; Koch, Gary

    2017-03-01

    Confirmatory randomized clinical trials with a stratified design may have ordinal response outcomes, ie, either ordered categories or continuous determinations that are not compatible with an interval scale. Also, multiple endpoints are often collected when 1 single endpoint does not represent the overall efficacy of the treatment. In addition, random baseline imbalances and missing values can add another layer of difficulty in the analysis plan. Therefore, the development of an approach that provides a consolidated strategy to all issues collectively is essential. For a real case example that is from a clinical trial comparing a test treatment and a control for the pain management for patients with osteoarthritis, which has all aforementioned issues, multivariate Mann-Whitney estimators with stratification adjustment are applicable to the strictly ordinal responses with stratified design. Randomization based nonparametric analysis of covariance is applied to account for the possible baseline imbalances. Several approaches that handle missing values are provided. A global test followed by a closed testing procedure controls the family wise error rate in the strong sense for the analysis of multiple endpoints. Four outcomes indicating joint pain, stiffness, and functional status were analyzed collectively and also individually through the procedures. Treatment efficacy was observed in the combined endpoint as well as in the individual endpoints. The proposed approach is effective in addressing the aforementioned problems simultaneously and straightforward to implement.

  9. Evaluation and QSAR modeling on multiple endpoints of estrogen activity based on different bioassays.

    PubMed

    Liu, Huanxiang; Papa, Ester; Gramatica, Paola

    2008-02-01

    There is a great need for an effective means of rapidly assessing endocrine-disrupting activity, especially estrogen-simulating activity, due to the large number of chemicals that have serious adverse effects on the environment. Many approaches using a variety of biological screening assays are used to identify endocrine disrupting chemicals. The present investigation analyzes the consistency and peculiarity of information from different experimental assays collected from a literature survey, by studying the correlation of the different endpoints. In addition, the activity values of more widely used selected bioassays have been combined by principle components analysis (PCA) to build one cumulative endpoint, the estrogen activity index (EAI), for priority setting to identify chemicals most likely possessing estrogen activity for early entry into screening. This index was then modeled using only a few theoretical molecular descriptors. The constructed MLR-QSAR model has been statistically validated for its predictive power, and can be proposed as a preliminary evaluative method to screen/prioritize estrogens according to their integrated estrogen activity, just starting from molecular structure.

  10. Sensitive embryonic endpoints with in ovo treatment for detecting androgenic and anti-androgenic effects of chemicals in Japanese quail (Coturnix japonica).

    PubMed

    Utsumi, T; Yoshimura, Y

    2009-05-01

    The aim of the current study was to establish the sensitive embryonic endpoints and a test system for detecting androgenic and anti-androgenic potential of chemicals using an in ovo treatment assay in Japanese quail. In ovo injection with 0 to 75 microg of cyproterone acetate (CA) was performed on d 12 of incubation, followed by 0 to 300 microg of testosterone propionate (TP) injection on d 13 and histological examination on d 16. Experimental groups were composed of control (twice injected corn oil injections; on d 12 and d 13, respectively), TP-L (corn oil and 30 microg of TP), TP-H (corn oil and 300 microg of TP), CA-L + TP-H (7.5 microg of CA and 300 microg of TP), and CA-H+ TP-H (75 microg of CA and 300 microg of TP). Histological examinations were performed in the cloacal gland, liver, kidneys, testes, ovaries, uropygial gland, and bursa of Fabricius. The cloacal gland consists of many glandular units (tubular gland structures) lined by developed or undeveloped glandular cells. The developed glandular cells were tall in height and contained mucous substance in the cytoplasm. The glandular units containing developed glandular cells were termed as the developing glandular units. The developing glandular units were observed in the TP-H, CA-L + TP-H, and CA-H + TP-H groups, but not in the control and TP-L groups, in both males and females. The ratio of developing glandular units to the total number of glandular units was significantly greater in TP-H than control and TP-L and was significantly decreased in CA-L + TP-H and CA-H + TP-H compared with TP-H in both males and females. The ratio was significantly greater in males than in females of CA-L + TP-H. No significant structural differences were observed in the other organs. These results suggest that the most sensitive endpoint of androgenic effects in quail embryo appeared in the cloacal glands. The ratio of the developing glandular units could be used for evaluation of androgenic and anti-androgenic effects

  11. Nonperturbative landscape of the Mott-Hubbard transition: Multiple divergence lines around the critical endpoint

    NASA Astrophysics Data System (ADS)

    Schäfer, T.; Ciuchi, S.; Wallerberger, M.; Thunström, P.; Gunnarsson, O.; Sangiovanni, G.; Rohringer, G.; Toschi, A.

    2016-12-01

    We analyze the highly nonperturbative regime surrounding the Mott-Hubbard metal-to-insulator transition (MIT) by means of dynamical mean field theory (DMFT) calculations at the two-particle level. By extending the results of Schäfer et al. [Phys. Rev. Lett. 110, 246405 (2013), 10.1103/PhysRevLett.110.246405] we show the existence of infinitely many lines in the phase diagram of the Hubbard model where the local Bethe-Salpeter equations, and the related irreducible vertex functions, become singular in the charge as well as the particle-particle channel. By comparing our numerical data for the Hubbard model with analytical calculations for exactly solvable systems of increasing complexity [disordered binary mixture (BM), Falicov-Kimball (FK), and atomic limit (AL)], we have (i) identified two different kinds of divergence lines; (ii) classified them in terms of the frequency structure of the associated singular eigenvectors; and (iii) investigated their relation to the emergence of multiple branches in the Luttinger-Ward functional. In this way, we could distinguish the situations where the multiple divergences simply reflect the emergence of an underlying, single energy scale ν* below which perturbation theory is no longer applicable, from those where the breakdown of perturbation theory affects, not trivially, different energy regimes. Finally, we discuss the implications of our results on the theoretical understanding of the nonperturbative physics around the MIT and for future developments of many-body algorithms applicable in this regime.

  12. A marginal rank-based inverse normal transformation approach to comparing multiple clinical trial endpoints.

    PubMed

    Cai, Xiaoyu; Li, Huiyun; Liu, Aiyi

    2016-08-30

    The increase in incidence of obesity and chronic diseases and their health care costs have raised the importance of quality diet on the health policy agendas. The healthy eating index is an important measure for diet quality which consists of 12 components derived from ratios of dependent variables with distributions hard to specify, measurement errors and excessive zero observations difficult to model parametrically. Hypothesis testing involving data of such nature poses challenges because the widely used multiple comparison procedures such as Hotelling's T(2) test and Bonferroni correction may suffer from substantial loss of efficiency. We propose a marginal rank-based inverse normal transformation approach to normalizing the marginal distribution of the data before employing a multivariate test procedure. Extensive simulation was conducted to demonstrate the ability of the proposed approach to adequately control the type I error rate as well as increase the power of the test, with data particularly from non-symmetric or heavy-tailed distributions. The methods are exemplified with data from a dietary intervention study for type I diabetic children. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

  13. Analyzing multiple endpoints in clinical trials of pain treatments: IMMPACT recommendations. Initiative on Methods, Measurement, and Pain Assessment in Clinical Trials.

    PubMed

    Turk, Dennis C; Dworkin, Robert H; McDermott, Michael P; Bellamy, Nicholas; Burke, Laurie B; Chandler, Julie M; Cleeland, Charles S; Cowan, Penney; Dimitrova, Rozalina; Farrar, John T; Hertz, Sharon; Heyse, Joseph F; Iyengar, Smriti; Jadad, Alejandro R; Jay, Gary W; Jermano, John A; Katz, Nathaniel P; Manning, Donald C; Martin, Susan; Max, Mitchell B; McGrath, Patrick; McQuay, Henry J; Quessy, Steve; Rappaport, Bob A; Revicki, Dennis A; Rothman, Margaret; Stauffer, Joseph W; Svensson, Ola; White, Richard E; Witter, James

    2008-10-31

    The increasing complexity of randomized clinical trials and the practice of obtaining a wide variety of measurements from study participants have made the consideration of multiple endpoints a critically important issue in the design, analysis, and interpretation of clinical trials. Failure to consider important outcomes can limit the validity and utility of clinical trials; specifying multiple endpoints for the evaluation of treatment efficacy, however, can increase the rate of false positive conclusions about the efficacy of a treatment. We describe the use of multiple endpoints in the design, analysis, and interpretation of pain clinical trials, and review available strategies and methods for addressing multiplicity. To decrease the probability of a Type I error (i.e., the likelihood of obtaining statistically significant results by chance) in pain clinical trials, the use of gatekeeping procedures and other methods that correct for multiple analyses is recommended when a single primary endpoint does not adequately reflect the overall benefits of treatment. We emphasize the importance of specifying in advance the outcomes and clinical decision rule that will serve as the basis for determining that a treatment is efficacious and the methods that will be used to control the overall Type I error rate.

  14. Statistical methods for down-selection of treatment regimens based on multiple endpoints, with application to HIV vaccine trials.

    PubMed

    Huang, Ying; Gilbert, Peter B; Fu, Rong; Janes, Holly

    2016-09-20

    SummaryBiomarker endpoints measuring vaccine-induced immune responses are essential to HIV vaccine development because of their potential to predict the effect of a vaccine in preventing HIV infection. A vaccine's immune response profile observed in phase I immunogenicity studies is a key factor in determining whether it is advanced for further study in phase II and III efficacy trials. The multiplicity of immune variables and scientific uncertainty in their relative importance, however, pose great challenges to the development of formal algorithms for selecting vaccines to study further. Motivated by the practical need to identify a set of promising vaccines from a pool of candidate regimens for inclusion in an upcoming HIV vaccine efficacy trial, we propose a new statistical framework for the selection of vaccine regimens based on their immune response profile. In particular, we propose superiority and non-redundancy criteria to be achieved in down-selection, and develop novel statistical algorithms that integrate hypothesis testing and ranking for selecting vaccine regimens satisfying these criteria. Performance of the proposed selection algorithms are evaluated through extensive numerical studies. We demonstrate the application of the proposed methods through the comparison of immune responses between several HIV vaccine regimens. The methods are applicable to general down-selection applications in clinical trials.

  15. Generative models: Human embryonic stem cells and multiple modeling relations.

    PubMed

    Fagan, Melinda Bonnie

    2016-04-01

    Model organisms are at once scientific models and concrete living things. It is widely assumed by philosophers of science that (1) model organisms function much like other kinds of models, and (2) that insofar as their scientific role is distinctive, it is in virtue of representing a wide range of biological species and providing a basis for generalizations about those targets. This paper uses the case of human embryonic stem cells (hESC) to challenge both assumptions. I first argue that hESC can be considered model organisms, analogous to classic examples such as Escherichia coli and Drosophila melanogaster. I then discuss four contrasts between the epistemic role of hESC in practice, and the assumptions about model organisms noted above. These contrasts motivate an alternative view of model organisms as a network of systems related constructively and developmentally to one another. I conclude by relating this result to other accounts of model organisms in recent philosophy of science.

  16. Transplantation of Human Embryonic Stem Cells in Patients with Multiple Sclerosis and Lyme Disease

    PubMed Central

    Shroff, Geeta

    2016-01-01

    Case series Patient: Male, 42 • Female, 30 Final Diagnosis: Human embryonic stem cells showed good therapeutic potential for treatment of multiple sclerosis with lyme disease Symptoms: Fatigue • weakness in limbs Medication: — Clinical Procedure: Human embryonic stem cells transplantation Specialty: Transplantology Objective: Rare disease Background: Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease in which the myelin sheath of nerve cells is damaged. It can cause delayed neurologic symptoms similar to those seen in Lyme disease (LD) patients. Thymus derived T-cells (myelin reactive) migrate to the blood brain barrier and stimulate an inflammatory cascade in the central nervous system. Cell based therapies play an important role in treating neurological diseases such as MS and LD. Case Report: Human embryonic stem cell (hESC) therapy was used to treat two patients with both MS and LD. The hESCs were administered via different routes including intramuscular, intravenous, and supplemental routes (e.g., deep spinal, caudal, intercostal through eye drops) to regenerate the injured cells. Both the patients showed remarkable improvement in their functional skills, overall stamina, cognitive abilities, and muscle strength. Furthermore, the improvement in the patients’ conditions were assessed by magnetic resonance tractography and single photon emission computed tomography (SPECT). Conclusions: Therapy with hESCs might emerge as an effective and safe treatment for patients with both MS and LD. Well-designed clinical trials and follow-up studies are needed to prove the long-term efficacy and safety of hESC therapy in the treatment of patients with MS and LD. PMID:27956736

  17. An evaluation of behavioural endpoints: The pharmaceutical pollutant fluoxetine decreases aggression across multiple contexts in round goby (Neogobius melanostomus).

    PubMed

    McCallum, Erin S; Bose, Aneesh P H; Warriner, Theresa R; Balshine, Sigal

    2017-05-01

    Fluoxetine (Prozac™) is designed to alter human behaviour; however, because many physiological pathways are conserved across vertebrates, this drug may affect the behaviour of fish living in fluoxetine-polluted environments. Although a number of studies have used behaviour to document the sub-lethal effects of fluoxetine, the repeatability of these effects across experiments, across behavioural contexts, and over different exposure durations are rarely considered. Here, we conducted two experiments and assessed how fluoxetine exposure affected a range of fitness-related behaviours in wild round goby (Neogobius melanostomus). We found that fluoxetine impacts round goby behaviour at high (40 μg/l) doses, but not at environmentally relevant low doses (1 μg/l). In both experiments, an acute 3-day exposure to fluoxetine reduced round goby aggression in multiple behavioural contexts, but had no detectable effect on overall activity or social affiliative behaviour. While a chronic 28-day exposure to fluoxetine exposure still reduced aggression, this reduction was only detectable in one behavioural context. Our findings demonstrate the importance of repeated behavioural testing (both between and within experiments) and contribute to a growing body of literature evaluating the effects of fluoxetine and other pharmaceuticals on animal behaviour.

  18. Analyzing the "correct" endpoint.

    PubMed

    Atherton, Pamela J; Novotny, Paul J; Tan, Angelina D

    2006-01-01

    The choice of QOL endpoints for a study should be based on which score will most likely change if the treatment is favorable. How the QOL change is calculated should be based on the expected amount of missing data, how many time points data will be collected, and whether extreme outliers in the scores impact results. The study should have sufficient power to detect a meaningful difference between arms (typically 10 points on a 0-100 point scale) in the chosen QOL endpoint. At the conclusion of a study, several secondary endpoints can be analyzed which can provide additional information and confirm primary endpoint results.

  19. Multiple telencephalic and extratelencephalic embryonic domains contribute neurons to the medial extended amygdala.

    PubMed

    Bupesh, Munisamy; Legaz, Isabel; Abellán, Antonio; Medina, Loreta

    2011-06-01

    Dysfunctions in emotional control and social behavior are behind human neuropsychiatric disorders, some of which are associated with an alteration of amygdalar development. The medial extended amygdala is a key telencephalic center for control of social behavior, but very little is known about its development. We used in vitro migration assays for analyzing the origin of the neurons of the medial extended amygdala in mouse embryos (E13.5-E16.5). We compared the migration assays with immunofluorescence/immunohistochemistry for calbindin and radial glial fibers and with mRNA expression of several genetic markers of distinct forebrain subdivisions. We provide experimental evidence for multiple embryonic origins of the principal neurons of the medial extended amygdala. In particular, we provide novel evidence indicating that a major part of the neurons derives from a caudoventral pallidal subdivision (previously called or included as part of the anterior peduncular area), forming a cell corridor with similar molecular features (expression of Lhx6 and calbindin), connectivity, and function, which relates to reproductive behavior. We also provide novel experimental evidence indicating that the ventral pallium produces some neurons for the medial amygdala, which correlates with data from Lhx9 expression. Our results also confirm that some neurons of the medial extended amygdala originate in the preoptic area (our results indicate that these cells specifically originate in its commissural subdivision) and the supraoptoparaventricular domain of the hypothalamus. Our study helps to set up the foundations for a better understanding of medial amygdalar control of behavior in normal and abnormal conditions.

  20. Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways

    PubMed Central

    Gruber, Andreas J.; Grandy, William A.; Balwierz, Piotr J.; Dimitrova, Yoana A.; Pachkov, Mikhail; Ciaudo, Constance; van Nimwegen, Erik; Zavolan, Mihaela

    2014-01-01

    The findings that microRNAs (miRNAs) are essential for early development in many species and that embryonic miRNAs can reprogram somatic cells into induced pluripotent stem cells suggest that these miRNAs act directly on transcriptional and chromatin regulators of pluripotency. To elucidate the transcription regulatory networks immediately downstream of embryonic miRNAs, we extended the motif activity response analysis approach that infers the regulatory impact of both transcription factors (TFs) and miRNAs from genome-wide expression states. Applying this approach to multiple experimental data sets generated from mouse embryonic stem cells (ESCs) that did or did not express miRNAs of the ESC-specific miR-290-295 cluster, we identified multiple TFs that are direct miRNA targets, some of which are known to be active during cell differentiation. Our results provide new insights into the transcription regulatory network downstream of ESC-specific miRNAs, indicating that these miRNAs act on cell cycle and chromatin regulators at several levels and downregulate TFs that are involved in the innate immune response. PMID:25030899

  1. Mutations in the embryonal subunit of the acetylcholine receptor (CHRNG) cause lethal and Escobar variants of multiple pterygium syndrome.

    PubMed

    Morgan, Neil V; Brueton, Louise A; Cox, Phillip; Greally, Marie T; Tolmie, John; Pasha, Shanaz; Aligianis, Irene A; van Bokhoven, Hans; Marton, Tamas; Al-Gazali, Lihadh; Morton, Jenny E V; Oley, Christine; Johnson, Colin A; Trembath, Richard C; Brunner, Han G; Maher, Eamonn R

    2006-08-01

    Multiple pterygium syndromes (MPSs) comprise a group of multiple-congenital-anomaly disorders characterized by webbing (pterygia) of the neck, elbows, and/or knees and joint contractures (arthrogryposis). In addition, a variety of developmental defects (e.g., vertebral anomalies) may occur. MPSs are phenotypically and genetically heterogeneous but are traditionally divided into prenatally lethal and nonlethal (Escobar) types. To elucidate the pathogenesis of MPS, we undertook a genomewide linkage scan of a large consanguineous family and mapped a locus to 2q36-37. We then identified germline-inactivating mutations in the embryonal acetylcholine receptor gamma subunit (CHRNG) in families with both lethal and nonlethal MPSs. These findings extend the role of acetylcholine receptor dysfunction in human disease and provide new insights into the pathogenesis and management of fetal akinesia syndromes.

  2. Scenario-targeted toxicity assessment through multiple endpoint bioassays in a soil posing unacceptable environmental risk according to regulatory screening values.

    PubMed

    Rodriguez-Ruiz, A; Etxebarria, J; Boatti, L; Marigómez, I

    2015-09-01

    Lanestosa is a chronically polluted site (derelict mine) where the soil (Lanestosa (LA) soil) exceeds screening values (SVs) of regulatory policies in force (Basque Country; Europe) for Zn, Pb and Cd. A scenario-targeted toxicity assessment was carried out on the basis of a multi-endpoint bioassay approach. Acute and chronic toxicity bioassays were conducted with selected test species (Vibrio fischeri, Dictyostelium discoideum, Lactuca sativa, Raphanus sativus and Eisenia fetida) in combination with chemical analysis of soils and elutriates and with bioaccumulation studies in earthworms. Besides, the toxicity profile was compared with that of the mine runoff (RO) soil and of a fresh artificially polluted soil (LAAPS) resembling LA soil pollutant profile. Extractability studies in LA soil revealed that Pb, Zn and Cd were highly available for exchange and/or release into the environment. Indeed, Pb and Zn were accumulated in earthworms and LA soil resulted to be toxic. Soil respiration, V. fischeri, vegetative and developmental cycles of D. discoideum and survival and juvenile production of E. fetida were severely affected. These results confirmed that LA soil had unacceptable environmental risk and demanded intervention. In contrast, although Pb and Zn concentrations in RO soil revealed also unacceptable risk, both metal extractability and toxicity were much lower than in LA soil. Thus, within the polluted site, the need for intervention varied between areas that posed dissimilar risk. Besides, since LAAPS, with a high exchangeable metal fraction, was the most toxic, ageing under in situ natural conditions seemingly contributed to attenuate LA soil risk. As a whole, combining multi-endpoint bioassays with scenario-targeted analysis (including leaching and ageing) provides reliable risk assessment in soils posing unacceptable environmental risk according to SVs, which is useful to optimise the required intervention measures.

  3. CD44 in Differentiated Embryonic Stem Cells: Surface Expression and Transcripts Encoding Multiple Variants

    PubMed Central

    Haegel, Hélène; Dierich, Andrée

    1994-01-01

    Expression of the surface-adhesion molecule CD44 was investigated during the in vitro differentiation of the embryonic stem (ES) cell line D3. By immunofluorescence analysis, totipotent, undifferentiated ES cells did not show surface expression of CD44, although two transcripts of approximately 1.6 and 3.3 kb were detected on Northern blots. Following 1 week of differentiation in either suspension or substrate-attached cultures, CD44 appeared on the surface of some D3 cells, and synthesis of an additional 4.5 kb mRNA species was detected on Northern blots. At this stage, at least three distinct transcripts encoding CD44 variants were induced within the cultures, resulting from alternative splicing of additional exons in the variable domains of CD44. From PCR analysis, they all appeared to contain the variable exon v10, and two of them in addition contained v6. Taken together, these results suggest that CD44 may play a role in cell migration and adhesion in the early development of the mouse embryo. PMID:7542511

  4. Analysis of phase II methodologies for single-arm clinical trials with multiple endpoints in rare cancers: An example in Ewing's sarcoma.

    PubMed

    Dutton, P; Love, S B; Billingham, L; Hassan, A B

    2016-09-01

    Trials run in either rare diseases, such as rare cancers, or rare sub-populations of common diseases are challenging in terms of identifying, recruiting and treating sufficient patients in a sensible period. Treatments for rare diseases are often designed for other disease areas and then later proposed as possible treatments for the rare disease after initial phase I testing is complete. To ensure the trial is in the best interests of the patient participants, frequent interim analyses are needed to force the trial to stop promptly if the treatment is futile or toxic. These non-definitive phase II trials should also be stopped for efficacy to accelerate research progress if the treatment proves to be particularly promising. In this paper, we review frequentist and Bayesian methods that have been adapted to incorporate two binary endpoints and frequent interim analyses. The Eurosarc Trial of Linsitinib in advanced Ewing Sarcoma (LINES) is used as a motivating example and provides a suitable platform to compare these approaches. The Bayesian approach provides greater design flexibility, but does not provide additional value over the frequentist approaches in a single trial setting when the prior is non-informative. However, Bayesian designs are able to borrow from any previous experience, using prior information to improve efficiency.

  5. Analysis of multiple end points in consumer research in support of switching drugs from prescription to over-the-counter status: the concept of end-point hierarchies.

    PubMed

    Brass, E P; Shay, L E; Leonard-Segal, A

    2009-04-01

    Clinical and regulatory decision making concerning over-the-counter (OTC) drugs requires research designed to understand how consumers will self-manage treatment using the candidate OTC drug. Consumer research for an OTC drug may include studies of label comprehension, self-selection, and actual use. Definition and analysis of end points for these trials have varied in the absence of consensus on optimal approaches. Research programs should prospectively prioritize the importance of label messages based on their roles in the safe and effective use of the drug. The assessment of messages for which failure to heed warnings will expose the consumer to increased risk or clinically relevant treatment failure should receive the highest priority as study end points. Based on the consequences of unheeded warnings, message-specific targets for appropriate response rates can be predefined. This prospective, hierarchical approach to end-point definition, combined with prespecification of targeted correct-response rates, has the potential to increase the scientific rigor and regulatory utility of these important research studies.

  6. Embryonic stem cells improve cardiac function in Doxorubicin-induced cardiomyopathy mediated through multiple mechanisms.

    PubMed

    Singla, Dinender K; Ahmed, Aisha; Singla, Reetu; Yan, Binbin

    2012-01-01

    Doxorubicin (DOX) is an effective antineoplastic agent used for the treatment of a variety of cancers. Unfortunately, its use is limited as this drug induces cardiotoxicity and heart failure as a side effect. There is no report that describes whether transplanted embryonic stem (ES) cells or their conditioned medium (CM) in DOX-induced cardiomyopathy (DIC) can repair and regenerate myocardium. Therefore, we transplanted ES cells or CM in DIC to examine apoptosis, fibrosis, cytoplasmic vacuolization, and myofibrillar loss and their associated Akt and ERK pathway. Moreover, we also determined activation of endogenous c-kit(+ve) cardiac stem cells (CSCs), levels of HGF and IGF-1, growth factors required for c-kit cell activation, and their differentiation into cardiac myocytes, which also contributes in cardiac regeneration and improved heart function. We generated DIC in C57Bl/6 mice (cumulative dose of DOX 12 mg/kg body weight, IP), and animals were treated with ES cells, CM, or cell culture medium in controls. Two weeks post-DIC, ES cells or CM transplanted hearts showed a significant (p < 0.05) decrease in cardiac apoptotic nuclei and their regulation with Akt and ERK pathway. Cardiac fibrosis observed in the ES cell or CM groups was significantly less compared with DOX and cell culture medium groups (p < 0.05). Next, cytoplasmic vacuolization and myofibrillar loss was reduced (p < 0.05) following treatment with ES cells or CM. Moreover, our data also demonstrated increased levels of c-kit(+ve) CSCs in ES cells or CM hearts and differentiated cardiac myocytes from these CSCs, suggesting endogenous cardiac regeneration. Importantly, the levels of HFG and IGF-1 were significantly increased in ES cells or CM transplanted hearts. In conclusion, we reported that transplanted ES cells or CM in DIC hearts significantly decreases various adverse pathological mechanisms as well as enhances cardiac regeneration that effectively contributes to improved heart function.

  7. Basonuclin 2 has a function in the multiplication of embryonic craniofacial mesenchymal cells and is orthologous to disco proteins

    PubMed Central

    Vanhoutteghem, Amandine; Maciejewski-Duval, Anna; Bouche, Cyril; Delhomme, Brigitte; Hervé, Françoise; Daubigney, Fabrice; Soubigou, Guillaume; Araki, Masatake; Araki, Kimi; Yamamura, Ken-ichi; Djian, Philippe

    2009-01-01

    Basonuclin 2 is a recently discovered zinc finger protein of unknown function. Its paralog, basonuclin 1, is associated with the ability of keratinocytes to multiply. The basonuclin zinc fingers are closely related to those of the Drosophila proteins disco and discorelated, but the relation between disco proteins and basonuclins has remained elusive because the function of the disco proteins in larval head development seems to have no relation to that of basonuclin 1 and because the amino acid sequence of disco, apart from the zinc fingers, also has no similarity to that of the basonuclins. We have generated mice lacking basonuclin 2. These mice die within 24 h of birth with a cleft palate and abnormalities of craniofacial bones and tongue. In the embryonic head, expression of the basonuclin 2 gene is restricted to mesenchymal cells in the palate, at the periphery of the tongue, and in the mesenchymal sheaths that surround the brain and the osteocartilagineous structures. In late embryos, the rate of multiplication of these mesenchymal cells is greatly diminished. Therefore, basonuclin 2 is essential for the multiplication of craniofacial mesenchymal cells during embryogenesis. Non-Drosophila insect databases available since 2008 reveal that the basonuclins and the disco proteins share much more extensive sequence and gene structure similarity than noted when only Drosophila sequences were examined. We conclude that basonuclin 2 is both structurally and functionally the vertebrate ortholog of the disco proteins. We also note the possibility that some human craniofacial abnormalities are due to a lack of basonuclin 2. PMID:19706529

  8. Statistical analysis of histopathological endpoints.

    PubMed

    Green, John W; Springer, Timothy A; Saulnier, Amy N; Swintek, Joe

    2014-05-01

    Histopathological assessments of fish from aquatic ecotoxicology studies are being performed with increasing frequency. Aquatic ecotoxicology studies performed for submission to regulatory agencies are usually conducted with multiple subjects (e.g., fish) in each of multiple vessels (replicates) within a water control and within each of several concentrations of a test substance. A number of histopathological endpoints are evaluated in each fish, and a severity score is generally recorded for each endpoint. The severity scores are often recorded using a nonquantitative scale of 0 to 4, with 0 indicating no effect, 1 indicating minimal effect, through 4 for severe effect. Statistical methods often used to analyze these scores suffer from several shortcomings: computing average scores as though scores were quantitative values, considering only the frequency of abnormality while ignoring severity, ignoring any concentration-response trend, and ignoring the possible correlation between responses of individuals within test vessels. A new test, the Rao-Scott Cochran-Armitage by Slices (RSCABS), is proposed that incorporates the replicate vessel experimental design and the biological expectation that the severity of the effect tends to increase with increasing doses or concentrations, while retaining the individual subject scores and taking into account the severity as well as frequency of scores. A power simulation and examples demonstrate the performance of the test. R-based software has been developed to carry out this test and is available free of charge at www.epa.gov/med/Prods_Pubs/rscabs.htm. The SAS-based RSCABS software is available from the first and third authors.

  9. The onion skin-like organization of the septum arises from multiple embryonic origins to form multiple adult neuronal fates.

    PubMed

    Wei, B; Huang, Z; He, S; Sun, C; You, Y; Liu, F; Yang, Z

    2012-10-11

    In the past several decades, tremendous progress has been achieved through developmental studies of the central nervous system structures such as the cerebral cortex. The septum, which receives reciprocal connections from a variety of brain structures, contains diverse projection neurons but few interneurons. However, the mechanisms underlying its development remain poorly understood. Here we show that the septum is organized into an onion skin-like structure composed of five groups of neurons. These neurons are parvalbumin, choline acetyltransferase, neuronal nitric oxide synthase, calretinin and calbindin immunoreactive. Using the BrdU birth-dating method, we found that these five groups of neurons in the septum are grossly generated following an outside-in pattern. Interestingly, the distinct molecular identities of these neuronal subtypes correspond to their heterogeneous subpallial origins. Using three specific transgenic mouse lines and focal in utero electroporation of Cre-reporter plasmid, we showed that septal neurons originate from not only local progenitor regions but also neighboring progenitor regions including the medial ganglionic eminence and preoptic area. Thus, the neuronal diversity of the septum is achieved through both temporal and spatial control. Our results also suggest that multiple neuronal subtypes arrive to the septum through both radial and tangential migration. Based on these findings, we proposed a novel developmental model involving multiple spatial-temporal origins of septal neurons. This study presents new perspectives for comprehensively exploring septal functions in brain circuits.

  10. A U.S. Human Well-being Index (HWBI) for Multiple Scales: Linking Services Provisioning to Human Well-being Endpoints (2000-2010)

    EPA Science Inventory

    objective of this report is to characterize well-being at multiple scales in order to evaluate the relationship of service flows in terms of sustainable well-being. The HWBI results presented represent snapshot assessments for the 2000-2010 time period. Based on the spatial and t...

  11. Ordered kinematic endpoints for 5-body cascade decays

    NASA Astrophysics Data System (ADS)

    Klimek, Matthew D.

    2016-12-01

    We present expressions for the kinematic endpoints of 5-body cascade decay chains proceeding through all possible combinations of 2-body and 3-body decays, with one stable invisible particle in the final decay stage. When an invariant mass can be formed in multiple ways by choosing different final state particles from a common vertex, we introduce techniques for finding the sub-leading endpoints for all indistinguishable versions of the invariant mass. In contrast to short decay chains, where sub-leading endpoints are linearly related to the leading endpoints, we find that in 5-body decays, they provide additional independent constraints on the mass spectrum.

  12. A synthetic small molecule for rapid induction of multiple pluripotency genes in mouse embryonic fibroblasts

    NASA Astrophysics Data System (ADS)

    Pandian, Ganesh N.; Nakano, Yusuke; Sato, Shinsuke; Morinaga, Hironobu; Bando, Toshikazu; Nagase, Hiroki; Sugiyama, Hiroshi

    2012-07-01

    Cellular reprogramming involves profound alterations in genome-wide gene expression that is precisely controlled by a hypothetical epigenetic code. Small molecules have been shown to artificially induce epigenetic modifications in a sequence independent manner. Recently, we showed that specific DNA binding hairpin pyrrole-imidazole polyamides (PIPs) could be conjugated with chromatin modifying histone deacetylase inhibitors like SAHA to epigenetically activate certain pluripotent genes in mouse fibroblasts. In our steadfast progress to improve the efficiency of SAHA-PIPs, we identified a novel compound termed, δ that could dramatically induce the endogenous expression of Oct-3/4 and Nanog. Genome-wide gene analysis suggests that in just 24 h and at nM concentration, δ induced multiple pluripotency-associated genes including Rex1 and Cdh1 by more than ten-fold. δ treated MEFs also rapidly overcame the rate-limiting step of epithelial transition in cellular reprogramming by switching ``'' the complex transcriptional gene network.

  13. Evolution of the cephalopod head complex by assembly of multiple molluscan body parts: Evidence from Nautilus embryonic development.

    PubMed

    Shigeno, Shuichi; Sasaki, Takenori; Moritaki, Takeya; Kasugai, Takashi; Vecchione, Michael; Agata, Kiyokazu

    2008-01-01

    Cephalopod head parts are among the most complex occurring in all invertebrates. Hypotheses for the evolutionary process require a drastic body-plan transition in relation to the life-style changes from benthos to active nekton. Determining these transitions, however, has been elusive because of scarcity of fossil records of soft tissues and lack of some of the early developmental stages of the basal species. Here we report the first embryological evidence in the nautiloid cephalopod Nautilus pompilius for the morphological development of the head complex by a unique assembly of multiple archetypical molluscan body parts. Using a specialized aquarium system, we successfully obtained a series of developmental stages that enabled us to test previous controversial scenarios. Our results demonstrate that the embryonic organs exhibit body plans that are primarily bilateral and antero-posteriorly elongated at stereotyped positions. The distinct cephalic compartment, foot, brain cords, mantle, and shell resemble the body plans of monoplacophorans and basal gastropods. The numerous digital tentacles of Nautilus develop from simple serial and spatially-patterned bud-like anlagen along the anterior-posterior axis, indicating that origins of digital tentacles or arms of all other cephalopods develop not from the head but from the foot. In middle and late embryos, the primary body plans largely change to those of juveniles or adults, and finally form a "head" complex assembled by anlagen of the foot, cephalic hood, collar, hyponome (funnel), and the foot-derived epidermal covers. We suggest that extensions of the collar-funnel compartment and free epidermal folds derived from multiple topological foot regions may play an important role in forming the head complex, which is thought to be an important feature during the body plan transition.

  14. Gli activity is critical at multiple stages of embryonic mammary and nipple development.

    PubMed

    Chandramouli, Anupama; Hatsell, Sarah J; Pinderhughes, Alicia; Koetz, Lisa; Cowin, Pamela

    2013-01-01

    Gli3 is a transcriptional regulator of Hedgehog (Hh) signaling that functions as a repressor (Gli3(R)) or activator (Gli3(A)) depending upon cellular context. Previously, we have shown that Gli3(R) is required for the formation of mammary placodes #3 and #5. Here, we report that this early loss of Gli3 results in abnormal patterning of two critical regulators: Bmp4 and Tbx3, within the presumptive mammary rudiment (MR) #3 zone. We also show that Gli3 loss leads to failure to maintain mammary mesenchyme specification and loss of epithelial Wnt signaling, which impairs the later development of remaining MRs: MR#2 showed profound evagination and ectopic hairs formed within the presumptive areola; MR#4 showed mild invagination defects and males showed inappropriate retention of mammary buds in Gli3(xt/xt) mice. Importantly, mice genetically manipulated to misactivate Hh signaling displayed the same phenotypic spectrum demonstrating that the repressor function of Gli3(R) is essential during multiple stages of mammary development. In contrast, positive Hh signaling occurs during nipple development in a mesenchymal cuff around the lactiferous duct and in muscle cells of the nipple sphincter. Collectively, these data show that repression of Hh signaling by Gli3(R) is critical for early placodal patterning and later mammary mesenchyme specification whereas positive Hh signaling occurs during nipple development.

  15. A multiple endpoint analysis of the effects of chronic exposure to sediment contaminated with Deepwater Horizon oil on juvenile Southern flounder and their associated microbiomes.

    PubMed

    Brown-Peterson, Nancy J; Krasnec, Michelle; Takeshita, Ryan; Ryan, Caitlin N; Griffitt, Kimberly J; Lay, Claire; Mayer, Gregory D; Bayha, Keith M; Hawkins, William E; Lipton, Ian; Morris, Jeffrey; Griffitt, Robert J

    2015-08-01

    Exposure to oiled sediments can negatively impact the health of fish species. Here, we examine the effects of chronic exposure of juvenile southern flounder, Paralichthys lethostigma, to a sediment-oil mixture. Oil:sediment mixtures are persistent over time and can become bioavailable following sediment perturbation or resuspension. Juvenile flounder were exposed for 32 days under controlled laboratory conditions to five concentrations of naturally weathered Macondo MC252 oil mixed into uncontaminated, field-collected sediments. The percent composition of individual polycyclic aromatic hydrocarbons (PAHs) of the weathered oil did not change after mixing with the sediment. Spiked exposure sediments contained 0.04-395mg/kg tPAH50 (sum of 50 individual PAH concentration measurements). Mortality increased with both exposure duration and concentration of sediment-associated PAHs, and flounder exposed to concentrations above 8mg/kg tPAH50 showed significantly reduced growth over the course of the experiment. Evident histopathologic changes were observed in liver and gill tissues of fish exposed to more than 8mg/kg tPAH50. All fish at these concentrations showed hepatic intravascular congestion, macrovesicular hepatic vacoulation, telangiectasia of secondary lamellae, and lamellar epithelial proliferation in gill tissues. Dose-dependent upregulation of Cyp1a expression in liver tissues was observed. Taxonomic analysis of gill and intestinal commensal bacterial assemblages showed that exposure to oiled sediments led to distinct shifts in commensal bacterial population structures. These data show that chronic exposure to environmentally-relevant concentrations of oiled sediments produces adverse effects in flounder at multiple biological levels.

  16. [Intermediate endpoints in clinical research].

    PubMed

    Peters, Sanne A E; Groenwold, Rolf H H; Bots, Michiel L

    2013-01-01

    An intermediate variable such as blood pressure is part of the causal pathway of mechanisms to a clinical outcome, e.g. myocardial infarction. An intervention affects a clinical outcome through its effect on that intermediate variable. In studies designed to assess the effects of interventions an intermediate variable may be used as surrogate for clinical outcomes. Such an endpoint is also known as an intermediate endpoint. Intervention studies with intermediate endpoints are commonly performed in medical research to evaluate the effects of an intervention on clinical outcomes. Intervention studies with an intermediate endpoint are conducted in a smaller study population and with a shorter duration of follow-up than studies using clinical outcomes. An intermediate variable is not eligible as an intermediate endpoint when the intervention also affects other biological mechanisms that subsequently affect the clinical endpoint. Due to a smaller sample size and shorter study duration, side effects of intervention are more difficult to evaluate in studies with an intermediate endpoint than in studies with clinical endpoints.

  17. Early events in xenograft development from the human embryonic stem cell line HS181--resemblance with an initial multiple epiblast formation.

    PubMed

    Gertow, Karin; Cedervall, Jessica; Jamil, Seema; Ali, Rouknuddin; Imreh, Marta P; Gulyas, Miklos; Sandstedt, Bengt; Ahrlund-Richter, Lars

    2011-01-01

    Xenografting is widely used for assessing in vivo pluripotency of human stem cell populations. Here, we report on early to late events in the development of mature experimental teratoma from a well-characterized human embryonic stem cell (HESC) line, HS181. The results show an embryonic process, increasingly chaotic. Active proliferation of the stem cell derived cellular progeny was detected already at day 5, and characterized by the appearance of multiple sites of engraftment, with structures of single or pseudostratified columnar epithelium surrounding small cavities. The striking histological resemblance to developing embryonic ectoderm, and the formation of epiblast-like structures was supported by the expression of the markers OCT4, NANOG, SSEA-4 and KLF4, but a lack of REX1. The early neural marker NESTIN was uniformly expressed, while markers linked to gastrulation, such as BMP-4, NODAL or BRACHYURY were not detected. Thus, observations on day 5 indicated differentiation comparable to the most early transient cell populations in human post implantation development. Confirming and expanding on previous findings from HS181 xenografts, these early events were followed by an increasingly chaotic development, incorporated in the formation of a benign teratoma with complex embryonic components. In the mature HS181 teratomas not all types of organs/tissues were detected, indicating a restricted differentiation, and a lack of adequate spatial developmental cues during the further teratoma formation. Uniquely, a kinetic alignment of rare complex structures was made to human embryos at diagnosed gestation stages, showing minor kinetic deviations between HS181 teratoma and the human counterpart.

  18. Patient reported outcomes as endpoints in medical research.

    PubMed

    Fairclough, Diane L

    2004-04-01

    This review covers a number of the many design and analytic issues associated with clinical trials that incorporate patient reported outcomes as primary or secondary endpoints. We use a clinical trial designed to evaluate a new therapy for the prevention of migraines to illustrate how endpoints are defined by the objectives of the study, the methods for handling longitudinal assessments with multiple scales or outcomes, and the methods of analysis in the presence of missing data.

  19. Surrogate Endpoints in Suicide Research

    ERIC Educational Resources Information Center

    Wortzel, Hal S.; Gutierrez, Peter M.; Homaifar, Beeta Y.; Breshears, Ryan E.; Harwood, Jeri E.

    2010-01-01

    Surrogate endpoints frequently substitute for rare outcomes in research. The ability to learn about completed suicides by investigating more readily available and proximate outcomes, such as suicide attempts, has obvious appeal. However, concerns with surrogates from the statistical science perspective exist, and mounting evidence from…

  20. Establishing a group of endpoints to support collective operations without specifying unique identifiers for any endpoints

    DOEpatents

    Archer, Charles J.; Blocksom, Michael A.; Ratterman, Joseph D.; Smith, Brian E.; Xue, Hanghon

    2016-02-02

    A parallel computer executes a number of tasks, each task includes a number of endpoints and the endpoints are configured to support collective operations. In such a parallel computer, establishing a group of endpoints receiving a user specification of a set of endpoints included in a global collection of endpoints, where the user specification defines the set in accordance with a predefined virtual representation of the endpoints, the predefined virtual representation is a data structure setting forth an organization of tasks and endpoints included in the global collection of endpoints and the user specification defines the set of endpoints without a user specification of a particular endpoint; and defining a group of endpoints in dependence upon the predefined virtual representation of the endpoints and the user specification.

  1. Comparative endpoint sensitivity of in vitro estrogen agonist assays.

    PubMed

    Dreier, David A; Connors, Kristin A; Brooks, Bryan W

    2015-07-01

    Environmental and human health implications of endocrine disrupting chemicals (EDCs), particularly xenoestrogens, have received extensive study. In vitro assays are increasingly employed as diagnostic tools to comparatively evaluate chemicals, whole effluent toxicity and surface water quality, and to identify causative EDCs during toxicity identification evaluations. Recently, the U.S. Environmental Protection Agency (USEPA) initiated ToxCast under the Tox21 program to generate novel bioactivity data through high throughput screening. This information is useful for prioritizing chemicals requiring additional hazard information, including endocrine active chemicals. Though multiple in vitro and in vivo techniques have been developed to assess estrogen agonist activity, the relative endpoint sensitivity of these approaches and agreement of their conclusions remain unclear during environmental diagnostic applications. Probabilistic hazard assessment (PHA) approaches, including chemical toxicity distributions (CTD), are useful for understanding the relative sensitivity of endpoints associated with in vitro and in vivo toxicity assays by predicting the likelihood of chemicals eliciting undesirable outcomes at or above environmentally relevant concentrations. In the present study, PHAs were employed to examine the comparative endpoint sensitivity of 16 in vitro assays for estrogen agonist activity using a diverse group of compounds from the USEPA ToxCast dataset. Reporter gene assays were generally observed to possess greater endpoint sensitivity than other assay types, and the Tox21 ERa LUC BG1 Agonist assay was identified as the most sensitive in vitro endpoint for detecting an estrogenic response. When the sensitivity of this most sensitive ToxCast in vitro endpoint was compared to the human MCF-7 cell proliferation assay, a common in vitro model for biomedical and environmental monitoring applications, the ERa LUC BG1 assay was several orders of magnitude less

  2. Evaluation of multiple mechanism-based toxicity endpoints in primary cultured human hepatocytes for the identification of drugs with clinical hepatotoxicity: Results from 152 marketed drugs with known liver injury profiles.

    PubMed

    Zhang, Jie; Doshi, Utkarsh; Suzuki, Ayako; Chang, Ching-Wei; Borlak, Jürgen; Li, Albert P; Tong, Weida

    2016-08-05

    We report here the results of a collaborative research program to develop a robust and reliable in vitro system to allow an accurate definition of the drug-induced liver injury (DILI) potential of new drug entities during drug development. The in vitro hepatotoxic potential of 152 drugs with known DILI profiles were evaluated in primary cultured human hepatocytes with four mechanistically-relevant endpoints: cellular ATP depletion, reactive oxygen species (ROS), glutathione (GSH) depletion, and caspase activation for apoptosis. The drugs, 80 in the testing set and 72 in the validation set, were classified based on serious clinical/regulatory outcomes as defined by reported acute liver failure, black-box warning, and/or withdrawal. The drugs were further sub-categorized for dominant types of liver injury. Logistic regression models were performed to calculate the area under the receiver operating characteristics curve (AUROC) and to evaluate the prediction potential of the selected endpoints for serious clinical/regulatory outcomes. The ROS/ATP ratio was found to yield an excellent AUROC in both the testing (0.8989, P < 0.0001) and validation set (0.8545, P < 0.0001), and was found to distinguish drugs associated with severe from non-severe DILI cases (p < 0.0001). The results suggest that evaluation of drugs in primary human hepatocytes using the ROS/ATP ratio endpoint may aid the definition of their potential to cause severe DILI.

  3. Src Family Kinase Inhibitors Antagonize the Toxicity of Multiple Serotypes of Botulinum Neurotoxin in Human Embryonic Stem Cell-Derived Motor Neurons

    PubMed Central

    Burnett, James C.; Nuss, Jonathan E.; Wanner, Laura M.; Peyser, Brian D.; Du, Hao T.; Gomba, Glenn Y.; Kota, Krishna P.; Panchal, Rekha G.; Gussio, Rick; Kane, Christopher D.; Tessarollo, Lino

    2015-01-01

    Botulinum neurotoxins (BoNTs), the causative agents of botulism, are potent inhibitors of neurotransmitter release from motor neurons. There are currently no drugs to treat BoNT intoxication after the onset of the disease symptoms. In this study, we explored how modulation of key host pathways affects the process of BoNT intoxication in human motor neurons, focusing on Src family kinase (SFK) signaling. Motor neurons derived from human embryonic stem (hES) cells were treated with a panel of SFK inhibitors and intoxicated with BoNT serotypes A, B, or E (which are responsible for >95 % of human botulism cases). Subsequently, it was found that bosutinib, dasatinib, KX2-391, PP1, PP2, Src inhibitor-1, and SU6656 significantly antagonized all three of the serotypes. Furthermore, the data indicated that the treatment of hES-derived motor neurons with multiple SFK inhibitors increased the antagonistic effect synergistically. Mechanistically, the small molecules appear to inhibit BoNTs by targeting host pathways necessary for intoxication and not by directly inhibiting the toxins’ proteolytic activity. Importantly, the identified inhibitors are all well-studied with some in clinical trials while others are FDA-approved drugs. Overall, this study emphasizes the importance of targeting host neuronal pathways, rather than the toxin’s enzymatic components, to antagonize multiple BoNT serotypes in motor neurons. PMID:25782580

  4. Behavioral endpoints for radiation injury

    NASA Astrophysics Data System (ADS)

    Rabin, B. M.; Joseph, J. A.; Hunt, W. A.; Dalton, T. B.; Kandasamy, S. B.; Harris, A. H.; Ludewig, B.

    1994-10-01

    The relative behavioral effectiveness of heavy particles was evaluated. Using the taste aversion paradigm in rats, the behavioral toxicity of most types of radiation (including 20Ne and 40Ar) was similar to that of 60Co photons. Only 56Fe and 93Nb particles and fission neutrons were significantly more effective. Using emesis in ferrets as the behavioral endpoint, 56Fe particles and neutrons were again the most effective; however, 60Co photons were significantly more effective than 18 MeV electrons. These results suggest that LET does not completely predict behavioral effectiveness. Additionally, exposing rats to 10 cGy of 56Fe particles attenuated amphetamine-induced taste aversion learning. This behavior is one of a broad class of behaviors which depends on the integrity of the dopaminergic system and suggests the possibility of alterations in these behaviors following exposure to heavy particles in a space radiation environment.

  5. Morphological abnormalities of embryonic cranial nerves after in utero exposure to valproic acid: implications for the pathogenesis of autism with multiple developmental anomalies.

    PubMed

    Tashiro, Yasura; Oyabu, Akiko; Imura, Yoshio; Uchida, Atsuko; Narita, Naoko; Narita, Masaaki

    2011-06-01

    Autism is often associated with multiple developmental anomalies including asymmetric facial palsy. In order to establish the etiology of autism with facial palsy, research into developmental abnormalities of the peripheral facial nerves is necessary. In the present study, to investigate the development of peripheral cranial nerves for use in an animal model of autism, rat embryos were treated with valproic acid (VPA) in utero and their cranial nerves were visualized by immunostaining. Treatment with VPA after embryonic day 9 had a significant effect on the peripheral fibers of several cranial nerves. Following VPA treatment, immunoreactivity within the trigeminal, facial, glossopharyngeal and vagus nerves was significantly reduced. Additionally, abnormal axonal pathways were observed in the peripheral facial nerves. Thus, the morphology of several cranial nerves, including the facial nerve, can be affected by prenatal VPA exposure as early as E13. Our findings indicate that disruption of early facial nerve development is involved in the etiology of asymmetric facial palsy, and may suggest a link to the etiology of autism.

  6. TACC3 is a microtubule plus end–tracking protein that promotes axon elongation and also regulates microtubule plus end dynamics in multiple embryonic cell types

    PubMed Central

    Nwagbara, Belinda U.; Faris, Anna E.; Bearce, Elizabeth A.; Erdogan, Burcu; Ebbert, Patrick T.; Evans, Matthew F.; Rutherford, Erin L.; Enzenbacher, Tiffany B.; Lowery, Laura Anne

    2014-01-01

    Microtubule plus end dynamics are regulated by a conserved family of proteins called plus end–tracking proteins (+TIPs). It is unclear how various +TIPs interact with each other and with plus ends to control microtubule behavior. The centrosome-associated protein TACC3, a member of the transforming acidic coiled-coil (TACC) domain family, has been implicated in regulating several aspects of microtubule dynamics. However, TACC3 has not been shown to function as a +TIP in vertebrates. Here we show that TACC3 promotes axon outgrowth and regulates microtubule dynamics by increasing microtubule plus end velocities in vivo. We also demonstrate that TACC3 acts as a +TIP in multiple embryonic cell types and that this requires the conserved C-terminal TACC domain. Using high-resolution live-imaging data on tagged +TIPs, we show that TACC3 localizes to the extreme microtubule plus end, where it lies distal to the microtubule polymerization marker EB1 and directly overlaps with the microtubule polymerase XMAP215. TACC3 also plays a role in regulating XMAP215 stability and localizing XMAP215 to microtubule plus ends. Taken together, our results implicate TACC3 as a +TIP that functions with XMAP215 to regulate microtubule plus end dynamics. PMID:25187649

  7. Elevated Nuclear and Cytoplasmic FTY720-Phosphate in Mouse Embryonic Fibroblasts Suggests the Potential for Multiple Mechanisms in FTY720-Induced Neural Tube Defects.

    PubMed

    Gardner, Nicole M; Riley, Ronald T; Showker, Jency L; Voss, Kenneth A; Sachs, Andrew J; Maddox, Joyce R; Gelineau-van Waes, Janee B

    2016-03-01

    FTY720 (fingolimod) is a U.S. Food and Drug Administration-approved drug to treat relapsing remitting multiple sclerosis. FTY720 treatment in pregnant inbred LM/Bc mice results in approximately 60% of embryos having a neural tube defect (NTD). Sphingosine kinases (Sphk1, Sphk2) phosphorylate FTY720 in vivo to form the bioactive metabolite FTY720-1-phosphate (FTY720-P). Cytoplasmic FTY720-P is an agonist for 4 of the 5 sphingosine-1-phosphate (S1P) receptors (S1P1, 3-5) and can also act as a functional antagonist of S1P1, whereas FTY720-P generated in the nucleus inhibits histone deacetylases (HDACs), leading to increased histone acetylation. This study demonstrates that treatment of LM/Bc mouse embryonic fibroblasts (MEFs) with FTY720 results in a significant accumulation of FTY720-P in both the cytoplasmic and nuclear compartments. Elevated nuclear FTY720-P is associated with decreased HDAC activity and increased histone acetylation at H3K18 and H3K23 in LM/Bc MEFs. Treatment of LM/Bc MEFs with FTY720 and a selective Sphk2 inhibitor, ABC294640, significantly reduces the amount of FTY720-P that accumulates in the nucleus. The data provide insight into the relative amounts of FTY720-P generated in the nuclear versus cytoplasmic subcellular compartments after FTY720 treatment and the specific Sphk isoforms involved. The results of this study suggest that FTY720-induced NTDs may involve multiple mechanisms, including: (1) sustained and/or altered S1P receptor activation and signaling by FTY720-P produced in the cytoplasm and (2) HDAC inhibition and histone hyperacetylation by FTY720-P generated in the nucleus that could lead to epigenetic changes in gene regulation.

  8. Surrogate endpoint analysis: an exercise in extrapolation.

    PubMed

    Baker, Stuart G; Kramer, Barnett S

    2013-03-06

    Surrogate endpoints offer the hope of smaller or shorter cancer trials. It is, however, important to realize they come at the cost of an unverifiable extrapolation that could lead to misleading conclusions. With cancer prevention, the focus is on hypothesis testing in small surrogate endpoint trials before deciding whether to proceed to a large prevention trial. However, it is not generally appreciated that a small surrogate endpoint trial is highly sensitive to a deviation from the key Prentice criterion needed for the hypothesis-testing extrapolation. With cancer treatment, the focus is on estimation using historical trials with both surrogate and true endpoints to predict treatment effect based on the surrogate endpoint in a new trial. Successively leaving out one historical trial and computing the predicted treatment effect in the left-out trial yields a standard error multiplier that summarizes the increased uncertainty in estimation extrapolation. If this increased uncertainty is acceptable, three additional extrapolation issues (biological mechanism, treatment following observation of the surrogate endpoint, and side effects following observation of the surrogate endpoint) need to be considered. In summary, when using surrogate endpoint analyses, an appreciation of the problems of extrapolation is crucial.

  9. Impact of weighted composite compared to traditional composite endpoints for the design of randomized controlled trials.

    PubMed

    Bakal, Jeffrey A; Westerhout, Cynthia M; Armstrong, Paul W

    2015-12-01

    Composite endpoints are commonly used in cardiovascular clinical trials. When using a composite endpoint a subject is considered to have an event when the first component endpoint has occurred. The use of composite endpoints offers the ability to incorporate several clinically important endpoint events thereby augmenting the event rate and increasing statistical power for a given sample size. One assumption of the composite is that all component events are of equal clinical importance. This assumption is rarely achieved given the diversity of component endpoints included. One means of adjusting for this diversity is to adjust the outcomes using severity weights determined a priori. The use of a weighted endpoint also allows for the incorporation of multiple endpoints per patient. Although weighting the outcomes lowers the effective number of events, it offers additional information that reduces the variance of the estimate. We created a series of simulation studies to examine the effect on power as the individual components of a typical composite were changed. In one study, we noted that the weighted composite was able to offer discriminative power when the component outcomes were altered, while the traditional method was not. In the other study, we noted that the weighted composite offered a similar level of power to the traditional composite when the change was driven by the more severe endpoints.

  10. [Immunological surrogate endpoints to evaluate vaccine efficacy].

    PubMed

    Jin, Pengfei; Li, Jingxin; Zhou, Yang; Zhu, Fengcai

    2015-12-01

    An immunological surrogate endpoints is a vaccine-induced immune response (either humoral or cellular immune) that predicts protection against clinical endpoints (infection or disease), and can be used to evaluate vaccine efficacy in clinical vaccine trials. Compared with field efficacy trials observing clinical endpoints, immunological vaccine trials could reduce the sample size or shorten the duration of a trial, which promote the license and development of new candidate vaccines. For these reasons, establishing immunological surrogate endpoints is one of 14 Grand Challenges of Global Health of the National Institutes of Health (NIH) and the Bill and Melinda Gates Foundation. From two parts of definition and statistical methods for evaluation of surrogate endpoints, this review provides a more comprehensive description.

  11. Evaluating endocrine endpoints relative to reproductive success in Japanese quail exposed to estrogenic chemicals [poster

    USGS Publications Warehouse

    Henry, P.F.P.; Russek-Cohen, E.; Casey, C.S.; Abdelnabi, M.A.; Ottinger, M.A.

    2000-01-01

    The standard US EPA guidelines for avian reproductive testing may not be sufficiently sensitive to detect effects of sublethal and chronic exposure to endocrine disrupting toxins. There is a need to evaluate endocrine endpoints as potential markers for contaminant effects, and to determine their effectiveness and sensitivity when applied to wildlife. To this end, a three generational test was conducted using the Japanese quail (Coturnix japonica) and a proven estrogenic PCB. Birds were exposed during embryonic development via maternal deposition and/or direct egg injection at day 4. Standard measures of reproductive success and productivity used in toxicological studies, as well as multiple measures of physiological and behavioral responses used in endocrine studies were collected. Long term effects on growth and apparent development were similar between treated and control offspring. Fertility of treated eggs decreased from 75%+ 4.4 (x + se) for P1, to 59% + 12.5 for F1 and 54% + 14.2 for F2. All paired control birds mated to produce viable eggs, whereas 27 % of the F1 and 41 % of the F2 treated pairs failed to produce at least 1 viable egg. Although some decreases in productivity can be related to direct toxic exposure, the response from one generation to the next was not linear with treatment, indicating a potential effect from behavioral or other endocrine alterations.

  12. Multiple positive and negative 5' regulatory elements control the cell-type-specific expression of the embryonic skeletal myosin heavy-chain gene.

    PubMed Central

    Bouvagnet, P F; Strehler, E E; White, G E; Strehler-Page, M A; Nadal-Ginard, B; Mahdavi, V

    1987-01-01

    To identify the DNA sequences that regulate the expression of the sarcomeric myosin heavy-chain (MHC) genes in muscle cells, a series of deletion constructs of the rat embryonic MHC gene was assayed for transient expression after introduction into myogenic and nonmyogenic cells. The sequences in 1.4 kilobases of 5'-flanking DNA were found to be sufficient to direct expression of the MHC gene constructs in a tissue-specific manner (i.e., in differentiated muscle cells but not in undifferentiated muscle and nonmuscle cells). Three main distinct regulatory domains have been identified: (i) the upstream sequences from positions -1413 to -174, which determine the level of expression of the MHC gene and are constituted of three positive regulatory elements and two negative ones; (ii) a muscle-specific regulatory element from positions -173 to -142, which restricts the expression of the MHC gene to muscle cells; and (iii) the promoter region, downstream from position -102, which directs transcription initiation. Introduction of the simian virus 40 enhancer into constructs where subportions of or all of the upstream sequences are deleted (up to position -173) strongly increases the level of expression of such truncated constructs but without changing their muscle specificity. These upstream sequences, which can be substituted for by the simian virus 40 enhancer, function in an orientation-, position-, and promoter-dependent fashion. The muscle-specific element is also promoter specific but does not support efficient expression of the MHC gene. The MHC promoter in itself is not muscle specific. These results underline the importance of the concerted action of multiple regulatory elements that are likely to represent targets for DNA-binding-regulatory proteins. Images PMID:2830491

  13. Automatic endpoint detection to support the systematic review process.

    PubMed

    Blake, Catherine; Lucic, Ana

    2015-08-01

    Preparing a systematic review can take hundreds of hours to complete, but the process of reconciling different results from multiple studies is the bedrock of evidence-based medicine. We introduce a two-step approach to automatically extract three facets - two entities (the agent and object) and the way in which the entities are compared (the endpoint) - from direct comparative sentences in full-text articles. The system does not require a user to predefine entities in advance and thus can be used in domains where entity recognition is difficult or unavailable. As with a systematic review, the tabular summary produced using the automatically extracted facets shows how experimental results differ between studies. Experiments were conducted using a collection of more than 2million sentences from three journals Diabetes, Carcinogenesis and Endocrinology and two machine learning algorithms, support vector machines (SVM) and a general linear model (GLM). F1 and accuracy measures for the SVM and GLM differed by only 0.01 across all three comparison facets in a randomly selected set of test sentences. The system achieved the best performance of 92% for objects, whereas the accuracy for both agent and endpoints was 73%. F1 scores were higher for objects (0.77) than for endpoints (0.51) or agents (0.47). A situated evaluation of Metformin, a drug to treat diabetes, showed system accuracy of 95%, 83% and 79% for the object, endpoint and agent respectively. The situated evaluation had higher F1 scores of 0.88, 0.64 and 0.62 for object, endpoint, and agent respectively. On average, only 5.31% of the sentences in a full-text article are direct comparisons, but the tabular summaries suggest that these sentences provide a rich source of currently underutilized information that can be used to accelerate the systematic review process and identify gaps where future research should be focused.

  14. Multi-Toxic Endpoints of the Foodborne Mycotoxins in Nematode Caenorhabditis elegans

    PubMed Central

    Yang, Zhendong; Xue, Kathy S.; Sun, Xiulan; Tang, Lili; Wang, Jia-Sheng

    2015-01-01

    Aflatoxins B1 (AFB1), deoxynivalenol (DON), fumonisin B1 (FB1), T-2 toxin (T-2), and zearalenone (ZEA) are the major foodborne mycotoxins of public health concerns. In the present study, the multiple toxic endpoints of these naturally-occurring mycotoxins were evaluated in Caenorhabditis elegans model for their lethality, toxic effects on growth and reproduction, as well as influence on lifespan. We found that the lethality endpoint was more sensitive for T-2 toxicity with the EC50 at 1.38 mg/L, the growth endpoint was relatively sensitive for AFB1 toxic effects, and the reproduction endpoint was more sensitive for toxicities of AFB1, FB1, and ZEA. Moreover, the lifespan endpoint was sensitive to toxic effects of all five tested mycotoxins. Data obtained from this study may serve as an important contribution to knowledge on assessment of mycotoxin toxic effects, especially for assessing developmental and reproductive toxic effects, using the C. elegans model. PMID:26633509

  15. Latent variable indirect response joint modeling of a continuous and a categorical clinical endpoint.

    PubMed

    Hu, Chuanpu; Szapary, Philippe O; Mendelsohn, Alan M; Zhou, Honghui

    2014-08-01

    Informative exposure-response modeling of clinical endpoints is important in drug development. There has been much recent progress in latent variable modeling of ordered categorical endpoints, including the application of indirect response (IDR) models and accounting for residual correlations between multiple categorical endpoints. This manuscript describes a framework of latent-variable-based IDR models that facilitate easy simultaneous modeling of a continuous and a categorical clinical endpoint. The model was applied to data from two phase III clinical trials of subcutaneously administered ustekinumab for the treatment of psoriatic arthritis, where Psoriasis Area and Severity Index scores and 20, 50, and 70 % improvement in the American College of Rheumatology response criteria were used as efficacy endpoints. Visual predictive check and external validation showed reasonable parameter estimation precision and model performance.

  16. Multi-Toxic Endpoints of the Foodborne Mycotoxins in Nematode Caenorhabditis elegans.

    PubMed

    Yang, Zhendong; Xue, Kathy S; Sun, Xiulan; Tang, Lili; Wang, Jia-Sheng

    2015-12-02

    Aflatoxins B₁ (AFB₁), deoxynivalenol (DON), fumonisin B₁ (FB₁), T-2 toxin (T-2), and zearalenone (ZEA) are the major foodborne mycotoxins of public health concerns. In the present study, the multiple toxic endpoints of these naturally-occurring mycotoxins were evaluated in Caenorhabditis elegans model for their lethality, toxic effects on growth and reproduction, as well as influence on lifespan. We found that the lethality endpoint was more sensitive for T-2 toxicity with the EC50 at 1.38 mg/L, the growth endpoint was relatively sensitive for AFB₁ toxic effects, and the reproduction endpoint was more sensitive for toxicities of AFB₁, FB₁, and ZEA. Moreover, the lifespan endpoint was sensitive to toxic effects of all five tested mycotoxins. Data obtained from this study may serve as an important contribution to knowledge on assessment of mycotoxin toxic effects, especially for assessing developmental and reproductive toxic effects, using the C. elegans model.

  17. Comparing Laboratory and Field Measured Bioaccumulation Endpoints

    EPA Science Inventory

    The report presents an approach that allows comparisons of all laboratory and field bioaccumulation endpoints measurements. The approach will enable the inclusion of large amounts of field data into evaluations of bioaccumulation potential for legacy chemicals. Currently, these...

  18. Critical endpoint behavior: A Wang Landau study

    NASA Astrophysics Data System (ADS)

    Landau, D. P.; Wang, Fugao; Tsai, Shan-Ho

    2008-07-01

    We study the critical endpoint behavior using an asymmetric Ising model with two- and three-body interactions on a triangular lattice, in the presence of an external field. The simulation method we use is Wang-Landau sampling in a two-dimensional parameter space. We observe a clear divergence of the curvature of the spectator phase boundary and of the magnetization coexistence diameter derivative at the critical endpoint, and the exponents for both divergences agree well with previous theoretical predictions.

  19. Mouse Embryonic Stem Cell Adherent Cell Differentiation and Cytotoxicity (ACDC) assay

    EPA Science Inventory

    The Embryonic Stem Cell Test (EST) is an assay which evaluates xenobiotic-induced effects using three endpoints: mouse embryonic stem cell (mESC) differentiation, mESC viability, and 3T3-cell viability. Our research goal was to develop an improved high-throughput assay by establi...

  20. Establishing a group of endpoints in a parallel computer

    DOEpatents

    Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.; Xue, Hanhong

    2016-02-02

    A parallel computer executes a number of tasks, each task includes a number of endpoints and the endpoints are configured to support collective operations. In such a parallel computer, establishing a group of endpoints receiving a user specification of a set of endpoints included in a global collection of endpoints, where the user specification defines the set in accordance with a predefined virtual representation of the endpoints, the predefined virtual representation is a data structure setting forth an organization of tasks and endpoints included in the global collection of endpoints and the user specification defines the set of endpoints without a user specification of a particular endpoint; and defining a group of endpoints in dependence upon the predefined virtual representation of the endpoints and the user specification.

  1. Molecular pathology endpoints useful for aging studies.

    PubMed

    Niedernhofer, L J; Kirkland, J L; Ladiges, W

    2016-10-06

    The first clinical trial aimed at targeting fundamental processes of aging will soon be launched (TAME: Targeting Aging with Metformin). In its wake is a robust pipeline of therapeutic interventions that have been demonstrated to extend lifespan or healthspan of preclinical models, including rapalogs, antioxidants, anti-inflammatory agents, and senolytics. This ensures that if the TAME trial is successful, numerous additional clinical trials are apt to follow. But a significant impediment to these trials remains the question of what endpoints should be measured? The design of the TAME trial very cleverly skirts around this based on the fact that there are decades of data on metformin in humans, providing unequaled clarity of what endpoints are most likely to yield a positive outcome. But for a new chemical entity, knowing what endpoints to measure remains a formidable challenge. For economy's sake, and to achieve results in a reasonable time frame, surrogate markers of lifespan and healthy aging are desperately needed. This review provides a comprehensive analysis of molecular endpoints that are currently being used as indices of age-related phenomena (e.g., morbidity, frailty, mortality) and proposes an approach for validating and prioritizing these endpoints.

  2. Ovarian cancer clinical trial endpoints: Society of Gynecologic Oncology white paper

    PubMed Central

    Herzog, Thomas J.; Armstrong, Deborah K.; Brady, Mark F.; Coleman, Robert L.; Einstein, Mark H.; Monk, Bradley J.; Mannel, Robert S.; Thigpen, J. Tate; Umpierre, Sharee A.; Villella, Jeannine A.; Alvarez, Ronald D.

    2015-01-01

    Objective To explore the value of multiple clinical endpoints in the unique setting of ovarian cancer. Methods A clinical trial workgroup was established by the Society of Gynecologic Oncology to develop a consensus statement via multiple conference calls, meetings and white paper drafts. Results Clinical trial endpoints have profound effects on late phase clinical trial design, result interpretation, drug development, and regulatory approval of therapeutics. Selection of the optimal clinical trial endpoint is particularly provocative in ovarian cancer where long overall survival (OS) is observed. The lack of new regulatory approvals and the lack of harmony between regulatory bodies globally for ovarian cancer therapeutics are of concern. The advantages and disadvantages of the numerous endpoints available are herein discussed within the unique context of ovarian cancer where both crossover and post-progression therapies potentially uncouple surrogacy between progression-free survival (PFS) and OS, the two most widely supported and utilized endpoints. The roles of patient reported outcomes (PRO) and health related quality of life (HRQoL) are discussed, but even these widely supported parameters are affected by the unique characteristics of ovarian cancer where a significant percentage of patients may be asymptomatic. Original data regarding the endpoint preferences of ovarian cancer advocates is presented. Conclusions Endpoint selection in ovarian cancer clinical trials should reflect the impact on disease burden and unique characteristics of the treatment cohort while reflecting true patient benefit. Both OS and PFS have led to regulatory approvals and are clinically important. OS remains the most objective and accepted endpoint because it is least vulnerable to bias; however, the feasibility of OS in ovarian cancer is compromised by the requirement for large trial size, prolonged time-line for final analysis, and potential for unintended loss of treatment effect

  3. Enabling communication concurrency through flexible MPI endpoints

    DOE PAGES

    Dinan, James; Grant, Ryan E.; Balaji, Pavan; ...

    2014-09-23

    MPI defines a one-to-one relationship between MPI processes and ranks. This model captures many use cases effectively; however, it also limits communication concurrency and interoperability between MPI and programming models that utilize threads. Our paper describes the MPI endpoints extension, which relaxes the longstanding one-to-one relationship between MPI processes and ranks. Using endpoints, an MPI implementation can map separate communication contexts to threads, allowing them to drive communication independently. Also, endpoints enable threads to be addressable in MPI operations, enhancing interoperability between MPI and other programming models. Furthermore, these characteristics are illustrated through several examples and an empirical study thatmore » contrasts current multithreaded communication performance with the need for high degrees of communication concurrency to achieve peak communication performance.« less

  4. Enabling communication concurrency through flexible MPI endpoints

    SciTech Connect

    Dinan, James; Grant, Ryan E.; Balaji, Pavan; Goodell, David; Miller, Douglas; Snir, Marc; Thakur, Rajeev

    2014-09-23

    MPI defines a one-to-one relationship between MPI processes and ranks. This model captures many use cases effectively; however, it also limits communication concurrency and interoperability between MPI and programming models that utilize threads. Our paper describes the MPI endpoints extension, which relaxes the longstanding one-to-one relationship between MPI processes and ranks. Using endpoints, an MPI implementation can map separate communication contexts to threads, allowing them to drive communication independently. Also, endpoints enable threads to be addressable in MPI operations, enhancing interoperability between MPI and other programming models. Furthermore, these characteristics are illustrated through several examples and an empirical study that contrasts current multithreaded communication performance with the need for high degrees of communication concurrency to achieve peak communication performance.

  5. Sublethal Toxicity Endpoints of Heavy Metals to the Nematode Caenorhabditis elegans.

    PubMed

    Jiang, Ying; Chen, Jiandong; Wu, Yue; Wang, Qiang; Li, Huixin

    2016-01-01

    Caenorhabditis elegans, a free-living nematode, is commonly used as a model organism in ecotoxicological studies. The current literatures have provided useful insight into the relative sensitivity of several endpoints, but few direct comparisons of multiple endpoints under a common set of experimental conditions. The objective of this study was to determine appropriate sublethal endpoints to develop an ecotoxicity screening and monitoring system. C. elegans was applied to explore the sublethal toxicity of four heavy metals (copper, zinc, cadmium and chromium). Two physiological endpoints (growth and reproduction), three behavioral endpoints (head thrash frequency, body bend frequency and feeding) and two enzymatic endpoints (acetylcholine esterase [AChE] and superoxide dismutase [SOD]) were selected for the assessment of heavy metal toxicity. The squared correlation coefficients (R2) between the responses observed and fitted by Logit function were higher than 0.90 and the RMSE were lower than 0.10, indicating a good significance statistically. There was no significant difference among the half effect concentration (EC50) endpoints in physiological and behavioral effects of the four heavy metals, indicating similar sensitivity of physiological and behavioral effects. AChE enzyme was more sensitive to copper, zinc, and cadmium than to other physiological and behavioral effects, and SOD enzyme was most sensitive to chromium. The EC50 of copper, zinc, and cadmium, to the AChE enzyme in the nematodes were 0.68 mg/L, 2.76 mg/L, and 0.92 mg/L respectively and the EC50 of chromium to the SOD enzyme in the nematode was 1.58 mg/L. The results of this study showed that there was a good concentration-response relationship between all four heavy metals and the sublethal toxicity effects to C. elegans. Considering these sublethal endpoints in terms of simplicity, accuracy, repeatability and costs of the experiments, feeding is the relatively ideal sublethal toxicity endpoint of

  6. Shift endpoint trace selection algorithm and wavelet analysis to detect the endpoint using optical emission spectroscopy

    NASA Astrophysics Data System (ADS)

    Ben Zakour, Sihem; Taleb, Hassen

    2016-06-01

    Endpoint detection (EPD) is very important undertaking on the side of getting a good understanding and figuring out if a plasma etching process is done on the right way. It is truly a crucial part of supplying repeatable effects in every single wafer. When the film to be etched has been completely erased, the endpoint is reached. In order to ensure the desired device performance on the produced integrated circuit, many sensors are used to detect the endpoint, such as the optical, electrical, acoustical/vibrational, thermal, and frictional. But, except the optical sensor, the other ones show their weaknesses due to the environmental conditions which affect the exactness of reaching endpoint. Unfortunately, some exposed area to the film to be etched is very low (<0.5%), reflecting low signal and showing the incapacity of the traditional endpoint detection method to determine the wind-up of the etch process. This work has provided a means to improve the endpoint detection sensitivity by collecting a huge numbers of full spectral data containing 1201 spectra for each run, then a new unsophisticated algorithm is proposed to select the important endpoint traces named shift endpoint trace selection (SETS). Then, a sensitivity analysis of linear methods named principal component analysis (PCA) and factor analysis (FA), and the nonlinear method called wavelet analysis (WA) for both approximation and details will be studied to compare performances of the methods mentioned above. The signal to noise ratio (SNR) is not only computed based on the main etch (ME) period but also the over etch (OE) period. Moreover, a new unused statistic for EPD, coefficient of variation (CV), is proposed to reach the endpoint in plasma etches process.

  7. Improvement in latent variable indirect response joint modeling of a continuous and a categorical clinical endpoint in rheumatoid arthritis.

    PubMed

    Hu, Chuanpu; Zhou, Honghui

    2016-02-01

    Improving the quality of exposure-response modeling is important in clinical drug development. The general joint modeling of multiple endpoints is made possible in part by recent progress on the latent variable indirect response (IDR) modeling for ordered categorical endpoints. This manuscript aims to investigate, when modeling a continuous and a categorical clinical endpoint, the level of improvement achievable by joint modeling in the latent variable IDR modeling framework through the sharing of model parameters for the individual endpoints, guided by the appropriate representation of drug and placebo mechanism. This was illustrated with data from two phase III clinical trials of intravenously administered mAb X for the treatment of rheumatoid arthritis, with the 28-joint disease activity score (DAS28) and 20, 50, and 70% improvement in the American College of Rheumatology (ACR20, ACR50, and ACR70) disease severity criteria were used as efficacy endpoints. The joint modeling framework led to a parsimonious final model with reasonable performance, evaluated by visual predictive check. The results showed that, compared with the more common approach of separately modeling the endpoints, it is possible for the joint model to be more parsimonious and yet better describe the individual endpoints. In particular, the joint model may better describe one endpoint through subject-specific random effects that would not have been estimable from data of this endpoint alone.

  8. Use of Zebrafish Larvae as a Multi-Endpoint Platform to Characterize the Toxicity Profile of Silica Nanoparticles

    PubMed Central

    Pham, Duc-Hung; De Roo, Bert; Nguyen, Xuan-Bac; Vervaele, Mattias; Kecskés, Angela; Ny, Annelii; Copmans, Daniëlle; Vriens, Hanne; Locquet, Jean-Pierre; Hoet, Peter; de Witte, Peter A. M.

    2016-01-01

    Nanomaterials are being extensively produced and applied in society. Human and environmental exposures are, therefore, inevitable and so increased attention is being given to nanotoxicity. While silica nanoparticles (NP) are one of the top five nanomaterials found in consumer and biomedical products, their toxicity profile is poorly characterized. In this study, we investigated the toxicity of silica nanoparticles with diameters 20, 50 and 80 nm using an in vivo zebrafish platform that analyzes multiple endpoints related to developmental, cardio-, hepato-, and neurotoxicity. Results show that except for an acceleration in hatching time and alterations in the behavior of zebrafish embryos/larvae, silica NPs did not elicit any developmental defects, nor any cardio- and hepatotoxicity. The behavioral alterations were consistent for both embryonic photomotor and larval locomotor response and were dependent on the concentration and the size of silica NPs. As embryos and larvae exhibited a normal touch response and early hatching did not affect larval locomotor response, the behavior changes observed are most likely the consequence of modified neuroactivity. Overall, our results suggest that silica NPs do not cause any developmental, cardio- or hepatotoxicity, but they pose a potential risk for the neurobehavioral system. PMID:27872490

  9. Scaling for interfacial tensions near critical endpoints.

    PubMed

    Zinn, Shun-Yong; Fisher, Michael E

    2005-01-01

    Parametric scaling representations are obtained and studied for the asymptotic behavior of interfacial tensions in the full neighborhood of a fluid (or Ising-type) critical endpoint, i.e., as a function both of temperature and of density/order parameter or chemical potential/ordering field. Accurate nonclassical critical exponents and reliable estimates for the universal amplitude ratios are included naturally on the basis of the "extended de Gennes-Fisher" local-functional theory. Serious defects in previous scaling treatments are rectified and complete wetting behavior is represented; however, quantitatively small, but unphysical residual nonanalyticities on the wetting side of the critical isotherm are smoothed out "manually." Comparisons with the limited available observations are presented elsewhere but the theory invites new, searching experiments and simulations, e.g., for the vapor-liquid interfacial tension on the two sides of the critical endpoint isotherm for which an amplitude ratio -3.25+/-0.05 is predicted.

  10. A specific endpoint assay for ubiquitin.

    PubMed Central

    Rose, I A; Warms, J V

    1987-01-01

    Simple endpoint assays for free ubiquitin (Ub) and for the Ub-activating enzyme are described. The method for measuring Ub makes use of the reaction of iodoacetamide-treated Ub-activating enzyme (E): [3H]ATP + Ub + E----E X [3H]AMP-Ub + PPi and PPi----2Pi (in the presence of pyrophosphatase). The Ub is then measured by determining the acid-insoluble radioactivity. The reaction is accompanied by a slow enzyme-catalyzed hydrolysis of the complex to AMP plus Ub. The presence of ubiquitin-activating enzyme in excess of Ub by approximately equal to 0.1 microM assures that the steady state will be close to the endpoint for total Ub. A preparation of the activating enzyme from human erythrocytes that does not depend on affinity chromatography is described. Several applications of the assay are presented. PMID:3031643

  11. Protein patterns as endpoints in environmental remediation

    SciTech Connect

    Bradley, B.; Brown, D.

    1995-12-31

    Biological endpoints can complement chemical analyses in monitoring environmental remediation. In some cases the levels of chemical detection are so low that the costs of clean-up to no detection would be prohibitive. And chemical tests do not indicate the availability of the contaminants to the biota. On the other hand many if not most biological tests lack specificity. The authors have investigated a protein expression assay to establish an endpoint for clean-up of sulfur mustard and breakdown products. Earthworms (Lumbricus terrestris) were exposed to sulfur mustard (SM), a breakdown product thiodiethanol (TDE), and ethylene glycol, the solvent for the two chemicals. Tissue from the lining of the coelomic cavity was taken from each of 6 worms in each treatment class. Soluble proteins were extracted and separated on one and two-dimensional (1D and 2D) gels. The 1 D gels showed no difference by eye but the patterns from control and solvent control worms on 2D gels differed from those of worms exposed to TDE and SM. The 1D gel data were digitized and analyzed by pattern recognition using artificial neural networks. The protein patterns under the two treatments and the two controls were learned in one set of data and successfully recognized in a second. This indicated that what was learned was useful in recognizing patterns induced by SM and TDE. Thus a possible endpoint for remediation would be the protein pattern at no effect levels of chemicals of interest.

  12. Biomarkers and surrogate endpoints in glaucoma clinical trials.

    PubMed

    Medeiros, Felipe A

    2015-05-01

    Surrogate endpoints are often used as replacements for true clinically relevant endpoints in several areas of medicine, as they enable faster and less expensive clinical trials. However, without proper validation, the use of surrogates may lead to incorrect conclusions about the efficacy and safety of treatments. This article reviews the general requirements for validating surrogate endpoints and provides a critical assessment of the use of intraocular pressure (IOP), visual fields, and structural measurements of the optic nerve as surrogate endpoints in glaucoma clinical trials. A valid surrogate endpoint must be able to predict the clinically relevant endpoint and fully capture the effect of an intervention on that endpoint. Despite its widespread use in clinical trials, no proper validation of IOP as a surrogate endpoint has ever been conducted for any class of IOP-lowering treatments. Evidence has accumulated with regard to the role of imaging measurements of optic nerve damage as surrogate endpoints in glaucoma. These measurements are predictive of functional losses in the disease and may explain, at least in part, treatment effects on clinically relevant endpoints. The use of composite endpoints in glaucoma trials may overcome weaknesses of the use of structural or functional endpoints in isolation. Unless research is dedicated to fully develop and validate suitable endpoints that can be used in glaucoma clinical trials, we run the risk of inappropriate judgments about the value of new therapies.

  13. Ecosystem Services as Assessment Endpoints in Ecological Risk Assessment

    EPA Science Inventory

    The focus of ecological risk assessment (ERA) is on assessment endpoints, explicit expressions of environmental values to be protected. Traditionally, the ecological entities identified in assessment endpoints have been components of ecosystems deemed by risk assessors to be impo...

  14. Magnetic-field induced critical endpoint

    NASA Astrophysics Data System (ADS)

    Rechenberger, Stefan

    2017-03-01

    The phase diagram of strong interaction matter is analyzed utilizing the Nambu-Jona-Lasinio model. Special emphasis is placed on its dependence on an external magnetic field and isospin chemical potential. Using flavor mixing induced by instanton effects the influence of isospin breaking due to the magnetic field and the isospin chemical potential is compared. It is found that at low temperatures and large quark chemical potential the magnetic field, depending on its strength, induces a new critical endpoint or a triple point.

  15. Nonalcoholic Steatohepatitis and Endpoints in Clinical Trials

    PubMed Central

    Hannah, William N.; Torres, Dawn M.

    2016-01-01

    Nonalcoholic fatty liver disease (NAFLD) is now the leading cause of liver disease in developed countries, and the rates of NAFLD continue to rise in conjunction with the obesity pandemic. While the majority of patients with isolated steatosis generally have a benign course, a diagnosis of nonalcoholic steatohepatitis (NASH) carries a significantly higher risk for progression of disease, cirrhosis, and death. Pharmacologic therapeutic interventions in NASH have largely proven to be ineffective or unappealing due to long-term side-effect profiles, and the majority of patients cannot achieve or sustain targeted weight loss goals, necessitating an urgent need for therapeutic trials and drug development. The complex molecular mechanisms leading to NASH and the long duration of time to develop complications of disease are challenges to developing meaningful clinical endpoints. Because of these challenges, surrogate endpoints that are linked to all-cause mortality, liver-related death, and complications of cirrhosis are much more likely to be beneficial in the majority of patients. PMID:28035202

  16. Strategies and Endpoints of Antifibrotic Drug Trials

    PubMed Central

    Torok, Natalie; Dranoff, Jonathan A.; Schuppan, Detlef; Friedman, Scott L.

    2015-01-01

    There is an urgent need to develop antifibrotic therapies for chronic liver disease, and to clarify which endpoints in antifibrotic trials will be acceptable to regulatory agencies. AASLD sponsored an endpoints conference to help accelerate the efficient testing of antifibrotic agents and to develop recommendations on clinical trial design for liver fibrosis. In this review we summarize the salient and novel elements of this conference and provide directions for future clinical trial design. The paper follows the structure of the conference and is organized into five areas: I) Antifibrotic trial design; II) Preclinical proof of concept studies; III) Pharmacologic targets: rationale and lessons to learn; IV) Rational drug design and development; V) Consensus and recommendations on design of clinical trials in liver fibrosis. Expert overviews and collaborative discussions helped to summarize the key unmet needs and directions for the future, including: 1) Greater clarification of at-risk populations and study groups; 2) Standardization of all elements of drug discovery and testing; 3) Standardization of clinical trial approaches; 4) Accelerated development of improved non-invasive markers; 5) Need for exploration of potential off-target toxicities of future antifibrotic drugs. PMID:25626988

  17. Flexible stopping boundaries when changing primary endpoints after unblinded interim analyses.

    PubMed

    Chen, Liddy M; Ibrahim, Joseph G; Chu, Haitao

    2014-01-01

    It has been widely recognized that interim analyses of accumulating data in a clinical trial can inflate type I error. Different methods, from group sequential boundaries to flexible alpha spending functions, have been developed to control the overall type I error at prespecified level. These methods mainly apply to testing the same endpoint in multiple interim analyses. In this article, we consider a group sequential design with preplanned endpoint switching after unblinded interim analyses. We extend the alpha spending function method to group sequential stopping boundaries when the parameters can be different between interim, or between interim and final analyses.

  18. Population growth rate determinants for Arbacia: Evaluating ecological relevance of toxicity test endpoints

    SciTech Connect

    Nacci, D.; Gleason, T.; Munns, W.R. Jr.

    1995-12-31

    A population dynamics model for the sea urchin, Arbacia punctulata, was recently developed incorporating life stage endpoints frequently measured in acute and chronic toxicity studies. Model elasticity analysis was used to demonstrate that population growth rate was influenced most by adult survival and least by early life stage success, calling into question the ecological relevance of results from standardized Arbacia fertilization and larval development toxicity tests. Two approaches were used to continue this evaluation. Actual and hypothetical dose-response curves for toxicant exposures over multiple life stages were used to evaluate contributions to population growth rate of stage-specific toxicant effects. Additionally, relationships between critical life stages were developed from laboratory data for Arbacia. The results of this analysis underscore the importance of understanding both endpoint sensitivity to toxicants and sensitivity of population growth rate to test endpoints in determining the ecological relevance of toxicity tests results.

  19. Elevated nuclear and cytoplasmic FTY720-phosphate in mouse embryonic fibroblasts suggests the potential for multiple mechanisms in FTY720-induced neural tube defects

    Technology Transfer Automated Retrieval System (TEKTRAN)

    FTY720 (fingolimod) is an FDA-approved drug to treat relapsing remitting multiple sclerosis. FTY720 treatment in pregnant inbred LM/Bc mice results in approximately 60% of embryos having a neural tube defect (NTD). Sphingosine kinases (Sphk1, Sphk2) phosphorylate FTY720 in vivo to form the bioactive...

  20. Determining Significant Endpoints for Ecological risk Analyses

    SciTech Connect

    Hinton, Thimas G.; Bedford, Joel

    1999-06-01

    Our interest is in obtaining a scientifically defensible endpoint for measuring ecological risks to populations exposed to chronic, low-level radiation, and radiation with concomitant exposure to chemicals. To do so, we believe that we must understand the extent to which molecular damage is detrimental at the individual and population levels of biological organization. Ecological risk analyses based on molecular damage, without an understanding of the impacts to higher levels of biological organization, could cause cleanup strategies on DOE sites to be overly conservative and unnecessarily expensive. Our goal is to determine the relevancy of sublethal cellular damage to the performance of individuals and populations. We think that we can achieve this by using novel biological dosimeters in controlled, manipulative dose/effects experiments, and by coupling changes in metabolic rates and energy allocation patterns to meaningful population response variables such as age-specific survivorship, reproductive output, age at maturity and longevity.

  1. Comparing laboratory and field measured bioaccumulation endpoints.

    PubMed

    Burkhard, Lawrence P; Arnot, Jon A; Embry, Michelle R; Farley, Kevin J; Hoke, Robert A; Kitano, Masaru; Leslie, Heather A; Lotufo, Guilherme R; Parkerton, Thomas F; Sappington, Keith G; Tomy, Gregg T; Woodburn, Kent B

    2012-01-01

    An approach for comparing laboratory and field measures of bioaccumulation is presented to facilitate the interpretation of different sources of bioaccumulation data. Differences in numerical scales and units are eliminated by converting the data to dimensionless fugacity (or concentration-normalized) ratios. The approach expresses bioaccumulation metrics in terms of the equilibrium status of the chemical, with respect to a reference phase. When the fugacity ratios of the bioaccumulation metrics are plotted, the degree of variability within and across metrics is easily visualized for a given chemical because their numerical scales are the same for all endpoints. Fugacity ratios greater than 1 indicate an increase in chemical thermodynamic activity in organisms with respect to a reference phase (e.g., biomagnification). Fugacity ratios less than 1 indicate a decrease in chemical thermodynamic activity in organisms with respect to a reference phase (e.g., biodilution). This method provides a holistic, weight-of-evidence approach for assessing the biomagnification potential of individual chemicals because bioconcentration factors, bioaccumulation factors, biota-sediment accumulation factors, biomagnification factors, biota-suspended solids accumulation factors, and trophic magnification factors can be included in the evaluation. The approach is illustrated using a total 2393 measured data points from 171 reports, for 15 nonionic organic chemicals that were selected based on data availability, a range of physicochemical partitioning properties, and biotransformation rates. Laboratory and field fugacity ratios derived from the various bioaccumulation metrics were generally consistent in categorizing substances with respect to either an increased or decreased thermodynamic status in biota, i.e., biomagnification or biodilution, respectively. The proposed comparative bioaccumulation endpoint assessment method could therefore be considered for decision making in a

  2. Population-scale assessment endpoints in ecological risk assessment part II: selection of assessment endpoint attributes.

    PubMed

    Landis, Wayne G; Kaminski, Laurel A

    2007-07-01

    Because ecological services often are tied to specific species, the risk to populations is a critical endpoint and important feature of ecological risk assessments. In Part 1 of this series it was demonstrated that population scale assessment endpoints are important expressions of the valued components of ecological structures. This commentary reviews several of the characteristics of populations that can be evaluated and used in population scale risk assessments. Two attributes are evaluated as promising. The 1st attribute is the change in potential productivity of the population over a specified time period. The 2nd attribute is the change in the age structure of a population, expressed graphically or as a normalized effects vector (NEV). The NEV is a description of the change in age structure due to a toxicant or other stressor and appears to be characteristic of specific stressor effects.

  3. Ecosystem services as assessment endpoints for ecological risk assessment.

    PubMed

    Munns, Wayne R; Rea, Anne W; Suter, Glenn W; Martin, Lawrence; Blake-Hedges, Lynne; Crk, Tanja; Davis, Christine; Ferreira, Gina; Jordan, Steve; Mahoney, Michele; Barron, Mace G

    2016-07-01

    Ecosystem services are defined as the outputs of ecological processes that contribute to human welfare or have the potential to do so in the future. Those outputs include food and drinking water, clean air and water, and pollinated crops. The need to protect the services provided by natural systems has been recognized previously, but ecosystem services have not been formally incorporated into ecological risk assessment practice in a general way in the United States. Endpoints used conventionally in ecological risk assessment, derived directly from the state of the ecosystem (e.g., biophysical structure and processes), and endpoints based on ecosystem services serve different purposes. Conventional endpoints are ecologically important and susceptible entities and attributes that are protected under US laws and regulations. Ecosystem service endpoints are a conceptual and analytical step beyond conventional endpoints and are intended to complement conventional endpoints by linking and extending endpoints to goods and services with more obvious benefit to humans. Conventional endpoints can be related to ecosystem services even when the latter are not considered explicitly during problem formulation. To advance the use of ecosystem service endpoints in ecological risk assessment, the US Environmental Protection Agency's Risk Assessment Forum has added generic endpoints based on ecosystem services (ES-GEAE) to the original 2003 set of generic ecological assessment endpoints (GEAEs). Like conventional GEAEs, ES-GEAEs are defined by an entity and an attribute. Also like conventional GEAEs, ES-GEAEs are broadly described and will need to be made specific when applied to individual assessments. Adoption of ecosystem services as a type of assessment endpoint is intended to improve the value of risk assessment to environmental decision making, linking ecological risk to human well-being, and providing an improved means of communicating those risks. Integr Environ Assess Manag

  4. Voluntary control of static endpoint stiffness during force regulation tasks.

    PubMed

    Perreault, Eric J; Kirsch, Robert F; Crago, Patrick E

    2002-06-01

    The goals of this study were to determine the degree to which subjects could voluntarily modulate static endpoint stiffness orientation and to quantify the effects of simultaneously generated voluntary endpoint forces on this ability. Static endpoint stiffness, which characterizes the relationship between externally imposed displacements of the hand and the elastic forces generated in response, was estimated in real time during the application of planar, stochastic perturbations of endpoint position. This estimation was accomplished using a real-time parametric identification algorithm on measured force and position data. Subjects were provided with real-time visual feedback of endpoint stiffness, and their ability to modulate the orientation of maximum static stiffness was measured for different endpoint force magnitudes and directions. We found that individuals can voluntarily change stiffness orientation but that the magnitude of these changes is small, the range of available stiffness orientations decreases as endpoint force exertion increases, and endpoint force direction significantly constrains direction and magnitude of the stiffness orientations that can be achieved. Given these findings it appears unlikely that static endpoint stiffness orientation is controlled independently of force by voluntary neural mechanisms during postural tasks.

  5. Evaluation of a Mouse Embryonic Stem Cell Adherent Cell Differentiation and Cytotoxicity (ACDC) assay (SOT)

    EPA Science Inventory

    The Embryonic Stem Cell Test (EST) has been used to evaluate the effects of xenobiotics using three endpoints, stem cell differentiation, stem cell viability and 3T3-cell viability. Our research goal is to establish amodel system that would evaluate chemical effects using a singl...

  6. Translational endpoints in fragile X syndrome.

    PubMed

    de Esch, Celine E F; Zeidler, Shimriet; Willemsen, Rob

    2014-10-01

    Fragile X syndrome (FXS) occurs in less than 10% of the intellectually disabled (ID) population. The cause of FXS is a CGG trinucleotide repeat longer than 200 CGG units within the first exon of the FMR1 gene, which leads to hypermethylation and consequently silencing of the FMR1 gene. The lack of FMR1's gene product, the fragile X mental retardation protein (FMRP) in neurons is the cause of the ID in patients with FXS. FMRP plays an important role in local protein synthesis at the synapse including modulation of synaptic plasticity. The advancing knowledge about the cellular function of FMRP has led to the identification of translational endpoints for future therapeutic intervention strategies. This review highlights the challenging routes to the identification of reliable outcome measures in preclinical studies using both cellular models and Fmr1 knockout mice. Finally, clinical studies carried out to correct intellectual and behavioral deficits in patients with FXS, using a variety of existing and new drugs, are discussed.

  7. Evaluation of Gene Expression Endpoints in the Context of a Xenopus laevis Metamorphosis-based Bioassay to Detect Thyroid Hormone Disruptors

    EPA Science Inventory

    This study accentuates the need to examine multiple tissues and provides critical information required for optimization of exposure regimens and endpoint assessments that focus on the detection of disruption in TH-regulatory systems.

  8. Computer Model for Prediction of PCB Dechlorination and Biodegradation Endpoints

    SciTech Connect

    Just, E.M.; Klasson, T.

    1999-04-19

    Mathematical modeling of polychlorinated biphenyl (PCB) transformation served as a means of predicting possible endpoints of bioremediation, thus allowing evaluation of several of the most common transformation patterns. Correlation between laboratory-observed and predicted endpoint data was, in some cases, as good as 0.98 (perfect correlation = 1.0).

  9. Uncertainty in the Bayesian meta-analysis of normally distributed surrogate endpoints.

    PubMed

    Bujkiewicz, Sylwia; Thompson, John R; Spata, Enti; Abrams, Keith R

    2015-08-13

    We investigate the effect of the choice of parameterisation of meta-analytic models and related uncertainty on the validation of surrogate endpoints. Different meta-analytical approaches take into account different levels of uncertainty which may impact on the accuracy of the predictions of treatment effect on the target outcome from the treatment effect on a surrogate endpoint obtained from these models. A range of Bayesian as well as frequentist meta-analytical methods are implemented using illustrative examples in relapsing-remitting multiple sclerosis, where the treatment effect on disability worsening is the primary outcome of interest in healthcare evaluation, while the effect on relapse rate is considered as a potential surrogate to the effect on disability progression, and in gastric cancer, where the disease-free survival has been shown to be a good surrogate endpoint to the overall survival. Sensitivity analysis was carried out to assess the impact of distributional assumptions on the predictions. Also, sensitivity to modelling assumptions and performance of the models were investigated by simulation. Although different methods can predict mean true outcome almost equally well, inclusion of uncertainty around all relevant parameters of the model may lead to less certain and hence more conservative predictions. When investigating endpoints as candidate surrogate outcomes, a careful choice of the meta-analytical approach has to be made. Models underestimating the uncertainty of available evidence may lead to overoptimistic predictions which can then have an effect on decisions made based on such predictions.

  10. Evaluation of 309 Environmental Chemicals Using a Mouse Embryonic Stem Cell Adherent Cell Differentiation and Cytotoxicity Assay

    PubMed Central

    Chandler, Kelly J.; Barrier, Marianne; Jeffay, Susan; Nichols, Harriette P.; Kleinstreuer, Nicole C.; Singh, Amar V.; Reif, David M.; Sipes, Nisha S.; Judson, Richard S.; Dix, David J.; Kavlock, Robert; Hunter, Edward S.; Knudsen, Thomas B.

    2011-01-01

    The vast landscape of environmental chemicals has motivated the need for alternative methods to traditional whole-animal bioassays in toxicity testing. Embryonic stem (ES) cells provide an in vitro model of embryonic development and an alternative method for assessing developmental toxicity. Here, we evaluated 309 environmental chemicals, mostly food-use pesticides, from the ToxCast™ chemical library using a mouse ES cell platform. ES cells were cultured in the absence of pluripotency factors to promote spontaneous differentiation and in the presence of DMSO-solubilized chemicals at different concentrations to test the effects of exposure on differentiation and cytotoxicity. Cardiomyocyte differentiation (α,β myosin heavy chain; MYH6/MYH7) and cytotoxicity (DRAQ5™/Sapphire700™) were measured by In-Cell Western™ analysis. Half-maximal activity concentration (AC50) values for differentiation and cytotoxicity endpoints were determined, with 18% of the chemical library showing significant activity on either endpoint. Mining these effects against the ToxCast Phase I assays (∼500) revealed significant associations for a subset of chemicals (26) that perturbed transcription-based activities and impaired ES cell differentiation. Increased transcriptional activity of several critical developmental genes including BMPR2, PAX6 and OCT1 were strongly associated with decreased ES cell differentiation. Multiple genes involved in reactive oxygen species signaling pathways (NRF2, ABCG2, GSTA2, HIF1A) were strongly associated with decreased ES cell differentiation as well. A multivariate model built from these data revealed alterations in ABCG2 transporter was a strong predictor of impaired ES cell differentiation. Taken together, these results provide an initial characterization of metabolic and regulatory pathways by which some environmental chemicals may act to disrupt ES cell growth and differentiation. PMID:21666745

  11. Equipment management risk rating system based on engineering endpoints.

    PubMed

    James, P J

    1999-01-01

    The equipment management risk ratings system outlined here offers two significant departures from current practice: risk classifications are based on intrinsic device risks, and the risk rating system is based on engineering endpoints. Intrinsic device risks are categorized as physical, clinical and technical, and these flow from the incoming equipment assessment process. Engineering risk management is based on verification of engineering endpoints such as clinical measurements or energy delivery. This practice eliminates the ambiguity associated with ranking risk in terms of physiologic and higher-level outcome endpoints such as no significant hazards, low significance, injury, or mortality.

  12. Prognostic factors versus markers of response to treatment versus surrogate endpoints: Three different concepts.

    PubMed

    Sormani, Maria Pia

    2017-03-01

    Multiple sclerosis is a highly heterogeneous disease; the quantitative assessment of disease progression is problematic for many reasons, including the lack of objective methods to measure disability and the long follow-up times needed to detect relevant and stable changes. For these reasons, the importance of prognostic markers, markers of response to treatments and of surrogate endpoints, is crucial in multiple sclerosis research. Aim of this report is to clarify some basic definitions and methodological issues about baseline factors to be considered prognostic markers or markers of response to treatment; to define the dynamic role that variables must have to be considered surrogate markers in relation to specific treatments.

  13. Embryonal cancers in Europe.

    PubMed

    Gatta, Gemma; Ferrari, Andrea; Stiller, Charles A; Pastore, Guido; Bisogno, Gianni; Trama, Annalisa; Capocaccia, Riccardo

    2012-07-01

    Embryonal cancers are a heterogeneous group of rare cancers which mainly occur in children and adolescents. The aim of the present study was to estimate the burden (incidence, prevalence, survival and proportion of cured) for the principal embryonal cancers in Europe (EU27), using population-based data from cancer registries (CRs) participating in RARECARE. We identified 3322 cases diagnosed from 1995 to 2002 (latest period for which data are available): 44% neuroblastoma, 35% nephroblastoma, 13% retinoblastoma and 6% hepatoblastoma. Very few cases of pulmonary blastoma (43 cases) and pancreatoblastoma (seven cases) were diagnosed. About 2000 new embryonal cancers were estimated every year in EU27, for an annual incidence rate of 4 per million (1.8 neuroblastoma, 1.4 nephroblastoma, and 0.5 retinoblastoma); 91% of cases occurred in patients under 15 years. Five-year relative survival for all embryonal cancers was 80% (99% retinoblastoma, 90% nephroblastoma, 71% hepatoblastoma and 68% neuroblastoma). Overall survival was lower in adolescents and adults than in those under 15 years. The cure rate was estimated at 80%. Slightly less than 40,000 persons were estimated alive in EU27 with a diagnosis of embryonal cancer in 2008. Nephroblastoma was the most prevalent (18,150 cases in EU27), followed by neuroblastoma (12,100), retinoblastoma (5200), hepatoblastoma (2700) and pulmonary blastoma (614). This is the first study to delineate the embryonal cancer burden in Europe by age, sex and European region. Survival/cure rate is generally high, but there are considerable gaps in our understanding of the natural histories of these rare diseases particularly in adults.

  14. Endpoint temperature prediction of molten steel in RH using improved case-based reasoning

    NASA Astrophysics Data System (ADS)

    Feng, Kai; Wang, Hong-bing; Xu, An-jun; He, Dong-feng

    2013-12-01

    An improved case-based reasoning (CBR) method was proposed to predict the endpoint temperature of molten steel in Ruhrstahl Heraeus (RH) process. Firstly, production data were analyzed by multiple linear regressions and a pairwise comparison matrix in analytic hierarchy process (AHP) was determined by this linear regression's coefficient. The weights of various influencing factors were obtained by AHP. Secondly, the dividable principles of case base including "0-1" and "breakpoint" were proposed, and the case base was divided into several homogeneous parts. Finally, the improved CBR was compared with ordinary CBR, which is based on the even weight and the single base. The results show that the improved CBR has a higher hit rate for predicting the endpoint temperature of molten steel in RH.

  15. Accurate measurement method for tube's endpoints based on machine vision

    NASA Astrophysics Data System (ADS)

    Liu, Shaoli; Jin, Peng; Liu, Jianhua; Wang, Xiao; Sun, Peng

    2017-01-01

    Tubes are used widely in aerospace vehicles, and their accurate assembly can directly affect the assembling reliability and the quality of products. It is important to measure the processed tube's endpoints and then fix any geometric errors correspondingly. However, the traditional tube inspection method is time-consuming and complex operations. Therefore, a new measurement method for a tube's endpoints based on machine vision is proposed. First, reflected light on tube's surface can be removed by using photometric linearization. Then, based on the optimization model for the tube's endpoint measurements and the principle of stereo matching, the global coordinates and the relative distance of the tube's endpoint are obtained. To confirm the feasibility, 11 tubes are processed to remove the reflected light and then the endpoint's positions of tubes are measured. The experiment results show that the measurement repeatability accuracy is 0.167 mm, and the absolute accuracy is 0.328 mm. The measurement takes less than 1 min. The proposed method based on machine vision can measure the tube's endpoints without any surface treatment or any tools and can realize on line measurement.

  16. Preliminary remediation goals for ecological endpoints

    SciTech Connect

    Efroymson, R.A.; Suter, G.W. II; Sample, B.E.; Jones, D.S.

    1996-07-01

    Preliminary remediation goals (PRGs) are useful for risk assessment and decision making at Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) sites. PRGs are upper concentration limits for specific chemicals in specific environmental media that are anticipated to protect human health or the environment. They can be used for multiple remedial investigations at multiple facilities. In addition to media and chemicals of potential concern, the development of PRGs generally requires some knowledge or anticipation of future land use. In Preliminary Remediation Goals for Use at the U.S. Department of Energy Oak Ridge Operations Office (Energy Systems 1995), PRGs intended to protect human health were developed with guidance from Risk Assessment Guidance for Superfund: Volume I - Human Health Evaluation Manual, Part B (RAGS) (EPA 1991). However, no guidance was given for PRGs based on ecological risk. The numbers that appear in this volume have, for the most part, been extracted from toxicological benchmarks documents for Oak Ridge National Laboratory (ORNL) and have previously been developed by ORNL. The sources of the quantities, and many of the uncertainties associated with their derivation, are described in this technical memorandum.

  17. Differences in end-point force trajectories elicited by electrical stimulation of individual human calf muscles

    PubMed Central

    Giordano, S B; Segal, R L; Abelew, T A

    2009-01-01

    The purpose of this study was to investigate the end-point force trajectories of the fibularis longus (FIB), lateral gastrocnemius (LG) and medial gastrocnemius (MG) muscles. Most information about individual muscle function has come from studies which use models based on electromyographic (EMG) recordings. In this study (N=20 subjects) we used electrical stimulation (20Hz) to elicit activity in individual muscles, recorded the end-point forces at the foot and verified the selectivity of stimulation by using magnetic resonance imaging. Unexpectedly, no significant differences were found between LG and MG force directions. Stimulation of LG and MG resulted in downward and medial or lateral forces depending on the subject. We found FIB end-point forces to be significantly different than those of LG and MG. In all subjects, stimulation of FIB resulted in downward and lateral forces. Based on our results, we suggest that there are multiple factors determining when and whether LG or MG will produce a medial or lateral force and FIB consistently plays a significant role in eversion/abduction and plantarflexion. We suggest that the inter-subject variability we found is not simply an artifact of experimental or technical error but is functionally relevant and should be addressed in future studies and models. PMID:20095454

  18. Gravity and embryonic development

    NASA Technical Reports Server (NTRS)

    Young, R. S.

    1976-01-01

    The relationship between the developing embryo (both plant and animal) and a gravitational field has long been contemplated. The difficulty in designing critical experiments on the surface of the earth because of its background of 1 g, has been an obstacle to a resolution of the problem. Biological responses to gravity (particularly in plants) are obvious in many cases; however, the influence of gravity as an environmental input to the developing embryo is not as obvious and has proven to be extremely difficult to define. In spite of this, over the years numerous attempts have been made using a variety of embryonic materials to come to grips with the role of gravity in development. Three research tools are available: the centrifuge, the clinostat, and the orbiting spacecraft. Experimental results are now available from all three sources. Some tenuous conclusions are drawn, and an attempt at a unifying theory of gravitational influence on embryonic development is made.

  19. Surrogate Endpoint Evaluation: Principal Stratification Criteria and the Prentice Definition.

    PubMed

    Gilbert, Peter B; Gabriel, Erin E; Huang, Ying; Chan, Ivan S F

    2015-09-01

    A common problem of interest within a randomized clinical trial is the evaluation of an inexpensive response endpoint as a valid surrogate endpoint for a clinical endpoint, where a chief purpose of a valid surrogate is to provide a way to make correct inferences on clinical treatment effects in future studies without needing to collect the clinical endpoint data. Within the principal stratification framework for addressing this problem based on data from a single randomized clinical efficacy trial, a variety of definitions and criteria for a good surrogate endpoint have been proposed, all based on or closely related to the "principal effects" or "causal effect predictiveness (CEP)" surface. We discuss CEP-based criteria for a useful surrogate endpoint, including (1) the meaning and relative importance of proposed criteria including average causal necessity (ACN), average causal sufficiency (ACS), and large clinical effect modification; (2) the relationship between these criteria and the Prentice definition of a valid surrogate endpoint; and (3) the relationship between these criteria and the consistency criterion (i.e., assurance against the "surrogate paradox"). This includes the result that ACN plus a strong version of ACS generally do not imply the Prentice definition nor the consistency criterion, but they do have these implications in special cases. Moreover, the converse does not hold except in a special case with a binary candidate surrogate. The results highlight that assumptions about the treatment effect on the clinical endpoint before the candidate surrogate is measured are influential for the ability to draw conclusions about the Prentice definition or consistency. In addition, we emphasize that in some scenarios that occur commonly in practice, the principal strata sub-populations for inference are identifiable from the observable data, in which cases the principal stratification framework has relatively high utility for the purpose of effect

  20. Image Segmentation Using Parametric Contours With Free Endpoints.

    PubMed

    Benninghoff, Heike; Garcke, Harald

    2016-04-01

    In this paper, we introduce a novel approach for active contours with free endpoints. A scheme for image segmentation is presented based on a discrete version of the Mumford-Shah functional where the contours can be both closed and open curves. Additional to a flow of the curves in normal direction, evolution laws for the tangential flow of the endpoints are derived. Using a parametric approach to describe the evolving contours together with an edge-preserving denoising, we obtain a fast method for image segmentation and restoration. The analytical and numerical schemes are presented followed by numerical experiments with artificial test images and with a real medical image.

  1. Image Segmentation Using Parametric Contours With Free Endpoints

    NASA Astrophysics Data System (ADS)

    Benninghoff, Heike; Garcke, Harald

    2016-04-01

    In this paper, we introduce a novel approach for active contours with free endpoints. A scheme is presented for image segmentation and restoration based on a discrete version of the Mumford-Shah functional where the contours can be both closed and open curves. Additional to a flow of the curves in normal direction, evolution laws for the tangential flow of the endpoints are derived. Using a parametric approach to describe the evolving contours together with an edge-preserving denoising, we obtain a fast method for image segmentation and restoration. The analytical and numerical schemes are presented followed by numerical experiments with artificial test images and with a real medical image.

  2. Sharp bounds on causal effects using a surrogate endpoint.

    PubMed

    Kuroki, Manabu

    2013-11-10

    This paper considers a problem of evaluating the causal effect of a treatment X on a true endpoint Y using a surrogate endpoint S, in the presence of unmeasured confounders between S and Y. Such confounders render the causal effect of X on Y unidentifiable from the causal effect of X on S and the joint probability of S and Y. To evaluate the causal effect of X on Y in such a situation, this paper derives closed-form formulas for the sharp bounds on the causal effect of X on Y based on both the causal effect of X on S and the joint probability of S and Y under various assumptions. In addition, we show that it is not always necessary to observe Y to test the null causal effect of X on Y under the monotonicity assumption between X and S. These bounds enable clinical practitioners and researchers to assess the causal effect of a treatment on a true endpoint using a surrogate endpoint with minimum computational effort.

  3. Predictive Modeling of Apical Toxicity Endpoints Using Data ...

    EPA Pesticide Factsheets

    The US EPA and other regulatory agencies face a daunting challenge of evaluating potential toxicity for tens of thousands of environmental chemicals about which little is currently known. The EPA’s ToxCast program is testing a novel approach to this problem by screening compounds using a variety of in vitro assays and using the results to prioritize chemicals for further, more detailed testing. Phase I of ToxCast is testing 320 chemicals (mainly pesticide active ingredients) against ~400 cell-based and biochemical assays. In order to anchor these studies, we are using in vivo guideline study data for subchronic, chronic, cancer, reproductive and developmental endpoints. This data is compiled in the EPA toxicity reference database, ToxRefDB. The main goal of ToxCast is the discovery and validation of “signatures” linking in vitro assay data to in vivo toxicity endpoints. These signatures will be collections of assays that are correlated with particular endpoints. These assay collections should also help define molecular-and cellular-level mechanisms of toxicity. This talk will discuss our strategy to use a combination of statistical and machine learning methods, coupled with biochemical network or systems biology approaches. Our initial examples will focus signatures for endpoints from 2 year rodent cancer bioassays. Most of the data we have analyzed is in dose or concentration response series, so to effectively use this data we have developed novel appro

  4. Is Suicide Ideation a Surrogate Endpoint for Geriatric Suicide?

    ERIC Educational Resources Information Center

    Links, Paul S.; Heisel, Marnin J.; Quastel, Adam

    2005-01-01

    The present study explored the validity of treating suicide ideation as a surrogate endpoint that can serve as a proxy for suicide in clinical intervention research with suicidal seniors. Two criteria; that suicide ideation is modulated by the proposed intervention and that modulation of suicide ideation leads to a quantitative reduction in…

  5. Developing a Cognition Endpoint for Traumatic Brain Injury Clinical Trials.

    PubMed

    Silverberg, Noah D; Crane, Paul K; Dams-O'Connor, Kristen; Holdnack, James; Ivins, Brian J; Lange, Rael T; Manley, Geoffrey T; McCrea, Michael; Iverson, Grant L

    2017-01-15

    Cognitive impairment is a core clinical feature of traumatic brain injury (TBI). After TBI, cognition is a key determinant of post-injury productivity, outcome, and quality of life. As a final common pathway of diverse molecular and microstructural TBI mechanisms, cognition is an ideal endpoint in clinical trials involving many candidate drugs and nonpharmacological interventions. Cognition can be reliably measured with performance-based neuropsychological tests that have greater granularity than crude rating scales, such as the Glasgow Outcome Scale-Extended, which remain the standard for clinical trials. Remarkably, however, there is no well-defined, widely accepted, and validated cognition endpoint for TBI clinical trials. A single cognition endpoint that has excellent measurement precision across a wide functional range and is sensitive to the detection of small improvements (and declines) in cognitive functioning would enhance the power and precision of TBI clinical trials and accelerate drug development research. We outline methodologies for deriving a cognition composite score and a research program for validation. Finally, we discuss regulatory issues and the limitations of a cognition endpoint.

  6. ECOLOGICAL ENDPOINT MODELING: EFFECTS OF SEDIMENT ON FISH POPULATIONS

    EPA Science Inventory

    Sediment is one of the main stressors of concern for TMDLs (Total Maximum Daily Loads) for streams, and often it is a concern because of its impact on biological endpoints. The National Research Council (NRC) has recommended that the EPA promote the development of models that ca...

  7. Expanding the ecotoxicological toolbox: the inclusion of polychaete reproductive endpoints.

    PubMed

    Lewis, Ceri; Watson, Gordon J

    2012-04-01

    In the last 15 years the diversity of pollutants and routes of impact have increased. However, the polychaete families, species and endpoints investigated have remained fairly constant. Reproductive outputs are more ecologically relevant than adult physiological or biochemical changes. Nevertheless, there remains a paucity of data on the reproductive responses of the popular species to pollutants which limits our ability to understand the true ecological impacts of such contaminants on natural populations. We highlight the current knowledge gaps in our understanding of the impacts of pollutants on the 'model' species' reproductive biology and therefore the potential ecological impacts of such contaminants on their natural populations, and the potential benefits of a wider use of polychaete reproductive endpoints for ecotoxicological assessments. The following priority areas are suggested for inclusion in the polychaete ecotoxicology toolbox: 1. Include reproductive endpoints as assessments of ecotoxicology for the traditional 'model' species and those that have different reproductive traits to ensure broad ecological relevance. 2. Nereids and Arenicola marina should be used to investigate the interaction of pollutants with the endocrine/environmental control of reproduction. 3. Polychaetes are ideal for addressing the under representation of male eco-toxicity effects. 4. Emerging pollutants should be assessed with reproductive endpoints together with the traditional biomarkers. 5. Effects of pollutants on larval behaviour need to be explored considering the limited but equivocal results so far.

  8. Comparison and Evaluation of Laboratory and Field Measured Bioaccumulation Endpoints

    EPA Science Inventory

    Evaluation of bioaccumulation endpoints on a fugacity basis allows provides a framework to assess the biomagnification potential of a chemical and assess data deficiencies, i.e., uncertainties and lack of data. In addition, it is suggested that additional guidance is needed in o...

  9. Improving Endpoint Detection to Support Automated Systematic Reviews

    PubMed Central

    Lucic, Ana; Blake, Catherine L.

    2016-01-01

    Authors of biomedical articles use comparison sentences to communicate the findings of a study, and to compare the results of the current study with earlier studies. The Claim Framework defines a comparison claim as a sentence that includes at least two entities that are being compared, and an endpoint that captures the way in which the entities are compared. Although automated methods have been developed to identify comparison sentences from the text, identifying the role that a specific noun plays (i.e. entity or endpoint) is much more difficult. Automated methods have been successful at identifying the second entity, but classification models were unable to clearly differentiate between the first entity and the endpoint. We show empirically that establishing if head noun is an amount or measure provides a statistically significant improvement that increases the endpoint precision from 0.42 to 0.56 on longer and from 0.51 to 0.58 on shorter sentences and recall from 0.64 to 0.71 on longer and from 0.69 to 0.74 on shorter sentences. The differences were not statistically significant for the second compared entity. PMID:28269949

  10. 21 CFR 601.41 - Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Approval based on a surrogate endpoint or on an... Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival or... well-controlled clinical trials establishing that the biological product has an effect on a...

  11. 21 CFR 601.41 - Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival...

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Approval based on a surrogate endpoint or on an... Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival or... well-controlled clinical trials establishing that the biological product has an effect on a...

  12. 21 CFR 314.510 - Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 5 2012-04-01 2012-04-01 false Approval based on a surrogate endpoint or on an... Serious or Life-Threatening Illnesses § 314.510 Approval based on a surrogate endpoint or on an effect on... the drug product has an effect on a surrogate endpoint that is reasonably likely, based...

  13. 21 CFR 601.41 - Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Approval based on a surrogate endpoint or on an... Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival or... well-controlled clinical trials establishing that the biological product has an effect on a...

  14. 21 CFR 314.510 - Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival...

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 5 2014-04-01 2014-04-01 false Approval based on a surrogate endpoint or on an... Serious or Life-Threatening Illnesses § 314.510 Approval based on a surrogate endpoint or on an effect on... the drug product has an effect on a surrogate endpoint that is reasonably likely, based...

  15. 21 CFR 314.510 - Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 5 2011-04-01 2011-04-01 false Approval based on a surrogate endpoint or on an... Serious or Life-Threatening Illnesses § 314.510 Approval based on a surrogate endpoint or on an effect on... the drug product has an effect on a surrogate endpoint that is reasonably likely, based...

  16. 21 CFR 314.510 - Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Approval based on a surrogate endpoint or on an... Serious or Life-Threatening Illnesses § 314.510 Approval based on a surrogate endpoint or on an effect on... the drug product has an effect on a surrogate endpoint that is reasonably likely, based...

  17. 21 CFR 601.41 - Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival...

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Approval based on a surrogate endpoint or on an... Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival or... well-controlled clinical trials establishing that the biological product has an effect on a...

  18. 21 CFR 314.510 - Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival...

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... the drug product has an effect on a surrogate endpoint that is reasonably likely, based on... 21 Food and Drugs 5 2013-04-01 2013-04-01 false Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival or irreversible morbidity. 314.510 Section 314.510...

  19. Defining Surrogate Endpoints for Clinical Trials in Severe Falciparum Malaria

    PubMed Central

    Plewes, Katherine; Maude, Richard J.; Hanson, Josh; Herdman, M. Trent; Leopold, Stije J.; Ngernseng, Thatsanun; Charunwatthana, Prakaykaew; Phu, Nguyen Hoan; Ghose, Aniruddha; Hasan, M. Mahtab Uddin; Fanello, Caterina I.; Faiz, Md Abul; Hien, Tran Tinh; Day, Nicholas P. J.; White, Nicholas J.; Dondorp, Arjen M.

    2017-01-01

    Background Clinical trials in severe falciparum malaria require a large sample size to detect clinically meaningful differences in mortality. This means few interventions can be evaluated at any time. Using a validated surrogate endpoint for mortality would provide a useful alternative allowing a smaller sample size. Here we evaluate changes in coma score and plasma lactate as surrogate endpoints for mortality in severe falciparum malaria. Methods Three datasets of clinical studies in severe malaria were re-evaluated: studies from Chittagong, Bangladesh (adults), the African ‘AQUAMAT’ trial comparing artesunate and quinine (children), and the Vietnamese ‘AQ’ study (adults) comparing artemether with quinine. The absolute change, relative change, slope of the normalization over time, and time to normalization were derived from sequential measurements of plasma lactate and coma score, and validated for their use as surrogate endpoint, including the proportion of treatment effect on mortality explained (PTE) by these surrogate measures. Results Improvements in lactate concentration or coma scores over the first 24 hours of admission, were strongly prognostic for survival in all datasets. In hyperlactataemic patients in the AQ study (n = 173), lower mortality with artemether compared to quinine closely correlated with faster reduction in plasma lactate concentration, with a high PTE of the relative change in plasma lactate at 8 and 12 hours of 0.81 and 0.75, respectively. In paediatric patients enrolled in the ‘AQUAMAT’ study with cerebral malaria (n = 785), mortality was lower with artesunate compared to quinine, but this was not associated with faster coma recovery. Conclusions The relative changes in plasma lactate concentration assessed at 8 or 12 hours after admission are valid surrogate endpoints for severe malaria studies on antimalarial drugs or adjuvant treatments aiming at improving the microcirculation. Measures of coma recovery are not valid

  20. Generalized optimal design for two-arm, randomized phase II clinical trials with endpoints from the exponential dispersion family.

    PubMed

    Jiang, Wei; Mahnken, Jonathan D; He, Jianghua; Mayo, Matthew S

    2016-11-01

    For two-arm randomized phase II clinical trials, previous literature proposed an optimal design that minimizes the total sample sizes subject to multiple constraints on the standard errors of the estimated event rates and their difference. The original design is limited to trials with dichotomous endpoints. This paper extends the original approach to be applicable to phase II clinical trials with endpoints from the exponential dispersion family distributions. The proposed optimal design minimizes the total sample sizes needed to provide estimates of population means of both arms and their difference with pre-specified precision. Its applications on data from specific distribution families are discussed under multiple design considerations. Copyright © 2016 John Wiley & Sons, Ltd.

  1. BRIDGING FROM CLINICAL ENDPOINTS TO ESTIMATES OF TREATMENT VALUE FOR EXTERNAL DECISION MAKERS

    PubMed Central

    ZHU, C.W.; LEIBMAN, C.; TOWNSEND, R.; MCLAUGHLIN, T.; SCARMEAS, N.; ALBERT, M.; BRANDT, J.; BLACKER, D.; SANO, M.; STERN, Y.

    2009-01-01

    .01), BDRS (r=0.610, p<0.01), behavior (r=.2633, p=0.0005), EPS (r=0.1910, p=0.0137) and psychotic symptoms (r=0.253, p<0.01); and at 4-year follow-up, DS scores were significantly correlated with MMSE (r=−0.3705, p=0.017), BDRS (r=0.6982, p<0.001). Correlations between DS and behavior (−0.0085, p=0.96), EPS (r=0.3824, p=0.0794), psychotic symptoms (r=0.130, ns) were not statistically significant at follow-up. DS scores were also significantly correlated with total costs at baseline (r=0.2615, p=0.0003) and follow-up (r=0.3359, p=0.0318). Discussion AD is associated with deficits in cognition, function and behavior, thus it is imperative that these constructs are assessed in trials of AD treatment. However, assessing multiple endpoints can lead to confusion for decision makers if treatments do not impact all endpoints similarly, especially if the measures are not used typically in practice. One potential method for translating these deficits into a more meaningful outcome would be to identify a separate construct, one that takes a broader view of the overall impact of the disease. Patient dependence, as measured by the DS, would appear to be a reasonable choice – it is associated with the three clinical endpoints, as well as measures of cost (medical and informal), thereby providing a bridge between measures of clinical efficacy and value in a single, transparent measure. PMID:19262963

  2. A latent variable approach for modeling categorical endpoints among patients with rheumatoid arthritis treated with golimumab plus methotrexate.

    PubMed

    Hu, Chuanpu; Xu, Zhenhua; Rahman, Mahboob U; Davis, Hugh M; Zhou, Honghui

    2010-08-01

    The need for accurate exposure-response modeling is critical in the drug development process. Few methods are available for linking discrete endpoints, especially ordered categorical variables, to mechanistic (e.g., indirect response) models. Here we describe a latent-variable approach that is proposed in conjunction with an inhibitory indirect response model to link the placebo/comedication effect and drug exposure to the endpoints. The model is parsimonious, with desirable characteristics at initial timepoints, and allows simultaneous modeling of multiple endpoints that are categorically ordered. Application of the model is demonstrated with data from a phase 3 clinical trial of golimumab, a human IgG1kappa monoclonal antibody that binds with high affinity and specificity to tumor necrosis factor (TNF)-alpha, in patients with rheumatoid arthritis. The efficacy endpoints were 20, 50, and 70% improvement in the American College of Rheumatology criteria (ACR20, ACR50, and ACR70, respectively) as measures of improvement in disease severity. The modeling results were shown to be consistent by using either a sequential or simultaneous pharmacokinetic/pharmacodynamic modeling approach. The suitability of likelihood profiling and proper use of bootstrap methods in assessing parameter estimation precision are also presented. More accurate, parsimonious models with appropriately quantified uncertainty can facilitate better drug development decisions.

  3. The validated embryonic stem cell test to predict embryotoxicity in vitro.

    PubMed

    Seiler, Andrea E M; Spielmann, Horst

    2011-06-16

    In the embryonic stem cell test (EST), differentiation of mouse embryonic stem cells (mESCs) is used as a model to assess embryotoxicity in vitro. The test was successfully validated by the European Center for the Validation of Alternative Methods (ECVAM) and models fundamental mechanisms in embryotoxicity, such as cytotoxicity and differentiation. In addition, differences in sensitivity between differentiated (adult) and embryonic cells are also taken into consideration. To predict the embryotoxic potential of a test substance, three endpoints are assessed: the inhibition of differentiation into beating cardiomyocytes, the cytotoxic effects on stem cells and the cytotoxic effects on 3T3 fibroblasts. A special feature of the EST is that it is solely based on permanent cell lines so that primary embryonic cells and tissues from pregnant animals are not needed. In this protocol, we describe the ECVAM-validated method, in which the morphological assessment of contracting cardiomyocytes is used as an endpoint for differentiation, and the molecular-based FACS-EST method, in which highly predictive protein markers specific for developing heart tissue were selected. With these methods, the embryotoxic potency of a compound can be assessed in vitro within 10 or 7 d, respectively.

  4. Endpoints for Mouse Abdominal Tumor Models: Refinement of Current Criteria

    PubMed Central

    Paster, Eden V; Villines, Kimberly A; Hickman, Debra L

    2009-01-01

    Accurate, rapid, and noninvasive health assessments are required to establish more appropriate endpoints in mouse cancer models where tumor size is not easily measured. We evaluated potential endpoints in mice with experimentally induced peritoneal lymphoma, an abdominal tumor model, by comparing body weight, body condition, and behavior with those of a control group of mice not developing lymphoma. Our hypothesis was that body weight would increase or plateau, whereas body condition and behavioral scores would decrease, as disease progressed. Results indicated that body weight did not differ significantly between the control and experimental groups, but the experimental group experienced significant decreases in both body condition and behavioral scores. Our results support the use of body condition and behavioral scoring as adjunctive assessment methods for mice involved in abdominal lymphoma tumor studies in which health may decline despite an increase or plateau in body weight. PMID:19619413

  5. A new end-point for ELISA titrations.

    PubMed

    Vidal, José

    2004-01-01

    This report describes a new ELISA procedure based on end-point titrations. This end-point ELISA takes advantage of the change of color intensity that occurs when peroxidase-containing wells of an ELISA plate are revealed with diaminobenzidine-nickel and further intensification with silver: as antibody concentration and, therefore, peroxidase concentration, decreased, the color became stronger in some wells and, afterwards (i.e., at lower antibody and peroxidase concentrations), the color faded toward clear background. It is proposed that the reciprocal of the sample dilution at which the color intensifies can be used as a measure of the sample antibody content. This report verifies the validity and precision of that procedure.

  6. Changing the endpoints for determining effective obesity management.

    PubMed

    Ross, Robert; Blair, Steve; de Lannoy, Louise; Després, Jean-Pierre; Lavie, Carl J

    2015-01-01

    Health authorities worldwide recommend weight loss as a primary endpoint for effective obesity management. Despite a growing public awareness of the importance of weight loss and the spending of billions of dollars by Americans in attempts to lose weight, obesity prevalence continues to rise. In this report we argue that effective obesity management in today's environment will require a shift in focus from weight loss as the primary endpoint, to improvements in the causal behaviors; diet and exercise/physical activity (PA). We reason that increases in PA combined with a balanced diet are associated with improvement in many of the intermediate risk factors including cardiorespiratory fitness (CRF) associated with obesity despite minimal or no weight loss. Consistent with this notion, we suggest that a focus on healthy behaviors for the prevention of additional weight gain may be an effective way of managing obesity in the short term.

  7. Research priorities in biomarkers and surrogate end-points.

    PubMed

    Aronson, Jeffrey K

    2012-06-01

    Ideal tests of the effects of therapeutic interventions measure the desired outcomes; however, the desired outcomes are not always easily measured or may be long-term objectives. Biomarkers and surrogate end-points are often cheaper and easier to measure and can be measured over a shorter time span. They can be used in screening, diagnosing, staging, and monitoring diseases, in monitoring responses to interventions, and in various aspects of drug discovery and development. They can be extrinsic to the body or intrinsic, and can relate to any point in the pharmacological chain, at the molecular, cellular, tissue, or organ level. Problems arise when the relation between the pathophysiology of the disease and the mechanism of action of the intervention is not properly understood; when adverse effects obviate therapeutic effects; when confounding factors, such as other drugs, alter the surrogate independently of the final end-point; when a biomarker persists after resolution of the disease; and when the concentration-effect curves for the effects of an intervention on the primary outcome and the surrogate are different. Use of biomarkers may also be hindered by poor reproducibility of measurement techniques. Challenges for clinical pharmacologists are to devise biomarker tests that are reliable, reproducible, sensitive, and specific, and surrogate end-points that are associated with the clinical outcomes of concern and useful. A robust taxonomy is needed of the relations that link the pathophysiology of disease, the mechanisms of action of interventions and their adverse effects, the desired clinical outcomes, and the surrogate end-points that predict them.

  8. Modeling Robot Dynamic Performance for Endpoint Force Control

    DTIC Science & Technology

    1988-08-01

    we consider is robot endpoint force control, also known as manipulator compliant motion control. Force control research has been quite popular...manipulator through a programmed trajectory consisting of a sequence of joint positions and velocities. Position and velocity sensors located at the robot ...may be located. 1.1 Force Control Research Background Research in robot compliant motion control has been in these areas: " Passive compliance schemes

  9. Congenital adrenal hyperplasia: classification of studies employing psychological endpoints.

    PubMed

    Stout, Stephanie A; Litvak, Margarita; Robbins, Natashia M; Sandberg, David E

    2010-01-01

    Psychological outcomes in persons with congenital adrenal hyperplasia (CAH) have received substantial attention. The objectives of this paper were to (1) catalog psychological endpoints assessed in CAH outcome studies and (2) classify the conceptual/theoretical model shaping the research design and interpretation of CAH-related psychological effects. A total of 98 original research studies, published between 1955 and 2009, were categorized based on psychological endpoints examined as well as the research design and conceptual model guiding analysis and interpretation of data. The majority of studies (68%) investigated endpoints related to psychosexual differentiation. The preponderance of studies (76%) examined a direct relationship (i.e., inferring causality) between prenatal androgen exposure and psychological outcomes. Findings are discussed in relation to the observed imbalance between theoretical interest in the role of prenatal androgens in shaping psychosexual differentiation and a broader conceptual model that examines the role of other potential factors in mediating or moderating the influence of CAH pathophysiology on psychological outcomes in both affected females and males. The latter approach offers to identify factors amenable to clinical intervention that enhance both health and quality of life outcomes in CAH as well as other disorders of sex development.

  10. Challenges assessing clinical endpoints in early Huntington disease

    PubMed Central

    Paulsen, Jane S.; Wang, Chiachi; Duff, Kevin; Barker, Roger; Nance, Martha; Beglinger, Leigh; Moser, David; Williams, Janet K.; Simpson, Sheila; Langbehn, Douglas; van Kammen, Daniel P.

    2010-01-01

    The primary aim of this study was to evaluate the current accepted standard clinical endpoint for the earliest-studied HD participants likely to be recruited into clinical trials. Since the advent of genetic testing for HD, it is possible to identify gene carriers prior to the diagnosis of disease, which opens up the possibility of clinical trials of disease-modifying treatments in clinically asymptomatic persons. Current accepted standard clinical endpoints were examined as part of a multi-national, 32-site, longitudinal, observational study of 786 research participants currently in the HD prodrome (gene-positive but not clinically diagnosed). Clinical signs and symptoms were used to prospectively predict functional loss as assessed by current accepted standard endpoints over 8 years of follow up. Functional capacity measures were not sensitive for HD in the prodrome; over 88% scored at ceiling. Prospective evaluation revealed that the first functional loss was in their accustomed work. In a survival analysis, motor, cognitive, and psychiatric measures were all predictors of job change. To our knowledge, this is the first prospective study ever conducted on the emergence of functional loss secondary to brain disease. We conclude that future clinical trials designed for very early disease will require the development of new and more sensitive measures of real-life function. PMID:20623772

  11. Exposing the cancer genome atlas as a SPARQL endpoint

    PubMed Central

    Deus, Helena F.; Veiga, Diogo F.; Freire, Pablo R.; Weinstein, John N.; Mills, Gordon B.; Almeida, Jonas S.

    2011-01-01

    The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to characterize several types of cancer. Datasets from biomedical domains such as TCGA present a particularly challenging task for those interested in dynamically aggregating its results because the data sources are typically both heterogeneous and distributed. The Linked Data best practices offer a solution to integrate and discover data with those characteristics, namely through exposure of data as Web services supporting SPARQL, the Resource Description Framework query language. Most SPARQL endpoints, however, cannot easily be queried by data experts. Furthermore, exposing experimental data as SPARQL endpoints remains a challenging task because, in most cases, data must first be converted to Resource Description Framework triples. In line with those requirements, we have developed an infrastructure to expose clinical, demographic and molecular data elements generated by TCGA as a SPARQL endpoint by assigning elements to entities of the Simple Sloppy Semantic Database (S3DB) management model. All components of the infrastructure are available as independent Representational State Transfer (REST) Web services to encourage reusability, and a simple interface was developed to automatically assemble SPARQL queries by navigating a representation of the TCGA domain. A key feature of the proposed solution that greatly facilitates assembly of SPARQL queries is the distinction between the TCGA domain descriptors and data elements. Furthermore, the use of the S3DB management model as a mediator enables queries to both public and protected data without the need for prior submission to a single data source. PMID:20851208

  12. Lethal multiple pterygium syndrome

    PubMed Central

    Joshi, Tulika; Noor, Nazia Nagori; Kural, Moolraj; Tripathi, Amita

    2016-01-01

    The multiple pterygium syndrome is consist of wide range of fetal malformations which have a genetic linkage. A defect in embryonic acetylcholine receptor which can be inherited as autosomal recessive, autosomal dominant, or X-linked fashion is the cause of this syndrome. We present a sporadic case of lethal multiple pterygium syndrome. PMID:27843868

  13. Cell size and the blockage of electron transfer in photosynthesis: proposed endpoints for algal assays and its application to soil alga Chlorococcum infusionum.

    PubMed

    Nam, Sun-Hwa; An, Youn-Joo

    2015-06-01

    This study evaluated multiple endpoints of algal assays to identify sensitive and easy to use endpoints that could be applied to evaluate algal toxicity in metal-polluted soil extracts. Soil algae play an important role in trophic levels; thus, Chlorococcum infusionum was selected as the test species. Soil extracts were used because they might help identify potential soil retention and ecological hazards caused by pollutants that are present in the soil aqueous phase. The multi-endpoints measured were growth yield, photosynthetic activities, and cell viabilities. Nine parameters were measured to evaluate photosynthetic activity; namely, specific energy fluxes per quinone A-reducing photosystem II reaction center (absorption flux, trapped energy flux, electron transport flux, and dissipated energy flux per reaction center), quantum yields (maximum quantum yield of primary photochemistry, quantum yield of electron transport, quantum yield of energy dissipation, and average quantum yield of primary photochemistry), and the blockage of electron transfer from the reaction center to the quinone pool. Cell viability was evaluated by measuring cell size, cell granularity, and the autofluorescence of chlorophyll using flow cytometry. The results showed that heavy metals reduced growth yield, cell viability, and the photosynthetic activity of C. infusionum in soil extracts. Out of the 13 tested endpoints, the blockage of electron transfer from the reaction center to the quinone pool and cell size represented the most sensitive endpoints. We propose that both endpoints should be measured, along with conventional growth yield, to determine the effect of soil pollutants and to lower pollutant concentrations in soils.

  14. Control of end-point forces of a multijoint limb by functional neuromuscular stimulation.

    PubMed

    Lan, N; Crago, P E; Chizeck, H J

    1991-10-01

    A multivariable feedback controller was designed and tested for regulating the magnitude and orientation of the force vector at the end point of a multijoint limb in contact with an isometric load. The force vector was produced by electrical stimulation of muscles. To achieve arbitrary control of end-point force magnitude and orientation, two coupling issues must be dealt with by the control system. First, there is a geometric coupling between the end-point force vector and joint torques. The amplitude and orientation of the force vector depend on the limb geometry. Second, torques at two joints may be coupled due to activation of muscles that cross them (biarticular coupling). To eliminate the geometric coupling, a transformation of controller error from the Cartesian space to the joint space was employed. A multivariable proportional-plus-integral (PI) control law was used to calculate muscle activation based on the transformed controller error. Centralized and decentralized controls were investigated for decoupling the effects of biarticular muscles. The results obtained from cat experiments showed that the magnitude and orientation of the end-point forces of the cat hindlimb could be regulated by this controller. In the presence of strong biarticular coupling, centralized control yielded better performance than decentralized control during transient responses. Both control strategies could decouple the biarticular muscle at steady state. When no biarticular coupling was present, centralized control sometimes performed worse than decentralized control. This is the first step in the simultaneous control of multiple joints by functional neuromuscular stimulation (FNS). The controller has broad potential applications in FNS neural prostheses.

  15. The risky reliance on small surrogate endpoint studies when planning a large prevention trial.

    PubMed

    Baker, Stuart G; Kramer, Barnett S

    2013-02-01

    The definitive evaluation of treatment to prevent a chronic disease with low incidence in middle age, such as cancer or cardiovascular disease, requires a trial with a large sample size of perhaps 20,000 or more. To help decide whether to implement a large true endpoint trial, investigators first typically estimate the effect of treatment on a surrogate endpoint in a trial with a greatly reduced sample size of perhaps 200 subjects. If investigators reject the null hypothesis of no treatment effect in the surrogate endpoint trial they implicitly assume they would likely correctly reject the null hypothesis of no treatment effect for the true endpoint. Surrogate endpoint trials are generally designed with adequate power to detect an effect of treatment on surrogate endpoint. However, we show that a small surrogate endpoint trial is more likely than a large surrogate endpoint trial to give a misleading conclusion about the beneficial effect of treatment on true endpoint, which can lead to a faulty (and costly) decision about implementing a large true endpoint prevention trial. If a small surrogate endpoint trial rejects the null hypothesis of no treatment effect, an intermediate-sized surrogate endpoint trial could be a useful next step in the decision-making process for launching a large true endpoint prevention trial.

  16. Endpoint-based parallel data processing in a parallel active messaging interface of a parallel computer

    DOEpatents

    Archer, Charles J; Blocksome, Michael E; Ratterman, Joseph D; Smith, Brian E

    2014-02-11

    Endpoint-based parallel data processing in a parallel active messaging interface ('PAMI') of a parallel computer, the PAMI composed of data communications endpoints, each endpoint including a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task, the compute nodes coupled for data communications through the PAMI, including establishing a data communications geometry, the geometry specifying, for tasks representing processes of execution of the parallel application, a set of endpoints that are used in collective operations of the PAMI including a plurality of endpoints for one of the tasks; receiving in endpoints of the geometry an instruction for a collective operation; and executing the instruction for a collective opeartion through the endpoints in dependence upon the geometry, including dividing data communications operations among the plurality of endpoints for one of the tasks.

  17. Endpoint-based parallel data processing in a parallel active messaging interface of a parallel computer

    DOEpatents

    Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

    2014-08-12

    Endpoint-based parallel data processing in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints, each endpoint including a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task, the compute nodes coupled for data communications through the PAMI, including establishing a data communications geometry, the geometry specifying, for tasks representing processes of execution of the parallel application, a set of endpoints that are used in collective operations of the PAMI including a plurality of endpoints for one of the tasks; receiving in endpoints of the geometry an instruction for a collective operation; and executing the instruction for a collective operation through the endpoints in dependence upon the geometry, including dividing data communications operations among the plurality of endpoints for one of the tasks.

  18. Clinical research and methodology: What usage and what hierarchical order for secondary endpoints?

    PubMed

    Laporte, Silvy; Diviné, Marine; Girault, Danièle

    2016-02-01

    In a randomised clinical trial, when the result of the primary endpoint shows a significant benefit, the secondary endpoints are scrutinised to identify additional effects of the treatment. However, this approach entails a risk of concluding that there is a benefit for one of these endpoints when such benefit does not exist (inflation of type I error risk). There are mainly two methods used to control the risk of drawing erroneous conclusions for secondary endpoints. The first method consists of distributing the risk over several co-primary endpoints, so as to maintain an overall risk of 5%. The second is the hierarchical test procedure, which consists of first establishing a hierarchy of the endpoints, then evaluating each endpoint in succession according to this hierarchy while the endpoints continue to show statistical significance. This simple method makes it possible to show the additional advantages of treatments and to identify the factors that differentiate them.

  19. Patient-specific dosimetric endpoints based treatment plan quality control in radiotherapy.

    PubMed

    Song, Ting; Staub, David; Chen, Mingli; Lu, Weiguo; Tian, Zhen; Jia, Xun; Li, Yongbao; Zhou, Linghong; Jiang, Steve B; Gu, Xuejun

    2015-11-07

    In intensity modulated radiotherapy (IMRT), the optimal plan for each patient is specific due to unique patient anatomy. To achieve such a plan, patient-specific dosimetric goals reflecting each patient's unique anatomy should be defined and adopted in the treatment planning procedure for plan quality control. This study is to develop such a personalized treatment plan quality control tool by predicting patient-specific dosimetric endpoints (DEs). The incorporation of patient specific DEs is realized by a multi-OAR geometry-dosimetry model, capable of predicting optimal DEs based on the individual patient's geometry. The overall quality of a treatment plan is then judged with a numerical treatment plan quality indicator and characterized as optimal or suboptimal. Taking advantage of clinically available prostate volumetric modulated arc therapy (VMAT) treatment plans, we built and evaluated our proposed plan quality control tool. Using our developed tool, six of twenty evaluated plans were identified as sub-optimal plans. After plan re-optimization, these suboptimal plans achieved better OAR dose sparing without sacrificing the PTV coverage, and the dosimetric endpoints of the re-optimized plans agreed well with the model predicted values, which validate the predictability of the proposed tool. In conclusion, the developed tool is able to accurately predict optimally achievable DEs of multiple OARs, identify suboptimal plans, and guide plan optimization. It is a useful tool for achieving patient-specific treatment plan quality control.

  20. Patient-specific dosimetric endpoints based treatment plan quality control in radiotherapy

    NASA Astrophysics Data System (ADS)

    Song, Ting; Staub, David; Chen, Mingli; Lu, Weiguo; Tian, Zhen; Jia, Xun; Li, Yongbao; Zhou, Linghong; Jiang, Steve B.; Gu, Xuejun

    2015-11-01

    In intensity modulated radiotherapy (IMRT), the optimal plan for each patient is specific due to unique patient anatomy. To achieve such a plan, patient-specific dosimetric goals reflecting each patient’s unique anatomy should be defined and adopted in the treatment planning procedure for plan quality control. This study is to develop such a personalized treatment plan quality control tool by predicting patient-specific dosimetric endpoints (DEs). The incorporation of patient specific DEs is realized by a multi-OAR geometry-dosimetry model, capable of predicting optimal DEs based on the individual patient’s geometry. The overall quality of a treatment plan is then judged with a numerical treatment plan quality indicator and characterized as optimal or suboptimal. Taking advantage of clinically available prostate volumetric modulated arc therapy (VMAT) treatment plans, we built and evaluated our proposed plan quality control tool. Using our developed tool, six of twenty evaluated plans were identified as sub-optimal plans. After plan re-optimization, these suboptimal plans achieved better OAR dose sparing without sacrificing the PTV coverage, and the dosimetric endpoints of the re-optimized plans agreed well with the model predicted values, which validate the predictability of the proposed tool. In conclusion, the developed tool is able to accurately predict optimally achievable DEs of multiple OARs, identify suboptimal plans, and guide plan optimization. It is a useful tool for achieving patient-specific treatment plan quality control.

  1. New science-based endpoints to accelerate oncology drug development.

    PubMed

    Kelloff, Gary J; Sigman, Caroline C

    2005-03-01

    Although several new oncology drugs have reached the market, more than 80% of drugs for all indications entering clinical development do not get marketing approval, with many failing late in development often in Phase III trials, because of unexpected safety issues or difficulty determining efficacy, including confounded outcomes. These factors contribute to the high costs of oncology drug development and clearly show the need for faster, more cost-effective strategies for evaluating oncology drugs and better definition of patients who will benefit from treatment. Remarkable advances in the understanding of neoplastic progression at the cellular and molecular levels have spurred the discovery of molecularly targeted drugs. This progress along with advances in imaging and bioassay technologies are the basis for describing and evaluating new biomarker endpoints as well as for defining other biomarkers for identifying patient populations, potential toxicity, and providing evidence of drug effect and efficacy. Definitions and classifications of these biomarkers for use in oncology drug development are presented in this paper. Science-based and practical criteria for validating biomarkers have been developed including considerations of mechanistic plausibility, available methods and technology, and clinical feasibility. New promising tools for measuring biomarkers have also been developed and are based on genomics and proteomics, direct visualisation by microscopy (e.g., confocal microscopy and computer-assisted image analysis of cellular features), nanotechnologies, and direct and remote imaging (e.g., fluorescence endoscopy and anatomical, functional and molecular imaging techniques). The identification and evaluation of potential surrogate endpoints and other biomarkers require access to and analysis of large amounts of data, new technologies and extensive research resources. Further, there is a requirement for a convergence of research, regulatory and drug developer

  2. Exploring a possible origin of the QCD critical endpoint

    SciTech Connect

    Bugaev, K. A. Petrov, V. K. Zinovjev, G. M.

    2013-03-15

    We develop a new model of the QCD critical endpoint by matching the deconfinement phase transition line of quark-gluon bags with the similar line at which the bag surface tension coefficient vanishes. Unlike all previous studies of such models the deconfined phase in our approach is defined not by an essential singularity of the isobaric partition function but its simple pole. As an unexpected result we find out that the first-order phase transition which is usually defined by a discontinuity of the first derivative of the bag system pressure results from a discontinuity of the derivative of surface tension coefficient of quark-gluon bags.

  3. Two-temperature LATE-PCR endpoint genotyping

    PubMed Central

    Sanchez, J Aquiles; Abramowitz, Jessica D; Salk, Jesse J; Reis, Arthur H; Rice, John E; Pierce, Kenneth E; Wangh, Lawrence J

    2006-01-01

    Background In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. Results Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE)-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA) and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of 2:1 and 1:2 ratios of the

  4. Impact of copula directional specification on multi-trial evaluation of surrogate endpoints

    PubMed Central

    Renfro, Lindsay A.; Shang, Hongwei; Sargent, Daniel J.

    2014-01-01

    Evaluation of surrogate endpoints using patient-level data from multiple trials is the gold standard, where multi-trial copula models are used to quantify both patient-level and trial-level surrogacy. While limited consideration has been given in the literature to copula choice (e.g., Clayton), no prior consideration has been given to direction of implementation (via survival versus distribution functions). We demonstrate that evenwith the “correct” copula family, directional misspecification leads to biased estimates of patient-level and trial-level surrogacy. We illustrate with a simulation study and a re-analysis of disease-free survival as a surrogate for overall survival in early stage colon cancer. PMID:24905465

  5. Assessment of toxicity test endpoints for freshwater mussel larvae (glochidia).

    PubMed

    Fritts, Andrea K; Barnhart, M Christopher; Bradley, Megan; Liu, Na; Cope, W Gregory; Hammer, Edward; Bringolf, Robert B

    2014-01-01

    The objectives of the present study were to determine if the viability of freshwater mussel larvae (glochidia) is an ecologically relevant endpoint for toxicity tests and to define the appropriate duration of those tests. The authors assessed 1) how viability (the shell closure response to sodium chloride) compares with infectivity (ability to attach to a host fish and successfully metamorphose to the juvenile stage), and 2) the decline of viability and infectivity over time after glochidia were released from female mussels. Glochidia of 7 mussel species were isolated from females, placed in water, and subsampled daily for 2 d to 5 d. Viability, when ≥90%, was generally a good predictor of infectivity; however, when viability was <90%, infectivity was often disproportionately low, especially for glochidia collected near the end of the brooding period. Viability and infectivity declined more rapidly in natural water and sediment compared to reconstituted water. Following 24-h exposure to a toxicant (sodium chloride or copper), infectivity of the viable glochidia did not differ among concentrations of toxicants. The results indicate that viability is a valid proxy for infectivity and an ecologically relevant endpoint for standard toxicity tests with freshwater mussels for any test duration with control viability >90%.

  6. Design and analysis of crossover trials for absorbing binary endpoints.

    PubMed

    Nason, Martha; Follmann, Dean

    2010-09-01

    The crossover is a popular and efficient trial design used in the context of patient heterogeneity to assess the effect of treatments that act relatively quickly and whose benefit disappears with discontinuation. Each patient can serve as her own control as within-individual treatment and placebo responses are compared. Conventional wisdom is that these designs are not appropriate for absorbing binary endpoints, such as death or HIV infection. We explore the use of crossover designs in the context of these absorbing binary endpoints and show that they can be more efficient than the standard parallel group design when there is heterogeneity in individuals' risks. We also introduce a new two-period design where first period "survivors" are rerandomized for the second period. This design combines the crossover design with the parallel design and achieves some of the efficiency advantages of the crossover design while ensuring that the second period groups are comparable by randomization. We discuss the validity of the new designs and evaluate both a mixture model and a modified Mantel-Haenszel test for inference. The mixture model assumes no carryover or period effects while the Mantel-Haenszel approach conditions out period effects. Simulations are used to compare the different designs and an example is provided to explore practical issues in implementation.

  7. Immediate skin responses to laser and light treatments: Warning endpoints: How to avoid side effects.

    PubMed

    Wanner, Molly; Sakamoto, Fernanda H; Avram, Mathew M; Anderson, R Rox

    2016-05-01

    Lasers are versatile, commonly used treatment tools in dermatology. While it is tempting to follow manufacturer's guidelines or other "recipes" for laser treatment, this approach alone can be a recipe for disaster. Specific and immediate skin responses or endpoints exist and are clinically useful because they correlate with underlying mechanisms that are either desirable (ie, therapeutic), undesirable (ie, warning signs of injury or side effects), or incidental. The observation of clinical endpoints is a safe and reliable guide for appropriate treatment. This article presents the warning endpoints during specific dermatologic laser treatments, and the accompanying article presents the therapeutic endpoints, their underlying mechanisms, and the utility of these endpoints.

  8. Endpoint Force Fluctuations Reveal Flexible Rather Than Synergistic Patterns of Muscle Cooperation

    PubMed Central

    Kutch, Jason J.; Kuo, Arthur D.; Bloch, Anthony M.; Rymer, William Z.

    2008-01-01

    We developed a new approach to investigate how the nervous system activates multiple redundant muscles by studying the endpoint force fluctuations during isometric force generation at a multi-degree-of-freedom joint. We hypothesized that, due to signal-dependent muscle force noise, endpoint force fluctuations would depend on the target direction of index finger force and that this dependence could be used to distinguish flexible from synergistic activation of the musculature. We made high-gain measurements of isometric forces generated to different target magnitudes and directions, in the plane of index finger metacarpophalangeal joint abduction–adduction/flexion–extension. Force fluctuations from each target were used to calculate a covariance ellipse, the shape of which varied as a function of target direction. Directions with narrow ellipses were approximately aligned with the estimated mechanical actions of key muscles. For example, targets directed along the mechanical action of the first dorsal interosseous (FDI) yielded narrow ellipses, with 88% of the variance directed along those target directions. It follows the FDI is likely a prime mover in this target direction and that, at most, 12% of the force variance could be explained by synergistic coupling with other muscles. In contrast, other target directions exhibited broader covariance ellipses with as little as 30% of force variance directed along those target directions. This is the result of cooperation among multiple muscles, based on independent electromyographic recordings. However, the pattern of cooperation across target directions indicates that muscles are recruited flexibly in accordance with their mechanical action, rather than in fixed groupings. PMID:18799603

  9. Functiogenesis of the embryonic central nervous system revealed by optical recording with a voltage-sensitive dye.

    PubMed

    Sato, Katsushige; Momose-Sato, Yoko

    2017-01-01

    Clarification of the functiogenesis of the embryonic central nervous system (CNS) has long been problematic, because conventional electrophysiological techniques have several limitations. First, early embryonic neurons are small and fragile, and the application of microelectrodes is challenging. Second, the simultaneous monitoring of electrical activity from multiple sites is limited, and as a consequence, spatiotemporal response patterns of neural networks cannot be assessed. We have applied multiple-site optical recording with a voltage-sensitive dye to the embryonic CNS and paved a new way to analyze the functiogenesis of the CNS. In this review, we discuss key points of optical recording in the embryonic CNS and introduce recent progress in optical investigations on the embryonic CNS with special emphasis on the development of the chick olfactory system. The studies clearly demonstrate the usefulness of voltage-sensitive dye recording as a powerful tool for elucidating the functional organization of the vertebrate embryonic CNS.

  10. Computation of eigenfunctions and eigenvalues for the Sturm-Liouville problem with Dirichlet boundary conditions at the left endpoint and Neumann conditions at the right endpoint

    NASA Astrophysics Data System (ADS)

    Khapaev, M. M.; Khapaeva, T. M.

    2016-10-01

    A functional-based variational method is proposed for finding the eigenfunctions and eigenvalues in the Sturm-Liouville problem with Dirichlet boundary conditions at the left endpoint and Neumann conditions at the right endpoint. Computations are performed for three potentials: sin(( x-π)2/π), cos(4 x), and a high nonisosceles triangle.

  11. 21 CFR 601.41 - Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Approval based on a surrogate endpoint or on an effect on a clinical endpoint other than survival or irreversible morbidity. 601.41 Section 601.41 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED)...

  12. Evaluation of embryotoxicity for major components of herbal extracts using the chick embryonic heart micromass and mouse D3 embryonic stem cell systems.

    PubMed

    Mohammed, Omar J; Latif, Muhammad Liaque; Pratten, Margaret K

    2016-01-01

    Herbal remedies are often used during the early stages of pregnancy, being considered 'harmless' and 'natural'. There are insufficient data regarding their potential embryotoxicity. The main components of selected herbs, including 6-gingerol from ginger, Ginkgolide A and Ginkgolide B from gingko biloba and Ginsenoside Rg1 from ginseng, have been investigated using chick embryonic heart micromass and Mouse D3 embryonic stem cells. The potential effects were evaluated via alteration in contractility, cell viability, and cell protein content. The myocytes in both systems were also demonstrated by immunocytochemistry using a specific cardiomyocyte marker (α-actinin). For 6-gingerol, Ginkgolide A, Ginkgolide B and Ginsenoside Rg1 in both methods, at moderate to high concentrations, there were alterations in the values for the endpoints. These data indicate that herbal remedies used in the first trimester of pregnancy might not be safe for fetal development.

  13. Evaluation of a multi-endpoint assay in rats, combining the bone-marrow micronucleus test, the Comet assay and the flow-cytometric peripheral blood micronucleus test.

    PubMed

    Bowen, Damian E; Whitwell, James H; Lillford, Lucinda; Henderson, Debbie; Kidd, Darren; Mc Garry, Sarah; Pearce, Gareth; Beevers, Carol; Kirkland, David J

    2011-05-18

    With the publication of revised draft ICH guidelines (Draft ICH S2), there is scope and potential to establish a combined multi-end point in vivo assay to alleviate the need for multiple in vivo assays, thereby reducing time, cost and use of animals. Presented here are the results of an evaluation trial in which the bone-marrow and peripheral blood (via MicroFlow(®) flow cytometry) micronucleus tests (looking at potential chromosome breakage and whole chromosome loss) in developing erythrocytes or young reticulocytes were combined with the Comet assay (measuring DNA strand-breakage), in stomach, liver and blood lymphocytes. This allowed a variety of potential target tissues (site of contact, site of metabolism and peripheral distribution) to be assessed for DNA damage. This combination approach was performed with minimal changes to the standard and regulatory recommended sampling times for the stand-alone assays. A series of eight in vivo genotoxins (2-acetylaminofluorene, benzo[a]pyrene, carbendazim, cyclophosphamide, dimethylnitrosamine, ethyl methanesulfonate, ethyl nitrosourea and mitomycin C), which are known to act via different modes of action (direct- and indirect-acting clastogens, alkylating agents, gene mutagens, cross-linking and aneugenic compounds) were tested. Male rats were dosed at 0, 24 and 45 h, and bone marrow and peripheral blood (micronucleus endpoint), liver, whole blood and stomach (Comet endpoint) were sampled at three hours after the last dose. Comet and micronucleus responses were as expected based on available data for conventional (acute) stand-alone assays. All compounds were detected as genotoxic in at least one of the endpoints. The importance of evaluating both endpoints was highlighted by the uniquely positive responses for certain chemicals (benzo[a]pyrene and 2-acetylaminofluorene) with the Comet endpoint and certain other chemicals (carbendazim and mitomycin C) with the micronucleus endpoint. The data generated from these

  14. Multiple roles of Activin/Nodal, bone morphogenetic protein, fibroblast growth factor and Wnt/β-catenin signalling in the anterior neural patterning of adherent human embryonic stem cell cultures

    PubMed Central

    Lupo, Giuseppe; Novorol, Claire; Smith, Joseph R.; Vallier, Ludovic; Miranda, Elena; Alexander, Morgan; Biagioni, Stefano; Pedersen, Roger A.; Harris, William A.

    2013-01-01

    Several studies have successfully produced a variety of neural cell types from human embryonic stem cells (hESCs), but there has been limited systematic analysis of how different regional identities are established using well-defined differentiation conditions. We have used adherent, chemically defined cultures to analyse the roles of Activin/Nodal, bone morphogenetic protein (BMP), fibroblast growth factor (FGF) and Wnt/β-catenin signalling in neural induction, anteroposterior patterning and eye field specification in hESCs. We show that either BMP inhibition or activation of FGF signalling is required for effective neural induction, but these two pathways have distinct outcomes on rostrocaudal patterning. While BMP inhibition leads to specification of forebrain/midbrain positional identities, FGF-dependent neural induction is associated with strong posteriorization towards hindbrain/spinal cord fates. We also demonstrate that Wnt/β-catenin signalling is activated during neural induction and promotes acquisition of neural fates posterior to forebrain. Therefore, inhibition of this pathway is needed for efficient forebrain specification. Finally, we provide evidence that the levels of Activin/Nodal and BMP signalling have a marked influence on further forebrain patterning and that constitutive inhibition of these pathways represses expression of eye field genes. These results show that the key mechanisms controlling neural patterning in model vertebrate species are preserved in adherent, chemically defined hESC cultures and reveal new insights into the signals regulating eye field specification. PMID:23576785

  15. Evolution of the mammalian embryonic pluripotency gene regulatory network

    PubMed Central

    Fernandez-Tresguerres, Beatriz; Cañon, Susana; Rayon, Teresa; Pernaute, Barbara; Crespo, Miguel; Torroja, Carlos; Manzanares, Miguel

    2010-01-01

    Embryonic pluripotency in the mouse is established and maintained by a gene-regulatory network under the control of a core set of transcription factors that include octamer-binding protein 4 (Oct4; official name POU domain, class 5, transcription factor 1, Pou5f1), sex-determining region Y (SRY)-box containing gene 2 (Sox2), and homeobox protein Nanog. Although this network is largely conserved in eutherian mammals, very little information is available regarding its evolutionary conservation in other vertebrates. We have compared the embryonic pluripotency networks in mouse and chick by means of expression analysis in the pregastrulation chicken embryo, genomic comparisons, and functional assays of pluripotency-related regulatory elements in ES cells and blastocysts. We find that multiple components of the network are either novel to mammals or have acquired novel expression domains in early developmental stages of the mouse. We also find that the downstream action of the mouse core pluripotency factors is mediated largely by genomic sequence elements nonconserved with chick. In the case of Sox2 and Fgf4, we find that elements driving expression in embryonic pluripotent cells have evolved by a small number of nucleotide changes that create novel binding sites for core factors. Our results show that the network in charge of embryonic pluripotency is an evolutionary novelty of mammals that is related to the comparatively extended period during which mammalian embryonic cells need to be maintained in an undetermined state before engaging in early differentiation events. PMID:21048080

  16. Trends in Utilization of Surrogate Endpoints in Contemporary Cardiovascular Clinical Trials.

    PubMed

    Patel, Ravi B; Vaduganathan, Muthiah; Samman-Tahhan, Ayman; Kalogeropoulos, Andreas P; Georgiopoulou, Vasiliki V; Fonarow, Gregg C; Gheorghiade, Mihai; Butler, Javed

    2016-06-01

    Surrogate endpoints facilitate trial efficiency but are variably linked to clinical outcomes, and limited data are available exploring their utilization in cardiovascular clinical trials over time. We abstracted data regarding primary clinical, intermediate, and surrogate endpoints from all phase II to IV cardiovascular clinical trials from 2001 to 2012 published in the 8 highest Web of Science impact factor journals. Two investigators independently classified the type of primary endpoint. Of the 1,224 trials evaluated, 677 (55.3%) primary endpoints were clinical, 165 (13.5%) intermediate, and 382 (31.2%) surrogate. The relative proportions of these endpoints remained constant over time (p = 0.98). Trials using surrogate endpoints were smaller (187 vs 1,028 patients) and enrolled patients more expeditiously (1.4 vs 0.9 patients per site per month) compared with trials using clinical endpoints (p <0.001 for both comparisons). Surrogate endpoint trials were independently more likely to meet their primary endpoint compared to trials with clinical endpoints (adjusted odds ratio 1.56, 95% CI 1.05 to 2.34; p = 0.03). Rates of positive results in clinical endpoint trials have decreased over time from 66.1% in 2001 to 2003 to 47.2% in 2010 to 2012 (p = 0.001), whereas these rates have remained stable over the same period for surrogate (72.0% to 69.3%, p = 0.27) and intermediate endpoints (74.4% to 71.4%, p = 0.98). In conclusion, approximately a third of contemporary cardiovascular trials use surrogate endpoints. These trials are completed more expeditiously and are more likely to meet their primary outcomes. The overall scientific contribution of these surrogate endpoint trials requires further attention given their variable association with definitive outcomes.

  17. The embryonic midbrain directs neuronal specification of embryonic stem cells at early stages of differentiation.

    PubMed

    Baizabal, José-Manuel; Covarrubias, Luis

    2009-01-01

    Specific neuronal differentiation of Embryonic Stem Cells (ESCs) depends on their capacity to interpret environmental cues. At present, it is not clear at which stage of differentiation ESCs become competent to produce multiple neuronal lineages in response to the niche of the embryonic brain. To unfold the developmental potential of ESC-derived precursors, we transplanted these cells into the embryonic midbrain explants, where neurogenesis occurs as in normal midbrain development. Using this experimental design, we show that the transition from ESCs to Embryoid Body (EB) precursors is necessary to differentiate into Lmx1a(+)/Ptx3(+)/TH(+) dopaminergic neurons around the ventral midline of the midbrain. In addition, EB cells placed at other dorsal-ventral levels of the midbrain give rise to Nkx6.1(+) red nucleus (RN) neurons, Nkx2.2(+) ventral interneurons and Pax7(+) dorsal neurons at the correct positions. Notably, differentiation of ESCs into Neural Precursor Cells (NPCs) prior to transplantation markedly reduces specification at the Lmx1a, Nkx6.1 and Pax7 expression domains, without affecting neuronal differentiation. Finally, exposure to Fgf8 and Shh in vitro promotes commitment of some ESC-derived NPCs to differentiate into putative Lmx1a(+) dopaminergic neurons in the midbrain. Our data demonstrate intrinsic developmental potential differences among ESC-derived precursor populations.

  18. The use of RT-PCR for determination of separate end-points for the strains IB H120 and IB D274 in titration of the combination vaccine Poulvac IB® primer.

    PubMed

    Geerligs, H J; Meinders, C A M; Snel, J; Duyves, W

    2013-11-01

    Poulvac IB® Primer is a lyophilized vaccine containing two attenuated infectious bronchitis strains in one vial, IB H120 and IB D274. For quantification of the viral content of the vaccine, dilution series of the final product are inoculated in embryonated chicken eggs. After the incubation period of seven days standard practice is for the embryos to be taken from each egg and examined visually for IB specific lesions; these readings are used to determine an end-point in viral titrations. The result is a titre value to which both strains contribute. However, it is not clear what the live virus titre is for strain IB H120 and for strain IB D274. In order to determine end-points in the titration for each of the two strains, we collected the allantoic fluids from each egg after the incubation period and tested these for the presence of IB H120 and IB D274 by a strain specific reverse phase PCR. Based on the data obtained by PCR we were able to determine an end-point for each of the two strains. For a given commercial batch of Poulvac IB primer we determined titres of 10(6.31) EID50 per vial for IB H120 and 10(6.59) EID50 for IB D274 using PCR for end-point determination. These end-points matched well with the end-point determined for both strains cumulatively after visual examination, i.e. 10(6.67) EID50 per vial. It is concluded that PCR is a suitable means to determine end-points in titrations of live viruses.

  19. Nucleotide Excision Repair Is Not Induced in Human Embryonic Lung Fibroblasts Treated with Environmental Pollutants

    PubMed Central

    Rossner, Pavel; Spatova, Milada; Rossnerova, Andrea; Libalova, Helena; Schmuczerova, Jana; Milcova, Alena; Topinka, Jan; Sram, Radim J.

    2013-01-01

    The cellular response to genotoxic treatment depends on the cell line used. Although tumor cell lines are widely used for genotoxicity tests, the interpretation of the results may be potentially hampered by changes in cellular processes caused by malignant transformation. In our study we used normal human embryonic lung fibroblasts (HEL12469 cells) and tested their response to treatment with benzo[a]pyrene (B[a]P) and extractable organic matter (EOM) from ambient air particles <2.5 µm (PM2.5) collected in two Czech cities differing in levels and sources of air pollution. We analyzed multiple endpoints associated with exposure to polycyclic aromatic hydrocarbons (PAHs) including the levels of bulky DNA adducts and the nucleotide excision repair (NER) response [expression of XPE, XPC and XPA genes on the level of mRNA and proteins, unscheduled DNA synthesis (UDS)]. EOMs were collected in the winter and summer of 2011 in two Czech cities with different levels and sources of air pollution. The effects of the studied compounds were analyzed in the presence (+S9) and absence (–S9) of the rat liver microsomal S9 fraction. The levels of bulky DNA adducts were highest after treatment with B[a]P, followed by winter EOMs; their induction by summer EOMs was weak. The induction of both mRNA and protein expression was observed, with the most pronounced effects after treatment with B[a]P (–S9); the response induced by EOMs from both cities and seasons was substantially weaker. The expression of DNA repair genes was not accompanied by the induction of UDS activity. In summary, our results indicate that the tested compounds induced low levels of DNA damage and affected the expression of NER genes; however, nucleotide excision repair was not induced. PMID:23894430

  20. Mechanotransduction in Embryonic Vascular Development

    PubMed Central

    Roman, Beth L.; Pekkan, Kerem

    2015-01-01

    A plethora of biochemical signals provides spatial and temporal cues that carefully orchestrate the complex process of vertebrate embryonic development. The embryonic vasculature develops not only in the context of these biochemical cues, but also in the context of the biomechanical forces imparted by blood flow. In the mature vasculature, different blood flow regimes induce distinct genetic programs, and significant progress has been made toward understanding how these forces are perceived by endothelial cells and transduced into biochemical signals. However, it cannot be assumed that paradigms that govern the mature vasculature are pertinent to the developing embryonic vasculature. The embryonic vasculature can respond to the mechanical forces of blood flow, and these responses are critical in vascular remodeling, certain aspects of sprouting angiogenesis, and maintenance of arterial-venous identity. Here, we review data regarding mechanistic aspects of endothelial cell mechanotransduction, with a focus on the response to shear stress, and elaborate upon the multifarious effects of shear stress on the embryonic vasculature. In addition, we discuss emerging predictive vascular growth models and highlight the prospect of combining signaling pathway information with computational modeling. We assert that correlation of precise measurements of hemodynamic parameters with effects on endothelial cell gene expression and cell behavior is required for fully understanding how blood flow-induced loading governs normal vascular development and shapes congenital cardiovascular abnormalities. PMID:22744845

  1. Embryonic death and the creation of human embryonic stem cells.

    PubMed

    Landry, Donald W; Zucker, Howard A

    2004-11-01

    The creation of human embryonic stem cells through the destruction of a human embryo pits the value of a potential therapeutic tool against that of an early human life. This contest of values has resulted in a polarized debate that neglects areas of common interest and perspective. We suggest that a common ground for pursuing research on human embryonic stem cells can be found by reconsidering the death of the human embryo and by applying to this research the ethical norms of essential organ donation.

  2. Semi-inclusive hadronic B decays in the endpoint region

    SciTech Connect

    Chay, Junegone; Kim, Chul; Leibovich, Adam K.; Zupan, Jure

    2006-10-01

    We consider in the soft-collinear effective theory semi-inclusive hadronic B decays, B{yields}XM, in which an energetic light meson M near the endpoint recoils against an inclusive jet X. We focus on a subset of decays where the spectator quark from the B meson ends up in the jet. The branching ratios and direct CP asymmetries are computed to next-to-leading order accuracy in {alpha}{sub s} and to leading order in 1/m{sub b}. The contribution of charming penguins is extensively discussed, and a method to extract it in semi-inclusive decays is suggested. Subleading 1/m{sub b} corrections and SU(3) breaking effects are discussed.

  3. DETERMINING SIGNIFICANT ENDPOINTS FOR ECOLOGICAL RISK ANALYS ES

    SciTech Connect

    Hinton, Thomas G.

    2000-12-31

    Our interest is in obtaining a scientifically defensible endpoint for measuring ecological risks to populations exposed to chronic, low-level radiation, and radiation with concomitant exposure to chemicals. To do so, we believe that we must understand the extent to which molecular damage is detrimental at the individual and population levels of biological organization. Ecological risk analyses based on molecular damage, without an understanding of the impacts to higher levels of biological organization, could cause cleanup strategies on DOE sites to be overly conservative and unnecessarily expensive. Our goal is to determine the relevancy of sublethal cellular damage to the performance of individuals and populations. We think that we can achieve this by using novel biological dosimeters in controlled, manipulative dose/effects experiments, and by coupling changes in metabolic rates and energy allocation patterns to meaningful population response variables (such as age-specific survivorship, reproductive output, age at maturity and longevity).

  4. Are Hemodynamics Surrogate Endpoints in Pulmonary Arterial Hypertension?

    PubMed Central

    Ventetuolo, Corey E.; Gabler, Nicole B.; Fritz, Jason S.; Smith, K. Akaya; Palevsky, Harold I.; Klinger, James R.; Halpern, Scott D.; Kawut, Steven M.

    2014-01-01

    Background While frequently assessed in trials and clinical practice, hemodynamic response to therapy has never been validated as a surrogate endpoint for clinical events in pulmonary arterial hypertension (PAH). Methods and Results We performed a patient-level pooled analysis of four randomized placebo-controlled trials to determine if treatment-induced changes in hemodynamic values at 12 weeks accounted for the relationship between treatment assignment and the probability of early clinical events (death, lung transplantation, atrial septostomy, PAH hospitalization, withdrawal for clinical worsening, escalation in PAH therapy). We included 1119 subjects with PAH. The median (interquartile range) age was 48 (37 – 59), and 23% were men. 656 (59%) received active therapy (101 [15%] iloprost, 118 [18%] sitaxsentan, 204 [31%] sildenafil, and 233 [36%] subcutaneous treprostinil). Active treatment significantly lowered right atrial pressure (RAP), mean pulmonary artery pressure (mPAP), and pulmonary vascular resistance and increased cardiac output and index (p < 0.01 for all). Changes in hemodynamic values (except for RAP and mPAP) were significantly associated with the risk of a clinical event (p ≤ 0.01 for all). While active treatment approximately halved the odds of a clinical event compared to placebo (p < 0.001), changes in hemodynamics accounted for only 1.2 – 13.9% of the overall treatment effect. Conclusions Treatment-induced changes in hemodynamics at 12 weeks only partially explain the impact of therapy on the probability of early clinical events in PAH. These findings suggest that resting hemodynamics are not valid surrogate endpoints for short-term events in PAH clinical trials. PMID:24951771

  5. A multivariate Bayesian model for embryonic growth.

    PubMed

    Willemsen, Sten P; Eilers, Paul H C; Steegers-Theunissen, Régine P M; Lesaffre, Emmanuel

    2015-04-15

    Most longitudinal growth curve models evaluate the evolution of each of the anthropometric measurements separately. When applied to a 'reference population', this exercise leads to univariate reference curves against which new individuals can be evaluated. However, growth should be evaluated in totality, that is, by evaluating all body characteristics jointly. Recently, Cole et al. suggested the Superimposition by Translation and Rotation (SITAR) model, which expresses individual growth curves by three subject-specific parameters indicating their deviation from a flexible overall growth curve. This model allows the characterization of normal growth in a flexible though compact manner. In this paper, we generalize the SITAR model in a Bayesian way to multiple dimensions. The multivariate SITAR model allows us to create multivariate reference regions, which is advantageous for prediction. The usefulness of the model is illustrated on longitudinal measurements of embryonic growth obtained in the first semester of pregnancy, collected in the ongoing Rotterdam Predict study. Further, we demonstrate how the model can be used to find determinants of embryonic growth.

  6. Towards better environmental performance of wastewater sludge treatment using endpoint approach in LCA methodology.

    PubMed

    Alyaseri, Isam; Zhou, Jianpeng

    2017-03-01

    The aim of this study is to use the life cycle assessment method to measure the environmental performance of the sludge incineration process in a wastewater treatment plant and to propose an alternative that can reduce the environmental impact. To show the damages caused by the treatment processes, the study aimed to use an endpoint approach in evaluating impacts on human health, ecosystem quality, and resources due to the processes. A case study was taken at Bissell Point Wastewater Treatment Plant in Saint Louis, Missouri, U.S. The plant-specific data along with literature data from technical publications were used to build an inventory, and then analyzed the environmental burdens from sludge handling unit in the year 2011. The impact assessment method chosen was ReCipe 2008. The existing scenario (dewatering-multiple hearth incineration-ash to landfill) was evaluated and three alternative scenarios (fluid bed incineration and anaerobic digestion with and without land application) with energy recovery from heat or biogas were proposed and analyzed to find the one with the least environmental impact. The existing scenario shows that the most significant impacts are related to depletion in resources and damage to human health. These impacts mainly came from the operation phase (electricity and fuel consumption and emissions related to combustion). Alternatives showed better performance than the existing scenario. Using ReCipe endpoint methodology, and among the three alternatives tested, the anaerobic digestion had the best overall environmental performance. It is recommended to convert to fluid bed incineration if the concerns were more about human health or to anaerobic digestion if the concerns were more about depletion in resources. The endpoint approach may simplify the outcomes of this study as follows: if the plant is converted to fluid bed incineration, it could prevent an average of 43.2 DALYs in human life, save 0.059 species in the area from extinction

  7. Anatomy of an experimental two-link flexible manipulator under end-point control

    NASA Technical Reports Server (NTRS)

    Oakley, Celia M.; Cannon, Robert H., Jr.

    1990-01-01

    The design and experimental implementation of an end-point controller for two-link flexible manipulators are presented. The end-point controller is based on linear quadratic Gaussian (LQG) theory and is shown to exhibit significant improvements in trajectory tracking over a conventional controller design. To understand the behavior of the manipulator structure under end-point control, a strobe sequence illustrating the link deflections during a typical slew maneuver is included.

  8. Assessment of the embryotoxicity of four Chinese herbal extracts using the embryonic stem cell test.

    PubMed

    Li, Lin-Yan; Cao, Fen-Fang; Su, Zhi-Jian; Zhang, Qi-Hao; Dai, Xiao-Yong; Xiao, Xue; Huang, Ya-Dong; Zheng, Qing; Xu, Hua

    2015-08-01

    Rhizoma Atractylodes macrocephala, Radix Isatidis, Coptis chinensis and Flos Genkwa are common herbal remedies used by pregnant woman in China. In this study, their potential embryotoxicity was assessed using the embryonic stem cell test (EST) and a prediction model. The potential embryotoxicity of the herbs was based on three endpoints: the concentrations of the compounds that inhibited the proliferation of 50% of embryonic stem cells (ESCs) (IC50ES), the concentrations that inhibited 50% of 3T3 cells (IC503T3), and the concentrations that inhibited the differentiation of 50% of ESCs (ID50ES). The results revealed that Rhizoma Atractylodes macrocephala and Radix Isatidis are non-embryotoxic compounds. Coptis chinensis extracts appeared to demonstrated weak embryotoxicity, and Flos Genkwa exhibited strong embryotoxicity. These results may be useful in guiding the clinical use of these herbs and in expanding the application of the EST to the field of traditional Chinese medicine.

  9. Multiple endpoints for somatic mutations in humans provide complementary views for biodosimetry, genotoxicity, and health risks

    SciTech Connect

    Jensen, R.H.; Bigbee, W.L.; Langlois, R.G.

    1989-07-24

    There are now four somatic cell mutation assays that are being used to determine in vivo mutagenesis in humans. Each assay is identified by an acronym that specifies the protein in which mutations are determined: HPRT assay, GPA assay, HLA assay, and Hb assay. Potentially, each assay can be used for either of two important applications; biodosimetry or cancer risk estimation. Biodosimetry is a means for determining the amount of exposure of an individual to a toxic agent by measuring the biological effect on the individual who was exposed. Based on the observation that many toxic chemicals and ionizing radiation are mutagenic to cells in culture and also to animals, the somatic mutation assays also should serve as biodosimeters for exposure of humans to these genotoxic phenomena. These four somatic mutation assays should contribute to the possibility of estimating each individual's risk of developing cancer by monitoring for the presence of genotoxicity events similar to cancer initiation events or cancer promotion events on suppressor genes. 16 refs., 4 tabs.

  10. Development of Effects-Based Nutrient Criteria using Biological Endpoints

    NASA Astrophysics Data System (ADS)

    Miltner, R.

    2005-05-01

    Ohio employs biological endpoints to judge the status of aquatic life in rivers and streams. Specifically, numeric criteria derived from biological indices have been incorporated into Ohio's water quality standards for fish and macroinvertebrate communities. When appropriate, chemical-specific water quality standards derived from dose-response curves are used in concert with the biological indices to ascribe the causes and sources of impairment to polluted streams. However, water quality criteria have not been established for all polluting agents, especially those, like nutrients, that do not elicit a simple dose-response curve. In such cases, where biological impairment is observed, the linkage between the impairment and causal agent is made inferentially. Ohio EPA is currently studying the relationship between nutrient concentrations, periphytic chlorophyll a concentrations, and biological indices to ascertain whether a direct relationship exists between nutrient concentration and the biological health of fish and macroinvertebrate communities, with the eventual goal of adopting effects-based nutrient criteria in Ohio's water quality standards. Results from the first field season show a strong relationship between chlorophyll a concentrations, and physical and land use variables. Additionally, 48 h dissolved oxygen flux correlated with periphytic chlorophyll a concentrations and the degree of canopy cover.

  11. Responsiveness of endpoints in osteoporosis clinical trials--an update.

    PubMed

    Cranney, A; Welch, V; Tugwell, P; Wells, G; Adachi, J D; McGowan, J; Shea, B

    1999-01-01

    As an update of our earlier paper, published as part of the Outcome Measures in Rheumatology Clinical Trials (OMERACT 3) proceedings in 1996, we surveyed the types of outcomes incorporated in recent clinical trials. A literature search was conducted on MEDLINE and Current Contents, from January 1996 to March 1998, using the search strategy recommended by the Cochrane Collaboration for the identification of randomized controlled trials (RCT). Two independent reviewers selected trials according to inclusion criteria. The same reviewers extracted data on clinical and radiographic fractures, pain, quality of life, and bone mineral density (BMD). Seventy-four RCT conducted on bone loss in postmenopausal women were identified. Most trials incorporated biochemical markers and BMD as outcome measures. Fewer trials included vertebral fractures, pain, height, and quality of life. The responsiveness is presented in terms of the sample size needed per group to show a statistically significant difference. The most responsive outcomes were pain, BMD, and biochemical markers. The number needed to treat to prevent one vertebral fracture ranged from 13 to 54, depending on the intervention and population. Investigators should examine the characteristics of the patient population and the nature of the intervention in determining the sample size required to demonstrate a significant effect. The selection of endpoints should be based on their responsiveness, feasibility, and the importance of using standardized outcomes. Standardized outcomes greatly facilitate the synthesis of available information into systematic reviews by groups such as the Cochrane Collaboration.

  12. Embryonic markers of cone differentiation

    PubMed Central

    Rodgers, Helen M.; Belcastro, Marycharmain; Sokolov, Maxim

    2016-01-01

    Purpose Photoreceptor cells are born in two distinct phases of vertebrate retinogenesis. In the mouse retina, cones are born primarily during embryogenesis, while rod formation occurs later in embryogenesis and early postnatal ages. Despite this dichotomy in photoreceptor birthdates, the visual pigments and phototransduction machinery are not reactive to visual stimulus in either type of photoreceptor cell until the second postnatal week. Several markers of early cone formation have been identified, including Otx2, Crx, Blimp1, NeuroD, Trβ2, Rorβ, and Rxrγ, and all are thought to be involved in cellular determination. However, little is known about the expression of proteins involved in cone visual transduction during early retinogenesis. Therefore, we sought to characterize visual transduction proteins that are expressed specifically in photoreceptors during mouse embryogenesis. Methods Eye tissue was collected from control and phosducin-null mice at embryonic and early postnatal ages. Immunohistochemistry and quantitative reverse transcriptase-PCR (qPCR) were used to measure the spatial and temporal expression patterns of phosducin (Pdc) and cone transducin γ (Gngt2) proteins and transcripts in the embryonic and early postnatal mouse retina. Results We identified the embryonic expression of phosducin (Pdc) and cone transducin γ (Gngt2) that coincides temporally and spatially with the earliest stages of cone histogenesis. Using immunohistochemistry, the phosducin protein was first detected in the retina at embryonic day (E)12.5, and cone transducin γ was observed at E13.5. The phosducin and cone transducin γ proteins were seen only in the outer neuroblastic layer, consistent with their expression in photoreceptors. At the embryonic ages, phosducin was coexpressed with Rxrγ, a known cone marker, and with Otx2, a marker of photoreceptors. Pdc and Gngt2 mRNAs were detected as early as E10.5 with qPCR, although at low levels. Conclusions Visual transduction

  13. Quantitative in vivo imaging of embryonic development: opportunities and challenges.

    PubMed

    Gregg, Chelsea L; Butcher, Jonathan T

    2012-07-01

    Animal models are critically important for a mechanistic understanding of embryonic morphogenesis. For decades, visualizing these rapid and complex multidimensional events has relied on projection images and thin section reconstructions. While much insight has been gained, fixed tissue specimens offer limited information on dynamic processes that are essential for tissue assembly and organ patterning. Quantitative imaging is required to unlock the important basic science and clinically relevant secrets that remain hidden. Recent advances in live imaging technology have enabled quantitative longitudinal analysis of embryonic morphogenesis at multiple length and time scales. Four different imaging modalities are currently being used to monitor embryonic morphogenesis: optical, ultrasound, magnetic resonance imaging (MRI), and micro-computed tomography (micro-CT). Each has its advantages and limitations with respect to spatial resolution, depth of field, scanning speed, and tissue contrast. In addition, new processing tools have been developed to enhance live imaging capabilities. In this review, we analyze each type of imaging source and its use in quantitative study of embryonic morphogenesis in small animal models. We describe the physics behind their function, identify some examples in which the modality has revealed new quantitative insights, and then conclude with a discussion of new research directions with live imaging.

  14. Statistical evaluation of surrogate endpoints with examples from cancer clinical trials.

    PubMed

    Buyse, Marc; Molenberghs, Geert; Paoletti, Xavier; Oba, Koji; Alonso, Ariel; Van der Elst, Wim; Burzykowski, Tomasz

    2016-01-01

    A surrogate endpoint is intended to replace a clinical endpoint for the evaluation of new treatments when it can be measured more cheaply, more conveniently, more frequently, or earlier than that clinical endpoint. A surrogate endpoint is expected to predict clinical benefit, harm, or lack of these. Besides the biological plausibility of a surrogate, a quantitative assessment of the strength of evidence for surrogacy requires the demonstration of the prognostic value of the surrogate for the clinical outcome, and evidence that treatment effects on the surrogate reliably predict treatment effects on the clinical outcome. We focus on these two conditions, and outline the statistical approaches that have been proposed to assess the extent to which these conditions are fulfilled. When data are available from a single trial, one can assess the "individual level association" between the surrogate and the true endpoint. When data are available from several trials, one can additionally assess the "trial level association" between the treatment effect on the surrogate and the treatment effect on the true endpoint. In the latter case, the "surrogate threshold effect" can be estimated as the minimum effect on the surrogate endpoint that predicts a statistically significant effect on the clinical endpoint. All these concepts are discussed in the context of randomized clinical trials in oncology, and illustrated with two meta-analyses in gastric cancer.

  15. Use of sublethal endpoints in sediment toxicity testing with the amphipod Hyalella azteca

    SciTech Connect

    Kemble, N.E.; Brunson, E.B.; Dwyer, F.J.; Ehrhardt, E.A.; Hardesty, D.K.; Haverland, P.S.; Ingersoll, C.G.

    1995-12-31

    ASTM and EPA standard methods for sediment toxicity tests with Hyalella azteca typically recommend use of lethality as the endpoint in a 10-d exposure. However, data from 10- to 28-d exposures with amphipods indicate sublethal endpoints (i.e., growth, sexual maturation, or reproduction) identify additional samples as toxic. The authors compared the frequency that lethal and sublethal endpoints identified a sediment sample as toxic in 14- and 28-d amphipod exposures. In the 14-d amphipod exposures, lethality identified 20% of the samples as toxic, and sublethal endpoints identified an additional 16% of the samples as toxic using sublethal endpoints only. Similarly, in the 28-d exposures, lethality identified 14% of the samples as toxic and sublethal endpoints identified an additional 18% of the samples as toxic. The authors are also currently evaluating Sediment Effect Concentrations (SECs) relative to both lethal and sublethal endpoints in H. azteca exposures. These SECs will be used to evaluate reliability in estimating toxicity of samples. Potential factors which may confound interpretation of sublethal endpoints in sediment tests include: (1) changes in sediment chemistry resulting from long-term storage or feeding (2) the influence of physical characteristics of sediment (grain size), and (3) effects of ammonia or hydrogen sulfide.

  16. 78 FR 46351 - Trial Designs and Endpoints for Liver Disease Secondary to Nonalcoholic Steatohepatitis; Public...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-31

    ... HUMAN SERVICES Food and Drug Administration Trial Designs and Endpoints for Liver Disease Secondary to... Research in cosponsorship with the American Association for the Study of Liver Diseases (AASLD) is announcing a 2-day public workshop entitled ``Trial Designs and Endpoints for Liver Disease Secondary...

  17. A Few Endpoint Geodesic Restriction Estimates for Eigenfunctions

    NASA Astrophysics Data System (ADS)

    Chen, Xuehua; Sogge, Christopher D.

    2014-07-01

    We prove a couple of new endpoint geodesic restriction estimates for eigenfunctions. In the case of general 3-dimensional compact manifolds, after a TT* argument, simply by using the L 2-boundedness of the Hilbert transform on , we are able to improve the corresponding L 2-restriction bounds of Burq, Gérard and Tzvetkov (Duke Math J 138:445-486, 2007) and Hu (Forum Math 6:1021-1052, 2009). Also, in the case of 2-dimensional compact manifolds with nonpositive curvature, we obtain improved L 4-estimates for restrictions to geodesics, which, by Hölder's inequality and interpolation, implies improved L p -bounds for all exponents p ≥ 2. We do this by using oscillatory integral theorems of Hörmander (Ark Mat 11:1-11, 1973), Greenleaf and Seeger (J Reine Angew Math 455:35-56, 1994) and Phong and Stein (Int Math Res Notices 4:49-60, 1991), along with a simple geometric lemma (Lemma 3.2) about properties of the mixed-Hessian of the Riemannian distance function restricted to pairs of geodesics in Riemannian surfaces. We are also able to get further improvements beyond our new results in three dimensions under the assumption of constant nonpositive curvature by exploiting the fact that, in this case, there are many totally geodesic submanifolds.

  18. Embryonic development during chronic acceleration

    NASA Technical Reports Server (NTRS)

    Smith, A. H.; Abbott, U. K.

    1982-01-01

    Experiments carried out on chicken eggs indicate that the embryo is affected during very early development, especially over the first four days, and during hatching. In the first four days, the brain develops as well as the anlage for all other organs. In addition, the heart commences to function and the extraembryonic membranes that compartmentalize the egg contents form. The latter require an appreciable extension and folding of tissue which may be disrupted by the mechanical load. Observations of embryonic abnormalities that occur during chronic acceleration suggest an inhibition of development of the axial skeleton, which is rarely seen otherwise, a general retardation of embryonic growth, and circulatory problems. The final stages of development (after 18 days) involve the uptake of fluids, the transition to aerial respiration, and the reorientation of the embryo into a normal hatching position. At 4 G mortality is very high during this period, with a majority of embryos failing to reorient into the normal hatching position.

  19. Electroporation of Embryonic Kidney Explants

    NASA Astrophysics Data System (ADS)

    Haddad, Nicholas; Houle, Daniel; Gupta, Indra R.

    Metanephric kidney development in the mouse begins at embryonic day (E) 10.5, when the ureteric bud (UB), an outgrowth of the epithelial nephric duct, invades the neighboring metanephric mesenchyme (MM). The ureteric bud then undergoes a series of branching events to form the collecting duct network of the adult kidney (Fig. 19.1). As each ureteric bud tip forms, the adjacent undifferentiated mesenchyme is induced to epithelialize and form a nephron, the functional unit of the adult kidney that filters waste. Rodent embryonic kidneys can be dissected and cultured as explants such that branching morphogenesis and nephrogenesis can be observed ex vivo (Rothenpieler and Dressler, 1993; Vega et al., 1996; Piscione et al., 1997; Gupta et al., 2003).

  20. Observations on Three Endpoint Properties and Their Relationship to Regulatory Outcomes of European Oncology Marketing Applications

    PubMed Central

    Stolk, Pieter; McAuslane, James Neil; Schellens, Jan; Breckenridge, Alasdair M.; Leufkens, Hubert

    2015-01-01

    Background. Guidance and exploratory evidence indicate that the type of endpoints and the magnitude of their outcome can define a therapy’s clinical activity; however, little empirical evidence relates specific endpoint properties with regulatory outcomes. Materials and Methods. We explored the relationship of 3 endpoint properties to regulatory outcomes by assessing 50 oncology marketing authorization applications (MAAs; reviewed from 2009 to 2013). Results. Overall, 16 (32%) had a negative outcome. The most commonly used hard endpoints were overall survival (OS) and the duration of response or stable disease. OS was a component of 91% approved and 63% failed MAAs. The most commonly used surrogate endpoints were progression-free survival (PFS), response rate, and health-related quality of life assessments. There was no difference (p = .3801) between the approved and failed MAA cohorts in the proportion of hard endpoints used. A mean of slightly more than four surrogate endpoints were used per approved MAA compared with slightly more than two for failed MAAs. Longer OS and PFS duration outcomes were generally associated with approvals, often when not statistically significant. The approved cohort was associated with a preponderance of statistically significant (p < .05) improvements in primary endpoints (p < .0001 difference between the approved and failed groups). Conclusion. Three key endpoint properties (type of endpoint [hard/surrogate], magnitude of an endpoint outcome, and its statistical significance) are consistent with the European Medicines Agency guidance and, notwithstanding the contribution of unique disease-specific circumstances, are associated with a predictable positive outcome for oncology MAAs. Implications for Practice: Regulatory decisions made by the European Medicines Agency determine which new medicines will be available to European prescribers and for which therapeutic indications. Regulatory success or failure can be influenced by many

  1. Integrative analysis of the mouse embryonic transcriptome

    PubMed Central

    Singh, Amar V; Knudsen, Kenneth B; Knudsen, Thomas B

    2007-01-01

    Monitoring global gene expression provides insight into how genes and regulatory signals work together to guide embryo development. The fields of developmental biology and teratology are now confronted with the need for automated access to a reference library of gene-expression signatures that benchmark programmed (genetic) and adaptive (environmental) regulation of the embryonic transcriptome. Such a library must be constructed from highly-distributed microarray data. Birth Defects Systems Manager (BDSM), an open access knowledge management system, provides custom software to mine public microarray data focused on developmental health and disease. The present study describes tools for seamless data integration in the BDSM library (MetaSample, MetaChip, CIAeasy) using the QueryBDSM module. A field test of the prototype was run using published microarray data series derived from a variety of laboratories, experiments, microarray platforms, organ systems, and developmental stages. The datasets focused on several developing systems in the mouse embryo, including preimplantation stages, heart and nerve development, testis and ovary development, and craniofacial development. Using BDSM data integration tools, a gene-expression signature for 346 genes was resolved that accurately classified samples by organ system and developmental sequence. The module builds a potential for the BDSM approach to decipher a large number developmental processes through comparative bioinformatics analysis of embryological systems at-risk for specific defects, using multiple scenarios to define the range of probabilities leading from molecular phenotype to clinical phenotype. We conclude that an integrative analysis of global gene-expression of the developing embryo can form the foundation for constructing a reference library of signaling pathways and networks for normal and abnormal regulation of the embryonic transcriptome. These tools are available free of charge from the web-site http

  2. Integrative analysis of the mouse embryonic transcriptome.

    PubMed

    Singh, Amar V; Knudsen, Kenneth B; Knudsen, Thomas B

    2007-04-10

    Monitoring global gene expression provides insight into how genes and regulatory signals work together to guide embryo development. The fields of developmental biology and teratology are now confronted with the need for automated access to a reference library of gene-expression signatures that benchmark programmed (genetic) and adaptive (environmental) regulation of the embryonic transcriptome. Such a library must be constructed from highly-distributed microarray data. Birth Defects Systems Manager (BDSM), an open access knowledge management system, provides custom software to mine public microarray data focused on developmental health and disease. The present study describes tools for seamless data integration in the BDSM library (MetaSample, MetaChip, CIAeasy) using the QueryBDSM module. A field test of the prototype was run using published microarray data series derived from a variety of laboratories, experiments, microarray platforms, organ systems, and developmental stages. The datasets focused on several developing systems in the mouse embryo, including preimplantation stages, heart and nerve development, testis and ovary development, and craniofacial development. Using BDSM data integration tools, a gene-expression signature for 346 genes was resolved that accurately classified samples by organ system and developmental sequence. The module builds a potential for the BDSM approach to decipher a large number developmental processes through comparative bioinformatics analysis of embryological systems at-risk for specific defects, using multiple scenarios to define the range of probabilities leading from molecular phenotype to clinical phenotype. We conclude that an integrative analysis of global gene-expression of the developing embryo can form the foundation for constructing a reference library of signaling pathways and networks for normal and abnormal regulation of the embryonic transcriptome. These tools are available free of charge from the web-site http

  3. Early and late damages induced by heavy charged particle irradiation in embryonic tissue of Arabidopsis seeds

    NASA Astrophysics Data System (ADS)

    Bork, U.; Gartenbach, K. E.; Kranz, A. R.

    Early and late effects of accelerated heavy ions (HZE) on the embryonic tissue of Arabidopsis thaliana seeds were investigated seeing that initial cells of the plant eumeristems resemble the original cells of animal and human tissues with continuous cell proliferation. The endpoints measured were lethality and tumorization in the M1-generation for early effects and embryonic lethality in the M2-generation for late effects. The biological endpoints are plotted as functions of the physical parameters of the irradiation i.e. ion fluence (p/cm2), dose (Gray), charge Z and linear energy transfer (LET). The results presented contribute to the estimation of the principles of biological HZE effects and thus may help to develop a unified theory which could explain the whole sequence from physical and chemical reactions to biological responses connected with heavy ion radiation. Additionally, the data of this paper may be used for the discussion of the quality factor for heavy ion irradiation needed for space missions and for HZE-application in radio-therapy by use of accelerators (UNILAC, (SIS/ESR), BEVALAC).

  4. PICKLE acts during germination to repress expression of embryonic traits

    PubMed Central

    Li, Hui-Chun; Chuang, King; Henderson, James T.; Rider, Stanley Dean; Bai, Yinglin; Zhang, Heng; Fountain, Matthew; Gerber, Jacob; Ogas, Joe

    2008-01-01

    SUMMARY PICKLE (PKL) codes for a CHD3 chromatin remodeling factor that plays multiple roles in Arabidopsis growth and development. Previous analysis of the expression of genes that exhibit PKL-dependent regulation suggested that PKL acts during germination to repress expression of embryonic traits. In this study, we examined the expression of PKL protein to investigate when and where PKL acts to regulate development. A PKL:eGFP translational fusion is preferentially localized in the nucleus of cells, consistent with the proposed role for PKL as a chromatin remodeling factor. A steroid-inducible version of PKL - a fusion of PKL to the glucocorticoid receptor (PKL:GR) - was used to examine when PKL acts to repress expression of embryonic traits. We found that activation of PKL:GR during germination was sufficient to repress expression of embryonic traits in the primary roots of pkl seedlings whereas activation of PKL:GR after germination had little effect. In contrast, we observed that PKL is required continuously after germination to repress expression of PHERES1, a type I MADS box gene that is normally expressed during early embryogenesis in wild-type plants. Thus PKL acts at multiple points during development to regulate patterns of gene expression in Arabidopsis. PMID:16359393

  5. PICKLE acts during germination to repress expression of embryonic traits.

    PubMed

    Li, Hui-Chun; Chuang, King; Henderson, James T; Rider, Stanley Dean; Bai, Yinglin; Zhang, Heng; Fountain, Matthew; Gerber, Jacob; Ogas, Joe

    2005-12-01

    PICKLE (PKL) codes for a CHD3 chromatin remodeling factor that plays multiple roles in Arabidopsis growth and development. Previous analysis of the expression of genes that exhibit PKL-dependent regulation suggested that PKL acts during germination to repress expression of embryonic traits. In this study, we examined the expression of PKL protein to investigate when and where PKL acts to regulate development. A PKL:eGFP translational fusion is preferentially localized in the nucleus of cells, consistent with the proposed role for PKL as a chromatin remodeling factor. A steroid-inducible version of PKL [a fusion of PKL to the glucocorticoid receptor (PKL:GR)] was used to examine when PKL acts to repress expression of embryonic traits. We found that activation of PKL:GR during germination was sufficient to repress expression of embryonic traits in the primary roots of pkl seedlings, whereas activation of PKL:GR after germination had little effect. In contrast, we observed that PKL is required continuously after germination to repress expression of PHERES1, a type I MADS box gene that is normally expressed during early embryogenesis in wild-type plants. Thus, PKL acts at multiple points during development to regulate patterns of gene expression in Arabidopsis.

  6. Food Safety: Recommendations for Determining Doneness in Consumer Egg Dish Recipes and Measurement of Endpoint Temperatures When Recipes Are Followed

    PubMed Central

    Godwin, Sandria; Maughan, Curtis; Chambers, Edgar

    2016-01-01

    Many consumers do not follow recommended food safety practices for cooking egg dishes, such as pies, quiches, and casseroles, potentially leading to foodborne illnesses such as Salmonellosis. The United States Department of Agriculture (USDA) recommends cooking egg mixtures until the center reaches 71 °C (160 °F). The objectives of this study were to determine what endpoint temperature information consumers receive from egg dish recipes, and if recipes would lead to safe temperatures when followed. Egg dish recipes (n = 226) from 65 websites, 50 cookbooks, and nine magazine titles (multiple issues of each) were analyzed. Time was the most frequently used indicator, given in 92% of the recipes, with 15% using only time. Other indicators included: set (89), browned (76), clean toothpick/knife (60), puffed (27), and jiggled (13). Only two recipes indicated final endpoint temperatures. Three recipes (a pie, a quiche, and an egg casserole) were chosen and prepared in triplicate to see if they would reach recommended temperatures. The pie and quiche were still liquid at 71 °C, and were well over the recommended temperature when cooked according to instructions, but the egg casserole was not consistently above 71 °C, when the recipe instructions indicated it was done and the center was light brown and “jiggled” This research indicates that consumers are not receiving information on endpoint temperatures in egg recipes, but the likelihood of foodborne illness is low since most dishes probably be cooked past the recommended temperature before the consumer considers them done unless there are many inclusions that may absorb liquid and reduce the appearance of liquid in the dish. PMID:28231140

  7. STATISTICAL METHODOLOGY FOR THE SIMULTANEOUS ANALYSIS OF MULTIPLE TYPES OF OUTCOMES IN NONLINEAR THRESHOLD MODELS.

    EPA Science Inventory

    Multiple outcomes are often measured on each experimental unit in toxicology experiments. These multiple observations typically imply the existence of correlation between endpoints, and a statistical analysis that incorporates it may result in improved inference. When both disc...

  8. Dimethadione embryotoxicity in the rat is neither correlated with maternal systemic drug concentrations nor embryonic tissue levels.

    PubMed

    Ozolinš, Terence R S; Weston, Andrea D; Perretta, Anthony; Thomson, Jason J; Brown, Nigel A

    2015-11-15

    Pregnant rats treated with dimethadione (DMO), the N-demethylated metabolite of the anticonvulsant trimethadione, produce offspring having a 74% incidence of congenital heart defects (CHD); however, the incidence of CHD has high inter-litter variability (40-100%) that presents a challenge when studying the initiating events prior to the presentation of an abnormal phenotype. We hypothesized that the variability in CHD incidence was the result of differences in maternal systemic concentrations or embryonic tissue concentrations of DMO. To test this hypothesis, dams were administered 300 mg/kg DMO every 12h from the evening of gestational day (GD) 8 until the morning of GD 11 (six total doses). Maternal serum levels of DMO were assessed on GD 11, 12, 13, 14, 15, 18 and 21. Embryonic tissue concentrations of DMO were assessed on GD 11, 12, 13 and 14. In a separate cohort of GD 12 embryos, DMO concentrations and parameters of growth and development were assessed to determine if tissue levels of DMO were correlated with these endpoints. Embryos were exposed directly to different concentrations of DMO with whole embryo culture (WEC) and their growth and development assessed. Key findings were that neither maternal systemic concentrations nor tissue concentrations of DMO identified embryos that were sensitive or resistant to DMO in vivo. Direct exposure of embryos to DMO via WEC also failed to show correlations between embryonic concentrations of DMO with developmental outcomes in vitro. We conclude that neither maternal serum nor embryonic tissue concentrations of DMO predict embryonic outcome.

  9. End-points and clinical trial design in pulmonary arterial hypertension: have we made progress?

    PubMed

    Peacock, A J; Naeije, R; Galiè, N; Rubin, L

    2009-07-01

    There is enormous interest in the treatment of pulmonary arterial hypertension (PAH), so it is appropriate to consider the design of trials of new therapies and the end-points to be measured when trying to decide whether or not a therapy is effective. In May 2003, the first meeting devoted solely to the discussion of end-points and trial design in PAH was held in Gleneagles, UK. At that time, most of the randomised controlled trials in PAH had used 6-min walking distance and/or resting haemodynamics as their primary end-points. The present article considers the progress that has been made since 2003. It deals with aspects of clinical trial design (such as noninferiority, superiority and withdrawal trials), considers end-points used in previous and current studies (such as 6-min walking distance, time to clinical worsening, haemodynamics, imaging and plasma brain natriuretic peptide), and considers what end-points might be used in the future. The second end-points meeting was held in Turnberry, UK, in June 2007. It had a similar format to the first meeting. Much of what is presented here is a summary of the workshops from that meeting. An attempt has been made to both summarise the current state of end-points and trial design and suggest new ways in which they could be improved. The present article forms one of a series being published in the European Respiratory Journal on pulmonary hypertension.

  10. Analysis of Coronary Vessels in Cleared Embryonic Hearts

    PubMed Central

    Ivins, Sarah; Roberts, Catherine; Vernay, Bertrand; Scambler, Peter J.

    2016-01-01

    Whole mount visualization of the embryonic coronary plexus from which the capillary and arterial networks will form is rendered problematic using standard microscopy techniques, due to the scattering of imaging light by the thick heart tissue, as these vessels are localized deep within the walls of the developing heart. As optical clearing of tissues using organic solvents such as BABB (1 part benzyl alcohol to 2 parts benzyl benzoate) has been shown to greatly improve the optical penetration depth that can be achieved, we combined clearance of whole, PECAM1-immunostained hearts, with laser-scanning confocal microscopy, in order to obtain high-resolution images of vessels throughout the entire heart. BABB clearance of embryonic hearts takes place rapidly and also acts to preserve the fluorescent signal for several weeks; in addition, samples can be imaged multiple times without loss of signal. This straightforward method is also applicable to imaging other types of blood vessels in whole embryos. PMID:28060348

  11. Analysis of Coronary Vessels in Cleared Embryonic Hearts.

    PubMed

    Ivins, Sarah; Roberts, Catherine; Vernay, Bertrand; Scambler, Peter J

    2016-12-07

    Whole mount visualization of the embryonic coronary plexus from which the capillary and arterial networks will form is rendered problematic using standard microscopy techniques, due to the scattering of imaging light by the thick heart tissue, as these vessels are localized deep within the walls of the developing heart. As optical clearing of tissues using organic solvents such as BABB (1 part benzyl alcohol to 2 parts benzyl benzoate) has been shown to greatly improve the optical penetration depth that can be achieved, we combined clearance of whole, PECAM1-immunostained hearts, with laser-scanning confocal microscopy, in order to obtain high-resolution images of vessels throughout the entire heart. BABB clearance of embryonic hearts takes place rapidly and also acts to preserve the fluorescent signal for several weeks; in addition, samples can be imaged multiple times without loss of signal. This straightforward method is also applicable to imaging other types of blood vessels in whole embryos.

  12. A Dynamical Modeling Approach for Analysis of Longitudinal Clinical Trials in the Presence of Missing Endpoints.

    PubMed

    Banks, H T; Hu, Shuhua; Rosenberg, Eric

    2017-01-01

    Randomized longitudinal clinical trials are the gold standard to evaluate the effectiveness of interventions among different patient treatment groups. However, analysis of such clinical trials becomes difficult in the presence of missing data, especially in the case where the study endpoints become difficult to measure because of subject dropout rates or/and the time to discontinue the assigned interventions are different among the patient groups. Here we report on using a validated mathematical model combined with an inverse problem approach to predict the values for the missing endpoints. A small randomized HIV clinical trial where endpoints for most of patients are missing is used to demonstrate this approach.

  13. Culture and Manipulation of Embryonic Cells

    PubMed Central

    Edgar, Lois G.; Goldstein, Bob

    2012-01-01

    The direct manipulation of embryonic cells is an important tool for addressing key questions in cell and developmental biology. C. elegans is relatively unique among genetic model systems in being amenable to manipulation of embryonic cells. Embryonic cell manipulation has allowed the identification of cell interactions by direct means, and it has been an important technique for dissecting mechanisms by which cell fates are specified, cell divisions are oriented, and morphogenesis is accomplished. Here, we present detailed methods for isolating, manipulating and culturing embryonic cells of C. elegans. PMID:22226523

  14. The asymptotic behaviour of the scattering matrix in a neighbourhood of the endpoints of a spectral gap

    NASA Astrophysics Data System (ADS)

    Nazarov, S. A.

    2017-01-01

    The behaviour of the scattering matrix is investigated as the spectral parameter approaches an endpoint of a spectral gap of a quantum waveguide from the inside or the outside. The waveguide has two sleeves, one is cylindrical and the other periodic. When the spectral parameter traverses the spectral gap, the scattering matrix is reshaped because the number of waves inside and outside the gap is different. Notwithstanding, the smaller scattering matrix (in size) is transformed continuously into an identical block in the bigger scattering matrix and, in addition, the latter takes block diagonal form in the limit at the endpoint of the gap, that is, at the spectral threshold. The unexpected phenomena are related to the other block. It is shown that in the limit this block can only take certain values at the threshold, and taking one or other of these values depends on the structure of the continuous spectrum and also on the structure of the subspace of `almost standing' waves at the threshold, which are solutions of the homogeneous problem that transfer no energy to infinity. A criterion for the existence of such solutions links the dimension of this subspace to the multiplicity of the eigenvalue -1 of the threshold scattering matrix. Asymptotic formulae are obtained, which show, in particular, that the phenomenon of anomalous scattering of high-amplitude waves at near-threshold frequencies, discovered by Weinstein in a special acoustic problem, also occurs in periodic waveguides. Bibliography: 38 titles.

  15. Developmental effects of embryonic exposure to toxaphene in the American alligator (Alligator mississippiensis).

    PubMed

    Milnes, Matthew R; Allen, Davina; Bryan, Teresa A; Sedacca, Cassidy D; Guillette, Louis J

    2004-05-01

    A variety of organochlorine pesticides have been shown to adversely affect embryonic development. A number of abnormalities have been documented in alligators (Alligator mississippiensis) from highly-contaminated Lake Apopka, FL, USA that are similar to the results of experimental studies exposing embryos to pesticides. In the current study, we exposed developing alligator embryos to varying concentrations of toxaphene, a broad-spectrum pesticide found in relatively high concentration in Lake Apopka alligator egg yolk. The toxaphene, dissolved in 50 microl of ethanol, was applied topically to the eggshell just prior to the sex-determining period of development. Shortly after hatching, we examined a number of morphological and physiological endpoints to determine the consequences of sub-lethal embryonic exposure to toxaphene. Our results indicate that toxaphene had little or no effect on the morphological endpoints examined including body mass (BM) and size, liver, thyroid, and gonad development. In addition, toxaphene failed to affect sexual differentiation, or in vitro thyroxin, testosterone (T), and estradiol production. However, male plasma T concentration was higher in animals treated with 10 and 0.01 microg toxaphene/kg (based on mean egg mass) than control males. Because in vitro T production was not different among control groups, we suggest the difference in plasma T could be due to differences in hypothalamic-pituitary stimulation of the gonad or hepatic steroid degradation. This study indicates that technical grade toxaphene, at the applied doses, does not induce the same developmental abnormalities associated with alligators living in Lake Apopka. Future studies should consider the effects of embryonic exposure to a mixture of chemicals, including toxaphene metabolites, on development in alligators to better evaluate the consequences of environmental contamination.

  16. PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)

    EPA Science Inventory

    Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

  17. 78 FR 73199 - Draft Guidance for Industry on Bioequivalence Studies With Pharmacokinetic Endpoints for Drugs...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-05

    ... as on scientific information that has become available to the Agency. We believe the revisions will... the Agency's current thinking on BE studies with pharmacokinetic endpoints for drug products...

  18. Autonomous Sub-Pixel Satellite Track Endpoint Determination for Space Based Images

    SciTech Connect

    Simms, L M

    2011-03-07

    An algorithm for determining satellite track endpoints with sub-pixel resolution in spaced-based images is presented. The algorithm allows for significant curvature in the imaged track due to rotation of the spacecraft capturing the image. The motivation behind the subpixel endpoint determination is first presented, followed by a description of the methodology used. Results from running the algorithm on real ground-based and simulated spaced-based images are shown to highlight its effectiveness.

  19. 40 CFR Appendix A to Part 68 - Table of Toxic Endpoints

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ....0011 75-78-5 Dimethyldichlorosilane 0.026 57-14-7 1,1-Dimethylhydrazine 0.012 106-89-8 Epichlorohydrin... Endpoints CAS No. Chemical name Toxic endpoint (mg/L) 107-02-8 Acrolein 0.0011 107-13-1 Acrylonitrile 0.076... Ammonia (anhydrous) 0.14 7664-41-7 Ammonia (conc 20% or greater) 0.14 7784-34-1 Arsenous trichloride...

  20. 40 CFR Appendix A to Part 68 - Table of Toxic Endpoints

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ....0011 75-78-5 Dimethyldichlorosilane 0.026 57-14-7 1,1-Dimethylhydrazine 0.012 106-89-8 Epichlorohydrin... Endpoints CAS No. Chemical name Toxic endpoint (mg/L) 107-02-8 Acrolein 0.0011 107-13-1 Acrylonitrile 0.076... Ammonia (anhydrous) 0.14 7664-41-7 Ammonia (conc 20% or greater) 0.14 7784-34-1 Arsenous trichloride...

  1. Evaluation of three soil toxicity tests used to monitor acceptable endpoints

    SciTech Connect

    Brinkmann, M.; Stroo, H.; Leuschner, A.; Leuteritz, D.; Stromberg, M.; Brourman, M.

    1995-12-31

    Three terrestrial toxicity tests were used to evaluate the efficacy of biological treatment of creosote and pentachlorophenol impacted soils at a Superfund site. Microtox, 5-day lettuce seed, and 14-day earthworm toxicity tests were performed on 10 soil samples at the beginning and end of 3 months of land treatment. Secondary endpoints of root length and earthworm weight loss were also evaluated. EC50 and LC50 values were calculated using a Trimmed Logit Statistical Program and compared to toxicity of 10 background samples collected from the site. Results for initial soils demonstrated toxicity with three of the five endpoints. End treatment results showed no measurable toxicity using all endpoints. Toxicity testing results are critical for obtaining regulatory approval for the full-scale treatment system. Post treatment closure requirements for the site will be based on bioassay results. Evaluation of the three tests used showed the Microtox test to be the most sensitive to this type of toxicity. Lettuce seed germination results were the least sensitive of the three primary endpoints chosen. Of the secondary endpoint criteria, root length demonstrated reliable EC50 values and showed toxicity trends similar to Microtox and earthworm tests. The earthworm weight loss endpoint was not a useful toxicity measurement at 14 days.

  2. Avian embryonic development in hyperdynamic environments

    NASA Technical Reports Server (NTRS)

    Abbott, U. K.; Smith, A. H.

    1983-01-01

    Embryos which developed for 24 hours in the oviduct of hens maintained at 2 G and which were subsequently incubated at Earth gravity had a 14% reduction in hatchability. Increased mortality during the first 4 days, and an increase in embryonic abnormalities were of the types usually found during the first mortality peak (2-3 days). Embryos in eggs that were produced at Earth gravity and continued their development on the centrifuge at fields of 2 G or less did not appear to be greatly affected by the treatment. At 4 G, 91% of the embryos died, mostly on the first and second days of incubation. Abnormalities prominent in the centrifuged eggs include: (a) a failure of the primitive streak to develop; (b) interference with the development of the axial skeleton; (c) multiple hemorrhages, mostly petechial which is consistent with capillary fragility; and (d) retardation of embryo growth, possibly caused by an interference with gaseous diffusion, the result of an acceleration-induced increase in gas density in the centrifuging incubator.

  3. Embryonic blood-cerebrospinal fluid barrier formation and function

    PubMed Central

    Bueno, David; Parvas, Maryam; Hermelo, Ismaïl; Garcia-Fernàndez, Jordi

    2014-01-01

    During embryonic development and adult life, brain cavities and ventricles are filled with cerebrospinal fluid (CSF). CSF has attracted interest as an active signaling medium that regulates brain development, homeostasis and disease. CSF is a complex protein-rich fluid containing growth factors and signaling molecules that regulate multiple cell functions in the central nervous system (CNS). The composition and substance concentrations of CSF are tightly controlled. In recent years, it has been demonstrated that embryonic CSF (eCSF) has a key function as a fluid pathway for delivering diffusible signals to the developing brain, thus contributing to the proliferation, differentiation and survival of neural progenitor cells, and to the expansion and patterning of the brain. From fetal stages through to adult life, CSF is primarily produced by the choroid plexus. The development and functional activities of the choroid plexus and other blood–brain barrier (BBB) systems in adults and fetuses have been extensively analyzed. However, eCSF production and control of its homeostasis in embryos, from the closure of the anterior neuropore when the brain cavities become physiologically sealed, to the formation of the functional fetal choroid plexus, has not been studied in as much depth and remains open to debate. This review brings together the existing literature, some of which is based on experiments conducted by our research group, concerning the formation and function of a temporary embryonic blood–CSF barrier in the context of the crucial roles played by the molecules in eCSF. PMID:25389383

  4. Exploring the relationship between the causal-inference and meta-analytic paradigms for the evaluation of surrogate endpoints.

    PubMed

    Van der Elst, Wim; Molenberghs, Geert; Alonso, Ariel

    2016-04-15

    Nowadays, two main frameworks for the evaluation of surrogate endpoints, based on causal-inference and meta-analysis, dominate the scene. Earlier work showed that the metrics of surrogacy introduced in both paradigms are related, although in a complex way that is difficult to study analytically. In the present work, this relationship is further examined using simulations and the analysis of a case study. The results indicate that the extent to which both paradigms lead to similar conclusions regarding the validity of the surrogate, depends on a complex interplay between multiple factors like the ratio of the between and within trial variability and the unidentifiable correlations between the potential outcomes. All the analyses were carried out using the newly developed R package Surrogate, which is freely available via CRAN.

  5. Infrared inhibition of embryonic hearts

    NASA Astrophysics Data System (ADS)

    Wang, Yves T.; Rollins, Andrew M.; Jenkins, Michael W.

    2016-06-01

    Infrared control is a new technique that uses pulsed infrared lasers to thermally alter electrical activity. Originally developed for nerves, we have applied this technology to embryonic hearts using a quail model, previously demonstrating infrared stimulation and, here, infrared inhibition. Infrared inhibition enables repeatable and reversible block, stopping cardiac contractions for several seconds. Normal beating resumes after the laser is turned off. The block can be spatially specific, affecting propagation on the ventricle or initiation on the atrium. Optical mapping showed that the block affects action potentials and not just calcium or contraction. Increased resting intracellular calcium was observed after a 30-s exposure to the inhibition laser, which likely resulted in reduced mechanical function. Further optimization of the laser illumination should reduce potential damage. Stopping cardiac contractions by disrupting electrical activity with infrared inhibition has the potential to be a powerful tool for studying the developing heart.

  6. Correlating behaviour and gene expression endpoints in the dopaminergic system after modafinil administration in mouse.

    PubMed

    De Ron, P; Dremier, S; Winlow, P; Jenkins, A; Hanon, E; Nogueira da Costa, A

    2016-04-01

    The mechanisms of action of modafinil continue to be poorly characterised and its potential for abuse in preclinical models remains controverted. The aim of this study was to further elucidate the mechanism of action of modafinil, through a potential behavioural and molecular association in the mouse. A conditioned place preference (CPP) paradigm was implemented to investigate the rewarding properties of modafinil. Whole genome expression and qRT-PCR analysis were performed on the ventral tegmental area (VTA), nucleus accumbens (NAC) and prefrontal cortex (PFC) of modafinil-treated and control animals. Modafinil administration (65 mg/kg) induced an increase in locomotor activity, an increase in the change of preference for the drug paired side after a conditioning period as well as changes to gene expression profiles in the VTA (120 genes), NAC (23 genes) and PFC (19 genes). A molecular signature consisting of twelve up-regulated genes was identified as common to the three brain regions. Multiple linear correlation analysis showed a strong correlation (R(2)>0.70) between the behavioural and molecular endpoints in the three brain regions. We show that modafinil had a concomitant effect on CPP, locomotor activity, and up-regulation of interferon-γ (IFN-γ) regulated genes (Gbp2, Gbp3, Gbp10, Cd274, Igtp), while correlating the latter set of genes with behaviour changes evaluated through the CPP. A potential association can be proposed based on the dysregulation of p47 family genes and Gbp family of IFN-γ induced GTPases. In conclusion, these findings suggest a link between the behavioural and molecular events in the context of modafinil administration.

  7. An Adaptive Staggered Dose Design for a Normal Endpoint.

    PubMed

    Wu, Joseph; Menon, Sandeep; Chang, Mark

    2015-01-01

    In a clinical trial where several doses are compared to a control, a multi-stage design that combines both the selection of the best dose and the confirmation of this selected dose is desirable. An example is the two-stage drop-the-losers or pick-the-winner design, where inferior doses are dropped after interim analysis. Selection of target dose(s) can be based on ranking of observed effects, hypothesis testing with adjustment for multiplicity, or other criteria at interim stages. A number of methods have been proposed and have made significant gains in trial efficiency. However, many of these designs started off with all doses with equal allocation and did not consider prioritizing the doses using existing dose-response information. We propose an adaptive staggered dose procedure that allows explicit prioritization of doses and applies error spending scheme that favors doses with assumed better responses. This design starts off with only a subset of the doses and adaptively adds new doses depending on interim results. Using simulation, we have shown that this design performs better in terms of increased statistical power than the drop-the-losers design given strong prior information of dose response.

  8. Generation of the Dimensional Embryology Application (App) for Visualization of Early Chick and Frog Embryonic Development

    ERIC Educational Resources Information Center

    Webb, Rebecca L.; Bilitski, James; Zerbee, Alyssa; Symans, Alexandra; Chop, Alexandra; Seitz, Brianne; Tran, Cindy

    2015-01-01

    The study of embryonic development of multiple organisms, including model organisms such as frogs and chicks, is included in many undergraduate biology programs, as well as in a variety of graduate programs. As our knowledge of biological systems increases and the amount of material to be taught expands, the time spent instructing students about…

  9. Role of microglia in embryonic neurogenesis

    PubMed Central

    Tong, Chih Kong

    2016-01-01

    Microglia begin colonizing the developing brain as early as embryonic day 9, prior to the emergence of neurons and other glia. Their ontogeny is also distinct from other central nervous system cells, as they derive from yolk sac hematopoietic progenitors and not neural progenitors. In this review, we feature these unique characteristics of microglia and assess the spatiotemporal similarities between microglia colonization of the central nervous system and embryonic neurogenesis. We also infer to existing evidence for microglia function from embryonic through to postnatal neurodevelopment to postulate roles for microglia in neurogenesis. PMID:27555616

  10. Latent variable indirect response modeling of categorical endpoints representing change from baseline.

    PubMed

    Hu, Chuanpu; Xu, Zhenhua; Mendelsohn, Alan M; Zhou, Honghui

    2013-02-01

    Accurate exposure-response modeling is important in drug development. Methods are still evolving in the use of mechanistic, e.g., indirect response (IDR) models to relate discrete endpoints, mostly of the ordered categorical form, to placebo/co-medication effect and drug exposure. When the discrete endpoint is derived using change-from-baseline measurements, a mechanistic exposure-response modeling approach requires adjustment to maintain appropriate interpretation. This manuscript describes a new modeling method that integrates a latent-variable representation of IDR models with standard logistic regression. The new method also extends to general link functions that cover probit regression or continuous clinical endpoint modeling. Compared to an earlier latent variable approach that constrained the baseline probability of response to be 0, placebo effect parameters in the new model formulation are more readily interpretable and can be separately estimated from placebo data, thus allowing convenient and robust model estimation. A general inherent connection of some latent variable representations with baseline-normalized standard IDR models is derived. For describing clinical response endpoints, Type I and Type III IDR models are shown to be equivalent, therefore there are only three identifiable IDR models. This approach was applied to data from two phase III clinical trials of intravenously administered golimumab for the treatment of rheumatoid arthritis, where 20, 50, and 70% improvement in the American College of Rheumatology disease severity criteria were used as efficacy endpoints. Likelihood profiling and visual predictive checks showed reasonable parameter estimation precision and model performance.

  11. Endpoint in plasma etch process using new modified w-multivariate charts and windowed regression

    NASA Astrophysics Data System (ADS)

    Zakour, Sihem Ben; Taleb, Hassen

    2017-02-01

    Endpoint detection is very important undertaking on the side of getting a good understanding and figuring out if a plasma etching process is done in the right way, especially if the etched area is very small (0.1%). It truly is a crucial part of supplying repeatable effects in every single wafer. When the film being etched has been completely cleared, the endpoint is reached. To ensure the desired device performance on the produced integrated circuit, the high optical emission spectroscopy (OES) sensor is employed. The huge number of gathered wavelengths (profiles) is then analyzed and pre-processed using a new proposed simple algorithm named Spectra peak selection (SPS) to select the important wavelengths, then we employ wavelet analysis (WA) to enhance the performance of detection by suppressing noise and redundant information. The selected and treated OES wavelengths are then used in modified multivariate control charts (MEWMA and Hotelling) for three statistics (mean, SD and CV) and windowed polynomial regression for mean. The employ of three aforementioned statistics is motivated by controlling mean shift, variance shift and their ratio (CV) if both mean and SD are not stable. The control charts show their performance in detecting endpoint especially W-mean Hotelling chart and the worst result is given by CV statistic. As the best detection of endpoint is given by the W-Hotelling mean statistic, this statistic will be used to construct a windowed wavelet Hotelling polynomial regression. This latter can only identify the window containing endpoint phenomenon.

  12. Treatment endpoints for resistant port wine stains with a 755 nm laser.

    PubMed

    Izikson, Leonid; Anderson, R Rox

    2009-03-01

    Laser therapy of port wine stains (PWS) resistant to pulsed dye laser is challenging and controversial. Based on the theory of selective photothermolysis, vessels in such lesions may be specifically targeted with the laser wavelength of 755 nm. There is much deeper penetration of the near-infrared light and it is difficult to visualize laser-induced changes within the deeper dermis. The recognition of an appropriate immediate endpoint response with this wavelength would be helpful. This is a clinical observations report. We present examples of an appropriate PWS tissue response endpoint based on our clinical observations in resistant PWS treated with a 755 nm laser at high fluences (40-100 J/cm(2)), 1.5-ms pulse duration, with dynamic cooling device (DCD) cooling. Mild-to-moderate PWS lightening was associated with the immediate endpoint of a transient gray color that gradually evolved into persistent deep purpura within several minutes. We also discuss the clinical endpoints that represent undertreatment and overtreatment of PWS. It is important to attain, and maintain, the correct endpoint when treating PWS with this deeply penetrating near-infrared laser at high fluences in order to (a) induce lesional lightening, and (b) avoid deep dermal burns that may produce scarring. Judicious use of the 755 nm laser can be beneficial for resistant PWS.

  13. Assembly of embryonic and extra-embryonic stem cells to mimic embryogenesis in vitro.

    PubMed

    Harrison, Sarah Ellys; Sozen, Berna; Christodoulou, Neophytos; Kyprianou, Christos; Zernicka-Goetz, Magdalena

    2017-03-02

    Mammalian embryogenesis requires intricate interactions between embryonic and extra-embryonic tissues to orchestrate and coordinate morphogenesis with changes in developmental potential. Here, we combine mouse embryonic stem cells (ESCs) and extra-embryonic trophoblast stem cells (TSCs) in a 3D-scaffold to generate structures whose morphogenesis is remarkably similar to natural embryos. By using genetically-modified stem cells and specific inhibitors, we show embryogenesis of ESC- and TSC-derived embryos, ETS-embryos, depends on crosstalk involving Nodal signaling. When ETS-embryos develop, they spontaneously initiate expression of mesoderm and primordial germ cell markers asymmetrically on the embryonic and extra-embryonic border, in response to Wnt and BMP signaling. Our study demonstrates the ability of distinct stem cell types to self-assemble in vitro to generate embryos whose morphogenesis, architecture, and constituent cell-types resemble natural embryos.

  14. Endpoints for Neural Connectivity Including Neurite Outgrowth, Synapse Formation, and Function

    EPA Science Inventory

    A strategy for alternative methods for developmental neurotoxicity testing (DNT) focuses on assessment of chemical effects on conserved neurodevelopmental processes. The development of the brain is an integrated series of steps from the commitment of embryonic cells to become neu...

  15. Swimming speed alteration in the early developmental stages of Paracentrotus lividus sea urchin as ecotoxicological endpoint.

    PubMed

    Morgana, Silvia; Gambardella, Chiara; Falugi, Carla; Pronzato, Roberto; Garaventa, Francesca; Faimali, Marco

    2016-04-01

    Behavioral endpoints have been used for decades to assess chemical impacts at concentrations unlikely to cause mortality. With recently developed techniques, it is possible to investigate the swimming behavior of several organisms under laboratory conditions. The aims of this study were: i) assessing for the first time the feasibility of swimming speed analysis of the early developmental stage sea urchin Paracentrotus lividus by an automatic recording system ii) investigating any Swimming Speed Alteration (SSA) on P. lividus early stages exposed to a chemical reference; iii) identifying the most suitable stage for SSA test. Results show that the swimming speed of all the developmental stages was easily recorded. The swimming speed was inhibited as a function of toxicant concentration. Pluteus were the most appropriate stage for evaluating SSA in P. lividus as ecotoxicological endpoint. Finally, swimming of sea urchin early stages represents a sensitive endpoint to be considered in ecotoxicological investigations.

  16. Missing data and measurement variability in assessing progression-free survival endpoint in randomized clinical trials.

    PubMed

    Sridhara, Rajeshwari; Mandrekar, Sumithra J; Dodd, Lori E

    2013-05-15

    Progression-free survival (PFS) is frequently used as the primary efficacy endpoint in the evaluation of cancer treatment that is considered for marketing approval. Missing or incomplete data problems become more acute with a PFS endpoint (compared with overall survival). In a given clinical trial, it is common to observe incomplete data due to premature treatment discontinuation, missed or flawed assessments, change of treatment, lack of follow-up, and unevaluable data. When incomplete data issues are substantial, interpretation of the data becomes tenuous. Plans to prevent, minimize, or properly analyze incomplete data are critical for generalizability of results from the clinical trial. Variability in progressive disease measurement between radiologists further contributes to data problems with a PFS endpoint. The repercussions of this on phase III clinical trials are complex and depend on several factors, including the magnitude of the variability and whether there is a systematic reader evaluation bias favoring one treatment arm particularly in open-label trials.

  17. Sample size determination in group-sequential clinical trials with two co-primary endpoints.

    PubMed

    Asakura, Koko; Hamasaki, Toshimitsu; Sugimoto, Tomoyuki; Hayashi, Kenichi; Evans, Scott R; Sozu, Takashi

    2014-07-30

    We discuss sample size determination in group-sequential designs with two endpoints as co-primary. We derive the power and sample size within two decision-making frameworks. One is to claim the test intervention's benefit relative to control when superiority is achieved for the two endpoints at the same interim timepoint of the trial. The other is when superiority is achieved for the two endpoints at any interim timepoint, not necessarily simultaneously. We evaluate the behaviors of sample size and power with varying design elements and provide a real example to illustrate the proposed sample size methods. In addition, we discuss sample size recalculation based on observed data and evaluate the impact on the power and Type I error rate.

  18. The Feynman trajectories: determining the path of a protein using fixed-endpoint assays.

    PubMed

    Ketteler, Robin

    2010-03-01

    Richard Feynman postulated in 1948 that the path of an electron can be best described by the sum or functional integral of all possible trajectories rather than by the notion of a single, unique trajectory. As a consequence, the position of an electron does not harbor any information about the paths that contributed to this position. This observation constitutes a classical endpoint observation. The endpoint assay is the desired type of experiment for high-throughput screening applications, mainly because of limitations in data acquisition and handling. Quite contrary to electrons, it is possible to extract information about the path of a protein using endpoint assays, and these types of applications are reviewed in this article.

  19. Radiation acquisition and RBF neural network analysis on BOF end-point control

    NASA Astrophysics Data System (ADS)

    Zhao, Qi; Wen, Hong-yuan; Zhou, Mu-chun; Chen, Yan-ru

    2008-12-01

    There are some problems in Basic Oxygen Furnace (BOF) steelmaking end-point control technology at present. A new BOF end-point control model was designed, which was based on the character of carbon oxygen reaction in Basic Oxygen Furnace steelmaking process. The image capture and transformation system was established by Video for Windows (VFW) library function, which is a video software development package promoted by Microsoft Corporation. In this paper, the Radial Basic Function (RBF) neural network model was established by using the real-time acquisition information. The input parameters can acquire easily online and the output parameter is the end-point time, which can compare with the actual value conveniently. The experience results show that the predication result is ideal and the experiment results show the model can work well in the steelmaking adverse environment.

  20. Effect of Pre-Fixation Delay and Freezing on Mink Testicular Endpoints for Environmental Research

    PubMed Central

    Spörndly-Nees, Ellinor; Ekstedt, Elisabeth; Magnusson, Ulf; Fakhrzadeh, Azadeh; Luengo Hendriks, Cris L.; Holm, Lena

    2015-01-01

    There is growing interest in using wild animals to monitor the real-life cocktail effect of environmental chemicals on male reproduction. However, practical difficulties, such as long distances to the laboratory, generally prolong the time between euthanisation and specimen handling. For instance, tissue fixation is often performed on frozen material or on material where deterioration has started, which may affect tissue morphology. This study examined the effect of pre-fixation delay and freezing on mink testicular endpoints in order to determine robust endpoints in suboptimally handled specimens. Sexually mature farmed mink (n=30) selected at culling were divided into six groups and subjected to different time intervals between euthanisation and fixation or freezing: 0 hours (fixed immediately post mortem), 6 hours, 18 hours, 30 hours, 42 hours, or frozen 6 hours post mortem and thawed overnight. Unaffected endpoints when pre-fixation storage was extended to 30 hours included: area and diameter of the seminiferous tubules, length and weight of the testes, and acrosomes marked with Gata-4. Epithelial height, Sertoli cells marked with Gata-4 and cell morphology were affected endpoints after 6 hours of storage. Freezing the tissue prior to fixation severely altered cell morphology and reduced testicular weight, tubular diameter and area. Morphological changes seen after 6 hours included shredded germ cells and excess cytoplasm in seminiferous tubular lumen, chromatin rearrangements and increased germ cell death. Extended delay before fixation and freezing affected many endpoints in the mink testicular tissue. Some of these endpoints may mimic chemically induced effects, which is important to consider when evaluating specimens from wild animals for environmental toxicity. PMID:25933113

  1. Medaka haploid embryonic stem cells.

    PubMed

    Hong, Yunhan

    2010-01-01

    The appearance of diploidy, the presence of two genomes or chromosome sets, is a fundamental hallmark of eukaryotic evolution and bisexual reproduction, because diploidy offers the basis for the bisexual life cycle, allowing for oscillation between diploid and haploid phases. Meiosis produces haploid gametes. At fertilization, male and female gametes fuse to restore diploidy in a zygote, which develops into a new life. At sex maturation, diploid cells enter into meiosis, culminating in the production of haploid gametes. Therefore, diploidy ensures pluripotency, cell proliferation, and functions, whereas haploidy is restricted only to the post-meiotic gamete phase of germline development and represents the end point of cell growth. Diploidy is advantageous for evolution. Haploidy is ideal for genetic analyses, because any recessive mutations of essential genes will show a clear phenotype in the absence of a second gene copy. Recently, my laboratory succeeded in the generation of medaka haploid embryonic stem (ES) cells capable of whole animal production. Therefore, haploidy in a vertebrate is able to support stable cell culture and pluripotency. This finding anticipates the possibility to generate haploid ES cells in other vertebrate species such as zebrafish. These medaka haploid ES cells elegantly combine haploidy and pluripotency, offering a unique yeast-like system for in vitro genetic analyses of molecular, cellular, and developmental events in various cell lineages. This chapter is aimed to describe the strategy of haploid ES cell derivation and their characteristics, and illustrate the perspectives of haploid ES cells for infertility treatment, genetic screens, and analyses.

  2. Embryonic development in Zungaro jahu.

    PubMed

    Marques, Camila; Faustino, Francine; Bertolucci, Bruno; Paes, Maria do Carmo Faria; Silva, Regiane Cristina da; Nakaghi, Laura Satiko Okada

    2017-02-01

    The aim of this study was to characterize the embryonic development of Zungaro jahu, a fresh water teleostei commonly known as 'jaú'. Samples were collected at pre-determined times from oocyte release to larval hatching and analysed under light microscopy, transmission electron microscopy and scanning electron microscopy. At the first collection times, the oocytes and eggs were spherical and yellowish, with an evident micropyle. Embryo development took place at 29.4 ± 1.5°C and was divided into seven stages: zygote, cleavage, morula, blastula, gastrula, organogenesis, and hatching. The differentiation of the animal and vegetative poles occured during the zygote stage, at 10 min post-fertilization (mpf), leading to the development of the egg cell at 15 mpf. From 20 to 75 mpf, successive cleavages resulted in the formation of 2, 4, 8, 16, 32 and 64 blastomeres. The morula stage was observed between 90 and 105 mpf, and the blastula and gastrula stage at 120 and 180 mpf; respectively. The end of the gastrula stage was characterized by the presence of the yolk plug at 360 mpf. Organogenesis followed, with differentiation of the cephalic and caudal regions, elongation of the embryo by the cephalo-caudal axis, and somitogenesis. Hatching occurred at 780 mpf, with mean larval total length of 3.79 ± 0.11 mm.

  3. Embryonal rhabdomyosarcoma: A rare oral tumor

    PubMed Central

    Datta, Sila; Ray, Jay Gopal; Deb, Tushar; Patsa, Santanu

    2016-01-01

    Rhabdomyosarcoma is the malignant neoplasm of striated muscle and a relatively uncommon tumor of the oral cavity. Embryonal variety is the most common subtype, observed in children below 10 years of age but occasionally seen in adolescents and young adults. The present report describes a case of embryonal rhabdomyosarcoma in the left posterior buccal mucosa, with extension in the adjacent alveolus, soft palate, oropharynx and nasopharynx of a 17-year-old female. PMID:27721622

  4. Calculation of a velocity distribution from particle trajectory end-points.

    USGS Publications Warehouse

    Rasmussen, Lowell A.

    1983-01-01

    The longitudinal component of the velocity of a particle at or near a glacier surface is considered, its position as a function of time being termed its trajectory. Functional relationships are derived for obtaining the trajectory from the spatial distribution of velocity and for obtaining the velocity distribution from the trajectory. It is established that the trajectory end-points impose only an integral condition on the velocity distribution and that no individual point on the velocity distribution can be determined if only the end-points are known.-from Author

  5. Movement trajectory smoothness is not associated with the endpoint accuracy of rapid multi-joint arm movements in young and older adults.

    PubMed

    Poston, Brach; Van Gemmert, Arend W A; Sharma, Siddharth; Chakrabarti, Somesh; Zavaremi, Shahrzad H; Stelmach, George

    2013-06-01

    The minimum variance theory proposes that motor commands are corrupted by signal-dependent noise and smooth trajectories with low noise levels are selected to minimize endpoint error and endpoint variability. The purpose of the study was to determine the contribution of trajectory smoothness to the endpoint accuracy and endpoint variability of rapid multi-joint arm movements. Young and older adults performed arm movements (4 blocks of 25 trials) as fast and as accurately as possible to a target with the right (dominant) arm. Endpoint accuracy and endpoint variability along with trajectory smoothness and error were quantified for each block of trials. Endpoint error and endpoint variance were greater in older adults compared with young adults, but decreased at a similar rate with practice for the two age groups. The greater endpoint error and endpoint variance exhibited by older adults were primarily due to impairments in movement extent control and not movement direction control. The normalized jerk was similar for the two age groups, but was not strongly associated with endpoint error or endpoint variance for either group. However, endpoint variance was strongly associated with endpoint error for both the young and older adults. Finally, trajectory error was similar for both groups and was weakly associated with endpoint error for the older adults. The findings are not consistent with the predictions of the minimum variance theory, but support and extend previous observations that movement trajectories and endpoints are planned independently.

  6. SEMICONDUCTOR TECHNOLOGY A signal processing method for the friction-based endpoint detection system of a CMP process

    NASA Astrophysics Data System (ADS)

    Chi, Xu; Dongming, Guo; Zhuji, Jin; Renke, Kang

    2010-12-01

    A signal processing method for the friction-based endpoint detection system of a chemical mechanical polishing (CMP) process is presented. The signal process method uses the wavelet threshold denoising method to reduce the noise contained in the measured original signal, extracts the Kalman filter innovation from the denoised signal as the feature signal, and judges the CMP endpoint based on the feature of the Kalman filter innovation sequence during the CMP process. Applying the signal processing method, the endpoint detection experiments of the Cu CMP process were carried out. The results show that the signal processing method can judge the endpoint of the Cu CMP process.

  7. ECOLOGICAL ENDPOINT MODELING FOR TMDLS: EFFECTS OF SEDIMENT ON FISH POPULATIONS

    EPA Science Inventory

    Sediment is one of the primary stressors of concern for Total Maximum Daily Loads (TMDLs) for streams, and often it is a concern because of its impact on ecological endpoints. A modeling approach relating sediment to stream fish population dynamics is presented. Equations are d...

  8. Selecting surrogate endpoints for estimating pesticide effects on avian reproductive success

    EPA Science Inventory

    A Markov chain nest productivity model (MCnest) has been developed for projecting the effects of a specific pesticide-use scenario on the annual reproductive success of avian species of concern. A critical element in MCnest is the use of surrogate endpoints, defined as measured ...

  9. EFFECTS OF COPPER ON COMMUNITY, FUNCTIONAL, AND BEHAVIORAL ENDPOINTS IN AN ARTIFICIAL STREAM STUDY

    EPA Science Inventory

    A study of the effects of copper on biota and behavioral endpoints was carried out at the U.S. EPA's Experimental Stream Facility (ESF), Milford OH. The objective of the study was to identify relationships between structural (macrobenthos and periphyton indices), functional (inte...

  10. Shape and Steepness of Toxicological Dose-Response Relationships of Continuous Endpoints

    EPA Science Inventory

    A re-analysis of a large number of historical dose-response data for continuous endpoints indicates that an exponential or a Hill model with four parameters both adequately describe toxicological dose-responses. The four parameters relate to the background response, the potency o...

  11. Development of a Computer Model for Prediction of PCB Degradation Endpoints

    SciTech Connect

    Just, E.M.; Klasson, T.

    1999-12-07

    Several researchers have demonstrated the transformation if polychlorinated biphenyls (PCBs) by both aerobic and anaerobic bacteria. This transformation, or conversion, is characteristic and often dependent on PCB congener structure and in addition, dictates the products or endpoints. Since transformation is linked to microbial activities, bioremediation has been hailed as a possible solution for PCB-contaminated soils and sediments, and several demonstration activities have verified laboratory results. This paper presents results from mathematical modeling of PCB transformation as a means of predicting possible endpoints of bioremediation. Since transformation can be influenced by both starting composition of the PCBs and microbial activity, this paper systematically evaluates several of the most common transformation patterns. The predicted data are also compared with experimental results. For example, the correlation between laboratory-observed and predicted endpoint data was, in some cases, as good as 0.98 (perfect correlation = 1.0). In addition to predicting chemical endpoints, the possible human effects of the PCBs are discussed through the use of documented dioxin-like toxicity and accumulation in humans before and after transformation.

  12. Predictive Signatures from ToxCast Data for Chronic, Developmental and Reproductive Toxicity Endpoints

    EPA Science Inventory

    The EPA ToxCast program is using in vitro assay data and chemical descriptors to build predictive models for in vivo toxicity endpoints. In vitro assays measure activity of chemicals against molecular targets such as enzymes and receptors (measured in cell-free and cell-based sys...

  13. Detecting Blending End-Point Using Mean Squares Successive Difference Test and Near-Infrared Spectroscopy.

    PubMed

    Khorasani, Milad; Amigo, José M; Bertelsen, Poul; Van Den Berg, Frans; Rantanen, Jukka

    2015-08-01

    An algorithm based on mean squares successive difference test applied to near-infrared and principal component analysis scores was developed to monitor and determine the blending profile and to assess the end-point in the statistical stabile phase. Model formulations consisting of an active compound (acetylsalicylic acid), together with microcrystalline cellulose and two grades of calcium carbonate with dramatically different particle shapes, were prepared. The formulation comprising angular-shaped calcium carbonate reached blending end-point slower when compared with the formulation comprising equant-shaped calcium carbonate. Utilizing the ring shear test, this distinction in end-point could be related to the difference in flowability of the formulations. On the basis of the two model formulations, a design of experiments was conducted to characterize the blending process by studying the effect of CaCO3 grades and fill level of the bin on blending end-point. Calcium carbonate grades, fill level, and their interaction were shown to have a significant impact on the blending process.

  14. Developing ecosystem services-based assessment endpoints for determining ecological risks to estuarine environments

    EPA Science Inventory

    Current U.S. EPA ecological risk assessment (ERA) guidance defines an assessment endpoint (AE) as an explicit expression of the environmental value that is to be protected, and recommends that AEs are selected based on ecological relevance, susceptibility to known or potential st...

  15. LIFE CYCLE IMPACT ASSESSMENT WORKSHOP SUMMARY - MIDPOINTS VERSUS ENDPOINTS: THE SACRIFICES AND BENEFITS

    EPA Science Inventory

    On 5/25-26/2000 in Brighton, England, the third international workshop was held under the umbrella of UNEP addressing issues in Life Cycle Impact Assessment (LCIA). The workshop provided a forum for experts to discuss midpoint vs. endpoint modeling. Midpoints are considered to be...

  16. 77 FR 49447 - Endpoints for Clinical Trials in Kidney Transplantation; Public Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-16

    ... HUMAN SERVICES Food and Drug Administration Endpoints for Clinical Trials in Kidney Transplantation... trials of drugs and therapeutic biologics in kidney transplantation. This public workshop is intended to... evaluate patient and allograft outcome in clinical trials of kidney transplantation. The meeting...

  17. Development of Pain Endpoint Models for Use in Prostate Cancer Clinical Trials and Drug Approval

    DTIC Science & Technology

    2013-10-01

    Study Endpoint and Label Development Team, and FDA Division of Anesthesia, Analgesia and Rheumatology Products, in order to establish discrete...Team, and FDA Division of Anesthesia, Analgesia and Rheumatology Products, in order to establish discrete guidelines and produce a publication

  18. Plasma creatinine results derived from an endpoint modification of the Jaffé method.

    PubMed

    Schurman, S J; Perlman, S A; Chamizo, W

    1998-06-01

    For values in the normal pediatric range, endpoint modifications of the Jaffé method for measuring plasma creatinine (PCr) yield higher results than other commonly used techniques. In an effort to evaluate the Olympus AU5000 endpoint method used by the large reference laboratory to which many of our patients are directed by their third-party payor, we compared results with a kinetic Jaffé technique using paired samples from the same specimens. In 46 samples, the kinetic method measured Pcr at < or =0.8 mg/dl, whereas the endpoint technique PCr was higher by 0.1 mg/dl in 6 (13%), 0.2 mg/dl in 23 (50%), and 0.3 mg/dl in 16 (35%) samples (P<0.0001). The combination of these higher values and the same reported normal range for all children ages 2-12 years (0.3-1.0 mg/dl) and 13-17 years (0.7-1.4 mg/dl) makes interpretation of Olympus AU5000 endpoint method results difficult, particularly for younger children. The results reinforce the need for each laboratory to provide comprehensive age- and sex-adjusted normal PCr ranges.

  19. 76 FR 51993 - Draft Guidance for Industry on Standards for Clinical Trial Imaging Endpoints; Availability

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-19

    ... standardization of imaging procedures when an important imaging endpoint is used in a clinical trial of a... outlines the major considerations for standardization of image acquisition, image interpretation methods... of image acquisition and interpretation standardization, a medical practice standard and a...

  20. Coulometric Titration of Ethylenediaminetetraacetate (EDTA) with Spectrophotometric Endpoint Detection: An Experiment for the Instrumental Analysis Laboratory

    ERIC Educational Resources Information Center

    Williams, Kathryn R.; Young, Vaneica Y.; Killian, Benjamin J.

    2011-01-01

    Ethylenediaminetetraacetate (EDTA) is commonly used as an anticoagulant in blood-collection procedures. In this experiment for the instrumental analysis laboratory, students determine the quantity of EDTA in commercial collection tubes by coulometric titration with electrolytically generated Cu[superscript 2+]. The endpoint is detected…

  1. QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP (QSAR) MODELS TO PREDICT CHEMICAL TOXICITY FOR VARIOUS HEALTH ENDPOINTS

    EPA Science Inventory

    Although ranking schemes based on exposure and toxicity have been developed to aid in the prioritization of research funds for identifying chemicals of regulatory concern, there are significant gaps in the availability of experimental toxicity data for most health endpoints. Pred...

  2. 77 FR 46444 - Gastroenterology Regulatory Endpoints and the Advancement of Therapeutics (GREAT); Public Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-03

    ..., pediatric and adult inflammatory bowel disease, and parenteral nutrition-associated liver disease. DATES... liver disease is to discuss endpoints and their measurement for clinical trials in which parenteral nutrition-induced liver disease is either an efficacy or safety outcome measure. Particpation In the...

  3. Can joint sound assess soft and hard endpoints of the Lachman test?: A preliminary study.

    PubMed

    Hattori, Koji; Ogawa, Munehiro; Tanaka, Kazunori; Matsuya, Ayako; Uematsu, Kota; Tanaka, Yasuhito

    2016-05-12

    The Lachman test is considered to be a reliable physical examination for anterior cruciate ligament (ACL) injury. Patients with a damaged ACL demonstrate a soft endpoint feeling. However, examiners judge the soft and hard endpoints subjectively. The purpose of our study was to confirm objective performance of the Lachman test using joint auscultation. Human and porcine knee joints were examined. Knee joint sound during the Lachman test (Lachman sound) was analyzed by fast Fourier transformation. As quantitative indices of Lachman sound, the peak sound as the maximum relative amplitude (acoustic pressure) and its frequency were used. The mean Lachman peak sound for healthy volunteer knees was 86.9 ± 12.9 Hz in frequency and -40 ± 2.5 dB in acoustic pressure. The mean Lachman peak sound for intact porcine knees was 84.1 ± 9.4 Hz and -40.5 ± 1.7 dB. Porcine knees with ACL deficiency had a soft endpoint feeling during the Lachman test. The Lachman peak sounds of porcine knees with ACL deficiency were dispersed into four distinct groups, with center frequencies of around 40, 160, 450, and 1600. The Lachman peak sound was capable of assessing soft and hard endpoints of the Lachman test objectively.

  4. Recent Developments in Whole Sediment Toxicity Identification Evaluations: Innovations in Manipulations and Endpoints

    EPA Science Inventory

    Whole sediment Toxicity Identification Evaluation (TIE) methods were developed primarily in the late 1990s and early 2000s in research programs dedicated to developing manipulations and endpoints to characterize and identify causes of toxicity to benthic freshwater and marine org...

  5. Assessment of embryonic growth in chicken eggs by means of visible transmission spectroscopy.

    PubMed

    Kemps, Bart J; Bamelis, Flip R; Mertens, Kristof; Decuypere, Eddy M; De Baerdemaeker, Josse G; De Ketelaere, Bart

    2010-01-01

    During this work, it was investigated whether spectral measurements can be used to monitor embryonic growth. An experiment was conducted in which both the transmission spectra and embryonic weight were determined on 240 eggs (Cobb, 37 weeks) between Day 5 and Day 10 of incubation. The spectral data were linked to embryonic weight by means of a partial least squares analysis. Different preprocessing procedures were compared during this work, that is, smoothing, multiplicative scatter correction (MSC), and first- and second-order derivative. Compared to the remainder of the preprocessing procedures, MSC leads to a considerable improvement of the prediction capability of the embryonic weight. The ratio of performance to deviation obtained for the MSC spectra equaled 4.5 indicating that a very accurate prediction of embryonic weight is feasible based on the VIS/NIR transmission measurements. Important regions for the prediction are situated around 685-740 nm. It is suggested that the spectral changes in these spectral regions result from the displacement of carotenoids from the yolk into the blood circuitry.

  6. Shortening and Improving the Embryonic Stem Cell Test through the Use of Gene Biomarkers of Differentiation

    PubMed Central

    Romero, Andrea C.; Vilanova, Eugenio; Sogorb, Miguel A.

    2011-01-01

    The embryonic Stem cell Test (EST) is a validated assay for testing embryotoxicity in vitro. The total duration of this protocol is 10 days, and its main end-point is based on histological determinations. It is suggested that improvements on EST must be focused toward molecular end-points and, if possible, to reduce the total assay duration. Five days of exposure of D3 cells in monolayers under spontaneous differentiation to 50 ng/mL of the strong embryotoxic 5-fluorouracil or to 75 μg/mL of the weak embryotoxic 5,5-diphenylhydeantoin caused between 20 and 74% of reductions in the expression of the following genes: Pnpla6, Afp, Hdac7, Vegfa, and Nes. The exposure to 1 mg/mL of nonembryotoxic saccharin only caused statistically significant reductions in the expression of Nes. These exposures reduced cell viability of D3 cells by 15, 28, and 34%. We applied these records to the mathematical discriminating function of the EST method to find that this approach is able to correctly predict the embryotoxicity of all three above-mentioned chemicals. Therefore, this work proposes the possibility of improve EST by reducing its total duration and by introducing gene expression as biomarker of differentiation, which might be very interesting for in vitro risk assessment embryotoxicity. PMID:21876691

  7. Alternative Endpoints and Approaches Selected for the Remediation of Contaminated Groundwater at Complex Sites

    NASA Astrophysics Data System (ADS)

    Deeb, R. A.; Hawley, E.

    2011-12-01

    This presentation will focus on findings, statistics, and case studies from a recently-completed report for the Department of Defense's Environmental Security Technology Certification Program (ESTCP) (Project ER-0832) on alternative endpoints and alternative remedial strategies for groundwater remediation under a variety of Federal and state cleanup programs, including technical impracticability (TI) and other Applicable or Relevant and Appropriate Requirement (ARAR) waivers, state and local designations such as groundwater management zones, Alternate Concentration Limits (ACLs), use of monitored natural attenuation (MNA) over long timeframes, and more. The primary objective of the project was to provide environmental managers and regulators with tools, metrics, and information needed to evaluate alternative endpoints for groundwater remediation at complex sites. A statistical analysis of Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) sites receiving TI waivers will be presented as well as case studies of other types of alternative endpoints and alternative remedial strategies to illustrate the variety of approaches used at complex sites and the technical analyses used to predict and document cost, timeframe, and potential remedial effectiveness. Case studies provide examples of the flexible, site-specific, application of alternative endpoints and alternative remedial strategies that have been used in the past to manage and remediate groundwater contamination at complex sites. For example, at least 13 states consider some designation for groundwater containment in their corrective action policies, such as groundwater management zones, containment zones, and groundwater classification exemption areas. These designations typically indicate that groundwater contamination is present above permissible levels. Soil and groundwater within these zones are managed to protect human health and the environment. Lesson learned for the analyses

  8. Linaclotide: Promising IBS-C Efficacy in an Era of Provisional Study Endpoints

    PubMed Central

    Sayuk, Gregory S.

    2013-01-01

    Recent disappointing developments in the pharmacotherapy of irritable bowel syndrome (IBS) have not dampened the enthusiasm surrounding linaclotide, a novel guanylate cyclase-C agonist for the management of constipation-predominant IBS (IBS-C). Two recent phase 3 studies reporting on a single, daily dose of linaclotide are presented in this issue of the American Journal of Gastroenterology. Importantly, these studies are the first to examine a provisional Food and Drug Administration (FDA) combined response endpoint for IBS-C, which mandates improvements of both abdominal pain and defecatory symptoms. Potential limitations of this FDA endpoint relate to a lack of inclusion of other potentially important IBS symptoms and an inability to directly compare findings with other recent IBS-C trials. Both studies successfully reached this endpoint in approximately one-third of study subjects, resulting in numbers needed to treat (NNT) of five to eight, to achieve an FDA responder. Individual symptom responses to linaclotide were seen in nearly 50% of participants, and potential explanations for these discrepancies when compared with the FDA endpoint are offered. Adequate relief measures also were assessed and, with NNTs of 3.4–6.8, compared favorably with other contemporary IBS-C studies. Overall, both linaclotide trials found the medication to be safe in terms of serious adverse events, though the secretagogue mechanism of action led to diarrhea in approximately one in five subjects. Together, these studies inspire several other important questions regarding linaclotide, including its role in the management of IBS-C relative to existing treatment options, such as lubiprostone. Greater clinical use of linaclotide will reveal whether the observed responses measured with the FDA provisional endpoint will translate into real-world experiences of improvement in IBS patients. “ In seeking absolute truth we aim at the unattainable and must be content with broken portions

  9. Linaclotide: promising IBS-C efficacy in an era of provisional study endpoints.

    PubMed

    Sayuk, Gregory S

    2012-11-01

    Recent disappointing developments in the pharmacotherapy of irritable bowel syndrome (IBS) have not dampened the enthusiasm surrounding linaclotide, a novel guanylate cyclase-C agonist for the management of constipation-predominant IBS (IBS-C). Two recent phase 3 studies reporting on a single, daily dose of linaclotide are presented in this issue of the American Journal of Gastroenterology. Importantly, these studies are the first to examine a provisional Food and Drug Administration (FDA) combined response endpoint for IBS-C, which mandates improvements of both abdominal pain and defecatory symptoms. Potential limitations of this FDA endpoint relate to a lack of inclusion of other potentially important IBS symptoms and an inability to directly compare findings with other recent IBS-C trials. Both studies successfully reached this endpoint in approximately one-third of study subjects, resulting in numbers needed to treat (NNT) of five to eight, to achieve an FDA responder. Individual symptom responses to linaclotide were seen in nearly 50% of participants, and potential explanations for these discrepancies when compared with the FDA endpoint are offered. Adequate relief measures also were assessed and, with NNTs of 3.4-6.8, compared favorably with other contemporary IBS-C studies. Overall, both linaclotide trials found the medication to be safe in terms of serious adverse events, though the secretagogue mechanism of action led to diarrhea in approximately one in five subjects. Together, these studies inspire several other important questions regarding linaclotide, including its role in the management of IBS-C relative to existing treatment options, such as lubiprostone. Greater clinical use of linaclotide will reveal whether the observed responses measured with the FDA provisional endpoint will translate into real-world experiences of improvement in IBS patients.

  10. Group-Sequential Strategies in Clinical Trials with Multiple Co-Primary Outcomes.

    PubMed

    Hamasaki, Toshimitsu; Asakura, Koko; Evans, Scott R; Sugimoto, Tomoyuki; Sozu, Takashi

    We discuss the decision-making frameworks for clinical trials with multiple co-primary endpoints in a group-sequential setting. The decision-making frameworks can account for flexibilities such as a varying number of analyses, equally or unequally spaced increments of information and fixed or adaptive Type I error allocation among endpoints. The frameworks can provide efficiency, i.e., potentially fewer trial participants, than the fixed sample size designs. We investigate the operating characteristics of the decision-making frameworks and provide guidance on constructing efficient group-sequential strategies in clinical trials with multiple co-primary endpoints.

  11. Scaffolding for Three-Dimensional Embryonic Vasculogenesis

    NASA Astrophysics Data System (ADS)

    Kraehenbuehl, Thomas P.; Aday, Sezin; Ferreira, Lino S.

    Biomaterial scaffolds have great potential to support efficient vascular differentiation of embryonic stem cells. Vascular cell fate-specific biochemical and biophysical cues have been identified and incorporated into three-dimensional (3D) biomaterials to efficiently direct embryonic vasculogenesis. The resulting vascular-like tissue can be used for regenerative medicine applications, further elucidation of biophysical and biochemical cues governing vasculogenesis, and drug discovery. In this chapter, we give an overview on the following: (1) developmental cues for directed differentiation of human embryonic stem cells (hESCs) into vascular cells, (2) 3D vascular differentiation in embryoid bodies (EBs), (3) preparation of 3D scaffolds for the vascular differentiation of hESCs, and (4) the most significant studies combining scaffolding and hESCs for development of vascular-like tissue.

  12. Fate of D3 mouse embryonic stem cells exposed to X-rays or carbon ions.

    PubMed

    Luft, S; Pignalosa, D; Nasonova, E; Arrizabalaga, O; Helm, A; Durante, M; Ritter, S

    2014-01-15

    The risk of radiation exposure during embryonic development is still a major problem in radiotoxicology. In this study we investigated the response of the murine embryonic stem cell (mESC) line D3 to two radiation qualities: sparsely ionizing X-rays and densely ionizing carbon ions. We analyzed clonogenic cell survival, proliferation, induction of chromosome aberrations as well as the capability of cells to differentiate to beating cardiomyocytes up to 3 days after exposure. Our results show that, for all endpoints investigated, carbon ions are more effective than X-rays at the same radiation dose. Additionally, in long term studies (≥8 days post-irradiation) chromosomal damage and the pluripotency state were investigated. These studies reveal that pluripotency markers are present in the progeny of cells surviving the exposure to both radiation types. However, only in the progeny of X-ray exposed cells the aberration frequency was comparable to that of the control population, while the progeny of carbon ion irradiated cells harbored significantly more aberrations than the control, generally translocations. We conclude that cells surviving the radiation exposure maintain pluripotency but may carry stable chromosomal rearrangements after densely ionizing radiation.

  13. Reducing sample sizes in two-stage phase II cancer trials by using continuous tumour shrinkage end-points.

    PubMed

    Wason, James M S; Mander, Adrian P; Eisen, Tim G

    2011-05-01

    Reducing the number of patients required for a clinical trial is important for shortening development time. Phase II cancer trials assess the tumour-shrinking effect of a novel compound through a binary end-point formed from the percentage change in total lesion diameter. We compare single-arm two-stage designs which use the binary end-point to those which directly use the continuous end-point. Using the continuous end-point results in lower expected and maximum sample sizes. For larger trials the reduction is around 37%. This assumes that the dichotomisation point of the continuous end-point is chosen to give the best sample size, with the trial design using the binary end-point performing even worse otherwise. We consider a previous trial designed using a Simon two-stage design and show that if the continuous end-point had been used, the expected and maximum sample sizes of the trial would be reduced by around 50%. Using the continuous end-point in a two-stage cancer trial results in large sample size reductions. The methods discussed in this paper work best when the number of complete responses is low, as is true in several types of cancer. We discuss what could be done if this is not the case.

  14. Embryonic stem cell patents and human dignity.

    PubMed

    Resnik, David B

    2007-09-01

    This article examines the assertion that human embryonic stem cells patents are immoral because they violate human dignity. After analyzing the concept of human dignity and its role in bioethics debates, this article argues that patents on human embryos or totipotent embryonic stem cells violate human dignity, but that patents on pluripotent or multipotent stem cells do not. Since patents on pluripotent or multipotent stem cells may still threaten human dignity by encouraging people to treat embryos as property, patent agencies should carefully monitor and control these patents to ensure that patents are not inadvertently awarded on embryos or totipotent stem cells.

  15. Embryonic Stem Cell Patents and Human Dignity

    PubMed Central

    Resnik, David B.

    2009-01-01

    This article examines the assertion that human embryonic stem cells patents are immoral because they violate human dignity. After analyzing the concept of human dignity and its role in bioethics debates, this article argues that patents on human embryos or totipotent embryonic stem cells violate human dignity, but that patents on pluripotent or multipotent stem cells do not. Since patents on pluripotent or multipotent stem cells may still threaten human dignity by encouraging people to treat embryos as property, patent agencies should carefully monitor and control these patents to ensure that patents are not inadvertently awarded on embryos or totipotent stem cells. PMID:17922198

  16. Embryonic Stem Cells: Isolation, Characterization and Culture

    NASA Astrophysics Data System (ADS)

    Amit, Michal; Itskovitz-Eldor, Joseph

    Embryonic stem cells are pluripotent cells isolated from the mammalian blastocyst. Traditionally, these cells have been derived and cultured with mouse embryonic fibroblast (MEF) supportive layers, which allow their continuous growth in an undifferentiated state. However, for any future industrial or clinical application hESCs should be cultured in reproducible, defined, and xeno-free culture system, where exposure to animal pathogens is prevented. From their derivation in 1998 the methods for culturing hESCs were significantly improved. This chapter wills discuss hESC characterization and the basic methods for their derivation and maintenance.

  17. Embryotoxicity hazard assessment of cadmium and arsenic compounds using embryonic stem cells.

    PubMed

    Stummann, T C; Hareng, L; Bremer, S

    2008-10-30

    The Embryonic Stem Cell Test (EST) has been successfully validated as an in vitro method for detecting embryotoxicity, showing a good overall test accuracy of 78% [Genschow, E., Spielmann, H., Scholz, G., Seiler, A., Brown, N., Piersma, A., Brady, M., Clemann, N., Huuskonen, H., Paillard, F., Bremer, S., Becker, K., 2002. The ECVAM international validation study on in vitro embryotoxicity tests: results of the definitive phase and evaluation of prediction models. European Centre for the Validation of Alternative Methods. Altern. Lab. Anim. 30, 151-176]. Methylmercury was the only strong in vivo embryotoxicant falsely predicted as non-embryotoxic making the metal the most significant outlayer [Genschow, E., Spielmann, H., Scholz, G., Pohl, I., Seiler, A., Clemann, N., Bremer, S., Becker, K., 2004. Validation of the Embryonic Stem Cell Test in the international ECVAM validation study on three in vitro embryotoxicity tests. Altern. Lab. Anim. 32, 209-244]. The misclassification of methylmercury and the potential environmental exposure to developmental toxic heavy metals promoted our investigation of whether the EST applicability domain covers cadmium and arsenic compounds. The EST misclassified cadmium, arsenite and arsenate compounds as non-embryotoxic, even when including arsenic metabolites (methylarsonate, methylarsonous and dimethylarsinic). The reasons were the lack of higher cytotoxicity towards embryonic stem cells as compared to more mature cells (3T3 fibroblasts) or the absence of inhibition of cardiac differentiation by specific mechanisms rather than general cytotoxicity. Including EST data on heavy metals from the literature (lithium, methylmercury, trivalent chromium and hexavalent chromium) revealed that the test correctly predicted the embryotoxic potential of three out of the seven heavy metals, indicating an insufficient predictivity for such metals. Refinement of the EST prediction model and inclusion of additional toxicological endpoints could

  18. Embryonic stem cells: testing the germ-cell theory.

    PubMed

    Hochedlinger, Konrad

    2011-10-25

    The exact cellular origin of embryonic stem cells remains elusive. Now a new study provides compelling evidence that embryonic stem cells, established under conventional culture conditions, originate from a transient germ-cell state.

  19. Fabrication of spintronic devices: etching endpoint detection by resistance measurement for magnetic tunnel junctions

    NASA Astrophysics Data System (ADS)

    Pong, Philip W. T.; Schmoueli, Moshe; Egelhoff, William F., Jr.

    2007-09-01

    Magnetic tunnel junctions (MTJs) have received tremendous interest since the discovery of substantial room temperature tunneling magnetoresistance (TMR) due to spin-dependent tunneling, and have been intensively investigated for applications in next-generation memory devices, hard disk drives, and magnetic sensors. In the fabrication of MTJs, etching is needed to remove the top cap layers, upper magnetic layers, and the middle oxide layer in order to form a tunneling junction. In view of this, we have devised an innovative, simple, low-cost endpoint detection method for fabricating MTJs. In this method, the endpoint is detected by measurement of the sheet resistance of the MTJ stack. Only a multimeter is needed in this method, hence it provides a simple low-cost alternative for spintronic device researchers to explore the research field of magnetic tunnel junctions. This technique is also of great use in other kinds of metallic stack etching experiments.

  20. Outcomes-Based CV Imaging Research Endpoints and Trial Design: From Pixels to Patient Satisfaction.

    PubMed

    Fordyce, Christopher B; Douglas, Pamela S

    2017-03-01

    The categories and quality of evidence documenting the value of noninvasive cardiovascular imaging have evolved substantially over the last several decades. From an initial emphasis on the diagnostic accuracy of various imaging modalities, cardiovascular imaging has matured into an outcomes-based field that now provides evidence on adverse events, safety, cost, and patient quality-of-life endpoints, and does so in the setting of large randomized trials. This review aims to highlight types of outcomes endpoints, including updating the hierarchy of evidence for diagnostic imaging as first proposed by Fryback and Thornbury, and critically reviewing their application in the current cardiovascular imaging evidence base. We describe the range of data categories generated to date for the various imaging modalities, and indicate how this provides insights into contemporary study design and future directions in cardiovascular imaging outcomes research.

  1. Coulometric trace determination of water by using Karl Fischer reagent and potentiometric end-point detection.

    PubMed

    Cedergren, A

    1974-06-01

    A new approach to the determination of water via the Karl Fischer reaction is described. Iodine is coulometrically generated and the end-point corresponding to a slight excess of iodine, is detected potentiometrically with a non-polarized platinum electrode. Samples of 1-500 mul containing 0.05-200 mug of water were analysed with a standard deviation of 0.015 mug in the range 0.05-20 mug of H(2)O. A specially constructed electrolysis cell was used in combination with an LKB 16300 Coulometric Analyzer and the time for a complete analysis was 1-4 min, depending on sample size. The reagent composition has been optimized in order to enhance the rate of the main reaction and to minimize the extent of side-reactions. Decreasing the temperature reduced the extent of side-reactions. The displacement of end-point potential on dilution was studied and a correction is discussed.

  2. Proposed Standardized Neurological Endpoints for Cardiovascular Clinical Trials: An Academic Research Consortium Initiative.

    PubMed

    Lansky, Alexandra J; Messé, Steven R; Brickman, Adam M; Dwyer, Michael; van der Worp, H Bart; Lazar, Ronald M; Pietras, Cody G; Abrams, Kevin J; McFadden, Eugene; Petersen, Nils H; Browndyke, Jeffrey; Prendergast, Bernard; Ng, Vivian G; Cutlip, Donald E; Kapadia, Samir; Krucoff, Mitchell W; Linke, Axel; Moy, Claudia Scala; Schofer, Joachim; van Es, Gerrit-Anne; Virmani, Renu; Popma, Jeffrey; Parides, Michael K; Kodali, Susheel; Bilello, Michel; Zivadinov, Robert; Akar, Joseph; Furie, Karen L; Gress, Daryl; Voros, Szilard; Moses, Jeffrey; Greer, David; Forrest, John K; Holmes, David; Kappetein, Arie P; Mack, Michael; Baumbach, Andreas

    2017-02-14

    Surgical and catheter-based cardiovascular procedures and adjunctive pharmacology have an inherent risk of neurological complications. The current diversity of neurological endpoint definitions and ascertainment methods in clinical trials has led to uncertainties in the neurological risk attributable to cardiovascular procedures and inconsistent evaluation of therapies intended to prevent or mitigate neurological injury. Benefit-risk assessment of such procedures should be on the basis of an evaluation of well-defined neurological outcomes that are ascertained with consistent methods and capture the full spectrum of neurovascular injury and its clinical effect. The Neurologic Academic Research Consortium is an international collaboration intended to establish consensus on the definition, classification, and assessment of neurological endpoints applicable to clinical trials of a broad range of cardiovascular interventions. Systematic application of the proposed definitions and assessments will improve our ability to evaluate the risks of cardiovascular procedures and the safety and effectiveness of preventive therapies.

  3. Establishing Good Practices for Exposure–Response Analysis of Clinical Endpoints in Drug Development

    PubMed Central

    Overgaard, RV; Ingwersen, SH; Tornøe, CW

    2015-01-01

    This tutorial aims at promoting good practices for exposure–response (E-R) analyses of clinical endpoints in drug development. The focus is on practical aspects of E-R analyses to assist modeling scientists with a process of performing such analyses in a consistent manner across individuals and projects and tailored to typical clinical drug development decisions. This includes general considerations for planning, conducting, and visualizing E-R analyses, and how these are linked to key questions. PMID:26535157

  4. Development of Pain Endpoint Models for Use in Prostate Cancer Clinical Trials and Drug Approval

    DTIC Science & Technology

    2015-10-01

    Award Number: W81XWH-11-1-0639 TITLE: Development of Pain Endpoint Models for Use in Prostate Cancer Clinical Trials and Drug Approval PRINCIPAL...Clinical Trials and Drug Approval 5b. GRANT NUMBER PC100563 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Betty Diamond 5d. PROJECT NUMBER Ethan Basch...meet regulatory requirements for drug approval and labeling. The primary aim of this award is to conduct an observational longitudinal study in men

  5. Muscle Synergies Heavily Influence the Neural Control of Arm Endpoint Stiffness and Energy Consumption

    PubMed Central

    Inouye, Joshua M.; Valero-Cuevas, Francisco J.

    2016-01-01

    Much debate has arisen from research on muscle synergies with respect to both limb impedance control and energy consumption. Studies of limb impedance control in the context of reaching movements and postural tasks have produced divergent findings, and this study explores whether the use of synergies by the central nervous system (CNS) can resolve these findings and also provide insights on mechanisms of energy consumption. In this study, we phrase these debates at the conceptual level of interactions between neural degrees of freedom and tasks constraints. This allows us to examine the ability of experimentally-observed synergies—correlated muscle activations—to control both energy consumption and the stiffness component of limb endpoint impedance. In our nominal 6-muscle planar arm model, muscle synergies and the desired size, shape, and orientation of endpoint stiffness ellipses, are expressed as linear constraints that define the set of feasible muscle activation patterns. Quadratic programming allows us to predict whether and how energy consumption can be minimized throughout the workspace of the limb given those linear constraints. We show that the presence of synergies drastically decreases the ability of the CNS to vary the properties of the endpoint stiffness and can even preclude the ability to minimize energy. Furthermore, the capacity to minimize energy consumption—when available—can be greatly affected by arm posture. Our computational approach helps reconcile divergent findings and conclusions about task-specific regulation of endpoint stiffness and energy consumption in the context of synergies. But more generally, these results provide further evidence that the benefits and disadvantages of muscle synergies go hand-in-hand with the structure of feasible muscle activation patterns afforded by the mechanics of the limb and task constraints. These insights will help design experiments to elucidate the interplay between synergies and the

  6. Muscle Synergies Heavily Influence the Neural Control of Arm Endpoint Stiffness and Energy Consumption.

    PubMed

    Inouye, Joshua M; Valero-Cuevas, Francisco J

    2016-02-01

    Much debate has arisen from research on muscle synergies with respect to both limb impedance control and energy consumption. Studies of limb impedance control in the context of reaching movements and postural tasks have produced divergent findings, and this study explores whether the use of synergies by the central nervous system (CNS) can resolve these findings and also provide insights on mechanisms of energy consumption. In this study, we phrase these debates at the conceptual level of interactions between neural degrees of freedom and tasks constraints. This allows us to examine the ability of experimentally-observed synergies--correlated muscle activations--to control both energy consumption and the stiffness component of limb endpoint impedance. In our nominal 6-muscle planar arm model, muscle synergies and the desired size, shape, and orientation of endpoint stiffness ellipses, are expressed as linear constraints that define the set of feasible muscle activation patterns. Quadratic programming allows us to predict whether and how energy consumption can be minimized throughout the workspace of the limb given those linear constraints. We show that the presence of synergies drastically decreases the ability of the CNS to vary the properties of the endpoint stiffness and can even preclude the ability to minimize energy. Furthermore, the capacity to minimize energy consumption--when available--can be greatly affected by arm posture. Our computational approach helps reconcile divergent findings and conclusions about task-specific regulation of endpoint stiffness and energy consumption in the context of synergies. But more generally, these results provide further evidence that the benefits and disadvantages of muscle synergies go hand-in-hand with the structure of feasible muscle activation patterns afforded by the mechanics of the limb and task constraints. These insights will help design experiments to elucidate the interplay between synergies and the mechanisms

  7. Energy metabolism and biotransformation as endpoints to pre-screen hepatotoxicity using a liver spheroid model

    SciTech Connect

    Xu Jinsheng . E-mail: jinsheng.xu@uwe.ac.uk; Purcell, Wendy M.

    2006-10-15

    The current study investigated liver spheroid culture as an in vitro model to evaluate the endpoints relevant to the status of energy metabolism and biotransformation after exposure to test toxicants. Mature rat liver spheroids were exposed to diclofenac, galactosamine, isoniazid, paracetamol, m-dinitrobenzene (m-DNB) and 3-nitroaniline (3-NA) for 24 h. Pyruvate uptake, galactose biotransformation, lactate release and glucose secretion were evaluated after exposure. The results showed that pyruvate uptake and lactate release by mature liver spheroids in culture were maintained at a relatively stable level. These endpoints, together with glucose secretion and galactose biotransformation, were related to and could reflect the status of energy metabolism and biotransformation in hepatocytes. After exposure, all of the test agents significantly reduced glucose secretion, which was shown to be the most sensitive endpoint of those evaluated. Diclofenac, isoniazid, paracetamol and galactosamine reduced lactate release (P < 0.01), but m-DNB increased lactate release (P < 0.01). Diclofenac, isoniazid and paracetamol also reduced pyruvate uptake (P < 0.01), while galactosamine had little discernible effect. Diclofenac, galactosamine, paracetamol and m-DNB also reduced galactose biotransformation (P < 0.01), by contrast, isoniazid did not. The metabolite of m-DNB, 3-NA, which served as a negative control, did not cause significant changes in lactate release, pyruvate uptake or galactose biotransformation. It is concluded that pyruvate uptake, galactose biotransformation, lactate release and glucose secretion can be used as endpoints for evaluating the status of energy metabolism and biotransformation after exposure to test agents using the liver spheroid model to pre-screen hepatotoxicity.

  8. Three-dimensional bioprinting of rat embryonic neural cells.

    PubMed

    Lee, Wonhye; Pinckney, Jason; Lee, Vivian; Lee, Jong-Hwan; Fischer, Krisztina; Polio, Samuel; Park, Je-Kyun; Yoo, Seung-Schik

    2009-05-27

    We present a direct cell printing technique to pattern neural cells in a three-dimensional (3D) multilayered collagen gel. A layer of collagen precursor was printed to provide a scaffold for the cells, and the rat embryonic neurons and astrocytes were subsequently printed on the layer. A solution of sodium bicarbonate was applied to the cell containing collagen layer as nebulized aerosols, which allowed the gelation of the collagen. This process was repeated layer-by-layer to construct the 3D cell-hydrogel composites. Upon characterizing the relationship between printing resolutions and the growth of printed neural cells, single/multiple layers of neural cell-hydrogel composites were constructed and cultured. The on-demand capability to print neural cells in a multilayered hydrogel scaffold offers flexibility in generating artificial 3D neural tissue composites.

  9. Transcriptional control of embryonic and induced pluripotent stem cells.

    PubMed

    Guenther, Matthew G

    2011-06-01

    Embryonic stem cells (ESCs) have the potential to generate virtually any cell type or tissue type in the body. This remarkable plasticity has yielded great interest in using these cells to understand early development and in treating human disease. In an effort to understand the basis of ESC pluripotency, genetic and genomic studies have revealed transcriptional regulatory circuitry that maintains the pluripotent cell state and poises the genome for downstream activation. Critical components of this circuitry include ESC transcription factors, chromatin regulators, histone modifications, signaling molecules and regulatory RNAs. This article will focus on our current understanding of these components and how they influence ESC and induced pluripotent stem cell states. Emerging themes include regulation of the pluripotent genome by a core set of transcription factors, transcriptional poising of developmental genes by chromatin regulatory complexes and the establishment of multiple layers of repression at key genomic loci.

  10. The somite-secreted factor Maeg promotes zebrafish embryonic angiogenesis

    PubMed Central

    Qi, Jialing; Qin, Yinyin; Shi, Yunwei; Zhang, Jie; Gong, Jie; Dong, Zhangji; Liu, Xiaoyu; Sun, Chen; Chai, Renjie; Le Noble, Ferdinand; Liu, Dong

    2016-01-01

    MAM and EGF containing gene (MAEG), also called Epidermal Growth Factor-like domain multiple 6 (EGFL6), belongs to the epidermal growth factor repeat superfamily. The role of Maeg in zebrafish angiogenesis remains unclear. It was demonstrated that maeg was dynamically expressed in zebrafish developing somite during a time window encompassing many key steps in embryonic angiogenesis. Maeg loss-of-function embryos showed reduced endothelial cell number and filopodia extensions of intersegmental vessels (ISVs). Maeg gain-of-function induced ectopic sprouting evolving into a hyperbranched and functional perfused vasculature. Mechanistically we demonstrate that Maeg promotes angiogenesis dependent on RGD domain and stimulates activation of Akt and Erk signaling in vivo. Loss of Maeg or Itgb1, augmented expression of Notch receptors, and inhibiting Notch signaling or Dll4 partially rescued angiogenic phenotypes suggesting that Notch acts downstream of Itgb1. We conclude that Maeg acts as a positive regulator of angiogenic cell behavior and formation of functional vessels. PMID:27780917

  11. ATP dependent chromatin remodeling enzymes in embryonic stem cells.

    PubMed

    Saladi, Srinivas Vinod; de la Serna, Ivana L

    2010-03-01

    Embryonic stem (ES) cells are pluripotent cells that can self renew or be induced to differentiate into multiple cell lineages, and thus have the potential to be utilized in regenerative medicine. Key pluripotency specific factors (Oct 4/Sox2/Nanog/Klf4) maintain the pluripotent state by activating expression of pluripotency specific genes and by inhibiting the expression of developmental regulators. Pluripotent ES cells are distinguished from differentiated cells by a specialized chromatin state that is required to epigenetically regulate the ES cell phenotype. Recent studies show that in addition to pluripotency specific factors, chromatin remodeling enzymes play an important role in regulating ES cell chromatin and the capacity to self-renew and to differentiate. Here we review recent studies that delineate the role of ATP dependent chromatin remodeling enzymes in regulating ES cell chromatin structure.

  12. Reduction of animal suffering in rabies vaccine potency testing by introduction of humane endpoints.

    PubMed

    Takayama-Ito, Mutsuyo; Lim, Chang-Kweng; Nakamichi, Kazuo; Kakiuchi, Satsuki; Horiya, Madoka; Posadas-Herrera, Guillermo; Kurane, Ichiro; Saijo, Masayuki

    2017-03-01

    Potency controls of inactivated rabies vaccines for human use are confirmed by the National Institutes of Health challenge test in which lethal infection with severe neurological symptoms should be observed in approximately half of the mice inoculated with the rabies virus. Weight loss, decreased body temperature, and the presence of rabies-associated neurological signs have been proposed as humane endpoints. The potential for reduction of animal suffering by introducing humane endpoints in the potency test for inactivated rabies vaccine for human use was investigated. The clinical signs were scored and body weight was monitored. The average times to death following inoculation were 10.49 and 10.99 days post-inoculation (dpi) by the potency and challenge control tests, respectively, whereas the average times to showing Score-2 signs (paralysis, trembling, and coma) were 6.26 and 6.55 dpi, respectively. Body weight loss of more than 15% appeared at 5.82 and 6.42 dpi. The data provided here support the introduction of obvious neuronal signs combined with a body weight loss of ≥15% as a humane endpoint to reduce the time of animal suffering by approximately 4 days.

  13. A New Test Unit for Disintegration End-Point Determination of Orodispersible Films.

    PubMed

    Low, Ariana; Kok, Si Ling; Khong, Yuet Mei; Chan, Sui Yung; Gokhale, Rajeev

    2015-11-01

    No standard time or pharmacopoeia disintegration test method for orodispersible films (ODFs) exists. The USP disintegration test for tablets and capsules poses significant challenges for end-point determination when used for ODFs. We tested a newly developed disintegration test unit (DTU) against the USP disintegration test. The DTU is an accessory to the USP disintegration apparatus. It holds the ODF in a horizontal position, allowing top-view of the ODF during testing. A Gauge R&R study was conducted to assign relative contributions of the total variability from the operator, sample or the experimental set-up. Precision was compared using commercial ODF products in different media. Agreement between the two measurement methods was analysed. The DTU showed improved repeatability and reproducibility compared to the USP disintegration system with tighter standard deviations regardless of operator or medium. There is good agreement between the two methods, with the USP disintegration test giving generally longer disintegration times possibly due to difficulty in end-point determination. The DTU provided clear end-point determination and is suitable for quality control of ODFs during product developmental stage or manufacturing. This may facilitate the development of a standardized methodology for disintegration time determination of ODFs.

  14. Effects of the polycyclic musk HHCB on individual- and population-level endpoints in Potamopyrgus antipodarum.

    PubMed

    Pedersen, Signe; Selck, Henriette; Salvito, Daniel; Forbes, Valery

    2009-05-01

    Although the polycyclic musk 1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethylcyclopenta[gamma]-2-benzopyran (HHCB) is frequently detected in aquatic sediments, very little is known about its effects on sediment-feeding organisms. Effects of sediment-associated HHCB on growth, feeding rate, survival and reproduction in the gastropod Potamopyrgus antipodarum were measured in the laboratory. Snails were exposed to six nominal HHCB concentrations: 0, 0.1, 1, 10, 30 and 100microg g(-1) dry weight (dw) sediment. Adult survival and growth were not affected by HHCB. However, juvenile growth and survival, reproduction, time to first reproduction and adult feeding rate were more sensitive endpoints and declined with increasing HHCB concentration. Individual-level endpoints for P. antipodarum were integrated into a population model to investigate the effects of HHCB on population growth rate. Under otherwise favorable laboratory conditions, population growth rate was slightly (by ca. 2%), but not significantly, reduced with increasing HHCB exposure concentration. Model simulations were performed to explore the consequences of HHCB exposure under more ecologically realistic conditions (i.e., survival and reproduction of unexposed snails were markedly reduced relative to the laboratory). The results suggest that despite detectable effects of HHCB on individual-level endpoints measured in the laboratory, impacts on population dynamics of this deposit feeder are not likely to occur at environmentally relevant exposure concentrations.

  15. Scientific and societal considerations in selecting assessment endpoints for environmental decision making.

    PubMed

    Strange, Elizabeth M; Lipton, Joshua; Beltman, Douglas; Snyder, Blaine D

    2002-03-08

    It is sometimes argued that, from an ecological point of view, population-, community-, and ecosystem-level endpoints are more relevant than individual-level endpoints for assessing the risks posed by human activities to the sustainability of natural resources. Yet society values amenities provided by natural resources that are not necessarily evaluated or protected by assessment tools that focus on higher levels of biological organization. For example, human-caused stressors can adversely affect recreational opportunities that are valued by society even in the absence of detectable population-level reductions in biota. If protective measures are not initiated until effects at higher levels of biological organization are apparent, natural resources that are ecologically important or highly valued by the public may not be adequately protected. Thus, environmental decision makers should consider both scientific and societal factors in selecting endpoints for ecological risk assessments. At the same time, it is important to clearly distinguish the role of scientists, which is to evaluate ecological effects, from the role of policy makers, which is to determine how to address the uncertainty in scientific assessment in making environmental decisions and to judge what effects are adverse based on societal values and policy goals.

  16. Superiority inferences on individual endpoints following noninferiority testing in clinical trials.

    PubMed

    Logan, Brent R; Tamhane, Ajit C

    2008-10-01

    We consider the problem of drawing superiority inferences on individual endpoints following non-inferiority testing. Röhmel et al. (2006) pointed out this as an important problem which had not been addressed by the previous procedures that only tested for global superiority. Röhmel et al. objected to incorporating the non-inferiority tests in the assessment of the global superiority test by exploiting the relationship between the two, since the results of the latter test then depend on the non-inferiority margins specified for the former test. We argue that this is justified, besides the fact that it enhances the power of the global superiority test. We provide a closed testing formulation which generalizes the three-step procedure proposed by Röhmel et al. for two endpoints. For the global superiority test, Röhmel et al. suggest using the Läuter (1996) test which is modified to make it monotone. The resulting test not only is complicated to use, but the modification does not readily extend to more than two endpoints, and it is less powerful in general than several of its competitors. This is verified in a simulation study. Instead, we suggest applying the one-sided likelihood ratio test used by Perlman and Wu (2004) or the union-intersection t(max) test used by Tamhane and Logan (2004).

  17. Pediatric phase I trial design using maximum target inhibition as the primary endpoint.

    PubMed

    Meany, Holly; Balis, Frank M; Aikin, Alberta; Whitcomb, Patricia; Murphy, Robert F; Steinberg, Seth M; Widemann, Brigitte C; Fox, Elizabeth

    2010-06-16

    The extent to which a drug inhibits a target responsible for a therapeutic effect is a more rational primary endpoint for dose-finding studies of more selective anticancer drugs than the conventional endpoint of dose-limiting toxicity (DLT) used for cytotoxic agents. An adaptive phase I trial design incorporating maximum target inhibition as the primary endpoint was developed to define the optimal dose of talabostat, a dipeptidyl peptidase (DPP) inhibitor, in children with relapsed or refractory solid tumors. The relationship between dose and effect (percent inhibition of serum DPP-4) was assessed using a maximum effect model. Maximum target inhibition was defined as greater than 90% DPP-4 inhibition in five or more of six patients 24 hours post-dose. If DLT was to occur, the trial would adapt to a traditional phase I design with a more conservative dose escalation. At the 600 microg/m(2) dose level, serum DPP-4 inhibition at 24 hours was 85%. No talabostat-related DLT occurred. The maximum effect model predicted that 1200 microg/m(2) of talabostat would maximally inhibit DPP-4. This adaptive trial design appears to be feasible, safe, and efficient and warrants further evaluation for development of molecularly targeted agents.

  18. Sensitivity Enhancement of RF Plasma Etch Endpoint Detection With K-means Cluster Analysis

    NASA Astrophysics Data System (ADS)

    Lee, Honyoung; Jang, Haegyu; Lee, Hak-Seung; Chae, Heeyeop

    2015-09-01

    Plasma etching process is the core process in semiconductor fabrication, and the etching endpoint detection is one of the essential FDC (Fault Detection and Classification) for yield management and mass production. In general, Optical emission spectrocopy (OES) has been used to detect endpoint because OES can be a non-invasive and real-time plasma monitoring tool. In OES, the trend of a few sensitive wavelengths is traced. However, in case of small-open area etch endpoint detection (ex. contact etch), it is at the boundary of the detection limit because of weak signal intensities of reaction reactants and products. Furthemore, the various materials covering the wafer such as photoresist, dielectric materials, and metals make the analysis of OES signals complicated. In this study, full spectra of optical emission signals were collected and the data were analyzed by a data-mining approach, modified K-means cluster analysis. The K-means cluster analysis is modified suitably to analyze a thousand of wavelength variables from OES. This technique can improve the sensitivity of EPD for small area oxide layer etching processes: about 1.0% oxide area. This technique is expected to be applied to various plasma monitoring applications including fault detections as well as EPD. Plasma Etch, EPD, K-means Cluster Analysis.

  19. End-point impedance measurements across dominant and nondominant hands and robotic assistance with directional damping.

    PubMed

    Erden, Mustafa Suphi; Billard, Aude

    2015-06-01

    The goal of this paper is to perform end-point impedance measurements across dominant and nondominant hands while doing airbrush painting and to use the results for developing a robotic assistance scheme. We study airbrush painting because it resembles in many ways manual welding, a standard industrial task. The experiments are performed with the 7 degrees of freedom KUKA lightweight robot arm. The robot is controlled in admittance using a force sensor attached at the end-point, so as to act as a free-mass and be passively guided by the human. For impedance measurements, a set of nine subjects perform 12 repetitions of airbrush painting, drawing a straight-line on a cartoon horizontally placed on a table, while passively moving the airbrush mounted on the robot's end-point. We measure hand impedance during the painting task by generating sudden and brief external forces with the robot. The results show that on average the dominant hand displays larger impedance than the nondominant in the directions perpendicular to the painting line. We find the most significant difference in the damping values in these directions. Based on this observation, we develop a "directional damping" scheme for robotic assistance and conduct a pilot study with 12 subjects to contrast airbrush painting with and without robotic assistance. Results show significant improvement in precision with both dominant and nondominant hands when using robotic assistance.

  20. Resummation of Large Endpoint Corrections to Color-Octet J/psi Photoproduction

    SciTech Connect

    Sean Fleming; Adam K. Leibovich; Thomas Mehen

    2006-07-27

    An unresolved problem in J/{psi} phenomenology is a systematic understanding of the differential photoproduction cross section, d{sigma}/dz [{gamma} + p {yields} J/{psi} + X], where z = E{sub {psi}}/E{sub {gamma}} in the proton rest frame. In the non-relativistic QCD (NRQCD) factorization formalism, fixed-order perturbative calculations of color-octet mechanisms suffer from large perturbative and nonperturbative corrections that grow rapidly in the endpoint region, z {yields} 1. In this paper, NRQCD and soft collinear effective theory are combined to resum these large corrections to the color-octet photoproduction cross section. We derive a factorization theorem for the endpoint differential cross section involving the parton distribution function and the color-octet J/{psi} shape functions. A one loop matching calculation explicitly confirms our factorization theorem at next-to-leading order. Large perturbative corrections are resummed using the renormalization group. The calculation of the color-octet contribution to d{sigma}/dz is in qualitative agreement with data. Quantitative tests of the universality of color-octet matrix elements require improved knowledge of shape functions entering these calculations as well as resummation of the color-singlet contribution which accounts for much of the total cross section and also peaks near the endpoint.

  1. Combining SVM and flame radiation to forecast BOF end-point

    NASA Astrophysics Data System (ADS)

    Wen, Hongyuan; Zhao, Qi; Xu, Lingfei; Zhou, Munchun; Chen, Yanru

    2009-05-01

    Because of complex reactions in Basic Oxygen Furnace (BOF) for steelmaking, the main end-point control methods of steelmaking have insurmountable difficulties. Aiming at these problems, a support vector machine (SVM) method for forecasting the BOF steelmaking end-point is presented based on flame radiation information. The basis is that the furnace flame is the performance of the carbon oxygen reaction, because the carbon oxygen reaction is the major reaction in the steelmaking furnace. The system can acquire spectrum and image data quickly in the steelmaking adverse environment. The structure of SVM and the multilayer feed-ward neural network are similar, but SVM model could overcome the inherent defects of the latter. The model is trained and forecasted by using SVM and some appropriate variables of light and image characteristic information. The model training process follows the structure risk minimum (SRM) criterion and the design parameter can be adjusted automatically according to the sampled data in the training process. Experimental results indicate that the prediction precision of the SVM model and the executive time both meet the requirements of end-point judgment online.

  2. Evaluation of reproduction as an endpoint in chronic toxicity tests with the amphipod Hyalella azteca

    SciTech Connect

    Brunson, E.L.; Dwyer, F.J.; Ingersoll, C.G.

    1995-12-31

    In 1994, USEPA published ``Methods for Measuring the Toxicity and Bioaccumulation of Sediment-associated Contaminants with Freshwater Invertebrates`` (EPA/600/R-94/024). Within that document a Hyalella azteca 10-d survival test for sediments is described. The 10-d survival test provides a measure of acute toxicity from moderately to highly contaminated sediments. In addition to survival, growth during the 10-d test can be measured and could be a more sensitive endpoint. However, the ecological significance of reduced growth is questionable. Reproduction may be a more sensitive endpoint than growth or survival and its ecological importance is not questionable. The objective of this research is to develop a Hyalella azteca sediment toxicity test with a reproductive endpoint. The reproductive test will closely resemble the 10-d test but will be longer in duration and may require isolation of amphipods from the sediment for reproduction. Presently, reproductive effects of different diets and water types have been evaluated. A preliminary test protocol has been developed and is being tested and refined. This presentation will provide the most current results of this ongoing research. This study will be used to develop standard methods for measuring chronic toxicity in sediments using Hyalella azteca.

  3. Clinical trial design principles and endpoint definitions for transcatheter mitral valve repair and replacement: part 2: endpoint definitions: A consensus document from the Mitral Valve Academic Research Consortium.

    PubMed

    Stone, Gregg W; Adams, David H; Abraham, William T; Kappetein, Arie Pieter; Généreux, Philippe; Vranckx, Pascal; Mehran, Roxana; Kuck, Karl-Heinz; Leon, Martin B; Piazza, Nicolo; Head, Stuart J; Filippatos, Gerasimos; Vahanian, Alec S

    2015-08-01

    Mitral regurgitation (MR) is one of the most prevalent valve disorders and has numerous aetiologies, including primary (organic) MR, due to underlying degenerative/structural mitral valve (MV) pathology, and secondary (functional) MR, which is principally caused by global or regional left ventricular remodelling and/or severe left atrial dilation. Diagnosis and optimal management of MR requires integration of valve disease and heart failure specialists, MV cardiac surgeons, interventional cardiologists with expertise in structural heart disease, and imaging experts. The introduction of trans- catheter MV therapies has highlighted the need for a consensus approach to pragmatic clinical trial design and uniform endpoint definitions to evaluate outcomes in patients with MR. The Mitral Valve Academic Research Consortium is a collaboration between leading academic research organizations and physician-scientists specializing in MV disease from the United States and Europe. Three in-person meetings were held in Virginia and New York during which 44 heart failure, valve, and imaging experts, MV surgeons and interventional cardiologists, clinical trial specialists and statisticians, and representatives from the U.S. Food and Drug Administration considered all aspects of MV pathophysiology, prognosis, and therapies, culminating in a 2-part document describing consensus recommendations for clinical trial design (Part 1) and endpoint definitions (Part 2) to guide evaluation of transcatheter and surgical therapies for MR. The adoption of these recommendations will afford robustness and consistency in the comparative effectiveness evaluation of new devices and approaches to treat MR. These principles may be useful for regulatory assessment of new transcatheter MV devices, as well as for monitoring local and regional outcomes to guide quality improvement initiatives.

  4. Idaho National Laboratory Test Area North: Application of Endpoints to Guide Adaptive Remediation at a Complex Site: INL Test Area North: Application of Endpoints

    SciTech Connect

    Lee, M. Hope; Truex, Mike; Freshley, Mark; Wellman, Dawn

    2016-09-01

    Complex sites are defined as those with difficult subsurface access, deep and/or thick zones of contamination, large areal extent, subsurface heterogeneities that limit the effectiveness of remediation, or where long-term remedies are needed to address contamination (e.g., because of long-term sources or large extent). The Test Area North at the Idaho National Laboratory, developed for nuclear fuel operations and heavy metal manufacturing, is used as a case study. Liquid wastes and sludge from experimental facilities were disposed in an injection well, which contaminated the subsurface aquifer located deep within fractured basalt. The wastes included organic, inorganic, and low-level radioactive constituents, with the focus of this case study on trichloroethylene. The site is used as an example of a systems-based framework that provides a structured approach to regulatory processes established for remediation under existing regulations. The framework is intended to facilitate remedy decisions and implementation at complex sites where restoration may be uncertain, require long timeframes, or involve use of adaptive management approaches. The framework facilitates site, regulator, and stakeholder interactions during the remedial planning and implementation process by using a conceptual model description as a technical foundation for decisions, identifying endpoints, which are interim remediation targets or intermediate decision points on the path to an ultimate end, and maintaining protectiveness during the remediation process. At the Test Area North, using a structured approach to implementing concepts in the endpoint framework, a three-component remedy is largely functioning as intended and is projected to meet remedial action objectives by 2095 as required. The remedy approach is being adjusted as new data become available. The framework provides a structured process for evaluating and adjusting the remediation approach, allowing site owners, regulators, and

  5. Embryonic Expression of the Chicken Krüppel-like (KLF) Transcription Factor Gene Family

    PubMed Central

    Antin, Parker B.; Pier, Maricela; Sesepasara, Terry; Yatskievych, Tatiana A; Darnell, Diana K.

    2010-01-01

    The Krüppel-like transcription factors are zinc finger proteins that activate and suppress target gene transcription. Although KLF factors have been implicated in regulating many developmental processes, a comprehensive gene expression analysis has not been reported. Here we present the chicken KLF gene family and expression during the first five days of embryonic development. Fourteen chicken KLF genes or expressed sequences have been previously identified. Through synteny analysis and cDNA mapping we have identified the KLF9 gene and determined that the gene presently named KLF1 is the true ortholog of KLF17 in other species. In situ hybridization expression analyses show that in general KLFs are broadly expressed in multiple cell and tissue types. Expression of KLFs 3, 7, 8, and 9, is widespread at all stages examined. KLFs 2, 4, 5, 6, 10, 11, 15 and 17 show more restricted patterns that suggest multiple functions during early stages of embryonic development. PMID:20503383

  6. Sourcing human embryos for embryonic stem cell lines: problems & perspectives.

    PubMed

    Mehta, Rajvi H

    2014-11-01

    The ability to successfully derive human embryonic stem cells (hESC) lines from human embryos following in vitro fertilization (IVF) opened up a plethora of potential applications of this technique. These cell lines could have been successfully used to increase our understanding of human developmental biology, transplantation medicine and the emerging science of regenerative medicine. The main source for human embryos has been 'discarded' or 'spare' fresh or frozen human embryos following IVF. It is a common practice to stimulate the ovaries of women undergoing any of the assisted reproductive technologies (ART) and retrieve multiple oocytes which subsequently lead to multiple embryos. Of these, only two or maximum of three embryos are transferred while the rest are cryopreserved as per the decision of the couple. in case a couple does not desire to 'cryopreserve' their embryos then all the embryos remaining following embryo transfer can be considered 'spare' or if a couple is no longer in need of the 'cryopreserved' embryos then these also can be considered as 'spare'. But, the question raised by the ethicists is, "what about 'slightly' over-stimulating a woman to get a few extra eggs and embryos? The decision becomes more difficult when it comes to 'discarded' embryos. As of today, the quality of the embryos is primarily assessed based on morphology and the rate of development mainly judged by single point assessment. Despite many criteria described in the literature, the quality assessment is purely subjective. The question that arises is on the decision of 'discarding' embryos. What would be the criteria for discarding embryos and the potential 'use' of ESC derived from the 'abnormal appearing' embryos? This paper discusses some of the newer methods to procure embryos for the derivation of embryonic stem cell lines which will respect the ethical concerns but still provide the source material.

  7. Assessing remediation of contaminated sediments using multiple biological endpoints: sediment toxicity, food web tissue contamination, biotic condition and DNA damage.

    EPA Science Inventory

    The Ottawa River is a component of the Maumee River Area of Concern (AOC) as defined by the International Joint Commission’s Great Lakes Water Quality Agreement. A sediment remediation project took place in the lower 14.2 km of the river where urban and industrial activitie...

  8. A logrank test-based method for sizing clinical trials with two co-primary time-to-event endpoints.

    PubMed

    Sugimoto, Tomoyuki; Sozu, Takashi; Hamasaki, Toshimitsu; Evans, Scott R

    2013-07-01

    We discuss sample size determination for clinical trials evaluating the joint effects of an intervention on two potentially correlated co-primary time-to-event endpoints. For illustration, we consider the most common case, a comparison of two randomized groups, and use typical copula families to model the bivariate endpoints. A correlation structure of the bivariate logrank statistic is specified to account for the correlation among the endpoints, although the between-group comparison is performed using the univariate logrank statistic. We propose methods to calculate the required sample size to compare the two groups and evaluate the performance of the methods and the behavior of required sample sizes via simulation.

  9. Transcriptome analysis uncovers key regulatory and metabolic aspects of soybean embryonic axes during germination.

    PubMed

    Bellieny-Rabelo, Daniel; De Oliveira, Eduardo Alves Gamosa; Ribeiro, Elaneda Silva; Costa, Evenilton Pessoa; Oliveira, Antônia Elenir Amâncio; Venancio, Thiago Motta

    2016-11-08

    Soybean (Glycine max) is a major legume crop worldwide, providing a critical source of protein and oil. The release of the soybean genome fuelled several transcriptome projects comprising multiple developmental stages and environmental conditions. Nevertheless, the global transcriptional patterns of embryonic axes during germination remain unknown. Here we report the analysis of ~1.58 billion RNA-Seq reads from soybean embryonic axes at five germination stages. Our results support the early activation of processes that are critical for germination, such as glycolysis, Krebs cycle and cell wall remodelling. Strikingly, only 3 hours after imbibition there is a preferential up-regulation of protein kinases and transcription factors, particularly from the LOB domain family, implying that transcriptional and post-transcriptional regulation play major roles early after imbibition. Lipid mobilization and glyoxylate pathways are also transcriptionally active in the embryonic axes, indicating that the local catabolism of oil reserves in the embryonic axes contributes to energy production during germination. We also present evidence supporting abscisic acid inactivation and the up-regulation of gibberellin, ethylene and brassinosteroid pathways. Further, there is a remarkable differential activation of paralogous genes in these hormone signalling pathways. Taken together, our results provide insights on the regulation and biochemistry of soybean germination.

  10. Transcriptome analysis uncovers key regulatory and metabolic aspects of soybean embryonic axes during germination

    PubMed Central

    Bellieny-Rabelo, Daniel; Alves Gamosa de Oliveira, Eduardo; da Silva Ribeiro, Elane; Pessoa Costa, Evenilton; Elenir Amâncio Oliveira, Antônia; Motta Venancio, Thiago

    2016-01-01

    Soybean (Glycine max) is a major legume crop worldwide, providing a critical source of protein and oil. The release of the soybean genome fuelled several transcriptome projects comprising multiple developmental stages and environmental conditions. Nevertheless, the global transcriptional patterns of embryonic axes during germination remain unknown. Here we report the analysis of ~1.58 billion RNA-Seq reads from soybean embryonic axes at five germination stages. Our results support the early activation of processes that are critical for germination, such as glycolysis, Krebs cycle and cell wall remodelling. Strikingly, only 3 hours after imbibition there is a preferential up-regulation of protein kinases and transcription factors, particularly from the LOB domain family, implying that transcriptional and post-transcriptional regulation play major roles early after imbibition. Lipid mobilization and glyoxylate pathways are also transcriptionally active in the embryonic axes, indicating that the local catabolism of oil reserves in the embryonic axes contributes to energy production during germination. We also present evidence supporting abscisic acid inactivation and the up-regulation of gibberellin, ethylene and brassinosteroid pathways. Further, there is a remarkable differential activation of paralogous genes in these hormone signalling pathways. Taken together, our results provide insights on the regulation and biochemistry of soybean germination. PMID:27824062

  11. Alternative Endpoints and Approaches for the Remediation of Contaminated Groundwater at Complex Sites - 13426

    SciTech Connect

    Deeb, Rula A.; Hawley, Elisabeth L.

    2013-07-01

    The goal of United States (U.S.) Department of Energy's (DOE)'s environmental remediation programs is to restore groundwater to beneficial use, similar to many other Federal and state environmental cleanup programs. Based on past experience, groundwater remediation to pre-contamination conditions (i.e., drinking water standards or non-detectable concentrations) can be successfully achieved at many sites. At a subset of the most complex sites, however, complete restoration is not likely achievable within the next 50 to 100 years using today's technology. This presentation describes several approaches used at complex sites in the face of these technical challenges. Many complex sites adopted a long-term management approach, whereby contamination was contained within a specified area using active or passive remediation techniques. Consistent with the requirements of their respective environmental cleanup programs, several complex sites selected land use restrictions and used risk management approaches to accordingly adopt alternative cleanup goals (alternative endpoints). Several sites used long-term management designations and approaches in conjunction with the alternative endpoints. Examples include various state designations for groundwater management zones, technical impracticability (TI) waivers or greater risk waivers at Superfund sites, and the use of Monitored Natural Attenuation (MNA) or other passive long-term management approaches over long time frames. This presentation will focus on findings, statistics, and case studies from a recently-completed report for the Department of Defense's Environmental Security Technology Certification Program (ESTCP) (Project ER-0832) on alternative endpoints and approaches for groundwater remediation at complex sites under a variety of Federal and state cleanup programs. The primary objective of the project was to provide environmental managers and regulators with tools, metrics, and information needed to evaluate

  12. [Detection of endpoint for segmentation between consonants and vowels in aphasia rehabilitation software based on artificial intelligence scheduling].

    PubMed

    Deng, Xingjuan; Chen, Ji; Shuai, Jie

    2009-08-01

    For the purpose of improving the efficiency of aphasia rehabilitation training, artificial intelligence-scheduling function is added in the aphasia rehabilitation software, and the software's performance is improved. With the characteristics of aphasia patient's voice as well as with the need of artificial intelligence-scheduling functions under consideration, the present authors have designed a set of endpoint detection algorithm. It determines the reference endpoints, then extracts every word and ensures the reasonable segmentation points between consonants and vowels, using the reference endpoints. The results of experiments show that the algorithm is able to attain the objects of detection at a higher accuracy rate. Therefore, it is applicable to the detection of endpoint on aphasia-patient's voice.

  13. Does bisphenol A induce superfeminization in Marisa cornuarietis? Part I: intra- and inter-laboratory variability in test endpoints.

    PubMed

    Forbes, Valery E; Selck, Henriette; Palmqvist, Annemette; Aufderheide, John; Warbritton, Ryan; Pounds, Nadine; Thompson, Roy; van der Hoeven, Nelly; Caspers, Norbert

    2007-03-01

    It has been claimed that bisphenol A (BPA) induces superfeminization in the freshwater gastropod, Marisa cornuarietis. To explore the reproducibility of prior work, here we present results from a three-laboratory study, the objectives of which were to determine the mean and variability in test endpoints (i.e., adult fecundity, egg hatchability, and juvenile growth) under baseline conditions and to identify the sources of variability. A major source of variability for all of the measured endpoints was due to differences within and among individuals. With few exceptions, variability among laboratories and among replicate tanks within laboratories contributed little to the observed variability in endpoints. The results highlight the importance of obtaining basic knowledge of husbandry requirements and baseline information on life-history traits of potential test species prior to designing toxicity test protocols. Understanding of the levels and sources of endpoint variability is essential so that statistically robust and ecologically relevant tests of chemicals can be conducted.

  14. End-point control of a two-link manipulator with a very flexible forearm - Issues and experiments

    NASA Technical Reports Server (NTRS)

    Oakley, Celia M.; Cannon, Robert H., Jr.

    1989-01-01

    For mechanical manipulators, a logical sensor location is at the manipulator end-point where tasks are performed. Unfortunately, when bending flexibility exists between an end-point sensor and a joint actuator, stability and performance are achieved only through sophisticated control design. Some of the issues involved in utilizing end-point sensing for two-link flexible manipulators are addressed. A modeling technique that properly represents the foreshortening of a flexible link undergoing deflections is presented. In order to realize fully the advantages of the assumed-modes modeling method, mode shapes are selected that allow a low-order model to be used effectively for simulation and control purposes. A nonlinear controller, incorporating state feedback and a constant-gain extended Kalman filter driven by end-point measurements, is designed and compared to a conventional proportional-plus-derivative controller that uses collocated sensors. Results from implementing these controllers on the experimental Stanford multilink flexible manipulator are given.

  15. Guidance for Using Non-Definitive Endpoints in Evaluating Risks to Listed and Non-listed Animal Species

    EPA Pesticide Factsheets

    Ensure consistency among OPP scientists in the use of non-definitive toxicity endpoints for terrestrial and aquatic animals when conducting ecological risk assessments for pesticides and federally listed and non-listed species.

  16. What is Normal? A Characterization of the Values and Variabilty in Reproductive Endpoints of the Fathead Minnow, Pimephales promelas

    EPA Science Inventory

    Jensen et al. investigated aspects of the normal reproductive biology of the fathead minnow (FHM, P. promelas), and subsequent studies have generated a large amount of additional reproductive data for endpoints such as plasma steroid hormone and vitellogenin concentrations, spa...

  17. OCT guided microinjections for mouse embryonic research

    NASA Astrophysics Data System (ADS)

    Larin, Kirill V.; Syed, Saba H.; Coughlin, Andrew J.; Wang, Shang; West, Jennifer L.; Dickinson, Mary E.; Larina, Irina V.

    2013-02-01

    Optical coherence tomography (OCT) is gaining popularity as live imaging tool for embryonic research in animal models. Recently we have demonstrated that OCT can be used for live imaging of cultured early mouse embryos (E7.5-E10) as well as later stage mouse embryos in utero (E12.5 to the end of gestation). Targeted delivery of signaling molecules, drugs, and cells is a powerful approach to study normal and abnormal development, and image guidance is highly important for such manipulations. Here we demonstrate that OCT can be used to guide microinjections of gold nanoshell suspensions in live mouse embryos. This approach can potentially be used for variety of applications such as guided injections of contrast agents, signaling molecules, pharmacological agents, cell transplantation and extraction, as well as other image-guided micromanipulations. Our studies also reveal novel potential for gold nanoshells in embryonic research.

  18. Mechanically patterning the embryonic airway epithelium.

    PubMed

    Varner, Victor D; Gleghorn, Jason P; Miller, Erin; Radisky, Derek C; Nelson, Celeste M

    2015-07-28

    Collections of cells must be patterned spatially during embryonic development to generate the intricate architectures of mature tissues. In several cases, including the formation of the branched airways of the lung, reciprocal signaling between an epithelium and its surrounding mesenchyme helps generate these spatial patterns. Several molecular signals are thought to interact via reaction-diffusion kinetics to create distinct biochemical patterns, which act as molecular precursors to actual, physical patterns of biological structure and function. Here, however, we show that purely physical mechanisms can drive spatial patterning within embryonic epithelia. Specifically, we find that a growth-induced physical instability defines the relative locations of branches within the developing murine airway epithelium in the absence of mesenchyme. The dominant wavelength of this instability determines the branching pattern and is controlled by epithelial growth rates. These data suggest that physical mechanisms can create the biological patterns that underlie tissue morphogenesis in the embryo.

  19. Mechanically patterning the embryonic airway epithelium

    PubMed Central

    Varner, Victor D.; Gleghorn, Jason P.; Miller, Erin; Radisky, Derek C.; Nelson, Celeste M.

    2015-01-01

    Collections of cells must be patterned spatially during embryonic development to generate the intricate architectures of mature tissues. In several cases, including the formation of the branched airways of the lung, reciprocal signaling between an epithelium and its surrounding mesenchyme helps generate these spatial patterns. Several molecular signals are thought to interact via reaction-diffusion kinetics to create distinct biochemical patterns, which act as molecular precursors to actual, physical patterns of biological structure and function. Here, however, we show that purely physical mechanisms can drive spatial patterning within embryonic epithelia. Specifically, we find that a growth-induced physical instability defines the relative locations of branches within the developing murine airway epithelium in the absence of mesenchyme. The dominant wavelength of this instability determines the branching pattern and is controlled by epithelial growth rates. These data suggest that physical mechanisms can create the biological patterns that underlie tissue morphogenesis in the embryo. PMID:26170292

  20. Deriving sulfamethoxazole dissipation endpoints in pasture soils using first order and biphasic kinetic models.

    PubMed

    Srinivasan, Prakash; Sarmah, Ajit K; Rohan, Maheswaran

    2014-08-01

    Single first-order (SFO) kinetic model is often used to derive the dissipation endpoints of an organic chemical in soil. This model is used due to its simplicity and requirement by regulatory agencies. However, using the SFO model for all types of decay pattern could lead to under- or overestimation of dissipation endpoints when the deviation from first-order is significant. In this study the performance of three biphasic kinetic models - bi-exponential decay (BEXP), first-order double exponential decay (FODED), and first-order two-compartment (FOTC) models was evaluated using dissipation datasets of sulfamethoxazole (SMO) antibiotic in three different soils under varying concentration, depth, temperature, and sterile conditions. Corresponding 50% (DT50) and 90% (DT90) dissipation times for the antibiotics were numerically obtained and compared against those obtained using the SFO model. The fit of each model to the measured values was evaluated based on an array of statistical measures such as coefficient of determination (R(2)adj), root mean square error (RMSE), chi-square (χ(2)) test at 1% significance, Bayesian Information Criteria (BIC) and % model error. Box-whisker residual plots were also used to compare the performance of each model to the measured datasets. The antibiotic dissipation was successfully predicted by all four models. However, the nonlinear biphasic models improved the goodness-of-fit parameters for all datasets. Deviations from datasets were also often less evident with the biphasic models. The fits of FOTC and FODED models for SMO dissipation datasets were identical in most cases, and were found to be superior to the BEXP model. Among the biphasic models, the FOTC model was found to be the most suitable for obtaining the endpoints and could provide a mechanistic explanation for SMO dissipation in the soils.

  1. Use of behavioral endpoints to determine protective concentrations of the insecticide fonofos for bluegill (Lepomis macrochirus)

    USGS Publications Warehouse

    Fairchild, J.F.; Little, E.E.

    1999-01-01

    This research compared the results of laboratory and mesocosm studies to determine the effectiveness of using behavioral measures of sublethal exposure to define environmental concentration ranges that are protective of free-ranging populations of bluegill (Lepomis macrochirus) exposed to the organophophate insecticide fonofos. Thirty-day laboratory chronic studies were conducted to determine the relative sensitivity of standard (e.g. survival and growth) and non-standard behavioral (e.g. swimming capacity, feeding efficiency, and aggression) endpoints in predicting concentrations of fonofos protective of bluegill growth and survival. The lowest observable effect concentration (LOECs) for the standard measures of survival and growth was 5.6 ??g/L. Two behavioral endpoints were of similar sensitivity to the standard measures: swimming capacity, LOEC of 5.6 ??g/L; and prey strike frequency, LOEC of 5.6 ??g/L. However, aggressive interactions were ten-fold more sensitive than swimming or feeding behavior with a LOEC occurring at 0.6 ??g/L. Lab results were compared to an aquatic mesocosm study which exposed adult and juvenile bluegill to a 9.41 ??g/L concentration of fonofos. The dissipation half-life of fonofos was 5 days in 0.1 hectare aquatic mesocosms. Significant mortality among caged bluegill occurred within 4 days of exposure at 9.41 ??g/L. However, the 9.41 ??g/L concentration of fonofos had no statistically significant effects on survival, growth, reproduction, or total biomass of free-ranging populations of bluegill. We conclude from these studies that laboratory data can accurately estimate concentrations that are lethal in the field and that the use of behavioral endpoints can provide ecologically relevant, yet conservative estimates of concentrations that are protective of field populations.

  2. Comparing toxicity endpoints on Lecane quadridentata (Rotifera: Monogononta) exposed to two anticholinesterases pesticides.

    PubMed

    Pérez-Legaspi, Ignacio Alejandro; Quintanar, J Luis; Rico-Martínez, Roberto

    2012-09-01

    Toxicity tests were performed on the freshwater rotifer Lecane quadridentata exposed to the pesticides carbaryl and methyl parathion (lethal, sublethal, and chronic) to compare the sensitivity between different endpoints: (a) 48-h mortality; (b) 30-min in vivo inhibition of esterase activity; (c) 5-day inhibition of the instantaneous growth rate. The emphasis of this work was to find the most appropriate endpoint to evaluate the toxicity of these pesticides in view of their sensitivity, duration, and ecological relevance. The comparison between the three toxicity tests show that the 5-day chronic tests have the lowest EC50 (2.22 and 6.6 mg/L), lowest-observed-effect concentration (2.5 and 2.5 mg/L), and no-observed-effect concentration (1.0 and 1.2 mg/L) values for carbaryl and methyl parathion, respectively. This indicates that the estimate of the instantaneous rate of natural increase r is the most sensitive endpoint regarding the toxicity of these pesticides. This sensitivity might be due to the effect on reducing the growth potential form the first generation on. Lethal and sublethal tests are closely related, suggesting that the immediate effect after inhibition of esterases is death. In general, the sensitivity of L. quadridentata is similar to other species of rotifers exposed to methyl parathion. Therefore, the 5-day chronic toxicity test with the freshwater rotifer L. quadridentata should be considered a good candidate to evaluate the effect of anticholinesterase pesticides, due to its high sensitivity and ecological relevance.

  3. The Sleep Apnea cardioVascular Endpoints (SAVE) Trial: Rationale, Ethics, Design, and Progress

    PubMed Central

    Antic, Nick A.; Heeley, Emma; Anderson, Craig S.; Luo, Yuanming; Wang, Jiguang; Neal, Bruce; Grunstein, Ron; Barbe, Ferran; Lorenzi-Filho, Geraldo; Huang, Shaoguang; Redline, Susan; Zhong, Nanshan; McEvoy, R. Doug

    2015-01-01

    The Sleep Apnea cardioVascular Endpoints (SAVE) study is an ongoing investigator-initiated and conducted, international, multicenter, open, blinded endpoint, randomized controlled trial that was designed to determine whether treatment of obstructive sleep apnea (OSA) with continuous positive airways pressure (CPAP) can reduce the risk of serious cardiovascular (CV) events in patients with established CV disease (clinical trial registration NCT00738179). The results of this study will have important implications for the provision of health care to patients with sleep apnea around the world. The SAVE study has brought together respiratory, sleep, CV and stroke clinicians-scientists in an interdisciplinary collaboration with industry and government sponsorship to conduct an ambitious clinical trial. Following its launch in Australia and China in late 2008, the recruitment network expanded across 89 sites that included New Zealand, India, Spain, USA, and Brazil for a total of 2,717 patients randomized by December 2013. These patients are being followed until December 2015 so that the average length of follow-up of the cohort will be over 4 y. This article describes the rationale for the SAVE study, considerations given to the design including how various cultural and ethical challenges were addressed, and progress in establishing and maintaining the recruitment network, patient follow-up, and adherence to CPAP and procedures. The assumptions underlying the original trial sample size calculation and why this was revised downward in 2012 are also discussed. Clinical Trials Registration Number: NCT00738179. Australia New Zealand Clinical Trials Registry Number: ACTRN12608000409370. Citation: Antic NA, Heeley E, Anderson CS, Luo Y, Wang J, Neal B, Grunstein R, Barbe F, Lorenzi-Filho G, Huang S, Redline S, Zhong N, McEvoy RD. The sleep apnea cardiovascular endpoints (SAVE) trial: rationale, ethics, design, and progress. SLEEP 2015;38(8):1247–1257. PMID:25669180

  4. Determination of Endpoint Energy and Bremsstrahlung Spectra for High-Energy Radiation-Therapy Beams

    NASA Astrophysics Data System (ADS)

    Landry, Danny Joe

    Few attempts have been made to experimentally determine thick-target bremsstrahlung spectra of megavoltage therapy beams. For spectral studies using the Compton scattering technique, sodium iodine (NaI) detectors with relatively poor energy resolution have been used. Other experimental techniques for determining spectra are generally not suited for a clinical environment with the inherent time and space constraints. To gather more spectral information than previously obtained in the region near the endpoint energy, the use of a high-resolution intrinsic-germanium (Ge) detector was proposed. A response function matrix was determined from experimentally obtained pulse height distributions on the multichannel analyzer. The distributions were for nine various monoenergetic sources between 280 adn 1525 keV. The response function was used to convert the measured pulse height distributions to photon flux spectra using an iterative approximation technique with a computer. Photon flux spectra from the Sagittaire Linear Accelerator were obtained at average-electron endpoint energies of 15, 20, and 25 MeV. Two spectra were measured at the 25 MeV setting; one spectrum was measured along the central axis and one spectrum at 4(DEGREES) off axis. Photon spectra were also obtained for a Van de Graaff generator at the nominal endpoint energies of 2.2, 2.35, and 2.5 MeV. The results for both the linac and the Van de Graaff generator were compared with theoretical spectra and previously measured spectra where available. Also, photon spectra from a Theratron-80 (('60)Co) unit were determined for three field sizes and for a 10 x 10 cm. field with a lucite tray or a 45(DEGREES) wedge in the beam. The resulting spectra were compared to previously measured ('60)Co spectra.

  5. A trade-off between embryonic development rate and immune function of avian offspring is concealed by embryonic temperature

    USGS Publications Warehouse

    Martin, Thomas E.; Arriero, Elena; Majewska, Ania

    2011-01-01

    Long embryonic periods are assumed to reflect slower intrinsic development that are thought to trade off to allow enhanced physiological systems, such as immune function. Yet, the relatively rare studies of this trade-off in avian offspring have not found the expected trade-off. Theory and tests have not taken into account the strong extrinsic effects of temperature on embryonic periods of birds. Here, we show that length of the embryonic period did not explain variation in two measures of immune function when temperature was ignored, based on studies of 34 Passerine species in tropical Venezuela (23 species) and north temperate Arizona (11 species). Variation in immune function was explained when embryonic periods were corrected for average embryonic temperature, in order to better estimate intrinsic rates of development. Immune function of offspring trades off with intrinsic rates of embryonic development once the extrinsic effects of embryonic temperatures are taken into account.

  6. Metabolic circadian rhythms in embryonic turtles.

    PubMed

    Loudon, Fiona Kay; Spencer, Ricky-John; Strassmeyer, Alana; Harland, Karen

    2013-07-01

    Oviparous species are model organisms for investigating embryonic development of endogenous physiological circadian rhythms without the influence of maternal biorhythms. Recent studies have demonstrated that heart rates and metabolic rates of embryonic turtles are not constant or always maximal and can be altered in response to the presence of embryos at a more advanced stage of development within the nest. A first step in understanding the physiological mechanisms underpinning these responses in embryonic ectothermic organisms is to develop metabolic profiles (e.g., heart rate) at different temperatures throughout incubation. Heart beat and rhythmic patterns or changes in development may represent important signals or cues within a nest and may be vital to coordinate synchronous hatching well in advance of the final stages of incubation. We developed baseline embryonic heart-rate profiles of embryos of the short-necked Murray River turtle (Emydura macquarii) to determine the stage of embryogenesis that metabolic circadian rhythms become established, if at all. Eggs were incubated at constant temperatures (26°C and 30°C) and heart rates were monitored at 6-h intervals over 24 h every 7-11 days until hatching. Circadian heart rate rhythms were detected at the mid-gestation period and were maintained until hatching. Heart rates throughout the day varied by up to 20% over 24 h and were not related to time of day. This study demonstrated that endogenous metabolic circadian rhythms in developing embryos in turtle eggs establish earlier in embryogenesis than those documented in other vertebrate taxa during embryogenesis. Early establishment of circadian rhythms in heart rates may be critical for communication among embryos and synchrony in hatching and emergence from the nest.

  7. Multisite Comparison of Anti-Human Immunodeficiency Virus Microbicide Activity in Explant Assays Using a Novel Endpoint Analysis ▿ †

    PubMed Central

    Richardson-Harman, Nicola; Lackman-Smith, Carol; Fletcher, Patricia S.; Anton, Peter A.; Bremer, James W.; Dezzutti, Charlene S.; Elliott, Julie; Grivel, Jean-Charles; Guenthner, Patricia; Gupta, Phalguni; Jones, Maureen; Lurain, Nell S.; Margolis, Leonid B.; Mohan, Swarna; Ratner, Deena; Reichelderfer, Patricia; Roberts, Paula; Shattock, Robin J.; Cummins, James E.

    2009-01-01

    Microbicide candidates with promising in vitro activity are often advanced for evaluations using human primary tissue explants relevant to the in vivo mucosal transmission of human immunodeficiency virus type 1 (HIV-1), such as tonsil, cervical, or rectal tissue. To compare virus growth or the anti-HIV-1 efficacies of candidate microbicides in tissue explants, a novel soft-endpoint method was evaluated to provide a single, objective measurement of virus growth. The applicability of the soft endpoint is shown across several different ex vivo tissue types, with the method performed in different laboratories, and for a candidate microbicide (PRO 2000). The soft-endpoint method was compared to several other endpoint methods, including (i) the growth of virus on specific days after infection, (ii) the area under the virus growth curve, and (iii) the slope of the virus growth curve. Virus growth at the assay soft endpoint was compared between laboratories, methods, and experimental conditions, using nonparametric statistical analyses. Intra-assay variability determinations using the coefficient of variation demonstrated higher variability for virus growth in rectal explants. Significant virus inhibition by PRO 2000 and significant differences in the growth of certain primary HIV-1 isolates were observed by the majority of laboratories. These studies indicate that different laboratories can provide consistent measurements of anti-HIV-1 microbicide efficacy when (i) the soft endpoint or another standardized endpoint is used, (ii) drugs and/or virus reagents are centrally sourced, and (iii) the same explant tissue type and method are used. Application of the soft-endpoint method reduces the inherent variability in comparisons of preclinical assays used for microbicide development. PMID:19726602

  8. Multisite comparison of anti-human immunodeficiency virus microbicide activity in explant assays using a novel endpoint analysis.

    PubMed

    Richardson-Harman, Nicola; Lackman-Smith, Carol; Fletcher, Patricia S; Anton, Peter A; Bremer, James W; Dezzutti, Charlene S; Elliott, Julie; Grivel, Jean-Charles; Guenthner, Patricia; Gupta, Phalguni; Jones, Maureen; Lurain, Nell S; Margolis, Leonid B; Mohan, Swarna; Ratner, Deena; Reichelderfer, Patricia; Roberts, Paula; Shattock, Robin J; Cummins, James E

    2009-11-01

    Microbicide candidates with promising in vitro activity are often advanced for evaluations using human primary tissue explants relevant to the in vivo mucosal transmission of human immunodeficiency virus type 1 (HIV-1), such as tonsil, cervical, or rectal tissue. To compare virus growth or the anti-HIV-1 efficacies of candidate microbicides in tissue explants, a novel soft-endpoint method was evaluated to provide a single, objective measurement of virus growth. The applicability of the soft endpoint is shown across several different ex vivo tissue types, with the method performed in different laboratories, and for a candidate microbicide (PRO 2000). The soft-endpoint method was compared to several other endpoint methods, including (i) the growth of virus on specific days after infection, (ii) the area under the virus growth curve, and (iii) the slope of the virus growth curve. Virus growth at the assay soft endpoint was compared between laboratories, methods, and experimental conditions, using nonparametric statistical analyses. Intra-assay variability determinations using the coefficient of variation demonstrated higher variability for virus growth in rectal explants. Significant virus inhibition by PRO 2000 and significant differences in the growth of certain primary HIV-1 isolates were observed by the majority of laboratories. These studies indicate that different laboratories can provide consistent measurements of anti-HIV-1 microbicide efficacy when (i) the soft endpoint or another standardized endpoint is used, (ii) drugs and/or virus reagents are centrally sourced, and (iii) the same explant tissue type and method are used. Application of the soft-endpoint method reduces the inherent variability in comparisons of preclinical assays used for microbicide development.

  9. Sensitivity, variability, and recovery of functional and structural endpoints of an aquatic community exposed to herbicides.

    PubMed

    Knauer, Katja; Hommen, Udo

    2012-04-01

    A mesocosm study with three photosystem-II inhibitors and an equipotent mixture was performed to address the value of functional and structural endpoints in evaluating the impact of herbicides on aquatic systems. The herbicides atrazine, diuron, and isoproturon were dosed in the ratio of their relative potencies as HC30 for the single substance treatments and as 1/3 HC30 for the mixture treatment to obtain comparable effect concentrations. To investigate the effects of the three herbicides and their mixture on photosynthesis of the whole system, the physical-chemical parameters pH, dissolved oxygen, and conductivity were monitored. To address effects on photosynthesis more specifically, the photosynthetic efficiency of phytoplankton and three submersed macrophytes (Elodea canadensis, Myriophyllum spicatum, and Potamogeton lucens) were investigated applying in vivo chlorophyll fluorescence as an indicator for their activity. As a structural endpoint, the species abundance and community structure of the phytoplankton community was determined. Effects were continuously monitored over a five week period of constant exposure, and during a 3 month post-exposure period. The sensitivity, expressed as maximum effect during constant exposure, was higher for the structural parameters (total and single species abundances and PRC) than for the functional parameters. The mean coefficient of variation (CV) for the physical-chemical parameters was below 10%, for the photosynthesis measurement of the phytoplankton and macrophytes below 10 and 30%, respectively. Structural parameters, however, yielded higher variability with mean CVs for phytoplankton abundance data and single sensitive species reaching up to 96%. Effects on the phytoplankton photosynthesis measured via in vivo chlorophyll fluorescence were constant during the exposure period; whereas macrophytes recovered quickly from photosynthesis inhibition despite constant exposure. Effects on total system photosynthesis

  10. An Application of Endpoint Detection to Bivariate Data in Tau-Path Order.

    PubMed

    Sampath, Srinath; Verducci, Joseph S

    2014-08-01

    The Fligner and Verducci (1988) multistage model for rankings is modified to create the moving average maximum likelihood estimator (MAMLE), a locally smooth estimator that measures stage-wise agreement between two long ranked lists, and provides a stopping rule for the detection of the endpoint of agreement. An application of this MAMLE stopping rule to bivariate data set in tau-path order (Yu, Verducci and Blower (2011)) is discussed. Data from the National Cancer Institute measuring associations between gene expression and compound potency are studied using this application, providing insights into the length of the relationship between the variables.

  11. Application of molecular endpoints in early life stage salmonid environmental biomonitoring.

    PubMed

    Marlatt, Vicki L; Sherrard, Ryan; Kennedy, Chris J; Elphick, James R; Martyniuk, Christopher J

    2016-04-01

    Molecular endpoints can enhance existing whole animal bioassays by more fully characterizing the biological impacts of aquatic pollutants. Laboratory and field studies were used to examine the utility of adopting molecular endpoints for a well-developed in situ early life stage (eyed embryo to onset of swim-up fry) salmonid bioassay to improve diagnostic assessments of water quality in the field. Coastal cutthroat trout (Oncorhynchus clarki clarki) were exposed in the laboratory to the model metal (zinc, 40μg/L) and the polycyclic aromatic hydrocarbon (pyrene, 100μg/L) in water to examine the resulting early life stage salmonid responses. In situ field exposures and bioassays were conducted in parallel to evaluate the water quality of three urban streams in British Columbia (two sites with anthropogenic inputs and one reference site). The endpoints measured in swim-up fry included survival, deformities, growth (weight and length), vitellogenin (vtg) and metallothionein (Mt) protein levels, and hepatic gene expression (e.g., metallothioneins [mta and mtb], endocrine biomarkers [vtg and estrogen receptors, esr] and xenobiotic-metabolizing enzymes [cytochrome P450 1A3, cyp1a3 and glutathione transferases, gstk]). No effects were observed in the zinc treatment, however exposure of swim-up fry to pyrene resulted in decreased survival, deformities and increased estrogen receptor alpha (er1) mRNA levels. In the field exposures, xenobiotic-metabolizing enzymes (cyp1a3, gstk) and zinc transporter (zntBigM103) mRNA were significantly increased in swim-up fry deployed at the sites with more anthropogenic inputs compared to the reference site. Cluster analysis revealed that gene expression profiles in individuals from the streams receiving anthropogenic inputs were more similar to each other than to the reference site. Collectively, the results obtained in this study suggest that molecular endpoints may be useful, and potentially more sensitive, indicators of site

  12. Adverse effect of agroecosystem pond water on biological endpoints of common toad (Rhinella arenarum) tadpoles.

    PubMed

    Babini, María Selene; Bionda, Clarisa de Lourdes; Salas, Nancy Edith; Martino, Adolfo Ludovico

    2016-08-01

    Chemical prroducts used in farming and wastes from livestock can contaminate pond water in agroecosystems due to runoff. Amphibians using these ponds for breeding are probably exposed to pollutants, and serious consequences might be observed afterward at the population level. Assessment biological endpoints of anuran to water quality give a realistic estimate of the probability of occurrence of adverse effects and provide an early warning signal. In this study, the ecotoxicity of agroecosystem ponds from the south of Córdoba province, Argentina, was investigated. Ponds in four sites with different degrees of human disturbance were selected: three agroecosystems (A1, A2, A3) and a site without crops or livestock (SM). The effect of pond water quality on the biological endpoint of Rhinella arenarum tadpoles was examined using microcosms with pond water from sites. Biological endpoints assessed were as follows: mortality, growth, development, morphological abnormalities (in body shape, gut, and labial tooth row formula), behavior, and blood cell parameters (micronucleus and nuclear abnormalities). Results indicated that water from agroecosystems has adverse effect on early life stage of R. arenarum. High mortality and fewer metamorphs were recorded in the A1 and A3 treatments. Tadpoles and metamorphs from A1 and A2 treatments had lower body condition. Tadpoles from A1 and A3 showed the highest prevalence of morphological abnormalities. The lowest amount of tadpoles feeding and the highest percentage of tadpoles swimming on the surface were observed in treatments with agroecosystem pond water. The higher frequencies of micronuclei and nuclear abnormalities were recorded in tadpoles from A1, A2, and A3 treatments. We check the sensitivity of the biological endpoints of R. arenarum tadpoles like early warning indicators of water quality. We found that the poor water quality of agroecosystem ponds has impact on the health of the tadpoles, and this could affect the

  13. Optimal Futility Interim Design: A Predictive Probability of Success Approach with Time-to-Event Endpoint.

    PubMed

    Tang, Zhongwen

    2015-01-01

    An analytical way to compute predictive probability of success (PPOS) together with credible interval at interim analysis (IA) is developed for big clinical trials with time-to-event endpoints. The method takes account of the fixed data up to IA, the amount of uncertainty in future data, and uncertainty about parameters. Predictive power is a special type of PPOS. The result is confirmed by simulation. An optimal design is proposed by finding optimal combination of analysis time and futility cutoff based on some PPOS criteria.

  14. Do embryonic polar bodies commit suicide?

    PubMed

    Fabian, Dušan; Čikoš, Štefan; Rehák, Pavol; Koppel, Juraj

    2014-02-01

    The extrusion and elimination of unnecessary gametic/embryonic material is one of the key events that determines the success of further development in all living organisms. Oocytes produce the first polar body to fulfill the maturation process just before ovulation, and release the second polar body immediately after fertilization. The aim of this study was to compile a physiological overview of elimination of polar bodies during early preimplantation development in mice. Our results show that three-quarters of the first polar bodies were lost even at the zygotic stage; the 4-cell stage embryos contained only one (second) polar body, and the elimination of second polar bodies proceeded continuously during later development. Both first and second polar bodies showed several typical features of apoptosis: phosphatidylserine redistribution (observed for the first time in the first polar body), specific DNA degradation, condensed nuclear morphology, and inability to exclude cationic dye from the nucleus during the terminal stage of the apoptotic process. Caspase-3 activity was recorded only in the second polar body. From the morphological point of view, mouse polar bodies acted very similarly to damaged embryonic cells which have lost contact with their neighboring blastomeres. In conclusion, polar bodies possess all the molecular equipment necessary for triggering and executing an active suicide process. Furthermore, similarly as in dying embryonic cells, stressing external conditions (culture in vitro) might accelerate and increase the incidence of apoptotic elimination of the polar bodies in embryos.

  15. Informing tendon tissue engineering with embryonic development.

    PubMed

    Glass, Zachary A; Schiele, Nathan R; Kuo, Catherine K

    2014-06-27

    Tendon is a strong connective tissue that transduces muscle-generated forces into skeletal motion. In fulfilling this role, tendons are subjected to repeated mechanical loading and high stress, which may result in injury. Tissue engineering with stem cells offers the potential to replace injured/damaged tissue with healthy, new living tissue. Critical to tendon tissue engineering is the induction and guidance of stem cells towards the tendon phenotype. Typical strategies have relied on adult tissue homeostatic and healing factors to influence stem cell differentiation, but have yet to achieve tissue regeneration. A novel paradigm is to use embryonic developmental factors as cues to promote tendon regeneration. Embryonic tendon progenitor cell differentiation in vivo is regulated by a combination of mechanical and chemical factors. We propose that these cues will guide stem cells to recapitulate critical aspects of tenogenesis and effectively direct the cells to differentiate and regenerate new tendon. Here, we review recent efforts to identify mechanical and chemical factors of embryonic tendon development to guide stem/progenitor cell differentiation toward new tendon formation, and discuss the role this work may have in the future of tendon tissue engineering.

  16. Embryonic development of Pelteobagrus fulvidraco (Richardson, 1846)

    NASA Astrophysics Data System (ADS)

    Wang, Weimin; Abbas, Khalid; Yan, Ansheng

    2006-12-01

    For production enhancement and procedure upgrade, the developmental phases of laboratory-reared eggs of catfish Pelteobagrus fulvidraco were investigated. Twenty mature females and 10 males were collected from Dadongmen wholesale fisheries market in Wuhan City on May 8, 2003. Zygotes were stripped from mature fish after hormone-induced ovulation, fertilized, and incubated through whole embryonic development. The fertilized eggs were stocked in density of 100 eggs/L in white square tanks of 10 L. Incubation water was dechlorinated tap water with continuous aeration. The tanks were lit directly with 60 W fluorescent bulbs with a 12 light: 12 dark photoperiod. Water temperature, dissolved oxygen and pH were 29.0±0.5°C, 6.7±0.4 mg/L and 7.4±2, respectively. The results showed that the eggs of P. fulvidraco were yellow, sticky and contained much yolk. The mean diameter of fertilized eggs was 2.03 mm. At the water temperature of 29.0±0.5°C, the ontogenesis spent about 33 h after fertilization. From fertilization to hatching, the embryonic development can be divided into 30 40 phases, which varies in the emphasis and direction of development. The detailed embryonic movement was also described.

  17. [Heart tissue from embryonic stem cells].

    PubMed

    Zimmermann, W-H

    2008-09-01

    Embryonic stem cells can give rise to all somatic cells, making them an attractive cell source for tissue engineering applications. The propensity of cells to form tissue-like structures in a culture dish has been well documented. We and others made use of this intrinsic property to generate bioartificial heart muscle. First proof-of-concept studies involved immature heart cells mainly from fetal chicken, neonatal rats and mice. They eventually provided evidence that force-generating heart muscle can be engineered in vitro. Recently, the focus shifted to the application of stem cells to eventually enable the generation of human heart muscle and reach following long-term goals: (1) development of a simplified in vitro model of heart muscle development; (2) generation of a human test-bed for drug screening and development; (3) allocation of surrogate heart tissue to myocardial repair applications. This overview will provide the background for cell-based myocardial repair, introduce the main myocardial tissue engineering concepts, discuss the use of embryonic and non-embryonic stem cells, and lays out the potential direct and indirect therapeutic use of human tissue engineered myocardium.

  18. Human embryonic stem cells and lung regeneration.

    PubMed

    Varanou, A; Page, C P; Minger, S L

    2008-10-01

    Human embryonic stem cells are pluripotent cells derived from the inner cell mass of preimplantation stage embryos. Their unique potential to give rise to all differentiated cell types has generated great interest in stem cell research and the potential that it may have in developmental biology, medicine and pharmacology. The main focus of stem cell research has been on cell therapy for pathological conditions with no current methods of treatment, such as neurodegenerative diseases, cardiac pathology, retinal dysfunction and lung and liver disease. The overall aim is to develop methods of application either of pure cell populations or of whole tissue parts to the diseased organ under investigation. In the field of pulmonary research, studies using human embryonic stem cells have succeeded in generating enriched cultures of type II pneumocytes in vitro. On account of their potential of indefinite proliferation in vitro, embryonic stem cells could be a source of an unlimited supply of cells available for transplantation and for use in gene therapy. Uncovering the ability to generate such cell types will expand our understanding of biological processes to such a degree that disease understanding and management could change dramatically.

  19. Mechanical signaling coordinates the embryonic heartbeat

    PubMed Central

    Chiou, Kevin K.; Rocks, Jason W.; Chen, Christina Yingxian; Cho, Sangkyun; Merkus, Koen E.; Rajaratnam, Anjali; Robison, Patrick; Tewari, Manorama; Vogel, Kenneth; Majkut, Stephanie F.; Prosser, Benjamin L.; Discher, Dennis E.; Liu, Andrea J.

    2016-01-01

    In the beating heart, cardiac myocytes (CMs) contract in a coordinated fashion, generating contractile wave fronts that propagate through the heart with each beat. Coordinating this wave front requires fast and robust signaling mechanisms between CMs. The primary signaling mechanism has long been identified as electrical: gap junctions conduct ions between CMs, triggering membrane depolarization, intracellular calcium release, and actomyosin contraction. In contrast, we propose here that, in the early embryonic heart tube, the signaling mechanism coordinating beats is mechanical rather than electrical. We present a simple biophysical model in which CMs are mechanically excitable inclusions embedded within the extracellular matrix (ECM), modeled as an elastic-fluid biphasic material. Our model predicts strong stiffness dependence in both the heartbeat velocity and strain in isolated hearts, as well as the strain for a hydrogel-cultured CM, in quantitative agreement with recent experiments. We challenge our model with experiments disrupting electrical conduction by perfusing intact adult and embryonic hearts with a gap junction blocker, β-glycyrrhetinic acid (BGA). We find this treatment causes rapid failure in adult hearts but not embryonic hearts—consistent with our hypothesis. Last, our model predicts a minimum matrix stiffness necessary to propagate a mechanically coordinated wave front. The predicted value is in accord with our stiffness measurements at the onset of beating, suggesting that mechanical signaling may initiate the very first heartbeats. PMID:27457951

  20. Informing tendon tissue engineering with embryonic development

    PubMed Central

    Glass, Zachary A.; Schiele, Nathan R.; Kuo, Catherine K.

    2014-01-01

    Tendon is a strong connective tissue that transduces muscle-generated forces into skeletal motion. In fulfilling this role, tendons are subjected to repeated mechanical loading and high stress, which may result in injury. Tissue engineering with stem cells offers the potential to replace injured/damaged tissue with healthy, new living tissue. Critical to tendon tissue engineering is the induction and guidance of stem cells towards the tendon phenotype. Typical strategies have relied on adult tissue homeostatic and healing factors to influence stem cell differentiation, but have yet to achieve tissue regeneration. A novel paradigm is to use embryonic developmental factors as cues to promote tendon regeneration. Embryonic tendon progenitor cell differentiation in vivo is regulated by a combination of mechanical and chemical factors. We propose that these cues will guide stem cells to recapitulate critical aspects of tenogenesis and effectively direct the cells to differentiate and regenerate new tendon. Here, we review recent efforts to identify mechanical and chemical factors of embryonic tendon development to guide stem/progenitor cell differentiation toward new tendon formation, and discuss the role this work may have in the future of tendon tissue engineering. PMID:24484642

  1. Embryonic and embryonic-like stem cells in heart muscle engineering.

    PubMed

    Zimmermann, Wolfram-Hubertus

    2011-02-01

    Cardiac muscle engineering is evolving rapidly and may ultimately be exploited to (1) model cardiac development, physiology, and pathology; (2) identify and validate drug targets; (3) assess drug safety and efficacy; and (4) provide therapeutic substitute myocardium. The ultimate success in any of these envisioned applications depends on the utility of human cells and their assembly into myocardial equivalents with structural and functional properties of mature heart muscle. Embryonic stem cells appear as a promising cell source in this respect, because they can be cultured reliably and differentiated robustly into cardiomyocytes. Despite their unambiguous cardiogenicity, data on advanced maturation and seamless myocardial integration of embryonic stem cell-derived cardiomyocytes in vivo are sparse. Additional concerns relate to the limited control over cardiomyogenic specification and cardiomyocyte maturation in vitro as well as the risk of teratocarcinoma formation and immune rejection of stem cell implants in vivo. Through the invent of embryonic-like stem cells - such as parthenogenetic stem cells, male germline stem cells, and induced pluripotent stem cells - some but certainly not all of these issues may be addressed, albeit at the expense of additional concerns. This review will discuss the applicability of embryonic and embryonic-like stem cells in myocardial tissue engineering and address issues that require particular attention before the potential of stem cell-based heart muscle engineering may be fully exploited. This article is part of a special issue entitled, "Cardiovascular Stem Cells Revisited".

  2. Morphology of the embryonic and hatchling American alligator ductus arteriosi and implications for embryonic cardiovascular shunting.

    PubMed

    Jacobs, Kimberley; Goy, Sarah K; Dzialowski, Edward M

    2012-02-01

    The ductus arteriosi (DA) are embryonic blood vessels found in amniotic vertebrates that shunt blood away from the pulmonary artery and lungs and toward the aorta. Here, we examine changes in morphology of the right and left DA (LDA), and right and left aorta (LAo) from embryonic and hatchling alligators. The developing alligator has two-patent DA that join the right and LAo. Both DA exhibit a muscular phenotype composed of an internal smooth muscle layer (2-4 cells thick). At hatching, the lumen diameter of both DA decreases as the vessels begin to close within the first 12 h of posthatch life. Between day 1 and day 12 posthatching, the vessel becomes fully occluded with endothelial and smooth muscle cells filling the lumen. A number of DA from hatchlings contained blood clots along their length. The lumen of the full term alligator DA is reduced in comparison with the full term chicken DA. The developing alligator embryo has an additional right-to-left shunt pathway in the LAo arising from the right ventricle. The embryonic LAo diameter is twice the diameter of either the right DA or LDA, providing a lower resistance pathway for blood leaving the right ventricle. On the basis of these findings, we propose that the paired DA of the embryonic alligator have a reduced role in the embryonic right-to-left shunt of blood from the right ventricle when compared with the avian DA.

  3. Comparison of adequate relief with symptom, global, and responder endpoints in linaclotide phase 3 trials in IBS-C

    PubMed Central

    Camilleri, Michael; Lembo, Anthony J; Lavins, Bernard J; MacDougall, James E; Carson, Robyn T; Williams, Valerie SL; Nelson, Lauren M; Shiff, Steven J; Currie, Mark G; Kurtz, Caroline B

    2015-01-01

    Background Optimal clinical trial endpoints for irritable bowel syndrome with constipation (IBS-C) are uncertain. Objective The objective of this article is to compare adequate relief (AR) to abdominal/bowel symptoms, global endpoints, and FDA and EMA responder criteria; and to use AR as an anchor to assess clinically meaningful change (CMC) in IBS-C symptoms. Methods Using pooled 12-week data from two phase 3 linaclotide clinical trials, daily abdominal/bowel symptoms and weekly global assessments were correlated with AR. Symptom CMC thresholds were estimated using AR as an anchor. Agreement between AR and FDA/EMA responder criteria was assessed. Results Correlations of AR with percentage change in abdominal symptoms, bowel symptoms, and global endpoints ranged from 0.48–0.54, 0.32–0.39, and 0.61–0.71, respectively. Using AR as an anchor, CMC thresholds were 29% improvement in abdominal pain, 29% improvement in abdominal discomfort, and 0.7/week increase in CSBMs, similar to thresholds for IBS-C responder endpoints recommended by the FDA and EMA. There was considerable agreement of weekly responder rates between AR and the FDA and EMA endpoints (on average, 70%–76% and 71%–82% of weeks with agreement, respectively). Conclusions AR bridges IBS-C clinical trials, putting into perspective the disparate primary endpoints recommended by professional societies and regulatory authorities, and allowing researchers, practitioners, and regulators to compare trial results. PMID:25653859

  4. Specialized mouse embryonic stem cells for studying vascular development.

    PubMed

    Glaser, Drew E; Burns, Andrew B; Hatano, Rachel; Medrzycki, Magdalena; Fan, Yuhong; McCloskey, Kara E

    2014-01-01

    Vascular progenitor cells are desirable in a variety of therapeutic strategies; however, the lineage commitment of endothelial and smooth muscle cell from a common progenitor is not well-understood. Here, we report the generation of the first dual reporter mouse embryonic stem cell (mESC) lines designed to facilitate the study of vascular endothelial and smooth muscle development in vitro. These mESC lines express green fluorescent protein (GFP) under the endothelial promoter, Tie-2, and Discomsoma sp. red fluorescent protein (RFP) under the promoter for alpha-smooth muscle actin (α-SMA). The lines were then characterized for morphology, marker expression, and pluripotency. The mESC colonies were found to exhibit dome-shaped morphology, alkaline phosphotase activity, as well as expression of Oct 3/4 and stage-specific embryonic antigen-1. The mESC colonies were also found to display normal karyotypes and are able to generate cells from all three germ layers, verifying pluripotency. Tissue staining confirmed the coexpression of VE (vascular endothelial)-cadherin with the Tie-2 GFP+ expression on endothelial structures and smooth muscle myosin heavy chain with the α-SMA RFP+ smooth muscle cells. Lastly, it was verified that the developing mESC do express Tie-2 GFP+ and α-SMA RFP+ cells during differentiation and that the GFP+ cells colocalize with the vascular-like structures surrounded by α-SMA-RFP cells. These dual reporter vascular-specific mESC permit visualization and cell tracking of individual endothelial and smooth muscle cells over time and in multiple dimensions, a powerful new tool for studying vascular development in real time.

  5. Histone H1 Depletion Impairs Embryonic Stem Cell Differentiation

    PubMed Central

    Cao, Kaixiang; Krauth, Beth; Ho, Po-Yi; Medrzycki, Magdalena; Berhe, Dawit T.; Pan, Chenyi; McDevitt, Todd C.; Fan, Yuhong

    2012-01-01

    Pluripotent embryonic stem cells (ESCs) are known to possess a relatively open chromatin structure; yet, despite efforts to characterize the chromatin signatures of ESCs, the role of chromatin compaction in stem cell fate and function remains elusive. Linker histone H1 is important for higher-order chromatin folding and is essential for mammalian embryogenesis. To investigate the role of H1 and chromatin compaction in stem cell pluripotency and differentiation, we examine the differentiation of embryonic stem cells that are depleted of multiple H1 subtypes. H1c/H1d/H1e triple null ESCs are more resistant to spontaneous differentiation in adherent monolayer culture upon removal of leukemia inhibitory factor. Similarly, the majority of the triple-H1 null embryoid bodies (EBs) lack morphological structures representing the three germ layers and retain gene expression signatures characteristic of undifferentiated ESCs. Furthermore, upon neural differentiation of EBs, triple-H1 null cell cultures are deficient in neurite outgrowth and lack efficient activation of neural markers. Finally, we discover that triple-H1 null embryos and EBs fail to fully repress the expression of the pluripotency genes in comparison with wild-type controls and that H1 depletion impairs DNA methylation and changes of histone marks at promoter regions necessary for efficiently silencing pluripotency gene Oct4 during stem cell differentiation and embryogenesis. In summary, we demonstrate that H1 plays a critical role in pluripotent stem cell differentiation, and our results suggest that H1 and chromatin compaction may mediate pluripotent stem cell differentiation through epigenetic repression of the pluripotency genes. PMID:22589736

  6. [The comparison of biologic character between mouse embryonic fibroblast and human embryonic fibroblast].

    PubMed

    Zhang, Yi; Zhao, Liansan; Wang, Chengxiao; Lei, Binjun

    2003-06-01

    To evaluate the feasibility of using human embryonic fibroblast(HEF) as feeder layer in the culture of human embryonic stem(ES) cells in vitro, we investigated the morphology, the sensitivity to 0.25% trypsin, the growth curve and cell cycle of HEF with DMEM(low glucose) +10% FBS used as culture medium, and then we compared HEF with mouse embryonic fibroblast (MEF). The results showed that both HEF and MEF are adherent cells in vitro, and HEF has longer life span and better growth ability than MEF. In room temperature, HEF is more sensitive to 0.25% trypsin. Our research suggested that HEF can be used as feeder layer in culture of ES cells. HEF has longer service life than MEF and is worthy to be studied further.

  7. Cell cycle regulation of embryonic stem cells and mouse embryonic fibroblasts lacking functional Pax7

    PubMed Central

    Czerwinska, Areta M.; Nowacka, Joanna; Aszer, Magdalena; Fogtman, Anna; Iwanicka-Nowicka, Roksana; Jańczyk-Ilach, Katarzyna; Ciemerych, Maria A.; Grabowska, Iwona

    2016-01-01

    ABSTRACT The transcription factor Pax7 plays a key role during embryonic myogenesis and in adult organisms in that it sustains the proper function of satellite cells, which serve as adult skeletal muscle stem cells. Recently we have shown that lack of Pax7 does not prevent the myogenic differentiation of pluripotent stem cells. In the current work we show that the absence of functional Pax7 in differentiating embryonic stem cells modulates cell cycle facilitating their proliferation. Surprisingly, deregulation of Pax7 function also positively impacts at the proliferation of mouse embryonic fibroblasts. Such phenotypes seem to be executed by modulating the expression of positive cell cycle regulators, such as cyclin E. PMID:27610933

  8. Hairy black holes and the endpoint of AdS4 charged superradiance

    NASA Astrophysics Data System (ADS)

    Dias, Óscar J. C.; Masachs, Ramon

    2017-02-01

    We construct hairy black hole solutions that merge with the anti-de Sitter (AdS4) Reissner-Nordström black hole at the onset of superradiance. These hairy black holes have, for a given mass and charge, higher entropy than the corresponding AdS4-Reissner-Nordström black hole. Therefore, they are natural candidates for the endpoint of the charged superradiant instability. On the other hand, hairy black holes never dominate the canonical and grand-canonical ensembles. The zero-horizon radius of the hairy black holes is a soliton (i.e. a boson star under a gauge transformation). We construct our solutions perturbatively, for small mass and charge, so that the properties of hairy black holes can be used to testify and compare with the endpoint of initial value simulations. We further discuss the near-horizon scalar condensation instability which is also present in global AdS4-Reissner-Nordström black holes. We highlight the different nature of the near-horizon and superradiant instabilities and that hairy black holes ultimately exist because of the non-linear instability of AdS.

  9. Using an Ecosystem Approach to complement protection schemes based on organism-level endpoints.

    PubMed

    Bradshaw, Clare; Kapustka, Lawrence; Barnthouse, Lawrence; Brown, Justin; Ciffroy, Philippe; Forbes, Valery; Geras'kin, Stanislav; Kautsky, Ulrik; Bréchignac, François

    2014-10-01

    Radiation protection goals for ecological resources are focussed on ecological structures and functions at population-, community-, and ecosystem-levels. The current approach to radiation safety for non-human biota relies on organism-level endpoints, and as such is not aligned with the stated overarching protection goals of international agencies. Exposure to stressors can trigger non-linear changes in ecosystem structure and function that cannot be predicted from effects on individual organisms. From the ecological sciences, we know that important interactive dynamics related to such emergent properties determine the flows of goods and services in ecological systems that human societies rely upon. A previous Task Group of the IUR (International Union of Radioecology) has presented the rationale for adding an Ecosystem Approach to the suite of tools available to manage radiation safety. In this paper, we summarize the arguments for an Ecosystem Approach and identify next steps and challenges ahead pertaining to developing and implementing a practical Ecosystem Approach to complement organism-level endpoints currently used in radiation safety.

  10. General description of electromagnetic radiation processes based on instantaneous charge acceleration in ''endpoints''

    SciTech Connect

    James, Clancy W.; Falcke, Heino; Huege, Tim; Ludwig, Marianne

    2011-11-15

    We present a methodology for calculating the electromagnetic radiation from accelerated charged particles. Our formulation - the 'endpoint formulation' - combines numerous results developed in the literature in relation to radiation arising from particle acceleration using a complete, and completely general, treatment. We do this by describing particle motion via a series of discrete, instantaneous acceleration events, or 'endpoints', with each such event being treated as a source of emission. This method implicitly allows for particle creation and destruction, and is suited to direct numerical implementation in either the time or frequency domains. In this paper we demonstrate the complete generality of our method for calculating the radiated field from charged particle acceleration, and show how it reduces to the classical named radiation processes such as synchrotron, Tamm's description of Vavilov-Cherenkov, and transition radiation under appropriate limits. Using this formulation, we are immediately able to answer outstanding questions regarding the phenomenology of radio emission from ultra-high-energy particle interactions in both the earth's atmosphere and the moon. In particular, our formulation makes it apparent that the dominant emission component of the Askaryan effect (coherent radio-wave radiation from high-energy particle cascades in dense media) comes from coherent 'bremsstrahlung' from particle acceleration, rather than coherent Vavilov-Cherenkov radiation.

  11. Contaminant effect endpoints in terrestrial vertebrates at and above the individual level

    USGS Publications Warehouse

    Rattner, B.A.; Cohen, J.B.; Golden, N.H.; Albers, P.H.; Heinz, G.H.; Ohlendorf, H.M.

    2000-01-01

    Use of biochemical, physiological, anatomical, reproductive and behavioral characteristics of wild terrestrial vertebrates to assess contaminant exposure and effects has become commonplace over the past 3 decades. At the level of the individual organism, response patterns have been associated with and sometimes causally linked to contaminant exposure. However, such responses at the organismal level are rarely associated with or causally linked to effects at the population level. Although the ultimate goal of ecotoxicology is the protection of populations, communities, and ecosystems, most of the existing science and regulatory legislation focus on the level of the individual. Consequently, much of this overview concentrates on contaminant effects at the organismal level, with some extrapolation to higher-level effects. In this chapter, we review the state of the science for the evaluation of biotic end-points used to assess contaminant exposure and effects at or above the level of the individual. In addition, we describe extant contaminant concentration thresholds, guidelines, or standards (toxicant criteria) in environmental matrices (e.g., water, soil, sediment, foods) that have been developed to protect wild terrestrial vertebrates. Suggestions are provided to develop and embellish the use and value of such endpoints and criteria for extrapolation of effects to higher levels of biological organization. Increasing focus on populations, communities, and ecosystems is needed to develop biologically meaningful regulatory guidelines that will protect natural resources.

  12. Safety and Efficacy Endpoints for Mesenchymal Stromal Cell Therapy in Renal Transplant Recipients

    PubMed Central

    Bank, J. R.; Rabelink, T. J.; de Fijter, J. W.; Reinders, M. E. J.

    2015-01-01

    Despite excellent short-term graft survival after renal transplantation, the long-term graft outcome remains compromised. It has become evident that a combination of sustained alloreactivity and calcineurin-inhibitor- (CNI-) related nephrotoxicity results in fibrosis and consequently dysfunction of the graft. New immunosuppressive regimens that can minimize or eliminate side effects, while maintaining efficacy, are required to improve long-term graft survival. In this perspective mesenchymal stromal cells (MSCs) are an interesting candidate, since MSCs have immunosuppressive and regenerative properties. The first clinical trials with MSCs in renal transplantation showed safety and feasibility and displayed promising results. Recently, the first phase II studies have been started. One of the most difficult and challenging aspects in those early phase trials is to define accurate endpoints that can measure safety and efficacy of MSC treatment. Since both graft losses and acute rejection rates declined, alternative surrogate markers such as renal function, histological findings, and immunological markers are used to measure efficacy and to provide mechanistic insight. In this review, we will discuss the current status of MSCs in renal transplantation with a focus on the endpoints used in the different experimental and clinical studies. PMID:26258149

  13. Challenges to the Therapeutic Pipeline for Irritable Bowel Syndrome: Endpoints and Regulatory Hurdles

    PubMed Central

    Camilleri, Michael; Chang, Lin

    2008-01-01

    Recent advances in our understanding of basic neuroenteric mechanisms and the role of effectors and transmitters in the brain-gut axis have provided opportunities to develop new therapeutic agents for irritable bowel syndrome (IBS). Furthermore, human pharmacodynamic studies utilizing transit, colonic or rectal sensitivity, and brain imaging have been useful in determining therapeutic efficacy (particularly for drugs that act on motor function). This review provides an overview of medications that have not yet been approved for treatment of patients with IBS, yet have shown promise in phase IIB trials. These include drugs that act on the serotonin receptor and transporter system, antidepressants, norepinephrine reuptake inhibitors, opioids, cholecystokinin antagonists, neurokinin-antagonists, chloride channel activators, guanylate cyclase C agonists, atypical benzodiazepines, probiotics and antibiotics. The changing landscape in the regulatory approval process has impacted the development of IBS drugs. Guidance documents from regulatory agencies in Europe and the United States have focused on patients’ reported outcomes and associated quality of life. After a decade of experience with different endpoints that have generated some data on psychometric validation and unprecedented information about responsiveness of the binary or global endpoints to drug therapy, it is necessary to pursue further validation studies before or during pivotal phase IIB or III trials. The hope of providing relief to patients should galvanize all parties to achieve these goals. PMID:18848833

  14. The sleep apnea cardiovascular endpoints (SAVE) trial: Rationale and start-up phase.

    PubMed

    McEvoy, R Doug; Anderson, Craig S; Antic, Nick A; Chen, Baoyuan; He, Quanying; Heeley, Emma; Huang, Shaoguang; Huang, Yining; Wang, Jiguang; Zhong, Nanshan

    2010-09-01

    THE SLEEP APNEA CARDIOVASCULAR ENDPOINTS (SAVE) STUDY (CLINICAL TRIALS REGISTRATION NUMBER: NCT00738170) is an academic initiated and conducted, multinational, open, blinded endpoint, randomised controlled trial designed to determine whether treatment of obstructive sleep apnea (OSA) with continuous positive airways pressure (CPAP) can reduce the incidence of serious cardiovascular events in patients with established cardiovascular disease. The answer to this question is of major importance to populations undergoing ageing and lifestyle changes all over the world. The SAVE study brings together respiratory, sleep and cardiovascular clinician-scientists in a unique interdisciplinary collaborative effort with industry sponsors to conduct the largest and most ambitious clinical trial yet conducted in the field of sleep apnea, with a global recruitment target of 5000 patients. Following its launch in Australia and China in late 2008, SAVE has now entered a phase of international expansion with new recruitment networks being established in New Zealand, India and Latin America. This article describes the rationale for the SAVE study, the considerations behind its design, and progress thus far in establishing the recruitment network. The report emphasises the important role that Chinese sleep and cardiovascular investigators have played in the start-up phase of this landmark international project.

  15. Environmental phthalate exposure in relation to reproductive outcomes and other health endpoints in humans.

    PubMed

    Swan, Shanna H

    2008-10-01

    After briefly discussing human exposure to phthalates--diesters of 1,2-benzenedicarboxylic acid (phthalic acid)--this article first presents recent findings from the Study for Future Families, a multi-center pregnancy study in which the human analogue of the phthalate syndrome was first identified. This is one of an increasing number of studies that have investigated human endpoints in relation to environmental exposure to these ubiquitous compounds. This literature, which includes a range of human health endpoints following prenatal, neonatal, childhood, and adult exposures, is then summarized. At least one significant association has been reported for urinary metabolites of di-n-butyl phthalate (DBP), butylbenzyl phthalate (BzBP), diethyl phthlate (DEP), and di-isononyl phthalate (DINP) and for three of the urinary metabolites of di(2-ethylhexyl) phthalate (DEHP). Many of the findings reported in humans--most of which have been in males--are consistent with the anti-androgenic action that has been demonstrated for several phthalates. Replication of the results described here and further mechanistic studies are needed to strengthen links between phthalates and adverse health outcomes.

  16. One-stage and two-stage designs for phase II clinical trials with survival endpoints.

    PubMed

    Whitehead, John

    2014-09-28

    This work is motivated by trials in rapidly lethal cancers or cancers for which measuring shrinkage of tumours is infeasible. In either case, traditional phase II designs focussing on tumour response are unsuitable. Usually, tumour response is considered as a substitute for the more relevant but longer-term endpoint of death. In rapidly lethal cancers such as pancreatic cancer, there is no need to use a surrogate, as the definitive endpoint is (sadly) available so soon. In uveal cancer, there is no counterpart to tumour response, and so, mortality is the only realistic response available. Cytostatic cancer treatments do not seek to kill tumours, but to mitigate their effects. Trials of such therapy might also be based on survival times to death or progression, rather than on tumour shrinkage. Phase II oncology trials are often conducted with all study patients receiving the experimental therapy, and this approach is considered here. Simple extensions of one-stage and two-stage designs based on binary responses are presented. Outcomes based on survival past a small number of landmark times are considered: here, the case of three such times is explored in examples. This approach allows exact calculations to be made for both design and analysis purposes. Simulations presented here show that calculations based on normal approximations can lead to loss of power when sample sizes are small. Two-stage versions of the procedure are also suggested.

  17. Special endpoint and product specific considerations in pharmaceutical acceptable daily exposure derivation.

    PubMed

    Gould, Janet; Callis, Courtney M; Dolan, David G; Stanard, Brad; Weideman, Patricia A

    2016-08-01

    Recently, a guideline has been published by the European Medicines Agency (EMA) on setting safe limits, permitted daily exposures (PDE) [also called acceptable daily exposures (ADE)], for medicines manufactured in multi-product facilities. The ADE provides a safe exposure limit for inadvertent exposure of a drug due to cross-contamination in manufacturing. The ADE determination encompasses a standard risk assessment, requiring an understanding of the toxicological and pharmacological effects, the mechanism of action, drug compound class, and the dose-response as well as the pharmacokinetic properties of the compound. While the ADE concept has broad application in pharmaceutical safety there are also nuances and specific challenges associated with some toxicological endpoints or drug product categories. In this manuscript we discuss considerations for setting ADEs when the following specific adverse health endpoints may constitute the critical effect: genotoxicity, developmental and reproductive toxicity (DART), and immune system modulation (immunostimulation or immunosuppression), and for specific drug classes, including antibody drug conjugates (ADCs), emerging medicinal therapeutic compounds, and compounds with limited datasets. These are challenging toxicological scenarios that require a careful evaluation of all of the available information in order to establish a health-based safe level.

  18. Transcriptomics-based identification of developmental toxicants through their interference with cardiomyocyte differentiation of embryonic stem cells

    SciTech Connect

    Dartel, Dorien A.M. van; Pennings, Jeroen L.A.; Schooten, Frederik J. van; Piersma, Aldert H.

    2010-03-15

    The embryonic stem cell test (EST) predicts developmental toxicity based on the inhibition of cardiomyocyte differentiation of embryonic stem cells (ESC). The subjective endpoint, the long culture duration together with the undefined applicability domain and related predictivity need further improvement to facilitate implementation of the EST into regulatory strategies. These aspects may be improved by studying gene expression changes in the ESC differentiation cultures and their modulation by compound exposure using transcriptomics. Here, we tested the developmental toxicants monobutyl phthalate and 6-aminonicotinamide. ESC were allowed to differentiated, and cardiomyocyte differentiation was assessed after 10 days of culture. RNA of solvent controls was collected after 0, 24, 48, 72 and 96 h of exposure, and RNA of developmental-toxicant-exposed cultures was collected after 24 and 96 h. Samples were hybridized to DNA microarrays, and 1355 genes were found differentially expressed among the unexposed experimental groups. These regulated genes were involved in differentiation-related processes, and Principal Component Analysis (PCA) based on these genes showed that the unexposed experimental groups appeared in chronological order in the PCA, which can therefore be regarded as a continuous representation of the differentiation track. The developmental-toxicant-exposed cultures appeared to deviate significantly from this differentiation track, which confirms the compound-modulating effects on the differentiation process. The incorporation of transcriptomics in the EST is expected to provide a more informative and improved endpoint in the EST as compared with morphology, allowing early detection of differentiation modulation. Furthermore, this approach may improve the definition of the applicability domain and predictivity of the EST.

  19. UST-ID robotics: Wireless communication and minimum conductor technology, and end-point tracking technology surveys

    SciTech Connect

    Holliday, M.A.

    1993-10-01

    This report is a technology review of the current state-of-the-art in two technologies applicable to the Underground Storage Tank (UST) program at the Hanford Nuclear Reservation. The first review is of wireless and minimal conductor technologies for in-tank communications. The second review is of advanced concepts for independent tool-point tracking. This study addresses the need to provide wireless transmission media or minimum conductor technology for in-tank communications and robot control. At present, signals are conducted via contacting transmission media, i.e., cables. Replacing wires with radio frequencies or invisible light are commonplace in the communication industry. This technology will be evaluated for its applicability to the needs of robotics. Some of these options are radio signals, leaky coax, infrared, microwave, and optical fiber systems. Although optical fiber systems are contacting transmission media, they will be considered because of their ability to reduce the number of conductors. In this report we will identify, evaluate, and recommend the requirements for wireless and minimum conductor technology to replace the present cable system. The second section is a technology survey of concepts for independent end-point tracking (tracking the position of robot end effectors). The position of the end effector in current industrial robots is determined by computing that position from joint information, which is basically a problem of locating a point in three-dimensional space. Several approaches are presently being used in industrial robotics, including: stereo-triangulation with a theodolite network and electrocamera system, photogrammetry, and multiple-length measurement with laser interferometry and wires. The techniques that will be evaluated in this survey are advanced applications of the aforementioned approaches. These include laser tracking (3-D and 5-D), ultrasonic tracking, vision-guided servoing, and adaptive robotic visual tracking.

  20. International Cartilage Repair Society (ICRS) Recommended Guidelines for Histological Endpoints for Cartilage Repair Studies in Animal Models and Clinical Trials

    PubMed Central

    Hoemann, Caroline; Kandel, Rita; Roberts, Sally; Saris, Daniel B.F.; Creemers, Laura; Mainil-Varlet, Pierre; Méthot, Stephane; Hollander, Anthony P.; Buschmann, Michael D.

    2011-01-01

    Cartilage repair strategies aim to resurface a lesion with osteochondral tissue resembling native cartilage, but a variety of repair tissues are usually observed. Histology is an important structural outcome that could serve as an interim measure of efficacy in randomized controlled clinical studies. The purpose of this article is to propose guidelines for standardized histoprocessing and unbiased evaluation of animal tissues and human biopsies. Methods were compiled from a literature review, and illustrative data were added. In animal models, treatments are usually administered to acute defects created in healthy tissues, and the entire joint can be analyzed at multiple postoperative time points. In human clinical therapy, treatments are applied to developed lesions, and biopsies are obtained, usually from a subset of patients, at a specific time point. In striving to standardize evaluation of structural endpoints in cartilage repair studies, 5 variables should be controlled: 1) location of biopsy/sample section, 2) timing of biopsy/sample recovery, 3) histoprocessing, 4) staining, and 5) blinded evaluation with a proper control group. Histological scores, quantitative histomorphometry of repair tissue thickness, percentage of tissue staining for collagens and glycosaminoglycan, polarized light microscopy for collagen fibril organization, and subchondral bone integration/structure are all relevant outcome measures that can be collected and used to assess the efficacy of novel therapeutics. Standardized histology methods could improve statistical analyses, help interpret and validate noninvasive imaging outcomes, and permit cross-comparison between studies. Currently, there are no suitable substitutes for histology in evaluating repair tissue quality and cartilaginous character. PMID:26069577

  1. [Microglial cells and development of the embryonic central nervous system].

    PubMed

    Legendre, Pascal; Le Corronc, Hervé

    2014-02-01

    Microglia cells are the macrophages of the central nervous system with a crucial function in the homeostasis of the adult brain. However, recent studies showed that microglial cells may also have important functions during early embryonic central nervous system development. In this review we summarize recent works on the extra embryonic origin of microglia, their progenitor niche, the pattern of their invasion of the embryonic central nervous system and on interactions between embryonic microglia and their local environment during invasion. We describe microglial functions during development of embryonic neuronal networks, including their roles in neurogenesis, in angiogenesis and developmental cell death. These recent discoveries open a new field of research on the functions of neural-microglial interactions during the development of the embryonic central nervous system.

  2. Volumetric optical mapping in early embryonic hearts using light-sheet microscopy

    PubMed Central

    Ma, Pei; Chan, Dennis C.; Gu, Shi; Watanabe, Michiko; Jenkins, Michael W.; Rollins, Andrew M.

    2016-01-01

    Optical mapping (OM) of electrical activity using voltage-sensitive fluorescent dyes is a powerful tool for the investigation of embryonic cardiac electrophysiology. However, because conventional OM integrates the signal in depth and projects it to a two-dimensional plane, information acquired is incomplete and dependent upon the orientation of the sample. This complicates interpretation of data, especially when comparing one heart to another. To overcome this limitation, we present volumetric OM using light-sheet microscopy, which enables high-speed capture of optically sectioned slices. Voltage-sensitive fluorescence images from multiple planes across entire early embryonic quail hearts were acquired, and complete, orientation-independent, four-dimensional maps of transmembrane potential are demonstrated. Volumetric OM data were collected while using optical pacing to control the heart rate, paving the way for physiological measurements and precise manipulation of the heartbeat in the future. PMID:28018729

  3. Wls is expressed in the epidermis and regulates embryonic hair follicle induction in mice.

    PubMed

    Huang, Sixia; Zhu, Xuming; Liu, Yanfang; Tao, Yixin; Feng, Guoyin; He, Lin; Guo, Xizhi; Ma, Gang

    2012-01-01

    Wnt proteins are secreted molecules that play multiple roles during hair follicle development and postnatal hair cycling. Wntless (Wls) is a cargo protein required for the secretion of various Wnt ligands. However, its role during hair follicle development and hair cycling remains unclear. Here, we examined the expression of Wls during hair follicle induction and postnatal hair cycling. We also conditionally deleted Wls with K14-cre to investigate its role in hair follicle induction. K14-cre;Wls(c/c) mice exhibited abnormal hair follicle development, which is possibly caused by impaired canonical Wnt signaling. Meanwhile, Wnt5a is also expressed in embryonic epidermis, but Wnt5a null mice showed no significant defect in embryonic hair follicle morphogenesis. Therefore, Wls may regulate hair follicle induction by mediating the Wnt/β-catenin pathway.

  4. The Genetic and Epigenetic Journey of Embryonic Stem Cells into Mature Neural Cells

    PubMed Central

    Olynik, Brendan M.; Rastegar, Mojgan

    2012-01-01

    Epigenetic changes occur throughout life from embryonic development into adulthood. This results in the timely expression of developmentally important genes, determining the morphology and identity of different cell types and tissues within the body. Epigenetics regulate gene expression and cellular morphology through multiple mechanisms without alteration in the underlying DNA sequences. Different epigenetic mechanisms include chromatin condensation, post-translational modification of histone proteins, DNA cytosine marks, and the activity of non-coding RNA molecules. Epigenetics play key roles in development, stem cell differentiation, and have high impact in human disease. In this review, we will discuss our current knowledge about these epigenetic mechanisms, with a focus on histone and DNA marks. We will then talk about the genetics and epigenetics of embryonic stem cell self-renewal and differentiation into neural stem cells, and further into specific neuronal cell types. PMID:22629283

  5. Root length of aquatic plant, Lemna minor L., as an optimal toxicity endpoint for biomonitoring of mining effluents.

    PubMed

    Gopalapillai, Yamini; Vigneault, Bernard; Hale, Beverley A

    2014-10-01

    Lemna minor, a free-floating macrophyte, is used for biomonitoring of mine effluent quality under the Metal Mining Effluent Regulations (MMER) of the Environmental Effects Monitoring (EEM) program in Canada and is known to be sensitive to trace metals commonly discharged in mine effluents such as Ni. Environment Canada's standard toxicity testing protocol recommends frond count (FC) and dry weight (DW) as the 2 required toxicity endpoints-this is similar to other major protocols such as those by the US Environmental Protection Agency (USEPA) and the Organisation for Economic Co-operation and Development (OECD)-that both require frond growth or biomass endpoints. However, we suggest that similar to terrestrial plants, average root length (RL) of aquatic plants will be an optimal and relevant endpoint. As expected, results demonstrate that RL is the ideal endpoint based on the 3 criteria: accuracy (i.e., toxicological sensitivity to contaminant), precision (i.e., lowest variance), and ecological relevance (metal mining effluents). Roots are known to play a major role in nutrient uptake in conditions of low nutrient conditions-thus having ecological relevance to freshwater from mining regions. Root length was the most sensitive and precise endpoint in this study where water chemistry varied greatly (pH and varying concentrations of Ca, Mg, Na, K, dissolved organic carbon, and an anthropogenic organic contaminant, sodium isopropyl xanthates) to match mining effluent ranges. Although frond count was a close second, dry weight proved to be an unreliable endpoint. We conclude that toxicity testing for the floating macrophyte should require average RL measurement as a primary endpoint.

  6. Monolayer cultivation of osteoprogenitors shortens duration of the embryonic stem cell test while reliably predicting developmental osteotoxicity.

    PubMed

    zur Nieden, Nicole I; Davis, Lesley A; Rancourt, Derrick E

    2010-11-09

    Osteotoxic compounds administered during pregnancy can initiate skeletal congenital anomalies in the embryo. In vitro, developmental osteotoxicity of a compound can be predicted with the embryonic stem cell test (EST), the only in vitro embryotoxicity model identified to date that entirely abrogates the use of animals. Although the previously identified endpoint osteocalcin mRNA expression robustly predicts developmental osteotoxicity, it can only be assayed after 5 weeks of in vitro culture with existing embryoid body (EB)-based differentiation protocols. Therefore, the goal of this study was to characterize novel earlier endpoints of developmental osteotoxicity for the EST. The currently used EB-based differentiation protocol was modified so that a monolayer culture of pre-differentiated cells was inoculated. The expression profile of five bone-specific mRNAs, including osteocalcin, over the course of 30 differentiation days suggested an acceleration of pre-osteoblast specification in the monolayer over the EB-based protocol. Similarly, calcification was already visible after 14 days of culture in monolayer cultures. Employing image and absorption-based techniques to measure the degree of mineralization in these cells after compound treatment, the three compounds Penicillin G, 5-fluorouracil (5-FU) and all-trans retinoic acid (RA) were then tested after 14 days in monolayer cultures and compared to embryoid body-based differentiations at day 30. By modifying the culture the three test substances were classified correctly into non- or strong osteotoxic. Moreover, we were successful in shortening the assay duration from 30 to 14 days.

  7. Effects of androstenedione exposure on fathead minnow (Pimephales promelas) reproduction and embryonic development.

    PubMed

    DeQuattro, Zachary A; Hemming, Jocelyn D C; Barry, Terence P

    2015-11-01

    High concentrations (300 ng/L) of androstenedione (A4) were identified in snowmelt runoff from fields fertilized with manure from livestock feeding operations in Wisconsin, USA. In fishes, A4 is an active androgen and substrate for biosynthesis of functional androgens (e.g., testosterone and 11-ketotestosterone) and estrogens (e.g., estradiol-17β). Thus, A4 has the potential to be a powerful endocrine disruptor. This hypothesis was tested by exposing reproductively mature fathead minnows to 0.0 ng/L, 4.5 ng/L, 74 ng/L, and 700 ng/L A4 for 26 d in a flow-through system. Various reproductive endpoints were measured including fecundity, fertilization success, secondary sexual characteristics, gonadosomatic index (GSI), and hepatic vitellogenin messenger RNA (mRNA) expression. In addition, fertilized embryos from the reproduction assay were used in an embryonic development assay to assess A4 effects on development and hatchability. In males, A4 significantly increased Vtg mRNA expression (estrogenic effect), significantly reduced GSI, and had no effect on tubercle expression (p = 0.067). In females, A4 induced tubercle development (androgenic effect) with no effects on GSI. Fecundity was not significantly impacted. Exposure to A4 had no effect on fertilization, embryonic development, or hatchability. These data indicate that exogenous A4, at environmentally relevant concentrations, can significantly modulate the reproductive physiology of the fathead minnows in a sex-specific manner and that A4 should be monitored as an endocrine disruptor.

  8. Maternal diet programs embryonic kidney gene expression.

    PubMed

    Welham, Simon J M; Riley, Paul R; Wade, Angie; Hubank, Mike; Woolf, Adrian S

    2005-06-16

    Human epidemiological data associating birth weight with adult disease suggest that organogenesis is "programmed" by maternal diet. In rats, protein restriction in pregnancy produces offspring with fewer renal glomeruli and higher systemic blood pressures than controls. We tested the hypothesis that maternal diet alters gene expression in the metanephros, the precursor of the definitive mammalian kidney. We demonstrated that maternal low-protein diet initiated when pregnancy starts and maintained to embryonic day 13, when the metanephros consists of mesenchyme surrounding a once-branched ureteric bud, is sufficient to significantly reduce glomerular numbers in offspring by about 20%. As assessed by representational difference analyses and real-time quantitative polymerase chain reactions, low-protein diet modulated gene expression in embryonic day 13 metanephroi. In particular, levels of prox-1, the ortholog of Drosophila transcription factor prospero, and cofilin-1, a regulator of the actin cytoskeleton, were reduced. During normal metanephrogenesis, prox-1 protein was first detected in mesenchymal cells around the ureteric tree and thereafter in nascent nephron epithelia, whereas cofilin-1 immunolocalized to bud derivatives and condensing mesenchyme. Previously, we reported that low-protein diets increased mesenchymal apoptosis cells when metanephrogenesis began and thereafter reduced numbers of precursor cells. Collectively, these studies prove that the maternal diet programs the embryonic kidney, altering cell turnover and gene expression at a time when nephrons and glomeruli have yet to form. The human implication is that the maternal diet ingested between conception and 5- 6-wk gestation contributes to the variation in glomerular numbers that are known to occur between healthy and hypertensive populations.

  9. Embryonic in vivo electroporation in the mouse.

    PubMed

    Saito, Tetsuichiro

    2010-01-01

    Electroporation combined with surgery is a quick and highly efficient method to transfect nucleic acids into various embryonic tissues in a spatiotemporally restricted manner. Forceps-type electrodes facilitate transfection by delivering electric pulses from outside of the embryo. Many electroporated embryos survive in the pregnant mouse, are born, and are reared. The developing central nervous system (CNS) is a good target for transfection, because there are many neural progenitors adjacent to the ventricle, into which nucleic acids are relatively easily injected. The expression of transfected genes persists in neurons for months.

  10. [Ethical aspects of embryonic stem cell research].

    PubMed

    Kostka, U

    2002-11-01

    Research using embryonic stem cells raises a variety of ethical questions, which will be explored in this article. At the core of the ethical controversy is the question of the status of the embryo and its availability for research. A range of countries have approved the use of "supernumerous" embryos from in-vitro fertilization. But ethical problems also arise in reproduction medicine, the informed consent of affected couples, and the targeted production of embryos and egg cell donation for research. The author discuss some of these neglected issues and develops suggestions for comprehensive ethical reflection.

  11. Imaging embryonic morphogenesis in C. elegans.

    PubMed

    Hardin, Jeff

    2011-01-01

    The Caenorhabditis elegans embryo is well suited to morphogenetic analysis via modern microscopy, due to its short generation time, transparency, invariant lineage, and the ability to generate transgenic embryos expressing various fluorescent proteins. This chapter provides an overview of microscopy techniques for imaging embryonic morphogenesis, including making agar mounts, capturing four-dimensional (4D) data using Nomarski microscopy, imaging of actin in embryos, factors important for optimizing 4D fluorescence microscopy, and recent techniques that leverage fluorescence microscopy for intracellular imaging of cellular components during morphogenesis.

  12. Using endophenotypes to examine molecules related to candidate genes as novel therapeutics: The "endophenotype-associated surrogate endpoint (EASE)" concept.

    PubMed

    Yamasue, Hidenori

    2015-10-01

    In this article, a new concept of an "endophenotype-associated surrogate endpoint (EASE)" is proposed. To examine effect of a novel therapeutic molecule on a target phenotype of a genotype associated with the molecule, state-dependent aspect of an endophenotype can be used as a surrogate endpoint. Desired characteristics for EASE are (1) a close relationship to the endophenotype associated with therapeutics, (2) longitudinal changes in illness severity, while the original "endophenotype" is primarily state independent, (3) a physical sign or laboratory measurement that occurs in association with a pathological process and has putative diagnostic and/or prognostic utility, and (4) serves as a substitute for a clinically meaningful endpoint. Advantages are expected for both surrogate endpoints in drug development and endophenotypes in uncovering pathogenesis. EASE are closer to molecules than clinically meaningful endpoints and can respond to administration of the molecule in a more direct manner. Therefore, a statistically significant effect is likely to be observed in clinical trials with smaller sample sizes and shorter durations. As with endophenotypes, reduced heterogeneity might be expected especially in heterogeneous syndromes such as psychiatric disorders. Potential interactions (e.g., elucidating biological mechanisms underlying novel treatments) can be further expected.

  13. Elastic collisions of classical point particles on a finite frictionless linear track with perfectly reflecting endpoints

    NASA Astrophysics Data System (ADS)

    DeLuca, R.

    2006-03-01

    Repeated elastic collisions of point particles on a finite frictionless linear track with perfectly reflecting endpoints are considered. The problem is analysed by means of an elementary linear algebra approach. It is found that, starting with a state consisting of a projectile particle in motion at constant velocity and a target particle at rest in a fixed known position, the points at which collisions occur on track, when plotted versus progressive numerals, corresponding to the collisions themselves, show periodic patterns for a rather large choice of values of the initial position x(0) and on the mass ratio r. For certain values of these parameters, however, only regular behaviour over a large number of collisions is detected.

  14. Bayesian decision sequential analysis with survival endpoint in phase II clinical trials.

    PubMed

    Zhao, Lili; Woodworth, George

    2009-04-30

    Chen and Chaloner (Statist. Med. 2006; 25:2956-2966. DOI: 10.1002/sim.2429) present a Bayesian stopping rule for a single-arm clinical trial with a binary endpoint. In some cases, earlier stopping may be possible by basing the stopping rule on the time to a binary event. We investigate the feasibility of computing exact, Bayesian, decision-theoretic time-to-event stopping rules for a single-arm group sequential non-inferiority trial relative to an objective performance criterion. For a conjugate prior distribution, exponential failure time distribution, and linear and threshold loss structures, we obtain the optimal Bayes stopping rule by backward induction. We compute frequentist operating characteristics of including Type I error, statistical power, and expected run length. We also briefly address design issues.

  15. Endpoint fragmentation index: a method for monitoring the evolution of microbial degradation of polysaccharide feedstocks.

    PubMed

    Green, Terrence R; Popa, Radu

    2011-02-01

    We describe a simple method for tracking the course of microbial degradation of polysaccharide-rich feedstocks. The method involves determining total polysaccharides present in the feedstock, measured in glucose equivalents, relative to the fractional component of polysaccharides exhibiting 2,3-dinitrosalycylic acid aldehyde activity. The ratio of total polysaccharide to aldehyde activity, defined as the end-point fragmentation (EPF) index, is then calculated and tracked as it shifts as microbial degradation of polysaccharide-rich feedstock progresses. While degradation occurs, the EPF index falls. It bottoms out at an asymptotic limit marking the point in time where further degradation of the polysaccharide-rich feedstock has ceased. The EPF index can be used to follow the progressive breakdown of composting polysaccharide-rich waste. It may also have applicability as a means of tracking the turnover of polysaccharides in other complex environments including soil, sediments, wetlands, and peat bogs.

  16. Probing electroweak physics for all B{yields}XM decays in the endpoint region

    SciTech Connect

    Chay, Junegone; Kim, Chul; Leibovich, Adam K.; Zupan, Jure

    2007-11-01

    Using soft-collinear effective theory we describe at leading order in 1/m{sub b} all the semi-inclusive hadronic B{yields}XM decays near the endpoint, where an energetic light meson M recoils against an inclusive jet X. Here we extend to the decays in which spectator quarks go into the jet X, and also include the decays involving {eta}, {eta}{sup '} mesons that receive additional contributions from gluonic operators. The predicted branching ratios and CP asymmetries depend on fewer hadronic parameters than the corresponding two-body B decays. This makes semi-inclusive hadronic B{yields}XM decays a powerful probe of the potential nonperturbative nature of charming penguins as well as a useful probe of new physics effects in electroweak flavor changing transitions. A comparison with B{yields}KX data from BABAR points to an enhanced charming penguin, albeit with large experimental errors.

  17. Comparison of three embryo culture methods for derivation of human embryonic stem cells from discarded embryos.

    PubMed

    Liu, Ying; Li, Yang; Hwang, Andrew; Wang, Shu-yu; Jia, Chan-wei; Yu, Lan; Li, Jian

    2011-06-01

    Human embryonic stem cells (hESC) are self-renewing and pluripotent cells that hold great promise. Our objective was to compare the effect of three different embryo culture methods for derivation of human embryonic stem cells from discarded embryos. A prospective and randomized trial was conducted using 381 discarded human embryos at days 2-3 postfertilization in Beijing Obstetrics and Gynecology Hospital IVF center. After removal of the zona pellucida, discarded human embryos were cultured by three different methods as multiple embryo aggregates, single embryo, and blastomeres. Outgrowth of embryos and hESC derivation were observed. The outgrowth rate of embryos cultured as multiple embryo aggregates was higher than that of those cultured as single embryos or blastomeres (p < 0.05). Three propagating hESC lines were derived from poor quality day 2-3 postfertilization nonblastocyst embryos cultured as multiple embryo aggregates. Derived hESC lines expressed hESC-specific markers of pluripotency and had normal diploid karyotype. The cells were able to form derivatives of all three germ layers in vivo as teratomas. Our results demonstrate that culturing these discarded embryos as multiple embryo aggregates was more profitable for outgrowth and derivation of ESC line than culturing these as single embryo or blastomeres.

  18. Establishment of Early Endpoints in Mouse Total-Body Irradiation Model

    PubMed Central

    Gulani, Jatinder; King, Gregory; Hieber, Kevin; Chappell, Mark; Ossetrova, Natalia

    2016-01-01

    Acute radiation sickness (ARS) following exposure to ionizing irradiation is characterized by radiation-induced multiorgan dysfunction/failure that refers to progressive dysfunction of two or more organ systems, the etiological agent being radiation damage to cells and tissues over time. Radiation sensitivity data on humans and animals has made it possible to describe the signs associated with ARS. A mouse model of total-body irradiation (TBI) has previously been developed that represents the likely scenario of exposure in the human population. Herein, we present the Mouse Intervention Scoring System (MISS) developed at the Veterinary Sciences Department (VSD) of the Armed Forces Radiobiology Research Institute (AFRRI) to identify moribund mice and decrease the numbers of mice found dead, which is therefore a more humane refinement to death as the endpoint. Survival rates were compared to changes in body weights and temperatures in the mouse (CD2F1 male) TBI model (6–14 Gy, 60Co γ-rays at 0.6 Gy min-1), which informed improvements to the Scoring System. Individual tracking of animals via implanted microchips allowed for assessment of criteria based on individuals rather than by group averages. From a total of 132 mice (92 irradiated), 51 mice were euthanized versus only four mice that were found dead (7% of non-survivors). In this case, all four mice were found dead after overnight periods between observations. Weight loss alone was indicative of imminent succumbing to radiation injury, however mice did not always become moribund within 24 hours while having weight loss >30%. Only one survivor had a weight loss of greater than 30%. Temperature significantly dropped only 2–4 days before death/euthanasia in 10 and 14 Gy animals. The score system demonstrates a significant refinement as compared to using subjective assessment of morbidity or death as the endpoint for these survival studies. PMID:27579862

  19. Correlation of Hip Fracture with Other Fracture Types: Toward a Rational Composite Hip Fracture Endpoint

    PubMed Central

    Colón-Emeric, Cathleen; Pieper, Carl F.; Grubber, Janet; Van Scoyoc, Lynn; Schnell, Merritt L; Van Houtven, Courtney Harold; Pearson, Megan; Lafleur, Joanne; Lyles, Kenneth W.; Adler, Robert A.

    2016-01-01

    Purpose With ethical requirements to the enrollment of lower risk subjects, osteoporosis trials are underpowered to detect reduction in hip fractures. Different skeletal sites have different levels of fracture risk and response to treatment. We sought to identify fracture sites which cluster with hip fracture at higher than expected frequency; if these sites respond to treatment similarly, then a composite fracture endpoint could provide a better estimate of hip fracture reduction. Methods Cohort study using Veterans Affairs and Medicare administrative data. Male Veterans (n=5,036,536) aged 50-99 years receiving VA primary care between1999-2009 were included. Fractures were ascertained using ICD9 and CPT codes and classified by skeletal site. Pearson correlation coefficients, logistic regression and kappa statistics, were used to describe the correlation between each fracture type and hip fracture within individuals, without regards to the timing of the events. Results 595,579 (11.8%) men suffered 1 or more fractures and 179,597 (3.6%) suffered 2 or more fractures during the time under study. Of those with one or more fractures, rib was the most common site (29%), followed by spine (22%), hip (21%) and femur (20%). The fracture types most highly correlated with hip fracture were pelvic/acetabular (Pearson correlation coefficient 0.25, p<0.0001), femur (0.15, p<0.0001), and shoulder (0.11, p<0.0001). Conclusions Pelvic, acetabular, femur, and shoulder fractures cluster with hip fractures within individuals at greater than expected frequency. If we observe similar treatment risk reductions within that cluster, subsequent trials could consider use of a composite endpoint to better estimate hip fracture risk. PMID:26151123

  20. Use of sublethal endpoints in sediment toxicity tests with the amphipod Hyalella azteca

    USGS Publications Warehouse

    Ingersoll, Chris G.; Brunson, Eric L.; Dwyer, F. James; Hardesty, Douglas K.; Kemble, Nile E.

    1998-01-01

    Short-term sediment toxicity tests that only measure effects on survival can be used to identify high levels of contamination but may not be able to identify marginally contaminated sediments. The objective of the present study was to develop a method for determining the potential sublethal effects of contaminants associated with sediment on the amphipod Hyalella azteca (e.g., reproduction). Exposures to sediment were started with 7- to 8-d-old amphipods. On day 28, amphipods were isolated from the sediment and placed in water-only chambers where reproduction was measured on day 35 and 42. Typically, amphipods were first in amplexus at about day 21 to 28 with release of the first brood between day 28 to 42. Endpoints measured included survival (day 28, 35, and 42), growth (as length and weight on day 28 and 42), and reproduction (number of young/female produced from day 28 to 42). This method was used to evaluate a formulated sediment and field-collected sediments with low to moderate concentrations of contaminants. Survival of amphipods in these sediments was typically >85% after the 28-d sediment exposures and the 14-d holding period in water to measure reproduction. Reproduction was more variable than growth; hence, more replicates might be needed to establish statistical differences among treatments. Previous studies have demonstrated that growth of H. azteca in sediment tests often provides unique information that can be used to discriminate toxic effects of exposure to contaminants. Either length or weight can be measured in sediment tests with H. azteca. However, additional statistical options are available if length is measured on individual amphipods, such as nested analysis of variance that can account for variance in length within replicates. Ongoing water-only studies testing select contaminants will provide additional data on the relative sensitivity and variability of sublethal endpoints in toxicity tests with H. azteca.

  1. Toward early safety alert endpoints: exploring biomarkers suggestive of microbicide failure.

    PubMed

    Mauck, Christine K; Lai, Jaim Jou; Weiner, Debra H; Chandra, Neelima; Fichorova, Raina N; Dezzutti, Charlene S; Hillier, Sharon L; Archer, David F; Creinin, Mitchell D; Schwartz, Jill L; Callahan, Marianne M; Doncel, Gustavo F

    2013-11-01

    Several microbicides, including nonoxynol-9 (N-9) and cellulose sulfate (CS), looked promising during early trials but failed in efficacy trials. We aimed to identify Phase I mucosal safety endpoints that might explain that failure. In a blinded, randomized, parallel trial, 60 healthy premenopausal sexually abstinent women applied Universal HEC placebo, 6% CS or 4% N-9 gel twice daily for 13½ days. Endpoints included immune biomarkers in cervicovaginal lavage (CVL) and endocervical cytobrushes, inflammatory infiltrates in vaginal biopsies, epithelial integrity by naked eye, colposcopy, and histology, CVL anti-HIV activity, vaginal microflora, pH, and adverse events. Twenty women enrolled per group. Soluble/cellular markers were similar with CS and placebo, except secretory leukocyte protease inhibitor (SLPI) levels decreased in CVL, and CD3(+) and CD45(+) cells increased in biopsies after CS use. Increases in interleukin (IL)-8, IL-1, IL-1RA, and myeloperoxidase (MPO) and decreases in SLPI were significant with N-9. CVL anti-HIV activity was significantly higher during CS use compared to N-9 or placebo. CS users tended to have a higher prevalence of intermediate Nugent score, Escherichia coli, and Enterococcus and fewer gram-negative rods. Most Nugent scores diagnostic for bacterial vaginosis were in N-9 users. All cases of histological inflammation or deep epithelial disruption occurred in N-9 users. While the surfactant N-9 showed obvious biochemical and histological signs of inflammation, more subtle changes, including depression of SLPI, tissue influx of CD45(+) and CD3(+) cells, and subclinical microflora shifts were associated with CS use and may help to explain the clinical failure of nonsurfactant microbicides.

  2. Predictors of Long‐term Clinical Endpoints in Patients With Refractory Angina

    PubMed Central

    Povsic, Thomas J.; Broderick, Samuel; Anstrom, Kevin J.; Shaw, Linda K.; Ohman, E. Magnus; Eisenstein, Eric L.; Smith, Peter K.; Alexander, John H.

    2015-01-01

    Background Clinical outcomes in patients with refractory angina (RA) are poorly characterized and variably described. Using the Duke Database for Cardiovascular Disease (DDCD), we explored characteristics that drive clinical endpoints in patients with class II to IV angina stabilized on medical therapy. Methods and Results We explored clinical endpoints and associated costs of patients who underwent catheterization at Duke University Medical Center from 1997 to 2010 for evaluation of coronary artery disease (CAD) and were found to have advanced CAD ineligible for additional revascularization, and were clinically stable for a minimum of 60 days. Of 77 257 cardiac catheterizations performed, 1908 patients met entry criteria. The 3‐year incidence of death; cardiac rehospitalization; and a composite of death, myocardial infarction, stroke, cardiac rehospitalization, and revascularization were 13.0%, 43.5%, and 52.2%, respectively. Predictors of mortality included age, ejection fraction (EF), low body mass index, multivessel CAD, low heart rate, diabetes, diastolic blood pressure, history of coronary artery bypass graft surgery, cigarette smoking, history of congestive heart failure (CHF), and race. Multivessel CAD, EF<45%, and history of CHF increased risk of mortality; angina class and prior revascularization did not. Total rehospitalization costs over a 3‐year period per patient were $10 185 (95% CI 8458, 11912) in 2012 US dollars. Conclusions Clinically stable patients with RA who are medically managed have a modest mortality, but a high incidence of hospitalization and resource use over 3 years. These findings point to the need for novel therapies aimed at symptom mitigation in this population and their potential impact on health care utilization and costs. PMID:25637344

  3. Copper Oxide Nanoparticles Impact Several Toxicological Endpoints and Cause Neurodegeneration in Caenorhabditis elegans

    PubMed Central

    Zanon, Tyler; Kappell, Anthony D.; Petrella, Lisa N.; Andersen, Erik C.; Hristova, Krassimira R.

    2016-01-01

    Engineered nanoparticles are becoming increasingly incorporated into technology and consumer products. In 2014, over 300 tons of copper oxide nanoparticles were manufactured in the United States. The increased production of nanoparticles raises concerns regarding the potential introduction into the environment or human exposure. Copper oxide nanoparticles commonly release copper ions into solutions, which contribute to their toxicity. We quantified the inhibitory effects of both copper oxide nanoparticles and copper sulfate on C. elegans toxicological endpoints to elucidate their biological effects. Several toxicological endpoints were analyzed in C. elegans, including nematode reproduction, feeding behavior, and average body length. We examined three wild C. elegans isolates together with the Bristol N2 laboratory strain to explore the influence of different genotypic backgrounds on the physiological response to copper challenge. All strains exhibited greater sensitivity to copper oxide nanoparticles compared to copper sulfate, as indicated by reduction of average body length and feeding behavior. Reproduction was significantly reduced only at the highest copper dose, though still more pronounced with copper oxide nanoparticles compared to copper sulfate treatment. Furthermore, we investigated the effects of copper oxide nanoparticles and copper sulfate on neurons, cells with known vulnerability to heavy metal toxicity. Degeneration of dopaminergic neurons was observed in up to 10% of the population after copper oxide nanoparticle exposure. Additionally, mutants in the divalent-metal transporters, smf-1 or smf-2, showed increased tolerance to copper exposure, implicating both transporters in copper-induced neurodegeneration. These results highlight the complex nature of CuO nanoparticle toxicity, in which a nanoparticle-specific effect was observed in some traits (average body length, feeding behavior) and a copper ion specific effect was observed for other traits

  4. Classical and biochemical endpoints in the evaluation of phytotoxic effects caused by the herbicide trichloroacetate.

    PubMed

    Radetski; Cotelle; Férard

    2000-11-01

    Three terrestrial plant species, oat (Avena sativa ), Chinese cabbage (Brassica campestris cv. chinensis) and lettuce (Lactuca sativa), were exposed to different concentrations of herbicide TCA (sodium trichloroacetate) in a growth test according to guideline OECD # 208. Classical (i.e. germination and biomass) and biochemical (i.e., antioxydant enzyme activities) endpoints were investigated. Germination rate decreased significantly at 3.9 mg TCA kg dry soil(-1) (for oat and lettuce) and 62.5 mg TCA kg dry soil(-1) (for Chinese cabbage). Biomass decreased significantly only at 1.9 mg TCA kg dry soil(-1) (for oat and lettuce) and 15.6 mg TCA kg dry soil(-1) (for Chinese cabbage). The activities of superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), peroxidase (EC 1.11.1.7) and glutathione reductase (EC 1.6.4.2) increased significantly at the lowest concentration of TCA tested, i.e. 0.03 mg TCA kg dry soil(-1) (for oat and lettuce) and 0.48 mg TCA kg dry soil(-1) (for Chinese cabbage). Our results showed a ranking of sensitivity among the different endpoints for the three plant species: enzyme activities>biomass>germination rate. The increase in antioxidant enzyme activities observed in this study ensured the detoxification of increased levels of active oxygen species, and presumably prevented the plants from undergoing oxidative stress damage. Thus, the use of enzyme activities will permit the detection of early injury in plant growth testing.

  5. Log-gamma directed polymer with fixed endpoints via the replica Bethe Ansatz

    NASA Astrophysics Data System (ADS)

    Thiery, Thimothée; Le Doussal, Pierre

    2014-10-01

    We study the model of a discrete directed polymer (DP) on a square lattice with homogeneous inverse gamma distribution of site random Boltzmann weights, introduced by Seppalainen (2012 Ann. Probab. 40 19-73). The integer moments of the partition sum, \\overline{Z^n} , are studied using a transfer matrix formulation, which appears as a generalization of the Lieb-Liniger quantum mechanics of bosons to discrete time and space. In the present case of the inverse gamma distribution the model is integrable in terms of a coordinate Bethe Ansatz, as discovered by Brunet. Using the Brunet-Bethe eigenstates we obtain an exact expression for the integer moments of \\overline{Z^n} for polymers of arbitrary lengths and fixed endpoint positions. Although these moments do not exist for all integer n, we are nevertheless able to construct a generating function which reproduces all existing integer moments and which takes the form of a Fredholm determinant (FD). This suggests an analytic continuation via a Mellin-Barnes transform and we thereby propose a FD ansatz representation for the probability distribution function (PDF) of Z and its Laplace transform. In the limit of a very long DP, this ansatz yields that the distribution of the free energy converges to the Gaussian unitary ensemble (GUE) Tracy-Widom distribution up to a non-trivial average and variance that we calculate. Our asymptotic predictions coincide with a result by Borodin et al (2013 Commun. Math. Phys. 324 215-32) based on a formula obtained by Corwin et al (2011 arXiv:1110.3489) using the geometric Robinson-Schensted-Knuth (gRSK) correspondence. In addition we obtain the dependence on the endpoint position and the exact elastic coefficient at a large time. We argue the equivalence between our formula and that of Borodin et al. As we will discuss, this provides a connection between quantum integrability and tropical combinatorics.

  6. Comparison of osteoblast and cardiomyocyte differentiation in the embryonic stem cell test for predicting embryotoxicity in vivo.

    PubMed

    de Jong, Esther; van Beek, Lianne; Piersma, Aldert H

    2014-09-01

    One of the most studied alternative embryotoxicity assays is the embryonic stem cell test, in which the effect of compounds on cardiomyocyte differentiation is evaluated (subsequently termed the ESTc). This single differentiation endpoint may limit the predictive value of the assay. We recently published a novel embryonic stem cell based osteoblast differentiation assay (subsequently termed the ESTo), in which we studied the effect of six embryotoxic compounds. Differentiation is monitored via the differential expression of three genes related to osteogenesis (Runx2, SPARC and collagen type I). In the current study, we evaluated the effect of 14 additional compounds in the ESTo, to assess its added value as compared to the ESTc. To this end, we compared the effects of the compounds in the ESTo to their effects in the ESTc and to their published in vivo developmental toxicity profiles. The results show that there is a high overall correlation between compound potencies as regards inhibition of osteoblast and cardiomyocyte differentiation. Moreover, the results in both the ESTo and ESTc showed a significant correlation to in vivo developmental toxicity potency ranking of compounds tested. Interestingly, the embryotoxic effect of TCDD could only be detected using the ESTo, which can be explained based on its mechanism of action and its known inhibitory effect on osteogenesis. The results of TCDD suggest that incorporating the ESTo into a testing battery together with the ESTc could improve the overall predictive value of the battery.

  7. Estimation of cellular fabric in embryonic epithelia.

    PubMed

    Iles, Peter J W; Brodland, G Wayne; Clausi, David A; Puddister, Shannon M

    2007-02-01

    Recent computational and analytical studies have shown that cellular fabric-as embodied by average cell size, aspect ratio and orientation-is a key indicator of the stresses acting in an embryonic epithelium. Cellular fabric in real embryonic tissues could not previously be measured automatically because the cell boundaries tend to be poorly defined, significant lighting and cell pigmentation differences occur and tissues contain a variety of cell geometries. To overcome these difficulties, four algorithms were developed: least squares ellipse fitting (LSEF), area moments (AM), correlation and axes search (CAS) and Gabor filters (GF). The AM method was found to be the most reliable of these methods, giving typical cell size, aspect ratio and orientation errors of 18%, 0.10 and 7.4 degrees, respectively, when evaluated against manually segmented images. The power of the AM algorithm to provide new insights into the mechanics of morphogenesis is demonstrated through a brief investigation of gastrulation, where fabric data suggest that key gastrulation movements are driven by epidermal tensions circumferential to the blastopore.

  8. Organotypic slice culture of embryonic brain tissue.

    PubMed

    Daza, Ray A M; Englund, Chris; Hevner, Robert F

    2007-12-01

    INTRODUCTIONThis protocol describes how to dissect, assemble, and cultivate mouse embryonic (E) brain tissue from age E11.5 to E18.5 (days) for organotypic slice culture. These preparations can be used for a variety of assays and studies including coculture of different brain regions, cell migration assays, axon guidance assays, and DNA electroporation experiments. During electroporation, an electric current is applied to the surface of a specific target area of the brain slice in order to open holes in the plasma membrane and introduce a plasmid of coding DNA. The floating slice-on-membrane construct helps to preserve the structural integrity of the brain slices, while maintaining easy experimental access and optimal viability. Experiments can be monitored in living slices (e.g., with confocal imaging), and further studies can be completed using slices that have been fixed and cryosectioned at the end of the experiment. Any region of embryonic brain or spinal tissue can be used in this protocol.

  9. Embryonic paratesticular rhabdomyosarcoma: a case report

    PubMed Central

    2013-01-01

    Introduction An embryonic paratesticular rhabdomyosarcoma is a very rare mesenchymal tumor. It is an intrascrotal tumor that is localized in paratesticular structures such as the epididymis or spermatic cord. Rhabdomyosarcoma is most often observed in children and adolescents, presenting as a painless scrotal mass. Case presentation Our patient was an 18-year-old Moroccan man who presented with a painless left scrotal mass that had evolved over four months. An inguinal orchiectomy was performed. A histological examination of the excised tissue revealed an embryonic rhabdomyosarcoma. Our patient had three sessions of chemotherapy with vincristine, actinomycin C and cyclophosphamide. Each chemotherapy session was conducted over five days, with a cycle of 21 days. Our patient was assessed two months after the last chemotherapy session and demonstrated good clinical improvement. Conclusion Paratesticular rhabdomyosarcoma is a rare aggressive tumor manifesting in children and very young adults. Localized forms have a good prognosis whereas metastatic tumors show very poor results. A well-defined treatment based on surgery and chemotherapy yields good results. PMID:23561643

  10. Embryonic stem cells: from markers to market.

    PubMed

    Deb, Kaushik Dilip; Jayaprakash, Anitha Devi; Sharma, Vijay; Totey, Satish

    2008-02-01

    ABSTRACT Embryonic stem cells are considered the mother of all kinds of tissues and cells and it is envisioned as the holy grail of regenerative medicine. However, their use in cell replacement therapies (CRT) has so far been limited and their potentials are yet to be fully realized. The use of human embryonic stem cells (hESC) involves many safety issues pertaining to culture conditions and epigenetic changes. The role and importance of an epigenomic signature in derivation and maintenance of hESC are discussed. We provide a list of important epigenetic markers, which should be studied for evaluation of safety in hESC-based cell replacement therapies. These genes also need to be screened to determine an epigenetic signature for pluripotency in the hESCs. Finally a comprehensive list of all known stemness signature genes and the marker genes for different germ line lineages are presented. This review aims at summing up most of the intriguing molecules that can play a role in the maintenance of pluripotency and can help in determining hESC differentiation to various lineages. Extensive understanding of these markers will eventually help the researchers to transform the hESC research from bench to the bedside. The use of hESCs in CRTs is still in its infancy; much effort is warranted to turn them into the much dreamed about magic wand of regenerative medicine.

  11. Human embryonic stem cells and cardiac repair.

    PubMed

    Zhu, Wei-Zhong; Hauch, Kip D; Xu, Chunhui; Laflamme, Michael A

    2009-01-01

    The muscle lost after a myocardial infarction is replaced with noncontractile scar tissue, often initiating heart failure. Whole-organ cardiac transplantation is the only currently available clinical means of replacing the lost muscle, but this option is limited by the inadequate supply of donor hearts. Thus, cell-based cardiac repair has attracted considerable interest as an alternative means of ameliorating cardiac injury. Because of their tremendous capacity for expansion and unquestioned cardiac potential, pluripotent human embryonic stem cells (hESCs) represent an attractive candidate cell source for obtaining cardiomyocytes and other useful mesenchymal cell types for such therapies. Human embryonic stem cell-derived cardiomyocytes exhibit a committed cardiac phenotype and robust proliferative capacity, and recent testing in rodent infarct models indicates that they can partially remuscularize injured hearts and improve contractile function. Although the latter successes give good reason for optimism, considerable challenges remain in the successful application of hESCs to cardiac repair, including the need for preparations of high cardiac purity, improved methods of delivery, and approaches to overcome immune rejection and other causes of graft cell death. This review will describe the phenotype of hESC-derived cardiomyocytes and preclinical experience with these cells and will consider strategies to overcoming the aforementioned challenges.

  12. Mechanical signaling coordinates the embryonic heart

    NASA Astrophysics Data System (ADS)

    Chiou, Kevin; Rocks, Jason; Prosser, Benjamin; Discher, Dennis; Liu, Andrea

    The heart is an active material which relies on robust signaling mechanisms between cells in order to produce well-timed, coordinated beats. Heart tissue is composed primarily of active heart muscle cells (cardiomyocytes) embedded in a passive extracellular matrix. During a heartbeat, cardiomyocyte contractions are coordinated across the heart to form a wavefront that propagates through the tissue to pump blood. In the adult heart, this contractile wave is coordinated via intercellular electrical signaling.Here we present theoretical and experimental evidence for mechanical coordination of embryonic heartbeats. We model cardiomyocytes as mechanically excitable Eshelby inclusions embedded in an overdamped elastic-fluid biphasic medium. For physiological parameters, this model replicates recent experimental measurements of the contractile wavefront which are not captured by electrical signaling models. We additionally challenge our model by pharmacologically blocking gap junctions, inhibiting electrical signaling between myocytes. We find that while adult hearts stop beating almost immediately after gap junctions are blocked, embryonic hearts continue beating even at significantly higher concentrations, providing strong support for a mechanical signaling mechanism.

  13. Proteome analysis of chick embryonic cerebrospinal fluid.

    PubMed

    Parada, Carolina; Gato, Angel; Aparicio, Mariano; Bueno, David

    2006-01-01

    During early stages of embryo development, the brain cavity is filled with embryonic cerebrospinal fluid (E-CSF), a complex fluid containing different protein fractions that contributes to the regulation of the survival, proliferation and neurogenesis of the neuroectodermal stem cells. Using 2-DE, protein sequencing and database searches, we identified and analyzed the proteome of the E-CSF from chick embryos (Gallus gallus). We identified 26 different gene products, including proteins related to the extracellular matrix, proteins associated with the regulation of osmotic pressure and metal transport, proteins related to cell survival, MAP kinase activators, proteins involved in the transport of retinol and vitamin D, antioxidant and antimicrobial proteins, intracellular proteins and some unknown proteins. Most of these gene products are involved in the regulation of developmental processes during embryogenesis in systems other than E-CSF. Interestingly, 14 of them are also present in adult human CSF proteome, and it has been reported that they are altered in the CSF of patients suffering neurodegenerative diseases and/or neurological disorders. Understanding these molecules and the mechanisms they control during embryonic neurogenesis is a key contribution to the general understanding of CNS development, and may also contribute to greater knowledge of these human diseases.

  14. Gene signature of the embryonic meniscus.

    PubMed

    Pazin, Dorothy E; Gamer, Laura W; Capelo, Luciane P; Cox, Karen A; Rosen, Vicki

    2014-01-01

    The meniscus is a fibrocartilagenous disc in the knee that protects the joint from damage. Meniscal injuries are common, however repair efforts are largely unsuccessful and are not able to prevent the degenerative changes that result in development of osteoarthritis. Tissue regeneration in adults often recapitulates events of embryonic development, suggesting the regulatory pathways controlling morphogenesis are candidate repair signals. Here we use laser capture microdissection to collect mouse embryonic day 16 (E16) meniscus, articular cartilage, and cruciate ligaments. RNA isolated from these tissues was then used to perform genome-wide microarray analysis. We found 38 genes were differentially expressed between E16 meniscus and articular cartilage and 43 genes were differentially expressed between E16 meniscus and cruciate ligaments. Included in our data set were extracellular matrix proteins, transcription factors, and growth factors, including TGF-β modulators (Lox, Dpt) and IGF-1 pathway members (Igf-1, Igfbp2, Igfbp3, Igfbp5). Ingenuity Pathway Analysis revealed that IGF-1 signaling was enriched in the meniscus compared to the other joint structures, while qPCR showed that Igf-1, Igfbp2, and Igfbp3 expression declined with age. We also found that several meniscus-enriched genes were expressed either in the inner or outer meniscus, establishing that regionalization of the meniscus occurs early in development.

  15. Disseminated Cerebrospinal Embryonal Tumor in the Adult

    PubMed Central

    Armocida, Daniele; Caporlingua, Federico; Lapadula, Gennaro; Elefante, Grazia Maria; Antonelli, Manila; Salvati, Maurizio

    2016-01-01

    Introduction. According to the 2016 World Health Organization classification of Tumors of the Central Nervous System, the term Primitive Neuroectodermal Tumor has been replaced by the term Embryonal Tumor (ET). We present a case of disseminated cerebrospinal ET presenting in an adult patient. Illustrative Case. A 49-year-old male presenting with low back pain, dysuria, and hypoesthesia of the lower extremities referred to our emergency department. Brain and whole spine contrast-enhanced MRI documented a diffusively disseminated heterogeneous neoplasm with intradural extra- and intramedullary involvement of the cervicothoracic tract and cauda equina. A primary biopsy of the lumbosacral localization was performed through L5 bilateral laminectomy. Histologic diagnosis was Embryonal Tumor Not Otherwise Specified. The patient underwent chemotherapy with postoperative adjuvant alternating Vincristine-Doxorubicin-Ifosfamide (VAI) and Ifosfamide-Etoposide (IE). Discussion. Spinal ETs are exceedingly rare especially when presenting in the adult patient. Neurosurgical and oncologic management is still unclear. When feasible, surgical removal should always be performed to obtain a histologic diagnosis. Postoperative adjuvant therapy might entail both chemo- and radiotherapy; however a consensus on this matter is still lacking. PMID:27818821

  16. Evaluating the effect of varying flux group endpoints on reaction rates of 238U

    SciTech Connect

    Jaffke, Patrick John

    2015-01-28

    This acts as a short note on the effects of varying the value of the endpoints of the thermal, epithermal, and fast flux groups. As expected, varying these endpoints can alter the value of the cross-section for a given nuclide. This effect is quantified in this note for an important nuclide in reactor simulations, 238U. Uranium-238 is responsible for the production of Plutonium in most reactors, making it critical to understand all of the 238U capture modes leading to Plutonium. We explicitly quantify the reaction rates for 238U that are altered when we use a given research reactor flux and vary the endpoint definitions of said flux as well as the reactor position.

  17. Free-time and fixed end-point optimal control theory in quantum mechanics: application to entanglement generation.

    PubMed

    Mishima, K; Yamashita, K

    2009-01-21

    We have constructed free-time and fixed end-point optimal control theory for quantum systems and applied it to entanglement generation between rotational modes of two polar molecules coupled by dipole-dipole interaction. The motivation of the present work is to solve optimal control problems more flexibly by extending the popular fixed time and fixed end-point optimal control theory for quantum systems to free-time and fixed end-point optimal control theory. As a demonstration, the theory that we have constructed in this paper will be applied to entanglement generation in rotational modes of NaCl-NaBr polar molecular systems that are sensitive to the strength of entangling interactions. Our method will significantly be useful for the quantum control of nonlocal interaction such as entangling interaction, which depends crucially on the strength of the interaction or the distance between the two molecules, and other general quantum dynamics, chemical reactions, and so on.

  18. Free-time and fixed end-point optimal control theory in quantum mechanics: Application to entanglement generation

    NASA Astrophysics Data System (ADS)

    Mishima, K.; Yamashita, K.

    2009-01-01

    We have constructed free-time and fixed end-point optimal control theory for quantum systems and applied it to entanglement generation between rotational modes of two polar molecules coupled by dipole-dipole interaction. The motivation of the present work is to solve optimal control problems more flexibly by extending the popular fixed time and fixed end-point optimal control theory for quantum systems to free-time and fixed end-point optimal control theory. As a demonstration, the theory that we have constructed in this paper will be applied to entanglement generation in rotational modes of NaCl-NaBr polar molecular systems that are sensitive to the strength of entangling interactions. Our method will significantly be useful for the quantum control of nonlocal interaction such as entangling interaction, which depends crucially on the strength of the interaction or the distance between the two molecules, and other general quantum dynamics, chemical reactions, and so on.

  19. Titration of human-bovine rotavirus reassortants using a tetrazolium-based colorimetric end-point dilution assay.

    PubMed

    DiStefano, D J; Gould, S L; Munshi, S; Robinson, D K

    1995-10-01

    A colorimetric end-point dilution assay was developed for the titration of rotavirus-containing samples that uses commercially available tetrazolium dyes as an indicator of virus infection. This assay offers several advantages over both plaque assays and traditional end-point dilution methods. The latter assays require manual counting of plaques or the scoring of wells for the presence of virus based on observed cytopathic effects. The colorimetric end-point dilution assay enables the scoring of wells based upon absorbance readings alone, thereby eliminating time-consuming and subjective manual screenings. This method also has the potential for automating the analysis of large numbers of samples. Virus titers of human-bovine rotavirus reassortants obtained using this method are comparable to those determined by plaque assay. The scoring of wells based on absorbance readings was also found to agree with manual scoring of cytopathic effects and with the production of viral antigen.

  20. Embryonal Rhabdomyosarcoma Occurring on Mandibular Gingiva in an Adult

    PubMed Central

    Patil, Gururaj; Halawar, Sangamesh; Sagari, Shitalkumar; Babannavar, Roopa; Purohit, Sharad

    2013-01-01

    An embryonal rhabdomyosarcoma (ERMS) is a primitive, malignant, soft tissue sarcoma that recapitulates the phenotypic and biological features of embryonic skeletal muscles. Occurrence of intraoral ERMS in adults is extremely rare. This unique case report highlights the clinical, radiographic, histopathological and immunohistochemical findings of an intraoral ERMS. PMID:24179953

  1. Critical endpoint behavior in an asymmetric Ising model: application of Wang-Landau sampling to calculate the density of states.

    PubMed

    Tsai, Shan-Ho; Wang, Fugao; Landau, D P

    2007-06-01

    Using the Wang-Landau sampling method with a two-dimensional random walk we determine the density of states for an asymmetric Ising model with two- and three-body interactions on a triangular lattice, in the presence of an external field. With an accurate density of states we were able to map out the phase diagram accurately and perform quantitative finite-size analyses at, and away from, the critical endpoint. We observe a clear divergence of the curvature of the spectator phase boundary and of the magnetization coexistence diameter derivative at the critical endpoint, and the exponents for both divergences agree well with previous theoretical predictions.

  2. Critical endpoint behavior in an asymmetric Ising model: Application of Wang-Landau sampling to calculate the density of states

    NASA Astrophysics Data System (ADS)

    Tsai, Shan-Ho; Wang, Fugao; Landau, D. P.

    2007-06-01

    Using the Wang-Landau sampling method with a two-dimensional random walk we determine the density of states for an asymmetric Ising model with two- and three-body interactions on a triangular lattice, in the presence of an external field. With an accurate density of states we were able to map out the phase diagram accurately and perform quantitative finite-size analyses at, and away from, the critical endpoint. We observe a clear divergence of the curvature of the spectator phase boundary and of the magnetization coexistence diameter derivative at the critical endpoint, and the exponents for both divergences agree well with previous theoretical predictions.

  3. Motor adaptation to Coriolis force perturbations of reaching movements: endpoint but not trajectory adaptation transfers to the nonexposed arm

    NASA Technical Reports Server (NTRS)

    Dizio, P.; Lackner, J. R.

    1995-01-01

    1. Reaching movements made in a rotating room generate Coriolis forces that are directly proportional to the cross product of the room's angular velocity and the arm's linear velocity. Such Coriolis forces are inertial forces not involving mechanical contact with the arm. 2. We measured the trajectories of arm movements made in darkness to a visual target that was extinguished at the onset of each reach. Prerotation subjects pointed with both the right and left arms in alternating sets of eight movements. During rotation at 10 rpm, the subjects reached only with the right arm. Postrotation, the subjects pointed with the left and right arms, starting with the left, in alternating sets of eight movements. 3. The initial perrotary reaching movements of the right arm were highly deviated both in movement path and endpoint relative to the prerotation reaches of the right arm. With additional movements, subjects rapidly regained straight movement paths and accurate endpoints despite the absence of visual or tactile feedback about reaching accuracy. The initial postrotation reaches of the left arm followed straight paths to the wrong endpoint. The initial postrotation reaches of the right arm had paths with mirror image curvature to the initial perrotation reaches of the right arm but went to the correct endpoint. 4. These observations are inconsistent with current equilibrium point models of movement control. Such theories predict accurate reaches under our experimental conditions. Our observations further show independent implementation of movement and posture, as evidenced by transfer of endpoint adaptation to the nonexposed arm without transfer of path adaptation. Endpoint control may occur at a relatively central stage that represents general constraints such as gravitoinertial force background or egocentric direction relative to both arms, and control of path may occur at a more peripheral stage that represents moments of inertia and muscle dynamics unique to each

  4. In vitro embryotoxicity testing of metals for dental use by differentiation of embryonic stem cell test.

    PubMed

    Imai, Koichi; Nakamura, Masaaki

    2006-03-01

    We examined embryotoxicity using the embryonic stem cell test (EST) protocol. Tests were conducted using standard reagents for the atomic absorption measurement of 11 metal ions, silver, cobalt, chromium, copper, mercury, nickel, palladium, antimony, tin, vanadium, and zinc from among metals comprising dental alloys. In addition, for four metals like silver, cobalt, chromium, and nickel, the tests were also conducted using a test solution extracted from powder in the cell culture medium. The embryotoxic potential was obtained from a biostatistics-based prediction model, which was calculated from three endpoints, the ID50, IC50ES and IC(50)3T3. Data with the standard reagents showed that chromium and mercury ions corresponded to class 3, that is, having a strong embryotoxicity, while antimony, tin, and vanadium ions exhibited a weak embryotoxicity. The other metal ions demonstrated no embryotoxicity. On the other hand, when extracts of metal powder in cell culture solutions were used, silver exhibited a weak embryotoxicity while all other metals exhibited no embryotoxicity. In the future, it will be important to clarify the embryotoxicity of the many dental materials that are in use today. In addition, it is necessary to develop substances to ensure they have no toxicity before use in dental applications.

  5. Assessment of embryotoxicity of compounds in cosmetics by the embryonic stem cell test.

    PubMed

    Chen, Rui; Chen, Jing; Cheng, Shujun; Qin, Jie; Li, Weiqiang; Zhang, Lirong; Jiao, Hong; Yu, Xinbing; Zhang, Xiuming; Lahn, Bruce T; Xiang, Andy Peng

    2010-03-01

    The new EU legislations for cosmetics (Seventh Amendment) have laid down deadlines for the replacement of animal tests in cosmetics. This policy stimulates the acceptance of in vitro approaches to test embryotoxic potentials of compounds in cosmetics products. The embryonic stem cell test (EST) designed by The European Centre for the Validation of Alternative Methods (ECVAM) is currently the most promising in vitro assay to predict the embryotoxic potential of compounds. In this study, six selected compounds (hydroquinone, eugenol, dibutyl phthalate, antimony (III) oxide, neodymium (III) nitrate hydrate, melamine) formerly involved in cosmetic products were selected to test their embryotoxic potentials by the EST. 5-Fluorouracil and penicillin G were separately set as positive and negative control. The embryotoxic potential was determined by the prediction model (PM), which was calculated from three endpoints, the IC(50) 3T3, IC(50) ES, and ID(50). Hydroquinone, eugenol, and antimony (III) oxide indicated with strong embryotoxicity, while dibutyl phthalate, neodymium (III) nitrate hydrate, and melamine exhibited a weak embryotoxicity. These results may provide a valuable attempt to expand the application of EST to the cosmetics field.

  6. Diverse neurotoxicants target the differentiation of embryonic neural stem cells into neuronal and glial phenotypes.

    PubMed

    Slotkin, Theodore A; Skavicus, Samantha; Card, Jennifer; Levin, Edward D; Seidler, Frederic J

    2016-11-30

    The large number of compounds that needs to be tested for developmental neurotoxicity drives the need to establish in vitro models to evaluate specific neurotoxic endpoints. We used neural stem cells derived from rat neuroepithelium on embryonic day 14 to evaluate the impact of diverse toxicants on their ability to differentiate into glia and neurons: a glucocorticoid (dexamethasone), organophosphate insecticides (chlorpyrifos, diazinon, parathion), insecticides targeting the GABAA receptor (dieldrin, fipronil), heavy metals (Ni(2+), Ag(+)), nicotine and tobacco smoke extract. We found three broad groupings of effects. One diverse set of compounds, dexamethasone, the organophosphate pesticides, Ni(2+) and nicotine, suppressed expression of the glial phenotype while having little or no effect on the neuronal phenotype. The second pattern was restricted to the pesticides acting on GABAA receptors. These compounds promoted the glial phenotype and suppressed the neuronal phenotype. Notably, the actions of compounds eliciting either of these differentiation patterns were clearly unrelated to deficits in cell numbers: dexamethasone, dieldrin and fipronil all reduced cell numbers, whereas organophosphates and Ni(2+) had no effect. The third pattern, shared by Ag(+) and tobacco smoke extract, clearly delineated cytotoxicity, characterized by major cell loss with suppression of differentiation into both glial and neuronal phenotypes; but here again, there was some selectivity in that glia were suppressed more than neurons. Our results, from this survey with diverse compounds, point to convergence of neurotoxicant effects on a specific "decision node" that controls the emergence of neurons and glia from neural stem cells.

  7. Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis.

    PubMed

    Shaikh, T H; Kurahashi, H; Saitta, S C; O'Hare, A M; Hu, P; Roe, B A; Driscoll, D A; McDonald-McGinn, D M; Zackai, E H; Budarf, M L; Emanuel, B S

    2000-03-01

    The 22q11.2 deletion syndrome, which includes DiGeorge and velocardiofacial syndromes (DGS/VCFS), is the most common microdeletion syndrome. The majority of deleted patients share a common 3 Mb hemizygous deletion of 22q11.2. The remaining patients include those who have smaller deletions that are nested within the 3 Mb typically deleted region (TDR) and a few with rare deletions that have no overlap with the TDR. The identification of chromosome 22-specific duplicated sequences or low copy repeats (LCRs) near the end-points of the 3 Mb TDR has led to the hypothesis that they mediate deletions of 22q11.2. The entire 3 Mb TDR has been sequenced, permitting detailed investigation of the LCRs and their involvement in the 22q11.2 deletions. Sequence analysis has identified four LCRs within the 3 Mb TDR. Although the LCRs differ in content and organization of shared modules, those modules that are common between them share 97-98% sequence identity with one another. By fluorescence in situ hybridization (FISH) analysis, the end-points of four variant 22q11.2 deletions appear to localize to the LCRs. Pulsed-field gel electrophoresis and Southern hybridization have been used to identify rearranged junction fragments from three variant deletions. Analysis of junction fragments by PCR and sequencing of the PCR products implicate the LCRs directly in the formation of 22q11.2 deletions. The evolutionary origin of the duplications on chromosome 22 has been assessed by FISH analysis of non-human primates. Multiple signals in Old World monkeys suggest that the duplication events may have occurred at least 20-25 million years ago.

  8. 4D embryonic cardiography using gated optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Jenkins, M. W.; Rothenberg, F.; Roy, D.; Nikolski, V. P.; Hu, Z.; Watanabe, M.; Wilson, D. L.; Efimov, I. R.; Rollins, A. M.

    2006-01-01

    Simultaneous imaging of very early embryonic heart structure and function has technical limitations of spatial and temporal resolution. We have developed a gated technique using optical coherence tomography (OCT) that can rapidly image beating embryonic hearts in four-dimensions (4D), at high spatial resolution (10-15 μm), and with a depth penetration of 1.5 - 2.0 mm that is suitable for the study of early embryonic hearts. We acquired data from paced, excised, embryonic chicken and mouse hearts using gated sampling and employed image processing techniques to visualize the hearts in 4D and measure physiologic parameters such as cardiac volume, ejection fraction, and wall thickness. This technique is being developed to longitudinally investigate the physiology of intact embryonic hearts and events that lead to congenital heart defects.

  9. The New Federalism: State Policies Regarding Embryonic Stem Cell Research.

    PubMed

    Acosta, Nefi D; Golub, Sidney H

    2016-09-01

    Stem cell policy in the United States is an amalgam of federal and state policies. The scientific development of human pluripotent embryonic stem cells (ESCs) triggered a contentious national stem cell policy debate during the administration of President George W. Bush. The Bush "compromise" that allowed federal funding to study only a very limited number of ESC derived cell lines did not satisfy either the researchers or the patient advocates who saw great medical potential being stifled. Neither more restrictive legislation nor expansion of federal funding proved politically possible and the federal impasse opened the door for a variety of state-based experiments. In 2004, California became the largest and most influential state venture into stem cell research by passing "Prop 71," a voter initiative that created a new stem cell agency and funded it with $3 billion. Several states followed suit with similar programs to protect the right of investigators to do stem cell research and in some cases to invest state funding in such projects. Other states devised legislation to restrict stem cell research and in five states, criminal penalties were included. Thus, the US stem cell policy is a patchwork of multiple, often conflicting, state and federal policies.

  10. Molecular signature of erythroblast enucleation in human embryonic stem cells.

    PubMed

    Rouzbeh, Shaghayegh; Kobari, Ladan; Cambot, Marie; Mazurier, Christelle; Hebert, Nicolas; Faussat, Anne-Marie; Durand, Charles; Douay, Luc; Lapillonne, Hélène

    2015-08-01

    While enucleation is a critical step in the terminal differentiation of human red blood cells, the molecular mechanisms underlying this unique process remain unclear. To investigate erythroblast enucleation, we studied the erythroid differentiation of human embryonic stem cells (hESCs), which provide a unique model for deeper understanding of the development and differentiation of multiple cell types. First, using a two-step protocol, we demonstrated that terminal erythroid differentiation from hESCs is directly dependent on the age of the embryoid bodies. Second, by choosing hESCs in two extreme conditions of erythroid culture, we obtained an original differentiation model which allows one to study the mechanisms underlying the enucleation of erythroid cells by analyzing the gene and miRNA (miR) expression profiles of cells from these two culture conditions. Third, using an integrated analysis of mRNA and miR expression profiles, we identified five miRs potentially involved in erythroblast enucleation. Finally, by selective knockdown of these five miRs we found miR-30a to be a regulator of erythroblast enucleation in hESCs.

  11. Mutator phenotype of MUTYH-null mouse embryonic stem cells.

    PubMed

    Hirano, Seiki; Tominaga, Yohei; Ichinoe, Akimasa; Ushijima, Yasuhiro; Tsuchimoto, Daisuke; Honda-Ohnishi, Yoko; Ohtsubo, Toshio; Sakumi, Kunihiko; Nakabeppu, Yusaku

    2003-10-03

    To evaluate the antimutagenic role of a mammalian mutY homolog, namely the Mutyh gene, which encodes adenine DNA glycosylase excising adenine misincorporated opposite 8-oxoguanine in the template DNA, we generated MUTYH-null mouse embryonic stem (ES) cells. In the MUTYH-null cells carrying no adenine DNA glycosylase activity, the spontaneous mutation rate increased 2-fold in comparison with wild type cells. The expression of wild type mMUTYH or mutant mMUTYH protein with amino acid substitutions at the proliferating cell nuclear antigen binding motif restored the increased spontaneous mutation rates of the MUTYH-null ES cells to the wild type level. The expression of a mutant mMUTYH protein with an amino acid substitution (G365D) that corresponds to a germ-line mutation (G382D) found in patients with multiple colorectal adenomas could not suppress the elevated spontaneous mutation rate of the MUTYH-null ES cells. Although the recombinant mMUTYH(G365D) purified from Escherichia coli cells had a substantial level of adenine DNA glycosylase activity as did wild type MUTYH, no adenine DNA glycosylase activity was detected in the MUTYH-null ES cells expressing the mMUTYH(G365D) mutant protein. The germ-line mutation (G382D) of the human MUTYH gene is therefore likely to be responsible for the occurrence of a mutator phenotype in these patients.

  12. Programming the genome in embryonic and somatic stem cells.

    PubMed

    Collas, Philippe; Noer, Agate; Timoskainen, Sanna

    2007-01-01

    In opposition to terminally differentiated cells, stem cells can self-renew and give rise to multiple cell types. Embryonic stem cells retain the ability of the inner cell mass of blastocysts to differentiate into all cell types of the body and have acquired in culture unlimited self-renewal capacity. Somatic stem cells are found in many adult tissues, have an extensive but finite lifespan and can differentiate into a more restricted array of cell types. A growing body of evidence indicates that multi-lineage differentiation ability of stem cells can be defined by the potential for expression of lineage-specification genes. Gene expression, or as emphasized here, potential for gene expression, is largely controlled by epigenetic modifications of DNA and chromatin on genomic regulatory and coding regions. These modifications modulate chromatin organization not only on specific genes but also at the level of the whole nucleus; they can also affect timing of DNA replication. This review highlights how mechanisms by which genes are poised for transcription in undifferentiated stem cells are being uncovered through primarily the mapping of DNA methylation, histone modifications and transcription factor binding throughout the genome. The combinatorial association of epigenetic marks on developmentally regulated and lineage-specifying genes in undifferentiated cells seems to define a pluripotent state.

  13. Electrophysiological Properties of Embryonic Stem Cell-Derived Neurons

    PubMed Central

    Risner-Janiczek, Jessica R.; Ungless, Mark A.; Li, Meng

    2011-01-01

    In vitro generation of functional neurons from embryonic stem (ES) cells and induced pluripotent stem cells offers exciting opportunities for dissecting gene function, disease modelling, and therapeutic drug screening. To realize the potential of stem cells in these biomedical applications, a complete understanding of the cell models of interest is required. While rapid advances have been made in developing the technologies for directed induction of defined neuronal subtypes, most published works focus on the molecular characterization of the derived neural cultures. To characterize the functional properties of these neural cultures, we utilized an ES cell model that gave rise to neurons expressing the green fluorescent protein (GFP) and conducted targeted whole-cell electrophysiological recordings from ES cell-derived neurons. Current-clamp recordings revealed that most neurons could fire single overshooting action potentials; in some cases multiple action potentials could be evoked by depolarization, or occurred spontaneously. Voltage-clamp recordings revealed that neurons exhibited neuronal-like currents, including an outward current typical of a delayed rectifier potassium conductance and a fast-activating, fast-inactivating inward current, typical of a sodium conductance. Taken together, these results indicate that ES cell-derived GFP+ neurons in culture display functional neuronal properties even at early stages of differentiation. PMID:21887381

  14. Endpoint-based parallel data processing with non-blocking collective instructions in a parallel active messaging interface of a parallel computer

    DOEpatents

    Archer, Charles J; Blocksome, Michael A; Cernohous, Bob R; Ratterman, Joseph D; Smith, Brian E

    2014-11-11

    Endpoint-based parallel data processing with non-blocking collective instructions in a PAMI of a parallel computer is disclosed. The PAMI is composed of data communications endpoints, each including a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task. The compute nodes are coupled for data communications through the PAMI. The parallel application establishes a data communications geometry specifying a set of endpoints that are used in collective operations of the PAMI by associating with the geometry a list of collective algorithms valid for use with the endpoints of the geometry; registering in each endpoint in the geometry a dispatch callback function for a collective operation; and executing without blocking, through a single one of the endpoints in the geometry, an instruction for the collective operation.

  15. Cadherins in cerebellar development: translation of embryonic patterning into mature functional compartmentalization.

    PubMed

    Redies, Christoph; Neudert, Franziska; Lin, Juntang

    2011-09-01

    Cadherins are cell adhesion molecules with multiple morphogenic functions in brain development, for example, in neuroblast migration and aggregation, axon navigation, neural circuit formation, and synaptogenesis. More than 100 members of the cadherin superfamily are expressed in the developing and mature brain. Most of the cadherins investigated, in particular classic cadherins and δ-protocadherins, are expressed in the cerebellum. For several cadherin subtypes, expression begins at early embryonic stages and persists until mature stages of cerebellar development. At intermediate stages, distinct Purkinje cell clusters exhibit unique rostrocaudal and mediolateral expression profiles for each cadherin. In the chicken, mouse, and other species, the Purkinje cell clusters are separated by intervening raphes of migrating granule cells. This pattern of Purkinje cell clusters/raphes is, at least in part, continuous with the parasagittal striping pattern that is apparent in the mature cerebellar cortex, for example, for zebrin II/aldolase C. Moreover, subregions of the deep cerebellar nuclei, vestibular nuclei and the olivary complex also express cadherins differentially. Neuroanatomical evidence suggests that the nuclear subregions and cortical domains that express the same cadherin subtype are connected to each other, to form neural subcircuits of the cerebellar system. Cadherins thus provide a molecular code that specifies not only embryonic structures but also functional cerebellar compartmentalization. By following the implementation of this code, it can be revealed how mature functional architecture emerges from embryonic patterning during cerebellar development. Dysfunction of some cadherins is associated with psychiatric diseases and developmental impairments and may also affect cerebellar function.

  16. Early embryonic development of frogs under intense magnetic fields up to 8 T

    NASA Astrophysics Data System (ADS)

    Ueno, S.; Iwasaka, M.; Shiokawa, K.

    1994-05-01

    A possible influence of intense magnetic fields on the embryonic development of frogs was studied in reference to a potential hazard in magnetic resonance imaging technology. Some of the most serious hazardous effects that could be induced by intense magnetic fields are teratogenic effects on developing embryos. In the present experiment, the possible influence of intense magnetic fields up to 8 T on the early embryonic development of Xenopus laevis was studied. Embryos were exposed to magnetic fields up to 8 T for the period from the precleavage stage to neurula in a small glass vial. Embryos were then cultured in Brown-Caston's medium until the feeding-tadpole stage. No apparent teratogenic effects were observed when embryos were cultured for 20 h from the stage of uncleaved fertilized egg to the neurula stage under magnetic fields of 8 T. We conclude that static magnetic fields up to 8 T do not appreciably affect the rapid cleavage and the following cell multiplication and differentiation in Xenopus laevis. We have also studied the early embryonic development of Xenopus laevis in a 40 nT magnetic field, or 1/1000 of the earth's magnetic field, and obtained negative results. Thus, again under this very low magnetic field, fertilized eggs developed normally and formed tadpoles with no appreciable abnormality.

  17. Gli1 is not required for Pdgfralpha expression during mouse embryonic development.

    PubMed

    Zhang, Xiao-Qun; Afink, Gijs B; Hu, Xin-Rong; Forsberg-Nilsson, Karin; Nistér, Monica

    2005-03-01

    Pdgfra is expressed in the mesenchyme of multiple organs during embryonic development and Pdgfralpha is involved in cell proliferation, differentiation, migration, and apoptosis in many tissues. A fine-tuned regulation of gene transcription is required to achieve these effects. To investigate if the Shh signaling pathway is involved in the tightly regulated Pdgfra expression during embryogenesis, we systematically compared Gli1 and Pdgfralpha mRNA expression patterns in vivo from mouse embryonic day 9.5 to 14.5. We found that an initial partly overlapping expression of Gli1 and Pdgfralpha in the mesenchyme of foregut and somites was changed to different expression patterns when the mesenchyme differentiated into specialized structures such as intestinal villi and chondrocytes. Gli1 and Pdgfra were also expressed differently in the developing lung, heart, central nervous system, skin, tooth, and eye. Importantly, neither Pdgfralpha mRNA patterns nor levels were altered in Ihh mutant embryos although Gli1 and Ptc mRNA levels were dramatically reduced. Our results demonstrate that Gli1 is not required to induce Pdgfra expression during embryonic bone development, and are consistent with previous findings that Pdgfralpha and Hh pathways serve different functions in, e.g., bone, gut, and lung development. However, we cannot exclude the possibility that Glis can have more complex regulatory effects on Pdgfra gene activity, nor can we exclude such effects in pathological conditions.

  18. The zinc finger transcription factor 191 is required for early embryonic development and cell proliferation

    SciTech Connect

    Li Jianzhong; Chen Xia; Yang Hua; Wang Shuiliang; Guo Baoyu; Yu Long; Wang Zhugang; Fu Jiliang . E-mail: fu825@mail.tongji.edu.cn

    2006-12-10

    Human zinc finger protein 191 (ZNF191/ZNF24) was cloned and characterized as a SCAN family member, which shows 94% identity to its mouse homologue zinc finger protein 191 (Zfp191). ZNF191 can specifically interact with an intronic polymorphic TCAT repeat (HUMTH01) in the tyrosine hydroxylase (TH) gene. Allelic variations of HUMTH01 have been stated to have a quantitative silencing effect on TH gene expression and to correlate with quantitative and qualitative changes in the binding by ZNF191. Zfp191 is widely expressed during embryonic development and in multiple tissues and organs in adult. To investigate the functions of Zfp191 in vivo, we have used homologous recombination to generate mice that are deficient in Zfp191. Heterozygous Zfp191 {sup +/-} mice are normal and fertile. Homozygous Zfp191 {sup -/-} embryos are severely retarded in development and die at approximately 7.5 days post-fertilization. Unexpectedly, in Zfp191 {sup -/-} and Zfp191 {sup +/-} embryos, TH gene expression is not affected. Blastocyst outgrowth experiments and the RNA interference-mediated knockdown of ZNF191 in cultured cells revealed an essential role for Zfp191 in cell proliferation. In further agreement with this function, no viable Zfp191 {sup -/-} cell lines were obtained by derivation of embryonic stem (ES) cells from blastocysts of Zfp191 {sup +/-} intercrosses or by forced homogenotization of heterozygous ES cells at high concentrations of G418. These data show that Zfp191 is indispensable for early embryonic development and cell proliferation.

  19. Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell

    PubMed Central

    2013-01-01

    Background While more and more long intergenic non-coding RNAs (lincRNAs) were identified to take important roles in both maintaining pluripotency and regulating differentiation, how these lincRNAs may define and drive cell fate decisions on a global scale are still mostly elusive. Systematical profiling and comprehensive annotation of embryonic stem cells lincRNAs may not only bring a clearer big picture of these novel regulators but also shed light on their functionalities. Results Based on multiple RNA-Seq datasets, we systematically identified 300 human embryonic stem cell lincRNAs (hES lincRNAs). Of which, one forth (78 out of 300) hES lincRNAs were further identified to be biasedly expressed in human ES cells. Functional analysis showed that they were preferentially involved in several early-development related biological processes. Comparative genomics analysis further suggested that around half of the identified hES lincRNAs were conserved in mouse. To facilitate further investigation of these hES lincRNAs, we constructed an online portal for biologists to access all their sequences and annotations interactively. In addition to navigation through a genome browse interface, users can also locate lincRNAs through an advanced query interface based on both keywords and expression profiles, and analyze results through multiple tools. Conclusions By integrating multiple RNA-Seq datasets, we systematically characterized and annotated 300 hES lincRNAs. A full functional web portal is available freely at http://scbrowse.cbi.pku.edu.cn. As the first global profiling and annotating of human embryonic stem cell lincRNAs, this work aims to provide a valuable resource for both experimental biologists and bioinformaticians. PMID:24564552

  20. Hermes III endpoint energy calculation from photonuclear activation of 197Au and 58Ni foils

    SciTech Connect

    Parzyck, Christopher Thomas

    2014-09-01

    A new process has been developed to characterize the endpoint energy of HERMES III on a shot-to-shot basis using standard dosimetry tools from the Sandia Radiation Measurements Laboratory. Photonuclear activation readings from nickel and gold foils are used in conjunction with calcium fluoride thermoluminescent dosimeters to derive estimated electron endpoint energies for a series of HERMES shots. The results are reasonably consistent with the expected endpoint voltages on those shots.

  1. Nutrient reference value: non-communicable disease endpoints--a conference report.

    PubMed

    Lupton, J R; Blumberg, J B; L'Abbe, M; LeDoux, M; Rice, H B; von Schacky, C; Yaktine, A; Griffiths, J C

    2016-03-01

    scientific evidence does exist to confirm a relationship between the intake of a specific bioactive constituent and enhanced health conditions or reduced risk of a chronic disease. Further, research on the putative mechanisms of action of various classes of bioactives is supported by national and pan-national government agencies, and academic institutions, as well as functional food and dietary supplement manufacturers. Consumers are becoming educated and are seeking to purchase products containing bioactives, yet there is no evaluative process in place to let the public know how strong the science is behind the benefits or the quantitative amounts needed to achieve these beneficial health effects or to avoid exceeding the upper level (UL). When one lacks an essential nutrient, overt deficiency with concomitant physiological determents and eventually death are expected. The absence of bioactive substances from the diet results in suboptimal health, e.g., poor cellular and/or physiological function, which is relative and not absolute. Regrettably at this time, there is no DRI process to evaluate bioactives, although a recent workshop convened by the National Institutes of Health (Options for Consideration of Chronic Disease Endpoints for Dietary Reference Intakes (DRIs); March 10-11, 2015; http://health.gov/dietaryguidelines/dri/ ) did explore the process to develop DVs for nutrients, the lack of which result in increased risk of chronic disease (non-communicable disease) endpoints. A final report is expected soon. This conference (CRN-International Scientific Symposium; "Nutrient Reference Value-Non-Communicable Disease (NRV-NCD) Endpoints," 20 November in Kronberg, Germany; http://www.crn-i.ch/2015symposium/ ) explores concepts related to the Codex NRV process, the public health opportunities in setting NRVs for bioactive constituents, and further research and details on the specific class of bioactives, n-3 long-chain polyunsaturated fatty acids (also termed omega-3 fatty

  2. Efficient introduction of specific TP53 mutations into mouse embryonic fibroblasts and embryonic stem cells.

    PubMed

    Wei, Quan-Xiang; van der Hoeven, Franciscus; Hollstein, Monica; Odell, Adam F

    2012-05-17

    This protocol describes a rapid, precise method for generating sets of embryonic stem (ES) cells or mouse embryonic fibroblasts (MEFs) harboring point mutations in the p53 tumor suppressor gene (officially known as Trp53). The strategy uses cells from the Trp53 (p53-null) 'platform' mouse, which allows site-specific integration of plasmid DNA into the Trp53 locus. Simple PCR protocols identify correctly targeted clones and immunoblots verify re-expression of the protein. We also present protocol modifications needed for efficient recovery of MEF clones expressing p53 constructs that retain wild-type function, including growth at low (3%) oxygen and transient downregulation of p53 regulators to forestall cell senescence of primary MEFs. A library of cell lines expressing various p53 mutants derived from the same population of primary fibroblasts or platform ES cells can be acquired and screened in less than 1 month.

  3. Pancreatic Differentiation from Murine Embryonic Stem Cells.

    PubMed

    Sakano, Daisuke; Shiraki, Nobuaki; Kume, Shoen

    2016-01-01

    Pluripotent stem cells are considered as a cell source for replacement therapies for pancreatic beta cells and other organs.We identified tetrabenazine (TBZ), vesicular monoamine transporter 2 (VMAT2) inhibitor as a promoter of late-stage differentiation of Pdx1-positive pancreatic progenitor cells into Ngn3-positive endocrine progenitor cells. A cell-permeable cAMP analog, dBu-cAMP promotes beta cell maturation in late stage of differentiation. The induced beta cells can secrete insulin in a glucose-dependent manner.Our protocol consists of a three -step differentiation process. ES cell recapitulate embryonic developmental processes in vitro. Therefore, the ES cell differentiation system is a useful model for the understanding of molecular mechanism of beta-cell differentiation and are useful for application for future regenerative medicine.

  4. Nucleofection of human embryonic stem cells.

    PubMed

    Siemen, Henrike; Nix, Michael; Endl, Elmar; Koch, Philipp; Itskovitz-Eldor, Joseph; Brüstle, Oliver

    2005-08-01

    Human embryonic stem (hES) cells provide an important tool for the study of human development, disease, and tissue regeneration. Technologies for efficient genetic modification are required to exploit hES cells fully for these applications. Here we present a customized protocol for the transfection of hES cells with the Nucleofector technology and compare its efficiency with conventional electroporation and lipofection. Cell survival and transfection efficiency were quantified using an enhanced green fluorescent protein (EGFP) reporter construct. Our optimized nucleofection parameters yielded survival rates >70%. Under these conditions, 66% of the surviving cells showed transgene expression 24 h after nucleofection. Transfected cells maintained expression of the pluripotency- associated markers Tra-1-60, Tra-1-81, and Oct4 and could be expanded to stably transgene-expressing clones. The low quantities of hES cells and DNA required for nucleofection could make this method an attractive tool for miniaturized high throughput screening (HTS) applications.

  5. Will embryonic stem cells change health policy?

    PubMed

    Sage, William M

    2010-01-01

    Embryonic stem cells are actively debated in political and public policy arenas. However, the connections between stem cell innovation and overall health care policy are seldom elucidated. As with many controversial aspects of medical care, the stem cell debate bridges to a variety of social conversations beyond abortion. Some issues, such as translational medicine, commercialization, patient and public safety, health care spending, physician practice, and access to insurance and health care services, are core health policy concerns. Other issues, such as economic development, technologic progress, fiscal politics, and tort reform, are only indirectly related to the health care system but are frequently seen through a health care lens. These connections will help determine whether the stem cell debate reaches a resolution, and what that resolution might be.

  6. Embryonal brain tumors and developmental control genes

    SciTech Connect

    Aguzzi, A.

    1995-12-31

    Cell proliferation in embryogenesis and neoplastic transformation is thought to be controlled by similar sets of regulatory genes. This is certainly true for tumors of embryonic origin, such as Ewing sarcoma, Wilms` tumor and retinoblastoma, in which developmental control genes are either activated as oncogenes to promote proliferation, or are inactivated to eliminate their growth suppressing function. However, to date little is known about the genetic events underlying the pathogenesis of medulloblastoma, the most common brain tumor in children, which still carries an unfavourable prognosis. None of the common genetic alterations identified in other neuroectodermal tumors, such as mutation of the p53 gene or amplification of tyrosine kinase receptor genes, could be uncovered as key events in the formation of medulloblastoma. The identification of regulatory genes which are expressed in this pediatric brain tumor may provide an alternative approach to gain insight into the molecular aspects of tumor formation.

  7. Myosin synthesis in embryonic chicken fibroblasts

    PubMed Central

    1979-01-01

    The rate of constitutive myosin synthesis was measured in cultures of replicating embryonic chicken skin fibroblasts by pulse labeling with [3H]leucine. These cells synthesized the 200,000-dalton heavy chain of myosin (MHC) at a rate of 3.2 x 10(3) molecules/cell/min. Additionally, an independent estimate of the MHC synthesis rate needed to maintain a constant level of constitutive MHC/cell was calculated from total protein content, percentage MHC, fibroblast doubling time, and MHC half- life. This calculated rate of approximately 2.9 x 10(3) molecules/cell/min was in close agreement with the measured rate. By comparison, the synthesis rate of myofibrillar MHC in fully activated muscle cell cultures was approximately 2.9 x 10(4) molecules/nucleus/min. PMID:479285

  8. Functional analysis of Scr during embryonic and post-embryonic development in the cockroach, Periplaneta americana.

    PubMed

    Hrycaj, Steven; Chesebro, John; Popadić, Aleksandar

    2010-05-01

    The cockroach, Periplaneta americana represents a basal insect lineage that undergoes the ancestral hemimetabolous mode of development. Here, we examine the embryonic and post-embryonic functions of the hox gene Scr in Periplaneta as a way of better understanding the roles of this gene in the evolution of insect body plans. During embryogenesis, Scr function is strictly limited to the head with no role in the prothorax. This indicates that the ancestral embryonic function of Scr was likely restricted to the head, and that the posterior expansion of expression in the T1 legs may have preceded any apparent gain of function during evolution. In addition, Scr plays a pivotal role in the formation of the dorsal ridge, a structure that separates the head and thorax in all insects. This is evidenced by the presence of a supernumerary segment that occurs between the labial and T1 segments of RNAiScr first nymphs and is attributed to an alteration in engrailed (en) expression. The fact that similar Scr phenotypes are observed in Tribolium but not in Drosophila or Oncopeltus reveals the presence of lineage-specific variation in the genetic architecture that controls the formation of the dorsal ridge. In direct contrast to the embryonic roles, Scr has no function in the head region during post-embryogenesis in Periplaneta, and instead, strictly acts to provide identity to the T1 segment. Furthermore, the strongest Periplaneta RNAiScr phenotypes develop ectopic wing-like tissue that originates from the posterior region of the prothoracic segment. This finding provides a novel insight into the current debate on the morphological origin of insect wings.

  9. Acute effects of a prooxidant herbicide on the microalga Chlamydomonas reinhardtii: Screening cytotoxicity and genotoxicity endpoints.

    PubMed

    Esperanza, Marta; Cid, Ángeles; Herrero, Concepción; Rioboo, Carmen

    2015-08-01

    Since recent evidence has demonstrated that many types of chemicals exhibit oxidative and/or genotoxic potential on living organisms, reactive oxygen species (ROS) formation and DNA damage are currently the best accepted paradigms to assess the potential hazardous biological effects of a wide range of contaminants. The goal of this study was to evaluate the sensitivity of different cytotoxicity and genotoxicity responses on the model microalga Chlamydomonas reinhardtii exposed to the prooxidant herbicide paraquat. In addition to the growth endpoint, cell viability, mitochondrial membrane potential and presence of reactive oxygen species (ROS) were assayed as potential markers of cytotoxicity using flow cytometry (FCM). To study the effects of paraquat on C. reinhardtii DNA, several genotoxicity approaches were implemented for the first time in an ecotoxicological study on microalgae. Oxidative DNA base damage was analysed by measuring the oxidative DNA lesion 8-OHdG by FCM. DNA fragmentation was analysed by different methods: comet assay, and cell cycle analysis by FCM, with a particular focus on the presence of subG1-nuclei. Finally, effects on morphology of nuclei were monitored through DAPI staining. The evaluation of these endpoints showed that several physiological and biochemical parameters reacted to oxidative stress disturbances with greater sensitivity than integrative parameters such as growth rates or cell viability. The experiments revealed concentration-dependent cytotoxicity (ROS formation, depolarization of mitochondrial membrane), genotoxicity (oxidative DNA damage, DNA strand breakage, alterations in nuclear morphology), and cell cycle disturbances (subG1-nuclei, decrease of 4N population) in paraquat-treated cells. Overall, the genotoxicity results indicate that the production of ROS caused by exposure to paraquat induces oxidative DNA damage followed by DNA single- and double-strand breaks and cell cycle alterations, possibly leading to apoptosis

  10. Quantitative three-dimensional analysis of embryonic chick morphogenesis via microcomputed tomography.

    PubMed

    Kim, Jun Sup; Min, Jouha; Recknagel, Andrew K; Riccio, Mark; Butcher, Jonathan T

    2011-01-01

    Embryonic development is a remarkably complex and rapidly evolving morphogenetic process. Although many of the early patterning events have been well described, understanding the anatomical changes at later stages where clinically relevant malformations are more likely to be survivable has been limited by the lack of quantitative 3D imaging tools. Microcomputed tomography (Micro-CT) has emerged as a powerful tool for embryonic imaging, but a quantitative analysis of organ and tissue growth has not been conducted. In this study, we present a simple method for acquiring highly detailed, quantitative 3D datasets of embryonic chicks with Micro-CT. Embryos between 4 and 12 days (HH23 and HH40) were labeled with osmium tetroxide (OT), which revealed highly detailed soft tissue anatomy when scanned at 25 μm resolution. We demonstrate tissue boundary and inter-tissue contrast fidelity in virtual 2D sections are quantitatively and qualitatively similar to those of histological sections. We then establish mathematical relationships for the volumetric growth of heart, limb, eye, and brain during this period of development. We show that some organs exhibit constant exponential growth (eye and heart), whereas others contained multiple phases of growth (forebrain and limb). Furthermore, we show that cardiac myocardial volumetric growth differs in a time and chamber specific manner. These results demonstrate Micro-CT is a powerful technique for quantitative imaging of embryonic growth. The data presented here establish baselines from which to compare the effects of genetic or experimental perturbations. Quantifying subtle differences in morphogenesis is increasingly important as research focuses on localized and conditional effects.

  11. YAP/TAZ enhance mammalian embryonic neural stem cell characteristics in a Tead-dependent manner

    SciTech Connect

    Han, Dasol; Byun, Sung-Hyun; Park, Soojeong; Kim, Juwan; Kim, Inhee; Ha, Soobong; Kwon, Mookwang; Yoon, Keejung

    2015-02-27

    Mammalian brain development is regulated by multiple signaling pathways controlling cell proliferation, migration and differentiation. Here we show that YAP/TAZ enhance embryonic neural stem cell characteristics in a cell autonomous fashion using diverse experimental approaches. Introduction of retroviral vectors expressing YAP or TAZ into the mouse embryonic brain induced cell localization in the ventricular zone (VZ), which is the embryonic neural stem cell niche. This change in cell distribution in the cortical layer is due to the increased stemness of infected cells; YAP-expressing cells were colabeled with Sox2, a neural stem cell marker, and YAP/TAZ increased the frequency and size of neurospheres, indicating enhanced self-renewal- and proliferative ability of neural stem cells. These effects appear to be TEA domain family transcription factor (Tead)–dependent; a Tead binding-defective YAP mutant lost the ability to promote neural stem cell characteristics. Consistently, in utero gene transfer of a constitutively active form of Tead2 (Tead2-VP16) recapitulated all the features of YAP/TAZ overexpression, and dominant negative Tead2-EnR resulted in marked cell exit from the VZ toward outer cortical layers. Taken together, these results indicate that the Tead-dependent YAP/TAZ signaling pathway plays important roles in neural stem cell maintenance by enhancing stemness of neural stem cells during mammalian brain development. - Highlights: • Roles of YAP and Tead in vivo during mammalian brain development are clarified. • Expression of YAP promotes embryonic neural stem cell characteristics in vivo in a cell autonomous fashion. • Enhancement of neural stem cell characteristics by YAP depends on Tead. • Transcriptionally active form of Tead alone can recapitulate the effects of YAP. • Transcriptionally repressive form of Tead severely reduces stem cell characteristics.

  12. An assay for permeability of the zebrafish embryonic neuroepithelium.

    PubMed

    Chang, Jessica T; Sive, Hazel

    2012-10-24

    The brain ventricular system is conserved among vertebrates and is composed of a series of interconnected cavities called brain ventricles, which form during the earliest stages of brain development and are maintained throughout the animal's life. The brain ventricular system is found in vertebrates, and the ventricles develop after neural tube formation, when the central lumen fills with cerebrospinal fluid (CSF) (1,2). CSF is a protein rich fluid that is essential for normal brain development and function(3-6). In zebrafish, brain ventricle inflation begins at approximately 18 hr post fertilization (hpf), after the neural tube is closed. Multiple processes are associated with brain ventricle formation, including formation of a neuroepithelium, tight junction formation that regulates permeability and CSF production. We showed that the Na,K-ATPase is required for brain ventricle inflation, impacting all these processes (7,8), while claudin 5a is necessary for tight junction formation (9). Additionally, we showed that "relaxation" of the embryonic neuroepithelium, via inhibition of myosin, is associated with brain ventricle inflation. To investigate the regulation of permeability during zebrafish brain ventricle inflation, we developed a ventricular dye retention assay. This method uses brain ventricle injection in a living zebrafish embryo, a technique previously developed in our lab(10), to fluorescently label the cerebrospinal fluid. Embryos are then imaged over time as the fluorescent dye moves through the brain ventricles and neuroepithelium. The distance the dye front moves away from the basal (non-luminal) side of the neuroepithelium over time is quantified and is a measure of neuroepithelial permeability (Figure 1). We observe that dyes 70 kDa and smaller will move through the neuroepithelium and can be detected outside the embryonic zebrafish brain at 24 hpf (Figure 2). This dye retention assay can be used to analyze neuroepithelial permeability in a

  13. Energy and nutrient utilisation by embryonic reptiles.

    PubMed

    Thompson, Michael B; Speake, Brian K

    2002-11-01

    Most reptiles are oviparous, with the developing embryos relying on the contents of the yolk to sustain development until hatching (lecithotrophy). The yolk is composed primarily of lipid and protein, which act as an energy source and the essential components to build embryonic tissue. Nevertheless, yolk and the resulting embryos contain many other nutrients, including inorganic ions, vitamins, carotenoids, water and hormones. Apart from water and oxygen, which may be taken up by eggs, and some inorganic ions that can come from the eggshell or even from outside the egg, everything required by the embryo must be in the egg when it is laid. Approximately 20% of squamate reptiles are viviparous, exhibiting a variety of placental complexities. Species with complex placentae have reduced yolk volumes, with the mother augmenting embryonic nutrition by provision across the placenta (placentotrophy). Despite assumed advantages of placentotrophy, only 5 out of approximately 100 lineages of viviparous squamates exhibit substantial placentotrophy. This paper reviews available and recent information on the yolk contents of a variety of squamate reptiles to ask the question, how are nutrients transported from the yolk to the embryo or across the placenta? Although, current available data suggest that, in broad terms, yolk is taken up by embryos without discrimination of the nutrients, there are some apparent exceptions, including the very long chain polyunsaturated fatty acids. In addition, fundamental differences in the patterns of energy utilisation in lizards and snakes suggest fundamental differences in lipid profiles in these taxa, which appear to reflect the differences between placentotrophic and lecithotrophic viviparous lizards.

  14. Embryonic development of the cricket Gryllus bimaculatus.

    PubMed

    Donoughe, Seth; Extavour, Cassandra G

    2016-03-01

    Extensive research into Drosophila melanogaster embryogenesis has improved our understanding of insect developmental mechanisms. However, Drosophila development is thought to be highly divergent from that of the ancestral insect and arthropod in many respects. We therefore need alternative models for arthopod development that are likely to be more representative of basally-branching clades. The cricket Gryllus bimaculatus is such a model, and currently has the most sophisticated functional genetic toolkit of any hemimetabolous insect. The existing cricket embryonic staging system is fragmentary, and it is based on morphological landmarks that are not easily visible on a live, undissected egg. To address this problem, here we present a complementary set of "egg stages" that serve as a guide for identifying the developmental progress of a cricket embryo from fertilization to hatching, based solely on the external appearance of the egg. These stages were characterized using a combination of brightfield timelapse microscopy, timed brightfield micrographs, confocal microscopy, and measurements of egg dimensions. These egg stages are particularly useful in experiments that involve egg injection (including RNA interference, targeted genome modification, and transgenesis), as injection can alter the speed of development, even in control treatments. We also use 3D reconstructions of fixed embryo preparations to provide a comprehensive description of the morphogenesis and anatomy of the cricket embryo during embryonic rudiment assembly, germ band formation, elongation, segmentation, and appendage formation. Finally, we aggregate and schematize a variety of published developmental gene expression patterns. This work will facilitate further studies on G. bimaculatus development, and serve as a useful point of reference for other studies of wild type and experimentally manipulated insect development in fields from evo-devo to disease vector and pest management.

  15. Use of murine embryonic stem cells in embryotoxicity assays: the embryonic stem cell test.

    PubMed

    Seiler, Andrea E M; Buesen, Roland; Visan, Anke; Spielmann, Horst

    2006-01-01

    The embryonic stem cell test (EST) takes advantage of the potential of murine embryonic stem (ES) cells to differentiate in culture to test embryotoxicity in vitro. The EST represents a scientifically validated in vitro system for the classification of compounds according to their teratogenic potential based on the morphological analysis of beating cardiomyocytes in embryoid body outgrowths compared to cytotoxic effects on murine ES cells and differentiated 3T3 fibroblasts. Through a number of prevalidation and validation studies, the EST has been demonstrated to be a reliable alternative method for embryotoxicity testing based on the most important mechanisms in embryotoxicity-cytotoxicity and differentiation--as well as on differences in sensitivity between differentiated and embryonic tissues. Improvements of the EST protocol using flow cytometry analysis showed that differential expression of sarcomeric myosin heavy chain and alpha-actinin proteins quantified under the influence of a test compound is a useful marker for detecting potential teratogenicity. The in vitro embryotoxicity test described in this chapter is rapid, simple, and sensitive and can be usefully employed as a component of the risk/hazard assessment process.

  16. A vision-based end-point control for a two-link flexible manipulator. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Obergfell, Klaus

    1991-01-01

    The measurement and control of the end-effector position of a large two-link flexible manipulator are investigated. The system implementation is described and an initial algorithm for static end-point positioning is discussed. Most existing robots are controlled through independent joint controllers, while the end-effector position is estimated from the joint positions using a kinematic relation. End-point position feedback can be used to compensate for uncertainty and structural deflections. Such feedback is especially important for flexible robots. Computer vision is utilized to obtain end-point position measurements. A look-and-move control structure alleviates the disadvantages of the slow and variable computer vision sampling frequency. This control structure consists of an inner joint-based loop and an outer vision-based loop. A static positioning algorithm was implemented and experimentally verified. This algorithm utilizes the manipulator Jacobian to transform a tip position error to a joint error. The joint error is then used to give a new reference input to the joint controller. The convergence of the algorithm is demonstrated experimentally under payload variation. A Landmark Tracking System (Dickerson, et al 1990) is used for vision-based end-point measurements. This system was modified and tested. A real-time control system was implemented on a PC and interfaced with the vision system and the robot.

  17. DEVELOPMENT OF QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIPS (QSARS) TO PREDICT TOXICITY FOR A VARIETY OF HUMAN AND ECOLOGICAL ENDPOINTS

    EPA Science Inventory

    A web accessible software tool is being developed to predict the toxicity of unknown chemicals for a wide variety of endpoints. The tool will enable a user to easily predict the toxicity of a query compound by simply entering its structure in a 2-dimensional (2-D) chemical sketc...

  18. A novel test to compare two treatments based on endpoints involving both nonfatal and fatal events.

    PubMed

    Potthoff, Richard F; Halabi, Susan

    2015-01-01

    In a clinical trial comparing two treatment groups, one commonly-used endpoint is time to death. Another is time until the first nonfatal event (if there is one) or until death (if not). Both endpoints have drawbacks. The wrong choice may adversely affect the value of the study by impairing power if deaths are too few (with the first endpoint) or by lessening the role of mortality if not (with the second endpoint). We propose a compromise that provides a simple test based on the time to death if the patient has died or time since randomization augmented by an increment otherwise. The test applies the ordinary two-sample Wilcoxon statistic to these values. The formula for the increment (the same for experimental and control patients) must be specified before the trial starts. In the simplest (and perhaps most useful) case, the increment assumes only two values, according to whether or not the (surviving) patient had a nonfatal event. More generally, the increment depends on the time of the first nonfatal event, if any, and the time since randomization. The test has correct Type I error even though it does not handle censoring in a customary way. For conditions where investigators would face no easy (advance) choice between the two older tests, simulation results favor the new test. An example using a renal-cancer trial is presented.

  19. Review of Dredging Elutriate Application Factors: Relevance to Acute-to-Chronic Protection, Contaminant, and Endpoint Specificity

    DTIC Science & Technology

    2015-07-01

    Particularly, use of the default AF is overly conservative when high levels of nonpersistent chemicals such as ammonia are present in elutriate... ammonia toxicity and the development toxicity test endpoint. DISCLAIMER: The contents of this report are not to be used for advertising, publication, or...Importance of ammonia in determining elutriate toxicity results ............................................. 6 Development toxicity tests and use of

  20. 76 FR 35450 - Draft Guidance for Industry on Clinical Trial Endpoints for the Approval of Non-Small Cell Lung...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-17

    ... the Approval of Non-Small Cell Lung Cancer Drugs and Biologics; Availability AGENCY: Food and Drug... Cell Lung Cancer Drugs and Biologics.'' This draft guidance provides recommendations to applicants on... draft guidance for industry entitled ``Clinical Trial Endpoints for the Approval of Non-Small Cell...

  1. Role of biomechanics and muscle activation strategy in the production of endpoint force patterns in the cat hindlimb.

    PubMed

    Lemay, Michel A; Bhowmik-Stoker, Manoshi; McConnell, George C; Grill, Warren M

    2007-01-01

    We used a musculoskeletal model of the cat hindlimb to compare the patterns of endpoint forces generated by all possible combination of 12 hindlimb muscles under three different muscle activation rules: homogeneous activation of muscles based on uniform activation levels, homogeneous activation of muscles based on uniform (normalized) force production, and activation based on the topography of spinal motoneuron pools. Force patterns were compared with the patterns obtained experimentally by microstimulation of the lumbar spinal cord in spinal intact cats. Magnitude and orientation of the force patterns were compared, as well as the proportion of the types found, and the proportions of patterns exhibiting points of zero force (equilibrium points). The force patterns obtained with the homogenous activation and motoneuron topography models were quite similar to those measured experimentally, with the differences being larger for the patterns from the normalized endpoint forces model. Differences in the proportions of types of force patterns between the three models and the experimental results were significant for each model. Both homogeneous activation and normalized endpoint force models produced similar proportions of equilibrium points as found experimentally. The results suggest that muscle biomechanics play an important role in limiting the number of endpoint force pattern types, and that muscle combinations activated at similar levels reproduced best the experimental results obtained with intraspinal microstimulation.

  2. On the relationship between the causal-inference and meta-analytic paradigms for the validation of surrogate endpoints.

    PubMed

    Alonso, Ariel; Van der Elst, Wim; Molenberghs, Geert; Buyse, Marc; Burzykowski, Tomasz

    2015-03-01

    The increasing cost of drug development has raised the demand for surrogate endpoints when evaluating new drugs in clinical trials. However, over the years, it has become clear that surrogate endpoints need to be statistically evaluated and deemed valid, before they can be used as substitutes of "true" endpoints in clinical studies. Nowadays, two paradigms, based on causal-inference and meta-analysis, dominate the scene. Nonetheless, although the literature emanating from these paradigms is wide, till now the relationship between them has largely been left unexplored. In the present work, we discuss the conceptual framework underlying both approaches and study the relationship between them using theoretical elements and the analysis of a real case study. Furthermore, we show that the meta-analytic approach can be embedded within a causal-inference framework on the one hand and that it can be heuristically justified why surrogate endpoints successfully evaluated using this approach will often be appealing from a causal-inference perspective as well, on the other. A newly developed and user friendly R package Surrogate is provided to carry out the evaluation exercise.

  3. Fourier-transform infrared spectroscopy as a novel approach to providing effect-based endpoints in duckweed toxicity testing.

    PubMed

    Hu, Li-Xin; Ying, Guang-Guo; Chen, Xiao-Wen; Huang, Guo-Yong; Liu, You-Sheng; Jiang, Yu-Xia; Pan, Chang-Gui; Tian, Fei; Martin, Francis L

    2017-02-01

    Traditional duckweed toxicity tests only measure plant growth inhibition as an endpoint, with limited effects-based data. The present study aimed to investigate whether Fourier-transform infrared (FTIR) spectroscopy could enhance the duckweed (Lemna minor L.) toxicity test. Four chemicals (Cu, Cd, atrazine, and acetochlor) and 4 metal-containing industrial wastewater samples were tested. After exposure of duckweed to the chemicals, standard toxicity endpoints (frond number and chlorophyll content) were determined; the fronds were also interrogated using FTIR spectroscopy under optimized test conditions. Biochemical alterations associated with each treatment were assessed and further analyzed by multivariate analysis. The results showed that comparable x% of effective concentration (ECx) values could be achieved based on FTIR spectroscopy in comparison with those based on traditional toxicity endpoints. Biochemical alterations associated with different doses of toxicant were mainly attributed to lipid, protein, nucleic acid, and carbohydrate structural changes, which helped to explain toxic mechanisms. With the help of multivariate analysis, separation of clusters related to different exposure doses could be achieved. The present study is the first to show successful application of FTIR spectroscopy in standard duckweed toxicity tests with biochemical alterations as new endpoints. Environ Toxicol Chem 2017;36:346-353. © 2016 SETAC.

  4. Controlling the duty cycle of holographic crossed gratings by in situ endpoint detection during development.

    PubMed

    Wang, Shiwei; Zeng, Lijiang

    2016-04-01

    A method of in situ development endpoint detection is proposed to control the duty cycle of holographic crossed gratings. Based on the observation that after the developer first touches the substrate surface the topography of the crossed grating undergoes an evolution process from a hole array of increasing diameter to a pillar array of decreasing diameter, we set up a development model. In this model, the shapes of both holes and pillars are assumed to have square in-plane cross sections, rotated 45° with respect to the main periodic directions, and straight side walls perpendicular to the grating plane. Thus, the main development process, including the transition from a hole array to a pillar array, can be characterized by a single parameter continuously, and the change of diffraction efficiency during the process can be theoretically calculated. Two different in situ development monitoring conditions were simulated and tested experimentally. Using this method, crossed gratings with various duty cycles were fabricated under different incident and monitoring conditions.

  5. An end-point method based on graphene oxide for RNase H analysis and inhibitors screening.

    PubMed

    Zhao, Chuan; Fan, Jialong; Peng, Lan; Zhao, Lijian; Tong, Chunyi; Wang, Wei; Liu, Bin

    2017-04-15

    As a highly conserved damage repair protein, RNase H can hydrolysis DNA-RNA heteroduplex endonucleolytically and cleave RNA-DNA junctions as well. In this study, we have developed an accurate and sensitive RNase H assay based on fluorophore-labeled chimeric substrate hydrolysis and the differential affinity of graphene oxide on RNA strand with different length. This end-point measurement method can detect RNase H in a range of 0.01 to 1 units /mL with a detection limit of 5.0×10(-3) units/ mL under optimal conditions. We demonstrate the utility of the assay by screening antibiotics, resulting in the identification of gentamycin, streptomycin and kanamycin as inhibitors with IC50 of 60±5µM, 70±8µM and 300±20µM, respectively. Furthermore, the assay was reliably used to detect RNase H in complicated biosamples and found that RNase H activity in tumor cells was inhibited by gentamycin and streptomycin sulfate in a concentration-dependent manner. The average level of RNase H in serums of HBV infection group was similar to that of control group. In summary, the assay provides an alternative tool for biochemical analysis for this enzyme and indicates the feasibility of high throughput screening inhibitors of RNase H in vitro and in vivo.

  6. Endpoints for sediment toxicity tests with the freshwater bivalve Sphaerium corneum

    SciTech Connect

    Looise, B.A.S.; Holwerda, D.A.; Foekema, E.M.

    1994-12-31

    Being a participant in the EU project `Sediment toxicity tests for poorly water soluble substances` the authors examined toxicological endpoints with the freshwater bivalve Sphaerium corneum. These included induction of two biotransformation enzymes, glutathione S-transferase and catalase, and survival time under anoxic stress. Animals were taken from the field and exposed to sediments spiked with contaminants or to contaminants in a water-only system. Also a field sediment from a contaminated area was included. Spiking substances were lindane, dieldrin, benzo[a]pyrene, and PCB. After 1--5 weeks of exposure to contaminated sediments or water, animals were examined for induction of the biotransformation enzymes glutathione S-transferase (GST) and catalase. GST activity in whole body soft tissue was measured spectrophotometrically by the amount of conjugate formed, using 1-chloro-2,4-dinitrobenzene as a substrate and glutathione as a co-substrate. Catalase activity was also measured spectrophotometrically by the transformation rate of the substrate, hydrogen peroxide. None of the treatments resulted in a significant increase of GST or catalase activities. After 2--5 weeks of exposure to contaminated sediment, the animals were transferred to individual 10-mL bottles. Results show significant decrease of survival times of animals exposed to contaminated sediments.

  7. Critical exponents of the quark-gluon bags model with a critical endpoint

    NASA Astrophysics Data System (ADS)

    Ivanytskyi, A. I.; Bugaev, K. A.; Sorin, A. S.; Zinovjev, G. M.

    2012-12-01

    The critical indices α', β, γ', and δ of the Quark Gluon Bags with Surface Tension Model that has a critical endpoint are calculated and compared with the exponents of other models. These indices are expressed in terms of the most general parameters of the model. Despite the usual expectations the found critical indices do not depend on the Fisher exponent τ and on the parameter ϰ which relates the mean bag surface to its volume. The scaling relations for the obtained critical exponents are verified, and it is demonstrated that for the standard definition of the index α' the Fisher and the Griffiths scaling inequalities are not fulfilled in general case, whereas the Liberman scaling inequality is always obeyed. This is not surprising for the phase diagram with the asymmetric properties of pure phases, but the present model also provides us with the first and explicit example that the specially defined index αs' does not recover the scaling relations as well. Therefore, here we suggest the physically motivated definition of the index α'=αc' and demonstrate that such a definition recovers the Fisher scaling inequality, while it is shown that the Griffiths inequality should be generalized for the phase diagram with the asymmetric properties. The critical exponents of several systems that belong to different universality classes are successfully described by the parameters of the present model, and hence its equation of state can be used for a variety of practical applications.

  8. Natural Gas Residual Fluids: Sources, Endpoints, and Organic Chemical Composition after Centralized Waste Treatment in Pennsylvania.

    PubMed

    Getzinger, Gordon J; O'Connor, Megan P; Hoelzer, Kathrin; Drollette, Brian D; Karatum, Osman; Deshusses, Marc A; Ferguson, P Lee; Elsner, Martin; Plata, Desiree L

    2015-07-21

    Volumes of natural gas extraction-derived wastewaters have increased sharply over the past decade, but the ultimate fate of those waste streams is poorly characterized. Here, we sought to (a) quantify natural gas residual fluid sources and endpoints to bound the scope of potential waste stream impacts and (b) describe the organic pollutants discharged to surface waters following treatment, a route of likely ecological exposure. Our findings indicate that centralized waste treatment facilities (CWTF) received 9.5% (8.5 × 10(8) L) of natural gas residual fluids in 2013, with some facilities discharging all effluent to surface waters. In dry months, discharged water volumes were on the order of the receiving body flows for some plants, indicating that surface waters can become waste-dominated in summer. As disclosed organic compounds used in high volume hydraulic fracturing (HVHF) vary greatly in physicochemical properties, we deployed a suite of analytical techniques to characterize CWTF effluents, covering 90.5% of disclosed compounds. Results revealed that, of nearly 1000 disclosed organic compounds used in HVHF, only petroleum distillates and alcohol polyethoxylates were present. Few analytes targeted by regulatory agencies (e.g., benzene or toluene) were observed, highlighting the need for expanded and improved monitoring efforts at CWTFs.

  9. Speech endpoint detection with non-language speech sounds for generic speech processing applications

    NASA Astrophysics Data System (ADS)

    McClain, Matthew; Romanowski, Brian

    2009-05-01

    Non-language speech sounds (NLSS) are sounds produced by humans that do not carry linguistic information. Examples of these sounds are coughs, clicks, breaths, and filled pauses such as "uh" and "um" in English. NLSS are prominent in conversational speech, but can be a significant source of errors in speech processing applications. Traditionally, these sounds are ignored by speech endpoint detection algorithms, where speech regions are identified in the audio signal prior to processing. The ability to filter NLSS as a pre-processing step can significantly enhance the performance of many speech processing applications, such as speaker identification, language identification, and automatic speech recognition. In order to be used in all such applications, NLSS detection must be performed without the use of language models that provide knowledge of the phonology and lexical structure of speech. This is especially relevant to situations where the languages used in the audio are not known apriori. We present the results of preliminary experiments using data from American and British English speakers, in which segments of audio are classified as language speech sounds (LSS) or NLSS using a set of acoustic features designed for language-agnostic NLSS detection and a hidden-Markov model (HMM) to model speech generation. The results of these experiments indicate that the features and model used are capable of detection certain types of NLSS, such as breaths and clicks, while detection of other types of NLSS such as filled pauses will require future research.

  10. Determining significant endpoints for ecological risk analyses. 1997 annual progress report

    SciTech Connect

    Hinton, T.G.; Congdon, J.; Rowe, C.; Scott, D.; Bedford, J.; Whicker, F.W.

    1997-11-01

    'This report summarizes the first year''s progress of research funded under the Department of Energy''s Environmental Management Science Program. The research was initiated to better determine ecological risks from toxic and radioactive contaminants. More precisely, the research is designed to determine the relevancy of sublethal cellular damage to the performance of individuals and to identify characteristics of non-human populations exposed to chronic, low-level radiation, as is typically found on many DOE sites. The authors propose to establish a protocol to assess risks to non-human species at higher levels of biological organization by relating molecular damage to more relevant responses that reflect population health. They think that they can achieve this by coupling changes in metabolic rates and energy allocation patterns to meaningful population response variables, and by using novel biological dosimeters in controlled, manipulative dose/effects experiments. They believe that a scientifically defensible endpoint for measuring ecological risks can only be determined once its understood the extent to which molecular damage from contaminant exposure is detrimental at the individual and population levels of biological organization.'

  11. Prediction of organ toxicity endpoints by QSAR modeling based on precise chemical-histopathology annotations.

    PubMed

    Myshkin, Eugene; Brennan, Richard; Khasanova, Tatiana; Sitnik, Tatiana; Serebriyskaya, Tatiana; Litvinova, Elena; Guryanov, Alexey; Nikolsky, Yuri; Nikolskaya, Tatiana; Bureeva, Svetlana

    2012-09-01

    The ability to accurately predict the toxicity of drug candidates from their chemical structure is critical for guiding experimental drug discovery toward safer medicines. Under the guidance of the MetaTox consortium (Thomson Reuters, CA, USA), which comprised toxicologists from the pharmaceutical industry and government agencies, we created a comprehensive ontology of toxic pathologies for 19 organs, classifying pathology terms by pathology type and functional organ substructure. By manual annotation of full-text research articles, the ontology was populated with chemical compounds causing specific histopathologies. Annotated compound-toxicity associations defined histologically from rat and mouse experiments were used to build quantitative structure-activity relationship models predicting subcategories of liver and kidney toxicity: liver necrosis, liver relative weight gain, liver lipid accumulation, nephron injury, kidney relative weight gain, and kidney necrosis. All models were validated using two independent test sets and demonstrated overall good performance: initial validation showed 0.80-0.96 sensitivity (correctly predicted toxic compounds) and 0.85-1.00 specificity (correctly predicted non-toxic compounds). Later validation against a test set of compounds newly added to the database in the 2 years following initial model generation showed 75-87% sensitivity and 60-78% specificity. General hepatotoxicity and nephrotoxicity models were less accurate, as expected for more complex endpoints.

  12. Update of the International Consensus on Palliative Radiotherapy Endpoints for Future Clinical Trials in Bone Metastases

    SciTech Connect

    Chow, Edward; Hoskin, Peter; Mitera, Gunita; Zeng Liang; Lutz, Stephen; Roos, Daniel; Hahn, Carol; Linden, Yvette van der; Hartsell, William; Kumar, Eshwar

    2012-04-01

    Purpose: To update the international consensus on palliative radiotherapy endpoints for future clinical trials in bone metastases by surveying international experts regarding previous uncertainties within the 2002 consensus, changes that may be necessary based on practice pattern changes and research findings since that time. Methods and Materials: A two-phase survey was used to determine revisions and new additions to the 2002 consensus. A total of 49 experts from the American Society for Radiation Oncology, the European Society for Therapeutic Radiology and Oncology, the Faculty of Radiation Oncology of the Royal Australian and New Zealand College of Radiologists, and the Canadian Association of Radiation Oncology who are directly involved in the care of patients with bone metastases participated in this survey. Results: Consensus was established in areas involving response definitions, eligibility criteria for future trials, reirradiation, changes in systemic therapy, radiation techniques, parameters at follow-up, and timing of assessments. Conclusion: An outline for trials in bone metastases was updated based on survey and consensus. Investigators leading trials in bone metastases are encouraged to adopt the revised guideline to promote consistent reporting. Areas for future research were identified. It is intended for the consensus to be re-examined in the future on a regular basis.

  13. Evaluation of New Drugs for Asthma and COPD: Endpoints, Biomarkers and Clinical Trial Design.

    PubMed

    Singh, Dave

    2017-01-01

    There remains a considerable need to develop novel therapies for patients with asthma and chronic obstructive pulmonary disease (COPD). The greatest challenge at the moment is measuring the effects of novel anti-inflammatory drugs, as these drugs often cause only small effects on lung function. Measurements that demonstrate the pharmacological and clinical effects of these drugs are needed. Furthermore, we now recognise that only subgroups of patients are likely to respond to these novel drugs, so using biomarkers to determine the clinical phenotype most suitable for such therapies is important. An endotype is a subtype of a (clinical) condition defined by a distinct pathophysiological mechanism. An endotype-driven approach may be more helpful in drug development, enabling drugs to be targeted specifically towards specific biological mechanisms rather than clinical characteristics. This requires the development of biomarkers to define endotypes and/or to measure drug effects. This newer approach should continue alongside efforts to optimise the measurement of clinical endpoints, including patient-reported outcome measurements, required by drug regulatory authorities.

  14. Early Proctoscopy is a Surrogate Endpoint of Late Rectal Toxicity in Prostate Cancer Treated With Radiotherapy

    SciTech Connect

    Ippolito, Edy; Massaccesi, Mariangela; Digesu, Cinzia; Deodato, Francesco; Macchia, Gabriella; Pirozzi, Giuseppe Antonio; Cilla, Savino; Cuscuna, Daniele; Di Lallo, Alessandra; Mattiucci, Gian Carlo; Mantini, Giovanna; Pacelli, Fabio; Valentini, Vincenzo; Cellini, Numa; Ingrosso, Marcello; Morganti, Alessio Giuseppe

    2012-06-01

    Purpose: To predict the grade and incidence of late clinical rectal toxicity through short-term (1 year) mucosal alterations. Methods and Materials: Patients with prostate adenocarcinoma treated with curative or adjuvant radiotherapy underwent proctoscopy a year after the course of radiotherapy. Mucosal changes were classified by the Vienna Rectoscopy Score (VRS). Late toxicity data were analyzed according to the Kaplan-Meier method. Comparison between prognosis groups was performed by log-rank analysis. Results: After a median follow-up time of 45 months (range, 18-99), the 3-year incidence of grade {>=}2 rectal late toxicity according to the criteria of the European Organization for Research and Treatment of Cancer and the Radiation Therapy Oncology Group was 24%, with all patients (24/24; 100%) experiencing rectal bleeding. The occurrence of grade {>=}2 clinical rectal late toxicity was higher in patients with grade {>=}2 (32% vs. 15 %, p = 0.02) or grade {>=}3 VRS telangiectasia (47% vs. 17%, p {<=} 0.01) and an overall VRS score of {>=}2 (31% vs. 16 %, p = 0.04) or {>=}3 (48% vs. 17%, p = 0.01) at the 1-year proctoscopy. Conclusions: Early proctoscopy (1 year) predicts late rectal bleeding and therefore can be used as a surrogate endpoint for late rectal toxicity in studies aimed at reducing this frequent complication.

  15. Analysis of In-Situ Vibration Monitoring for End-Point Detection of CMP Planarization Processes

    SciTech Connect

    Hetherington, Dale L.; Lauffer, James P.; Shingledecker, David M.; Stein, David J.; Wyckoff, Edward E.

    1999-05-14

    This paper details the analysis of vibration monitoring for end-point control in oxide CMP processes. Two piezoelectric accelerometers were integrated onto the backside of a stainless steel polishing head of an IPEC 472 polisher. One sensor was placed perpendicular to the carrier plate (vertical) and the other parallel to the plate (horizontal). Wafers patterned with metal and coated with oxide material were polished at different speeds and pressures. Our results show that it is possible to sense a change in the vibration signal over time during planarization of oxide material on patterned wafers. The horizontal accelerometer showed more sensitivity to change in vibration amplitude compared to the vertical accelerometer for a given polish condition. At low carrier and platen rotation rates, the change in vibration signal over time at fixed frequencies decreased approximately ½ - 1 order of magnitude (over the 2 to 10 psi polish pressure ranges). At high rotation speeds, the vibration signal remained essentially constant indicating that other factors dominated the vibration signaL These results show that while it is possible to sense changes in acceleration during polishing, more robust hardware and signal processing algorithms are required to ensure its use over a wide range of process conditions.

  16. Phagocytosis in earthworms: An environmentally acceptable endpoint to assess immunotoxic potential of contaminated soils

    SciTech Connect

    Giggleman, M.A.; Fitzpatrick, L.C.; Goven, A.J.; Venables, B.J.; Callahan, C.A.

    1995-12-31

    Phagocytosis, a host-defense mechanism phylogenetically conserved throughout the animal kingdom, by earthworm (Lumbricus terrestris) coelomocytes has potential as a surrogate for vertebrates to be used as an environmentally acceptable endpoint to assess sublethal immunotoxic risks of contaminated soils to environmental (eg. higher wildlife) and public health. Coelomocytes can be exposed in vivo to complex contaminated parent soils by placing earthworms in situ at hazardous waste sites (HWS) or into soil samples and their dilutions with artificial soil (AS) in the laboratory, or in vitro to soil extracts and their fractionations. Here the authors report on phagocytosis by coelomocytes in earthworms exposed to pentachlorophenol (PCP) contaminated soils from a wood treatment HWS, PCP-spiked AS and PCP treated filter paper (FP). HWS soil was diluted to 25% with AS to a sublethal concentration (ca. 125 mg kg{sup {minus}1}) and earthworms exposed for 14d at 10 C under light conditions. AS was spiked at ca. 125 mg kg{sup {minus}1} PCP and earthworms were similarly exposed. Controls for both consisted of earthworms exposed to 100% AS. Earthworms were exposed to FP treated with a sublethal PCP concentration (15 {micro}g cm{sup {minus}2}) at 10 C under dark conditions for 96H. Controls were similarly exposed without PCP. Phagocytosis by coelomocytes in earthworms exposed to HWS soil, spiked AS and treated FP was suppressed 37, 41 and 29%, respectively. Results are discussed in terms of PCP body burdens and exposure protocols.

  17. Sample preparation and characterization for a study of environmentally acceptable endpoints for hydrocarbon-contaminated soil

    SciTech Connect

    Kreitinger, J.P.; Finn, J.T.

    1995-12-31

    In the past, the interdisciplinary research effort required to investigate the acceptable cleanup endpoints for hydrocarbon-impacted soils has been limited by the lack of standardized soils for testing. To support the efforts of the various researchers participating in the EAE research initiative, soil samples were collected from ten sites representing hydrocarbon-impacted soils typical of exploration/production, refinery, and bulk storage terminal operations. The hydrocarbons in the standard soils include crude oil, mixed refinery products, diesel, gasoline, and jet fuel. Physical characterization included analysis of soil texture, water retention, particle density, nanoporosity, pH, electrical conductivity, cation exchange capacity, buffer capacity, organic carbon, sodium adsorption ratio, and clay mineralogy. Chemical characterization included analysis of total recoverable petroleum hydrocarbons, total volatile and semivolatile organic compounds and metals, and TCLP for metals and organics. An analysis of the aliphatic and aromatic hydrocarbon fractions was performed on each soil to support the use of various models for assessing soil toxicity. Screening-level toxicity tests were conducted using Microtox{trademark}, plant seed germination and growth, and earthworm mortality and growth. Biodegradability screening tests were performed in slurry shake flasks to estimate the availability of hydrocarbon fractions to soil microorganisms.

  18. Head movement: a novel serotonin-sensitive behavioral endpoint for tail suspension test analysis.

    PubMed

    Lockridge, Amber; Newland, Brett; Printen, Spencer; Romero, Gabriel E; Yuan, Li-Lian

    2013-06-01

    The tail suspension test (TST) as an antidepressant and depression-related behavior screen, has many advantages over the forced swim test (FST) in terms of procedural simplicity and consistent SSRI response. However, the FST has traditionally offered more specific neuromodulatory information by differentiating between serotonin (5-HT) and norepinephrine sensitive behavior categories. Head movement is a newly characterized behavior endpoint in the FST and TST with a selective 5-HT sensitivity. In this investigation, we show that the baseline and drug response profile of head movement previously found in the 129S6 strain of mice (Lockridge et al., 2010) is reproducible in the C57 strain. Head movement is inversely correlated to FST swimming and elevated in the TST by SSRI administration. The use of a weighted bin sample analysis method differentiates TST behaviors into fluoxetine-responsive head movement and desipramine-responsive struggling. The use of 5-HT subtype receptor agonists, after depleting endogenous 5-HT with pCPA, shows the head movement suppressing effect of 5-HT2A and 5-HT2C postsynaptic receptor activation. 5-HT1A and 5-HT1B agonists were ineffective. We propose that a head movement focused analysis can add sensitive and reliable 5-HT detection capability to mouse TST testing with minimal effort but significant reward.

  19. Augmented case-only designs for randomized clinical trials with failure time endpoints

    PubMed Central

    2015-01-01

    Summary Under suitable assumptions and by exploiting the independence between inherited genetic susceptibility and treatment assignment, the case-only design yields efficient estimates for subgroup treatment effects and gene-treatment interaction in a Cox model. However it cannot provide estimates of the genetic main effect and baseline hazards, that are necessary to compute the absolute disease risk. For two-arm, placebo-controlled trials with rare failure time endpoints, we consider augmenting the case-only design with random samples of controls from both arms, as in the classical case-cohort sampling scheme, or with a random sample of controls from the active treatment arm only. The latter design is motivated by vaccine trials for cost-effective use of resources and specimens so that host genetics and vaccine-induced immune responses can be studied simultaneously in a bigger set of participants. We show that these designs can identify all parameters in a Cox model and that the efficient case-only estimator can be incorporated in a two-step plug-in procedure. Results in simulations and a data example suggest that incorporating case-only estimators in the classical case-cohort design improves the precision of all estimated parameters; sampling controls only in the active treatment arm attains a similar level of efficiency. PMID:26347982

  20. Use of sublethal endpoints in sediment toxicity tests with the amphipod, Hyalella azteca

    SciTech Connect

    Ingersoll, C.G.; Brunson, E.L.; Dwyer, F.J.; Hardesty, D.K.; Kemble, N.E.

    1998-08-01

    Short-term sediment toxicity tests that only measure effects on survival can be used to identify high levels of contamination but may not be able to identify marginally contaminated sediments. The objective of the present study was to develop a method for determining the potential sublethal effects of contaminants associated with sediment on the amphipod Hyalella azteca (e.g., reproduction). This method was used to evaluate a formulated sediment and field-collected sediments with low to moderate concentrations of contaminants. Survival of amphipods in these sediments was typically >85% after the 28-d sediment exposures are the 14-d holding period in water to measure reproduction. Reproduction was more variable than growth; hence, more replicates in sediment tests often provides unique information that can be used to discriminate toxic effects of exposure to contaminants. Either length or weight can be measured in sediment tests with H. azteca. However, additional statistical options are available if length is measured on individual amphipods, such as nested analysis of variance that can account for variance in length within replicates. Ongoing water-only studies testing select contaminants will provide additional data on the relative sensitivity and variability of sublethal endpoints in toxicity tests with H. azteca.

  1. Bioavailability-based toxicity endpoints of bifenthrin for Hyalella azteca and Chironomus dilutus.

    PubMed

    Harwood, Amanda D; Landrum, Peter F; Lydy, Michael J

    2013-01-01

    Recent studies have determined that techniques, such as solid phase microextraction (SPME) fibers and Tenax beads, can predict bioaccumulation and potentially could predict toxicity for several compounds and species. Toxicity of bifenthrin was determined using two standard sediment toxicity tests with the benthic species Hyalella azteca and Chironomus dilutus in three reference sediments with different characteristics. The objectives of the current study were to establish bioavailability-based median lethal concentrations (LC50) and median effect concentrations (EC50) of the pyrethroid insecticide bifenthrin, compare their ability to assess toxicity to the use of whole sediment concentrations, as well as to make comparisons of the concentrations derived using each method in order to make assessments of accuracy and extrapolation potential. Four metrics were compared including SPME fiber concentration, pore water concentration derived using SPMEs, 6 h Tenax extractable concentration, and 24 h Tenax extractable concentration. The variation among the LC50s and EC50s in each sediment derived using bioavailability-based methods was comparable to variation among organic carbon normalized sediment concentrations, but improved over whole sediment concentrations. There was a significant linear relationship between SPME or Tenax and organic carbon normalized sediment concentrations. Additionally, there was a significant relationship between the SPME and Tenax concentrations across sediments. The significant linear relationship between SPME and Tenax concentrations further demonstrates that these bioavailability-based endpoints are interrelated. This study derived bioavailability-based benchmarks that may prove to be more accurate than sediment-based ones in predicting toxicity across sediment types.

  2. Juveniles exposed to embryonic corticosterone have enhanced flight performance

    PubMed Central

    Chin, Eunice H.; Love, Oliver P.; Verspoor, Jan J.; Williams, Tony D.; Rowley, Kyle; Burness, Gary

    2008-01-01

    Exposure to maternally derived glucocorticoids during embryonic development impacts offspring phenotype. Although many of these effects appear to be transiently ‘negative’, embryonic exposure to maternally derived stress hormones is hypothesized to induce preparative responses that increase survival prospects for offspring in low-quality environments; however, little is known about how maternal stress influences longer-term survival-related performance traits in free-living individuals. Using an experimental elevation of yolk corticosterone (embryonic signal of low maternal quality), we examined potential impacts of embryonic exposure to maternally derived stress on flight performance, wing loading, muscle morphology and muscle physiology in juvenile European starlings (Sturnus vulgaris). Here we report that fledglings exposed to experimentally increased corticosterone in ovo performed better during flight performance trials than control fledglings. Consistent with differences in performance, individuals exposed to elevated embryonic corticosterone fledged with lower wing loading and had heavier and more functionally mature flight muscles compared with control fledglings. Our results indicate that the positive effects on a survival-related trait in response to embryonic exposure to maternally derived stress hormones may balance some of the associated negative developmental costs that have recently been reported. Moreover, if embryonic experience is a good predictor of the quality or risk of future environments, a preparative phenotype associated with exposure to apparently negative stimuli during development may be adaptive. PMID:18842541

  3. Ecological risk assessment of bisphenol A in surface waters of China based on both traditional and reproductive endpoints.

    PubMed

    Guo, Lei; Li, Zhengyan; Gao, Pei; Hu, Hong; Gibson, Mark

    2015-11-01

    Bisphenol A (BPA) occurs widely in natural waters with both traditional and reproductive toxicity to various aquatic species. The water quality criteria (WQC), however, have not been established in China, which hinders the ecological risk assessment for the pollutant. This study therefore aims to derive the water quality criteria for BPA based on both acute and chronic toxicity endpoints and to assess the ecological risk in surface waters of China. A total of 15 acute toxicity values tested with aquatic species resident in China were found in published literature, which were simulated with the species sensitivity distribution (SSD) model for the derivation of criterion maximum concentration (CMC). 18 chronic toxicity values with traditional endpoints were simulated for the derivation of traditional criterion continuous concentration (CCC) and 12 chronic toxicity values with reproductive endpoints were for reproductive CCC. Based on the derived WQC, the ecological risk of BPA in surface waters of China was assessed with risk quotient (RQ) method. The results showed that the CMC, traditional CCC and reproductive CCC were 1518μgL(-1), 2.19μgL(-1) and 0.86μgL(-1), respectively. The acute risk of BPA was negligible with RQ values much lower than 0.1. The chronic risk was however much higher with RQ values of between 0.01-3.76 and 0.03-9.57 based on traditional and reproductive CCC, respectively. The chronic RQ values on reproductive endpoints were about threefold as high as those on traditional endpoints, indicating that ecological risk assessment based on traditional effects may not guarantee the safety of aquatic biota.

  4. Screening of nanoparticle embryotoxicity using embryonic stem cells.

    PubMed

    Campagnolo, Luisa; Fenoglio, Ivana; Massimiani, Micol; Magrini, Andrea; Pietroiusti, Antonio

    2013-01-01

    Due to the increasing use of engineered nanoparticles in many consumer products, rapid and economic tests for evaluating possible adverse effects on human health are urgently needed. In the present chapter the use of mouse embryonic stem cells as a valuable tool to in vitro screen nanoparticle toxicity on embryonic tissues is described. This in vitro method is a modification of the embryonic stem cell test, which has been widely used to screen soluble chemical compounds for their embryotoxic potential. The test offers an alternative to animal experimentation, reducing experimental costs and ethical issues.

  5. Multiple Sclerosis

    MedlinePlus

    Multiple sclerosis Overview By Mayo Clinic Staff Multiple sclerosis (MS) is a potentially disabling disease of the brain and spinal cord (central nervous system). In MS, the immune system attacks the protective ...

  6. Multiple Sclerosis

    MedlinePlus

    Multiple sclerosis (MS) is a nervous system disease that affects your brain and spinal cord. It damages the ... attacks healthy cells in your body by mistake. Multiple sclerosis affects women more than men. It often begins ...

  7. Multiple myeloma

    MedlinePlus

    Plasma cell dyscrasia; Plasma cell myeloma; Malignant plasmacytoma; Plasmacytoma of bone; Myeloma - multiple ... Multiple myeloma most commonly causes: Low red blood cell count ( anemia ), which can lead to fatigue and ...

  8. Embryonic stem cell lines of nonhuman primates.

    PubMed

    Nakatsuji, Norio; Suemori, Hirofumi

    2002-06-26

    Human embryonic stem (ES) cell lines have opened great potential and expectation for cell therapy and regenerative medicine. Monkey and human ES cell lines, which are very similar to each other, have been established from monkey blastocysts and surplus human blastocysts from fertility clinics. Nonhuman primate ES cell lines provide important research tools for basic and applicative research. Firstly, they provide wider aspects of investigation of the regulative mechanisms of stem cells and cell differentiation among primate species. Secondly, their usage does not need clearance or permission from the regulative rules in many countries that are associated with the ethical aspects of human ES cells, although human and nonhuman embryos and fetuses are very similar to each other. Lastly and most importantly, they are indispensable for animal models of cell therapy to test effectiveness, safety, and immunological reaction of the allogenic transplantation in a setting similar to the treatment of human diseases. So far, ES cell lines have been established from rhesus monkey (Macaca mulatta), common marmoset (Callithrix jacchus), and cynomolgus monkey (Macaca fascicularis), using blastocysts produced naturally or by in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI). These cell lines seem to have very similar characteristics. They express alkaline phosphatase activity and stage-specific embryonic antigen (SSEA)-4 and, in most cases, SSEA-3. Their pluripotency was confirmed by the formation of embryoid bodies and differentiation into various cell types in culture and also by the formation of teratomas that contained many types of differentiated tissues including derivatives of three germ layers after transplantation into the severe combined immunodeficiency (SCID) mice. The noneffectiveness of the leukemia inhibitory factor (LIF) signal makes culture of primate and human ES cell lines prone to undergo spontaneous differentiation and thus it is

  9. Sertad1 encodes a novel transcriptional co-activator of SMAD1 in mouse embryonic hearts

    SciTech Connect

    Peng, Yin; Zhao, Shaomin; Song, Langying; Wang, Manyuan; Jiao, Kai

    2013-11-29

    Highlights: •SERTAD1 interacts with SMAD1. •Sertad1 is expressed in mouse embryonic hearts. •SERTAD1 is localized in both cytoplasm and nucleus of cardiomyocytes. •SERTAD1 enhances expression of BMP target cardiogenic genes as a SMAD1 co-activator. -- Abstract: Despite considerable advances in surgical repairing procedures, congenital heart diseases (CHDs) remain the leading noninfectious cause of infant morbidity and mortality. Understanding the molecular/genetic mechanisms underlying normal cardiogenesis will provide essential information for the development of novel diagnostic and therapeutic strategies against CHDs. BMP signaling plays complex roles in multiple cardiogenic processes in mammals. SMAD1 is a canonical nuclear mediator of BMP signaling, the activity of which is critically regulated through its interaction partners. We screened a mouse embryonic heart yeast two-hybrid library using Smad1 as bait and identified SERTAD1 as a novel interaction partner of SMAD1. SERTAD1 contains multiple potential functional domains, including two partially overlapping transactivation domains at the C terminus. The SERTAD1-SMAD1 interaction in vitro and in mammalian cells was further confirmed through biochemical assays. The expression of Sertad1 in developing hearts was demonstrated using RT-PCR, western blotting and in situ hybridization analyses. We also showed that SERTAD1 was localized in both the cytoplasm and nucleus of immortalized cardiomyocytes and primary embryonic cardiomyocyte cultures. The overexpression of SERTAD1 in cardiomyocytes not only enhanced the activity of two BMP reporters in a dose-dependent manner but also increased the expression of several known BMP/SMAD regulatory targets. Therefore, these data suggest that SERTAD1 acts as a SMAD1 transcriptional co-activator to promote the expression of BMP target genes during mouse cardiogenesis.

  10. Embryonic testicular regression sequence: A part of the clinical spectrum of 46,XY gonadal dysgenesis

    SciTech Connect

    Marcantonio, S.M.; Fechner, P.Y.; Migeon, C.J.; Perlman, E.J.; Berkovitz, G.D.

    1994-01-01

    The authors report on a group of 9 subjects who had a 46,XY karyotype, ambiguous genitalia, abnormalities of sexual duct formation, and lack of gonadal tissue on one or both sides. This is sometimes referred to as {open_quotes}embryonic testicular regression.{close_quotes} Previous investigators have suggested that this condition results from loss of testes at a critical stage in development. The authors examined the possibility that embryonic testicular regression is part of the clinical spectrum of 46,XY gonadal dysgenesis. Four subjects totally lacked gonadal tissue, three of them having ambiguous genitalia, and one a micropenis. The development of incongruous sexual ducts (presence of Muellerian ducts in the subject with micropenis, and absence of Muellerian and Wolffian ducts in two subjects with ambiguous genitalia) suggests that the embryonic gonads were intrinsically functionally abnormal before their disappearance. Five subjects had unilateral gonadal tissue, ambiguous genitalia, and a mix of Wolffian and Muellerian structures. The development of incongruous sexual ducts in 3 of them, the presence of ambiguous external genitalia in 5, and the presence of abnormal gonadal histology in 2 patients all indicate an underlying abnormality of gonadal differentiation in these subjects. The occurrence of testicular regression in several subjects in the family of one patient suggests a genetic basis for the condition. The presence of multiple congenital anomalies in other subjects in the study suggests either a mutation in a single gene that functions in several developmental pathways, or a defect of multiple genes that might be the result of a chromosome deletion. The sex-determining region Y (SRY) gene was sequenced in five subjects and was normal in all of them, suggesting that the underlying genetic abnormality in these subjects is located in one of several genes that function subsequent to SRY in the early stages of testis differentiation. 37 refs., 2 tabs.

  11. A1 demonstrates restricted tissue distribution during embryonic development and functions to protect against cell death.

    PubMed Central

    Carrió, R.; López-Hoyos, M.; Jimeno, J.; Benedict, M. A.; Merino, R.; Benito, A.; Fernández-Luna, J. L.; Núñez, G.; García-Porrero, J. A.; Merino, J.

    1996-01-01

    Members of the bcl-2 gene family are essential regulators of cell survival in a wide range of biological processes. A1, a member of the family, is known to be expressed in certain adult tissues. However, the precise tissue distribution and function of A1 remains poorly understood. We show here that A1 is expressed in multiple tissues during murine embryonic development. In the embryo, A1 was detected first at embryonic day 11.5 in liver, brain, and limbs. At day 13.5 of gestation, A1 expression was observed in the central nervous system, liver, perichondrium, and digital zones of developing limbs in a pattern different from that of bcl-X. In the central nervous system of 15.5-day embryos, A1 was expressed at high levels in the ventricular zone and cortical plate of brain cortex. Significantly, the interdigital zones of limbs and the intermediate region of the developing brain cortex, two sites associated with extensive cell death, were devoid of A1 and bcl-X. The expression of A1 was retained in many adult tissues. To assess the ability of A1 to modulate cell death, stable transfectants expressing different amounts of A1 protein were generated in K562 cells. Expression of A1 was associated with retardation of apoptotic cell death induced by actinomycin D and cycloheximide as well as by okadaic acid. Confocal microscopy showed that the A1 protein was localized to the cytoplasm in a pattern similar to that of Bcl-2. These results demonstrate that the expression of A1 is wider than previously reported in adult tissues. Furthermore, its distribution in multiple tissues of the embryo suggests that A1 plays a role in the regulation of physiological cell death during embryonic development. Images Figure 1 Figure 2 Figure 3 Figure 5 PMID:8952545

  12. The critical indices of the quark gluon bags with surface tension model with tricritical endpoint

    NASA Astrophysics Data System (ADS)

    Ivanytskyi, A. I.

    2012-04-01

    The critical indices α', β, γ' and δ of the quark gluon bags with surface tension model with the tricritical endpoint are calculated as functions of the usual parameters of this model and two newly introduces parameters (indices) in order to perform a thorough comparison with the critical exponents of other models. It is shown that for the newly introduced indices χ=0 and ξT⩽1 there is a branch of solutions for which the critical exponents of the present model and the statistical multifragmentation model coincide, otherwise these models have different critical exponents. The critical exponents α', β, γ' and δ of ordinary liquids and 3-dimensional Ising model are reproduced by several sets of the model parameters, but the resulting range of the Fisher exponent τ is rather narrow and lies between 20/11 and 2. The scaling relations for the found critical exponents are verified and it is demonstrated that for the standard definition of the index α' the Fisher and Griffiths scaling inequalities are not fulfilled for some values of the model parameters, whereas the Liberman scaling inequality is always obeyed. It is also shown that the specially defined index αs' recovers the scaling relations. A thorough analysis of the critical exponents obeying the scaling relations along with the condition αs'>-β is performed. The found solutions enable us to reproduce the critical exponents of the 3-dimensional O(4) spin model and to show that for this case the exponent τ falls almost in the same range of values as for the ordinary liquids.

  13. Determining significant endpoints for ecological risk analyses. 1998 annual progress report

    SciTech Connect

    Hinton, T.G.; Congdon, J.; Scott, D.; Rowe, C.; Bedford, J.; Whicker, W.

    1998-06-01

    'The goal of this report is to establish a protocol for assessing risks to non-human populations exposed to environmental stresses typically found on many DOE sites. The authors think that they can achieve this by using novel biological dosimeters in controlled, manipulative dose/effects experiments, and by coupling changes in metabolic rates and energy allocation patterns to meaningful population response variables (such as age-specific survivorship, reproductive output, age at maturity and longevity). This research is needed to determine the relevancy of sublethal cellular damage to the performance of individuals and populations exposed to chronic, low-level radiation, and radiation with concomitant exposure to chemicals. They believe that a scientifically defensible endpoint for measuring ecological risks can only be determined once its understood the extent to which molecular damage from contaminant exposure is detrimental at the individual and population levels of biological organization. The experimental facility will allow them to develop a credible assessment tool for appraising ecological risks, and to evaluate the effects of radionuclide/chemical synergisms on non-human species. This report summarizes work completed midway of a 3-year project that began in November 1996. Emphasis to date has centered on three areas: (1) developing a molecular probe to measure stable chromosomal aberrations known as reciprocal translocations, (2) constructing an irradiation facility where the statistical power inherent in replicated mesocosms can be used to address the response of non-human organisms to exposures from low levels of radiation and metal contaminants, and (3) quantifying responses of organisms living in contaminated mesocosms and field sites.'

  14. Relative Biological Effectiveness of HZE Particles for Chromosomal Exchanges and Other Surrogate Cancer Risk Endpoints

    SciTech Connect

    Cacao, Eliedonna; Hada, Megumi; Saganti, Premkumar B.; George, Kerry A.; Cucinotta, Francis A.

    2016-04-25

    The biological effects of high charge and energy (HZE) particle exposures are of interest in space radiation protection of astronauts and cosmonauts, and estimating secondary cancer risks for patients undergoing Hadron therapy for primary cancers. The large number of particles types and energies that makeup primary or secondary radiation in HZE particle exposures precludes tumor induction studies in animal models for all but a few particle types and energies, thus leading to the use of surrogate endpoints to investigate the details of the radiation quality dependence of relative biological effectiveness (RBE) factors. In this report we make detailed RBE predictions of the charge number and energy dependence of RBE’s using a parametric track structure model to represent experimental results for the low dose response for chromosomal exchanges in normal human lymphocyte and fibroblast cells with comparison to published data for neoplastic transformation and gene mutation. RBE’s are evaluated against acute doses of γ-rays for doses near 1 Gy. Models that assume linear or non-targeted effects at low dose are considered. Modest values of RBE (<10) are found for simple exchanges using a linear dose response model, however in the non-targeted effects model for fibroblast cells large RBE values (>10) are predicted at low doses <0.1 Gy. The radiation quality dependence of RBE’s against the effects of acute doses γ-rays found for neoplastic transformation and gene mutation studies are similar to those found for simple exchanges if a linear response is assumed at low HZE particle doses. Finally, we discuss comparisons of the resulting model parameters to those used in the NASA radiation quality factor function.

  15. Relative Biological Effectiveness of HZE Particles for Chromosomal Exchanges and Other Surrogate Cancer Risk Endpoints

    DOE PAGES

    Cacao, Eliedonna; Hada, Megumi; Saganti, Premkumar B.; ...

    2016-04-25

    The biological effects of high charge and energy (HZE) particle exposures are of interest in space radiation protection of astronauts and cosmonauts, and estimating secondary cancer risks for patients undergoing Hadron therapy for primary cancers. The large number of particles types and energies that makeup primary or secondary radiation in HZE particle exposures precludes tumor induction studies in animal models for all but a few particle types and energies, thus leading to the use of surrogate endpoints to investigate the details of the radiation quality dependence of relative biological effectiveness (RBE) factors. In this report we make detailed RBE predictionsmore » of the charge number and energy dependence of RBE’s using a parametric track structure model to represent experimental results for the low dose response for chromosomal exchanges in normal human lymphocyte and fibroblast cells with comparison to published data for neoplastic transformation and gene mutation. RBE’s are evaluated against acute doses of γ-rays for doses near 1 Gy. Models that assume linear or non-targeted effects at low dose are considered. Modest values of RBE (<10) are found for simple exchanges using a linear dose response model, however in the non-targeted effects model for fibroblast cells large RBE values (>10) are predicted at low doses <0.1 Gy. The radiation quality dependence of RBE’s against the effects of acute doses γ-rays found for neoplastic transformation and gene mutation studies are similar to those found for simple exchanges if a linear response is assumed at low HZE particle doses. Finally, we discuss comparisons of the resulting model parameters to those used in the NASA radiation quality factor function.« less

  16. Transmission Assessment Surveys (TAS) to Define Endpoints for Lymphatic Filariasis Mass Drug Administration: A Multicenter Evaluation

    PubMed Central

    Chu, Brian K.; Deming, Michael; Biritwum, Nana-Kwadwo; Bougma, Windtaré R.; Dorkenoo, Améyo M.; El-Setouhy, Maged; Fischer, Peter U.; Gass, Katherine; Gonzalez de Peña, Manuel; Mercado-Hernandez, Leda; Kyelem, Dominique; Lammie, Patrick J.; Flueckiger, Rebecca M.; Mwingira, Upendo J.; Noordin, Rahmah; Offei Owusu, Irene; Ottesen, Eric A.; Pavluck, Alexandre; Pilotte, Nils; Rao, Ramakrishna U.; Samarasekera, Dilhani; Schmaedick, Mark A.; Settinayake, Sunil; Simonsen, Paul E.; Supali, Taniawati; Taleo, Fasihah; Torres, Melissa; Weil, Gary J.; Won, Kimberly Y.

    2013-01-01

    Background Lymphatic filariasis (LF) is targeted for global elimination through treatment of entire at-risk populations with repeated annual mass drug administration (MDA). Essential for program success is defining and confirming the appropriate endpoint for MDA when transmission is presumed to have reached a level low enough that it cannot be sustained even in the absence of drug intervention. Guidelines advanced by WHO call for a transmission assessment survey (TAS) to determine if MDA can be stopped within an LF evaluation unit (EU) after at least five effective rounds of annual treatment. To test the value and practicality of these guidelines, a multicenter operational research trial was undertaken in 11 countries covering various geographic and epidemiological settings. Methodology The TAS was conducted twice in each EU with TAS-1 and TAS-2 approximately 24 months apart. Lot quality assurance sampling (LQAS) formed the basis of the TAS survey design but specific EU characteristics defined the survey site (school or community), eligible population (6–7 year olds or 1st–2nd graders), survey type (systematic or cluster-sampling), target sample size, and critical cutoff (a statistically powered threshold below which transmission is expected to be no longer sustainable). The primary diagnostic tools were the immunochromatographic (ICT) test for W. bancrofti EUs and the BmR1 test (Brugia Rapid or PanLF) for Brugia spp. EUs. Principal Findings/Conclusions In 10 of 11 EUs, the number of TAS-1 positive cases was below the critical cutoff, indicating that MDA could be stopped. The same results were found in the follow-up TAS-2, therefore, confirming the previous decision outcome. Sample sizes were highly sex and age-representative and closely matched the target value after factoring in estimates of non-participation. The TAS was determined to be a practical and effective evaluation tool for stopping MDA although its validity for longer-term post-MDA surveillance

  17. Coupling biological measurement endpoints used in ecological risk assessment with chemical measurements

    SciTech Connect

    Goodrich, M.; Mahato, M.

    1995-12-31

    Collections of surface water, sediments, and the benthic community were made in support of an ecological risk assessment for a stream on a US Air Force base in Oklahoma. Over 250 chemicals were detected within water and sediments, of which over 30 of those screened were classified as chemicals of potential ecological concern (COPEC) based on available toxicity benchmarks. Many of the chemicals detected were clustered in specific samples and in various concentration combinations, To address the complexity of this mixture of chemicals and chemical concentrations, the results of 28-day chronic Hyalella azteca bulk sediment toxicity tests, early life-stage, 7-day fathead minnow toxicity tests, 7-day survival and reproduction results with Ceriodaphnia dubia, and benthic community indices (i.e. biotic index(ices), number of taxa, number of individuals) were evaluated for correlations and associations with the chemicals detected. The resultant evaluation was useful in discriminating those COPEC`s within the various samples that were associated and predictive of the observed ecological measurement endpoints. Additional parameters such as, sulfide analysis of the overlying water from the sediment samples, was enlightening especially regarding an apparent reversal of the correlation between metal concentrations and toxicity. Benthic community indices were also useful in evaluating relationships between chemical concentrations, toxicological effects and aquatic hazard quotients. The approach presented is believed to be superior to the triad approach based on its ability to address mixtures of chemicals and variable chemical concentrations in combination. The results of this evaluation were able to more concisely identify the COPEC`s as well as, establish a priority system and clarify the risk assessment in the context of the complexity of chemical mixtures.

  18. SU-F-BRD-11: Prediction of Dosimetric Endpoints From Patient Geometry Using Neural Nets

    SciTech Connect

    O'Connell, D; Chow, P; Agazaryan, N; Jani, S; Low, D; Lamb, J

    2014-06-15

    Purpose: The previously-published overlap volume histogram (OVH) technique lends itself naturally to prediction of the dose received by a given volume of tissue (e.g. D90) in intensity-modulated radiotherapy (IMRT) treatment plans. Here we extend the OVH technique using artificial neural networks in order to predict the volume of tissue receiving a given dose (e.g. V90) in both prostate IMRT and conventional breast radiotherapy. Methods: Twenty-nine prostate treatment plans and forty-three breast treatment plans were analyzed. The spatial relationships between the prostate and rectum and between the breast and ipsilateral lung were characterized using OVHs. The OVH is a cumulative histogram representing the fractional volume of the risk organ overlapped by a series of isotropic expansions of the planning target volume (PTV). Seven cases were identified as outliers and replanned. OVH points were used as inputs to a one hidden layer feed forward artificial neural network with quality parameters of the corresponding plan, such as the rectum V50, as targets. A 3-fold cross-validation was used to estimate the prediction error. Results: The root mean square (RMS) error between the predicted rectum V50s and the planned values was 2.3, which was 35% of the standard deviation of V50 for the twenty-nine plans. The RMS error of prediction of V20 of the ipsilateral lung in breast cases was 3.9, which was 90% of the standard deviation of the V20 values in the breast plan database. Conclusion: This study demonstrates that artificial neural nets can be used to extend the OVH technique to predict dosimetric endpoints taking the form of a volume receiving a given dose, rather than the minimum dose received by a given volume. Prediction of ipsilateral lung dose in breast radiotherapy using the OVH technique remains a work in progress.

  19. Extended Gaussian quadratures for functions with an end-point singularity of logarithmic type

    NASA Astrophysics Data System (ADS)

    Pachucki, K.; Puchalski, M.; Yerokhin, V. A.

    2014-11-01

    The extended Gaussian quadrature rules are shown to be an efficient tool for numerical integration of wide class of functions with singularities of logarithmic type. The quadratures are exact for the functions pol1n-1(x)+lnx pol2n-1(x), where pol1n-1(x) and pol2n-1(x) are two arbitrary polynomials of degree n-1 and n is the order of the quadrature formula. We present an implementation of numerical algorithm that calculates the nodes and the weights of the quadrature formulas, provide a Fortran code for numerical integration, and test the performance of different kinds of Gaussian quadratures for functions with logarithmic singularities. Catalogue identifier: AETP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETP_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2535 No. of bytes in distributed program, including test data, etc.: 39 963 Distribution format: tar.gz Programming language: Mathematica, Fortran. Computer: PCs or higher performance computers. Operating system: Linux, Windows, MacOS. RAM: Kilobytes. Classification: 4.11. Nature of problem: Quadrature formulas for numerical integration, effective for a wide class of functions with end-point singularities of logarithmic type. Solution method: The method of solution is based on the algorithm developed in Ref. [1] with some modifications. Running time: Milliseconds to minutes. J. Ma, V. Rokhlin, S. Wandzura, Generalized Gaussian quadrature rules for systems of arbitrary functions, Soc. Indust. Appl. Math. J. Numer. Anal. 33 (3) (1996) 971-996.

  20. In vitro PFOS exposure on immune endpoints in bottlenose dolphins (Tursiops truncatus) and mice.

    PubMed

    Wirth, Jena R; Peden-Adams, Margie M; White, Natasha D; Bossart, Gregory D; Fair, Patricia A

    2014-06-01

    Previous studies in our lab have shown that perfluorooctane sulfonate (PFOS) modulates immune function in mice and correlates with many immune parameters in bottlenose dolphins (Tursiops truncatus). In this study, bottlenose dolphin peripheral blood leukocytes (PBLs) and adult female B6C3F1 mouse splenocytes were exposed to environmentally relevant PFOS concentrations (0-5 µg ml(-1)) in vitro; and natural killer (NK) cell activity and lymphocyte proliferation (T and B cell) were assessed using the parallelogram approach for risk assessment. The objectives were: to corroborate results from the correlative studies in bottlenose dolphins with in vitro PFOS exposures; to evaluate the sensitivity of the mouse model as compared with bottlenose dolphins; and to assess risk using the parallelogram approach. In mouse cells, NK cell activity was decreased at in vitro doses of 0.01, 0.5, 0.1, 0.5 and 1 µg PFOS ml(-1) and increased at 5 µg ml(-1). Additionally, B cell proliferation was not altered, but T cell proliferation was decreased at all in vitro PFOS exposures. In dolphin cells, NK cell activity and T cell proliferation were not altered by in vitro PFOS exposure, but B cell proliferation exhibited a positive association in relation to PFOS dose. Overall, the data indicates that: the in vitro exposures of bottlenose dolphin PBLs exhibited results similar to reported correlative fields studies; that mice were generally more sensitive (for these selected endpoints) than were dolphins; and that the parallelogram approach could be used two-thirds of the time to predict the effects in bottlenose dolphins.

  1. Predictive validity of endpoints used in electrophysiological modelling of migraine in the trigeminovascular system.

    PubMed

    Farkas, Bence; Kardos, Péter; Orosz, Szabolcs; Tarnawa, István; Csekő, Csongor; Lévay, György; Farkas, Sándor; Lendvai, Balázs; Kovács, Péter

    2015-11-02

    The trigeminovascular system has a pivotal role in the pathomechanism of migraine. The aim of the present study was to further develop existing models of migraine making them more suitable for testing the effects of compounds with presumed antimigraine activity in anaesthetised rats. Simultaneous recording of ongoing activity of spontaneously active neurons in the trigeminocervical complex as well as their discharges evoked by electrical stimulation of the dura mater via activation of A- and C-sensory fibres were carried out. Effects of sumatriptan, propranolol and topiramate were evaluated prior to and after application of a mixture containing inflammatory mediators on the dura. Propranolol (10 mg/kg s.c) and topiramate (30 mg/kg s.c.) resulted in a tendency to decrease the level of both spontaneous and evoked activity, while sumatriptan (1 mg/kg s.c.) did not exhibit any effect on recorded parameters. Application of an inflammatory soup to the dura mater boosted up spontaneous activity, which could be significantly attenuated by propranolol and topiramate but not by sumatriptan. In addition, all compounds prevented the delayed increase of spontaneous firing. In contrast to the ongoing activity, evoked responses were not augmented by inflammatory mediators. Nevertheless, inhibitory effect of propranolol and topiramate was evident when considering A- or C-fibre responses. Findings do not support the view that electrically evoked responses are useful for the measurement of trigeminal sensitization. It is proposed however, that inhibition of enhanced firing (immediate and/or delayed) evoked by inflammatory mediators as an endpoint have higher predictive validity regarding the clinical effectiveness of compounds.

  2. Relative Biological Effectiveness of HZE Particles for Chromosomal Exchanges and Other Surrogate Cancer Risk Endpoints

    PubMed Central

    Cacao, Eliedonna; Hada, Megumi; Saganti, Premkumar B.; George, Kerry A.; Cucinotta, Francis A.

    2016-01-01

    The biological effects of high charge and energy (HZE) particle exposures are of interest in space radiation protection of astronauts and cosmonauts, and estimating secondary cancer risks for patients undergoing Hadron therapy for primary cancers. The large number of particles types and energies that makeup primary or secondary radiation in HZE particle exposures precludes tumor induction studies in animal models for all but a few particle types and energies, thus leading to the use of surrogate endpoints to investigate the details of the radiation quality dependence of relative biological effectiveness (RBE) factors. In this report we make detailed RBE predictions of the charge number and energy dependence of RBE’s using a parametric track structure model to represent experimental results for the low dose response for chromosomal exchanges in normal human lymphocyte and fibroblast cells with comparison to published data for neoplastic transformation and gene mutation. RBE’s are evaluated against acute doses of γ-rays for doses near 1 Gy. Models that assume linear or non-targeted effects at low dose are considered. Modest values of RBE (<10) are found for simple exchanges using a linear dose response model, however in the non-targeted effects model for fibroblast cells large RBE values (>10) are predicted at low doses <0.1 Gy. The radiation quality dependence of RBE’s against the effects of acute doses γ-rays found for neoplastic transformation and gene mutation studies are similar to those found for simple exchanges if a linear response is assumed at low HZE particle doses. Comparisons of the resulting model parameters to those used in the NASA radiation quality factor function are discussed. PMID:27111667

  3. The circadian rest-activity rhythm, a potential safety pharmacology endpoint of cancer chemotherapy.

    PubMed

    Ortiz-Tudela, Elisabet; Iurisci, Ida; Beau, Jacques; Karaboue, Abdoulaye; Moreau, Thierry; Rol, Maria Angeles; Madrid, Juan Antonio; Lévi, Francis; Innominato, Pasquale F

    2014-06-01

    The robustness of the circadian timing system (CTS) was correlated to quality of life and predicted for improved survival in cancer patients. However, chemotherapy disrupted the CTS according to dose and circadian timing in mice. A continuous and repeated measures longitudinal design was implemented here to characterize CTS dynamics in patients receiving a fixed circadian-based chemotherapy protocol. The rest-activity rhythm of 49 patients with advanced cancer was monitored using a wrist actigraph for 13 days split into four consecutive spans of 3-4 days each, i.e., before, during, right after and late after a fixed chronotherapy course. The relative amount of activity in bed vs. out of bed (Iendpoint), the autocorrelation coefficient r24, the relative 24-hr amplitude (Amp), interdaily stability (IS) and intradaily variability (IV) were compared according to study span. Circadian disruption (I

  4. A toolbox to explore the mechanics of living embryonic tissues.

    PubMed

    Campàs, Otger

    2016-07-01

    The sculpting of embryonic tissues and organs into their functional morphologies involves the spatial and temporal regulation of mechanics at cell and tissue scales. Decades of in vitro work, complemented by some in vivo studies, have shown the relevance of mechanical cues in the control of cell behaviors that are central to developmental processes, but the lack of methodologies enabling precise, quantitative measurements of mechanical cues in vivo have hindered our understanding of the role of mechanics in embryonic development. Several methodologies are starting to enable quantitative studies of mechanics in vivo and in situ, opening new avenues to explore how mechanics contributes to shaping embryonic tissues and how it affects cell behavior within developing embryos. Here we review the present methodologies to study the role of mechanics in living embryonic tissues, considering their strengths and drawbacks as well as the conditions in which they are most suitable.

  5. Analysis of the prognostic risk factors of idiopathic membranous nephropathy using a new surrogate end-point

    PubMed Central

    ZHANG, BO; CHENG, MING; YANG, MING; HAN, SHUAI; ZHANG, YING-HUI; SHI, HONG-GUANG; ZHU, LIANG; ZHAO, XUE-ZHI

    2016-01-01

    Idiopathic membranous nephropathy (IMN) is one of the most common causes of nephrotic syndrome (NS) in adults. The latest study of the chronic kidney disease-prognosis consortium showed that a 30% decrease in the estimated glomerular filtration rate (eGFR) within 2 years could cover more patients and showed a better correlation with end-stage renal disease (ESRD), as compared with serum creatinine (SCr). The aim of the present study was to analyze prognostic factors of ESRD using a 30% decrease in eGFR within 2 years as the end-point. The medical records of patients who were diagnosed as having IMN by clinical pathology between February 2011 and August 2012 and had been followed up for ≥24 months were analyzed retrospectively. A 30% decrease in eGFR or the occurrence of ESRD were the end-points. Factors affecting the prognosis were analyzed by the χ2 test and multivariate logistic regression analysis, and the cumulative risk of risk factors was analyzed by Kaplan-Meier curve. A total of 73 patients with IMN were confirmed by clinical pathology. Blood pressure, tubulointerstitial injury area (TIA), glomerular sclerosis ratio, SCr, blood urea nitrogen, cystatin C, serum albumin and 24-h urine protein. In total, 28 patients (38.4%) reached the observation end-point. Multivariate logistic regression analysis showed that only age ≥60 years, serum albumin <25 g/l and TIA >25% were independent risk factors for predicting the occurrence of end-point events in the two groups (P<0.05), which increased the risk of the occurrence of end-point events in IMN patients by 3.471-, 3.195- and 6.724-fold, respectively. Kaplan-Meier curve showed that the occurrence of end-point events within 2 years was significantly higher in IMN patients whose age was ≥60 years, serum albumin <25 g/l and TIA >25% (log-rank P=0.004, P=0.024 and P=0.001). The results of the present study revealed that age ≥60 years, low serum albumin concentrations and severe tubulointerstitial injury are

  6. Coriolis-force-induced trajectory and endpoint deviations in the reaching movements of labyrinthine-defective subjects

    NASA Technical Reports Server (NTRS)

    DiZio, P.; Lackner, J. R.

    2001-01-01

    When reaching movements are made during passive constant velocity body rotation, inertial Coriolis accelerations are generated that displace both movement paths and endpoints in their direction. These findings directly contradict equilibrium point theories of movement control. However, it has been argued that these movement errors relate to subjects sensing their body rotation through continuing vestibular activity and making corrective movements. In the present study, we evaluated the reaching movements of five labyrinthine-defective subjects (lacking both semicircular canal and otolith function) who cannot sense passive body rotation in the dark and five age-matched, normal control subjects. Each pointed 40 times in complete darkness to the location of a just extinguished visual target before, during, and after constant velocity rotation at 10 rpm in the center of a fully enclosed slow rotation room. All subjects, including the normal controls, always felt completely stationary when making their movements. During rotation, both groups initially showed large deviations of their movement paths and endpoints in the direction of the transient Coriolis forces generated by their movements. With additional per-rotation movements, both groups showed complete adaptation of movement curvature (restoration of straight-line reaches) during rotation. The labyrinthine-defective subjects, however, failed to regain fully accurate movement endpoints after 40 reaches, unlike the control subjects who did so within 11 reaches. Postrotation, both groups' movements initially had mirror image curvatures to their initial per-rotation reaches; the endpoint aftereffects were significantly different from prerotation baseline for the control subjects but not for the labyrinthine-defective subjects reflecting the smaller amount of endpoint adaptation they achieved during rotation. The labyrinthine-defective subjects' movements had significantly lower peak velocity, higher peak elevation

  7. Coriolis-force-induced trajectory and endpoint deviations in the reaching movements of labyrinthine-defective subjects.

    PubMed

    DiZio, P; Lackner, J R

    2001-02-01

    When reaching movements are made during passive constant velocity body rotation, inertial Coriolis accelerations are generated that displace both movement paths and endpoints in their direction. These findings directly contradict equilibrium point theories of movement control. However, it has been argued that these movement errors relate to subjects sensing their body rotation through continuing vestibular activity and making corrective movements. In the present study, we evaluated the reaching movements of five labyrinthine-defective subjects (lacking both semicircular canal and otolith function) who cannot sense passive body rotation in the dark and five age-matched, normal control subjects. Each pointed 40 times in complete darkness to the location of a just extinguished visual target before, during, and after constant velocity rotation at 10 rpm in the center of a fully enclosed slow rotation room. All subjects, including the normal controls, always felt completely stationary when making their movements. During rotation, both groups initially showed large deviations of their movement paths and endpoints in the direction of the transient Coriolis forces generated by their movements. With additional per-rotation movements, both groups showed complete adaptation of movement curvature (restoration of straight-line reaches) during rotation. The labyrinthine-defective subjects, however, failed to regain fully accurate movement endpoints after 40 reaches, unlike the control subjects who did so within 11 reaches. Postrotation, both groups' movements initially had mirror image curvatures to their initial per-rotation reaches; the endpoint aftereffects were significantly different from prerotation baseline for the control subjects but not for the labyrinthine-defective subjects reflecting the smaller amount of endpoint adaptation they achieved during rotation. The labyrinthine-defective subjects' movements had significantly lower peak velocity, higher peak elevation

  8. Multiplicity Counting

    SciTech Connect

    Geist, William H.

    2015-12-01

    This set of slides begins by giving background and a review of neutron counting; three attributes of a verification item are discussed: 240Pueff mass; α, the ratio of (α,n) neutrons to spontaneous fission neutrons; and leakage multiplication. It then takes up neutron detector systems – theory & concepts (coincidence counting, moderation, die-away time); detector systems – some important details (deadtime, corrections); introduction to multiplicity counting; multiplicity electronics and example distributions; singles, doubles, and triples from measured multiplicity distributions; and the point model: multiplicity mathematics.

  9. Endpoint-based parallel data processing with non-blocking collective instructions in a parallel active messaging interface of a parallel computer

    DOEpatents

    Archer, Charles J; Blocksome, Michael A; Cernohous, Bob R; Ratterman, Joseph D; Smith, Brian E

    2014-11-18

    Methods, apparatuses, and computer program products for endpoint-based parallel data processing with non-blocking collective instructions in a parallel active messaging interface (`PAMI`) of a parallel computer are provided. Embodiments include establishing by a parallel application a data communications geometry, the geometry specifying a set of endpoints that are used in collective operations of the PAMI, including associating with the geometry a list of collective algorithms valid for use with the endpoints of the geometry. Embodiments also include registering in each endpoint in the geometry a dispatch callback function for a collective operation and executing without blocking, through a single one of the endpoints in the geometry, an instruction for the collective operation.

  10. Gene trapping in embryonic stem cells.

    PubMed

    Stanford, William L; Epp, Trevor; Reid, Tammy; Rossant, Janet

    2006-01-01

    Gene trapping in embryonic stem cells (ESCs) generates random, sequence-tagged insertional mutations, which can often report the gene expression pattern of the mutated gene. This mutagenesis strategy has often been coupled to expression or function-based assays in gene discovery screens. The availability of the mouse genome sequence has shifted gene trapping from a gene discovery platform to a high-throughput mutagenesis platform. At present, a concerted worldwide effort is underway to develop a library of loss-of-function mutations in all mouse genes. The International Gene Trap Consortium (IGTC) is leading the way by making a first pass of the genome by random mutagenesis before a high-throughput gene targeting program takes over. In this chapter, we provide a methods guidebook to exploring and using the IGTC resource, explain the different kinds of vectors and insertions that reside in the different libraries, and provide advice and methods for investigators to design novel expression-based "cottage industry" screens.

  11. The epigenomics of embryonic stem cell differentiation.

    PubMed

    Kraushaar, Daniel C; Zhao, Keji

    2013-01-01

    Embryonic stem cells (ESCs) possess an open and highly dynamic chromatin landscape, which underlies their plasticity and ultimately maintains ESC pluripotency. The ESC epigenome must not only maintain the transcription of pluripotency-associated genes but must also, through gene priming, facilitate rapid and cell type-specific activation of developmental genes upon lineage commitment. Trans-generational inheritance ensures that the ESC chromatin state is stably transmitted from one generation to the next; yet at the same time, epigenetic marks are highly dynamic, reversible and responsive to extracellular cues. Once committed to differentiation, the ESC epigenome is remodeled and resolves into a more compact chromatin state. A thorough understanding of the role of chromatin modifiers in ESC fate and differentiation will be important if they are to be used for therapeutic purposes. Recent technical advances, particularly in next-generation sequencing technologies, have provided a genome-scale view of epigenetic marks and chromatin modifiers. More affordable and faster sequencing platforms have led to a comprehensive characterization of the ESC epigenome and epigenomes of differentiated cell types. In this review, we summarize and discuss the recent progress that has highlighted the central role of histone modifications, histone variants, DNA methylation and chromatin modifiers in ESC pluripotency and ESC fate. We provide a detailed and comprehensive discussion of genome-wide studies that are pertinent to our understanding of mammalian development.

  12. Molecular imaging of human embryonic stem cells.

    PubMed

    Narsinh, Kazim H; Cao, Feng; Wu, Joseph C

    2009-01-01

    Human embryonic stem cells (hESCs) are a renewable source of differentiated cell types that may be employed in various tissue regeneration strategies. However, clinical implementation of cell transplantation therapy is hindered by legitimate concerns regarding the in vivo teratoma formation of undifferentiated hESCs and host immune reactions to allogenic cells. Investigating in vivo hESC behaviour and the ultimate feasibility of cell transplantation therapy necessitates the development of novel molecular imaging techniques to longitudinally monitor hESC localization, proliferation, and viability in living subjects. An innovative approach to harness the respective strengths of various imaging platforms is the creation and use of a fusion reporter construct composed of red fluorescent protein (RFP), firefly luciferase (fluc), and herpes simplex virus thymidine kinase (HSV-tk). The imaging modalities made available by use of this construct, including optical fluorescence, bioluminescence, and positron emission tomography (PET), mat be adapted to investigate a variety of physiological phenomena, including the spatio-temporal kinetics of hESC engraftment and proliferation in living subjects. This chapter describes the applications of reporter gene imaging to accelerate basic science research and clinical studies involving hESCs through (1) isolation of a homogenous hESC population, (2) noninvasive, longitudinal tracking of the location and proliferation of hESCs administered to a living subject, and (3) ablation of the hESC graft in the event of cellular misbehavior.

  13. Embryonic cuticle establishment: the great (apoplastic) divide.

    PubMed

    Moussu, Steven; San-Bento, Rita; Galletti, Roberta; Creff, Audrey; Farcot, Etienne; Ingram, Gwyneth

    2013-01-01

    The plant cuticle, a dynamic interface between plants and their environment, is formed by the secretion of hydrophobic lipids and waxes into the outer wall of aerial epidermal cells. Cuticle formation is such a ubiquitous feature of epidermal cells, and is of such fundamental importance for plant survival, that identifying and understanding specific developmental roles for this structure has been a major challenge for plant scientists. In recent work, we have tried to understand the functional relationships between a signaling feedback loop required for epidermal cell specification in developing plant embryos, and a seed specific signaling cascade, involving components localized both in the embryo and in the embryo surrounding endosperm, and necessary for embryo cuticle function. Analysis of the strongly synergistic genetic relationships between these 2 independent pathways, combined with mathematical simulations of the behavior of the signaling feedback loop, have allowed us to propose an important, and hitherto unsuspected, role for the embryonic cuticle as an apoplastic diffusion barrier, necessary for preventing the excessive diffusion of developmentally important signaling molecules away from developing embryo into surrounding tissues.

  14. Ornithine-δ-Aminotransferase Inhibits Neurogenesis During Xenopus Embryonic Development

    PubMed Central

    Peng, Ying; Cooper, Sandra K.; Li, Yi; Mei, Jay M.; Qiu, Shuwei; Borchert, Gregory L.; Donald, Steven P.; Kung, Hsiang-fu; Phang, James M.

    2015-01-01

    Purpose. In humans, deficiency of ornithine-δ-aminotransferase (OAT) results in progressive degeneration of the neural retina (gyrate atrophy) with blindness in the fourth decade. In this study, we used the Xenopus embryonic developmental model to study functions of the OAT gene on embryonic development. Methods. We cloned and sequenced full-length OAT cDNA from Xenopus oocytes (X-OAT) and determined X-OAT expression in various developmental stages of Xenopus embryos and in a variety of adult tissues. The phenotype, gene expression of neural developmental markers, and enzymatic activity were detected by gain-of-function and loss-of-function manipulations. Results. We showed that X-OAT is essential for Xenopus embryonic development, and overexpression of X-OAT produces a ventralized phenotype characterized by a small head, lack of axial structure, and defective expression of neural developmental markers. Using X-OAT mutants based on mutations identified in humans, we found that substitution of both Arg 180 and Leu 402 abrogated both X-OAT enzymatic activity and ability to modulate the developmental phenotype. Neurogenesis is inhibited by X-OAT during Xenopus embryonic development. Conclusions. Neurogenesis is inhibited by X-OAT during Xenopus embryonic development, but it is essential for Xenopus embryonic development. The Arg 180 and Leu 402 are crucial for these effects of the OAT molecule in development. PMID:25783604

  15. Embryonal Tumors With Abundant Neuropil and True Rosettes

    PubMed Central

    Gessi, Marco; Giangaspero, Felice; Lauriola, Libero; Gardiman, Marina; Scheithauer, Bernd W.; Halliday, William; Hawkins, Cynthia; Rosenblum, Marc K.; Burger, Peter C.; Eberhart, Charles G.

    2015-01-01

    Embryonal neoplasms of the central nervous system (CNS) generally arise in the early years of life and behave in a clinically aggressive manner, but vary somewhat in their microscopic appearance. Several groups have reported examples of an embryonal tumor with combined histologic features of ependymoblastoma and neuroblastoma, a lesion referred to as “embryonal tumor with abundant neuropil and true rosettes” (ETANTR). Herein, we present 22 new cases, and additional clinical follow-up on our 7 initially reported cases, to better define the histologic features and clinical behavior of this distinctive neoplasm. It affects infants and arises most often in cerebral cortex, the cerebellum and brainstem being less frequent sites. Unlike other embryonal tumors of the CNS, girls are more commonly affected than boys. On neuroimaging, the tumors appear as large, demarcated, solid masses featuring patchy or no contrast enhancement. Five of our cases (18%) were at least partly cystic. Distinctive microscopic features include a prominent background of mature neuropil punctuated by true rosettes formed of pseudo-stratified embryonal cells circumferentially disposed about a central lumen (true rosettes). Of the 25 cases with available follow-up, 19 patients have died, their median survival being 9 months. Performed on 2 cases, cytogenetic analysis revealed extra copies of chromosome 2 in both. We believe that the ETANTR represents a histologically distinctive form of CNS embryonal tumor. PMID:18987548

  16. Critical Transitions in Early Embryonic Aortic Arch Patterning and Hemodynamics

    PubMed Central

    Kowalski, William J.; Dur, Onur; Wang, Yajuan; Patrick, Michael J.; Tinney, Joseph P.; Keller, Bradley B.; Pekkan, Kerem

    2013-01-01

    Transformation from the bilaterally symmetric embryonic aortic arches to the mature great vessels is a complex morphogenetic process, requiring both vasculogenic and angiogenic mechanisms. Early aortic arch development occurs simultaneously with rapid changes in pulsatile blood flow, ventricular function, and downstream impedance in both invertebrate and vertebrate species. These dynamic biomechanical environmental landscapes provide critical epigenetic cues for vascular growth and remodeling. In our previous work, we examined hemodynamic loading and aortic arch growth in the chick embryo at Hamburger-Hamilton stages 18 and 24. We provided the first quantitative correlation between wall shear stress (WSS) and aortic arch diameter in the developing embryo, and observed that these two stages contained different aortic arch patterns with no inter-embryo variation. In the present study, we investigate these biomechanical events in the intermediate stage 21 to determine insights into this critical transition. We performed fluorescent dye microinjections to identify aortic arch patterns and measured diameters using both injection recordings and high-resolution optical coherence tomography. Flow and WSS were quantified with 3D computational fluid dynamics (CFD). Dye injections revealed that the transition in aortic arch pattern is not a uniform process and multiple configurations were documented at stage 21. CFD analysis showed that WSS is substantially elevated compared to both the previous (stage 18) and subsequent (stage 24) developmental time-points. These results demonstrate that acute increases in WSS are followed by a period of vascular remodeling to restore normative hemodynamic loading. Fluctuations in blood flow are one possible mechanism that impacts the timing of events such as aortic arch regression and generation, leading to the variable configurations at stage 21. Aortic arch variations noted during normal rapid vascular remodeling at stage 21 identify a

  17. Brief Embryonic Strychnine Exposure in Zebrafish Causes Long-Term Adult Behavioral Impairment with Indications of Embryonic Synaptic Changes

    PubMed Central

    Roy, Nicole M.; Arpie, Brianna; Lugo, Joseph; Linney, Elwood; Levin, Edward D.; Cerutti, Daniel

    2015-01-01

    Zebrafish provide a powerful model of the impacts of embryonic toxicant exposure on neural development that may result in long-term behavioral dysfunction. In this study, zebrafish embryos were treated with 1.5 mM strychnine for short embryonic time windows to induce transient changes in inhibitory neural signaling, and were subsequently raised in untreated water until adulthood. PCR analysis showed indications that strychnine exposure altered expression of some genes related to glycinergic, GABAergic and glutamatergic neuronal synapses during embryonic development. In adulthood, treated fish showed significant changes in swimming speed and tank diving behavior compared to controls. Taken together, these data show that a short embryonic exposure to a neurotoxicant can alter development of neural synapses and lead to changes in adult behavior. PMID:23022260

  18. Phylogenetic analyses of termite post-embryonic sequences illuminate caste and developmental pathway evolution.

    PubMed

    Legendre, Frédéric; Whiting, Michael F; Grandcolas, Philippe

    2013-01-01

    Termites are highly eusocial insects with a caste polyphenism (i.e., discontinuous morphological differences between castes) and elaborated behaviors. While the developmental pathways leading to caste occurrence are well-known in many species, the evolutionary origin of these pathways is still obscure. Recent molecular phylogenetic studies suggest multiple independent origins of sterile castes in termites, reviving a 30 years old debate. We demonstrate here that diploid sterile castes ("true" workers) evolved several times independently in this group and that this caste was lost at least once in a lineage with developmentally more flexible workers called pseudergates or "false" workers. We also infer that flexibility in post-embryonic development was acquired multiple times independently during termite evolution. We suggest that focusing on detailed developmental pathways in phylogenetic analyses is essential for elucidating the origin of caste polyphenism in termites.

  19. On stability and passivity of haptic devices characterized by a series elastic actuation and considerable end-point mass.

    PubMed

    Oblak, Jakob; Matjačić, Zlatko

    2011-01-01

    Series elastic actuators have considerable potential in rehabilitation robotics. However, the reflected mass of the motor and considerable robot's end-point mass, both linked by an elastic element, result in a potentially unstable coupled mechanical oscillator. Since rehabilitation devices are in constant contact with patients, safety concerns and consequently the devices' stability are very important. In this study, the conservative conditions that guarantee the stability of the haptic device (with a considerable end-point mass and driven by a series elastic actuator) were established. We have shown that sufficient damping should be presented in parallel to the spring in order to achieve the passivity of the haptic device. Theoretical results were confirmed in an experimental evaluation on previously developed rehabilitation device.

  20. Lethal and sublethal endpoints observed for Artemia exposed to two reference toxicants and an ecotoxicological concern organic compound.

    PubMed

    Manfra, Loredana; Canepa, Sara; Piazza, Veronica; Faimali, Marco

    2016-01-01

    Swimming speed alteration and mortality assays with the marine crustacean Artemia franciscana were carried out. EC50 and LC50 values after 24-48h exposures were calculated for two reference toxicants, copper sulphate pentahydrate (CuSO4·5H2O) and Sodium Dodecyl Sulphate (SDS), and an ecotoxicological concern organic compound, Diethylene Glycol (DEG). Different end-points have been evaluated, in order to point out their sensitivity levels. The swimming speed alteration (SSA) was compared to mortality values and also to the hatching rate inhibition (literature data). SSA resulted to be more sensitive than the mortality and with a sensitivity comparable to (or even higher than) the hatching rate endpoint.

  1. QED contribution to the color-singlet J/{psi} production in {Upsilon} decay near the endpoint

    SciTech Connect

    Liu Xiaohui

    2010-02-01

    A recent study indicates that the {alpha}{sup 2{alpha}}{sub s}{sup 2} order QED processes of {Upsilon}{yields}J/{psi}+X decay are compatible with those of QCD processes. However, in the endpoint region, the nonrelativistic QED calculation breaks down since the collinear degrees of freedom are missing under the framework of this effective theory. In this paper we apply the soft-collinear effective theory (SCET) to study the color-singlet QED process at the kinematic limit. Within this approach we are able to sum the kinematic logarithms by running operators using the renormalization group equations of soft-collinear effective theory, which will lead to a dramatic change in the momentum distribution near the endpoint and the spectrum shape consistent with the experimental results.

  2. Early improvement with pregabalin predicts endpoint response in patients with generalized anxiety disorder: an integrated and predictive data analysis.

    PubMed

    Montgomery, Stuart A; Lyndon, Gavin; Almas, Mary; Whalen, Ed; Prieto, Rita

    2017-01-01

    Generalized anxiety disorder (GAD), a common mental disorder, has several treatment options including pregabalin. Not all patients respond to treatment; quickly determining which patients will respond is an important treatment goal. Patient-level data were pooled from nine phase II and III randomized, double-blind, short-term, placebo-controlled trials of pregabalin for the treatment of GAD. Efficacy outcomes included the change from baseline in the Hamilton Anxiety Scale (HAM-A) total score and psychic and somatic subscales. Predictive modelling assessed baseline characteristics and early clinical responses to determine those predictive of clinical improvement at endpoint. A total of 2155 patients were included in the analysis (1447 pregabalin, 708 placebo). Pregabalin significantly improved the HAM-A total score compared with the placebo at endpoint, treatment difference (95% confidence interval), -2.61 (-3.21 to -2.01), P<0.0001. Pregabalin significantly improved HAM-A psychic and somatic scores compared with placebo, -1.52 (-1.85 to -1.18), P<0.0001, and -1.10 (-1.41 to -0.80), P<0.0001, respectively. Response to pregabalin in the first 1-2 weeks (≥20 or ≥30% improvement in HAM-A total, psychic or somatic score) was predictive of an endpoint greater than or equal to 50% improvement in the HAM-A total score. Pregabalin is an effective treatment option for patients with GAD. Patients with early response to pregabalin are more likely to respond significantly at endpoint.

  3. Recommendations for the development of rare disease drugs using the accelerated approval pathway and for qualifying biomarkers as primary endpoints.

    PubMed

    Kakkis, Emil D; O'Donovan, Mary; Cox, Gerald; Hayes, Mark; Goodsaid, Federico; Tandon, P K; Furlong, Pat; Boynton, Susan; Bozic, Mladen; Orfali, May; Thornton, Mark

    2015-02-10

    For rare serious and life-threatening disorders, there is a tremendous challenge of transforming scientific discoveries into new drug treatments. This challenge has been recognized by all stakeholders who endorse the need for flexibility in the regulatory review process for novel therapeutics to treat rare diseases. In the United States, the best expression of this flexibility was the creation of the Accelerated Approval (AA) pathway. The AA pathway is critically important for the development of treatments for diseases with high unmet medical need and has been used extensively for drugs used to treat cancer and infectious diseases like HIV.In 2012, the AA provisions were amended to enhance the application of the AA pathway to expedite the development of drugs for rare disorders under the Food and Drug Administration Safety and Innovation Act (FDASIA). FDASIA, among many provisions, requires the development of a more relevant FDA guidance on the types of evidence that may be acceptable in support of using a novel surrogate endpoint. The application of AA to rare diseases requires more predictability to drive greater access to appropriate use of AA for more rare disease treatments that might not be developed otherwise.This white paper proposes a scientific framework for assessing biomarker endpoints to enhance the development of novel therapeutics for rare and devastating diseases currently without adequate treatment and is based on the opinions of experts in drug development and rare disease patient groups. Specific recommendations include: 1) Establishing regulatory rationale for increased AA access in rare disease programs; 2) Implementing a Biomarker Qualification Request Process to provide the opportunity for an early determination of biomarker acceptance; and 3) A proposed scientific framework for qualifying biomarkers as primary endpoints. The paper's final section highlights case studies of successful examples that have incorporated biomarker endpoints into

  4. Influence of nutrient medium composition on uranium toxicity and choice of the most sensitive growth related endpoint in Lemna minor.

    PubMed

    Horemans, Nele; Van Hees, May; Saenen, Eline; Van Hoeck, Arne; Smolders, Valérie; Blust, Ronny; Vandenhove, Hildegarde

    2016-01-01

    Uranium (U) toxicity is known to be highly dependent on U speciation and bioavailability. To assess the impact of uranium on plants, a growth inhibition test was set up in the freshwater macrophyte Lemna minor. First growth media with different compositions were tested in order to find a medium fit for testing U toxicity in L. minor. Following arguments were used for medium selection: the ability to sustain L. minor growth, a high solubility of U in the medium and a high percentage of the more toxic U-species namely UO2(2+). Based on these selection criteria a with a low phosphate concentration of 0.5 mg L(-1) and supplemented with 5 mM MES (2-(N-morpholino)ethanesulfonic acid) to ensure pH stability was chosen. This medium also showed highest U toxicity compared to the other tested media. Subsequently a full dose response curve for U was established by exposing L. minor plants to U concentrations ranging from 0.05 μM up to 150 μM for 7 days. Uranium was shown to adversely affect growth of L. minor in a dose dependent manner with EC10, EC30 and EC50 values ranging between 1.6 and 4.8 μM, 7.7-16.4 μM and 19.4-37.2 μM U, respectively, depending on the growth endpoint. Four different growth related endpoints were tested: frond area, frond number, fresh weight and dry weight. Although differences in relative growth rates and associated ECx-values calculated on different endpoints are small (maximal twofold difference), frond area is recommended to be used to measure U-induced growth effects as it is a sensitive growth endpoint and easy to measure in vivo allowing for measurements over time.

  5. Eating Quality Traits of Hanwoo longissimus dorsi Muscle as a Function of End-Point Cooking Temperature.

    PubMed

    Yang, Jieun; Jeong, Dawoon; Na, Chong-Sam; Hwang, Inho

    2016-01-01

    Interaction between carcass quality grade and end-point cooking temperature on eating quality of Hanwoo m. longissimus was investigated. Ten (10) of steers were sampled from a commercial population; carcasses with QG 1(++) (n=5) and QG 1 (n=5) were chosen. Samples were cooked by electric oven at 60 or 82℃ and compared with uncooked control samples. The pH was not affected by cooking temperature but decreased the redness after cooking and steaks cooked at 60℃ were more reddish than steaks cooked at 82℃ in both QG groups. Higher cooking temperature greatly (p<0.05) increased the cooking loss, but there was no significant interaction between cooking temperature and QG on the cooking loss. Moisture is negatively correlated with temperature in both QG while the proportionate relationship between crude fat and end-point temperature found in QG 1(++). WBSF values were significantly (p<0.05) high for QG 1, while that was significantly (p<0.05) increased when the temperature continues to increase. The increasing quality grade of beef resulted in significant higher (p<0.01) level of TBARS and cooking temperature increased TBARS content. Fatty acid composition was not altered by cooking at both temperatures and also the amount of fat intake was not changed. The current study indicates that eating quality of beef m. longissimus was greatly influenced by end-point temperature being interacted with QG. However, the amount and composition of fat were stable regardless of end-point temperatures. These results will provide a consumer reference to determine cooking conditions and intramuscular fat content.

  6. Eating Quality Traits of Hanwoo longissimus dorsi Muscle as a Function of End-Point Cooking Temperature

    PubMed Central

    2016-01-01

    Interaction between carcass quality grade and end-point cooking temperature on eating quality of Hanwoo m. longissimus was investigated. Ten (10) of steers were sampled from a commercial population; carcasses with QG 1++ (n=5) and QG 1 (n=5) were chosen. Samples were cooked by electric oven at 60 or 82℃ and compared with uncooked control samples. The pH was not affected by cooking temperature but decreased the redness after cooking and steaks cooked at 60℃ were more reddish than steaks cooked at 82℃ in both QG groups. Higher cooking temperature greatly (p<0.05) increased the cooking loss, but there was no significant interaction between cooking temperature and QG on the cooking loss. Moisture is negatively correlated with temperature in both QG while the proportionate relationship between crude fat and end-point temperature found in QG 1++. WBSF values were significantly (p<0.05) high for QG 1, while that was significantly (p<0.05) increased when the temperature continues to increase. The increasing quality grade of beef resulted in significant higher (p<0.01) level of TBARS and cooking temperature increased TBARS content. Fatty acid composition was not altered by cooking at both temperatures and also the amount of fat intake was not changed. The current study indicates that eating quality of beef m. longissimus was greatly influenced by end-point temperature being interacted with QG. However, the amount and composition of fat were stable regardless of end-point temperatures. These results will provide a consumer reference to determine cooking conditions and intramuscular fat content. PMID:27433099

  7. Early Change in Proteinuria as a Surrogate Endpoint for Kidney Disease Progression: An Individual Patient Meta-analysis

    PubMed Central

    Inker, Lesley A.; Levey, Andrew S.; Pandya, Kruti; Stoycheff, Nicholas; Okparavero, Aghogho; Greene, Tom

    2014-01-01

    Background It is controversial whether proteinuria is a valid surrogate endpoint for randomized trials in chronic kidney disease. Study Design Meta-analysis of individual patient level data. Setting & Population Individual patient data on 9008 patients from 32 randomized trials evaluating five intervention types. Selection Criteria for Studies Randomized controlled trials of kidney disease progression until 2007 with measurements of proteinuria both at baseline and during the first year of follow-up, with at least one further year of follow-up for the clinical outcome. Predictor Early change in proteinuria. Outcomes Doubling of serum creatinine, end stage renal disease or death. Results Early decline in proteinuria was associated with a lower risk of the clinical outcome (pooled HR, 0.74 per 50% reduction in proteinuria); this association was stronger at higher levels of baseline proteinuria. Pooled estimates for the proportion of treatment effect on the clinical outcome explained by early decline in proteinuria ranged from −7.0% (95% CI, −40.6% to 26.7%) to 43.9% (95% CI, 25.3% to 62.6%) across five intervention types. The direction of the pooled treatment effects on early change in proteinuria agreed with the direction of the treatment effect on the clinical outcome for all 5 intervention types, with the magnitudes of the pooled treatment effects on the two endpoints agreeing for 4 of the 5 intervention types. The pooled treatment effects on both endpoints were simultaneously stronger at higher levels of proteinuria. However, statistical power was insufficient to determine if differences in treatment effects on the clinical outcome corresponded to differences in treatment effects on proteinuria between individual studies. Limitations Limited variety of interventions tested and low statistical power for many chronic kidney disease clinical trials. Conclusions These results provide new evidence supporting the use of an early reduction in proteinuria as a

  8. Induced Wnt5a expression perturbs embryonic outgrowth and intestinal elongation, but is well-tolerated in adult mice.

    PubMed

    Bakker, Elvira R M; Raghoebir, Lalini; Franken, Patrick F; Helvensteijn, Werner; van Gurp, Léon; Meijlink, Frits; van der Valk, Martin A; Rottier, Robbert J; Kuipers, Ernst J; van Veelen, Wendy; Smits, Ron

    2012-09-01

    Wnt5a is essential during embryonic development, as indicated by mouse Wnt5a knockout embryos displaying outgrowth defects of multiple structures including the gut. The dynamics of Wnt5a involvement in these processes is unclear, and perinatal lethality of Wnt5a knockout embryos has hampered investigation of Wnt5a during postnatal stages in vivo. Although in vitro studies have suggested a relevant role for Wnt5a postnatally, solid evidence for a significant impact of Wnt5a within the complexity of an adult organism is lacking. We generated a tightly-regulated inducible Wnt5a transgenic mouse model and investigated the effects of Wnt5a induction during different time-frames of embryonic development and in adult mice, focusing on the gastrointestinal tract. When induced in embryos from 10.5 dpc onwards, Wnt5a expression led to severe outgrowth defects affecting the gastrointestinal tracts, limbs, facial structures and tails, closely resembling the defects observed in Wnt5a knockout mice. However, Wnt5a induction from 13.5 dpc onwards did not cause this phenotype, indicating that the most critical period for Wnt5a in embryonic development is prior to 13.5 dpc. In adult mice, induced Wnt5a expression did not reveal abnormalities, providing the first in vivo evidence that Wnt5a has no major impact on mouse intestinal homeostasis postnatally. Protein expression of Wnt5a receptor Ror2 was strongly reduced in adult intestine compared to embryonic stages. Moreover, we uncovered a regulatory process where induction of Wnt5a causes downregulation of its receptor Ror2. Taken together, our results indicate a role for Wnt5a during a restricted time-frame of embryonic development, but suggest no impact during homeostatic postnatal stages.

  9. Translating neurobehavioural endpoints of developmental neurotoxicity tests into in vitro assays and readouts.

    PubMed

    van Thriel, Christoph; Westerink, Remco H S; Beste, Christian; Bale, Ambuja S; Lein, Pamela J; Leist, Marcel

    2012-08-01

    The developing nervous system is particularly vulnerable to chemical insults. Exposure to chemicals can result in neurobehavioural alterations, and these have been used as sensitive readouts to assess neurotoxicity in animals and man. Deconstructing neurobehaviour into relevant cellular and molecular components may allow for detection of specific neurotoxic effects in cell-based systems, which in turn may allow an easier examination of neurotoxic pathways and modes of actions and eventually inform the regulatory assessment of chemicals with potential developmental neurotoxicity. Here, current developments towards these goals are reviewed. Imaging genetics (CB) provides new insights into the neurobiological correlates of cognitive function that are being used to delineate neurotoxic mechanisms. The gaps between in vivo neurobehaviour and real-time in vitro measurements of neuronal function are being bridged by ex vivo measurements of synaptic plasticity (RW). An example of solvent neurotoxicity demonstrates how an in vivo neurological defect can be linked via the N-methyl-d-aspartate (NMDA)-glutamate receptor as a common target to in vitro readouts (AB). Axonal and dendritic morphology in vitro proved to be good correlates of neuronal connectivity and neurobehaviour in animals exposed to polychlorinated biphenyls and organophosphorus pesticides (PJL). Similarly, chemically induced changes in neuronal morphology affected the formation of neuronal networks on structured surfaces. Such network formation may become an important readout for developmental neurotoxicity in vitro (CvT), especially when combined with human neurons derived from embryonic stem cells (ML). We envision that future in vitro test systems for developmental neurotoxicity will combine the above approaches with exposure information, and we suggest a strategy for test system development and cell-based risk assessment.

  10. Bridging the gap between cadaveric and in vivo experiments: a biomechanical model evaluating thumb-tip endpoint forces.

    PubMed

    Wohlman, Sarah J; Murray, Wendy M

    2013-03-15

    The thumb is required for a majority of tasks of daily living. Biomechanical modeling is a valuable tool, with the potential to help us bridge the gap between our understanding of the mechanical actions of individual thumb muscles, derived from anatomical cadaveric experiments, and our understanding of how force is produced by the coordination of all of the thumb muscles, derived from studies involving human subjects. However, current biomechanical models do not replicate muscle force production at the thumb-tip. We hypothesized that accurate representations of the axes of rotation of the thumb joints were necessary to simulate the magnitude of endpoint forces produced by human subjects. We augmented a musculoskeletal model with axes of rotation derived from experimental measurements (Holzbaur et al., 2005) by defining muscle-tendon paths and maximum isometric force-generating capacity for the five intrinsic muscles. We then evaluated if this augmented model replicated a broad range of experimental data from the literature and identified which parameters most influenced model performance. The simulated endpoint forces generated by the combined action of all thumb muscles in our model yielded comparable forces in magnitude to those produced by nonimpaired subjects. A series of 8 sets of Monte Carlo simulations demonstrated that the difference in the axes of rotation of the thumb joints between studies best explains the improved performance of our model relative to previous work. In addition, we demonstrate that the endpoint forces produced by individual muscles cannot be replicated with existing experimental data describing muscle moment arms.

  11. The role of categorization and scale endpoint comparisons in numerical information processing: A two-process model.

    PubMed

    Tao, Tao; Wyer, Robert S; Zheng, Yuhuang

    2017-03-01

    We propose a two-process conceptualization of numerical information processing to describe how people form impressions of a score that is described along a bounded scale. According to the model, people spontaneously categorize a score as high or low. Furthermore, they compare the numerical discrepancy between the score and the endpoint of the scale to which it is closer, if they are not confident of their categorization, and use implications of this comparison as a basis for judgment. As a result, their evaluation of the score is less extreme when the range of numbers along the scale is large (e.g., from 0 to 100) than when it is small (from 0 to 10). Six experiments support this two-process model and demonstrate its generalizability. Specifically, the magnitude of numbers composing the scale has less impact on judgments (a) when the score being evaluated is extreme, (b) when individuals are unmotivated to engage in endpoint comparison processes (i.e., they are low in need for cognition), and (c) when they are unable to do so (i.e., they are under cognitive load). Moreover, the endpoint to which individuals compare