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Sample records for targeted rejection predicts

  1. The significance of parenchymal changes of acute cellular rejection in predicting chronic liver graft rejection

    NARCIS (Netherlands)

    Gouw, ASH; van den Heuvel, MC; van den Berg, AP; Slooff, NJH; de Jong, KP; Poppema, S

    2002-01-01

    Background. Chronic rejection (CR) in liver allografts shows a rapid onset and progressive course, leading to graft failure within the first year after transplantation. Most cases are preceded by episodes of acute cellular rejection (AR), but histological features predictive for the transition

  2. Prediction of acute cardiac rejection using radionuclide techniques

    International Nuclear Information System (INIS)

    Novitzky, D.; Bonioszczuk, J.; Cooper, D.K.C.; Isaacs, S.; Rose, A.G.; Smith, J.A.; Uys, C.J.; Barnard, C.N.; Fraser, R.

    1984-01-01

    Radionuclide scanning of the donor left ventricle using technetium-99m-labelled red cells was used to monitor acute rejection after heterotopic heart transplantation and compared with histopathological evidence of rejection obtained at examination of an endomyocardial biopsy specimen. The ejection fraction and end-diastolic, end-systolic and stroke volumes were calculated at each examination; an equation was derived from these data to predict the degree of acute rejection, using histopathological examination of endomyocardial biopsy specimens as criteria of the presence and severity of rejection. A highly significant multiple correlation between radionuclide scanning parameters and endomyocardial biopsy was found. The advantages of non-invasive radionuclide scanning over the invasive procedure of endomyocardial biopsy are discussed

  3. Somatostatin receptor scintigraphy predicts impending cardiac allograft rejection before endomyocardial biopsy

    Energy Technology Data Exchange (ETDEWEB)

    Aparici, C.M.; Martin, J.C.; Tembl, A.; Flotats, A.; Estorch, M.; Catafau, A.M.; Berna, L.; Carrio, I. [Nuclear Medicine Department, Hospital Sant Pau, Barcelona (Spain); Narula, J.; Puig, M.; Camprecios, M.; Ballester, M. [Cardiology Department, Sant Pau Hospital, Barcelona (Spain)

    2000-12-01

    following week. These preliminary results indicate the feasibility of targeting activated lymphocytes with somatostatin receptor imaging in the detection of cardiac allograft rejection. Somatostatin receptor imaging may predict impending rejection at least 1 week before the endomyocardial biopsy becomes positive. The late appearance of diagnostic endomyocardial biopsy probably reflects a lag-time between lymphocytic activation and induction of myocyte damage. Furthermore, somatostatin receptor imaging at 4 h may in any case allow earlier intervention in the event of rejection, given the time required for histological processing of endomyocardial biopsy. (orig.)

  4. Prediction of Kidney Graft Rejection Using Artificial Neural Network.

    Science.gov (United States)

    Tapak, Leili; Hamidi, Omid; Amini, Payam; Poorolajal, Jalal

    2017-10-01

    Kidney transplantation is the best renal replacement therapy for patients with end-stage renal disease. Several studies have attempted to identify predisposing factors of graft rejection; however, the results have been inconsistent. We aimed to identify prognostic factors associated with kidney transplant rejection using the artificial neural network (ANN) approach and to compare the results with those obtained by logistic regression (LR). The study used information regarding 378 patients who had undergone kidney transplantation from a retrospective study conducted in Hamadan, Western Iran, from 1994 to 2011. ANN was used to identify potential important risk factors for chronic nonreversible graft rejection. Recipients' age, creatinine level, cold ischemic time, and hemoglobin level at discharge were identified as the most important prognostic factors by ANN. The ANN model showed higher total accuracy (0.75 vs. 0.55 for LR), and the area under the ROC curve (0.88 vs. 0.75 for LR) was better than that obtained with LR. The results of this study indicate that the ANN model outperformed LR in the prediction of kidney transplantation failure. Therefore, this approach is a promising classifier for predicting graft failure to improve patients' survival and quality of life, and it should be further investigated for the prediction of other clinical outcomes.

  5. Predicting acute cardiac rejection from donor heart and pre-transplant recipient blood gene expression.

    Science.gov (United States)

    Hollander, Zsuzsanna; Chen, Virginia; Sidhu, Keerat; Lin, David; Ng, Raymond T; Balshaw, Robert; Cohen-Freue, Gabriela V; Ignaszewski, Andrew; Imai, Carol; Kaan, Annemarie; Tebbutt, Scott J; Wilson-McManus, Janet E; McMaster, Robert W; Keown, Paul A; McManus, Bruce M

    2013-02-01

    Acute rejection in cardiac transplant patients remains a contributory factor to limited survival of implanted hearts. Currently, there are no biomarkers in clinical use that can predict, at the time of transplantation, the likelihood of post-transplant acute cellular rejection. Such a development would be of great value in personalizing immunosuppressive treatment. Recipient age, donor age, cold ischemic time, warm ischemic time, panel-reactive antibody, gender mismatch, blood type mismatch and human leukocyte antigens (HLA-A, -B and -DR) mismatch between recipients and donors were tested in 53 heart transplant patients for their power to predict post-transplant acute cellular rejection. Donor transplant biopsy and recipient pre-transplant blood were also examined for the presence of genomic biomarkers in 7 rejection and 11 non-rejection patients, using non-targeted data mining techniques. The biomarker based on the 8 clinical variables had an area under the receiver operating characteristic curve (AUC) of 0.53. The pre-transplant recipient blood gene-based panel did not yield better performance, but the donor heart tissue gene-based panel had an AUC = 0.78. A combination of 25 probe sets from the transplant donor biopsy and 18 probe sets from the pre-transplant recipient whole blood had an AUC = 0.90. Biologic pathways implicated include VEGF- and EGFR-signaling, and MAPK. Based on this study, the best predictive biomarker panel contains genes from recipient whole blood and donor myocardial tissue. This panel provides clinically relevant prediction power and, if validated, may personalize immunosuppressive treatment and rejection monitoring. Copyright © 2013 International Society for Heart and Lung Transplantation. Published by Elsevier Inc. All rights reserved.

  6. Targeted inhibition of renal Rho kinase reduces macrophage infiltration and lymphangiogenesis in acute renal allograft rejection

    NARCIS (Netherlands)

    Poosti, Fariba; Yazdani, Saleh; Dolman, M. Emmy M.; Kok, Robbert Jan; Chen, Cheng; Ding, Guohua; Lacombe, Marie; Prakash, Jai; van den Born, Jacob; Hillebrands, Jan-Luuk; van Goor, Harry; de Borst, Martin H.

    2012-01-01

    The Rho kinase pathway plays an important role in epithelial dedifferentiation and inflammatory cell infiltration. Recent studies suggest that inflammation promotes lymphangiogenesis, which has been associated with renal allograft rejection. We investigated whether targeted inhibition of the Rho

  7. Accept or Reject? Predicting Ideation Outcomes through Enterprise Social Media

    Directory of Open Access Journals (Sweden)

    Rozaidi Nik Ahmad

    2017-01-01

    Full Text Available Implementing social media in the workplace may make it easier for employees to participate in knowledge sharing activities such as Q&A and ideation. However, vetting the quality of answers and ideas becomes more complex when anyone in the company can contribute. Research on the use of social media for Q&A has shown that certain characteristics and reputation algorithms can help determine the best answers. Less is known about the ideation process and the way it plays out in social media. This paper explores the use of enterprise social media (ESM for ideation by employees in a large Russian organization distributed across nine time zones. In particular, we explore which characteristics of both ideas and their contributors predict whether ideas get accepted or rejected. Our analysis is based on logistic regression analysis of a sample of 488 ideas contributed in an ESM tool used in the organization as well as a content analysis of the types of ideas generated. Our results suggest that rather than being truly democratic and decentralized, ideation in ESM is driven by those in (or proximate to positions of organizational power.

  8. Profile of the Pleximmune blood test for transplant rejection risk prediction

    OpenAIRE

    Sindhi, Rakesh; Ashokkumar, Chethan; Higgs, Brandon W; Levy, Samantha; Soltys, Kyle; Bond, Geoffrey; Mazariegos, George; Ranganathan, Sarangarajan; Zeevi, Adriana

    2016-01-01

    The Pleximmune? test (Plexision Inc., Pittsburgh, PA, USA) is the first cell-based test approved by the US FDA, which predicts acute cellular rejection in children with liver- or intestine transplantation. The test addresses an unmet need to improve management of immunosuppression, which incurs greater risks of opportunistic infections and Epstein?Barr virus-induced malignancy during childhood. High-dose immunosuppression and recurrent rejection after intestine transplantation also result in ...

  9. Predicting cellular rejection with a cell-based assay: Pre-clinical evaluation in children

    Science.gov (United States)

    Ashokkumar, Chethan; Soltys, Kyle; Mazariegos, George; Bond, Geoffrey; Higgs, Brandon W.; Ningappa, Mylarappa; Sun, Qing; Brown, Amanda; White, Jaimie; Levy, Samantha; Fazzolare, Tamara; Remaley, Lisa; Dirling, Katie; Harris, Patti; Hartle, Tara; Kachmar, Pam; Nicely, Megan; O'Toole, Lindsay; Boehm, Brittany; Jativa, Nicole; Stanley, Paula; Jaffe, Ronald; Ranganathan, Sarangarajan; Zeevi, Adriana; Sindhi, Rakesh

    2015-01-01

    Background Allospecific CD154+T-cytotoxic memory cells (CD154+TcM) predict acute cellular rejection (ACR) after liver or intestine transplantation (LTx, ITx) in small cohorts of children and can enhance immunosuppression management, but await validation and clinical implementation. Methods To establish safety and probable benefit, CD154+TcM were measured in cryopreserved samples from 214 children 1 implies increased rejection-risk. Results Training and validation set subjects were demographically similar. Mean coefficient of test variation was <10% under several conditions. Logistic regression incorporating several confounding variables identified separate pre-transplant and post-transplant IR thresholds for prediction of rejection in respective training set samples. An IR ≥ 1.1 in post-transplant training samples, and IR ≥1.23 in pre-transplant training samples predicted LTx or ITx rejection in corresponding validation set samples in the 60-day post-sampling period with sensitivity, specificity, positive and negative predictive values of 84%, 80%, 64%, and 92%, respectively (AUC 0.792), and 57%, 89%, 78%, and 74%, respectively (AUC 0.848). No adverse events were encountered due to phlebotomy. Conclusions Allospecific CD154+T-cytotoxic memory cells predict acute cellular rejection after liver or intestine transplantation in children. Adjunctive use can enhance clinical outcomes. PMID:26950712

  10. The Role of Conspiracist Ideation and Worldviews in Predicting Rejection of Science

    Science.gov (United States)

    Lewandowsky, Stephan; Gignac, Gilles E.; Oberauer, Klaus

    2013-01-01

    Background Among American Conservatives, but not Liberals, trust in science has been declining since the 1970's. Climate science has become particularly polarized, with Conservatives being more likely than Liberals to reject the notion that greenhouse gas emissions are warming the globe. Conversely, opposition to genetically-modified (GM) foods and vaccinations is often ascribed to the political Left although reliable data are lacking. There are also growing indications that rejection of science is suffused by conspiracist ideation, that is the general tendency to endorse conspiracy theories including the specific beliefs that inconvenient scientific findings constitute a “hoax.” Methodology/Principal findings We conducted a propensity weighted internet-panel survey of the U.S. population and show that conservatism and free-market worldview strongly predict rejection of climate science, in contrast to their weaker and opposing effects on acceptance of vaccinations. The two worldview variables do not predict opposition to GM. Conspiracist ideation, by contrast, predicts rejection of all three scientific propositions, albeit to greatly varying extents. Greater endorsement of a diverse set of conspiracy theories predicts opposition to GM foods, vaccinations, and climate science. Conclusions Free-market worldviews are an important predictor of the rejection of scientific findings that have potential regulatory implications, such as climate science, but not necessarily of other scientific issues. Conspiracist ideation, by contrast, is associated with the rejection of all scientific propositions tested. We highlight the manifold cognitive reasons why conspiracist ideation would stand in opposition to the scientific method. The involvement of conspiracist ideation in the rejection of science has implications for science communicators. PMID:24098391

  11. Stochastic disturbance rejection in model predictive control by randomized algorithms

    NARCIS (Netherlands)

    Batina, Ivo; Stoorvogel, Antonie Arij; Weiland, Siep

    2001-01-01

    In this paper we consider model predictive control with stochastic disturbances and input constraints. We present an algorithm which can solve this problem approximately but with arbitrary high accuracy. The optimization at each time step is a closed loop optimization and therefore takes into

  12. Profile of the Pleximmune blood test for transplant rejection risk prediction

    Science.gov (United States)

    Sindhi, Rakesh; Ashokkumar, Chethan; Higgs, Brandon W; Levy, Samantha; Soltys, Kyle; Bond, Geoffrey; Mazariegos, George; Ranganathan, Sarangarajan; Zeevi, Adriana

    2016-01-01

    Summary The Pleximmune™ test (Plexision Inc., Pittsburgh, PA, USA) is the first cell-based test approved by the US FDA, which predicts acute cellular rejection in children with liver- or intestine transplantation. The test addresses an unmet need to improve management of immunosuppression, which incurs greater risks of opportunistic infections and Epstein–Barr virus-induced malignancy during childhood. High-dose immunosuppression and recurrent rejection after intestine transplantation also result in a 5-year graft loss rate of up to 50%. Such outcomes seem increasingly unacceptable because children can experience rejection-free survival with reduced immunosuppression. Pleximmune test sensitivity and specificity for predicting acute cellular rejection is 84% and 81% respectively in training set–validation set testing of 214 children. Among existing gold standards, the biopsy detects but cannot predict rejection. Anti-donor antibodies, which presage antibody-mediated injury, reflect late-stage allosensitization as a downstream effect of engagement between recipient and donor cells. Therefore, durable graft and patient outcomes also require an accurate management of cellular immune responses in clinical practice. PMID:26760313

  13. T-Cell Cytokines as Predictive Markers of the Risk of Allograft Rejection.

    Science.gov (United States)

    Brunet, Mercè; Millán López, Olga; López-Hoyos, Marcos

    2016-04-01

    Over the last decade, several biomarkers and surrogate markers have surfaced as promising predictive markers of risk of rejection in solid organ transplantation. The monitoring of these markers can help to improve graft and recipient care by personalizing immunomodulatory therapies. The complex immune system response against an implanted graft can change during long-term follow-up, and the dynamic balance between effector and regulatory T-cell populations is a crucial factor in antidonor response, risk of rejection, and immunosuppression requirements. Therefore, at any time before and after transplantation, T-effector activity, which is associated with increased production and release of proinflammatory cytokines, can be a surrogate marker of the risk of rejection and need for immunosuppression. In addition, immunosuppressive drugs may have a different effect in each individual patient. The pharmacokinetics and pharmacodynamics of these drugs show high interpatient variability, and pharmacodynamic markers, strongly associated with the specific mechanism of action, can potentially be used to measure individual susceptibility to a specific immunosuppressive agent. The monitoring of a panel of valid biomarkers can improve patient stratification and the selection of immunosuppressive drugs. After transplantation, therapy can be adjusted based on the prediction of rejection episodes (maintained alloreactivity), the prognosis of allograft damage, and the individual's response to the drugs. This review will focus on current data indicating that changes in the T-cell production of the intracellular cytokines interferon-γ and interleukin-2 could be used to predict the risk of rejection and to guide immunosuppressive therapy in transplant recipients.

  14. Vascular Endothelium as a Target of Immune Response in Renal Transplant Rejection

    Science.gov (United States)

    Piotti, Giovanni; Palmisano, Alessandra; Maggiore, Umberto; Buzio, Carlo

    2014-01-01

    This review of clinical and experimental studies aims at analyzing the interplay between graft endothelium and host immune system in renal transplantation, and how it affects the survival of the graft. Graft endothelium is indeed the first barrier between self and non-self that is encountered by host lymphocytes upon reperfusion of vascularized solid transplants. Endothelial cells (EC) express all the major sets of antigens (Ag) that elicit host immune response, and therefore represent a preferential target in organ rejection. Some of the Ag expressed by EC are target of the antibody-mediated response, such as the AB0 blood group system, the human leukocyte antigens (HLA), and MHC class I related chain A antigens (MICA) systems, and the endothelial cell-restricted Ag; for each of these systems, the mechanisms of interaction and damage of both preformed and de novo donor-specific antibodies are reviewed along with their impact on renal graft survival. Moreover, the rejection process can force injured EC to expose cryptic self-Ag, toward which an autoimmune response mounts, overlapping to the allo-immune response in the damaging of the graft. Not only are EC a passive target of the host immune response but also an active player in lymphocyte activation; therefore, their interaction with allogenic T-cells is analyzed on the basis of experimental in vitro and in vivo studies, according to the patterns of expression of the HLA class I and II and the co-stimulatory molecules specific for cytotoxic and helper T-cells. Finally, as the response that follows transplantation has proven to be not necessarily destructive, the factors that foster graft endothelium functioning in spite of rejection, and how they could be therapeutically harnessed to promote long-term graft acceptance, are described: accommodation that is resistance of EC to donor-specific antibodies, and endothelial cell ability to induce Foxp3+ regulatory T-cells, that are crucial mediators of tolerance. PMID

  15. Attachment dismissal predicts frontal slow-wave ERPs during rejection by unfamiliar peers.

    Science.gov (United States)

    White, Lars O; Wu, Jia; Borelli, Jessica L; Rutherford, Helena J V; David, Daryn H; Kim-Cohen, Julia; Mayes, Linda C; Crowley, Michael J

    2012-08-01

    Attachment representations are thought to provide a cognitive-affective template, guiding the way individuals interact with unfamiliar social partners. To examine the neural correlates of this process, we sampled event-related potentials (ERPs) during exclusion by unfamiliar peers to differentiate insecure-dismissing from securely attached youth, as indexed by the child attachment interview. Thirteen secure and 10 dismissing 11- to 15-year-olds were ostensibly connected with two peers via the Internet to play a computerized ball-toss game. Actually, peers were computer generated, first distributing the ball evenly, but eventually excluding participants. Afterward children rated their distress. As in previous studies, distress was related to a negative left frontal slow wave (500-900 ms) during rejection, a waveform implicated in negative appraisals and less approach motivation. Though attachment classifications were comparable in frontal ERPs and distress, an attachment-related dismissal dimension predicted a negative left frontal slow wave during rejection, suggesting that high dismissal potentially involves elevated anticipation of rejection. As expected, dismissal and self-reported distress were uncorrelated. Yet, a new approach to quantifying the dissociation between self-reports and rejection-related ERPs revealed that dismissal predicted underreporting of distress relative to ERPs. Our findings imply that evaluations and regulatory strategies linked to attachment generalize to distressing social contexts in early adolescence.

  16. Mechanisms and Mediators of Inflammation: Potential Models for Skin Rejection and Targeted Therapy in Vascularized Composite Allotransplantation

    Directory of Open Access Journals (Sweden)

    Theresa Hautz

    2012-01-01

    Full Text Available Vascularized composite allotransplantation (VCA is an effective treatment option for patients suffering from limb loss or severe disfigurement. However, postoperative courses of VCA recipients have been complicated by skin rejection, and long-term immunosuppression remains a necessity for allograft survival. To widen the scope of this quality-of-life improving procedure minimization of immunosuppression in order to limit risks and side effects is needed. In some aspects, the molecular mechanisms and dynamics of skin allograft rejection seem similar to inflammatory skin conditions. T cells are key players in skin rejection and are recruited to the skin via activation of adhesion molecules, cytokines, and chemokines. Blocking these molecules has not only shown success in the treatment of inflammatory dermatoses, but also prolonged graft survival in various models of solid organ transplantation. In addition to T cell recruitment, ectopic lymphoid structures within the allograft associated with chronic rejection in solid organ transplantation might contribute to the strong alloimmune response towards the skin. Selectively targeting the molecules involved offers exciting novel therapeutic options in the prevention and treatment of skin rejection after VCA.

  17. Predicting excessive body image concerns among British university students: the unique role of Appearance-based Rejection Sensitivity.

    Science.gov (United States)

    Calogero, Rachel M; Park, Lora E; Rahemtulla, Zara K; Williams, Katherine C D

    2010-01-01

    The present research examined the extent to which interpersonal concerns about rejection based on appearance, or Appearance-based Rejection Sensitivity (Appearance-RS), serves as an indicator of risk for excessive body image concerns. Extending previous research, we examined the association between Appearance-RS and symptoms of body dysmorphic disorder (BDD) and cosmetic surgery attitudes among 106 British university students. Consistent with predictions, Appearance-RS uniquely predicted greater degree of BDD symptoms after controlling for other known predictor variables. Also, as expected, Appearance-RS uniquely predicted acceptance of cosmetic surgery for both intrapersonal and social reasons and greater consideration of having cosmetic surgery in the future. These findings highlight the importance of assessing individuals' sensitivity to rejection from others based on their physical appearance in investigations of excessive body image concerns. Copyright 2009 Elsevier Ltd. All rights reserved.

  18. Predictive current control of permanent magnet synchronous motor based on linear active disturbance rejection control

    Science.gov (United States)

    Li, Kunpeng

    2017-01-01

    The compatibility problem between rapidity and overshooting in the traditional predictive current control structure is inevitable and difficult to solve by reason of using PI controller. A novel predictive current control (PCC) algorithm for permanent magnet synchronous motor (PMSM) based on linear active disturbance rejection control (LADRC) is presented in this paper. In order to displace PI controller, the LADRC strategy which consisted of linear state error feedback (LSEF) control algorithm and linear extended state observer (LESO), is designed based on the mathematic model of PMSM. The purpose of LSEF is to make sure fast response to load mutation and system uncertainties, and LESO is designed to estimate the uncertain disturbances. The principal structures of the proposed system are speed outer loop based on LADRC and current inner loop based on predictive current control. Especially, the instruction value of qaxis current in inner loop is derived from the control quantity which is designed in speed outer loop. The simulation is carried out in Matlab/Simulink software, and the results illustrate that the dynamic and static performances of proposed system are satisfied. Moreover the robust against model parameters mismatch is enhanced obviously.

  19. Developing and testing ScrollQuest: A video game targeting rejection sensitivity in adolescents

    NARCIS (Netherlands)

    Tuijnman, A.; Granic, I.; Whitkin, J.; Engels, R.C.M.E.

    2017-01-01

    Depression affects a large proportion of adolescents and current interventions only have moderate effects. With the potential of video games for emotional and mental health in mind, we developed a video game for rejection sensitivity, which is a major risk factor for depression. A process of

  20. T cells targeting a neuronal paraneoplastic antigen mediate tumor rejection and trigger CNS autoimmunity with humoral activation.

    Science.gov (United States)

    Blachère, Nathalie E; Orange, Dana E; Santomasso, Bianca D; Doerner, Jessica; Foo, Patricia K; Herre, Margaret; Fak, John; Monette, Sébastien; Gantman, Emily C; Frank, Mayu O; Darnell, Robert B

    2014-11-01

    Paraneoplastic neurologic diseases (PND) involving immune responses directed toward intracellular antigens are poorly understood. Here, we examine immunity to the PND antigen Nova2, which is expressed exclusively in central nervous system (CNS) neurons. We hypothesized that ectopic expression of neuronal antigen in the periphery could incite PND. In our C57BL/6 mouse model, CNS antigen expression limits antigen-specific CD4+ and CD8+ T-cell expansion. Chimera experiments demonstrate that this tolerance is mediated by antigen expression in nonhematopoietic cells. CNS antigen expression does not limit tumor rejection by adoptively transferred transgenic T cells but does limit the generation of a memory population that can be expanded upon secondary challenge in vivo. Despite mediating cancer rejection, adoptively transferred transgenic T cells do not lead to paraneoplastic neuronal targeting. Preliminary experiments suggest an additional requirement for humoral activation to induce CNS autoimmunity. This work provides evidence that the requirements for cancer immunity and neuronal autoimmunity are uncoupled. Since humoral immunity was not required for tumor rejection, B-cell targeting therapy, such as rituximab, may be a rational treatment option for PND that does not hamper tumor immunity. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. KIR gene and KIR ligand analysis to predict graft rejection after renal transplantation.

    NARCIS (Netherlands)

    Kreijveld, E.; Meer, A. van der; Tijssen, H.J.; Hilbrands, L.B.; Joosten, I.

    2007-01-01

    BACKGROUND: The identification of transplant patients at high risk for rejection after reduction of immunosuppression would allow minimization of immunosuppression and avoidance of side effects in low-risk patients. Next to T cells, innate natural killer (NK) cells may contribute to graft rejection.

  2. Perceived mother and father acceptance-rejection predict four unique aspects of child adjustment across nine countries

    Science.gov (United States)

    Putnick, Diane L.; Bornstein, Marc H.; Lansford, Jennifer E.; Malone, Patrick S.; Pastorelli, Concetta; Skinner, Ann T.; Sorbring, Emma; Tapanya, Sombat; Tirado, Liliana Maria Uribe; Zelli, Arnaldo; Alampay, Liane Peña; Al-Hassan, Suha M.; Bacchini, Dario; Bombi, Anna Silvia; Chang, Lei; Deater-Deckard, Kirby; Di Giunta, Laura; Dodge, Kenneth A.; Oburu, Paul

    2014-01-01

    Background It is generally believed that parental rejection of children leads to child maladaptation. However, the specific effects of perceived parental acceptance-rejection on diverse domains of child adjustment and development have been incompletely documented, and whether these effects hold across diverse populations and for mothers and fathers are still open questions. Methods This study assessed children's perceptions of mother and father acceptance-rejection in 1247 families from China, Colombia, Italy, Jordan, Kenya, the Philippines, Sweden, Thailand, and the United States as antecedent predictors of later internalizing and externalizing behavior problems, school performance, prosocial behavior, and social competence. Results Higher perceived parental rejection predicted increases in internalizing and externalizing behavior problems and decreases in school performance and prosocial behavior across three years controlling for within-wave relations, stability across waves, and parental age, education, and social desirability bias. Patterns of relations were similar across mothers and fathers and, with a few exceptions, all 9 countries. Conclusions Children's perceptions of maternal and paternal acceptance-rejection have small but nearly universal effects on multiple aspects of their adjustment and development regardless of the family's country of origin. PMID:25492267

  3. Prediction of acute cardiac rejection by changes in left ventricular volumes

    International Nuclear Information System (INIS)

    Novitzky, D.; Cooper, D.K.; Boniaszczuk, J.

    1988-01-01

    Sixteen patients underwent heart transplantation (11 orthotopic, five heterotopic). Monitoring for acute rejection was by both endomyocardial biopsy (EMB) and multigated equilibrium blood pool scanning with technetium 99m-labelled red blood cells. From the scans information was obtained on left ventricular volumes (stroke, end-diastolic, and end-systolic), ejection fraction, and heart rate. Studies (208) were made in the 16 patients. There was a highly significant correlation between the reduction in stroke volume and end-diastolic volume (and a less significant correlation in end-systolic volume) and increasing acute rejection seen on EMB. Heart rate and ejection fraction did not correlate with the development of acute rejection. Correlation of a combination of changes in stroke volume and end-diastolic volume with EMB showed a sensitivity of 85% and a specificity of 96%. Radionuclide scanning is therefore a useful noninvasive tool for monitoring acute rejection

  4. Predicting the Reliability of Drug-target Interaction Predictions with Maximum Coverage of Target Space.

    Science.gov (United States)

    Peón, Antonio; Naulaerts, Stefan; Ballester, Pedro J

    2017-06-19

    Many computational methods to predict the macromolecular targets of small organic molecules have been presented to date. Despite progress, target prediction methods still have important limitations. For example, the most accurate methods implicitly restrict their predictions to a relatively small number of targets, are not systematically validated on drugs (whose targets are harder to predict than those of non-drug molecules) and often lack a reliability score associated with each predicted target. Here we present a systematic validation of ligand-centric target prediction methods on a set of clinical drugs. These methods exploit a knowledge-base covering 887,435 known ligand-target associations between 504,755 molecules and 4,167 targets. Based on this dataset, we provide a new estimate of the polypharmacology of drugs, which on average have 11.5 targets below IC 50 10 µM. The average performance achieved across clinical drugs is remarkable (0.348 precision and 0.423 recall, with large drug-dependent variability), especially given the unusually large coverage of the target space. Furthermore, we show how a sparse ligand-target bioactivity matrix to retrospectively validate target prediction methods could underestimate prospective performance. Lastly, we present and validate a first-in-kind score capable of accurately predicting the reliability of target predictions.

  5. Rejection Positivity Predicts Trial-to-Trial Reaction Times in an Auditory Selective Attention Task: A Computational Analysis of Inhibitory Control

    Directory of Open Access Journals (Sweden)

    Sufen eChen

    2014-08-01

    Full Text Available A series of computer simulations using variants of a formal model of attention (Melara & Algom, 2003 probed the role of rejection positivity (RP, a slow-wave electroencephalographic (EEG component, in the inhibitory control of distraction. Behavioral and EEG data were recorded as participants performed auditory selective attention tasks. Simulations that modulated processes of distractor inhibition accounted well for reaction-time (RT performance, whereas those that modulated target excitation did not. A model that incorporated RP from actual EEG recordings in estimating distractor inhibition was superior in predicting changes in RT as a function of distractor salience across conditions. A model that additionally incorporated momentary fluctuations in EEG as the source of trial-to-trial variation in performance precisely predicted individual RTs within each condition. The results lend support to the linking proposition that RP controls the speed of responding to targets through the inhibitory control of distractors.

  6. Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant

    Directory of Open Access Journals (Sweden)

    Silvia Pineda

    2017-12-01

    Full Text Available Transplant rejection is the critical clinical end-point limiting indefinite survival after histocompatibility antigen (HLA mismatched organ transplantation. The predominant cause of late graft loss is antibody-mediated rejection (AMR, a process whereby injury to the organ is caused by donor-specific antibodies, which bind to HLA and non-HLA (nHLA antigens. AMR is incompletely diagnosed as donor/recipient (D/R matching is only limited to the HLA locus and critical nHLA immunogenic antigens remain to be identified. We have developed an integrative computational approach leveraging D/R exome sequencing and gene expression to predict clinical post-transplant outcome. We performed a rigorous statistical analysis of 28 highly annotated D/R kidney transplant pairs with biopsy-confirmed clinical outcomes of rejection [either AMR or T-cell-mediated rejection (CMR] and no-rejection (NoRej, identifying a significantly higher number of mismatched nHLA variants in AMR (ANOVA—p-value = 0.02. Using Fisher’s exact test, we identified 123 variants associated mainly with risk of AMR (p-value < 0.001. In addition, we applied a machine-learning technique to circumvent the issue of statistical power and we found a subset of 65 variants using random forest, that are predictive of post-tx AMR showing a very low error rate. These variants are functionally relevant to the rejection process in the kidney and AMR as they relate to genes and/or expression quantitative trait loci (eQTLs that are enriched in genes expressed in kidney and vascular endothelium and underlie the immunobiology of graft rejection. In addition to current D/R HLA mismatch evaluation, additional mismatch nHLA D/R variants will enhance the stratification of post-tx AMR risk even before engraftment of the organ. This innovative study design is applicable in all solid organ transplants, where the impact of mitigating AMR on graft survival may be greater, with considerable benefits on

  7. Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection

    Directory of Open Access Journals (Sweden)

    Marius Rutkauskas

    2015-03-01

    Full Text Available CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against foreign nucleic acids. In type I CRISPR-Cas systems, invading DNA is detected by a large ribonucleoprotein surveillance complex called Cascade. The crRNA component of Cascade is used to recognize target sites in foreign DNA (protospacers by formation of an R-loop driven by base-pairing complementarity. Using single-molecule supercoiling experiments with near base-pair resolution, we probe here the mechanism of R-loop formation and detect short-lived R-loop intermediates on off-target sites bearing single mismatches. We show that R-loops propagate directionally starting from the protospacer-adjacent motif (PAM. Upon reaching a mismatch, R-loop propagation stalls and collapses in a length-dependent manner. This unambiguously demonstrates that directional zipping of the R-loop accomplishes efficient target recognition by rapidly rejecting binding to off-target sites with PAM-proximal mutations. R-loops that reach the protospacer end become locked to license DNA degradation by the auxiliary Cas3 nuclease/helicase without further target verification.

  8. The modelling of avian visual perception predicts behavioural rejection responses to foreign egg colours

    Czech Academy of Sciences Publication Activity Database

    Cassey, P.; Honza, Marcel; Grim, T.; Hauber, M. E.

    2008-01-01

    Roč. 4, č. 5 (2008), s. 515-517 ISSN 1744-9561 Institutional research plan: CEZ:AV0Z60930519 Keywords : brood parasitism * egg rejection * eggshell colour * visual perception * birds Subject RIV: EG - Zoology Impact factor: 3.000, year: 2008

  9. Bowman Capsulitis Predicts Poor Kidney Allograft Outcome in T Cell-Mediated Rejection.

    Science.gov (United States)

    Gallan, Alexander J; Chon, W James; Josephson, Michelle A; Cunningham, Patrick N; Henriksen, Kammi J; Chang, Anthony

    2018-02-28

    Acute T cell-mediated rejection (TCMR) is an important cause of renal allograft loss. The Banff classification for tubulointerstitial (type I) rejection is based on the extent of both interstitial inflammation and tubulitis. Lymphocytes may also be present between parietal epithelial cells and Bowman capsules in this setting, which we have termed "capsulitis." We conducted this study to determine the clinical significance of capsulitis. We identified 42 patients from the pathology archives at the University of Chicago with isolated Banff type I TCMR from 2010-2015. Patient demographic data, Banff classification, and graft outcome measurements were compared between capsulitis and non-capsulitis groups using Mann-Whitney U test. Capsulitis was present in 26 (62%), and was more frequently seen in Banff IB than IA TCMR (88% vs 44%, P=.01). Patients with capsulitis had a higher serum creatinine at biopsy (4.6 vs 2.9mg/dL, P=.04) and were more likely to progress to dialysis (42% vs 13%, P=.06) with fewer recovering their baseline serum creatinine (12% vs 38%, P=.08). Patients with both Banff IA TCMR and capsulitis have clinical outcomes similar or possibly worse than Banff IB TCMR compared to those with Banff IA and an absence of capsulitis. Capsulitis is an important pathologic parameter in the evaluation of kidney transplant biopsies with potential diagnostic, prognostic, and therapeutic implications in the setting of TCMR. Copyright © 2018. Published by Elsevier Inc.

  10. Predictive geophysics: geochemical simulations to geophysical targets

    Science.gov (United States)

    Chopping, R. G.; Cleverley, J.

    2017-12-01

    With an increasing focus on deep exploration for covered targets, new methods are required to target mineral systems under cover. Geophysical responses are driven by physical property contrasts; for example, density contrasts provide a gravity signal, acoustic impedance contrasts provide a seismic reflection signal. In turn, the physical properties for basement, crystalline rocks which host the vast majority of mineral systems are determined almost wholly by the mineralogy of the rocks in question. Mineral systems, through the transport of heat and reactive fluids, will serve to modify the physical properties of country rock as they chemically alter the hosting strata. To understand these changes, we have performed 2D reactive transport modelling that simulates the formation of Archean gold deposits of the Yilgarn Craton, Western Australia. From this, we derive a model of mineralogy that we can use to predict the density, magnetic susceptibility and seismic reflection changes associated with ore formation. It is then possible to predict the gravity, magnetic and seismic reflection responses associated with these deposits. Scenario mapping, such as testing the ability to resolve buried ore bodies or the geophysical survey spacing required to resolve the mineral system, can be performed to produce geophysical targets from these geochemical simulations. We find that there is a gravity response of around 9% of the unaltered response for deposits even buried by 1km of cover, and there is a magnetic spike associated with proximal alteration of the ore system. Finally, seismic reflection response is mostly characterised by additional reflections along faults that plumb the alteration system.

  11. Anxious Solitude and Peer Exclusion Predict Social Helplessness, Upset Affect, and Vagal Regulation in Response to Behavioral Rejection by a Friend

    Science.gov (United States)

    Gazelle, Heidi; Druhen, Madelynn J.

    2009-01-01

    It was hypothesized that combined individual child vulnerability (anxious solitude) and interpersonal stress (peer exclusion) would predict the strongest responses to experimentally manipulated behavioral peer rejection. Results indicated that in a sample of 3rd graders (N = 160, 59% girls), anxious solitary excluded children displayed more…

  12. Prediction of RO/NF membrane rejections of PhACs and organic compounds : A statistical analysis

    NARCIS (Netherlands)

    Yangali-Quintanilla, V.; Kim, T.U.; Kennedy, M.; Amy, G.

    2008-01-01

    OA fund TU Delft Rejections of pharmaceutical compounds (Ibuprofen, Diclofenac, Clofibric acid, Naproxen, Primidone, Phenacetin) and organic compounds (Dichloroacetic acid, Trichloroacetic acid, Chloroform, Bromoform, Trichloroethene, Perchloroethene, Car-bontetrachloride, Carbontetrabromide) by NF

  13. Combinatorial microRNA target predictions

    DEFF Research Database (Denmark)

    Krek, Azra; Grün, Dominic; Poy, Matthew N.

    2005-01-01

    in different cell types and may coordinately regulate cell-specific target genes. Here, we present PicTar, a computational method for identifying common targets of microRNAs. Statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar's ability to specifically recover published micro...... suggest widespread coordinate control executed by microRNAs. In particular, we experimentally validate common regulation of Mtpn by miR-375, miR-124 and let-7b and thus provide evidence for coordinate microRNA control in mammals....

  14. Prediction of potential drug targets based on simple sequence properties

    Directory of Open Access Journals (Sweden)

    Lai Luhua

    2007-09-01

    Full Text Available Abstract Background During the past decades, research and development in drug discovery have attracted much attention and efforts. However, only 324 drug targets are known for clinical drugs up to now. Identifying potential drug targets is the first step in the process of modern drug discovery for developing novel therapeutic agents. Therefore, the identification and validation of new and effective drug targets are of great value for drug discovery in both academia and pharmaceutical industry. If a protein can be predicted in advance for its potential application as a drug target, the drug discovery process targeting this protein will be greatly speeded up. In the current study, based on the properties of known drug targets, we have developed a sequence-based drug target prediction method for fast identification of novel drug targets. Results Based on simple physicochemical properties extracted from protein sequences of known drug targets, several support vector machine models have been constructed in this study. The best model can distinguish currently known drug targets from non drug targets at an accuracy of 84%. Using this model, potential protein drug targets of human origin from Swiss-Prot were predicted, some of which have already attracted much attention as potential drug targets in pharmaceutical research. Conclusion We have developed a drug target prediction method based solely on protein sequence information without the knowledge of family/domain annotation, or the protein 3D structure. This method can be applied in novel drug target identification and validation, as well as genome scale drug target predictions.

  15. Common features of microRNA target prediction tools

    Directory of Open Access Journals (Sweden)

    Sarah M. Peterson

    2014-02-01

    Full Text Available The human genome encodes for over 1800 microRNAs, which are short noncoding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one microRNA to target multiple gene transcripts, microRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of microRNA targets is a critical initial step in identifying microRNA:mRNA target interactions for experimental validation. The available tools for microRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to microRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all microRNA target prediction tools, four main aspects of the microRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MicroRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output.

  16. Motion prediction of a non-cooperative space target

    Science.gov (United States)

    Zhou, Bang-Zhao; Cai, Guo-Ping; Liu, Yun-Meng; Liu, Pan

    2018-01-01

    Capturing a non-cooperative space target is a tremendously challenging research topic. Effective acquisition of motion information of the space target is the premise to realize target capture. In this paper, motion prediction of a free-floating non-cooperative target in space is studied and a motion prediction algorithm is proposed. In order to predict the motion of the free-floating non-cooperative target, dynamic parameters of the target must be firstly identified (estimated), such as inertia, angular momentum and kinetic energy and so on; then the predicted motion of the target can be acquired by substituting these identified parameters into the Euler's equations of the target. Accurate prediction needs precise identification. This paper presents an effective method to identify these dynamic parameters of a free-floating non-cooperative target. This method is based on two steps, (1) the rough estimation of the parameters is computed using the motion observation data to the target, and (2) the best estimation of the parameters is found by an optimization method. In the optimization problem, the objective function is based on the difference between the observed and the predicted motion, and the interior-point method (IPM) is chosen as the optimization algorithm, which starts at the rough estimate obtained in the first step and finds a global minimum to the objective function with the guidance of objective function's gradient. So the speed of IPM searching for the global minimum is fast, and an accurate identification can be obtained in time. The numerical results show that the proposed motion prediction algorithm is able to predict the motion of the target.

  17. Me After You: Partner Influence and Individual Effort Predict Rejection of Self-Aspects and Self-Concept Clarity After Relationship Dissolution.

    Science.gov (United States)

    Slotter, Erica B; Emery, Lydia F; Luchies, Laura B

    2014-07-01

    Individuals in ongoing romantic relationships incorporate attributes from their partner into their own self-concepts. However, little research has investigated what happens to these attributes should the relationship end. Across three studies, the present research sought to examine factors that predicted whether individuals retain or reject attributes from their self-concept that they initially gained during a relationship. We predicted that individuals would be more likely to reject attributes from their self post-dissolution if their ex-partner was influential in them adding those attributes to the self in the first place. However, we expected this effect to be moderated such that individuals who exerted greater, versus lesser, effort in maintaining relevant attributes would retain them as part of the self, regardless of whether the attribute originated from the partner. In addition, in two of our three studies, we explored the roles of partner influence, effort, and attribute rejection on individuals' post-dissolution self-concept clarity. © 2014 by the Society for Personality and Social Psychology, Inc.

  18. Deep-Learning-Based Drug-Target Interaction Prediction.

    Science.gov (United States)

    Wen, Ming; Zhang, Zhimin; Niu, Shaoyu; Sha, Haozhi; Yang, Ruihan; Yun, Yonghuan; Lu, Hongmei

    2017-04-07

    Identifying interactions between known drugs and targets is a major challenge in drug repositioning. In silico prediction of drug-target interaction (DTI) can speed up the expensive and time-consuming experimental work by providing the most potent DTIs. In silico prediction of DTI can also provide insights about the potential drug-drug interaction and promote the exploration of drug side effects. Traditionally, the performance of DTI prediction depends heavily on the descriptors used to represent the drugs and the target proteins. In this paper, to accurately predict new DTIs between approved drugs and targets without separating the targets into different classes, we developed a deep-learning-based algorithmic framework named DeepDTIs. It first abstracts representations from raw input descriptors using unsupervised pretraining and then applies known label pairs of interaction to build a classification model. Compared with other methods, it is found that DeepDTIs reaches or outperforms other state-of-the-art methods. The DeepDTIs can be further used to predict whether a new drug targets to some existing targets or whether a new target interacts with some existing drugs.

  19. DASPfind: new efficient method to predict drug–target interactions

    KAUST Repository

    Ba Alawi, Wail

    2016-03-16

    Background Identification of novel drug–target interactions (DTIs) is important for drug discovery. Experimental determination of such DTIs is costly and time consuming, hence it necessitates the development of efficient computational methods for the accurate prediction of potential DTIs. To-date, many computational methods have been proposed for this purpose, but they suffer the drawback of a high rate of false positive predictions. Results Here, we developed a novel computational DTI prediction method, DASPfind. DASPfind uses simple paths of particular lengths inferred from a graph that describes DTIs, similarities between drugs, and similarities between the protein targets of drugs. We show that on average, over the four gold standard DTI datasets, DASPfind significantly outperforms other existing methods when the single top-ranked predictions are considered, resulting in 46.17 % of these predictions being correct, and it achieves 49.22 % correct single top ranked predictions when the set of all DTIs for a single drug is tested. Furthermore, we demonstrate that our method is best suited for predicting DTIs in cases of drugs with no known targets or with few known targets. We also show the practical use of DASPfind by generating novel predictions for the Ion Channel dataset and validating them manually. Conclusions DASPfind is a computational method for finding reliable new interactions between drugs and proteins. We show over six different DTI datasets that DASPfind outperforms other state-of-the-art methods when the single top-ranked predictions are considered, or when a drug with no known targets or with few known targets is considered. We illustrate the usefulness and practicality of DASPfind by predicting novel DTIs for the Ion Channel dataset. The validated predictions suggest that DASPfind can be used as an efficient method to identify correct DTIs, thus reducing the cost of necessary experimental verifications in the process of drug discovery. DASPfind

  20. Investigation of Killer Immunoglobulin-like Receptor (KIR) and HLA Genotypes to Predict the Occurrence of Acute Allograft Rejection after Kidney Transplantation.

    Science.gov (United States)

    Jafari, Davood; Nafar, Mohsen; Yekaninejad, Mir Saeed; Abdolvahabi, Razieh; Lesan Pezeshki, Mahboob; Razaghi, Efat; Amirzargar, Ali Akbar

    2017-06-01

    After kidney transplantation, natural killer (NK) cells play a pivotal role in triggering the immune response to the allogeneic grafts primarily by their killer-cell immunoglobulin-like receptors (KIR). This process may be one mechanism that contributes to graft rejection. In this study, we have evaluated whether acute rejection after kidney transplantation was associated with predicted NK cell alloreactivity based on KIR gene and ligand along with KIR/HLA compound genotype analysis. After kidney transplantation, natural killer (NK) cells play a pivotal role in triggering the immune response to the allogeneic grafts primarily by their killer-cell immunoglobulin-like receptors (KIR). This process may be one mechanism that contributes to graft rejection. In this study, we have evaluated whether acute rejection after kidney transplantation was associated with predicted NK cell alloreactivity based on KIR gene and ligand along with KIR/HLA compound genotype analysis. DNA from 65 patients with biopsy-proven acute kidney allograft rejection (AKAR), 61 clinically stable graft function (SGF) recipients and 176 healthy subjects were identified for the presence or absence of 10 variable KIR genes (both activating and inhibitory receptors) and their HLA ligands using polymerase chain reaction-sequence specific primers (PCR-SSP) assay. Although no significant difference in the frequency of individual KIR genes, was found the gene content, and the haplotypic distribution between the three categories were detected, the frequency of the KIR3DL1+HLA-Bw4*A allele combination was significantly lower in AKAR patients compared to SGF recipients (p=0.004, OR=0.34, CI=0.16-0.72) and healthy subjects (p=0.019, OR=0.47, CI=0.25-0.89). Kaplan-Meier survival test showed that the KIR3DL1+HLA-Bw4*A allele combination could be considered protective for AKAR (p=0.04 by log-rank). The results of this study suggest that KIR/HLA polymorphism may be a genetic susceptibility factor to alloreactivity

  1. miRNA-target prediction based on transcriptional regulation

    Directory of Open Access Journals (Sweden)

    Fujiwara Toyofumi

    2013-02-01

    Full Text Available Abstract Background microRNAs (miRNAs are tiny endogenous RNAs that have been discovered in animals and plants, and direct the post-transcriptional regulation of target mRNAs for degradation or translational repression via binding to the 3'UTRs and the coding exons. To gain insight into the biological role of miRNAs, it is essential to identify the full repertoire of mRNA targets (target genes. A number of computer programs have been developed for miRNA-target prediction. These programs essentially focus on potential binding sites in 3'UTRs, which are recognized by miRNAs according to specific base-pairing rules. Results Here, we introduce a novel method for miRNA-target prediction that is entirely independent of existing approaches. The method is based on the hypothesis that transcription of a miRNA and its target genes tend to be co-regulated by common transcription factors. This hypothesis predicts the frequent occurrence of common cis-elements between promoters of a miRNA and its target genes. That is, our proposed method first identifies putative cis-elements in a promoter of a given miRNA, and then identifies genes that contain common putative cis-elements in their promoters. In this paper, we show that a significant number of common cis-elements occur in ~28% of experimentally supported human miRNA-target data. Moreover, we show that the prediction of human miRNA-targets based on our method is statistically significant. Further, we discuss the random incidence of common cis-elements, their consensus sequences, and the advantages and disadvantages of our method. Conclusions This is the first report indicating prevalence of transcriptional regulation of a miRNA and its target genes by common transcription factors and the predictive ability of miRNA-targets based on this property.

  2. Predicting target displacements using ultrasound elastography and finite element modeling.

    Science.gov (United States)

    op den Buijs, Jorn; Hansen, Hendrik H G; Lopata, Richard G P; de Korte, Chris L; Misra, Sarthak

    2011-11-01

    Soft tissue displacements during minimally invasive surgical procedures may cause target motion and subsequent misplacement of the surgical tool. A technique is presented to predict target displacements using a combination of ultrasound elastography and finite element (FE) modeling. A cubic gelatin/agar phantom with stiff targets was manufactured to obtain pre- and post-loading ultrasound radio frequency (RF) data from a linear array transducer. The RF data were used to compute displacement and strain images, from which the distribution of elasticity was reconstructed using an inverse FE-based approach. The FE model was subsequently used to predict target displacements upon application of different boundary and loading conditions to the phantom. The influence of geometry was investigated by application of the technique to a breast-shaped phantom. The distribution of elasticity in the phantoms as determined from the strain distribution agreed well with results from mechanical testing. Upon application of different boundary and loading conditions to the cubic phantom, the FE model-predicted target motion were consistent with ultrasound measurements. The FE-based approach could also accurately predict the displacement of the target upon compression and indentation of the breast-shaped phantom. This study provides experimental evidence that organ geometry and boundary conditions surrounding the organ are important factors influencing target motion. In future work, the technique presented in this paper could be used for preoperative planning of minimally invasive surgical interventions.

  3. Quantitative self-assembly prediction yields targeted nanomedicines

    Science.gov (United States)

    Shamay, Yosi; Shah, Janki; Işık, Mehtap; Mizrachi, Aviram; Leibold, Josef; Tschaharganeh, Darjus F.; Roxbury, Daniel; Budhathoki-Uprety, Januka; Nawaly, Karla; Sugarman, James L.; Baut, Emily; Neiman, Michelle R.; Dacek, Megan; Ganesh, Kripa S.; Johnson, Darren C.; Sridharan, Ramya; Chu, Karen L.; Rajasekhar, Vinagolu K.; Lowe, Scott W.; Chodera, John D.; Heller, Daniel A.

    2018-02-01

    Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of sulfated indocyanines into particles with ultrahigh drug loadings of up to 90%. We devised quantitative structure-nanoparticle assembly prediction (QSNAP) models to identify and validate electrotopological molecular descriptors as highly predictive indicators of nano-assembly and nanoparticle size. The resulting nanoparticles selectively targeted kinase inhibitors to caveolin-1-expressing human colon cancer and autochthonous liver cancer models to yield striking therapeutic effects while avoiding pERK inhibition in healthy skin. This finding enables the computational design of nanomedicines based on quantitative models for drug payload selection.

  4. Drug-target interaction prediction from PSSM based evolutionary information.

    Science.gov (United States)

    Mousavian, Zaynab; Khakabimamaghani, Sahand; Kavousi, Kaveh; Masoudi-Nejad, Ali

    2016-01-01

    The labor-intensive and expensive experimental process of drug-target interaction prediction has motivated many researchers to focus on in silico prediction, which leads to the helpful information in supporting the experimental interaction data. Therefore, they have proposed several computational approaches for discovering new drug-target interactions. Several learning-based methods have been increasingly developed which can be categorized into two main groups: similarity-based and feature-based. In this paper, we firstly use the bi-gram features extracted from the Position Specific Scoring Matrix (PSSM) of proteins in predicting drug-target interactions. Our results demonstrate the high-confidence prediction ability of the Bigram-PSSM model in terms of several performance indicators specifically for enzymes and ion channels. Moreover, we investigate the impact of negative selection strategy on the performance of the prediction, which is not widely taken into account in the other relevant studies. This is important, as the number of non-interacting drug-target pairs are usually extremely large in comparison with the number of interacting ones in existing drug-target interaction data. An interesting observation is that different levels of performance reduction have been attained for four datasets when we change the sampling method from the random sampling to the balanced sampling. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization.

    Science.gov (United States)

    Ezzat, Ali; Zhao, Peilin; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

    2017-01-01

    Experimental determination of drug-target interactions is expensive and time-consuming. Therefore, there is a continuous demand for more accurate predictions of interactions using computational techniques. Algorithms have been devised to infer novel interactions on a global scale where the input to these algorithms is a drug-target network (i.e., a bipartite graph where edges connect pairs of drugs and targets that are known to interact). However, these algorithms had difficulty predicting interactions involving new drugs or targets for which there are no known interactions (i.e., "orphan" nodes in the network). Since data usually lie on or near to low-dimensional non-linear manifolds, we propose two matrix factorization methods that use graph regularization in order to learn such manifolds. In addition, considering that many of the non-occurring edges in the network are actually unknown or missing cases, we developed a preprocessing step to enhance predictions in the "new drug" and "new target" cases by adding edges with intermediate interaction likelihood scores. In our cross validation experiments, our methods achieved better results than three other state-of-the-art methods in most cases. Finally, we simulated some "new drug" and "new target" cases and found that GRMF predicted the left-out interactions reasonably well.

  6. Social Causes and Consequences of Rejection Sensitivity

    Science.gov (United States)

    London, Bonita; Downey, Geraldine; Bonica, Cheryl; Paltin, Iris

    2007-01-01

    Predictions from the Rejection Sensitivity (RS) model concerning the social causes and consequences of RS were examined in a longitudinal study of 150 middle school students. Peer nominations of rejection, self-report measures of anxious and angry rejection expectations, and social anxiety, social withdrawal, and loneliness were assessed at two…

  7. Labor market position after a rejection of a disability pension application: a register-based cohort study.

    Science.gov (United States)

    Laaksonen, Mikko; Gould, Raija; Liukko, Jyri

    2017-08-17

    To study labor market positions of rejected disability pension applicants and to examine which characteristics predict ending up in these positions after the rejection. Nationwide Finnish register data was used to describe employment, unemployment and disability pension trajectories of rejected applicants (n = 5740) from four years before to four years after the rejection. Demographic, occupational and health-related determinants of labor market position after the rejection were examined among those employed and not employed at the time of the rejection. The proportion of the employed steeply decreased and that of unemployed increased before the rejection of a disability pension application. Four years after the rejection, 30% of the rejected applicants were employed, 24% were unemployed and 30% received disability pension. Employment at the time of the rejection, younger age, shorter unemployment history, public sector employment and milder work disability increased future employment. Manual work, public sector employment and previous long-term unemployment predicted future unemployment. Apart from higher age, associations with receiving disability pension were relatively weak. For many rejected disability pension applicants return to work is challenging. Special efforts should be targeted to support the remaining work ability and to promote employment opportunities of the rejected applicants. Implications for Rehabilitation Employment, unemployment and receiving disability pension were equally common labor market positions four years after the rejection. Rejected DP applicants with unemployment history need special efforts to increase their employability. As a disability pension application, even if rejected, clearly indicates some degree of work ability problems, rehabilitation should be targeted at this time point to support employment.

  8. Assessment of CASP7 structure predictions for template free targets.

    Science.gov (United States)

    Jauch, Ralf; Yeo, Hock Chuan; Kolatkar, Prasanna R; Clarke, Neil D

    2007-01-01

    In CASP7, protein structure prediction targets that lacked substantial similarity to a protein in the PDB at the time of assessment were considered to be free modeling targets (FM). We assessed predictions for 14 FM targets as well as four other targets that were deemed to be on the borderline between FM targets and template based modeling targets (TBM/FM). GDT_TS was used as one measure of model quality. Model quality was also assessed by visual inspection. Visual inspection was performed by three independent assessors who were blinded to GDT_TS scores and other quantitative measures of model quality. The best models by visual inspection tended to rank among the top few percent by GDT_TS, but were typically not the highest scoring models. Thus, visual inspection remains an essential component of assessment for FM targets. Overall, group TS020 (Baker) performed best, but success on individual targets was widely distributed among many groups. Among these other groups, TS024 and TS025 (Zhang and Zhang server) performed notably well without exceptionally large computing resources. This should be considered encouraging for future CASPs. There was a sense of progress in template FM relative to CASP6, but we were unable to demonstrate this progress objectively. (c) 2007 Wiley-Liss, Inc.

  9. Predicting selective drug targets in cancer through metabolic networks

    Science.gov (United States)

    Folger, Ori; Jerby, Livnat; Frezza, Christian; Gottlieb, Eyal; Ruppin, Eytan; Shlomi, Tomer

    2011-01-01

    The interest in studying metabolic alterations in cancer and their potential role as novel targets for therapy has been rejuvenated in recent years. Here, we report the development of the first genome-scale network model of cancer metabolism, validated by correctly identifying genes essential for cellular proliferation in cancer cell lines. The model predicts 52 cytostatic drug targets, of which 40% are targeted by known, approved or experimental anticancer drugs, and the rest are new. It further predicts combinations of synthetic lethal drug targets, whose synergy is validated using available drug efficacy and gene expression measurements across the NCI-60 cancer cell line collection. Finally, potential selective treatments for specific cancers that depend on cancer type-specific downregulation of gene expression and somatic mutations are compiled. PMID:21694718

  10. Large-scale prediction of drug-target relationships

    DEFF Research Database (Denmark)

    Kuhn, Michael; Campillos, Mónica; González, Paula

    2008-01-01

    , but also provides a more global view on drug-target relations. Here we review recent attempts to apply large-scale computational analyses to predict novel interactions of drugs and targets from molecular and cellular features. In this context, we quantify the family-dependent probability of two proteins...... to bind the same ligand as function of their sequence similarity. We finally discuss how phenotypic data could help to expand our understanding of the complex mechanisms of drug action....

  11. TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models.

    Science.gov (United States)

    Yao, Zhi-Jiang; Dong, Jie; Che, Yu-Jing; Zhu, Min-Feng; Wen, Ming; Wang, Ning-Ning; Wang, Shan; Lu, Ai-Ping; Cao, Dong-Sheng

    2016-05-01

    Drug-target interactions (DTIs) are central to current drug discovery processes and public health fields. Analyzing the DTI profiling of the drugs helps to infer drug indications, adverse drug reactions, drug-drug interactions, and drug mode of actions. Therefore, it is of high importance to reliably and fast predict DTI profiling of the drugs on a genome-scale level. Here, we develop the TargetNet server, which can make real-time DTI predictions based only on molecular structures, following the spirit of multi-target SAR methodology. Naïve Bayes models together with various molecular fingerprints were employed to construct prediction models. Ensemble learning from these fingerprints was also provided to improve the prediction ability. When the user submits a molecule, the server will predict the activity of the user's molecule across 623 human proteins by the established high quality SAR model, thus generating a DTI profiling that can be used as a feature vector of chemicals for wide applications. The 623 SAR models related to 623 human proteins were strictly evaluated and validated by several model validation strategies, resulting in the AUC scores of 75-100 %. We applied the generated DTI profiling to successfully predict potential targets, toxicity classification, drug-drug interactions, and drug mode of action, which sufficiently demonstrated the wide application value of the potential DTI profiling. The TargetNet webserver is designed based on the Django framework in Python, and is freely accessible at http://targetnet.scbdd.com .

  12. TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models

    Science.gov (United States)

    Yao, Zhi-Jiang; Dong, Jie; Che, Yu-Jing; Zhu, Min-Feng; Wen, Ming; Wang, Ning-Ning; Wang, Shan; Lu, Ai-Ping; Cao, Dong-Sheng

    2016-05-01

    Drug-target interactions (DTIs) are central to current drug discovery processes and public health fields. Analyzing the DTI profiling of the drugs helps to infer drug indications, adverse drug reactions, drug-drug interactions, and drug mode of actions. Therefore, it is of high importance to reliably and fast predict DTI profiling of the drugs on a genome-scale level. Here, we develop the TargetNet server, which can make real-time DTI predictions based only on molecular structures, following the spirit of multi-target SAR methodology. Naïve Bayes models together with various molecular fingerprints were employed to construct prediction models. Ensemble learning from these fingerprints was also provided to improve the prediction ability. When the user submits a molecule, the server will predict the activity of the user's molecule across 623 human proteins by the established high quality SAR model, thus generating a DTI profiling that can be used as a feature vector of chemicals for wide applications. The 623 SAR models related to 623 human proteins were strictly evaluated and validated by several model validation strategies, resulting in the AUC scores of 75-100 %. We applied the generated DTI profiling to successfully predict potential targets, toxicity classification, drug-drug interactions, and drug mode of action, which sufficiently demonstrated the wide application value of the potential DTI profiling. The TargetNet webserver is designed based on the Django framework in Python, and is freely accessible at http://targetnet.scbdd.com.

  13. RFMirTarget: predicting human microRNA target genes with a random forest classifier.

    Directory of Open Access Journals (Sweden)

    Mariana R Mendoza

    Full Text Available MicroRNAs are key regulators of eukaryotic gene expression whose fundamental role has already been identified in many cell pathways. The correct identification of miRNAs targets is still a major challenge in bioinformatics and has motivated the development of several computational methods to overcome inherent limitations of experimental analysis. Indeed, the best results reported so far in terms of specificity and sensitivity are associated to machine learning-based methods for microRNA-target prediction. Following this trend, in the current paper we discuss and explore a microRNA-target prediction method based on a random forest classifier, namely RFMirTarget. Despite its well-known robustness regarding general classifying tasks, to the best of our knowledge, random forest have not been deeply explored for the specific context of predicting microRNAs targets. Our framework first analyzes alignments between candidate microRNA-target pairs and extracts a set of structural, thermodynamics, alignment, seed and position-based features, upon which classification is performed. Experiments have shown that RFMirTarget outperforms several well-known classifiers with statistical significance, and that its performance is not impaired by the class imbalance problem or features correlation. Moreover, comparing it against other algorithms for microRNA target prediction using independent test data sets from TarBase and starBase, we observe a very promising performance, with higher sensitivity in relation to other methods. Finally, tests performed with RFMirTarget show the benefits of feature selection even for a classifier with embedded feature importance analysis, and the consistency between relevant features identified and important biological properties for effective microRNA-target gene alignment.

  14. Predicting targets of compounds against neurological diseases using cheminformatic methodology

    Science.gov (United States)

    Nikolic, Katarina; Mavridis, Lazaros; Bautista-Aguilera, Oscar M.; Marco-Contelles, José; Stark, Holger; do Carmo Carreiras, Maria; Rossi, Ilaria; Massarelli, Paola; Agbaba, Danica; Ramsay, Rona R.; Mitchell, John B. O.

    2015-02-01

    Recently developed multi-targeted ligands are novel drug candidates able to interact with monoamine oxidase A and B; acetylcholinesterase and butyrylcholinesterase; or with histamine N-methyltransferase and histamine H3-receptor (H3R). These proteins are drug targets in the treatment of depression, Alzheimer's disease, obsessive disorders, and Parkinson's disease. A probabilistic method, the Parzen-Rosenblatt window approach, was used to build a "predictor" model using data collected from the ChEMBL database. The model can be used to predict both the primary pharmaceutical target and off-targets of a compound based on its structure. Molecular structures were represented based on the circular fingerprint methodology. The same approach was used to build a "predictor" model from the DrugBank dataset to determine the main pharmacological groups of the compound. The study of off-target interactions is now recognised as crucial to the understanding of both drug action and toxicology. Primary pharmaceutical targets and off-targets for the novel multi-target ligands were examined by use of the developed cheminformatic method. Several multi-target ligands were selected for further study, as compounds with possible additional beneficial pharmacological activities. The cheminformatic targets identifications were in agreement with four 3D-QSAR (H3R/D1R/D2R/5-HT2aR) models and by in vitro assays for serotonin 5-HT1a and 5-HT2a receptor binding of the most promising ligand ( 71/MBA-VEG8).

  15. Imbalanced target prediction with pattern discovery on clinical data repositories.

    Science.gov (United States)

    Chan, Tak-Ming; Li, Yuxi; Chiau, Choo-Chiap; Zhu, Jane; Jiang, Jie; Huo, Yong

    2017-04-20

    Clinical data repositories (CDR) have great potential to improve outcome prediction and risk modeling. However, most clinical studies require careful study design, dedicated data collection efforts, and sophisticated modeling techniques before a hypothesis can be tested. We aim to bridge this gap, so that clinical domain users can perform first-hand prediction on existing repository data without complicated handling, and obtain insightful patterns of imbalanced targets for a formal study before it is conducted. We specifically target for interpretability for domain users where the model can be conveniently explained and applied in clinical practice. We propose an interpretable pattern model which is noise (missing) tolerant for practice data. To address the challenge of imbalanced targets of interest in clinical research, e.g., deaths less than a few percent, the geometric mean of sensitivity and specificity (G-mean) optimization criterion is employed, with which a simple but effective heuristic algorithm is developed. We compared pattern discovery to clinically interpretable methods on two retrospective clinical datasets. They contain 14.9% deaths in 1 year in the thoracic dataset and 9.1% deaths in the cardiac dataset, respectively. In spite of the imbalance challenge shown on other methods, pattern discovery consistently shows competitive cross-validated prediction performance. Compared to logistic regression, Naïve Bayes, and decision tree, pattern discovery achieves statistically significant (p-values pattern discovery is consistently comparable to the best achievable performance. Pattern discovery has demonstrated to be robust and valuable for target prediction on existing clinical data repositories with imbalance and noise. The prediction results and interpretable patterns can provide insights in an agile and inexpensive way for the potential formal studies.

  16. Clustering and its application in multi-target prediction.

    Science.gov (United States)

    Liu, William; Johnson, Dale E

    2009-01-01

    Drug discovery teams are beginning to apply non-screening techniques to make early associations between chemical structure and various biological and druggability characteristics of compound series. The increasing availability of multiple data sets and models of target potency, ADME characteristics, and toxicity allows a researcher from any discipline to draw quick associations with multiple endpoints on sets of compounds or chemical scaffolds. Cluster analysis, for instance, can be used to correlate screening potency with data predicted from both freely available and commercially available models. In the future researchers will be able to draw chemical-biological associations 'on-the-fly' using various clustering or similarity techniques to determine whether the proposed toxicity of a drug is related to its chemical structure or its proposed efficacy mechanism. In this review associations are illustrated with target potency data gleaned from the literature associated with CYP450 substrate predictions from GeneGo's MetaDrug.

  17. Enhanced clinical pharmacy service targeting tools: risk-predictive algorithms.

    Science.gov (United States)

    El Hajji, Feras W D; Scullin, Claire; Scott, Michael G; McElnay, James C

    2015-04-01

    This study aimed to determine the value of using a mix of clinical pharmacy data and routine hospital admission spell data in the development of predictive algorithms. Exploration of risk factors in hospitalized patients, together with the targeting strategies devised, will enable the prioritization of clinical pharmacy services to optimize patient outcomes. Predictive algorithms were developed using a number of detailed steps using a 75% sample of integrated medicines management (IMM) patients, and validated using the remaining 25%. IMM patients receive targeted clinical pharmacy input throughout their hospital stay. The algorithms were applied to the validation sample, and predicted risk probability was generated for each patient from the coefficients. Risk threshold for the algorithms were determined by identifying the cut-off points of risk scores at which the algorithm would have the highest discriminative performance. Clinical pharmacy staffing levels were obtained from the pharmacy department staffing database. Numbers of previous emergency admissions and admission medicines together with age-adjusted co-morbidity and diuretic receipt formed a 12-month post-discharge and/or readmission risk algorithm. Age-adjusted co-morbidity proved to be the best index to predict mortality. Increased numbers of clinical pharmacy staff at ward level was correlated with a reduction in risk-adjusted mortality index (RAMI). Algorithms created were valid in predicting risk of in-hospital and post-discharge mortality and risk of hospital readmission 3, 6 and 12 months post-discharge. The provision of ward-based clinical pharmacy services is a key component to reducing RAMI and enabling the full benefits of pharmacy input to patient care to be realized. © 2014 John Wiley & Sons, Ltd.

  18. Repeated measurements of NT-pro-B-type natriuretic peptide, troponin T or C-reactive protein do not predict future allograft rejection in heart transplant recipients.

    Science.gov (United States)

    Battes, Linda C; Caliskan, Kadir; Rizopoulos, Dimitris; Constantinescu, Alina A; Robertus, Jan L; Akkerhuis, Martijn; Manintveld, Olivier C; Boersma, Eric; Kardys, Isabella

    2015-03-01

    Studies on the prognostic value of serial biomarker assays for future occurrence of allograft rejection (AR) are scarce. We examined whether repeated measurements of NT-pro-B-type natriuretic peptide (NT-proBNP), troponin T (TropT) and C-reactive protein (CRP) predict AR. From 2005 to 2010, 77 consecutive heart transplantation (HTx) recipients were included. The NT-proBNP, TropT, and CRP were measured at 16 ± 4 (mean ± standard deviation) consecutive routine endomyocardial biopsy surveillance visits during the first year of follow-up. Allograft rejection was defined as International Society for Heart and Lung Transplantation (ISHLT) grade 2R or higher at endomyocardial biopsy. Joint modeling was used to assess the association between repeated biomarker measurements and occurrence of future AR. Joint modeling accounts for dependence among repeated observations in individual patients. The mean age of the patients at HTx was 49 ± 9.2 years, and 68% were men. During the first year of follow-up, 1,136 biopsies and concurrent blood samples were obtained, and 56 patients (73%) experienced at least one episode of AR. All biomarkers were elevated directly after HTx and achieved steady-state after ∼ 12 weeks, both in patients with or without AR. No associations were present between the repeated measurements of NT-proBNP, TropT, or CRP and AR both early (weeks 0-12) and late (weeks 13-52) in the course after HTx (hazard ratios for weeks 13-52: 0.96 (95% confidence interval, 0.55-1.68), 0.67 (0.27-1.69), and 1.44 (0.90-2.30), respectively, per ln[unit]). Combining the three biomarkers in one model also rendered null results. The temporal evolution of NT-proBNP, TropT, and CRP before AR did not predict occurrence of acute AR both in the early and late course of the first year after HTx.

  19. Prediction of Human Drug Targets and Their Interactions Using Machine Learning Methods: Current and Future Perspectives.

    Science.gov (United States)

    Nath, Abhigyan; Kumari, Priyanka; Chaube, Radha

    2018-01-01

    Identification of drug targets and drug target interactions are important steps in the drug-discovery pipeline. Successful computational prediction methods can reduce the cost and time demanded by the experimental methods. Knowledge of putative drug targets and their interactions can be very useful for drug repurposing. Supervised machine learning methods have been very useful in drug target prediction and in prediction of drug target interactions. Here, we describe the details for developing prediction models using supervised learning techniques for human drug target prediction and their interactions.

  20. Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes

    Directory of Open Access Journals (Sweden)

    Hall Ross S

    2010-04-01

    Full Text Available Abstract Background New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Saccharomyces cerevisiae, to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset. Results Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from Ancylostoma caninum and Haemonchus contortus - two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools. Conclusions The present study demonstrates the utility of using orthology information from multiple, diverse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.

  1. CD25, CD28 and CD38 expression in peripheral blood lymphocytes as a tool to predict acute rejection after liver transplantation.

    Science.gov (United States)

    Boleslawski, Emmanuel; BenOthman, Samia; Grabar, Sophie; Correia, Leonor; Podevin, Philippe; Chouzenoux, Sandrine; Soubrane, Olivier; Calmus, Yvon; Conti, Filomena

    2008-01-01

    The aim of this study was to determine whether the expression of CD25, CD28 and CD38 (which reflects the degree of T-cell activation) by peripheral blood mononuclear cells constitutes a useful means of measuring the immune status of liver transplant recipients. Fifty-two patients enrolled in a prospective randomized study comparing cyclosporine and tacrolimus as the principal immunosuppressive drugs were monitored prospectively. The expression of CD25, CD28 and CD38 was analyzed on CD3-, CD4- and CD8-positive cells from whole blood using flow cytometry. The prognostic value of baseline and day 14 measurements regarding acute rejection was examined using Kaplan-Meier estimates for univariate analyses and the Cox model for multivariate analyses. The mean frequencies of CD28 and CD38-expressing T cells were significantly higher in patients with acute rejection (p = 0.01 and p = 0.001, respectively), whereas the frequency CD25-expressing T cells did not differ significantly. Under univariate analysis, baseline CD25 levels, the type of calcineurin inhibitor, as well as the CD28 and CD38 frequencies obtained at day 14 were associated with the subsequent development of acute rejection. Under multivariate analysis, only CD28 and CD38 frequencies obtained at day 14 were independently associated with acute rejection. The evaluation of CD28 and CD38 expression in peripheral blood lymphocytes is a simple marker that could be used routinely in clinical practice to assess the level of immunosuppression.

  2. DIANA-microT web server: elucidating microRNA functions through target prediction.

    Science.gov (United States)

    Maragkakis, M; Reczko, M; Simossis, V A; Alexiou, P; Papadopoulos, G L; Dalamagas, T; Giannopoulos, G; Goumas, G; Koukis, E; Kourtis, K; Vergoulis, T; Koziris, N; Sellis, T; Tsanakas, P; Hatzigeorgiou, A G

    2009-07-01

    Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

  3. Comparison and Integration of Target Prediction Algorithms for microRNA Studies

    Directory of Open Access Journals (Sweden)

    Zhang Yanju

    2010-12-01

    Full Text Available microRNAs are short RNA fragments that have the capacity of regulating hundreds of target gene expression. Currently, due to lack of high-throughput experimental methods for miRNA target identification, a collection of computational target prediction approaches have been developed. However, these approaches deal with different features or factors are weighted differently resulting in diverse range of predictions. The prediction accuracy remains uncertain. In this paper, three commonly used target prediction algorithms are evaluated and further integrated using algorithm combination, ranking aggregation and Bayesian Network classification. Our results revealed that each individual prediction algorithm displays its advantages as was shown on different test data sets. Among different integration strategies, the application of Bayesian Network classifier on the features calculated from multiple prediction methods significantly improved target prediction accuracy.

  4. Online prediction of others' actions: the contribution of the target object, action context and movement kinematics

    NARCIS (Netherlands)

    Stapel, J.C.; Hunnius, S.; Bekkering, H.

    2012-01-01

    Previous research investigated the contributions of target objects, situational context and movement kinematics to action prediction separately. The current study addresses how these three factors combine in the prediction of observed actions. Participants observed an actor whose movements were

  5. How do target predictability and precueing affect the production of express saccades in monkeys?

    Science.gov (United States)

    Schiller, Peter H; Haushofer, Johannes; Kendall, Geoffery

    2004-04-01

    The extent to which target predictability and precueing affect express saccade generation was determined in Rhesus monkeys. Target predictability, as manipulated by the probability with which targets appeared at various locations, had a strong influence on express saccade generation. Pre-cueing the location of the appearance of an impending single target with an identical stimulus was effective in increasing express saccade generation when there was a gap of 50-150 ms between fixation spot termination and target onset. However, precueing was not effective when the gap time was set to 0 ms in the single target task, when several simultaneous targets appeared requiring a visual discrimination to be made using an oddity task, or when the precue was not identical to the target. These findings indicate that express saccades are facilitated by a restricted set of conditions that increase the predictability of target location and identity.

  6. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets

    NARCIS (Netherlands)

    Biswas, A.; Gagnon, J.N.; Brouns, S.J.J.; Fineran, P.C.; Brown, C.M.

    2013-01-01

    The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are

  7. Statistical model based gender prediction for targeted NGS clinical panels

    Directory of Open Access Journals (Sweden)

    Palani Kannan Kandavel

    2017-12-01

    The reference test dataset are being used to test the model. The sensitivity on predicting the gender has been increased from the current “genotype composition in ChrX” based approach. In addition, the prediction score given by the model can be used to evaluate the quality of clinical dataset. The higher prediction score towards its respective gender indicates the higher quality of sequenced data.

  8. Variable Heat Rejection (VHR)

    Data.gov (United States)

    National Aeronautics and Space Administration — Develop advanced technologies to enable a variable heat rejection Thermal Control System (TCS) capable of operating through a wide range of thermal environments...

  9. SSFinder: High Throughput CRISPR-Cas Target Sites Prediction Tool

    Directory of Open Access Journals (Sweden)

    Santosh Kumar Upadhyay

    2014-01-01

    Full Text Available Clustered regularly interspaced short palindromic repeats (CRISPR and CRISPR-associated protein (Cas system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets. The SSFinder is a user-friendly tool, compatible with Windows, Mac OS, and Linux operating systems, and freely available online.

  10. Predictive Models of target organ and Systemic toxicities (BOSC)

    Science.gov (United States)

    The objective of this work is to predict the hazard classification and point of departure (PoD) of untested chemicals in repeat-dose animal testing studies. We used supervised machine learning to objectively evaluate the predictive accuracy of different classification and regress...

  11. Toxicological relationships between proteins obtained from protein target predictions of large toxicity databases

    International Nuclear Information System (INIS)

    Nigsch, Florian; Mitchell, John B.O.

    2008-01-01

    The combination of models for protein target prediction with large databases containing toxicological information for individual molecules allows the derivation of 'toxiclogical' profiles, i.e., to what extent are molecules of known toxicity predicted to interact with a set of protein targets. To predict protein targets of drug-like and toxic molecules, we built a computational multiclass model using the Winnow algorithm based on a dataset of protein targets derived from the MDL Drug Data Report. A 15-fold Monte Carlo cross-validation using 50% of each class for training, and the remaining 50% for testing, provided an assessment of the accuracy of that model. We retained the 3 top-ranking predictions and found that in 82% of all cases the correct target was predicted within these three predictions. The first prediction was the correct one in almost 70% of cases. A model built on the whole protein target dataset was then used to predict the protein targets for 150 000 molecules from the MDL Toxicity Database. We analysed the frequency of the predictions across the panel of protein targets for experimentally determined toxicity classes of all molecules. This allowed us to identify clusters of proteins related by their toxicological profiles, as well as toxicities that are related. Literature-based evidence is provided for some specific clusters to show the relevance of the relationships identified

  12. TBC2target: A Resource of Predicted Target Genes of Tea Bioactive Compounds.

    Science.gov (United States)

    Zhang, Shihua; Zhang, Liang; Wang, Yijun; Yang, Jian; Liao, Mingzhi; Bi, Shoudong; Xie, Zhongwen; Ho, Chi-Tang; Wan, Xiaochun

    2018-01-01

    Tea is one of the most popular non-alcoholic beverages consumed worldwide. Numerous bioactive constituents of tea were confirmed to possess healthy benefits via the mechanisms of regulating gene expressions or protein activities. However, a complete interacting profile between tea bioactive compounds (TBCs) and their target genes is lacking, which put an obstacle in the study of healthy function of tea. To fill this gap, we developed a database of target genes of TBCs (TBC2target, http://camellia.ahau.edu.cn/TBC2target) based on a pharmacophore mapping approach. In TBC2target, 6,226 interactions between 240 TBCs and 673 target genes were documented. TBC2target contains detailed information about each interacting entry, such as TBC, CAS number, PubChem CID, source of compound (e.g., green, black), compound type, target gene(s) of TBC, gene symbol, gene ID, ENSEMBL ID, PDB ID, TBC bioactivity and the reference. Using the TBC-target associations, we constructed a bipartite network and provided users the global network and local sub-network visualization and topological analyses. The entire database is free for online browsing, searching and downloading. In addition, TBC2target provides a BLAST search function to facilitate use of the database. The particular strengths of TBC2target are the inclusion of the comprehensive TBC-target interactions, and the capacity to visualize and analyze the interacting networks, which may help uncovering the beneficial effects of tea on human health as a central resource in tea health community.

  13. TBC2target: A Resource of Predicted Target Genes of Tea Bioactive Compounds

    Directory of Open Access Journals (Sweden)

    Shihua Zhang

    2018-02-01

    Full Text Available Tea is one of the most popular non-alcoholic beverages consumed worldwide. Numerous bioactive constituents of tea were confirmed to possess healthy benefits via the mechanisms of regulating gene expressions or protein activities. However, a complete interacting profile between tea bioactive compounds (TBCs and their target genes is lacking, which put an obstacle in the study of healthy function of tea. To fill this gap, we developed a database of target genes of TBCs (TBC2target, http://camellia.ahau.edu.cn/TBC2target based on a pharmacophore mapping approach. In TBC2target, 6,226 interactions between 240 TBCs and 673 target genes were documented. TBC2target contains detailed information about each interacting entry, such as TBC, CAS number, PubChem CID, source of compound (e.g., green, black, compound type, target gene(s of TBC, gene symbol, gene ID, ENSEMBL ID, PDB ID, TBC bioactivity and the reference. Using the TBC-target associations, we constructed a bipartite network and provided users the global network and local sub-network visualization and topological analyses. The entire database is free for online browsing, searching and downloading. In addition, TBC2target provides a BLAST search function to facilitate use of the database. The particular strengths of TBC2target are the inclusion of the comprehensive TBC-target interactions, and the capacity to visualize and analyze the interacting networks, which may help uncovering the beneficial effects of tea on human health as a central resource in tea health community.

  14. Predicting drug-target interaction for new drugs using enhanced similarity measures and super-target clustering.

    Science.gov (United States)

    Shi, Jian-Yu; Yiu, Siu-Ming; Li, Yiming; Leung, Henry C M; Chin, Francis Y L

    2015-07-15

    Predicting drug-target interaction using computational approaches is an important step in drug discovery and repositioning. To predict whether there will be an interaction between a drug and a target, most existing methods identify similar drugs and targets in the database. The prediction is then made based on the known interactions of these drugs and targets. This idea is promising. However, there are two shortcomings that have not yet been addressed appropriately. Firstly, most of the methods only use 2D chemical structures and protein sequences to measure the similarity of drugs and targets respectively. However, this information may not fully capture the characteristics determining whether a drug will interact with a target. Secondly, there are very few known interactions, i.e. many interactions are "missing" in the database. Existing approaches are biased towards known interactions and have no good solutions to handle possibly missing interactions which affect the accuracy of the prediction. In this paper, we enhance the similarity measures to include non-structural (and non-sequence-based) information and introduce the concept of a "super-target" to handle the problem of possibly missing interactions. Based on evaluations on real data, we show that our similarity measure is better than the existing measures and our approach is able to achieve higher accuracy than the two best existing algorithms, WNN-GIP and KBMF2K. Our approach is available at http://web.hku.hk/∼liym1018/projects/drug/drug.html or http://www.bmlnwpu.org/us/tools/PredictingDTI_S2/METHODS.html. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Postural control of elderly: moving to predictable and unpredictable targets.

    NARCIS (Netherlands)

    Jongman, Vera; Lamoth, Claudine J C; van Keeken, Helco; Caljouw, Simone R

    2012-01-01

    Impaired postural control with muscle weakness is an important predictor of falls within the elderly population.Particular daily activities that require weight shifting in order to be able to reach a specific target (a cup on a table) require continuous adjustments to keep the body's center of mass

  16. Drug-target interaction prediction via class imbalance-aware ensemble learning

    OpenAIRE

    Ezzat, Ali; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

    2016-01-01

    Background Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data on known drug-target interactions to train classifiers with the purpose of predicting new undiscovered interactions. However, a key challenge regarding this data that has not yet been addressed by these methods, namely class imbalance, is potentially degrading the prediction performance. Class imbalance can be divided ...

  17. Extended Active Disturbance Rejection Controller

    Science.gov (United States)

    Gao, Zhiqiang (Inventor); Tian, Gang (Inventor)

    2016-01-01

    Multiple designs, systems, methods and processes for controlling a system or plant using an extended active disturbance rejection control (ADRC) based controller are presented. The extended ADRC controller accepts sensor information from the plant. The sensor information is used in conjunction with an extended state observer in combination with a predictor that estimates and predicts the current state of the plant and a co-joined estimate of the system disturbances and system dynamics. The extended state observer estimates and predictions are used in conjunction with a control law that generates an input to the system based in part on the extended state observer estimates and predictions as well as a desired trajectory for the plant to follow.

  18. In silico prediction of novel therapeutic targets using gene-disease association data.

    Science.gov (United States)

    Ferrero, Enrico; Dunham, Ian; Sanseau, Philippe

    2017-08-29

    Target identification and validation is a pressing challenge in the pharmaceutical industry, with many of the programmes that fail for efficacy reasons showing poor association between the drug target and the disease. Computational prediction of successful targets could have a considerable impact on attrition rates in the drug discovery pipeline by significantly reducing the initial search space. Here, we explore whether gene-disease association data from the Open Targets platform is sufficient to predict therapeutic targets that are actively being pursued by pharmaceutical companies or are already on the market. To test our hypothesis, we train four different classifiers (a random forest, a support vector machine, a neural network and a gradient boosting machine) on partially labelled data and evaluate their performance using nested cross-validation and testing on an independent set. We then select the best performing model and use it to make predictions on more than 15,000 genes. Finally, we validate our predictions by mining the scientific literature for proposed therapeutic targets. We observe that the data types with the best predictive power are animal models showing a disease-relevant phenotype, differential expression in diseased tissue and genetic association with the disease under investigation. On a test set, the neural network classifier achieves over 71% accuracy with an AUC of 0.76 when predicting therapeutic targets in a semi-supervised learning setting. We use this model to gain insights into current and failed programmes and to predict 1431 novel targets, of which a highly significant proportion has been independently proposed in the literature. Our in silico approach shows that data linking genes and diseases is sufficient to predict novel therapeutic targets effectively and confirms that this type of evidence is essential for formulating or strengthening hypotheses in the target discovery process. Ultimately, more rapid and automated target

  19. Prediction of drug-target interaction networks from the integration of chemical and genomic spaces.

    Science.gov (United States)

    Yamanishi, Yoshihiro; Araki, Michihiro; Gutteridge, Alex; Honda, Wataru; Kanehisa, Minoru

    2008-07-01

    The identification of interactions between drugs and target proteins is a key area in genomic drug discovery. Therefore, there is a strong incentive to develop new methods capable of detecting these potential drug-target interactions efficiently. In this article, we characterize four classes of drug-target interaction networks in humans involving enzymes, ion channels, G-protein-coupled receptors (GPCRs) and nuclear receptors, and reveal significant correlations between drug structure similarity, target sequence similarity and the drug-target interaction network topology. We then develop new statistical methods to predict unknown drug-target interaction networks from chemical structure and genomic sequence information simultaneously on a large scale. The originality of the proposed method lies in the formalization of the drug-target interaction inference as a supervised learning problem for a bipartite graph, the lack of need for 3D structure information of the target proteins, and in the integration of chemical and genomic spaces into a unified space that we call 'pharmacological space'. In the results, we demonstrate the usefulness of our proposed method for the prediction of the four classes of drug-target interaction networks. Our comprehensively predicted drug-target interaction networks enable us to suggest many potential drug-target interactions and to increase research productivity toward genomic drug discovery. Softwares are available upon request. Datasets and all prediction results are available at http://web.kuicr.kyoto-u.ac.jp/supp/yoshi/drugtarget/.

  20. Neutrino interaction event reconstruction and analysis in the Opera emulsion targets and charmed background rejection in the τ → 3h channel

    International Nuclear Information System (INIS)

    Besnier, M.

    2008-07-01

    OPERA (Gran-Sasso, Italy) is a long-baseline neutrino experiment dedicated to the tau neutrino detection in a pure muon neutrino beam, produced at CERN (730 km away). The main goal is to observe the ν μ → ν τ oscillation. The experiment uses a hybrid technology with electronic detectors and target blocks made of lead plates interleaved with nuclear emulsion sheets, in order to sign efficiently the ν τ interactions. The fundamental features of OPERA are its particle reconstruction performances achieved in spatial and angular resolutions. The first studies done in this thesis concern the development of several analysis tools like the particle momentum determination using the multiple coulomb scattering in target, and a method of neutrino interaction reconstruction for multi-vertex events. Then it has been possible to develop a multivariable analysis in order to separate τ and charmed events in the τ decay channel into three charged hadrons. These tools have been tested with neutrino interactions observed first with the OPERA test-beam called PEANUT, then with the OPERA events accumulated during the first CNGS (CERN Neutrino to Gran Sasso) run in 2007. The combined analysis of these events has shown that both the analysis method and the OPERA detector behaviour are well understood. (author)

  1. On Why Targets Evoke P3 Components in Prediction Tasks: Drawing an Analogy between Prediction and Matching Tasks

    Science.gov (United States)

    Verleger, Rolf; Cäsar, Stephanie; Siller, Bastian; Śmigasiewicz, Kamila

    2017-01-01

    P3 is the most conspicuous component in recordings of stimulus-evoked EEG potentials from the human scalp, occurring whenever some task has to be performed with the stimuli. The process underlying P3 has been assumed to be the updating of expectancies. More recently, P3 has been related to decision processing and to activation of established stimulus-response associations (S/R-link hypothesis). However, so far this latter approach has not provided a conception about how to explain the occurrence of P3 with predicted stimuli, although P3 was originally discovered in a prediction task. The present article proposes such a conception. We assume that the internal responses right or wrong both become associatively linked to each predicted target and that one of these two response alternatives gets activated as a function of match or mismatch of the target to the preceding prediction. This seems similar to comparison tasks where responses depend on the matching of the target stimulus with a preceding first stimulus (S1). Based on this idea, this study compared the effects of frequencies of first events (predictions or S1) on target-evoked P3s in prediction and comparison tasks. Indeed, frequencies not only of targets but also of first events had similar effects across tasks on target-evoked P3s. These results support the notion that P3 evoked by predicted stimuli reflects activation of appropriate internal “match” or “mismatch” responses, which is compatible with S/R-link hypothesis. PMID:29066965

  2. Statistical learning for predictive targeting in online advertising

    DEFF Research Database (Denmark)

    Fruergaard, Bjarne Ørum

    , an international online advertising technology partner. This also means that the analyses and methods in this work are developed with particular use-cases within Adform in mind and thus need also to be applicable in Adform’s technology stack. This implies extra thought on scalability and performance......The focus in this thesis is investigation of machine learning methods with applications in computational advertising. Computational advertising is the broad discipline of building systems which can reach audiences browsing the Internet with targeted advertisements. At the core of such systems......, algorithms are needed for making decisions. It is in one such particular instance of computational advertising, namely in web banner advertising, that we investigate machine learning methods to assist and make decisions in order to optimize the placements of ads. The industrial partner in this work is Adform...

  3. Design of a tripartite network for the prediction of drug targets

    Science.gov (United States)

    Kunimoto, Ryo; Bajorath, Jürgen

    2018-02-01

    Drug-target networks have aided in many target prediction studies aiming at drug repurposing or the analysis of side effects. Conventional drug-target networks are bipartite. They contain two different types of nodes representing drugs and targets, respectively, and edges indicating pairwise drug-target interactions. In this work, we introduce a tripartite network consisting of drugs, other bioactive compounds, and targets from different sources. On the basis of analog relationships captured in the network and so-called neighbor targets of drugs, new drug targets can be inferred. The tripartite network was found to have a stable structure and simulated network growth was accompanied by a steady increase in assortativity, reflecting increasing correlation between degrees of connected nodes leading to even network connectivity. Local drug environments in the tripartite network typically contained neighbor targets and revealed interesting drug-compound-target relationships for further analysis. Candidate targets were prioritized. The tripartite network design extends standard drug-target networks and provides additional opportunities for drug target prediction.

  4. Large-scale prediction of drug–target interactions using protein sequences and drug topological structures

    International Nuclear Information System (INIS)

    Cao Dongsheng; Liu Shao; Xu Qingsong; Lu Hongmei; Huang Jianhua; Hu Qiannan; Liang Yizeng

    2012-01-01

    Highlights: ► Drug–target interactions are predicted using an extended SAR methodology. ► A drug–target interaction is regarded as an event triggered by many factors. ► Molecular fingerprint and CTD descriptors are used to represent drugs and proteins. ► Our approach shows compatibility between the new scheme and current SAR methodology. - Abstract: The identification of interactions between drugs and target proteins plays a key role in the process of genomic drug discovery. It is both consuming and costly to determine drug–target interactions by experiments alone. Therefore, there is an urgent need to develop new in silico prediction approaches capable of identifying these potential drug–target interactions in a timely manner. In this article, we aim at extending current structure–activity relationship (SAR) methodology to fulfill such requirements. In some sense, a drug–target interaction can be regarded as an event or property triggered by many influence factors from drugs and target proteins. Thus, each interaction pair can be represented theoretically by using these factors which are based on the structural and physicochemical properties simultaneously from drugs and proteins. To realize this, drug molecules are encoded with MACCS substructure fingerings representing existence of certain functional groups or fragments; and proteins are encoded with some biochemical and physicochemical properties. Four classes of drug–target interaction networks in humans involving enzymes, ion channels, G-protein-coupled receptors (GPCRs) and nuclear receptors, are independently used for establishing predictive models with support vector machines (SVMs). The SVM models gave prediction accuracy of 90.31%, 88.91%, 84.68% and 83.74% for four datasets, respectively. In conclusion, the results demonstrate the ability of our proposed method to predict the drug–target interactions, and show a general compatibility between the new scheme and current SAR

  5. Prediction of drug-target interactions for drug repositioning only based on genomic expression similarity.

    Directory of Open Access Journals (Sweden)

    Kejian Wang

    Full Text Available Small drug molecules usually bind to multiple protein targets or even unintended off-targets. Such drug promiscuity has often led to unwanted or unexplained drug reactions, resulting in side effects or drug repositioning opportunities. So it is always an important issue in pharmacology to identify potential drug-target interactions (DTI. However, DTI discovery by experiment remains a challenging task, due to high expense of time and resources. Many computational methods are therefore developed to predict DTI with high throughput biological and clinical data. Here, we initiatively demonstrate that the on-target and off-target effects could be characterized by drug-induced in vitro genomic expression changes, e.g. the data in Connectivity Map (CMap. Thus, unknown ligands of a certain target can be found from the compounds showing high gene-expression similarity to the known ligands. Then to clarify the detailed practice of CMap based DTI prediction, we objectively evaluate how well each target is characterized by CMap. The results suggest that (1 some targets are better characterized than others, so the prediction models specific to these well characterized targets would be more accurate and reliable; (2 in some cases, a family of ligands for the same target tend to interact with common off-targets, which may help increase the efficiency of DTI discovery and explain the mechanisms of complicated drug actions. In the present study, CMap expression similarity is proposed as a novel indicator of drug-target interactions. The detailed strategies of improving data quality by decreasing the batch effect and building prediction models are also effectively established. We believe the success in CMap can be further translated into other public and commercial data of genomic expression, thus increasing research productivity towards valid drug repositioning and minimal side effects.

  6. Computational Challenges in miRNA Target Predictions: To Be or Not to Be a True Target?

    Directory of Open Access Journals (Sweden)

    Christian Barbato

    2009-01-01

    Full Text Available All microRNA (miRNA target—finder algorithms return lists of candidate target genes. How valid is that output in a biological setting? Transcriptome analysis has proven to be a useful approach to determine mRNA targets. Time course mRNA microarray experiments may reliably identify downregulated genes in response to overexpression of specific miRNA. The approach may miss some miRNA targets that are principally downregulated at the protein level. However, the high-throughput capacity of the assay makes it an effective tool to rapidly identify a large number of promising miRNA targets. Finally, loss and gain of function miRNA genetics have the clear potential of being critical in evaluating the biological relevance of thousands of target genes predicted by bioinformatic studies and to test the degree to which miRNA-mediated regulation of any “validated” target functionally matters to the animal or plant.

  7. An efficient numerical target strength prediction model: Validation against analysis solutions

    NARCIS (Netherlands)

    Fillinger, L.; Nijhof, M.J.J.; Jong, C.A.F. de

    2014-01-01

    A decade ago, TNO developed RASP (Rapid Acoustic Signature Prediction), a numerical model for the prediction of the target strength of immersed underwater objects. The model is based on Kirchhoff diffraction theory. It is currently being improved to model refraction, angle dependent reflection and

  8. Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction.

    Directory of Open Access Journals (Sweden)

    Yong Liu

    2016-02-01

    Full Text Available In pharmaceutical sciences, a crucial step of the drug discovery process is the identification of drug-target interactions. However, only a small portion of the drug-target interactions have been experimentally validated, as the experimental validation is laborious and costly. To improve the drug discovery efficiency, there is a great need for the development of accurate computational approaches that can predict potential drug-target interactions to direct the experimental verification. In this paper, we propose a novel drug-target interaction prediction algorithm, namely neighborhood regularized logistic matrix factorization (NRLMF. Specifically, the proposed NRLMF method focuses on modeling the probability that a drug would interact with a target by logistic matrix factorization, where the properties of drugs and targets are represented by drug-specific and target-specific latent vectors, respectively. Moreover, NRLMF assigns higher importance levels to positive observations (i.e., the observed interacting drug-target pairs than negative observations (i.e., the unknown pairs. Because the positive observations are already experimentally verified, they are usually more trustworthy. Furthermore, the local structure of the drug-target interaction data has also been exploited via neighborhood regularization to achieve better prediction accuracy. We conducted extensive experiments over four benchmark datasets, and NRLMF demonstrated its effectiveness compared with five state-of-the-art approaches.

  9. Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction.

    Science.gov (United States)

    Liu, Yong; Wu, Min; Miao, Chunyan; Zhao, Peilin; Li, Xiao-Li

    2016-02-01

    In pharmaceutical sciences, a crucial step of the drug discovery process is the identification of drug-target interactions. However, only a small portion of the drug-target interactions have been experimentally validated, as the experimental validation is laborious and costly. To improve the drug discovery efficiency, there is a great need for the development of accurate computational approaches that can predict potential drug-target interactions to direct the experimental verification. In this paper, we propose a novel drug-target interaction prediction algorithm, namely neighborhood regularized logistic matrix factorization (NRLMF). Specifically, the proposed NRLMF method focuses on modeling the probability that a drug would interact with a target by logistic matrix factorization, where the properties of drugs and targets are represented by drug-specific and target-specific latent vectors, respectively. Moreover, NRLMF assigns higher importance levels to positive observations (i.e., the observed interacting drug-target pairs) than negative observations (i.e., the unknown pairs). Because the positive observations are already experimentally verified, they are usually more trustworthy. Furthermore, the local structure of the drug-target interaction data has also been exploited via neighborhood regularization to achieve better prediction accuracy. We conducted extensive experiments over four benchmark datasets, and NRLMF demonstrated its effectiveness compared with five state-of-the-art approaches.

  10. Accurate microRNA target prediction correlates with protein repression levels

    Directory of Open Access Journals (Sweden)

    Simossis Victor A

    2009-09-01

    Full Text Available Abstract Background MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pairing of the microRNA to sites in the messenger RNA of protein coding genes. Since experimental identification of miRNA target genes poses difficulties, computational microRNA target prediction is one of the key means in deciphering the role of microRNAs in development and disease. Results DIANA-microT 3.0 is an algorithm for microRNA target prediction which is based on several parameters calculated individually for each microRNA and combines conserved and non-conserved microRNA recognition elements into a final prediction score, which correlates with protein production fold change. Specifically, for each predicted interaction the program reports a signal to noise ratio and a precision score which can be used as an indication of the false positive rate of the prediction. Conclusion Recently, several computational target prediction programs were benchmarked based on a set of microRNA target genes identified by the pSILAC method. In this assessment DIANA-microT 3.0 was found to achieve the highest precision among the most widely used microRNA target prediction programs reaching approximately 66%. The DIANA-microT 3.0 prediction results are available online in a user friendly web server at http://www.microrna.gr/microT

  11. Drug-target interaction prediction via class imbalance-aware ensemble learning.

    Science.gov (United States)

    Ezzat, Ali; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

    2016-12-22

    Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data on known drug-target interactions to train classifiers with the purpose of predicting new undiscovered interactions. However, a key challenge regarding this data that has not yet been addressed by these methods, namely class imbalance, is potentially degrading the prediction performance. Class imbalance can be divided into two sub-problems. Firstly, the number of known interacting drug-target pairs is much smaller than that of non-interacting drug-target pairs. This imbalance ratio between interacting and non-interacting drug-target pairs is referred to as the between-class imbalance. Between-class imbalance degrades prediction performance due to the bias in prediction results towards the majority class (i.e. the non-interacting pairs), leading to more prediction errors in the minority class (i.e. the interacting pairs). Secondly, there are multiple types of drug-target interactions in the data with some types having relatively fewer members (or are less represented) than others. This variation in representation of the different interaction types leads to another kind of imbalance referred to as the within-class imbalance. In within-class imbalance, prediction results are biased towards the better represented interaction types, leading to more prediction errors in the less represented interaction types. We propose an ensemble learning method that incorporates techniques to address the issues of between-class imbalance and within-class imbalance. Experiments show that the proposed method improves results over 4 state-of-the-art methods. In addition, we simulated cases for new drugs and targets to see how our method would perform in predicting their interactions. New drugs and targets are those for which no prior interactions are known. Our method displayed satisfactory prediction performance and was

  12. The role of CD8+ T cells during allograft rejection

    Directory of Open Access Journals (Sweden)

    V. Bueno

    2002-11-01

    Full Text Available Organ transplantation can be considered as replacement therapy for patients with end-stage organ failure. The percent of one-year allograft survival has increased due, among other factors, to a better understanding of the rejection process and new immunosuppressive drugs. Immunosuppressive therapy used in transplantation prevents activation and proliferation of alloreactive T lymphocytes, although not fully preventing chronic rejection. Recognition by recipient T cells of alloantigens expressed by donor tissues initiates immune destruction of allogeneic transplants. However, there is controversy concerning the relative contribution of CD4+ and CD8+ T cells to allograft rejection. Some animal models indicate that there is an absolute requirement for CD4+ T cells in allogeneic rejection, whereas in others CD4-depleted mice reject certain types of allografts. Moreover, there is evidence that CD8+ T cells are more resistant to immunotherapy and tolerance induction protocols. An intense focal infiltration of mainly CD8+CTLA4+ T lymphocytes during kidney rejection has been described in patients. This suggests that CD8+ T cells could escape from immunosuppression and participate in the rejection process. Our group is primarily interested in the immune mechanisms involved in allograft rejection. Thus, we believe that a better understanding of the role of CD8+ T cells in allograft rejection could indicate new targets for immunotherapy in transplantation. Therefore, the objective of the present review was to focus on the role of the CD8+ T cell population in the rejection of allogeneic tissue.

  13. Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations.

    Science.gov (United States)

    Zong, Nansu; Kim, Hyeoneui; Ngo, Victoria; Harismendy, Olivier

    2017-08-01

    A heterogeneous network topology possessing abundant interactions between biomedical entities has yet to be utilized in similarity-based methods for predicting drug-target associations based on the array of varying features of drugs and their targets. Deep learning reveals features of vertices of a large network that can be adapted in accommodating the similarity-based solutions to provide a flexible method of drug-target prediction. We propose a similarity-based drug-target prediction method that enhances existing association discovery methods by using a topology-based similarity measure. DeepWalk, a deep learning method, is adopted in this study to calculate the similarities within Linked Tripartite Network (LTN), a heterogeneous network generated from biomedical linked datasets. This proposed method shows promising results for drug-target association prediction: 98.96% AUC ROC score with a 10-fold cross-validation and 99.25% AUC ROC score with a Monte Carlo cross-validation with LTN. By utilizing DeepWalk, we demonstrate that: (i) this method outperforms other existing topology-based similarity computation methods, (ii) the performance is better for tripartite than with bipartite networks and (iii) the measure of similarity using network topology outperforms the ones derived from chemical structure (drugs) or genomic sequence (targets). Our proposed methodology proves to be capable of providing a promising solution for drug-target prediction based on topological similarity with a heterogeneous network, and may be readily re-purposed and adapted in the existing of similarity-based methodologies. The proposed method has been developed in JAVA and it is available, along with the data at the following URL: https://github.com/zongnansu1982/drug-target-prediction . nazong@ucsd.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  14. Combining Results from Distinct MicroRNA Target Prediction Tools Enhances the Performance of Analyses.

    Science.gov (United States)

    Oliveira, Arthur C; Bovolenta, Luiz A; Nachtigall, Pedro G; Herkenhoff, Marcos E; Lemke, Ney; Pinhal, Danillo

    2017-01-01

    Target prediction is generally the first step toward recognition of bona fide microRNA (miRNA)-target interactions in living cells. Several target prediction tools are now available, which use distinct criteria and stringency to provide the best set of candidate targets for a single miRNA or a subset of miRNAs. However, there are many false-negative predictions, and consensus about the optimum strategy to select and use the output information provided by the target prediction tools is lacking. We compared the performance of four tools cited in literature-TargetScan (TS), miRanda-mirSVR (MR), Pita, and RNA22 (R22), and we determined the most effective approach for analyzing target prediction data (individual, union, or intersection). For this purpose, we calculated the sensitivity, specificity, precision, and correlation of these approaches using 10 miRNAs (miR-1-3p, miR-17-5p, miR-21-5p, miR-24-3p, miR-29a-3p, miR-34a-5p, miR-124-3p, miR-125b-5p, miR-145-5p, and miR-155-5p) and 1,400 genes (700 validated and 700 non-validated) as targets of these miRNAs. The four tools provided a subset of high-quality predictions and returned few false-positive predictions; however, they could not identify several known true targets. We demonstrate that union of TS/MR and TS/MR/R22 enhanced the quality of in silico prediction analysis of miRNA targets. We conclude that the union rather than the intersection of the aforementioned tools is the best strategy for maximizing performance while minimizing the loss of time and resources in subsequent in vivo and in vitro experiments for functional validation of miRNA-target interactions.

  15. A multi-label approach to target prediction taking ligand promiscuity into account.

    Science.gov (United States)

    Afzal, Avid M; Mussa, Hamse Y; Turner, Richard E; Bender, Andreas; Glen, Robert C

    2015-01-01

    According to Cobanoglu et al., it is now widely acknowledged that the single target paradigm (one protein/target, one disease, one drug) that has been the dominant premise in drug development in the recent past is untenable. More often than not, a drug-like compound (ligand) can be promiscuous - it can interact with more than one target protein. In recent years, in in silico target prediction methods the promiscuity issue has generally been approached computationally in three main ways: ligand-based methods; target-protein-based methods; and integrative schemes. In this study we confine attention to ligand-based target prediction machine learning approaches, commonly referred to as target-fishing. The target-fishing approaches that are currently ubiquitous in cheminformatics literature can be essentially viewed as single-label multi-classification schemes; these approaches inherently bank on the single target paradigm assumption that a ligand can zero in on one single target. In order to address the ligand promiscuity issue, one might be able to cast target-fishing as a multi-label multi-class classification problem. For illustrative and comparison purposes, single-label and multi-label Naïve Bayes classification models (denoted here by SMM and MMM, respectively) for target-fishing were implemented. The models were constructed and tested on 65,587 compounds/ligands and 308 targets retrieved from the ChEMBL17 database. On classifying 3,332 test multi-label (promiscuous) compounds, SMM and MMM performed differently. At the 0.05 significance level, a Wilcoxon signed rank test performed on the paired target predictions yielded by SMM and MMM for the test ligands gave a p-value promiscuous) compounds; McNemar's test yielded χ (2) values of 15.657, 16.500 and 16.405 (with corresponding p-values of 7.594 × 10(-05), 4.865 × 10(-05) and 5.115 × 10(-05)), respectively, for three test sets, in favour of MMM. The models performed similarly on the fourth set

  16. Supplementary Material for: DASPfind: new efficient method to predict drug–target interactions

    KAUST Repository

    Ba Alawi, Wail

    2016-01-01

    Abstract Background Identification of novel drug–target interactions (DTIs) is important for drug discovery. Experimental determination of such DTIs is costly and time consuming, hence it necessitates the development of efficient computational methods for the accurate prediction of potential DTIs. To-date, many computational methods have been proposed for this purpose, but they suffer the drawback of a high rate of false positive predictions. Results Here, we developed a novel computational DTI prediction method, DASPfind. DASPfind uses simple paths of particular lengths inferred from a graph that describes DTIs, similarities between drugs, and similarities between the protein targets of drugs. We show that on average, over the four gold standard DTI datasets, DASPfind significantly outperforms other existing methods when the single top-ranked predictions are considered, resulting in 46.17 % of these predictions being correct, and it achieves 49.22 % correct single top ranked predictions when the set of all DTIs for a single drug is tested. Furthermore, we demonstrate that our method is best suited for predicting DTIs in cases of drugs with no known targets or with few known targets. We also show the practical use of DASPfind by generating novel predictions for the Ion Channel dataset and validating them manually. Conclusions DASPfind is a computational method for finding reliable new interactions between drugs and proteins. We show over six different DTI datasets that DASPfind outperforms other state-of-the-art methods when the single top-ranked predictions are considered, or when a drug with no known targets or with few known targets is considered. We illustrate the usefulness and practicality of DASPfind by predicting novel DTIs for the Ion Channel dataset. The validated predictions suggest that DASPfind can be used as an efficient method to identify correct DTIs, thus reducing the cost of necessary experimental verifications in the process of drug discovery

  17. Modeling rejection immunity

    Directory of Open Access Journals (Sweden)

    Gaetano Andrea De

    2012-05-01

    Full Text Available Abstract Background Transplantation is often the only way to treat a number of diseases leading to organ failure. To overcome rejection towards the transplanted organ (graft, immunosuppression therapies are used, which have considerable side-effects and expose patients to opportunistic infections. The development of a model to complement the physician’s experience in specifying therapeutic regimens is therefore desirable. The present work proposes an Ordinary Differential Equations model accounting for immune cell proliferation in response to the sudden entry of graft antigens, through different activation mechanisms. The model considers the effect of a single immunosuppressive medication (e.g. cyclosporine, subject to first-order linear kinetics and acting by modifying, in a saturable concentration-dependent fashion, the proliferation coefficient. The latter has been determined experimentally. All other model parameter values have been set so as to reproduce reported state variable time-courses, and to maintain consistency with one another and with the experimentally derived proliferation coefficient. Results The proposed model substantially simplifies the chain of events potentially leading to organ rejection. It is however able to simulate quantitatively the time course of graft-related antigen and competent immunoreactive cell populations, showing the long-term alternative outcomes of rejection, tolerance or tolerance at a reduced functional tissue mass. In particular, the model shows that it may be difficult to attain tolerance at full tissue mass with acceptably low doses of a single immunosuppressant, in accord with clinical experience. Conclusions The introduced model is mathematically consistent with known physiology and can reproduce variations in immune status and allograft survival after transplantation. The model can be adapted to represent different therapeutic schemes and may offer useful indications for the optimization of

  18. Modeling rejection immunity.

    Science.gov (United States)

    De Gaetano, Andrea; Matone, Alice; Agnes, Annamaria; Palumbo, Pasquale; Ria, Francesco; Magalini, Sabina

    2012-05-20

    Transplantation is often the only way to treat a number of diseases leading to organ failure. To overcome rejection towards the transplanted organ (graft), immunosuppression therapies are used, which have considerable side-effects and expose patients to opportunistic infections. The development of a model to complement the physician's experience in specifying therapeutic regimens is therefore desirable. The present work proposes an Ordinary Differential Equations model accounting for immune cell proliferation in response to the sudden entry of graft antigens, through different activation mechanisms. The model considers the effect of a single immunosuppressive medication (e.g. cyclosporine), subject to first-order linear kinetics and acting by modifying, in a saturable concentration-dependent fashion, the proliferation coefficient. The latter has been determined experimentally. All other model parameter values have been set so as to reproduce reported state variable time-courses, and to maintain consistency with one another and with the experimentally derived proliferation coefficient. The proposed model substantially simplifies the chain of events potentially leading to organ rejection. It is however able to simulate quantitatively the time course of graft-related antigen and competent immunoreactive cell populations, showing the long-term alternative outcomes of rejection, tolerance or tolerance at a reduced functional tissue mass. In particular, the model shows that it may be difficult to attain tolerance at full tissue mass with acceptably low doses of a single immunosuppressant, in accord with clinical experience. The introduced model is mathematically consistent with known physiology and can reproduce variations in immune status and allograft survival after transplantation. The model can be adapted to represent different therapeutic schemes and may offer useful indications for the optimization of therapy protocols in the transplanted patient.

  19. Drug-target interaction prediction using ensemble learning and dimensionality reduction.

    Science.gov (United States)

    Ezzat, Ali; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

    2017-10-01

    Experimental prediction of drug-target interactions is expensive, time-consuming and tedious. Fortunately, computational methods help narrow down the search space for interaction candidates to be further examined via wet-lab techniques. Nowadays, the number of attributes/features for drugs and targets, as well as the amount of their interactions, are increasing, making these computational methods inefficient or occasionally prohibitive. This motivates us to derive a reduced feature set for prediction. In addition, since ensemble learning techniques are widely used to improve the classification performance, it is also worthwhile to design an ensemble learning framework to enhance the performance for drug-target interaction prediction. In this paper, we propose a framework for drug-target interaction prediction leveraging both feature dimensionality reduction and ensemble learning. First, we conducted feature subspacing to inject diversity into the classifier ensemble. Second, we applied three different dimensionality reduction methods to the subspaced features. Third, we trained homogeneous base learners with the reduced features and then aggregated their scores to derive the final predictions. For base learners, we selected two classifiers, namely Decision Tree and Kernel Ridge Regression, resulting in two variants of ensemble models, EnsemDT and EnsemKRR, respectively. In our experiments, we utilized AUC (Area under ROC Curve) as an evaluation metric. We compared our proposed methods with various state-of-the-art methods under 5-fold cross validation. Experimental results showed EnsemKRR achieving the highest AUC (94.3%) for predicting drug-target interactions. In addition, dimensionality reduction helped improve the performance of EnsemDT. In conclusion, our proposed methods produced significant improvements for drug-target interaction prediction. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Novel Data Fusion Method and Exploration of Multiple Information Sources for Transcription Factor Target Gene Prediction

    Science.gov (United States)

    Dai, Xiaofeng; Yli-Harja, Olli; Lähdesmäki, Harri

    2010-12-01

    Background. Revealing protein-DNA interactions is a key problem in understanding transcriptional regulation at mechanistic level. Computational methods have an important role in predicting transcription factor target gene genomewide. Multiple data fusion provides a natural way to improve transcription factor target gene predictions because sequence specificities alone are not sufficient to accurately predict transcription factor binding sites. Methods. Here we develop a new data fusion method to combine multiple genome-level data sources and study the extent to which DNA duplex stability and nucleosome positioning information, either alone or in combination with other data sources, can improve the prediction of transcription factor target gene. Results. Results on a carefully constructed test set of verified binding sites in mouse genome demonstrate that our new multiple data fusion method can reduce false positive rates, and that DNA duplex stability and nucleosome occupation data can improve the accuracy of transcription factor target gene predictions, especially when combined with other genome-level data sources. Cross-validation and other randomization tests confirm the predictive performance of our method. Our results also show that nonredundant data sources provide the most efficient data fusion.

  1. Novel computational methods to predict drug–target interactions using graph mining and machine learning approaches

    KAUST Repository

    Olayan, Rawan S.

    2017-12-01

    Computational drug repurposing aims at finding new medical uses for existing drugs. The identification of novel drug-target interactions (DTIs) can be a useful part of such a task. Computational determination of DTIs is a convenient strategy for systematic screening of a large number of drugs in the attempt to identify new DTIs at low cost and with reasonable accuracy. This necessitates development of accurate computational methods that can help focus on the follow-up experimental validation on a smaller number of highly likely targets for a drug. Although many methods have been proposed for computational DTI prediction, they suffer the high false positive prediction rate or they do not predict the effect that drugs exert on targets in DTIs. In this report, first, we present a comprehensive review of the recent progress in the field of DTI prediction from data-centric and algorithm-centric perspectives. The aim is to provide a comprehensive review of computational methods for identifying DTIs, which could help in constructing more reliable methods. Then, we present DDR, an efficient method to predict the existence of DTIs. DDR achieves significantly more accurate results compared to the other state-of-theart methods. As supported by independent evidences, we verified as correct 22 out of the top 25 DDR DTIs predictions. This validation proves the practical utility of DDR, suggesting that DDR can be used as an efficient method to identify 5 correct DTIs. Finally, we present DDR-FE method that predicts the effect types of a drug on its target. On different representative datasets, under various test setups, and using different performance measures, we show that DDR-FE achieves extremely good performance. Using blind test data, we verified as correct 2,300 out of 3,076 DTIs effects predicted by DDR-FE. This suggests that DDR-FE can be used as an efficient method to identify correct effects of a drug on its target.

  2. Rejection Sensitivity Moderates the Impact of Rejection on Self-Concept Clarity

    Science.gov (United States)

    Ayduk, Özlem; Gyurak, Anett; Luerssen, Anna

    2014-01-01

    Self-concept clarity (SCC) refers to the extent to which self-knowledge is clearly and confidently defined, internally consistent, and temporally stable. Research shows that SCC can be undermined by failures in valued goal domains. Because preventing rejection is an important self-relevant goal for people high in rejection sensitivity (RS), it is hypothesized here that failures to attain this goal would cause them to experience diminished SCC. Study 1, an experimental study, showed that high-RS people’s SCC was undermined following rejection but not following an aversive experience unrelated to rejection. Study 2, a daily diary study of couples in relationships, used occurrence of partner conflicts to operationalize rejection. Replicating the findings in Study 1, having a conflict on any given diary day predicted a greater reduction in the SCC of high- compared to low-RS people on the following day. The implications for understanding the conditions under which rejection negatively affects the self-concept are discussed. PMID:19713567

  3. The effects of incidentally learned temporal and spatial predictability on response times and visual fixations during target detection and discrimination.

    Science.gov (United States)

    Beck, Melissa R; Hong, S Lee; van Lamsweerde, Amanda E; Ericson, Justin M

    2014-01-01

    Responses are quicker to predictable stimuli than if the time and place of appearance is uncertain. Studies that manipulate target predictability often involve overt cues to speed up response times. However, less is known about whether individuals will exhibit faster response times when target predictability is embedded within the inter-trial relationships. The current research examined the combined effects of spatial and temporal target predictability on reaction time (RT) and allocation of overt attention in a sustained attention task. Participants responded as quickly as possible to stimuli while their RT and eye movements were measured. Target temporal and spatial predictability were manipulated by altering the number of: 1) different time intervals between a response and the next target; and 2) possible spatial locations of the target. The effects of target predictability on target detection (Experiment 1) and target discrimination (Experiment 2) were tested. For both experiments, shorter RTs as target predictability increased across both space and time were found. In addition, the influences of spatial and temporal target predictability on RT and the overt allocation of attention were task dependent; suggesting that effective orienting of attention relies on both spatial and temporal predictability. These results indicate that stimulus predictability can be increased without overt cues and detected purely through inter-trial relationships over the course of repeated stimulus presentations.

  4. The effects of incidentally learned temporal and spatial predictability on response times and visual fixations during target detection and discrimination.

    Directory of Open Access Journals (Sweden)

    Melissa R Beck

    Full Text Available Responses are quicker to predictable stimuli than if the time and place of appearance is uncertain. Studies that manipulate target predictability often involve overt cues to speed up response times. However, less is known about whether individuals will exhibit faster response times when target predictability is embedded within the inter-trial relationships. The current research examined the combined effects of spatial and temporal target predictability on reaction time (RT and allocation of overt attention in a sustained attention task. Participants responded as quickly as possible to stimuli while their RT and eye movements were measured. Target temporal and spatial predictability were manipulated by altering the number of: 1 different time intervals between a response and the next target; and 2 possible spatial locations of the target. The effects of target predictability on target detection (Experiment 1 and target discrimination (Experiment 2 were tested. For both experiments, shorter RTs as target predictability increased across both space and time were found. In addition, the influences of spatial and temporal target predictability on RT and the overt allocation of attention were task dependent; suggesting that effective orienting of attention relies on both spatial and temporal predictability. These results indicate that stimulus predictability can be increased without overt cues and detected purely through inter-trial relationships over the course of repeated stimulus presentations.

  5. Rejection sensitivity as a vulnerability marker for depressive symptom deterioration in men.

    Directory of Open Access Journals (Sweden)

    Jannika De Rubeis

    Full Text Available Consistent across time and cultures, men and male adolescents older than 14 years of age appear underrepresented in mood disorders, and are far less likely than women to seek psychological help. The much higher rate of suicide amongst males suggests that depression in men might be underreported. One of the core human motives is to seek acceptance by others and avoid rejection. Rejection Sensitivity (RS has been conceptualized as the cognitive-affective processing disposition to anxiously expect, readily perceive, and intensely respond to cues of rejection in the behavior of others. RS has been previously linked with the onset and course of depression, but-as yet-has not been investigated longitudinally in a clinical population. We investigated the predictive role of RS to symptom deterioration 6 months after end-of- treatment in 72 male inpatients with depressive spectrum disorder. The BDI was administered at intake, end-of-treatment and 6 month follow-up. RS scores were obtained at intake. Rejection Sensitivity had additional predictive power on BDI scores at 6 months follow-up controlling for BDI scores at end-of-treatment (ΔR2 = .095. The results are discussed in terms of the importance of targeting RS during treatment, and highlight the fact that therapeutic follow-up care is paramount. Future research should investigate possible mediators of the RS-relapse-to-depression association, such as self-blame, rumination, neuroticism, pessimism, emotion dysregulation, and low self-esteem.

  6. Rejection sensitivity as a vulnerability marker for depressive symptom deterioration in men.

    Science.gov (United States)

    De Rubeis, Jannika; Lugo, Ricardo G; Witthöft, Michael; Sütterlin, Stefan; Pawelzik, Markus R; Vögele, Claus

    2017-01-01

    Consistent across time and cultures, men and male adolescents older than 14 years of age appear underrepresented in mood disorders, and are far less likely than women to seek psychological help. The much higher rate of suicide amongst males suggests that depression in men might be underreported. One of the core human motives is to seek acceptance by others and avoid rejection. Rejection Sensitivity (RS) has been conceptualized as the cognitive-affective processing disposition to anxiously expect, readily perceive, and intensely respond to cues of rejection in the behavior of others. RS has been previously linked with the onset and course of depression, but-as yet-has not been investigated longitudinally in a clinical population. We investigated the predictive role of RS to symptom deterioration 6 months after end-of- treatment in 72 male inpatients with depressive spectrum disorder. The BDI was administered at intake, end-of-treatment and 6 month follow-up. RS scores were obtained at intake. Rejection Sensitivity had additional predictive power on BDI scores at 6 months follow-up controlling for BDI scores at end-of-treatment (ΔR2 = .095). The results are discussed in terms of the importance of targeting RS during treatment, and highlight the fact that therapeutic follow-up care is paramount. Future research should investigate possible mediators of the RS-relapse-to-depression association, such as self-blame, rumination, neuroticism, pessimism, emotion dysregulation, and low self-esteem.

  7. Large-scale prediction of drug-target interactions using protein sequences and drug topological structures

    Energy Technology Data Exchange (ETDEWEB)

    Cao Dongsheng [Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha 410083 (China); Liu Shao [Xiangya Hospital, Central South University, Changsha 410008 (China); Xu Qingsong [School of Mathematical Sciences and Computing Technology, Central South University, Changsha 410083 (China); Lu Hongmei; Huang Jianhua [Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha 410083 (China); Hu Qiannan [Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071 (China); Liang Yizeng, E-mail: yizeng_liang@263.net [Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha 410083 (China)

    2012-11-08

    Highlights: Black-Right-Pointing-Pointer Drug-target interactions are predicted using an extended SAR methodology. Black-Right-Pointing-Pointer A drug-target interaction is regarded as an event triggered by many factors. Black-Right-Pointing-Pointer Molecular fingerprint and CTD descriptors are used to represent drugs and proteins. Black-Right-Pointing-Pointer Our approach shows compatibility between the new scheme and current SAR methodology. - Abstract: The identification of interactions between drugs and target proteins plays a key role in the process of genomic drug discovery. It is both consuming and costly to determine drug-target interactions by experiments alone. Therefore, there is an urgent need to develop new in silico prediction approaches capable of identifying these potential drug-target interactions in a timely manner. In this article, we aim at extending current structure-activity relationship (SAR) methodology to fulfill such requirements. In some sense, a drug-target interaction can be regarded as an event or property triggered by many influence factors from drugs and target proteins. Thus, each interaction pair can be represented theoretically by using these factors which are based on the structural and physicochemical properties simultaneously from drugs and proteins. To realize this, drug molecules are encoded with MACCS substructure fingerings representing existence of certain functional groups or fragments; and proteins are encoded with some biochemical and physicochemical properties. Four classes of drug-target interaction networks in humans involving enzymes, ion channels, G-protein-coupled receptors (GPCRs) and nuclear receptors, are independently used for establishing predictive models with support vector machines (SVMs). The SVM models gave prediction accuracy of 90.31%, 88.91%, 84.68% and 83.74% for four datasets, respectively. In conclusion, the results demonstrate the ability of our proposed method to predict the drug-target

  8. Improved prediction of drug-target interactions using regularized least squares integrating with kernel fusion technique

    International Nuclear Information System (INIS)

    Hao, Ming; Wang, Yanli; Bryant, Stephen H.

    2016-01-01

    Identification of drug-target interactions (DTI) is a central task in drug discovery processes. In this work, a simple but effective regularized least squares integrating with nonlinear kernel fusion (RLS-KF) algorithm is proposed to perform DTI predictions. Using benchmark DTI datasets, our proposed algorithm achieves the state-of-the-art results with area under precision–recall curve (AUPR) of 0.915, 0.925, 0.853 and 0.909 for enzymes, ion channels (IC), G protein-coupled receptors (GPCR) and nuclear receptors (NR) based on 10 fold cross-validation. The performance can further be improved by using a recalculated kernel matrix, especially for the small set of nuclear receptors with AUPR of 0.945. Importantly, most of the top ranked interaction predictions can be validated by experimental data reported in the literature, bioassay results in the PubChem BioAssay database, as well as other previous studies. Our analysis suggests that the proposed RLS-KF is helpful for studying DTI, drug repositioning as well as polypharmacology, and may help to accelerate drug discovery by identifying novel drug targets. - Graphical abstract: Flowchart of the proposed RLS-KF algorithm for drug-target interaction predictions. - Highlights: • A nonlinear kernel fusion algorithm is proposed to perform drug-target interaction predictions. • Performance can further be improved by using the recalculated kernel. • Top predictions can be validated by experimental data.

  9. Improved prediction of drug-target interactions using regularized least squares integrating with kernel fusion technique

    Energy Technology Data Exchange (ETDEWEB)

    Hao, Ming; Wang, Yanli, E-mail: ywang@ncbi.nlm.nih.gov; Bryant, Stephen H., E-mail: bryant@ncbi.nlm.nih.gov

    2016-02-25

    Identification of drug-target interactions (DTI) is a central task in drug discovery processes. In this work, a simple but effective regularized least squares integrating with nonlinear kernel fusion (RLS-KF) algorithm is proposed to perform DTI predictions. Using benchmark DTI datasets, our proposed algorithm achieves the state-of-the-art results with area under precision–recall curve (AUPR) of 0.915, 0.925, 0.853 and 0.909 for enzymes, ion channels (IC), G protein-coupled receptors (GPCR) and nuclear receptors (NR) based on 10 fold cross-validation. The performance can further be improved by using a recalculated kernel matrix, especially for the small set of nuclear receptors with AUPR of 0.945. Importantly, most of the top ranked interaction predictions can be validated by experimental data reported in the literature, bioassay results in the PubChem BioAssay database, as well as other previous studies. Our analysis suggests that the proposed RLS-KF is helpful for studying DTI, drug repositioning as well as polypharmacology, and may help to accelerate drug discovery by identifying novel drug targets. - Graphical abstract: Flowchart of the proposed RLS-KF algorithm for drug-target interaction predictions. - Highlights: • A nonlinear kernel fusion algorithm is proposed to perform drug-target interaction predictions. • Performance can further be improved by using the recalculated kernel. • Top predictions can be validated by experimental data.

  10. Prediction of pesticide acute toxicity using two-dimensional chemical descriptors and target species classification.

    Science.gov (United States)

    Martin, T M; Lilavois, C R; Barron, M G

    2017-06-01

    Previous modelling of the median lethal dose (oral rat LD 50 ) has indicated that local class-based models yield better correlations than global models. We evaluated the hypothesis that dividing the dataset by pesticidal mechanisms would improve prediction accuracy. A linear discriminant analysis (LDA) based-approach was utilized to assign indicators such as the pesticide target species, mode of action, or target species - mode of action combination. LDA models were able to predict these indicators with about 87% accuracy. Toxicity is predicted utilizing the QSAR model fit to chemicals with that indicator. Toxicity was also predicted using a global hierarchical clustering (HC) approach which divides data set into clusters based on molecular similarity. At a comparable prediction coverage (~94%), the global HC method yielded slightly higher prediction accuracy (r 2 = 0.50) than the LDA method (r 2 ~ 0.47). A single model fit to the entire training set yielded the poorest results (r 2 = 0.38), indicating that there is an advantage to clustering the dataset to predict acute toxicity. Finally, this study shows that whilst dividing the training set into subsets (i.e. clusters) improves prediction accuracy, it may not matter which method (expert based or purely machine learning) is used to divide the dataset into subsets.

  11. Predicting range performance of sampled imagers by treating aliased signal as target-dependent noise.

    Science.gov (United States)

    Vollmerhausen, Richard H; Driggers, Ronald G; Wilson, David L

    2008-08-01

    This paper presents a new theory to predict the impact of sampling on target acquisition. The aliased signal that results from sampling is treated as noise. The aliased signal is different from detector noise in two ways. First, aliasing disappears as the target contrast decreases. Second, the image corruption due to aliasing gets worse with increased range. This is because sampling is constant in angle space, and targets become poorly sampled as range increases. The theory is presented, along with the results of three experiments. The match between model and experiment is excellent.

  12. CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization.

    Science.gov (United States)

    Zhu, Houxiang; Misel, Lauren; Graham, Mitchell; Robinson, Michael L; Liang, Chun

    2016-05-23

    The CRISPR system holds much promise for successful genome engineering, but therapeutic, industrial, and research applications will place high demand on improving the specificity and efficiency of this tool. CT-Finder (http://bioinfolab.miamioh.edu/ct-finder) is a web service to help users design guide RNAs (gRNAs) optimized for specificity. CT-Finder accommodates the original single-gRNA Cas9 system and two specificity-enhancing paired-gRNA systems: Cas9 D10A nickases (Cas9n) and dimeric RNA-guided FokI nucleases (RFNs). Optimal target candidates can be chosen based on the minimization of predicted off-target effects. Graphical visualization of on-target and off-target sites in the genome is provided for target validation. Major model organisms are covered by this web service.

  13. Cell-Free DNA and Active Rejection in Kidney Allografts.

    Science.gov (United States)

    Bloom, Roy D; Bromberg, Jonathan S; Poggio, Emilio D; Bunnapradist, Suphamai; Langone, Anthony J; Sood, Puneet; Matas, Arthur J; Mehta, Shikha; Mannon, Roslyn B; Sharfuddin, Asif; Fischbach, Bernard; Narayanan, Mohanram; Jordan, Stanley C; Cohen, David; Weir, Matthew R; Hiller, David; Prasad, Preethi; Woodward, Robert N; Grskovic, Marica; Sninsky, John J; Yee, James P; Brennan, Daniel C

    2017-07-01

    Histologic analysis of the allograft biopsy specimen is the standard method used to differentiate rejection from other injury in kidney transplants. Donor-derived cell-free DNA (dd-cfDNA) is a noninvasive test of allograft injury that may enable more frequent, quantitative, and safer assessment of allograft rejection and injury status. To investigate this possibility, we prospectively collected blood specimens at scheduled intervals and at the time of clinically indicated biopsies. In 102 kidney recipients, we measured plasma levels of dd-cfDNA and correlated the levels with allograft rejection status ascertained by histology in 107 biopsy specimens. The dd-cfDNA level discriminated between biopsy specimens showing any rejection (T cell-mediated rejection or antibody-mediated rejection [ABMR]) and controls (no rejection histologically), P rejection at a cutoff of 1.0% dd-cfDNA were 61% and 84%, respectively. The AUC for discriminating ABMR from samples without ABMR was 0.87 (95% CI, 0.75 to 0.97). Positive and negative predictive values for ABMR at a cutoff of 1.0% dd-cfDNA were 44% and 96%, respectively. Median dd-cfDNA was 2.9% (ABMR), 1.2% (T cell-mediated types ≥IB), 0.2% (T cell-mediated type IA), and 0.3% in controls ( P =0.05 for T cell-mediated rejection types ≥IB versus controls). Thus, dd-cfDNA may be used to assess allograft rejection and injury; dd-cfDNA levels rejection (T cell-mediated type ≥IB or ABMR) and levels >1% indicate a probability of active rejection. Copyright © 2017 by the American Society of Nephrology.

  14. Peer victimization and peer rejection during early childhood

    Science.gov (United States)

    Godleski, Stephanie A.; Kamper, Kimberly E.; Ostrov, Jamie M.; Hart, Emily J.; Blakely-McClure, Sarah J.

    2014-01-01

    Objective The development and course of the subtypes of peer victimization is a relatively understudied topic despite the association of victimization with important developmental and clinical outcomes. Moreover, understanding potential predictors, such as peer rejection and emotion regulation, in early childhood may be especially important to elucidate possible bi-directional pathways between relational and physical victimization and rejection. The current study (N = 97) was designed to explore several gaps and limitations in the peer victimization and peer rejection literature. In particular, the prospective associations between relational and physical victimization and peer rejection over the course of 3.5 months during early childhood (i.e., 3- to 5- years-old) were investigated in an integrated model. Method The study consisted of 97 (42 girls) preschool children recruited from four early childhood schools in the northeast of the US. Using observations, research assistant report and teacher report, relational and physical aggression, relational and physical victimization, peer rejection, and emotion regulation were measured in a short-term longitudinal study. Path analyses were conducted to test the overall hypothesized model. Results Peer rejection was found to predict increases in relational victimization. In addition, emotion regulation was found to predict decreases in peer rejection and physical victimization. Conclusions Implications for research and practice are discussed, including teaching coping strategies for peer rejection and emotional distress. PMID:25133659

  15. Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

    Science.gov (United States)

    Jiang, Jing; Lu, Weiqiang; Li, Weihua; Liu, Guixia; Zhou, Weixing; Huang, Jin; Tang, Yun

    2012-01-01

    Drug-target interaction (DTI) is the basis of drug discovery and design. It is time consuming and costly to determine DTI experimentally. Hence, it is necessary to develop computational methods for the prediction of potential DTI. Based on complex network theory, three supervised inference methods were developed here to predict DTI and used for drug repositioning, namely drug-based similarity inference (DBSI), target-based similarity inference (TBSI) and network-based inference (NBI). Among them, NBI performed best on four benchmark data sets. Then a drug-target network was created with NBI based on 12,483 FDA-approved and experimental drug-target binary links, and some new DTIs were further predicted. In vitro assays confirmed that five old drugs, namely montelukast, diclofenac, simvastatin, ketoconazole, and itraconazole, showed polypharmacological features on estrogen receptors or dipeptidyl peptidase-IV with half maximal inhibitory or effective concentration ranged from 0.2 to 10 µM. Moreover, simvastatin and ketoconazole showed potent antiproliferative activities on human MDA-MB-231 breast cancer cell line in MTT assays. The results indicated that these methods could be powerful tools in prediction of DTIs and drug repositioning. PMID:22589709

  16. The Limitations of Existing Approaches in Improving MicroRNA Target Prediction Accuracy.

    Science.gov (United States)

    Loganantharaj, Rasiah; Randall, Thomas A

    2017-01-01

    MicroRNAs (miRNAs) are small (18-24 nt) endogenous RNAs found across diverse phyla involved in posttranscriptional regulation, primarily downregulation of mRNAs. Experimentally determining miRNA-mRNA interactions can be expensive and time-consuming, making the accurate computational prediction of miRNA targets a high priority. Since miRNA-mRNA base pairing in mammals is not perfectly complementary and only a fraction of the identified motifs are real binding sites, accurately predicting miRNA targets remains challenging. The limitations and bottlenecks of existing algorithms and approaches are discussed in this chapter.A new miRNA-mRNA interaction algorithm was implemented in Python (TargetFind) to capture three different modes of association and to maximize detection sensitivity to around 95% for mouse (mm9) and human (hg19) reference data. For human (hg19) data, the prediction accuracy with any one feature among evolutionarily conserved score, multiple targets in a UTR or changes in free energy varied within a close range from 63.5% to 66%. When the results of these features are combined with majority voting, the expected prediction accuracy increases to 69.5%. When all three features are used together, the average best prediction accuracy with tenfold cross validation from the classifiers naïve Bayes, support vector machine, artificial neural network, and decision tree were, respectively, 66.5%, 67.1%, 69%, and 68.4%. The results reveal the advantages and limitations of these approaches.When comparing different sets of features on their strength in predicting true hg19 targets, evolutionarily conserved score slightly outperformed all other features based on thermostability, and target multiplicity. The sophisticated supervised learning algorithms did not improve the prediction accuracy significantly compared to a simple threshold based approach on conservation score or combining the results of each feature with majority agreements. The targets from randomly

  17. Modified linear predictive coding approach for moving target tracking by Doppler radar

    Science.gov (United States)

    Ding, Yipeng; Lin, Xiaoyi; Sun, Ke-Hui; Xu, Xue-Mei; Liu, Xi-Yao

    2016-07-01

    Doppler radar is a cost-effective tool for moving target tracking, which can support a large range of civilian and military applications. A modified linear predictive coding (LPC) approach is proposed to increase the target localization accuracy of the Doppler radar. Based on the time-frequency analysis of the received echo, the proposed approach first real-time estimates the noise statistical parameters and constructs an adaptive filter to intelligently suppress the noise interference. Then, a linear predictive model is applied to extend the available data, which can help improve the resolution of the target localization result. Compared with the traditional LPC method, which empirically decides the extension data length, the proposed approach develops an error array to evaluate the prediction accuracy and thus, adjust the optimum extension data length intelligently. Finally, the prediction error array is superimposed with the predictor output to correct the prediction error. A series of experiments are conducted to illustrate the validity and performance of the proposed techniques.

  18. The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data.

    Science.gov (United States)

    Awale, Mahendra; Reymond, Jean-Louis

    2017-01-01

    Several web-based tools have been reported recently which predict the possible targets of a small molecule by similarity to compounds of known bioactivity using molecular fingerprints (fps), however predictions in each case rely on similarities computed from only one or two fps. Considering that structural similarity and therefore the predicted targets strongly depend on the method used for comparison, it would be highly desirable to predict targets using a broader set of fps simultaneously. Herein, we present the polypharmacology browser (PPB), a web-based platform which predicts possible targets for small molecules by searching for nearest neighbors using ten different fps describing composition, substructures, molecular shape and pharmacophores. PPB searches through 4613 groups of at least 10 same target annotated bioactive molecules from ChEMBL and returns a list of predicted targets ranked by consensus voting scheme and p value. A validation study across 670 drugs with up to 20 targets showed that combining the predictions from all 10 fps gives the best results, with on average 50% of the known targets of a drug being correctly predicted with a hit rate of 25%. Furthermore, when profiling a new inhibitor of the calcium channel TRPV6 against 24 targets taken from a safety screen panel, we observed inhibition in 5 out of 5 targets predicted by PPB and in 7 out of 18 targets not predicted by PPB. The rate of correct (5/12) and incorrect (0/12) predictions for this compound by PPB was comparable to that of other web-based prediction tools. PPB offers a versatile platform for target prediction based on multi-fingerprint comparisons, and is freely accessible at www.gdb.unibe.ch as a valuable support for drug discovery.Graphical abstract.

  19. Ranking of microRNA target prediction scores by Pareto front analysis.

    Science.gov (United States)

    Sahoo, Sudhakar; Albrecht, Andreas A

    2010-12-01

    Over the past ten years, a variety of microRNA target prediction methods has been developed, and many of the methods are constantly improved and adapted to recent insights into miRNA-mRNA interactions. In a typical scenario, different methods return different rankings of putative targets, even if the ranking is reduced to selected mRNAs that are related to a specific disease or cell type. For the experimental validation it is then difficult to decide in which order to process the predicted miRNA-mRNA bindings, since each validation is a laborious task and therefore only a limited number of mRNAs can be analysed. We propose a new ranking scheme that combines ranked predictions from several methods and - unlike standard thresholding methods - utilises the concept of Pareto fronts as defined in multi-objective optimisation. In the present study, we attempt a proof of concept by applying the new ranking scheme to hsa-miR-21, hsa-miR-125b, and hsa-miR-373 and prediction scores supplied by PITA and RNAhybrid. The scores are interpreted as a two-objective optimisation problem, and the elements of the Pareto front are ranked by the STarMir score with a subsequent re-calculation of the Pareto front after removal of the top-ranked mRNA from the basic set of prediction scores. The method is evaluated on validated targets of the three miRNA, and the ranking is compared to scores from DIANA-microT and TargetScan. We observed that the new ranking method performs well and consistent, and the first validated targets are elements of Pareto fronts at a relatively early stage of the recurrent procedure, which encourages further research towards a higher-dimensional analysis of Pareto fronts. Copyright © 2010 Elsevier Ltd. All rights reserved.

  20. Role of retinal slip in the prediction of target motion during smooth and saccadic pursuit.

    Science.gov (United States)

    de Brouwer, S; Missal, M; Lefèvre, P

    2001-08-01

    Visual tracking of moving targets requires the combination of smooth pursuit eye movements with catch-up saccades. In primates, catch-up saccades usually take place only during pursuit initiation because pursuit gain is close to unity. This contrasts with the lower and more variable gain of smooth pursuit in cats, where smooth eye movements are intermingled with catch-up saccades during steady-state pursuit. In this paper, we studied in detail the role of retinal slip in the prediction of target motion during smooth and saccadic pursuit in the cat. We found that the typical pattern of pursuit in the cat was a combination of smooth eye movements with saccades. During smooth pursuit initiation, there was a correlation between peak eye acceleration and target velocity. During pursuit maintenance, eye velocity oscillated at approximately 3 Hz around a steady-state value. The average gain of smooth pursuit was approximately 0.5. Trained cats were able to continue pursuing in the absence of a visible target, suggesting a role of the prediction of future target motion in this species. The analysis of catch-up saccades showed that the smooth-pursuit motor command is added to the saccadic command during catch-up saccades and that both position error and retinal slip are taken into account in their programming. The influence of retinal slip on catch-up saccades showed that prediction about future target motion is used in the programming of catch-up saccades. Altogether, these results suggest that pursuit systems in primates and cats are qualitatively similar, with a lower average gain in the cat and that prediction affects both saccades and smooth eye movements during pursuit.

  1. Some Remarks on Prediction of Drug-Target Interaction with Network Models.

    Science.gov (United States)

    Zhang, Shao-Wu; Yan, Xiao-Ying

    2017-01-01

    System-level understanding of the relationships between drugs and targets is very important for enhancing drug research, especially for drug function repositioning. The experimental methods used to determine drug-target interactions are usually time-consuming, tedious and expensive, and sometimes lack reproducibility. Thus, it is highly desired to develop computational methods for efficiently and effectively analyzing and detecting new drug-target interaction pairs. With the explosive growth of different types of omics data, such as genome, pharmacology, phenotypic, and other kinds of molecular networks, numerous computational approaches have been developed to predict Drug-Target Interactions (DTI). In this review, we make a survey on the recent advances in predicting drug-target interaction with network-based models from the following aspects: i) Available public data sources and benchmark datasets; ii) Drug/target similarity metrics; iii) Network construction; iv) Common network algorithms; v) Performance comparison of existing network-based DTI predictors. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  2. Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes.

    Directory of Open Access Journals (Sweden)

    Scott Schaeffer

    Full Text Available Plastids are actively involved in numerous plant processes critical to growth, development and adaptation. They play a primary role in photosynthesis, pigment and monoterpene synthesis, gravity sensing, starch and fatty acid synthesis, as well as oil, and protein storage. We applied two complementary methods to analyze the recently published apple genome (Malus × domestica to identify putative plastid-targeted proteins, the first using TargetP and the second using a custom workflow utilizing a set of predictive programs. Apple shares roughly 40% of its 10,492 putative plastid-targeted proteins with that of the Arabidopsis (Arabidopsis thaliana plastid-targeted proteome as identified by the Chloroplast 2010 project and ∼57% of its entire proteome with Arabidopsis. This suggests that the plastid-targeted proteomes between apple and Arabidopsis are different, and interestingly alludes to the presence of differential targeting of homologs between the two species. Co-expression analysis of 2,224 genes encoding putative plastid-targeted apple proteins suggests that they play a role in plant developmental and intermediary metabolism. Further, an inter-specific comparison of Arabidopsis, Prunus persica (Peach, Malus × domestica (Apple, Populus trichocarpa (Black cottonwood, Fragaria vesca (Woodland Strawberry, Solanum lycopersicum (Tomato and Vitis vinifera (Grapevine also identified a large number of novel species-specific plastid-targeted proteins. This analysis also revealed the presence of alternatively targeted homologs across species. Two separate analyses revealed that a small subset of proteins, one representing 289 protein clusters and the other 737 unique protein sequences, are conserved between seven plastid-targeted angiosperm proteomes. Majority of the novel proteins were annotated to play roles in stress response, transport, catabolic processes, and cellular component organization. Our results suggest that the current state of

  3. Novel Methods for Drug-Target Interaction Prediction using Graph Mining

    KAUST Repository

    Ba Alawi, Wail

    2016-08-31

    The problem of developing drugs that can be used to cure diseases is important and requires a careful approach. Since pursuing the wrong candidate drug for a particular disease could be very costly in terms of time and money, there is a strong interest in minimizing such risks. Drug repositioning has become a hot topic of research, as it helps reduce these risks significantly at the early stages of drug development by reusing an approved drug for the treatment of a different disease. Still, finding new usage for a drug is non-trivial, as it is necessary to find out strong supporting evidence that the proposed new uses of drugs are plausible. Many computational approaches were developed to narrow the list of possible candidate drug-target interactions (DTIs) before any experiments are done. However, many of these approaches suffer from unacceptable levels of false positives. We developed two novel methods based on graph mining networks of drugs and targets. The first method (DASPfind) finds all non-cyclic paths that connect a drug and a target, and using a function that we define, calculates a score from all the paths. This score describes our confidence that DTI is correct. We show that DASPfind significantly outperforms other state-of-the-art methods in predicting the top ranked target for each drug. We demonstrate the utility of DASPfind by predicting 15 novel DTIs over a set of ion channel proteins, and confirming 12 out of these 15 DTIs through experimental evidence reported in literature and online drug databases. The second method (DASPfind+) modifies DASPfind in order to increase the confidence and reliability of the resultant predictions. Based on the structure of the drug-target interaction (DTI) networks, we introduced an optimization scheme that incrementally alters the network structure locally for each drug to achieve more robust top 1 ranked predictions. Moreover, we explored effects of several similarity measures between the targets on the prediction

  4. Diagnosis of cardiac allograft rejection with MR imaging

    International Nuclear Information System (INIS)

    Soulen, R.L.; Fraser, C.D.; Hutchins, G.M.; Baumgartner, W.A.; Reitz, B.A.

    1987-01-01

    Serial MR images and endomyocardial biopsy specimens of heterotopic cervical cardiac allotransplants were obtained in six dogs during 2 weeks of immunosuppression followed by 1 week without such therapy. A surface coil and gated spin-echo technique were used. Myocardial intensity (MI) measurements and histopathologic interpretations were performed independently. All six dogs showed a decrease in MI between their first and second MR studies, while showing no rejection. One dog had no rejection and died; in five dogs studies gated to every other beat showed progressive increase in MI that correlated significantly with increasing rejection, though absolute MI values did not correlated with a specific biopsy score. Severe rejection also caused overt increase in myocardial mass. The MI in the early postoperative period may reflect reperfusion injury. Absolute intensity values cannot predict rejection. Serial studies in transplant patients may prove clinically useful

  5. Radionuclide diagnosis of allograft rejection

    International Nuclear Information System (INIS)

    George, E.A.

    1982-01-01

    Interaction with one or more anatomical and physiopathological characteristics of the rejecting renal allograft is suggested by those radioagents utilized specifically for the diagnosis of allograft rejection. Rejection, the most common cause of declining allograft function, is frequently mimicked clinically or masked by other immediate or long term post transplant complications. Understanding of the anatomical pathological features and kinetics of rejection and their modification by immunosuppressive maintenance and therapy are important for the proper clinical utilization of these radioagents. Furthermore, in selecting these radionuclides, one has to consider the comparative availability, preparatory and procedural simplicity, acquisition and display techniques and the possibility of timely report. The clinical utilities of radiofibrinogen, /sup 99m/Tc sulfur colloid and 67 Ga in the diagnosis of allograft rejection have been evaluated to a variable extent in the past. The potential usefulness of the recently developed preparations of 111 In labeled autologous leukocytes and platelets are presently under investigation

  6. Predictive Diagnostic Pathology in the Target Therapy Era in Breast Cancer.

    Science.gov (United States)

    Marchio, Caterina; Balmativola, Davide; Castiglione, Roberta; Annaratone, Laura; Sapino, Anna

    2017-01-01

    Treatment strategies in oncology are nowadays largely based on the "target therapy model", which allows to personalize the cure of each patient depending on distinctive host and disease features. As a general concept "targeted drugs" are effective only when the tumor exhibits the "target", which in breast cancer pathology may correspond to the expression of estrogen receptors and/or of HER2. These biomarkers are evaluated on breast cancer tissues by companion diagnostic tests, however, evidence suggests that the first step in breast cancer predictive pathology is still represented by morphology. For instance, histological types, such as tubular and cribriform carcinomas, define patients who may not need any treatments other than surgical excision. Neoadjuvant studies have shown that patients affected by lobular carcinomas are not likely to have any beneficial effects from chemotherapy. The second step in prediction is represented by immunophenotyping. If the immunohistochemical evaluation of four markers (estrogen and progesterone receptors, HER2 and Ki67) remains the best practice for breast cancer predictive pathology, molecular pathology has certainly reshaped the way we approach breast cancer diagnosis. The aim of this review is to discuss current knowledge in predictive pathology for the management of breast cancer patients, focusing on the benefits and drawbacks of traditional tools and of novel improvements of molecular biology.

  7. Predicting the Types of Ion Channel-Targeted Conotoxins Based on AVC-SVM Model.

    Science.gov (United States)

    Xianfang, Wang; Junmei, Wang; Xiaolei, Wang; Yue, Zhang

    2017-01-01

    The conotoxin proteins are disulfide-rich small peptides. Predicting the types of ion channel-targeted conotoxins has great value in the treatment of chronic diseases, epilepsy, and cardiovascular diseases. To solve the problem of information redundancy existing when using current methods, a new model is presented to predict the types of ion channel-targeted conotoxins based on AVC (Analysis of Variance and Correlation) and SVM (Support Vector Machine). First, the F value is used to measure the significance level of the feature for the result, and the attribute with smaller F value is filtered by rough selection. Secondly, redundancy degree is calculated by Pearson Correlation Coefficient. And the threshold is set to filter attributes with weak independence to get the result of the refinement. Finally, SVM is used to predict the types of ion channel-targeted conotoxins. The experimental results show the proposed AVC-SVM model reaches an overall accuracy of 91.98%, an average accuracy of 92.17%, and the total number of parameters of 68. The proposed model provides highly useful information for further experimental research. The prediction model will be accessed free of charge at our web server.

  8. A model for predicting magnetic targeting of multifunctional particles in the microvasculature

    Energy Technology Data Exchange (ETDEWEB)

    Furlani, Edward J. [Institute for Lasers, Photonics and Biophotonics, University at Buffalo (SUNY), Buffalo 14260, NY (United States); Furlani, Edward P. [Institute for Lasers, Photonics and Biophotonics, University at Buffalo (SUNY), Buffalo 14260, NY (United States)]. E-mail: efurlani@buffalo.edu

    2007-05-15

    A mathematical model is presented for predicting magnetic targeting of multifunctional carrier particles that are designed to deliver therapeutic agents to malignant tissue in vivo. These particles consist of a nonmagnetic core material that contains embedded magnetic nanoparticles and therapeutic agents such as photodynamic sensitizers. For in vivo therapy, the particles are injected into the vascular system upstream from malignant tissue, and captured at the tumor using an applied magnetic field. The applied field couples to the magnetic nanoparticles inside the carrier particle and produces a force that attracts the particle to the tumor. In noninvasive therapy, the applied field is produced by a permanent magnet positioned outside the body. In this paper, a mathematical model is developed for predicting noninvasive magnetic targeting of therapeutic carrier particles in the microvasculature. The model takes into account the dominant magnetic and fluidic forces on the particles and leads to an analytical expression for predicting their trajectory. An analytical expression is also derived for predicting the volume fraction of embedded magnetic nanoparticles required to ensure capture of the carrier particle at the tumor. The model enables rapid parametric analysis of magnetic targeting as a function of key variables including the size of the carrier particle, the properties and volume fraction of the embedded magnetic nanoparticles, the properties of the magnet, the microvessel, the hematocrit of the blood and its flow rate.

  9. Tracking Maneuvering Group Target with Extension Predicted and Best Model Augmentation Method Adapted

    Directory of Open Access Journals (Sweden)

    Linhai Gan

    2017-01-01

    Full Text Available The random matrix (RM method is widely applied for group target tracking. The assumption that the group extension keeps invariant in conventional RM method is not yet valid, as the orientation of the group varies rapidly while it is maneuvering; thus, a new approach with group extension predicted is derived here. To match the group maneuvering, a best model augmentation (BMA method is introduced. The existing BMA method uses a fixed basic model set, which may lead to a poor performance when it could not ensure basic coverage of true motion modes. Here, a maneuvering group target tracking algorithm is proposed, where the group extension prediction and the BMA adaption are exploited. The performance of the proposed algorithm will be illustrated by simulation.

  10. Interactome of Radiation-Induced microRNA-Predicted Target Genes

    Directory of Open Access Journals (Sweden)

    Tenzin W. Lhakhang

    2012-01-01

    Full Text Available The microRNAs (miRNAs function as global negative regulators of gene expression and have been associated with a multitude of biological processes. The dysfunction of the microRNAome has been linked to various diseases including cancer. Our laboratory recently reported modulation in the expression of miRNA in a variety of cell types exposed to ionizing radiation (IR. To further understand miRNA role in IR-induced stress pathways, we catalogued a set of common miRNAs modulated in various irradiated cell lines and generated a list of predicted target genes. Using advanced bioinformatics tools we identified cellular pathways where miRNA predicted target genes function. The miRNA-targeted genes were found to play key roles in previously identified IR stress pathways such as cell cycle, p53 pathway, TGF-beta pathway, ubiquitin-mediated proteolysis, focal adhesion pathway, MAPK signaling, thyroid cancer pathway, adherens junction, insulin signaling pathway, oocyte meiosis, regulation of actin cytoskeleton, and renal cell carcinoma pathway. Interestingly, we were able to identify novel targeted pathways that have not been identified in cellular radiation response, such as aldosterone-regulated sodium reabsorption, long-term potentiation, and neutrotrophin signaling pathways. Our analysis indicates that the miRNA interactome in irradiated cells provides a platform for comprehensive modeling of the cellular stress response to IR exposure.

  11. Prediction problem for target events based on the inter-event waiting time

    Science.gov (United States)

    Shapoval, A.

    2010-11-01

    In this paper we address the problem of forecasting the target events of a time series given the distribution ξ of time gaps between target events. Strong earthquakes and stock market crashes are the two types of such events that we are focusing on. In the series of earthquakes, as McCann et al. show [W.R. Mc Cann, S.P. Nishenko, L.R. Sykes, J. Krause, Seismic gaps and plate tectonics: seismic potential for major boundaries, Pure and Applied Geophysics 117 (1979) 1082-1147], there are well-defined gaps (called seismic gaps) between strong earthquakes. On the other hand, usually there are no regular gaps in the series of stock market crashes [M. Raberto, E. Scalas, F. Mainardi, Waiting-times and returns in high-frequency financial data: an empirical study, Physica A 314 (2002) 749-755]. For the case of seismic gaps, we analytically derive an upper bound of prediction efficiency given the coefficient of variation of the distribution ξ. For the case of stock market crashes, we develop an algorithm that predicts the next crash within a certain time interval after the previous one. We show that this algorithm outperforms random prediction. The efficiency of our algorithm sets up a lower bound of efficiency for effective prediction of stock market crashes.

  12. Optimal marker-strategy clinical trial design to detect predictive markers for targeted therapy.

    Science.gov (United States)

    Zang, Yong; Liu, Suyu; Yuan, Ying

    2016-07-01

    In developing targeted therapy, the marker-strategy design (MSD) provides an important approach to evaluate the predictive marker effect. This design first randomizes patients into non-marker-based or marker-based strategies. Patients allocated to the non-marker-based strategy are then further randomized to receive either the standard or targeted treatments, while patients allocated to the marker-based strategy receive treatments based on their marker statuses. Little research has been done on the statistical properties of the MSD, which has led to some widespread misconceptions and placed clinical researchers at high risk of using inefficient designs. In this article, we show that the commonly used between-strategy comparison has low power to detect the predictive effect and is valid only under a restrictive condition that the randomization ratio within the non-marker-based strategy matches the marker prevalence. We propose a Wald test that is generally valid and also uniformly more powerful than the between-strategy comparison. Based on that, we derive an optimal MSD that maximizes the power to detect the predictive marker effect by choosing the optimal randomization ratios between the two strategies and treatments. Our numerical study shows that using the proposed optimal designs can substantially improve the power of the MSD to detect the predictive marker effect. We use a lung cancer trial to illustrate the proposed optimal designs. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies

    Directory of Open Access Journals (Sweden)

    Jennifer D. Atkins

    2015-08-01

    Full Text Available The role and function of a given protein is dependent on its structure. In recent years, however, numerous studies have highlighted the importance of unstructured, or disordered regions in governing a protein’s function. Disordered proteins have been found to play important roles in pivotal cellular functions, such as DNA binding and signalling cascades. Studying proteins with extended disordered regions is often problematic as they can be challenging to express, purify and crystallise. This means that interpretable experimental data on protein disorder is hard to generate. As a result, predictive computational tools have been developed with the aim of predicting the level and location of disorder within a protein. Currently, over 60 prediction servers exist, utilizing different methods for classifying disorder and different training sets. Here we review several good performing, publicly available prediction methods, comparing their application and discussing how disorder prediction servers can be used to aid the experimental solution of protein structure. The use of disorder prediction methods allows us to adopt a more targeted approach to experimental studies by accurately identifying the boundaries of ordered protein domains so that they may be investigated separately, thereby increasing the likelihood of their successful experimental solution.

  14. Predictive markers of efficacy for an angiopoietin-2 targeting therapeutic in xenograft models.

    Directory of Open Access Journals (Sweden)

    Gallen Triana-Baltzer

    Full Text Available The clinical efficacy of anti-angiogenic therapies has been difficult to predict, and biomarkers that can predict responsiveness are sorely needed in this era of personalized medicine. CVX-060 is an angiopoietin-2 (Ang2 targeting therapeutic, consisting of two peptides that bind Ang2 with high affinity and specificity, covalently fused to a scaffold antibody. In order to optimize the use of this compound in the clinic the construction of a predictive model is described, based on the efficacy of CVX-060 in 13 cell line and 2 patient-derived xenograft models. Pretreatment size tumors from each of the models were profiled for the levels of 27 protein markers of angiogenesis, SNP haplotype in 5 angiogenesis genes, and somatic mutation status for 11 genes implicated in tumor growth and/or vascularization. CVX-060 efficacy was determined as tumor growth inhibition (TGI% at termination of each study. A predictive statistical model was constructed based on the correlation of these efficacy data with the marker profiles, and the model was subsequently tested by prospective analysis in 11 additional models. The results reveal a range of CVX-060 efficacy in xenograft models of diverse tissue types (0-64% TGI, median = 27% and define a subset of 3 proteins (Ang1, EGF, Emmprin, the levels of which may be predictive of TGI by Ang2 blockade. The direction of the associations is such that better efficacy correlates with high levels of target and low levels of compensatory/antagonizing molecules. This effort has revealed a set of candidate predictive markers for CVX-060 efficacy that will be further evaluated in ongoing clinical trials.

  15. Predictive markers of efficacy for an angiopoietin-2 targeting therapeutic in xenograft models.

    Science.gov (United States)

    Triana-Baltzer, Gallen; Pavlicek, Adam; Goulart, Ariadne; Huang, Hanhua; Pirie-Shepherd, Steven; Levin, Nancy

    2013-01-01

    The clinical efficacy of anti-angiogenic therapies has been difficult to predict, and biomarkers that can predict responsiveness are sorely needed in this era of personalized medicine. CVX-060 is an angiopoietin-2 (Ang2) targeting therapeutic, consisting of two peptides that bind Ang2 with high affinity and specificity, covalently fused to a scaffold antibody. In order to optimize the use of this compound in the clinic the construction of a predictive model is described, based on the efficacy of CVX-060 in 13 cell line and 2 patient-derived xenograft models. Pretreatment size tumors from each of the models were profiled for the levels of 27 protein markers of angiogenesis, SNP haplotype in 5 angiogenesis genes, and somatic mutation status for 11 genes implicated in tumor growth and/or vascularization. CVX-060 efficacy was determined as tumor growth inhibition (TGI%) at termination of each study. A predictive statistical model was constructed based on the correlation of these efficacy data with the marker profiles, and the model was subsequently tested by prospective analysis in 11 additional models. The results reveal a range of CVX-060 efficacy in xenograft models of diverse tissue types (0-64% TGI, median = 27%) and define a subset of 3 proteins (Ang1, EGF, Emmprin), the levels of which may be predictive of TGI by Ang2 blockade. The direction of the associations is such that better efficacy correlates with high levels of target and low levels of compensatory/antagonizing molecules. This effort has revealed a set of candidate predictive markers for CVX-060 efficacy that will be further evaluated in ongoing clinical trials.

  16. Genome-Scale Screening and Validation of Targets for Identification of Salmonella enterica and Serovar Prediction.

    Science.gov (United States)

    Zhou, Xiujuan; Zhang, Lida; Shi, Chunlei; Fratamico, Pina M; Liu, Bin; Paoli, George C; Dan, Xianlong; Zhuang, Xiaofei; Cui, Yan; Wang, Dapeng; Shi, Xianming

    2016-03-01

    Salmonella enterica is the most common foodborne pathogen worldwide, with 2,500 recognized serovars. Detection of S. enterica and its classification into serovars are essential for food safety surveillance and clinical diagnosis. The PCR method is useful for these applications because of its rapidity and high accuracy. We obtained 412 candidate detection targets for S. enterica using a comparative genomics mining approach. Gene ontology (GO) functional enrichment analysis of these candidate targets revealed that the GO term with the largest number of unigenes with known function (38 of 177, 21.5%) was significantly involved in pathogenesis (P enterica by verification with 151 S. enterica strains and 34 non-Salmonella strains. The phylogenetic trees of verified targets were highly comparable with those of housekeeping genes, especially for differentiating S. enterica strains into serovars. The serovar prediction ability was validated by sequencing one target (S9) for 39 S. enterica strains belonging to six serovars. Identical mutation sites existed in the same serovar, and different mutation sites were found in diverse serovars. Our findings revealed that 15 verified targets can be potentially used for molecular detection, and some of them can be used for serotyping of S. enterica strains.

  17. Mining predicted essential genes of Brugia malayi for nematode drug targets.

    Directory of Open Access Journals (Sweden)

    Sanjay Kumar

    Full Text Available We report results from the first genome-wide application of a rational drug target selection methodology to a metazoan pathogen genome, the completed draft sequence of Brugia malayi, a parasitic nematode responsible for human lymphatic filariasis. More than 1.5 billion people worldwide are at risk of contracting lymphatic filariasis and onchocerciasis, a related filarial disease. Drug treatments for filariasis have not changed significantly in over 20 years, and with the risk of resistance rising, there is an urgent need for the development of new anti-filarial drug therapies. The recent publication of the draft genomic sequence for B. malayi enables a genome-wide search for new drug targets. However, there is no functional genomics data in B. malayi to guide the selection of potential drug targets. To circumvent this problem, we have utilized the free-living model nematode Caenorhabditis elegans as a surrogate for B. malayi. Sequence comparisons between the two genomes allow us to map C. elegans orthologs to B. malayi genes. Using these orthology mappings and by incorporating the extensive genomic and functional genomic data, including genome-wide RNAi screens, that already exist for C. elegans, we identify potentially essential genes in B. malayi. Further incorporation of human host genome sequence data and a custom algorithm for prioritization enables us to collect and rank nearly 600 drug target candidates. Previously identified potential drug targets cluster near the top of our prioritized list, lending credibility to our methodology. Over-represented Gene Ontology terms, predicted InterPro domains, and RNAi phenotypes of C. elegans orthologs associated with the potential target pool are identified. By virtue of the selection procedure, the potential B. malayi drug targets highlight components of key processes in nematode biology such as central metabolism, molting and regulation of gene expression.

  18. Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy.

    Science.gov (United States)

    Jung, Jinmyung; Kwon, Mijin; Bae, Sunghwa; Yim, Soorin; Lee, Doheon

    2018-03-05

    Muscle atrophy, an involuntary loss of muscle mass, is involved in various diseases and sometimes leads to mortality. However, therapeutics for muscle atrophy thus far have had limited effects. Here, we present a new approach for therapeutic target prediction using Petri net simulation of the status of phosphorylation, with a reasonable assumption that the recovery of abnormally phosphorylated proteins can be a treatment for muscle atrophy. The Petri net model was employed to simulate phosphorylation status in three states, i.e. reference, atrophic and each gene-inhibited state based on the myocyte-specific phosphorylation network. Here, we newly devised a phosphorylation specific Petri net that involves two types of transitions (phosphorylation or de-phosphorylation) and two types of places (activation with or without phosphorylation). Before predicting therapeutic targets, the simulation results in reference and atrophic states were validated by Western blotting experiments detecting five marker proteins, i.e. RELA, SMAD2, SMAD3, FOXO1 and FOXO3. Finally, we determined 37 potential therapeutic targets whose inhibition recovers the phosphorylation status from an atrophic state as indicated by the five validated marker proteins. In the evaluation, we confirmed that the 37 potential targets were enriched for muscle atrophy-related terms such as actin and muscle contraction processes, and they were also significantly overlapping with the genes associated with muscle atrophy reported in the Comparative Toxicogenomics Database (p-value net. We generated a list of the potential therapeutic targets whose inhibition recovers abnormally phosphorylated proteins in an atrophic state. They were evaluated by various approaches, such as Western blotting, GO terms, literature, known muscle atrophy-related genes and shortest path analysis. We expect the new proposed strategy to provide an understanding of phosphorylation status in muscle atrophy and to provide assistance towards

  19. lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics.

    Science.gov (United States)

    Hu, Ruifeng; Sun, Xiaobo

    2016-08-01

    Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .

  20. MirZ: an integrated microRNA expression atlas and target prediction resource.

    Science.gov (United States)

    Hausser, Jean; Berninger, Philipp; Rodak, Christoph; Jantscher, Yvonne; Wirth, Stefan; Zavolan, Mihaela

    2009-07-01

    MicroRNAs (miRNAs) are short RNAs that act as guides for the degradation and translational repression of protein-coding mRNAs. A large body of work showed that miRNAs are involved in the regulation of a broad range of biological functions, from development to cardiac and immune system function, to metabolism, to cancer. For most of the over 500 miRNAs that are encoded in the human genome the functions still remain to be uncovered. Identifying miRNAs whose expression changes between cell types or between normal and pathological conditions is an important step towards characterizing their function as is the prediction of mRNAs that could be targeted by these miRNAs. To provide the community the possibility of exploring interactively miRNA expression patterns and the candidate targets of miRNAs in an integrated environment, we developed the MirZ web server, which is accessible at www.mirz.unibas.ch. The server provides experimental and computational biologists with statistical analysis and data mining tools operating on up-to-date databases of sequencing-based miRNA expression profiles and of predicted miRNA target sites in species ranging from Caenorhabditis elegans to Homo sapiens.

  1. Combination of Supervised and Unsupervised Approaches for miRNA Target Prediction.

    Science.gov (United States)

    Sedaghat, Nafiseh; Fathy, Mahmood; Modarressi, Mohammad Hossein; Shojaie, Ali

    2017-07-13

    MicroRNAs (miRNAs) are short non-coding RNAs which target mRNAs by binding to them and regulating their expression. Involvement of miRNAs has been discovered in many diseases, so it is fruitful to investigate the miRNAs and their targets to develop new therapeutic ways by designing anti-miRNA oligonucleotides. There are various computational methods to predict the target genes, however, their precisions are not good enough. In this paper, we apply a two-step approach to refine the results of sequence-based prediction algorithms. The first step is based on consensus learning according to our previous research, then the second step includes utilizing Support Vector Machine (SVM) classifier in unary and binary modes to identify validated interactions based on binding features as well as network features of genes in constructed gene regulatory network. Experimental results on two real data sets from TCGA database show the binary SVM classification significantly increases the precision of finding validated interactions.

  2. Prediction of Effective Drug Combinations by Chemical Interaction, Protein Interaction and Target Enrichment of KEGG Pathways

    Directory of Open Access Journals (Sweden)

    Lei Chen

    2013-01-01

    Full Text Available Drug combinatorial therapy could be more effective in treating some complex diseases than single agents due to better efficacy and reduced side effects. Although some drug combinations are being used, their underlying molecular mechanisms are still poorly understood. Therefore, it is of great interest to deduce a novel drug combination by their molecular mechanisms in a robust and rigorous way. This paper attempts to predict effective drug combinations by a combined consideration of: (1 chemical interaction between drugs, (2 protein interactions between drugs’ targets, and (3 target enrichment of KEGG pathways. A benchmark dataset was constructed, consisting of 121 confirmed effective combinations and 605 random combinations. Each drug combination was represented by 465 features derived from the aforementioned three properties. Some feature selection techniques, including Minimum Redundancy Maximum Relevance and Incremental Feature Selection, were adopted to extract the key features. Random forest model was built with its performance evaluated by 5-fold cross-validation. As a result, 55 key features providing the best prediction result were selected. These important features may help to gain insights into the mechanisms of drug combinations, and the proposed prediction model could become a useful tool for screening possible drug combinations.

  3. Prediction of Effective Drug Combinations by Chemical Interaction, Protein Interaction and Target Enrichment of KEGG Pathways

    Science.gov (United States)

    Chen, Lei; Zheng, Ming-Yue; Zhang, Jian; Feng, Kai-Yan; Cai, Yu-Dong

    2013-01-01

    Drug combinatorial therapy could be more effective in treating some complex diseases than single agents due to better efficacy and reduced side effects. Although some drug combinations are being used, their underlying molecular mechanisms are still poorly understood. Therefore, it is of great interest to deduce a novel drug combination by their molecular mechanisms in a robust and rigorous way. This paper attempts to predict effective drug combinations by a combined consideration of: (1) chemical interaction between drugs, (2) protein interactions between drugs' targets, and (3) target enrichment of KEGG pathways. A benchmark dataset was constructed, consisting of 121 confirmed effective combinations and 605 random combinations. Each drug combination was represented by 465 features derived from the aforementioned three properties. Some feature selection techniques, including Minimum Redundancy Maximum Relevance and Incremental Feature Selection, were adopted to extract the key features. Random forest model was built with its performance evaluated by 5-fold cross-validation. As a result, 55 key features providing the best prediction result were selected. These important features may help to gain insights into the mechanisms of drug combinations, and the proposed prediction model could become a useful tool for screening possible drug combinations. PMID:24083237

  4. Open-source chemogenomic data-driven algorithms for predicting drug-target interactions.

    Science.gov (United States)

    Hao, Ming; Bryant, Stephen H; Wang, Yanli

    2018-02-06

    While novel technologies such as high-throughput screening have advanced together with significant investment by pharmaceutical companies during the past decades, the success rate for drug development has not yet been improved prompting researchers looking for new strategies of drug discovery. Drug repositioning is a potential approach to solve this dilemma. However, experimental identification and validation of potential drug targets encoded by the human genome is both costly and time-consuming. Therefore, effective computational approaches have been proposed to facilitate drug repositioning, which have proved to be successful in drug discovery. Doubtlessly, the availability of open-accessible data from basic chemical biology research and the success of human genome sequencing are crucial to develop effective in silico drug repositioning methods allowing the identification of potential targets for existing drugs. In this work, we review several chemogenomic data-driven computational algorithms with source codes publicly accessible for predicting drug-target interactions (DTIs). We organize these algorithms by model properties and model evolutionary relationships. We re-implemented five representative algorithms in R programming language, and compared these algorithms by means of mean percentile ranking, a new recall-based evaluation metric in the DTI prediction research field. We anticipate that this review will be objective and helpful to researchers who would like to further improve existing algorithms or need to choose appropriate algorithms to infer potential DTIs in the projects. The source codes for DTI predictions are available at: https://github.com/minghao2016/chemogenomicAlg4DTIpred. Published by Oxford University Press 2018. This work is written by US Government employees and is in the public domain in the US.

  5. Predicting mitochondrial targeting by small molecule xenobiotics within living cells using QSAR models.

    Science.gov (United States)

    Horobin, Richard W

    2015-01-01

    Whether small molecule xenobiotics (biocides, drugs, probes, toxins) will target mitochondria in living cells can be predicted using an algorithm derived from QSAR modeling. Application of the algorithm requires the chemical structures of all ionic species of the xenobiotic compound in question to be defined, and for certain numerical structure parameters (AI, CBN, log P, pKa, and Z) to be obtained for all such species. How the chemical structures are specified, how the structure parameters are obtained or estimated, and how the algorithm is used are described in an explicit protocol.

  6. Predictive Biomarkers in Colorectal Cancer: From the Single Therapeutic Target to a Plethora of Options

    Directory of Open Access Journals (Sweden)

    Daniela Rodrigues

    2016-01-01

    Full Text Available Colorectal cancer (CRC is one of the most frequent cancers and is a leading cause of cancer death worldwide. Treatments used for CRC may include some combination of surgery, radiation therapy, chemotherapy, and targeted therapy. The current standard drugs used in chemotherapy are 5-fluorouracil and leucovorin in combination with irinotecan and/or oxaliplatin. Most recently, biologic agents have been proven to have therapeutic benefits in metastatic CRC alone or in association with standard chemotherapy. However, patients present different treatment responses, in terms of efficacy and toxicity; therefore, it is important to identify biological markers that can predict the response to therapy and help select patients that would benefit from specific regimens. In this paper, authors review CRC genetic markers that could be useful in predicting the sensitivity/resistance to chemotherapy.

  7. Distribution of the alphaGal- and the non-alphaGal T-antigens in the pig kidney: potential targets for rejection in pig-to-man xenotransplantation

    DEFF Research Database (Denmark)

    Kirkeby, Svend; Mikkelsen, Hanne B

    2008-01-01

    Carbohydrate antigens, present on pig vascular endothelial cells, seem to be the prime agents responsible for graft rejection, and although genetically modified animals that express less amounts of carbohydrate antigen are available, it is still useful to decide the localization of the reactive...... forming the glomeruli and in the capillaries surrounding the convoluted tubules, but showed stronger staining in capillaries surrounding the limbs of Henle. In addition, the brush border and basement membranes of the convoluted tubules strongly reacted with the GS1-B4-lectin. Finally, the Galalpha1-3Gal...

  8. Predicting the dynamics of bacterial growth inhibition by ribosome-targeting antibiotics

    Science.gov (United States)

    Greulich, Philip; Doležal, Jakub; Scott, Matthew; Evans, Martin R.; Allen, Rosalind J.

    2017-12-01

    Understanding how antibiotics inhibit bacteria can help to reduce antibiotic use and hence avoid antimicrobial resistance—yet few theoretical models exist for bacterial growth inhibition by a clinically relevant antibiotic treatment regimen. In particular, in the clinic, antibiotic treatment is time-dependent. Here, we use a theoretical model, previously applied to steady-state bacterial growth, to predict the dynamical response of a bacterial cell to a time-dependent dose of ribosome-targeting antibiotic. Our results depend strongly on whether the antibiotic shows reversible transport and/or low-affinity ribosome binding (‘low-affinity antibiotic’) or, in contrast, irreversible transport and/or high affinity ribosome binding (‘high-affinity antibiotic’). For low-affinity antibiotics, our model predicts that growth inhibition depends on the duration of the antibiotic pulse, and can show a transient period of very fast growth following removal of the antibiotic. For high-affinity antibiotics, growth inhibition depends on peak dosage rather than dose duration, and the model predicts a pronounced post-antibiotic effect, due to hysteresis, in which growth can be suppressed for long times after the antibiotic dose has ended. These predictions are experimentally testable and may be of clinical significance.

  9. Predicting human miRNA target genes using a novel evolutionary methodology

    KAUST Repository

    Aigli, Korfiati

    2012-01-01

    The discovery of miRNAs had great impacts on traditional biology. Typically, miRNAs have the potential to bind to the 3\\'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. The experimental identification of their targets has many drawbacks including cost, time and low specificity and these are the reasons why many computational approaches have been developed so far. However, existing computational approaches do not include any advanced feature selection technique and they are facing problems concerning their classification performance and their interpretability. In the present paper, we propose a novel hybrid methodology which combines genetic algorithms and support vector machines in order to locate the optimal feature subset while achieving high classification performance. The proposed methodology was compared with two of the most promising existing methodologies in the problem of predicting human miRNA targets. Our approach outperforms existing methodologies in terms of classification performances while selecting a much smaller feature subset. © 2012 Springer-Verlag.

  10. Swing-leg trajectory of running guinea fowl suggests task-level priority of force regulation rather than disturbance rejection.

    Directory of Open Access Journals (Sweden)

    Yvonne Blum

    Full Text Available To achieve robust and stable legged locomotion in uneven terrain, animals must effectively coordinate limb swing and stance phases, which involve distinct yet coupled dynamics. Recent theoretical studies have highlighted the critical influence of swing-leg trajectory on stability, disturbance rejection, leg loading and economy of walking and running. Yet, simulations suggest that not all these factors can be simultaneously optimized. A potential trade-off arises between the optimal swing-leg trajectory for disturbance rejection (to maintain steady gait versus regulation of leg loading (for injury avoidance and economy. Here we investigate how running guinea fowl manage this potential trade-off by comparing experimental data to predictions of hypothesis-based simulations of running over a terrain drop perturbation. We use a simple model to predict swing-leg trajectory and running dynamics. In simulations, we generate optimized swing-leg trajectories based upon specific hypotheses for task-level control priorities. We optimized swing trajectories to achieve i constant peak force, ii constant axial impulse, or iii perfect disturbance rejection (steady gait in the stance following a terrain drop. We compare simulation predictions to experimental data on guinea fowl running over a visible step down. Swing and stance dynamics of running guinea fowl closely match simulations optimized to regulate leg loading (priorities i and ii, and do not match the simulations optimized for disturbance rejection (priority iii. The simulations reinforce previous findings that swing-leg trajectory targeting disturbance rejection demands large increases in stance leg force following a terrain drop. Guinea fowl negotiate a downward step using unsteady dynamics with forward acceleration, and recover to steady gait in subsequent steps. Our results suggest that guinea fowl use swing-leg trajectory consistent with priority for load regulation, and not for steadiness of gait

  11. Swing-Leg Trajectory of Running Guinea Fowl Suggests Task-Level Priority of Force Regulation Rather than Disturbance Rejection

    Science.gov (United States)

    Blum, Yvonne; Vejdani, Hamid R.; Birn-Jeffery, Aleksandra V.; Hubicki, Christian M.; Hurst, Jonathan W.; Daley, Monica A.

    2014-01-01

    To achieve robust and stable legged locomotion in uneven terrain, animals must effectively coordinate limb swing and stance phases, which involve distinct yet coupled dynamics. Recent theoretical studies have highlighted the critical influence of swing-leg trajectory on stability, disturbance rejection, leg loading and economy of walking and running. Yet, simulations suggest that not all these factors can be simultaneously optimized. A potential trade-off arises between the optimal swing-leg trajectory for disturbance rejection (to maintain steady gait) versus regulation of leg loading (for injury avoidance and economy). Here we investigate how running guinea fowl manage this potential trade-off by comparing experimental data to predictions of hypothesis-based simulations of running over a terrain drop perturbation. We use a simple model to predict swing-leg trajectory and running dynamics. In simulations, we generate optimized swing-leg trajectories based upon specific hypotheses for task-level control priorities. We optimized swing trajectories to achieve i) constant peak force, ii) constant axial impulse, or iii) perfect disturbance rejection (steady gait) in the stance following a terrain drop. We compare simulation predictions to experimental data on guinea fowl running over a visible step down. Swing and stance dynamics of running guinea fowl closely match simulations optimized to regulate leg loading (priorities i and ii), and do not match the simulations optimized for disturbance rejection (priority iii). The simulations reinforce previous findings that swing-leg trajectory targeting disturbance rejection demands large increases in stance leg force following a terrain drop. Guinea fowl negotiate a downward step using unsteady dynamics with forward acceleration, and recover to steady gait in subsequent steps. Our results suggest that guinea fowl use swing-leg trajectory consistent with priority for load regulation, and not for steadiness of gait. Swing

  12. Prediction of TF target sites based on atomistic models of protein-DNA complexes

    Directory of Open Access Journals (Sweden)

    Collado-Vides Julio

    2008-10-01

    Full Text Available Abstract Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition.

  13. Distance to Thrombus in Acute Middle Cerebral Artery Occlusion Predicts Target Mismatch and Ischemic Penumbra.

    Science.gov (United States)

    Gawlitza, Matthias; Friedrich, Benjamin; Hobohm, Carsten; Schaudinn, Alexander; Schob, Stefan; Quäschling, Ulf; Hoffmann, Karl-Titus; Lobsien, Donald

    2016-02-01

    In patients with occlusion of the middle cerebral artery (MCA) treated by intravenous thrombolysis (IVT), the distance to thrombus (DT) has been proposed as a predictor of outcome. The purpose of the present study was to investigate how DT relates to dynamic susceptibility contrast perfusion metrics. Retrospective analysis was undertaken of patients who were diagnosed with acute MCA occlusion by magnetic resonance imaging and treated with IVT. Volumes of time-to-maximum (Tmax) perfusion deficits and diffusion-weighted imaging (DWI) lesions, diffusion-perfusion mismatch volumes, and the presence of target mismatch were determined. Correlations between the above stoke measures and DT were then calculated. Fifty-five patients were included. DT showed significant inverse correlations with Tmax greater than 4, 6, 8, and 10 seconds, respectively, and mismatch volumes. Using the DT group median (14 mm) as a separator, significant intergroup differences were observed for Tmax greater than 4, 6, and 8 seconds, respectively, and for mismatch volumes. Grouping DT into quartiles showed significant intergroup differences regarding mismatch volumes and Tmax values greater than 4 and 6 seconds. Binary logistic regression identified DT (odds ratio [OR] = .89; 95% confidence interval [CI], .81-.99) and DWI lesion volumes (OR = .92; 95% CI, .86-.97) as independent predictors of target mismatch. A low DT predicted target mismatch with an area under the curve of .69. DT correlates inversely with Tmax perfusion deficits and mismatch volumes and acts as an independent predictor of target mismatch. Copyright © 2015 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  14. Noninvasive monitoring of cardiac allograft rejection by intramyocardial electrogram recordings.

    Science.gov (United States)

    Warnecke, H; Schüler, S; Goetze, H J; Matheis, G; Süthoff, U; Müller, J; Tietze, U; Hetzer, R

    1986-11-01

    Rejection after cardiac transplantation was monitored in nine patients by control of intramyocardial electrogram (IMEG) recordings transmitted by an implanted telemetric pacemaker. Under immunosuppression with cyclosporin A and prednisolone, 33 out of a total of 119 endomyocardial biopsy specimens showed moderate rejection (infiltrate with myocytolysis). Twenty-nine of these rejection episodes could be correctly predicted from IMEG recordings with a voltage drop above 15% used as a criterion (sensitivity 87.9%). Eighty-three of 86 negative biopsy results corresponded to negative IMEG results (specificity 96.5%). In this group of patients, amplitude of body surface electrocardiograms was not useful for the diagnosis of rejection because of the broad range of spontaneous variation. Control of IMEG voltage amplitude appears to be more accurate than body surface electrocardiogram amplitude in the detection of rejection episodes. Thus the onset of rejection during biopsy intervals is more readily detected and treatment is instituted earlier. The method is suitable for ambulatory patient monitoring by the patient's local physician.

  15. A Generic Multi-Compartmental CNS Distribution Model Structure for 9 Drugs Allows Prediction of Human Brain Target Site Concentrations

    NARCIS (Netherlands)

    Yamamoto, Yumi; Valitalo, Pyry A.; van den Berg, Dirk-Jan; Hartman, Robin; van den Brink, Willem; Wong, Yin Cheong; Huntjens, Dymphy R.; Proost, Johannes H.; Vermeulen, An; Krauwinkel, Walter; Bakshi, Suruchi; Aranzana-Climent, Vincent; Marchand, Sandrine; Dahyot-Fizelier, Claire; Couet, William; Danhof, Meindert; van Hasselt, Johan G. C.; de lange, Elizabeth C. M.

    Purpose Predicting target site drug concentration in the brain is of key importance for the successful development of drugs acting on the central nervous system. We propose a generic mathematical model to describe the pharmacokinetics in brain compartments, and apply this model to predict human

  16. Endothelial cell chimerism after renal transplantation and vascular rejection.

    NARCIS (Netherlands)

    Lagaaij, E.L.; Cramer-Knijnenburg, G.F.; Kemenade, F.J. van; Es, L.A. van; Bruijn, J.A.; Krieken, J.H.J.M. van

    2001-01-01

    BACKGROUND: The blood vessels of a transplanted organ are the interface between donor and recipient. The endothelium in the blood vessels is thought to be the major target for graft rejection. Endothelial cells of a transplanted organ are believed to remain of donor origin after transplantation. We

  17. Apoptotic tubular cell death during acute renal allograft rejection

    NARCIS (Netherlands)

    Wever, P. C.; Aten, J.; Rentenaar, R. J.; Hack, C. E.; Koopman, G.; Weening, J. J.; ten Berge, I. J.

    1998-01-01

    Tubular cells are important targets during acute renal allograft rejection and induction of apoptosis might be a mechanism of tubular cell destruction. Susceptibility to induction of apoptosis is regulated by the homologous Bcl-2 and Bax proteins. Expression of Bcl-2 and Bax is regulated by p53,

  18. A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction.

    Science.gov (United States)

    Öztürk, Hakime; Ozkirimli, Elif; Özgür, Arzucan

    2016-03-18

    Molecular structures can be represented as strings of special characters using SMILES. Since each molecule is represented as a string, the similarity between compounds can be computed using SMILES-based string similarity functions. Most previous studies on drug-target interaction prediction use 2D-based compound similarity kernels such as SIMCOMP. To the best of our knowledge, using SMILES-based similarity functions, which are computationally more efficient than the 2D-based kernels, has not been investigated for this task before. In this study, we adapt and evaluate various SMILES-based similarity methods for drug-target interaction prediction. In addition, inspired by the vector space model of Information Retrieval we propose cosine similarity based SMILES kernels that make use of the Term Frequency (TF) and Term Frequency-Inverse Document Frequency (TF-IDF) weighting approaches. We also investigate generating composite kernels by combining our best SMILES-based similarity functions with the SIMCOMP kernel. With this study, we provided a comparison of 13 different ligand similarity functions, each of which utilizes the SMILES string of molecule representation. Additionally, TF and TF-IDF based cosine similarity kernels are proposed. The more efficient SMILES-based similarity functions performed similarly to the more complex 2D-based SIMCOMP kernel in terms of AUC-ROC scores. The TF-IDF based cosine similarity obtained a better AUC-PR score than the SIMCOMP kernel on the GPCR benchmark data set. The composite kernel of TF-IDF based cosine similarity and SIMCOMP achieved the best AUC-PR scores for all data sets.

  19. Multi-Source Multi-Target Dictionary Learning for Prediction of Cognitive Decline.

    Science.gov (United States)

    Zhang, Jie; Li, Qingyang; Caselli, Richard J; Thompson, Paul M; Ye, Jieping; Wang, Yalin

    2017-06-01

    Alzheimer's Disease (AD) is the most common type of dementia. Identifying correct biomarkers may determine pre-symptomatic AD subjects and enable early intervention. Recently, Multi-task sparse feature learning has been successfully applied to many computer vision and biomedical informatics researches. It aims to improve the generalization performance by exploiting the shared features among different tasks. However, most of the existing algorithms are formulated as a supervised learning scheme. Its drawback is with either insufficient feature numbers or missing label information. To address these challenges, we formulate an unsupervised framework for multi-task sparse feature learning based on a novel dictionary learning algorithm. To solve the unsupervised learning problem, we propose a two-stage Multi-Source Multi-Target Dictionary Learning (MMDL) algorithm. In stage 1, we propose a multi-source dictionary learning method to utilize the common and individual sparse features in different time slots. In stage 2, supported by a rigorous theoretical analysis, we develop a multi-task learning method to solve the missing label problem. Empirical studies on an N = 3970 longitudinal brain image data set, which involves 2 sources and 5 targets, demonstrate the improved prediction accuracy and speed efficiency of MMDL in comparison with other state-of-the-art algorithms.

  20. Boolean network model for cancer pathways: predicting carcinogenesis and targeted therapy outcomes.

    Directory of Open Access Journals (Sweden)

    Herman F Fumiã

    Full Text Available A Boolean dynamical system integrating the main signaling pathways involved in cancer is constructed based on the currently known protein-protein interaction network. This system exhibits stationary protein activation patterns--attractors--dependent on the cell's microenvironment. These dynamical attractors were determined through simulations and their stabilities against mutations were tested. In a higher hierarchical level, it was possible to group the network attractors into distinct cell phenotypes and determine driver mutations that promote phenotypic transitions. We find that driver nodes are not necessarily central in the network topology, but at least they are direct regulators of central components towards which converge or through which crosstalk distinct cancer signaling pathways. The predicted drivers are in agreement with those pointed out by diverse census of cancer genes recently performed for several human cancers. Furthermore, our results demonstrate that cell phenotypes can evolve towards full malignancy through distinct sequences of accumulated mutations. In particular, the network model supports routes of carcinogenesis known for some tumor types. Finally, the Boolean network model is employed to evaluate the outcome of molecularly targeted cancer therapies. The major find is that monotherapies were additive in their effects and that the association of targeted drugs is necessary for cancer eradication.

  1. Smooth Pursuit Eye Movement Deficits in Patients With Whiplash and Neck Pain are Modulated by Target Predictability.

    Science.gov (United States)

    Janssen, Malou; Ischebeck, Britta K; de Vries, Jurryt; Kleinrensink, Gert-Jan; Frens, Maarten A; van der Geest, Jos N

    2015-10-01

    This is a cross-sectional study. The purpose of this study is to support and extend previous observations on oculomotor disturbances in patients with neck pain and whiplash-associated disorders (WADs) by systematically investigating the effect of static neck torsion on smooth pursuit in response to both predictably and unpredictably moving targets using video-oculography. Previous studies showed that in patients with neck complaints, for instance due to WAD, extreme static neck torsion deteriorates smooth pursuit eye movements in response to predictably moving targets compared with healthy controls. Eye movements in response to a smoothly moving target were recorded with video-oculography in a heterogeneous group of 55 patients with neck pain (including 11 patients with WAD) and 20 healthy controls. Smooth pursuit performance was determined while the trunk was fixed in 7 static rotations relative to the head (from 45° to the left to 45° to right), using both predictably and unpredictably moving stimuli. Patients had reduced smooth pursuit gains and smooth pursuit gain decreased due to neck torsion. Healthy controls showed higher gains for predictably moving targets compared with unpredictably moving targets, whereas patients with neck pain had similar gains in response to both types of target movements. In 11 patients with WAD, increased neck torsion decreased smooth pursuit performance, but only for predictably moving targets. Smooth pursuit of patients with neck pain is affected. The previously reported WAD-specific decline in smooth pursuit due to increased neck torsion seems to be modulated by the predictability of the movement of the target. The observed oculomotor disturbances in patients with WAD are therefore unlikely to be induced by impaired neck proprioception alone. 3.

  2. In Vitro Drug Sensitivity Tests to Predict Molecular Target Drug Responses in Surgically Resected Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Ryohei Miyazaki

    Full Text Available Epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs and anaplastic lymphoma kinase (ALK inhibitors have dramatically changed the strategy of medical treatment of lung cancer. Patients should be screened for the presence of the EGFR mutation or echinoderm microtubule-associated protein-like 4 (EML4-ALK fusion gene prior to chemotherapy to predict their clinical response. The succinate dehydrogenase inhibition (SDI test and collagen gel droplet embedded culture drug sensitivity test (CD-DST are established in vitro drug sensitivity tests, which may predict the sensitivity of patients to cytotoxic anticancer drugs. We applied in vitro drug sensitivity tests for cyclopedic prediction of clinical responses to different molecular targeting drugs.The growth inhibitory effects of erlotinib and crizotinib were confirmed for lung cancer cell lines using SDI and CD-DST. The sensitivity of 35 cases of surgically resected lung cancer to erlotinib was examined using SDI or CD-DST, and compared with EGFR mutation status.HCC827 (Exon19: E746-A750 del and H3122 (EML4-ALK cells were inhibited by lower concentrations of erlotinib and crizotinib, respectively than A549, H460, and H1975 (L858R+T790M cells were. The viability of the surgically resected lung cancer was 60.0 ± 9.8 and 86.8 ± 13.9% in EGFR-mutants vs. wild types in the SDI (p = 0.0003. The cell viability was 33.5 ± 21.2 and 79.0 ± 18.6% in EGFR mutants vs. wild-type cases (p = 0.026 in CD-DST.In vitro drug sensitivity evaluated by either SDI or CD-DST correlated with EGFR gene status. Therefore, SDI and CD-DST may be useful predictors of potential clinical responses to the molecular anticancer drugs, cyclopedically.

  3. A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information.

    Science.gov (United States)

    Luo, Yunan; Zhao, Xinbin; Zhou, Jingtian; Yang, Jinglin; Zhang, Yanqing; Kuang, Wenhua; Peng, Jian; Chen, Ligong; Zeng, Jianyang

    2017-09-18

    The emergence of large-scale genomic, chemical and pharmacological data provides new opportunities for drug discovery and repositioning. In this work, we develop a computational pipeline, called DTINet, to predict novel drug-target interactions from a constructed heterogeneous network, which integrates diverse drug-related information. DTINet focuses on learning a low-dimensional vector representation of features, which accurately explains the topological properties of individual nodes in the heterogeneous network, and then makes prediction based on these representations via a vector space projection scheme. DTINet achieves substantial performance improvement over other state-of-the-art methods for drug-target interaction prediction. Moreover, we experimentally validate the novel interactions between three drugs and the cyclooxygenase proteins predicted by DTINet, and demonstrate the new potential applications of these identified cyclooxygenase inhibitors in preventing inflammatory diseases. These results indicate that DTINet can provide a practically useful tool for integrating heterogeneous information to predict new drug-target interactions and repurpose existing drugs.Network-based data integration for drug-target prediction is a promising avenue for drug repositioning, but performance is wanting. Here, the authors introduce DTINet, whose performance is enhanced in the face of noisy, incomplete and high-dimensional biological data by learning low-dimensional vector representations.

  4. 7 CFR 58.136 - Rejected milk.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Rejected milk. 58.136 Section 58.136 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Milk § 58.136 Rejected milk. A plant shall reject specific milk from a producer if the milk fails to...

  5. Peer Group Rejection and Children's Outgroup Prejudice

    Science.gov (United States)

    Nesdale, Drew; Durkin, Kevin; Maass, Anne; Kiesner, Jeff; Griffiths, Judith; Daly, Josh; McKenzie, David

    2010-01-01

    Two simulation studies examined the effect of peer group rejection on 7 and 9 year old children's outgroup prejudice. In Study 1, children (n = 88) pretended that they were accepted or rejected by their assigned group, prior to competing with a lower status outgroup. Results indicated that rejected versus accepted children showed increased…

  6. On fiber rejection loss in flotation deinking

    Science.gov (United States)

    J.Y. Zhu; Freya Tan

    2005-04-01

    Reducing fiber rejection loss in flotation deinking is very important to conserve natural resources and reduce the cost of secondary fibers in paper recycling. This study examined two aspects of the problem, fiber consistency in the rejection stream and rate of Froth (or wet stream) rejection. Flotation experiments were conducted using both nylon and wood fibers in...

  7. Constructing a minority group identity out of shared rejection : The case of international students

    NARCIS (Netherlands)

    Schmitt, MT; Spears, R; Branscombe, NR

    2003-01-01

    With a sample of international students, we investigated how perceptions of rejection by the host community are related to a sense of identification with other international students. Based on the rejection-identification model (Branscombe, Schmitt, & Harvey, 1999) we predicted that perceiving

  8. Prediction of novel target genes and pathways involved in irinotecan-resistant colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Precious Takondwa Makondi

    Full Text Available Acquired drug resistance to the chemotherapeutic drug irinotecan (the active metabolite of which is SN-38 is one of the significant obstacles in the treatment of advanced colorectal cancer (CRC. The molecular mechanism or targets mediating irinotecan resistance are still unclear. It is urgent to find the irinotecan response biomarkers to improve CRC patients' therapy.Genetic Omnibus Database GSE42387 which contained the gene expression profiles of parental and irinotecan-resistant HCT-116 cell lines was used. Differentially expressed genes (DEGs between parental and irinotecan-resistant cells, protein-protein interactions (PPIs, gene ontologies (GOs and pathway analysis were performed to identify the overall biological changes. The most common DEGs in the PPIs, GOs and pathways were identified and were validated clinically by their ability to predict overall survival and disease free survival. The gene-gene expression correlation and gene-resistance correlation was also evaluated in CRC patients using The Cancer Genomic Atlas data (TCGA.The 135 DEGs were identified of which 36 were upregulated and 99 were down regulated. After mapping the PPI networks, the GOs and the pathways, nine genes (GNAS, PRKACB, MECOM, PLA2G4C, BMP6, BDNF, DLG4, FGF2 and FGF9 were found to be commonly enriched. Signal transduction was the most significant GO and MAPK pathway was the most significant pathway. The five genes (FGF2, FGF9, PRKACB, MECOM and PLA2G4C in the MAPK pathway were all contained in the signal transduction and the levels of those genes were upregulated. The FGF2, FGF9 and MECOM expression were highly associated with CRC patients' survival rate but not PRKACB and PLA2G4C. In addition, FGF9 was also associated with irinotecan resistance and poor disease free survival. FGF2, FGF9 and PRKACB were positively correlated with each other while MECOM correlated positively with FGF9 and PLA2G4C, and correlated negatively with FGF2 and PRKACB after doing gene

  9. Band rejection filter for measurement of electron cyclotron emission during electron cyclotron heating

    International Nuclear Information System (INIS)

    Iwase, Makoto; Ohkubo, Kunizo; Kubo, Shin; Idei, Hiroshi.

    1996-05-01

    For the measurement of electron cyclotron emission from the high temperature plasma, a band rejection filter in the range of 40-60 GHz is designed to reject the 53.2 GHz signal with large amplitude from the gyrotron for the purpose of plasma electron heating. The filter developed with ten sets of three quarters-wavelength coupled by TE 111 mode of tunable resonant cavity has rejection of 50 dB and 3 dB bandwidth of 500 MHz. The modified model of Tschebysheff type for the prediction of rejection is proposed. It is confirmed that the measured rejection as a function of frequency agrees well with the experimental results for small coupling hole, and also clarified that the rejection ratio increases for the large coupling hole. (author)

  10. Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics

    Directory of Open Access Journals (Sweden)

    Jaehee V. Shim

    2017-09-01

    Full Text Available Tyrosine kinase inhibitors (TKIs are highly potent cancer therapeutics that have been linked with serious cardiotoxicity, including left ventricular dysfunction, heart failure, and QT prolongation. TKI-induced cardiotoxicity is thought to result from interference with tyrosine kinase activity in cardiomyocytes, where these signaling pathways help to control critical processes such as survival signaling, energy homeostasis, and excitation–contraction coupling. However, mechanistic understanding is limited at present due to the complexities of tyrosine kinase signaling, and the wide range of targets inhibited by TKIs. Here, we review the use of TKIs in cancer and the cardiotoxicities that have been reported, discuss potential mechanisms underlying cardiotoxicity, and describe recent progress in achieving a more systematic understanding of cardiotoxicity via the use of mechanistic models. In particular, we argue that future advances are likely to be enabled by studies that combine large-scale experimental measurements with Quantitative Systems Pharmacology (QSP models describing biological mechanisms and dynamics. As such approaches have proven extremely valuable for understanding and predicting other drug toxicities, it is likely that QSP modeling can be successfully applied to cardiotoxicity induced by TKIs. We conclude by discussing a potential strategy for integrating genome-wide expression measurements with models, illustrate initial advances in applying this approach to cardiotoxicity, and describe challenges that must be overcome to truly develop a mechanistic and systematic understanding of cardiotoxicity caused by TKIs.

  11. DDR: Efficient computational method to predict drug–target interactions using graph mining and machine learning approaches

    KAUST Repository

    Olayan, Rawan S.

    2017-11-23

    Motivation Finding computationally drug-target interactions (DTIs) is a convenient strategy to identify new DTIs at low cost with reasonable accuracy. However, the current DTI prediction methods suffer the high false positive prediction rate. Results We developed DDR, a novel method that improves the DTI prediction accuracy. DDR is based on the use of a heterogeneous graph that contains known DTIs with multiple similarities between drugs and multiple similarities between target proteins. DDR applies non-linear similarity fusion method to combine different similarities. Before fusion, DDR performs a pre-processing step where a subset of similarities is selected in a heuristic process to obtain an optimized combination of similarities. Then, DDR applies a random forest model using different graph-based features extracted from the DTI heterogeneous graph. Using five repeats of 10-fold cross-validation, three testing setups, and the weighted average of area under the precision-recall curve (AUPR) scores, we show that DDR significantly reduces the AUPR score error relative to the next best start-of-the-art method for predicting DTIs by 34% when the drugs are new, by 23% when targets are new, and by 34% when the drugs and the targets are known but not all DTIs between them are not known. Using independent sources of evidence, we verify as correct 22 out of the top 25 DDR novel predictions. This suggests that DDR can be used as an efficient method to identify correct DTIs.

  12. Rejection index for pressure tubes

    International Nuclear Information System (INIS)

    Mitchell, A.B.; Meneley, D.

    1989-10-01

    The objective of the present study was to establish a set of criteria (or Rejection Index) which could be used to decide whether a zirconium-2 1/2 w/o niobium pressure tube in a CANDU reactor should be removed from service due to in-service degradation. A critique of key issues associated with establishing a realistic rejection index was prepared. Areas of uncertainty in available information were identified and recommendations for further analysis and laboratory testing made. A Rejection Index based on the following limits has been recommended: 1) Limits related to design intent and normal operation: any garter spring must remain within the tolerance band specified for its design location; the annulus gas system must normally be operated in a circulating mode with a procedure in place for purging to prevent accumulation of deuterium. It must remain sensitive to leaks into any part of the systems; and pressure tube dimensions and distortions must be limited to maintain the fuel channels within the original design intent; 2) Limits related to defect tolerance: adequate time margins between occurrence of a leaking crack and unstable failure must be demonstrated for all fuel channels; long lap-type flaws are unacceptable; crack-like defects of any size are unacceptable; and score marks, frat marks and other defects with contoured profiles must fall below certain depth, length and stress intensity limits; and 3) Limits related to property degradation: at operating temperature each pressure tube must be demonstrated to have a critical length in excess of a stipulated value; the maximum equivalent hydrogen level in any pressure tube should not exceed a limit which should be defined taking into account the known history of that tube; the maximum equivalent hydrogen level in any rolled joint should not exceed a limit which is presently recommended as 200 ppm equivalent hydrogen; and the maximum diametral creep strain should be limited to less than 5%

  13. Graft rejection by cytolytic T cells. Specificity of the effector mechanism in the rejection of allogeneic marrow

    International Nuclear Information System (INIS)

    Nakamura, H.; Gress, R.E.

    1990-01-01

    Cellular effector mechanisms of allograft rejection remain incompletely described. Characterizing the rejection of foreign-marrow allografts rather than solid-organ grafts has the advantage that the cellular composition of the marrow graft, as a single cell suspension, can be altered to include cellular components with differing antigen expression. Rejection of marrow grafts is sensitive to lethal doses of radiation in the mouse but resistant to sublethal levels of radiation. In an effort to identify cells mediating host resistance, lymphocytes were isolated and cloned from spleens of mice 7 days after sublethal TBI (650 cGy) and inoculation with allogeneic marrow. All clones isolated were cytolytic with specificity for MHC encoded gene products of the allogeneic marrow donor. When cloned cells were transferred in vivo into lethally irradiated (1025 cGy) recipients unable to reject allogeneic marrow, results utilizing splenic 125IUdR uptake indicated that these MHC-specific cytotoxic clones could suppress marrow proliferation. In order to characterize the effector mechanism and the ability of the clones to affect final engraftment, double donor chimeras were constructed so that 2 target cell populations differing at the MHC from each other and from the host were present in the same marrow allograft. Results directly demonstrated an ability of CTL of host MHC type to mediate graft rejection and characterized the effector mechanism as one with specificity for MHC gene products

  14. Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures.

    Science.gov (United States)

    Nithin, Chandran; Patwa, Nisha; Thomas, Amal; Bahadur, Ranjit Prasad; Basak, Jolly

    2015-06-12

    MicroRNAs (miRNAs) are endogenous, noncoding, short RNAs directly involved in regulating gene expression at the post-transcriptional level. In spite of immense importance, limited information of P. vulgaris miRNAs and their expression patterns prompted us to identify new miRNAs in P. vulgaris by computational methods. Besides conventional approaches, we have used the simple sequence repeat (SSR) signatures as one of the prediction parameter. Moreover, for all other parameters including normalized Shannon entropy, normalized base pairing index and normalized base-pair distance, instead of taking a fixed cut-off value, we have used 99% probability range derived from the available data. We have identified 208 mature miRNAs in P. vulgaris belonging to 118 families, of which 201 are novel. 97 of the predicted miRNAs in P. vulgaris were validated with the sequencing data obtained from the small RNA sequencing of P. vulgaris. Randomly selected predicted miRNAs were also validated using qRT-PCR. A total of 1305 target sequences were identified for 130 predicted miRNAs. Using 80% sequence identity cut-off, proteins coded by 563 targets were identified. The computational method developed in this study was also validated by predicting 229 miRNAs of A. thaliana and 462 miRNAs of G. max, of which 213 for A. thaliana and 397 for G. max are existing in miRBase 20. There is no universal SSR that is conserved among all precursors of Viridiplantae, but conserved SSR exists within a miRNA family and is used as a signature in our prediction method. Prediction of known miRNAs of A. thaliana and G. max validates the accuracy of our method. Our findings will contribute to the present knowledge of miRNAs and their targets in P. vulgaris. This computational method can be applied to any species of Viridiplantae for the successful prediction of miRNAs and their targets.

  15. Increase of peripheral Th17 lymphocytes during acute cellular rejection in liver transplant recipients.

    Science.gov (United States)

    Fan, Hua; Li, Li-Xin; Han, Dong-Dong; Kou, Jian-Tao; Li, Ping; He, Qiang

    2012-12-15

    Although many human inflammatory and autoimmune diseases were previously considered to be mediated by T helper type 1 (Th1) cells, the recently described Th17 cells play dominant roles in several of these diseases. We and others speculated that allograft rejection after organ transplantation may also involve Th17 cells. Episodes of acute rejection occur in 30% of liver transplants. This study aimed to determine the frequency of circulating Th17 cells in patients who had received liver transplants for benign end-stage liver disease and to identify any association between acute rejection episodes and levels of Th17 cells in the peripheral blood. A prospective study compared Th17 cells from 76 consecutive benign end-stage liver disease patients who had undergone orthotopic liver transplantation from 2007 to 2011 with those from 20 age-matched healthy individuals. Peripheral blood samples were collected at different time points within one year after transplant. Blood samples and liver biopsies were also collected at the diagnosis of acute rejection. Percentages of circulating CD4+IL-17+ cells were measured by flow cytometry. The transplant patients were classified into two groups: a rejection group consisting of 17 patients who had an episode of acute rejection, and a non-rejection group comprising the remaining 59 patients with no acute rejection episodes. Percentages of circulating Th17 cells were compared between the two groups and controls. The levels of circulating CD4+IL-17+ T cells in the rejection group were higher during acute rejection than those in the non-rejection group (2.56+/-0.43% versus 1.79+/-0.44%, Pblood was positively correlated with the rejection activity index (r=0.79, P=0.0002). Circulating Th17 cells may be useful as a surrogate marker for predicting acute rejection in liver transplant recipients.

  16. Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction

    Science.gov (United States)

    2012-01-01

    Background Previous studies have noted that drug targets appear to be associated with higher-degree or higher-centrality proteins in interaction networks. These studies explicitly or tacitly make choices of different source databases, data integration strategies, representation of proteins and complexes, and data reliability assumptions. Here we examined how the use of different data integration and representation techniques, or different notions of reliability, may affect the efficacy of degree and centrality as features in drug target prediction. Results Fifty percent of drug targets have a degree of less than nine, and ninety-five percent have a degree of less than ninety. We found that drug targets are over-represented in higher degree bins – this relationship is only seen for the consolidated interactome and it is not dependent on n-ary interaction data or its representation. Degree acts as a weak predictive feature for drug-target status and using more reliable subsets of the data does not increase this performance. However, performance does increase if only cancer-related drug targets are considered. We also note that a protein’s membership in pathway records can act as a predictive feature that is better than degree and that high-centrality may be an indicator of a drug that is more likely to be withdrawn. Conclusions These results show that protein interaction data integration and cleaning is an important consideration when incorporating network properties as predictive features for drug-target status. The provided scripts and data sets offer a starting point for further studies and cross-comparison of methods. PMID:23146171

  17. In-silico prediction of drug targets, biological activities, signal pathways and regulating networks of dioscin based on bioinformatics.

    Science.gov (United States)

    Yin, Lianhong; Zheng, Lingli; Xu, Lina; Dong, Deshi; Han, Xu; Qi, Yan; Zhao, Yanyan; Xu, Youwei; Peng, Jinyong

    2015-03-05

    Inverse docking technology has been a trend of drug discovery, and bioinformatics approaches have been used to predict target proteins, biological activities, signal pathways and molecular regulating networks affected by drugs for further pharmacodynamic and mechanism studies. In the present paper, inverse docking technology was applied to screen potential targets from potential drug target database (PDTD). Then, the corresponding gene information of the obtained drug-targets was applied to predict the related biological activities, signal pathways and processes networks of the compound by using MetaCore platform. After that, some most relevant regulating networks were considered, which included the nodes and relevant pathways of dioscin. 71 potential targets of dioscin from humans, 7 from rats and 8 from mice were screened, and the prediction results showed that the most likely targets of dioscin were cyclin A2, calmodulin, hemoglobin subunit beta, DNA topoisomerase I, DNA polymerase lambda, nitric oxide synthase and UDP-N-acetylhexosamine pyrophosphorylase, etc. Many diseases including experimental autoimmune encephalomyelitis of human, temporal lobe epilepsy of rat and ankylosing spondylitis of mouse, may be inhibited by dioscin through regulating immune response alternative complement pathway, G-protein signaling RhoB regulation pathway and immune response antiviral actions of interferons, etc. The most relevant networks (5 from human, 3 from rat and 5 from mouse) indicated that dioscin may be a TOP1 inhibitor, which can treat cancer though the cell cycle- transition and termination of DNA replication pathway. Dioscin can down regulate EGFR and EGF to inhibit cancer, and also has anti-inflammation activity by regulating JNK signaling pathway. The predictions of the possible targets, biological activities, signal pathways and relevant regulating networks of dioscin provide valuable information to guide further investigation of dioscin on pharmacodynamics and

  18. Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction

    Directory of Open Access Journals (Sweden)

    Mora Antonio

    2012-11-01

    Full Text Available Abstract Background Previous studies have noted that drug targets appear to be associated with higher-degree or higher-centrality proteins in interaction networks. These studies explicitly or tacitly make choices of different source databases, data integration strategies, representation of proteins and complexes, and data reliability assumptions. Here we examined how the use of different data integration and representation techniques, or different notions of reliability, may affect the efficacy of degree and centrality as features in drug target prediction. Results Fifty percent of drug targets have a degree of less than nine, and ninety-five percent have a degree of less than ninety. We found that drug targets are over-represented in higher degree bins – this relationship is only seen for the consolidated interactome and it is not dependent on n-ary interaction data or its representation. Degree acts as a weak predictive feature for drug-target status and using more reliable subsets of the data does not increase this performance. However, performance does increase if only cancer-related drug targets are considered. We also note that a protein’s membership in pathway records can act as a predictive feature that is better than degree and that high-centrality may be an indicator of a drug that is more likely to be withdrawn. Conclusions These results show that protein interaction data integration and cleaning is an important consideration when incorporating network properties as predictive features for drug-target status. The provided scripts and data sets offer a starting point for further studies and cross-comparison of methods.

  19. HuMiTar: A sequence-based method for prediction of human microRNA targets

    Directory of Open Access Journals (Sweden)

    Chen Ke

    2008-12-01

    Full Text Available Abstract Background MicroRNAs (miRs are small noncoding RNAs that bind to complementary/partially complementary sites in the 3' untranslated regions of target genes to regulate protein production of the target transcript and to induce mRNA degradation or mRNA cleavage. The ability to perform accurate, high-throughput identification of physiologically active miR targets would enable functional characterization of individual miRs. Current target prediction methods include traditional approaches that are based on specific base-pairing rules in the miR's seed region and implementation of cross-species conservation of the target site, and machine learning (ML methods that explore patterns that contrast true and false miR-mRNA duplexes. However, in the case of the traditional methods research shows that some seed region matches that are conserved are false positives and that some of the experimentally validated target sites are not conserved. Results We present HuMiTar, a computational method for identifying common targets of miRs, which is based on a scoring function that considers base-pairing for both seed and non-seed positions for human miR-mRNA duplexes. Our design shows that certain non-seed miR nucleotides, such as 14, 18, 13, 11, and 17, are characterized by a strong bias towards formation of Watson-Crick pairing. We contrasted HuMiTar with several representative competing methods on two sets of human miR targets and a set of ten glioblastoma oncogenes. Comparison with the two best performing traditional methods, PicTar and TargetScanS, and a representative ML method that considers the non-seed positions, NBmiRTar, shows that HuMiTar predictions include majority of the predictions of the other three methods. At the same time, the proposed method is also capable of finding more true positive targets as a trade-off for an increased number of predictions. Genome-wide predictions show that the proposed method is characterized by 1.99 signal

  20. Targeted intervention: Computational approaches to elucidate and predict relapse in alcoholism.

    Science.gov (United States)

    Heinz, Andreas; Deserno, Lorenz; Zimmermann, Ulrich S; Smolka, Michael N; Beck, Anne; Schlagenhauf, Florian

    2017-05-01

    Alcohol use disorder (AUD) and addiction in general is characterized by failures of choice resulting in repeated drug intake despite severe negative consequences. Behavioral change is hard to accomplish and relapse after detoxification is common and can be promoted by consumption of small amounts of alcohol as well as exposure to alcohol-associated cues or stress. While those environmental factors contributing to relapse have long been identified, the underlying psychological and neurobiological mechanism on which those factors act are to date incompletely understood. Based on the reinforcing effects of drugs of abuse, animal experiments showed that drug, cue and stress exposure affect Pavlovian and instrumental learning processes, which can increase salience of drug cues and promote habitual drug intake. In humans, computational approaches can help to quantify changes in key learning mechanisms during the development and maintenance of alcohol dependence, e.g. by using sequential decision making in combination with computational modeling to elucidate individual differences in model-free versus more complex, model-based learning strategies and their neurobiological correlates such as prediction error signaling in fronto-striatal circuits. Computational models can also help to explain how alcohol-associated cues trigger relapse: mechanisms such as Pavlovian-to-Instrumental Transfer can quantify to which degree Pavlovian conditioned stimuli can facilitate approach behavior including alcohol seeking and intake. By using generative models of behavioral and neural data, computational approaches can help to quantify individual differences in psychophysiological mechanisms that underlie the development and maintenance of AUD and thus promote targeted intervention. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Multi-target QSPR modeling for simultaneous prediction of multiple gas-phase kinetic rate constants of diverse chemicals

    Science.gov (United States)

    Basant, Nikita; Gupta, Shikha

    2018-03-01

    The reactions of molecular ozone (O3), hydroxyl (•OH) and nitrate (NO3) radicals are among the major pathways of removal of volatile organic compounds (VOCs) in the atmospheric environment. The gas-phase kinetic rate constants (kO3, kOH, kNO3) are thus, important in assessing the ultimate fate and exposure risk of atmospheric VOCs. Experimental data for rate constants are not available for many emerging VOCs and the computational methods reported so far address a single target modeling only. In this study, we have developed a multi-target (mt) QSPR model for simultaneous prediction of multiple kinetic rate constants (kO3, kOH, kNO3) of diverse organic chemicals considering an experimental data set of VOCs for which values of all the three rate constants are available. The mt-QSPR model identified and used five descriptors related to the molecular size, degree of saturation and electron density in a molecule, which were mechanistically interpretable. These descriptors successfully predicted three rate constants simultaneously. The model yielded high correlations (R2 = 0.874-0.924) between the experimental and simultaneously predicted endpoint rate constant (kO3, kOH, kNO3) values in test arrays for all the three systems. The model also passed all the stringent statistical validation tests for external predictivity. The proposed multi-target QSPR model can be successfully used for predicting reactivity of new VOCs simultaneously for their exposure risk assessment.

  2. Insights from computational modeling in inflammation and acute rejection in limb transplantation.

    Directory of Open Access Journals (Sweden)

    Dolores Wolfram

    Full Text Available Acute skin rejection in vascularized composite allotransplantation (VCA is the major obstacle for wider adoption in clinical practice. This study utilized computational modeling to identify biomarkers for diagnosis and targets for treatment of skin rejection. Protein levels of 14 inflammatory mediators in skin and muscle biopsies from syngeneic grafts [n = 10], allogeneic transplants without immunosuppression [n = 10] and allografts treated with tacrolimus [n = 10] were assessed by multiplexed analysis technology. Hierarchical Clustering Analysis, Principal Component Analysis, Random Forest Classification and Multinomial Logistic Regression models were used to segregate experimental groups. Based on Random Forest Classification, Multinomial Logistic Regression and Hierarchical Clustering Analysis models, IL-4, TNF-α and IL-12p70 were the best predictors of skin rejection and identified rejection well in advance of histopathological alterations. TNF-α and IL-12p70 were the best predictors of muscle rejection and also preceded histopathological alterations. Principal Component Analysis identified IL-1α, IL-18, IL-1β, and IL-4 as principal drivers of transplant rejection. Thus, inflammatory patterns associated with rejection are specific for the individual tissue and may be superior for early detection and targeted treatment of rejection.

  3. Modeling of RO/NF membrane rejections of PhACs and organic compounds: a statistical analysis

    Directory of Open Access Journals (Sweden)

    G. Amy

    2008-07-01

    Full Text Available Rejections of pharmaceutical compounds (Ibuprofen, Diclofenac, Clofibric acid, Naproxen, Primidone, Phenacetin and organic compounds (Dichloroacetic acid, Trichloroacetic acid, Chloroform, Bromoform, Trichloroethene, Perchloroethene, Carbontetrachloride, Carbontetrabromide by NF (Filmtec, Saehan and RO (Filmtec, Saehan, Toray, Koch membranes were studied. Chloroform presented the lowest rejection due to small molar volume, equivalent width and length. Diclofenac and Primidone showed high rejections related to high molar volume and length. Dichloroacetic acid and Trichloroacetic acid presented good rejections caused by charge exclusion instead of steric hindrance mechanism influencing rejection. Bromoform and Trichloroethene showed low rejections due to small length and equivalent width. Carbontetrabromide, Perchloroethene and Carbontetrachloride with higher equivalent width than BF and TCE presented better rejections. A qualitative analysis of variables using Principal Component Analysis was successfully implemented for reduction of physical-chemical compound properties that influence membrane rejection of PhACs and organic compounds. Properties such as dipole moment, molar volume, hydrophobicity/hydrophilicity, molecular length and equivalent width were found to be important descriptors for simulation of membrane rejection. For membranes used in the experiments, we may conclude that charge repulsion was an important mechanism of rejection for ionic compounds. After analysis with Multiple Linear Regression, we also may conclude that membrane rejection of neutral compounds was well predicted by molar volume, length, equivalent width, hydrophobicity/hydrophilicity and dipole moment. Molecular weight was a poor descriptor variable for rejection modelling. We were able to provide acceptable statistical significance for important results.

  4. A Predictive Model for Selective Targeting of the Warburg Effect through GAPDH Inhibition with a Natural Product.

    Science.gov (United States)

    Liberti, Maria V; Dai, Ziwei; Wardell, Suzanne E; Baccile, Joshua A; Liu, Xiaojing; Gao, Xia; Baldi, Robert; Mehrmohamadi, Mahya; Johnson, Marc O; Madhukar, Neel S; Shestov, Alexander A; Chio, Iok I Christine; Elemento, Olivier; Rathmell, Jeffrey C; Schroeder, Frank C; McDonnell, Donald P; Locasale, Jason W

    2017-10-03

    Targeted cancer therapies that use genetics are successful, but principles for selectively targeting tumor metabolism that is also dependent on the environment remain unknown. We now show that differences in rate-controlling enzymes during the Warburg effect (WE), the most prominent hallmark of cancer cell metabolism, can be used to predict a response to targeting glucose metabolism. We establish a natural product, koningic acid (KA), to be a selective inhibitor of GAPDH, an enzyme we characterize to have differential control properties over metabolism during the WE. With machine learning and integrated pharmacogenomics and metabolomics, we demonstrate that KA efficacy is not determined by the status of individual genes, but by the quantitative extent of the WE, leading to a therapeutic window in vivo. Thus, the basis of targeting the WE can be encoded by molecular principles that extend beyond the status of individual genes. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. LATE RENAL GRAFT REJECTION: PATHOLOGY AND PROGNOSIS

    Directory of Open Access Journals (Sweden)

    E.S. Stolyarevich

    2014-01-01

    Full Text Available Rejection has always been one of the most important cause of late renal graft dysfunction. Aim of the study was to analyze the prevalence of different clinico-pathological variants of rejection that cause late graft dysfunction, and evaluate their impact on long-term outcome. Materials and methods. This is a retrospective study that analyzed 294 needle core biopsy specimens from 265 renal transplant recipients with late (48,8 ± 46,1 months after transplantation allograft dysfunction caused by late acute rejection (LAR, n = 193 or chronic rejection (CR, n = 78 or both (n = 23. C4d staining was performed by immunofl uorescence (IF on frozen sections using a standard protocol. Results. Peritubular capillary C4d deposition was identifi ed in 36% samples with acute rejection and in 62% cases of chronic rejection (including 67% cases of transplant glomerulopathy, and 50% – of isolated chronic vasculopathy. 5-year graft survival for LAR vs CR vs their combination was 47, 13 and 25%, respectively. The outcome of C4d– LAR was (p < 0,01 better than of C4d+ acute rejection: at 60 months graft survival for diffuse C4d+ vs C4d− was 33% vs 53%, respectively. In cases of chronic rejection C4d+ vs C4d– it was not statistically signifi cant (34% vs 36%. Conclusion. In long-term allograft biopsy C4d positivity is more haracteristic for chronic rejection than for acute rejection. Only diffuse C4d staining affects the outcome. C4d– positivity is associated with worse allograft survival in cases of late acute rejection, but not in cases of chronic rejection

  6. Critical appraisal on the use of everolimus in renal transplantation as an immunosuppressant to prevent organ transplant rejection

    Directory of Open Access Journals (Sweden)

    Fernando Giron

    2010-01-01

    Full Text Available Fernando Giron, Yenny BaezKidney Transplant Service, Colombiana de Trasplantes, Bogota, ColombiaAbstract: Everolimus is a proliferation inhibitor designed to target chronic allograft nephropathy including prevention of acute rejection. Acute renal allograft rejection incidence varies with the therapy used for immunosuppression. Registry data show that 15% to 35% of kidney recipients will undergo treatment for at least one episode of acute rejection within the first post-transplant year. Everolimus has been used as therapy with full- or reduced-dose cyclosporine A without evidence of increasing the acute rejection incidence. This review will summarize the available clinical trial data on the use of everolimus and its role in preventing acute rejection incidence in renal transplantation.Keywords: calcineurin inhibitors, cyclosporine, everolimus, biopsy-proven acute rejection, renal transplantation, acute rejection

  7. Human amygdala engagement moderated by early life stress exposure is a biobehavioral target for predicting recovery on antidepressants.

    Science.gov (United States)

    Goldstein-Piekarski, Andrea N; Korgaonkar, Mayuresh S; Green, Erin; Suppes, Trisha; Schatzberg, Alan F; Hastie, Trevor; Nemeroff, Charles B; Williams, Leanne M

    2016-10-18

    Amygdala circuitry and early life stress (ELS) are both strongly and independently implicated in the neurobiology of depression. Importantly, animal models have revealed that the contribution of ELS to the development and maintenance of depression is likely a consequence of structural and physiological changes in amygdala circuitry in response to stress hormones. Despite these mechanistic foundations, amygdala engagement and ELS have not been investigated as biobehavioral targets for predicting functional remission in translational human studies of depression. Addressing this question, we integrated human neuroimaging and measurement of ELS within a controlled trial of antidepressant outcomes. Here we demonstrate that the interaction between amygdala activation engaged by emotional stimuli and ELS predicts functional remission on antidepressants with a greater than 80% cross-validated accuracy. Our model suggests that in depressed people with high ELS, the likelihood of remission is highest with greater amygdala reactivity to socially rewarding stimuli, whereas for those with low-ELS exposure, remission is associated with lower amygdala reactivity to both rewarding and threat-related stimuli. This full model predicted functional remission over and above the contribution of demographics, symptom severity, ELS, and amygdala reactivity alone. These findings identify a human target for elucidating the mechanisms of antidepressant functional remission and offer a target for developing novel therapeutics. The results also offer a proof-of-concept for using neuroimaging as a target for guiding neuroscience-informed intervention decisions at the level of the individual person.

  8. The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.

    Science.gov (United States)

    Indio, Valentina; Martelli, Pier Luigi; Savojardo, Castrense; Fariselli, Piero; Casadio, Rita

    2013-04-15

    Targeting peptides are the most important signal controlling the import of nuclear encoded proteins into mitochondria and plastids. In the lack of experimental information, their prediction is an essential step when proteomes are annotated for inferring both the localization and the sequence of mature proteins. We developed TPpred a new predictor of organelle-targeting peptides based on Grammatical-Restrained Hidden Conditional Random Fields. TPpred is trained on a non-redundant dataset of proteins where the presence of a target peptide was experimentally validated, comprising 297 sequences. When tested on the 297 positive and some other 8010 negative examples, TPpred outperformed available methods in both accuracy and Matthews correlation index (96% and 0.58, respectively). Given its very low-false-positive rate (3.0%), TPpred is, therefore, well suited for large-scale analyses at the proteome level. We predicted that from ∼4 to 9% of the sequences of human, Arabidopsis thaliana and yeast proteomes contain targeting peptides and are, therefore, likely to be localized in mitochondria and plastids. TPpred predictions correlate to a good extent with the experimental annotation of the subcellular localization, when available. TPpred was also trained and tested to predict the cleavage site of the organelle-targeting peptide: on this task, the average error of TPpred on mitochondrial and plastidic proteins is 7 and 15 residues, respectively. This value is lower than the error reported by other methods currently available. The TPpred datasets are available at http://biocomp.unibo.it/valentina/TPpred/. TPpred is available on request from the authors. Supplementary data are available at Bioinformatics online.

  9. Predicting success of oligomerized pool engineering (OPEN for zinc finger target site sequences

    Directory of Open Access Journals (Sweden)

    Goodwin Mathew J

    2010-11-01

    Full Text Available Abstract Background Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligomerized Pool ENgineering (OPEN is a recently developed method for engineering C2H2 zinc finger proteins (ZFPs designed to bind specific DNA sequences with high affinity and specificity in vivo. Because generation of ZFPs using OPEN requires considerable effort, a computational method for identifying the sites in any given gene that are most likely to be successfully targeted by this method is desirable. Results Analysis of the base composition of experimentally validated ZFP target sites identified important constraints on the DNA sequence space that can be effectively targeted using OPEN. Using alternate encodings to represent ZFP target sites, we implemented Naïve Bayes and Support Vector Machine classifiers capable of distinguishing "active" targets, i.e., ZFP binding sites that can be targeted with a high rate of success, from those that are "inactive" or poor targets for ZFPs generated using current OPEN technologies. When evaluated using leave-one-out cross-validation on a dataset of 135 experimentally validated ZFP target sites, the best Naïve Bayes classifier, designated ZiFOpT, achieved overall accuracy of 87% and specificity+ of 90%, with an ROC AUC of 0.89. When challenged with a completely independent test set of 140 newly validated ZFP target sites, ZiFOpT performance was comparable in terms of overall accuracy (88% and specificity+ (92%, but with reduced ROC AUC (0.77. Users can rank potentially active ZFP target sites using a confidence score derived from the posterior probability returned by ZiFOpT. Conclusion ZiFOpT, a machine learning classifier trained to identify DNA sequences amenable for targeting by OPEN-generated zinc finger arrays, can guide users to target sites that are most likely to function

  10. DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches.

    Science.gov (United States)

    Olayan, Rawan S; Ashoor, Haitham; Bajic, Vladimir B

    2018-04-01

    Finding computationally drug-target interactions (DTIs) is a convenient strategy to identify new DTIs at low cost with reasonable accuracy. However, the current DTI prediction methods suffer the high false positive prediction rate. We developed DDR, a novel method that improves the DTI prediction accuracy. DDR is based on the use of a heterogeneous graph that contains known DTIs with multiple similarities between drugs and multiple similarities between target proteins. DDR applies non-linear similarity fusion method to combine different similarities. Before fusion, DDR performs a pre-processing step where a subset of similarities is selected in a heuristic process to obtain an optimized combination of similarities. Then, DDR applies a random forest model using different graph-based features extracted from the DTI heterogeneous graph. Using 5-repeats of 10-fold cross-validation, three testing setups, and the weighted average of area under the precision-recall curve (AUPR) scores, we show that DDR significantly reduces the AUPR score error relative to the next best start-of-the-art method for predicting DTIs by 34% when the drugs are new, by 23% when targets are new and by 34% when the drugs and the targets are known but not all DTIs between them are not known. Using independent sources of evidence, we verify as correct 22 out of the top 25 DDR novel predictions. This suggests that DDR can be used as an efficient method to identify correct DTIs. The data and code are provided at https://bitbucket.org/RSO24/ddr/. vladimir.bajic@kaust.edu.sa. Supplementary data are available at Bioinformatics online.

  11. T2K Replica Target Hadron Production Measurements in NA61/SHINE and T2K Neutrino Flux Predictions

    CERN Document Server

    AUTHOR|(SzGeCERN)710687

    Accelerator based neutrino experiments generate their neutrino beams by impinging high energy protons on thick targets. The neutrino beam predictions are thus based on modeling the interactions of the beam protons inside the targets. Different hadronic models can be used with different accuracies depending on the energy range of the incident protons and on the target material. Nevertheless, none of the models can be seen as perfectly describing all different interactions. In order to reach high precision neutrino flux predictions, it is thus mandatory to be able to test and constrain the models with hadron production measurements. The T2K experiment in Japan uses the ancillary NA61/SHINE facility at CERN to constrain the production of hadrons resulting from the interactions of proton beam particles impinging on a 90cm long graphite target. Data taken by NA61/SHINE with a 30 GeV proton beam on a thin (4% interaction length) graphite target have been recorded in 2007 and 2009. They have been analysed and extens...

  12. Ensemble-sensitivity Analysis Based Observation Targeting for Mesoscale Convection Forecasts and Factors Influencing Observation-Impact Prediction

    Science.gov (United States)

    Hill, A.; Weiss, C.; Ancell, B. C.

    2017-12-01

    The basic premise of observation targeting is that additional observations, when gathered and assimilated with a numerical weather prediction (NWP) model, will produce a more accurate forecast related to a specific phenomenon. Ensemble-sensitivity analysis (ESA; Ancell and Hakim 2007; Torn and Hakim 2008) is a tool capable of accurately estimating the proper location of targeted observations in areas that have initial model uncertainty and large error growth, as well as predicting the reduction of forecast variance due to the assimilated observation. ESA relates an ensemble of NWP model forecasts, specifically an ensemble of scalar forecast metrics, linearly to earlier model states. A thorough investigation is presented to determine how different factors of the forecast process are impacting our ability to successfully target new observations for mesoscale convection forecasts. Our primary goals for this work are to determine: (1) If targeted observations hold more positive impact over non-targeted (i.e. randomly chosen) observations; (2) If there are lead-time constraints to targeting for convection; (3) How inflation, localization, and the assimilation filter influence impact prediction and realized results; (4) If there exist differences between targeted observations at the surface versus aloft; and (5) how physics errors and nonlinearity may augment observation impacts.Ten cases of dryline-initiated convection between 2011 to 2013 are simulated within a simplified OSSE framework and presented here. Ensemble simulations are produced from a cycling system that utilizes the Weather Research and Forecasting (WRF) model v3.8.1 within the Data Assimilation Research Testbed (DART). A "truth" (nature) simulation is produced by supplying a 3-km WRF run with GFS analyses and integrating the model forward 90 hours, from the beginning of ensemble initialization through the end of the forecast. Target locations for surface and radiosonde observations are computed 6, 12, and

  13. New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0.

    Science.gov (United States)

    Clark, Alex M; Sarker, Malabika; Ekins, Sean

    2014-01-01

    We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP_6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool.

  14. Identification of common blood gene signatures for the diagnosis of renal and cardiac acute allograft rejection.

    Directory of Open Access Journals (Sweden)

    Li Li

    Full Text Available To test, whether 10 genes, diagnostic of renal allograft rejection in blood, are able to diagnose and predict cardiac allograft rejection, we analyzed 250 blood samples from heart transplant recipients with and without acute rejection (AR and with cytomegalovirus (CMV infection by QPCR. A QPCR-based logistic regression model was built on 5 of these 10 genes (AR threshold composite score >37%  = AR and tested for AR prediction in an independent set of 109 samples, where it correctly diagnosed AR with 89% accuracy, with no misclassifications for AR ISHLT grade 1b. CMV infection did not confound the AR score. The genes correctly diagnosed AR in a blood sample within 6 months prior to biopsy diagnosis with 80% sensitivity and untreated grade 1b AR episodes had persistently elevated scores until 6 months after biopsy diagnosis. The gene score was also correlated with presence or absence of cardiac allograft vasculopathy (CAV irrespective of rejection grade. In conclusion, there is a common transcriptional axis of immunological trafficking in peripheral blood in both renal and cardiac organ transplant rejection, across a diverse recipient age range. A common gene signature, initially identified in the setting of renal transplant rejection, can be utilized serially after cardiac transplantation, to diagnose and predict biopsy confirmed acute heart transplant rejection.

  15. Social skills and perceived maternal acceptance-rejection in relation to depression in infertile women.

    Science.gov (United States)

    Yazdkhasti, Fariba

    2011-07-01

    This study examines the relationship between infertile women's social skills and their perception of their own mothers' acceptance or rejection, and the role this relationship plays in predicting self-reported depression. This was a correlational study. 60 infertile women aged 25 to 35 years participated in a self-evaluation. A Social Skills Inventory, Parental Acceptance and Rejection Questionnaire and Beck Depression Inventory were used to measure social skills, acceptance rejection and depression. Data was analyzed by SPSS software, using independent two-sample t test, logistic regression, and ANOVA. Findings showed that there are significant differences between depressed and not depressed infertile women in their perceptions of acceptance and rejection by their mothers. Further, women's perceptions of rejection are a more significant predictor of depression among less socially skilled infertile women than among those who are more socially skilled. Less socially skilled women did not show symptoms of depression when they experienced their mothers as accepting. In general the results of this study revealed that poorer social skills were more predictive of depression while good social skills moderate the effect of infertile women's perceptions of their mothers' rejection. At the same time, the findings showed that infertile women's perceptions of acceptance moderated the effects of poorer social skills in predicting depression. Results suggest that the perception of mothers' rejection and poor social skills are the key factors that make infertile women prone to depression.

  16. Multiple pathway assessment to predict anti-atherogenic efficacy of drugs targeting macrophages in atherosclerotic plaques

    NARCIS (Netherlands)

    Alaarg, Amr Muhmed Sabry Abdelhakeem; Zheng, K.H.; van der Valk, F.M.; Eduardo Da Silva, Acarilia; Versloot, M.; Quarles van Ufford, Linda C.; Schulte, D.M.; Storm, Gerrit; Metselaar, Josbert Maarten; Stroes, E.S.; Hamers, A.A.J.

    2016-01-01

    Background Macrophages play a central role in atherosclerosis development and progression, hence, targeting macrophage activity is considered an attractive therapeutic. Recently, we documented nanomedicinal delivery of the anti-inflammatory compound prednisolone to atherosclerotic plaque macrophages

  17. Prediction of position estimation errors for 3D target trajetories estimated from cone-beam CT projections

    DEFF Research Database (Denmark)

    Poulsen, Per Rugaard; Cho, Byungchul; Keall, Paul

    2010-01-01

    . The mathematical formalism of the method includes an individualized measure of the position estimation error in terms of an estimated 1D Gaussian distribution for the unresolved target position[2]. The present study investigates how well this 1D Gaussian predicts the actual distribution of position estimation...... errors. Over 5000 CBCT acquisitions were simulated from a 46-patient thoracic/abdominal and a 17-patient prostate tumor motion database. The 1D Gaussian predicted the actual root-mean-square and 95th percentile of the position estimation error with mean errors ≤0.04mm and maximum errors ≤0.48mm....... This finding indicates that individualized root-mean-square errors and 95% confidence intervals can be applied reliably to the estimated target trajectories....

  18. CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool.

    Directory of Open Access Journals (Sweden)

    Manuel Stemmer

    Full Text Available Engineering of the CRISPR/Cas9 system has opened a plethora of new opportunities for site-directed mutagenesis and targeted genome modification. Fundamental to this is a stretch of twenty nucleotides at the 5' end of a guide RNA that provides specificity to the bound Cas9 endonuclease. Since a sequence of twenty nucleotides can occur multiple times in a given genome and some mismatches seem to be accepted by the CRISPR/Cas9 complex, an efficient and reliable in silico selection and evaluation of the targeting site is key prerequisite for the experimental success. Here we present the CRISPR/Cas9 target online predictor (CCTop, http://crispr.cos.uni-heidelberg.de to overcome limitations of already available tools. CCTop provides an intuitive user interface with reasonable default parameters that can easily be tuned by the user. From a given query sequence, CCTop identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. CCTop was experimentally validated for gene inactivation, non-homologous end-joining as well as homology directed repair. Thus, CCTop provides the bench biologist with a tool for the rapid and efficient identification of high quality target sites.

  19. 21 CFR 1230.47 - Rejected containers.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Rejected containers. 1230.47 Section 1230.47 Food... FEDERAL CAUSTIC POISON ACT Imports § 1230.47 Rejected containers. (a) In all cases where the containers... notification to the importer that the containers must be exported under customs supervision within 3 months...

  20. A bedside technique for the diagnosis of acute rejection in renal transplants using 111-In platelets

    International Nuclear Information System (INIS)

    Chandler, S.T.; Buckels, J.A.C.; Drolc, Z.; Hawker, R.J.; Barnes, A.D.; McCollum, C.N.

    1982-01-01

    A total of 33 patients was studied with the aim of developing a bedside method for providing early diagnosis of acute rejection using 111-In labelled platelets. Platelet deposition was detected in all patients suffering acute rejection. A significant increase in kidney/aortic arch ratio, as measured by the portable bedside system, preceded the clinical diagnosis in 70% of patients. Using this system, it appeared possible not only to diagnose acute rejection at an earlier stage but also to predict irrecoverable transplant loss even in the presence of tubular necrosis. By labelling the platelets repeatedly for at least two weeks after transplantation, the period of highest risk for acute rejection and other complications. The gamma camera should still be employed in the event of markedly increased platelet deposition to differentiate between rejection and vascular complications

  1. Heightened male aggression toward sexualized women following romantic rejection: The mediating role of sex goal activation.

    Science.gov (United States)

    Blake, Khandis R; Bastian, Brock; Denson, Thomas F

    2018-01-01

    Research from a variety of disciplines suggests a positive relationship between Western cultural sexualization and women's likelihood of suffering harm. In the current experiment, 157 young men were romantically rejected by a sexualized or non-sexualized woman then given the opportunity to blast the woman with loud bursts of white noise. We tested whether the activation of sexual goals in men would mediate the relationship between sexualization and aggressive behavior after romantic rejection. We also tested whether behaving aggressively toward a woman after romantic rejection would increase men's feelings of sexual dominance. Results showed that interacting with a sexualized woman increased men's sex goals. Heightened sex goal activation, in turn, predicted increased aggression after romantic rejection. This result remained significant despite controlling for the effects of trait aggressiveness and negative affect. The findings suggest that heightened sex goal activation may lead men to perpetrate aggression against sexualized women who reject them. © 2017 Wiley Periodicals, Inc.

  2. The Search for Biosignatures on Mars: Using Predictive Geology to Optimize Exploration Targets

    Science.gov (United States)

    Oehler, Dorothy Z.; Allen, Carlton C.

    2011-01-01

    Predicting geologic context from satellite data is a method used on Earth for exploration in areas with limited ground truth. The method can be used to predict facies likely to contain organic-rich shales. Such shales concentrate and preserve organics and are major repositories of organic biosignatures on Earth [1]. Since current surface conditions on Mars are unfavorable for development of abundant life or for preservation of organic remains of past life, the chances are low of encountering organics in surface samples. Thus, focusing martian exploration on sites predicted to contain organic-rich shales would optimize the chances of discovering evidence of life, if it ever existed on that planet.

  3. MR imaging of renal transplant rejection

    International Nuclear Information System (INIS)

    Hanna, S.; Helenon, O.; Legendre, C.; Chichie, J.F.; Di Stefano, D.; Kreis, H.; Moreau, J.F.; Hopital Necker, 75 - Paris

    1991-01-01

    The results of 62 consecutive MR examinations were correlated with the subsequent clinical course and histologic results. Twenty-six cases of rejection showed a marked diminution of cortico-medullary differentiation (CMD). The renal parenchymal vascular pattern and visibility of renal sinus fat were not markedly altered in rejection and there was no difference between normal and rejected allograft shape. The ability of MR imaging to diagnose renal transplant rejection is only based on CMD, which, however, is non-specific. In 2 cases of severe rejection, T2 weighted images showed an abnormal signal intensity of the cortex due to renal infarction. Our preliminary results in 8 patients with Gd-DOTA injection showed 2 cases with necrosis seen as areas with absent contrast enhancement. This technique seems to be promising in the detection of perfusion defects. (orig.)

  4. Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors.

    Science.gov (United States)

    Mitra, A K; Mukherjee, U K; Harding, T; Jang, J S; Stessman, H; Li, Y; Abyzov, A; Jen, J; Kumar, S; Rajkumar, V; Van Ness, B

    2016-05-01

    Multiple myeloma (MM) is characterized by significant genetic diversity at subclonal levels that have a defining role in the heterogeneity of tumor progression, clinical aggressiveness and drug sensitivity. Although genome profiling studies have demonstrated heterogeneity in subclonal architecture that may ultimately lead to relapse, a gene expression-based prediction program that can identify, distinguish and quantify drug response in sub-populations within a bulk population of myeloma cells is lacking. In this study, we performed targeted transcriptome analysis on 528 pre-treatment single cells from 11 myeloma cell lines and 418 single cells from 8 drug-naïve MM patients, followed by intensive bioinformatics and statistical analysis for prediction of proteasome inhibitor sensitivity in individual cells. Using our previously reported drug response gene expression profile signature at the single-cell level, we developed an R Statistical analysis package available at https://github.com/bvnlabSCATTome, SCATTome (single-cell analysis of targeted transcriptome), that restructures the data obtained from Fluidigm single-cell quantitative real-time-PCR analysis run, filters missing data, performs scaling of filtered data, builds classification models and predicts drug response of individual cells based on targeted transcriptome using an assortment of machine learning methods. Application of SCATT should contribute to clinically relevant analysis of intratumor heterogeneity, and better inform drug choices based on subclonal cellular responses.

  5. Prediction of Bispectral Index during Target-controlled Infusion of Propofol and Remifentanil: A Deep Learning Approach.

    Science.gov (United States)

    Lee, Hyung-Chul; Ryu, Ho-Geol; Chung, Eun-Jin; Jung, Chul-Woo

    2018-03-01

    The discrepancy between predicted effect-site concentration and measured bispectral index is problematic during intravenous anesthesia with target-controlled infusion of propofol and remifentanil. We hypothesized that bispectral index during total intravenous anesthesia would be more accurately predicted by a deep learning approach. Long short-term memory and the feed-forward neural network were sequenced to simulate the pharmacokinetic and pharmacodynamic parts of an empirical model, respectively, to predict intraoperative bispectral index during combined use of propofol and remifentanil. Inputs of long short-term memory were infusion histories of propofol and remifentanil, which were retrieved from target-controlled infusion pumps for 1,800 s at 10-s intervals. Inputs of the feed-forward network were the outputs of long short-term memory and demographic data such as age, sex, weight, and height. The final output of the feed-forward network was the bispectral index. The performance of bispectral index prediction was compared between the deep learning model and previously reported response surface model. The model hyperparameters comprised 8 memory cells in the long short-term memory layer and 16 nodes in the hidden layer of the feed-forward network. The model training and testing were performed with separate data sets of 131 and 100 cases. The concordance correlation coefficient (95% CI) were 0.561 (0.560 to 0.562) in the deep learning model, which was significantly larger than that in the response surface model (0.265 [0.263 to 0.266], P < 0.001). The deep learning model-predicted bispectral index during target-controlled infusion of propofol and remifentanil more accurately compared to the traditional model. The deep learning approach in anesthetic pharmacology seems promising because of its excellent performance and extensibility.

  6. Effect of HMG-CoA reductase inhibitors on chronic allograft rejection.

    Science.gov (United States)

    Katznelson, S

    1999-07-01

    Although chronic rejection is the most important cause of late allograft loss, none of the currently available immunosuppressive agents successfully target this problem. Clinical and laboratory studies suggest that 3-hydroxy-3-methyl-glutaryl co-enzyme A (HMG-CoA) reductase inhibitors (HRIs) may decrease the incidence of and pathophysiologic factors leading to chronic rejection. A number of clinical and laboratory investigations have been designed to evaluate the effect of HRIs on chronic rejection. Clinical trials in heart transplant patients suggest that HRIs decrease the incidence of chronic rejection in a manner that may be independent of lipid lowering. Subsequent studies in animal transplant models confirm that HRIs reduce chronic rejection. In further studies to elucidate the possible mechanisms of this effect, it has been observed that HRIs have an inhibitory effect on an number of lymphoid cell lines and vascular smooth muscle cells. HRIs may also prevent chronic rejection by protecting the endothelium from injury and dysfunction, perhaps by up-regulating nitric oxide synthesis. HRIs may be the first agents to be effective in preventing chronic rejection. Although the mechanism behind this protective effect is unclear, it seems likely that HRIs may affect multiple factors that could lead to chronic rejection.

  7. Expression of Mitochondrial-Encoded Genes in Blood Differentiate Acute Renal Allograft Rejection

    Directory of Open Access Journals (Sweden)

    Silke Roedder

    2017-11-01

    Full Text Available Despite potent immunosuppression, clinical and biopsy confirmed acute renal allograft rejection (AR still occurs in 10–15% of recipients, ~30% of patients demonstrate subclinical rejection on biopsy, and ~50% of them can show molecular inflammation, all which increase the risk of chronic dysfunction and worsened allograft outcomes. Mitochondria represent intracellular endogenous triggers of inflammation, which can regulate immune cell differentiation, and expansion and cause antigen-independent graft injury, potentially enhancing the development of acute rejection. In the present study, we investigated the role of mitochondrial DNA encoded gene expression in biopsy matched peripheral blood (PB samples from kidney transplant recipients. Quantitative PCR was performed in 155 PB samples from 115 unique pediatric (<21 years and adult (>21 years renal allograft recipients at the point of AR (n = 61 and absence of rejection (n = 94 for the expression of 11 mitochondrial DNA encoded genes. We observed increased expression of all genes in adult recipients compared to pediatric recipients; separate analyses in both cohorts demonstrated increased expression during rejection, which also differentiated borderline rejection and showed an increasing pattern in serially collected samples (0–3 months prior to and post rejection. Our results provide new insights on the role of mitochondria during rejection and potentially indicate mitochondria as targets for novel immunosuppression.

  8. Targeted editing of goat genome with modular-assembly zinc finger nucleases based on activity prediction by computational molecular modeling.

    Science.gov (United States)

    Xiong, Kai; Li, Shanshan; Zhang, Hongxiao; Cui, Ye; Yu, Debing; Li, Yan; Sun, Wenxing; Fu, Yingying; Teng, Yun; Liu, Zhi; Zhou, Xiaolong; Xiao, Peng; Li, Juan; Liu, Honglin; Chen, Jie

    2013-07-01

    Zinc finger nuclease (ZFN) technology can mediate targeted genome modification to produce transgenic animals in a high-efficient and biological-safe way. Modular assembly is a rapid, convenient and open-source method for the synthesis of ZFNs. However, this biotechnology is hampered by multistep construction, low-efficiency editing and off-target cleavage. Here we synthesized and tested six pairs of three- or four-finger ZFNs to target one site in goat beta-lactoglobulin (BLG, a dominant allergen in goat milk) gene. Homology modeling was applied to build the structure model of ZFNs to predict their editing activities targeting at goat BLG gene. Goat fibroblast cells were transfected with plasmids that encoded ZFN pairs, and genomic DNA was isolated 72 h later for genome editing efficiency assay. The results of editing efficiency assay demonstrated that ZFNs with optimal interaction modes can edit goat BLG gene more efficiently, whereas ZFNs with unexpected interaction modes showed lower activities in editing BLG gene. We concluded that modular-assembly ZFNs can provide a rapid, public-available, and easy-to-practice platform for transgenic animal research and molecular modeling would help as a useful tool for ZFNs activity prediction.

  9. Image rejects/retakes--radiographic challenges.

    Science.gov (United States)

    Waaler, D; Hofmann, B

    2010-01-01

    A general held position among radiological personnel prior to digitalisation was that the problem of image rejects/retakes should more or less vanish. However, rejects/retakes still impose several challenges within radiographic imaging; they occupy unnecessary resources, expose patients to unnecessary ionizing radiation and may also indicate suboptimal quality management. The latter is the main objective of this paper, which is based on a survey of international papers published both for screen/film and digital technology. The digital revolution in imaging seems to have reduced the percentage of image rejects/retakes from 10-15 to 3-5 %. The major contribution to the decrease appears to be the dramatic reduction of incorrect exposures. At the same time, rejects/retakes due to lack of operator competence (positioning, etc.) are almost unchanged, or perhaps slightly increased (due to lack of proper technical competence, incorrect organ coding, etc.). However, the causes of rejects/retakes are in many cases defined and reported with reference to radiographers' subjective evaluations. Thus, unless radiographers share common views on image quality and acceptance criteria, objective measurements and assessments of reject/retake rates are challenging tasks. Interestingly, none of the investigated papers employs image quality parameters such as 'too much noise' as categories for rejects/retakes. Surprisingly, no reject/retake analysis seems yet to have been conducted for direct digital radiography departments. An increased percentage of rejects/retakes is related to 'digital skills' of radiographers and therefore points to areas for extended education and training. Furthermore, there is a need to investigate the inter-subjectivity of radiographers' perception of, and attitude towards, both technical and clinical image quality criteria. Finally, there may be a need to validate whether reject/retake rate analysis is such an effective quality indicator as has been asserted.

  10. Image rejects/retakes-radiographic challenges

    International Nuclear Information System (INIS)

    Waaler, D.; Hofmann, B.

    2010-01-01

    A general held position among radiological personnel prior to digitalisation was that the problem of image rejects/retakes should more or less vanish. However, rejects/retakes still impose several challenges within radiographic imaging; they occupy unnecessary resources, expose patients to unnecessary ionizing radiation and may also indicate suboptimal quality management. The latter is the main objective of this paper, which is based on a survey of international papers published both for screen/film and digital technology. The digital revolution in imaging seems to have reduced the percentage of image rejects/retakes from 10-15 to 3-5%. The major contribution to the decrease appears to be the dramatic reduction of incorrect exposures. At the same time, rejects/retakes due to lack of operator competence (positioning, etc.) are almost unchanged, or perhaps slightly increased (due to lack of proper technical competence, incorrect organ coding, etc.). However, the causes of rejects/retakes are in many cases defined and reported with reference to radiographers' subjective evaluations. Thus, unless radiographers share common views on image quality and acceptance criteria, objective measurements and assessments of reject/retake rates are challenging tasks. Interestingly, none of the investigated papers employs image quality parameters such as 'too much noise' as categories for rejects/retakes. Surprisingly, no reject/retake analysis seems yet to have been conducted for direct digital radiography departments. An increased percentage of rejects/retakes is related to 'digital skills' of radiographers and therefore points to areas for extended education and training. Furthermore, there is a need to investigate the inter subjectivity of radiographers' perception of, and attitude towards, both technical and clinical image quality criteria. Finally, there may be a need to validate whether reject/retake rate analysis is such an effective quality indicator as has been asserted

  11. Molecular Imaging to Predict Response to Targeted Therapies in Renal Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Ingrid Leguerney

    2017-01-01

    Full Text Available Molecular magnetic resonance imaging targeted to an endothelial integrin involved in neoangiogenesis was compared to DCE-US and immunochemistry to assess the early response of three different therapeutic agents in renal cell carcinoma. Human A498 renal cells carcinoma was subcutaneously inoculated into 24 nude mice. Mice received either phosphate-buffered saline solution, sunitinib, everolimus, or bevacizumab during 4 days. DCE-US and molecular MRI targeting αvβ3 were performed at baseline and 4 days after treatment initiation. PI, AUC, relaxation rate variations ΔR2⁎, and percentage of vessels area quantified on CD31-stained microvessels were compared. Significant decreases were observed for PI and AUC parameters measured by DCE-US for bevacizumab group as early as 4 days, whereas molecular αvβ3-targeted MRI was able to detect significant changes in both bevacizumab and everolimus groups. Percentage of CD31-stained microvessels was significantly correlated with DCE-US parameters, PI (R=0.87, p=0.0003 and AUC (R=0.81, p=0.0013. The percentage of vessel tissue area was significantly reduced (p<0.01 in both sunitinib and bevacizumab groups. We report an early detection of neoangiogenesis modification after induction of targeted therapies, using DCE-US or αvβ3-targeted MRI. We consider these outcomes should encourage clinical trial developments to further evaluate the potential of this molecular MRI technique.

  12. A NETWORK-BASED APPROACH FOR PREDICTING HSP27 KNOCK-OUT TARGETS IN MOUSE SKELETAL MUSCLES

    Directory of Open Access Journals (Sweden)

    Malek Kammoun

    2013-03-01

    Full Text Available Thanks to genomics, we have previously identified markers of beef tenderness, and computed a bioinformatic analysis that enabled us to build an interactome in which we found Hsp27 at a crucial node. Here, we have used a network-based approach for understanding the contribution of Hsp27 to tenderness through the prediction of its interactors related to tenderness. We have revealed the direct interactors of Hsp27. The predicted partners of Hsp27 included proteins involved in different functions, e.g. members of Hsp families (Hsp20, Cryab, Hsp70a1a, and Hsp90aa1, regulators of apoptosis (Fas, Chuk, and caspase-3, translation factors (Eif4E, and Eif4G1, cytoskeletal proteins (Desmin and antioxidants (Sod1. The abundances of 15 proteins were quantified by Western blotting in two muscles of HspB1-null mice and their controls. We observed changes in the amount of most of the Hsp27 predicted targets in mice devoid of Hsp27 mainly in the most oxidative muscle. Our study demonstrates the functional links between Hsp27 and its predicted targets. It suggests that Hsp status, apoptotic processes and protection against oxidative stress are crucial for post-mortem muscle metabolism, subsequent proteolysis, and therefore for beef tenderness.

  13. Role of Soluble ST2 as a Marker for Rejection after Heart Transplant.

    Science.gov (United States)

    Lee, Ga Yeon; Choi, Jin-Oh; Ju, Eun-Seon; Lee, Yoo-Jung; Jeon, Eun-Seok

    2016-11-01

    Endomyocardial biopsy is obligatory during the first year after heart transplant (HTx) for the surveillance of acute rejection. Previous attempts using cardiac biomarkers for the detection of rejection failed to show enough evidence to substitute endomyocardial biopsy. Therefore, this study sought the possibility of using soluble ST2 (sST2), a novel cardiovascular marker, as a surrogate marker for acute allograft rejection after HTx. A total of 494 blood samples acquired at the time of endomyocardial biopsy were analyzed in 67 HTx cases from September 2006 to August 2014. Significant rejection was defined as International Society of Heart and Lung Transplant (ISHLT) score ≥2R and humoral rejection accompanied by hemodynamic instability. Twenty cases of HTx with 22 blood samples showed significant rejection in endomyocardial biopsy at 4.0 (2.0-9.0) months after HTx. The level of sST2 showed positive correlation with cardiac troponin I, and N-terminal pro-B-type natriuretic peptide (all prejection) (p=0.003). However, when we studied within-subject effects of sST2 using a mixed model, the sST2 level according to the predefined time point was not different according to the presence of significant rejection (p for interaction=0.94). Although sST2 is known as a promising predictor for cardiovascular events, its role in HTx patients to predict acute allograft rejection seems to be limited.

  14. Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity.

    Science.gov (United States)

    Penrod, Nadia M; Greene, Casey S; Moore, Jason H

    2014-01-01

    Molecularly targeted drugs promise a safer and more effective treatment modality than conventional chemotherapy for cancer patients. However, tumors are dynamic systems that readily adapt to these agents activating alternative survival pathways as they evolve resistant phenotypes. Combination therapies can overcome resistance but finding the optimal combinations efficiently presents a formidable challenge. Here we introduce a new paradigm for the design of combination therapy treatment strategies that exploits the tumor adaptive process to identify context-dependent essential genes as druggable targets. We have developed a framework to mine high-throughput transcriptomic data, based on differential coexpression and Pareto optimization, to investigate drug-induced tumor adaptation. We use this approach to identify tumor-essential genes as druggable candidates. We apply our method to a set of ER(+) breast tumor samples, collected before (n = 58) and after (n = 60) neoadjuvant treatment with the aromatase inhibitor letrozole, to prioritize genes as targets for combination therapy with letrozole treatment. We validate letrozole-induced tumor adaptation through coexpression and pathway analyses in an independent data set (n = 18). We find pervasive differential coexpression between the untreated and letrozole-treated tumor samples as evidence of letrozole-induced tumor adaptation. Based on patterns of coexpression, we identify ten genes as potential candidates for combination therapy with letrozole including EPCAM, a letrozole-induced essential gene and a target to which drugs have already been developed as cancer therapeutics. Through replication, we validate six letrozole-induced coexpression relationships and confirm the epithelial-to-mesenchymal transition as a process that is upregulated in the residual tumor samples following letrozole treatment. To derive the greatest benefit from molecularly targeted drugs it is critical to design combination

  15. Perceived childhood paternal acceptance-rejection among adults

    International Nuclear Information System (INIS)

    Hussain, S.; Alvi, T.; Zeeshan, A.; Nadeem, S.

    2013-01-01

    Objective: To determine the childhood perceptual difference of paternal acceptance-rejection between those having psychological disorders and non-clinical population during adulthood. Study Design: Comparative study. Place and Duration of Study: Karwan-e-Hayat, Psychiatric Care and Rehabilitation Centre, Keamari, Karachi, Pakistan, from January to August 2011. Methodology: To test our hypotheses, 69 participants were selected from Karwan-e-Hayat Psychiatric Care and Rehabilitation Centre, Karachi on the basis of purposive sampling technique and 79 from Karachi city on the basis of convenient sampling technique. To measure their perceived paternal acceptance-rejection during childhood, Adult Parental acceptance-rejection questionnaire (PARQ)/control: father-short form (Urdu translation) was administered. The statistical analysis of data was done with the predictive analytics software (PASW). Results: One hundred and forty eight (78 males and 70 females) participants with mean age of 31.28 +- 9.54 years were included. Out of them 69 (40 males and 29 females) were clinical cases of depression, mania and psychosis with mean age of 33.26 +- 9.51 years. Seventy nine (38 males and 41 females) were normal individuals with mean age of 29.54 +- 9.29 years of the demographics corresponding to the clinical population. Independent t-test revealed a significant difference in perceived childhood father acceptance-rejection between clinical and non-clinical population (p < 0.05) and significant gender difference (p < 0.05). Conclusion: The studied clinical population and male participants perceived to be more rejected by their father during their childhood than non-clinical population and female participants. (author)

  16. Radiographic rejection index using statistical process control

    International Nuclear Information System (INIS)

    Savi, M.B.M.B.; Camozzato, T.S.C.; Soares, F.A.P.; Nandi, D.M.

    2015-01-01

    The Repeat Analysis Index (IRR) is one of the items contained in the Quality Control Program dictated by brazilian law of radiological protection and should be performed frequently, at least every six months. In order to extract more and better information of IRR, this study presents the Statistical Quality Control applied to reject rate through Statistical Process Control (Control Chart for Attributes ρ - GC) and the Pareto Chart (GP). Data collection was performed for 9 months and the last four months of collection was given on a daily basis. The Limits of Control (LC) were established and Minitab 16 software used to create the charts. IRR obtained for the period was corresponding to 8.8% ± 2,3% and the generated charts analyzed. Relevant information such as orders for X-ray equipment and processors were crossed to identify the relationship between the points that exceeded the control limits and the state of equipment at the time. The GC demonstrated ability to predict equipment failures, as well as the GP showed clearly what causes are recurrent in IRR. (authors) [pt

  17. Bayesian Nonparametric Estimation of Targeted Agent Effects on Biomarker Change to Predict Clinical Outcome

    Science.gov (United States)

    Graziani, Rebecca; Guindani, Michele; Thall, Peter F.

    2015-01-01

    Summary The effect of a targeted agent on a cancer patient's clinical outcome putatively is mediated through the agent's effect on one or more early biological events. This is motivated by pre-clinical experiments with cells or animals that identify such events, represented by binary or quantitative biomarkers. When evaluating targeted agents in humans, central questions are whether the distribution of a targeted biomarker changes following treatment, the nature and magnitude of this change, and whether it is associated with clinical outcome. Major difficulties in estimating these effects are that a biomarker's distribution may be complex, vary substantially between patients, and have complicated relationships with clinical outcomes. We present a probabilistically coherent framework for modeling and estimation in this setting, including a hierarchical Bayesian nonparametric mixture model for biomarkers that we use to define a functional profile of pre-versus-post treatment biomarker distribution change. The functional is similar to the receiver operating characteristic used in diagnostic testing. The hierarchical model yields clusters of individual patient biomarker profile functionals, and we use the profile as a covariate in a regression model for clinical outcome. The methodology is illustrated by analysis of a dataset from a clinical trial in prostate cancer using imatinib to target platelet-derived growth factor, with the clinical aim to improve progression-free survival time. PMID:25319212

  18. A linear perturbation computation method applied to hydrodynamic instability growth predictions in ICF targets

    International Nuclear Information System (INIS)

    Clarisse, J.M.; Boudesocque-Dubois, C.; Leidinger, J.P.; Willien, J.L.

    2006-01-01

    A linear perturbation computation method is used to compute hydrodynamic instability growth in model implosions of inertial confinement fusion direct-drive and indirect-drive designed targets. Accurate descriptions of linear perturbation evolutions for Legendre mode numbers up to several hundreds have thus been obtained in a systematic way, motivating further improvements of the physical modeling currently handled by the method. (authors)

  19. How Do Discrepancies between Victimization and Rejection Expectations in Gay and Bisexual Men Relate to Mental Health Problems?

    Science.gov (United States)

    Sattler, Frank A; Christiansen, Hanna

    2017-01-01

    Introduction: Victimization and rejection expectations predict mental health problems in gay and bisexual men. Furthermore, it was shown that victimization predicts rejection expectations. Nevertheless, the levels of these two variables do not necessarily correspond as indicated by low inter-correlations, resulting in the question "How do discrepancies in the two variables relate to mental health problems?" This study tests if non-corresponding levels of victimization and rejection expectations in gay and bisexual men relate to mental health problems differently than corresponding levels of victimization and rejection expectations. It furthermore tests for linear and curvilinear relationships between victimization, rejection expectations, and mental health problems. Methods: Data from N = 1423 gay and bisexual men were obtained online. Victimization and rejection expectations were tested for discrepant values (differing 0.5 SD or more) and those that were in agreement (differing less than 0.5): 33.7% of participants were in agreement, 33.0% reported higher rejection expectations than victimization, and 33.3% v.v. Then, a polynomial regression and a surface analysis were conducted. Results: Discrepant values in victimization and rejection expectations or the direction of the discrepancy did not relevantly predict mental health problems. Findings indicate that victimization and rejection expectations predict mental health problems linearly as well as convexly (upward curving) in gay and bisexual men. Discussion: This study replicates findings that gay and bisexual men with more experiences of victimization and rejection expectations demonstrated more mental health problems. Furthermore, this study is the first one to find a convex relationship between these predictors and mental health problems, implicating that disproportionally high mental health problems exist in those gay and bisexual men with high levels of victimization and rejection expectations. On the other

  20. ERROR VS REJECTION CURVE FOR THE PERCEPTRON

    OpenAIRE

    PARRONDO, JMR; VAN DEN BROECK, Christian

    1993-01-01

    We calculate the generalization error epsilon for a perceptron J, trained by a teacher perceptron T, on input patterns S that form a fixed angle arccos (J.S) with the student. We show that the error is reduced from a power law to an exponentially fast decay by rejecting input patterns that lie within a given neighbourhood of the decision boundary J.S = 0. On the other hand, the error vs. rejection curve epsilon(rho), where rho is the fraction of rejected patterns, is shown to be independent ...

  1. Prediction of pesticide acute toxicity using two-dimensional chemical descriptors and target species classification

    Science.gov (United States)

    Previous modelling of the median lethal dose (oral rat LD50) has indicated that local class-based models yield better correlations than global models. We evaluated the hypothesis that dividing the dataset by pesticidal mechanisms would improve prediction accuracy. A linear discri...

  2. Targeting chronic illness together. Health plans support providers through predictive analytics.

    Science.gov (United States)

    Raths, David

    2012-05-01

    Health insurers that used to focus on individual claims are now looking across their entire membership to better define the appropriate level of financial risk to assign and to drive the right kinds of interventions. Many are making a determined effort to share their predictive analytics findings with clinicians.

  3. Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef.

    Directory of Open Access Journals (Sweden)

    Mahdi Sarmady

    Full Text Available Virus proteins alter protein pathways of the host toward the synthesis of viral particles by breaking and making edges via binding to host proteins. In this study, we developed a computational approach to predict viral sequence hotspots for binding to host proteins based on sequences of viral and host proteins and literature-curated virus-host protein interactome data. We use a motif discovery algorithm repeatedly on collections of sequences of viral proteins and immediate binding partners of their host targets and choose only those motifs that are conserved on viral sequences and highly statistically enriched among binding partners of virus protein targeted host proteins. Our results match experimental data on binding sites of Nef to host proteins such as MAPK1, VAV1, LCK, HCK, HLA-A, CD4, FYN, and GNB2L1 with high statistical significance but is a poor predictor of Nef binding sites on highly flexible, hoop-like regions. Predicted hotspots recapture CD8 cell epitopes of HIV Nef highlighting their importance in modulating virus-host interactions. Host proteins potentially targeted or outcompeted by Nef appear crowding the T cell receptor, natural killer cell mediated cytotoxicity, and neurotrophin signaling pathways. Scanning of HIV Nef motifs on multiple alignments of hepatitis C protein NS5A produces results consistent with literature, indicating the potential value of the hotspot discovery in advancing our understanding of virus-host crosstalk.

  4. sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization.

    Directory of Open Access Journals (Sweden)

    Xiaomin Ying

    Full Text Available BACKGROUND: Bacterial sRNAs are a class of small regulatory RNAs involved in regulation of expression of a variety of genes. Most sRNAs act in trans via base-pairing with target mRNAs, leading to repression or activation of translation or mRNA degradation. To date, more than 1,000 sRNAs have been identified. However, direct targets have been identified for only approximately 50 of these sRNAs. Computational predictions can provide candidates for target validation, thereby increasing the speed of sRNA target identification. Although several methods have been developed, target prediction for bacterial sRNAs remains challenging. RESULTS: Here, we propose a novel method for sRNA target prediction, termed sTarPicker, which was based on a two-step model for hybridization between an sRNA and an mRNA target. This method first selects stable duplexes after screening all possible duplexes between the sRNA and the potential mRNA target. Next, hybridization between the sRNA and the target is extended to span the entire binding site. Finally, quantitative predictions are produced with an ensemble classifier generated using machine-learning methods. In calculations to determine the hybridization energies of seed regions and binding regions, both thermodynamic stability and site accessibility of the sRNAs and targets were considered. Comparisons with the existing methods showed that sTarPicker performed best in both performance of target prediction and accuracy of the predicted binding sites. CONCLUSIONS: sTarPicker can predict bacterial sRNA targets with higher efficiency and determine the exact locations of the interactions with a higher accuracy than competing programs. sTarPicker is available at http://ccb.bmi.ac.cn/starpicker/.

  5. GLRS-R 2-colour retroreflector target design and predicted performance

    Science.gov (United States)

    Lund, Glenn

    1993-01-01

    This paper reports on the retroreflector ground-target design for the GLRS-R spaceborne dual-wavelength laser ranging system. The described passive design flows down from the requirements of high station autonomy, high global FOV (up to 60 degrees zenith angle), little or no multiple pulse returns, and adequate optical cross section for most ranging geometries. The proposed solution makes use of 5 hollow cube-corner retroreflectors of which one points to the zenith and the remaining four are inclined from the vertical at uniform azimuthal spacings. The need for fairly large (is approximately 10 cm) retroreflectors is expected (within turbulence limitations) to generate quite narrow diffraction lobes, thus placing non-trivial requirements on the vectorial accuracy of velocity aberration corrections. A good compromise solution is found by appropriately spoiling just one of the retroreflector dihedral angles from 90 degrees, thus generating two symmetrically oriented diffraction lobes in the return beam. The required spoil angles are found to have little dependence on ground target latitude. Various link budget analyses are presented, showing the influence of such factors as point-ahead optimization, turbulence, ranging angle, atmospheric visibility and ground target thermal deformations.

  6. Rejection sensitivity and symptom severity in patients with borderline personality disorder: effects of childhood maltreatment and self-esteem.

    Science.gov (United States)

    Bungert, Melanie; Liebke, Lisa; Thome, Janine; Haeussler, Katrin; Bohus, Martin; Lis, Stefanie

    2015-01-01

    Interpersonal dysfunction in Borderline Personality Disorder (BPD) is characterized by an 'anxious preoccupation with real or imagined abandonment' (DSM-5). This symptom description bears a close resemblance to that of rejection sensitivity, a cognitive affective disposition that affects perceptions, emotions and behavior in the context of social rejection. The present study investigates the level of rejection sensitivity in acute and remitted BPD patients and its relation to BPD symptom severity, childhood maltreatment, and self-esteem. Data were obtained from 167 female subjects: 77 with acute BPD, 15 with remitted BPD, and 75 healthy controls who were matched with the patients for age and education. The instruments used for assessment were the Rejection Sensitivity Questionnaire, the short version of the Borderline Symptom List, the Childhood Trauma Questionnaire, and the Rosenberg Self-Esteem Scale. Both acute and remitted BPD patients had higher scores on the Rejection Sensitivity Questionnaire than did healthy controls. Lower self-esteem was found to be positively correlated with both increased BPD symptom severity and higher rejection sensitivity, and mediated the relation between the two. History of childhood maltreatment did not correlate with rejection sensitivity, BPD symptom severity, or self-esteem. Our findings support the hypothesis that rejection sensitivity is an important component in BPD, even for remitted BPD patients. Level of self-esteem appears to be a relevant factor in the relationship between rejection sensitivity and BPD symptom severity. Therapeutic interventions for BPD would do well to target rejection sensitivity.

  7. Social Skills and Perceived Maternal Acceptance-Rejection in Relation to Depression in Infertile Women

    OpenAIRE

    Yazdkhasti, Fariba

    2011-01-01

    Background This study examines the relationship between infertile women’s social skills and their perception of their own mothers’ acceptance or rejection, and the role this relationship plays in predicting self-reported depression. Materials and Methods This was a correlational study. 60 infertile women aged 25 to 35 years participated in a self-evaluation. A Social Skills Inventory, Parental Acceptance and Rejection Questionnaire and Beck Depression Inventory were used to measure social ski...

  8. Rare oncogenic mutations of predictive markers for targeted therapy in triple-negative breast cancer.

    Science.gov (United States)

    Grob, Tobias J; Heilenkötter, Uwe; Geist, Stefan; Paluchowski, Peter; Wilke, Christian; Jaenicke, Fritz; Quaas, Alexander; Wilczak, Waldemar; Choschzick, Matthias; Sauter, Guido; Lebeau, Annette

    2012-07-01

    Women with triple-negative breast cancer (TNBC) do not benefit from endocrine therapy or trastuzumab. Chemotherapy is the only systemic therapy currently available. To reduce the elevated risk of disease progression in these patients, better treatment options are needed, which are less toxic and more targeted to this patient population. We performed a comprehensive analysis of potential targetable genetic aberrations affecting the receptor tyrosine kinase/RAS/MAPK pathway, which are observed at higher frequencies in adenocarcinomas of other organs. Sixty-five individual TNBCs were studied by sequence analysis for HER2 (exon 18-23), EGFR (exon 18-21), KRAS (exon 2), and BRAF (exon 15) mutations. In addition, a tissue microarray was constructed to screen for EGFR gene copy gain and EML4-ALK fusion by FISH. Triple-negative status was confirmed by immunohistochemistry and FISH on tissue microarray sections. EGFR and CK5/6 immunohistochemical analyses were performed for identification of the basal-like phenotype. In addition, mutation analysis of TP53 (exon 5-8) was included. Sequence analysis revealed HER2 gene mutation in only one patient (heterozygous missense mutation in exon 19: p.L755S). No mutations were found in EGFR, KRAS, and BRAF. High polysomy of EGFR was detected in 5 of the 62 informative cases by FISH. True EGFR gene amplification accompanied by strong membranous EGFR protein expression was observed in only one case. No rearrangement of the ALK gene was detected. Basal-like phenotype was identified in 38 of the 65 TNBCs (58.5 %). TP53 gene mutation was found in 36/63 (57.1 %) tumors. We conclude that targetable genetic aberrations in the receptor tyrosine kinase/RAS/MAPK pathway occur rarely in TNBC.

  9. Pyrrhonism and Hume's rejection of induction

    OpenAIRE

    Bogdanovski, Mašan

    2012-01-01

    Sextus' rejection of induction poses a serious problem for Charlotte Stough's classical interpretation of Pyrrhonism. Her explanation of Pyrrhonist action is not available to the classical interpretation, because it implies that a Pyrrhonean has beliefs about his future impressions. In this article, the main premises of Hume's rejection of induction are reconstructed from Sextus' account of commemorative and indicative signs. The Pyrrhonean is not entitled to hold rational beliefs about his f...

  10. Reviewing the pathogenesis of antibody-mediated rejection and renal graft pathology after kidney transplantation.

    Science.gov (United States)

    Morozumi, Kunio; Takeda, Asami; Otsuka, Yasuhiro; Horike, Keiji; Gotoh, Norihiko; Narumi, Shunji; Watarai, Yoshihiko; Kobayashi, Takaaki

    2016-07-01

    The clinicopathological context of rejection after kidney transplantation was well recognized. Banff conferences greatly contributed to elucidate the pathogenesis and to establish the pathologic criteria of rejection after kidney transplantation. The most important current problem of renal transplantation is de novo donor-specific antibody (DSA) production leading chronic rejection and graft loss. Microvascular inflammation is considered as a reliable pathological marker for antibody-mediated rejection (AMR) in the presence of DSA. Electron microscopic study allowed us to evaluate early changes in peritubular capillaries in T-lymphocyte mediated rejection and transition to antibody-mediated rejection. Severe endothelial injuries with edema and activated lymphocyte invaded into subendothelial space with early multi-layering of peritubular capillary basement membrane suggest T-lymphocyte mediated rejection induce an unbounded chain of antibody-mediated rejection. The risk factors of AMR after ABO-incompatible kidney transplantation are important issues. Anti-ABO blood type antibody titre of IgG excess 32-fold before transplant operation is the only predictable factor for acute AMR. Characteristics of chronic active antibody-mediated rejection (CAAMR) are one of the most important problems. Light microscopic findings and C4d stain of peritubular capillary and glomerular capillary are useful diagnostic criteria of CAAMR. Microvascular inflammation, double contour of glomerular capillary and thickening of peritubular capillary basement are good predictive factors of the presence of de novo DSA. C4d stain of linear glomerular capillary is a more sensitive marker for CAAMR than positive C4d of peritubular capillary. Early and sensitive diagnostic attempts of diagnosing CAAMR are pivotal to prevent chronic graft failure. © 2016 Asian Pacific Society of Nephrology.

  11. Social Skills and Perceived Maternal Acceptance-Rejection in Relation to Depression in Infertile Women

    Directory of Open Access Journals (Sweden)

    Fariba Yazdkhasti

    2011-01-01

    Full Text Available Background: This study examines the relationship between infertile women’s social skills andtheir perception of their own mothers’ acceptance or rejection, and the role this relationship playsin predicting self-reported depression.Materials and Methods: This was a correlational study. 60 infertile women aged 25 to 35 yearsparticipated in a self-evaluation. A Social Skills Inventory, Parental Acceptance and RejectionQuestionnaire and Beck Depression Inventory were used to measure social skills, acceptancerejection and depression. Data was analyzed by SPSS software, using independent two-sample ttest, logistic regression, and ANOVA.Results: Findings showed that there are significant differences between depressed and not depressedinfertile women in their perceptions of acceptance and rejection by their mothers. Further, women'sperceptions of rejection are a more significant predictor of depression among less socially skilledinfertile women than among those who are more socially skilled. Less socially skilled women didnot show symptoms of depression when they experienced their mothers as accepting. In generalthe results of this study revealed that poorer social skills were more predictive of depression whilegood social skills moderate the effect of infertile women’s perceptions of their mothers' rejection.At the same time, the findings showed that infertile women's perceptions of acceptance moderatedthe effects of poorer social skills in predicting depression.Conclusion: Results suggest that the perception of mothers’ rejection and poor social skills are thekey factors that make infertile women prone to depression.

  12. Fine and Predictable Tuning of TALEN Gene Editing Targeting for Improved T Cell Adoptive Immunotherapy.

    Science.gov (United States)

    Gautron, Anne-Sophie; Juillerat, Alexandre; Guyot, Valérie; Filhol, Jean-Marie; Dessez, Emilie; Duclert, Aymeric; Duchateau, Philippe; Poirot, Laurent

    2017-12-15

    Using a TALEN-mediated gene-editing approach, we have previously described a process for the large-scale manufacturing of "off-the-shelf" CAR T cells from third-party donor T cells by disrupting the gene encoding TCRα constant chain (TRAC). Taking advantage of a previously described strategy to control TALEN targeting based on the exclusion capacities of non-conventional RVDs, we have developed highly efficient and specific nucleases targeting a key T cell immune checkpoint, PD-1, to improve engineered CAR T cells' functionalities. Here, we demonstrate that this approach allows combined TRAC and PDCD1 TALEN processing at the desired locus while eliminating low-frequency off-site processing. Thus, by replacing few RVDs, we provide here an easy and rapid redesign of optimal TALEN combinations. We anticipate that this method can greatly benefit multiplex editing, which is of key importance especially for therapeutic applications where high editing efficiencies need to be associated with maximal specificity and safety. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  13. SVMRFE based approach for prediction of most discriminatory gene target for type II diabetes

    Directory of Open Access Journals (Sweden)

    Atul Kumar

    2017-06-01

    Full Text Available Type II diabetes is a chronic condition that affects the way our body metabolizes sugar. The body's important source of fuel is now becoming a chronic disease all over the world. It is now very necessary to identify the new potential targets for the drugs which not only control the disease but also can treat it. Support vector machines are the classifier which has a potential to make a classification of the discriminatory genes and non-discriminatory genes. SVMRFE a modification of SVM ranks the genes based on their discriminatory power and eliminate the genes which are not involved in causing the disease. A gene regulatory network has been formed with the top ranked coding genes to identify their role in causing diabetes. To further validate the results pathway study was performed to identify the involvement of the coding genes in type II diabetes. The genes obtained from this study showed a significant involvement in causing the disease, which may be used as a potential drug target.

  14. Fine and Predictable Tuning of TALEN Gene Editing Targeting for Improved T Cell Adoptive Immunotherapy

    Directory of Open Access Journals (Sweden)

    Anne-Sophie Gautron

    2017-12-01

    Full Text Available Using a TALEN-mediated gene-editing approach, we have previously described a process for the large-scale manufacturing of “off-the-shelf” CAR T cells from third-party donor T cells by disrupting the gene encoding TCRα constant chain (TRAC. Taking advantage of a previously described strategy to control TALEN targeting based on the exclusion capacities of non-conventional RVDs, we have developed highly efficient and specific nucleases targeting a key T cell immune checkpoint, PD-1, to improve engineered CAR T cells’ functionalities. Here, we demonstrate that this approach allows combined TRAC and PDCD1 TALEN processing at the desired locus while eliminating low-frequency off-site processing. Thus, by replacing few RVDs, we provide here an easy and rapid redesign of optimal TALEN combinations. We anticipate that this method can greatly benefit multiplex editing, which is of key importance especially for therapeutic applications where high editing efficiencies need to be associated with maximal specificity and safety.

  15. VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses.

    Science.gov (United States)

    Qureshi, Abid; Thakur, Nishant; Kumar, Manoj

    2013-12-11

    Selection of effective viral siRNA is an indispensable step in the development of siRNA based antiviral therapeutics. Despite immense potential, a viral siRNA efficacy prediction algorithm is still not available. Moreover, performances of the existing general mammalian siRNA efficacy predictors are not satisfactory for viral siRNAs. Therefore, we have developed "VIRsiRNApred" a support vector machine (SVM) based method for predicting the efficacy of viral siRNA. In the present study, we have employed a new dataset of 1725 viral siRNAs with experimentally verified quantitative efficacies tested under heterogeneous experimental conditions and targeting as many as 37 important human viruses including HIV, Influenza, HCV, HBV, SARS etc. These siRNAs were divided into training (T1380) and validation (V345) datasets. Important siRNA sequence features including mono to penta nucleotide frequencies, binary pattern, thermodynamic properties and secondary structure were employed for model development. During 10-fold cross validation on T1380 using hybrid approach, we achieved a maximum Pearson Correlation Coefficient (PCC) of 0.55 between predicted and actual efficacy of viral siRNAs. On V345 independent dataset, our best model achieved a maximum correlation of 0.50 while existing general siRNA prediction methods showed PCC from 0.05 to 0.18. However, using leave one out cross validation PCC was improved to 0.58 and 0.55 on training and validation datasets respectively. SVM performed better than other machine learning techniques used like ANN, KNN and REP Tree. VIRsiRNApred is the first algorithm for predicting inhibition efficacy of viral siRNAs which is developed using experimentally verified viral siRNAs. We hope this algorithm would be useful in predicting highly potent viral siRNA to aid siRNA based antiviral therapeutics development. The web server is freely available at http://crdd.osdd.net/servers/virsirnapred/.

  16. Structural Decoupling and Disturbance Rejection in a Distillation Column

    DEFF Research Database (Denmark)

    Bahar, Mehrdad; Jantzen, Jan; Commault, C.

    1996-01-01

    Introduction, distillation column model, input-output decoupling, disturbance rejection, concluding remarks, references.......Introduction, distillation column model, input-output decoupling, disturbance rejection, concluding remarks, references....

  17. Interrogating differences in expression of targeted gene sets to predict breast cancer outcome.

    Science.gov (United States)

    Andres, Sarah A; Brock, Guy N; Wittliff, James L

    2013-07-02

    Genomics provides opportunities to develop precise tests for diagnostics, therapy selection and monitoring. From analyses of our studies and those of published results, 32 candidate genes were identified, whose expression appears related to clinical outcome of breast cancer. Expression of these genes was validated by qPCR and correlated with clinical follow-up to identify a gene subset for development of a prognostic test. RNA was isolated from 225 frozen invasive ductal carcinomas,and qRT-PCR was performed. Univariate hazard ratios and 95% confidence intervals for breast cancer mortality and recurrence were calculated for each of the 32 candidate genes. A multivariable gene expression model for predicting each outcome was determined using the LASSO, with 1000 splits of the data into training and testing sets to determine predictive accuracy based on the C-index. Models with gene expression data were compared to models with standard clinical covariates and models with both gene expression and clinical covariates. Univariate analyses revealed over-expression of RABEP1, PGR, NAT1, PTP4A2, SLC39A6, ESR1, EVL, TBC1D9, FUT8, and SCUBE2 were all associated with reduced time to disease-related mortality (HR between 0.8 and 0.91, adjusted p data sets for the gene expression, clinical, and combined models were 0.65, 0.63, and 0.65 for disease mortality and 0.64, 0.63, and 0.66 for disease recurrence, respectively. Molecular signatures consisting of five genes (PGR, GABRP, TBC1D9, SLC39A6 and LRBA) for disease mortality and of six genes (PGR, ESR1, GABRP, TBC1D9, SLC39A6 and LRBA) for disease recurrence were identified. These signatures were as effective as standard clinical parameters in predicting recurrence/mortality, and when combined, offered some improvement relative to clinical information alone for disease recurrence (median difference in C-values of 0.03, 95% CI of -0.08 to 0.13). Collectively, results suggest that these genes form the basis for a clinical

  18. Interrogating differences in expression of targeted gene sets to predict breast cancer outcome

    International Nuclear Information System (INIS)

    Andres, Sarah A; Brock, Guy N; Wittliff, James L

    2013-01-01

    Genomics provides opportunities to develop precise tests for diagnostics, therapy selection and monitoring. From analyses of our studies and those of published results, 32 candidate genes were identified, whose expression appears related to clinical outcome of breast cancer. Expression of these genes was validated by qPCR and correlated with clinical follow-up to identify a gene subset for development of a prognostic test. RNA was isolated from 225 frozen invasive ductal carcinomas,and qRT-PCR was performed. Univariate hazard ratios and 95% confidence intervals for breast cancer mortality and recurrence were calculated for each of the 32 candidate genes. A multivariable gene expression model for predicting each outcome was determined using the LASSO, with 1000 splits of the data into training and testing sets to determine predictive accuracy based on the C-index. Models with gene expression data were compared to models with standard clinical covariates and models with both gene expression and clinical covariates. Univariate analyses revealed over-expression of RABEP1, PGR, NAT1, PTP4A2, SLC39A6, ESR1, EVL, TBC1D9, FUT8, and SCUBE2 were all associated with reduced time to disease-related mortality (HR between 0.8 and 0.91, adjusted p < 0.05), while RABEP1, PGR, SLC39A6, and FUT8 were also associated with reduced recurrence times. Multivariable analyses using the LASSO revealed PGR, ESR1, NAT1, GABRP, TBC1D9, SLC39A6, and LRBA to be the most important predictors for both disease mortality and recurrence. Median C-indexes on test data sets for the gene expression, clinical, and combined models were 0.65, 0.63, and 0.65 for disease mortality and 0.64, 0.63, and 0.66 for disease recurrence, respectively. Molecular signatures consisting of five genes (PGR, GABRP, TBC1D9, SLC39A6 and LRBA) for disease mortality and of six genes (PGR, ESR1, GABRP, TBC1D9, SLC39A6 and LRBA) for disease recurrence were identified. These signatures were as effective as standard clinical

  19. First-trimester multimarker prediction of gestational diabetes mellitus using targeted mass spectrometry

    DEFF Research Database (Denmark)

    Ravnsborg, Tina; Andersen, Lise Lotte T; Trabjerg, Natacha D.

    2016-01-01

    perinatal outcome, no single protein biomarker has yet proven useful for this purpose. In the present study, we hypothesised that multimarker panels of serum proteins can improve first-trimester prediction of GDM among obese and non-obese women compared with single markers. Methods: A nested case......–control study was performed on first-trimester serum samples from 199 GDM cases and 208 controls, each divided into an obese group (BMI ≥27 kg/m2) and a non-obese group (BMI 2). Based on their biological relevance to GDM or type 2 diabetes mellitus or on their previously reported potential as biomarkers...

  20. Adaptation of Rejection Algorithms for a Radar Clutter

    Directory of Open Access Journals (Sweden)

    D. Popov

    2017-09-01

    Full Text Available In this paper, the algorithms for adaptive rejection of a radar clutter are synthesized for the case of a priori unknown spectral-correlation characteristics at wobbulation of a repetition period of the radar signal. The synthesis of algorithms for the non-recursive adaptive rejection filter (ARF of a given order is reduced to determination of the vector of weighting coefficients, which realizes the best effectiveness index for radar signal extraction from the moving targets on the background of the received clutter. As the effectiveness criterion, we consider the averaged (over the Doppler signal phase shift improvement coefficient for a signal-to-clutter ratio (SCR. On the base of extreme properties of the characteristic numbers (eigennumbers of the matrices, the optimal vector (according to this criterion maximum is defined as the eigenvector of the clutter correlation matrix corresponding to its minimal eigenvalue. The general type of the vector of optimal ARF weighting coefficients is de-termined and specific adaptive algorithms depending upon the ARF order are obtained, which in the specific cases can be reduced to the known algorithms confirming its authenticity. The comparative analysis of the synthesized and known algorithms is performed. Significant bene-fits are established in clutter rejection effectiveness by the offered processing algorithms compared to the known processing algorithms.

  1. Campylobacter fetus subspecies: Comparative genomics and prediction of potential virulence targets

    DEFF Research Database (Denmark)

    Ali, Amjad; Soares, Siomar C.; Santos, Anderson R.

    2012-01-01

    The genus Campylobacter contains pathogens causing a wide range of diseases, targeting both humans and animals. Among them, the Campylobacter fetus subspecies fetus and venerealis deserve special attention, as they are the etiological agents of human bacterial gastroenteritis and bovine genital...... campylobacteriosis, respectively. We compare the whole genomes of both subspecies to get insights into genomic architecture, phylogenetic relationships, genome conservation and core virulence factors. Pan-genomic approach was applied to identify the core- and pan-genome for both C. fetus subspecies and members...... of the genus. The C. fetus subspecies conserved (76%) proteome were then analyzed for their subcellular localization and protein functions in biological processes. Furthermore, with pathogenomic strategies, unique candidate regions in the genomes and several potential core-virulence factors were identified...

  2. Identification and target prediction of miRNAs specifically expressed in rat neural tissue

    Directory of Open Access Journals (Sweden)

    Tu Kang

    2009-05-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are a large group of RNAs that play important roles in regulating gene expression and protein translation. Several studies have indicated that some miRNAs are specifically expressed in human, mouse and zebrafish tissues. For example, miR-1 and miR-133 are specifically expressed in muscles. Tissue-specific miRNAs may have particular functions. Although previous studies have reported the presence of human, mouse and zebrafish tissue-specific miRNAs, there have been no detailed reports of rat tissue-specific miRNAs. In this study, Home-made rat miRNA microarrays which established in our previous study were used to investigate rat neural tissue-specific miRNAs, and mapped their target genes in rat tissues. This study will provide information for the functional analysis of these miRNAs. Results In order to obtain as complete a picture of specific miRNA expression in rat neural tissues as possible, customized miRNA microarrays with 152 selected miRNAs from miRBase were used to detect miRNA expression in 14 rat tissues. After a general clustering analysis, 14 rat tissues could be clearly classified into neural and non-neural tissues based on the obtained expression profiles with p values Conclusion Our work provides a global view of rat neural tissue-specific miRNA profiles and a target map of miRNAs, which is expected to contribute to future investigations of miRNA regulatory mechanisms in neural systems.

  3. Rejection thresholds in solid chocolate-flavored compound coating.

    Science.gov (United States)

    Harwood, Meriel L; Ziegler, Gregory R; Hayes, John E

    2012-10-01

    Classical detection thresholds do not predict liking, as they focus on the presence or absence of a sensation. Recently however, Prescott and colleagues described a new method, the rejection threshold, where a series of forced choice preference tasks are used to generate a dose-response function to determine hedonically acceptable concentrations. That is, how much is too much? To date, this approach has been used exclusively in liquid foods. Here, we determined group rejection thresholds in solid chocolate-flavored compound coating for bitterness. The influences of self-identified preferences for milk or dark chocolate, as well as eating style (chewers compared to melters) on rejection thresholds were investigated. Stimuli included milk chocolate-flavored compound coating spiked with increasing amounts of sucrose octaacetate, a bitter and generally recognized as safe additive. Paired preference tests (blank compared to spike) were used to determine the proportion of the group that preferred the blank. Across pairs, spiked samples were presented in ascending concentration. We were able to quantify and compare differences between 2 self-identified market segments. The rejection threshold for the dark chocolate preferring group was significantly higher than the milk chocolate preferring group (P= 0.01). Conversely, eating style did not affect group rejection thresholds (P= 0.14), although this may reflect the amount of chocolate given to participants. Additionally, there was no association between chocolate preference and eating style (P= 0.36). Present work supports the contention that this method can be used to examine preferences within specific market segments and potentially individual differences as they relate to ingestive behavior. This work makes use of the rejection threshold method to study market segmentation, extending its use to solid foods. We believe this method has broad applicability to the sensory specialist and product developer by providing a

  4. Rejection versus escape: the tumor MHC dilemma.

    Science.gov (United States)

    Garrido, Federico; Ruiz-Cabello, Francisco; Aptsiauri, Natalia

    2017-02-01

    Most tumor cells derive from MHC-I-positive normal counterparts and remain positive at early stages of tumor development. T lymphocytes can infiltrate tumor tissue, recognize and destroy MHC class I (MHC-I)-positive cancer cells ("permissive" phase I). Later, MHC-I-negative tumor cell variants resistant to T-cell killing emerge. During this process, tumors first acquire a heterogeneous MHC-I expression pattern and finally become uniformly MHC-I-negative. This stage (phase II) represents a "non-permissive" encapsulated structure with tumor nodes surrounded by fibrous tissue containing different elements including leukocytes, macrophages, fibroblasts, etc. Molecular mechanisms responsible for total or partial MHC-I downregulation play a crucial role in determining and predicting the antigen-presenting capacity of cancer cells. MHC-I downregulation caused by reversible ("soft") lesions can be upregulated by TH1-type cytokines released into the tumor microenvironment in response to different types of immunotherapy. In contrast, when the molecular mechanism of the tumor MHC-I loss is irreversible ("hard") due to a genetic defect in the gene/s coding for MHC-I heavy chains (chromosome 6) or beta-2-microglobulin (B2M) (chromosome 15), malignant cells are unable to upregulate MHC-I, remain undetectable by cytotoxic T-cells, and continue to grow and metastasize. Based on the tumor MHC-I molecular analysis, it might be possible to define MHC-I phenotypes present in cancer patients in order to distinguish between non-responders, partial/short-term responders, and likely durable responders. This highlights the need for designing strategies to enhance tumor MHC-I expression that would allow CTL-mediated tumor rejection.

  5. B-cell-mediated strategies to fight chronic allograft rejection

    Directory of Open Access Journals (Sweden)

    Ali H Dalloul

    2013-12-01

    Full Text Available Solid organs have been transplanted for decades. Since the improvement in graft selection and in medical and surgical procedures, the likelihood of graft function after one year is now close to 90%. Nonetheless even well-matched recipients continue to need medications for the rest of their lives hence adverse side effects and enhanced morbidity. Understanding Immune rejection mechanisms, is of increasing importance since the greater use of living-unrelated donors and genetically unmatched individuals. Chronic rejection is devoted to T-cells, however the role of B-cells in rejection has been appreciated recently by the observation that B-cell depletion improve graft survival. By contrast however, B-cells can be beneficial to the grafted tissue. This protective effect is secondary to either the secretion of protective antibodies or the induction of B-cells that restrain excessive inflammatory responses, chiefly by local provision of IL-10, or inhibit effector T-cells by direct cellular interactions. As a proof of concept B-cell-mediated infectious transplantation tolerance could be achieved in animal models, and evidence emerged that the presence of such B-cells in transplanted patients correlate with a favorable outcome. Among these populations, regulatory B-cells constitute a recently described population. These cells may develop as a feedback mechanism to prevent uncontrolled reactivity to antigens and inflammatory stimuli. The difficult task for the clinician, is to quantify the respective ratios and functions of tolerant vs effector B-cells within a transplanted organ, at a given time point in order to modulate B-cell-directed therapy. Several receptors at the B-cell membrane as well as signaling molecules, can now be targeted for this purpose. Understanding the temporal expansion of regulatory B-cells in grafted patients and the stimuli that activate them will help in the future to implement specific strategies aimed at fighting chronic

  6. Identification and targeting of a TACE-dependent autocrine loopwhich predicts poor prognosis in breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Kenny, Paraic A.; Bissell, Mina J.

    2005-06-15

    The ability to proliferate independently of signals from other cell types is a fundamental characteristic of tumor cells. Using a 3D culture model of human breast cancer progression, we have delineated a protease-dependent autocrine loop which provides an oncogenic stimulus in the absence of proto-oncogene mutation. Inhibition of this protease, TACE/ADAM17, reverts the malignant phenotype by preventing mobilization of two crucial growth factors, Amphiregulin and TGF{alpha}. We show further that the efficacy of EGFR inhibitors is overcome by physiological levels of growth factors and that successful EGFR inhibition is dependent on reducing ligand bioavailability. Using existing patient outcome data, we demonstrate a strong correlation between TACE and TGF{alpha} expression in human breast cancers that is predictive of poor prognosis.

  7. Exploiting Reject Option in Classification for Social Discrimination Control

    KAUST Repository

    Kamiran, Faisal

    2017-09-29

    Social discrimination is said to occur when an unfavorable decision for an individual is influenced by her membership to certain protected groups such as females and minority ethnic groups. Such discriminatory decisions often exist in historical data. Despite recent works in discrimination-aware data mining, there remains the need for robust, yet easily usable, methods for discrimination control. In this paper, we utilize reject option in classification, a general decision theoretic framework for handling instances whose labels are uncertain, for modeling and controlling discriminatory decisions. Specifically, this framework permits a formal treatment of the intuition that instances close to the decision boundary are more likely to be discriminated in a dataset. Based on this framework, we present three different solutions for discrimination-aware classification. The first solution invokes probabilistic rejection in single or multiple probabilistic classifiers while the second solution relies upon ensemble rejection in classifier ensembles. The third solution integrates one of the first two solutions with situation testing which is a procedure commonly used in the court of law. All solutions are easy to use and provide strong justifications for the decisions. We evaluate our solutions extensively on four real-world datasets and compare their performances with previously proposed discrimination-aware classifiers. The results demonstrate the superiority of our solutions in terms of both performance and flexibility of applicability. In particular, our solutions are effective at removing illegal discrimination from the predictions.

  8. Advantages of C2 monitoring to avoid acute rejection in pediatric heart transplant recipients.

    Science.gov (United States)

    Schubert, S; Abdul-Khaliq, H; Lehmkuhl, H B; Hübler, M; Abd El Rahman, M Y; Miera, O; Ewert, P; Weng, Y; Wei, H; Krüdewagen, B; Hetzer, R; Berger, F

    2006-06-01

    Inadequate cyclosporine (CsA) blood levels are a major risk factor for acute rejection in transplant recipients. The CsA trough level (C0 level) measured just before the next dose is commonly used to adjust the oral dosage. However, the 2-hour post-CsA dose concentration (C2 level) is favored as the best single-point correlate of CsA area-under-the-curve concentration and may better reflect the immunosuppressive effect of CsA. Because an adequate C2 level has not yet been defined, this study was performed to assess the value of C2 monitoring for the prevention of acute rejection and to define target levels in pediatric heart transplant recipients. C2 levels were assessed in 50 pediatric heart transplant patients with oral CsA therapy and compared with trough C0 levels using full blood sampling, mass spectrometry and a blinded analysis. Acute graft rejection was detected using intramyocardial electrocardiogram (IMEG) and serial conventional and tissue Doppler echocardiography (TDE). Rejection was confirmed or excluded by endomyocardial biopsy. C2 and not C0 levels were significantly reduced in patients with acute graft rejection (ISHLT Grade > or =2). Patients with a C2 level 600 ng/ml should be the target to prevent acute rejection.

  9. Image rejects in general direct digital radiography

    International Nuclear Information System (INIS)

    Hofmann, Bjørn; Rosanowsky, Tine Blomberg; Jensen, Camilla; Wah, Kenneth Hong Ching

    2015-01-01

    The number of rejected images is an indicator of image quality and unnecessary imaging at a radiology department. Image reject analysis was frequent in the film era, but comparably few and small studies have been published after converting to digital radiography. One reason may be a belief that rejects have been eliminated with digitalization. To measure the extension of deleted images in direct digital radiography (DR), in order to assess the rates of rejects and unnecessary imaging and to analyze reasons for deletions, in order to improve the radiological services. All exposed images at two direct digital laboratories at a hospital in Norway were reviewed in January 2014. Type of examination, number of exposed images, and number of deleted images were registered. Each deleted image was analyzed separately and the reason for deleting the image was recorded. Out of 5417 exposed images, 596 were deleted, giving a deletion rate of 11%. A total of 51.3% were deleted due to positioning errors and 31.0% due to error in centering. The examinations with the highest percentage of deleted images were the knee, hip, and ankle, 20.6%, 18.5%, and 13.8% respectively. The reject rate is at least as high as the deletion rate and is comparable with previous film-based imaging systems. The reasons for rejection are quite different in digital systems. This falsifies the hypothesis that digitalization would eliminates rejects. A deleted image does not contribute to diagnostics, and therefore is an unnecessary image. Hence, the high rates of deleted images have implications for management, training, education, as well as for quality

  10. Target-based drug discovery for [Formula: see text]-globin disorders: drug target prediction using quantitative modeling with hybrid functional Petri nets.

    Science.gov (United States)

    Mehraei, Mani; Bashirov, Rza; Tüzmen, Şükrü

    2016-10-01

    Recent molecular studies provide important clues into treatment of [Formula: see text]-thalassemia, sickle-cell anaemia and other [Formula: see text]-globin disorders revealing that increased production of fetal hemoglobin, that is normally suppressed in adulthood, can ameliorate the severity of these diseases. In this paper, we present a novel approach for drug prediction for [Formula: see text]-globin disorders. Our approach is centered upon quantitative modeling of interactions in human fetal-to-adult hemoglobin switch network using hybrid functional Petri nets. In accordance with the reverse pharmacology approach, we pose a hypothesis regarding modulation of specific protein targets that induce [Formula: see text]-globin and consequently fetal hemoglobin. Comparison of simulation results for the proposed strategy with the ones obtained for already existing drugs shows that our strategy is the optimal as it leads to highest level of [Formula: see text]-globin induction and thereby has potential beneficial therapeutic effects on [Formula: see text]-globin disorders. Simulation results enable verification of model coherence demonstrating that it is consistent with qPCR data available for known strategies and/or drugs.

  11. Friendship quantity and quality as predictors of rejection sensitivity in adolescents

    Directory of Open Access Journals (Sweden)

    Gabriela Šeboková

    2014-12-01

    Full Text Available The current study examines friendship quality and quantity as unique predictors of rejection sensitivity in adolescents. The purpose of the study was to analyze whether the unique contributions of friendship quality and quantity differ in adolescent boys and girls. Rejection sensitivity is conceptualized as the disposition to anxiously expect, readily perceive and intensively react to social rejection. That is why rejection sensitivity is considered to be a cognitive-affective mechanism which leads to increase of internalizing problems in children and adolescents (loneliness, social anxiety, depression.... Friendship variables have been found to predict the level of internalizing problems in adolescents. Little to no research, however, has examined friendship quality and quantity as predictors of level of rejection sensitivity. Participants in this study were 184 students (98 girls and 86 boys, aged from 13 to 16 (M=13.83, SD=1. Adolescents completed measures assessing number of their friends, quality of best friendship (self-report questionnaire Friendship qualities scale, Bukowski, Hoza, Boivin, 1994 and rejection sensitivity (self-report questionnaire Rejection sensitivity scale, Downey, Feldman, 1996. Regression analysis indicated that friendship features (companionship, balance, help, security, closeness, friendship quantity and overall friendship quality are significant unique predictors of sensitivity rejection in adolescents with. Results suggest that adolescents with higher number of and higher quality friendships have lower concerns about the possibility and expectation of rejection, which can lead to minimizing the risk of development of internalizing problems. However, only a small proportion of variance was accounted for in rejection sensitivity by the friendship variables (small to medium effect size. This suggests that different kind of peer relationships (peer acceptance, popularity, peer victimization make unique, differential

  12. Happy eating: the single target implicit association test predicts overeating after positive emotions.

    Science.gov (United States)

    Bongers, Peggy; Jansen, Anita; Houben, Katrijn; Roefs, Anne

    2013-08-01

    For many years, questionnaires have been considered the standard when examining emotional eating behavior. However, recently, some controversy has arisen about these questionnaires, and their usefulness in identifying emotional eaters has been questioned. The current study aimed to investigate the Single Target Implicit Association Test (ST-IAT) as a measure of emotional eating. Two ST-IATs (assessing food-positive and food-negative associations respectively) and the Dutch Eating Behaviour Questionnaire (DEBQ) were compared in undergraduate students. A positive, negative or neutral mood was induced by means of a film clip, and milkshake consumption was measured during and after the mood induction. It was hypothesized that participants with strong emotion-food associations on the ST-IATs (i.e., IAT-emotional eaters) would consume more food in the emotion induction condition corresponding to that emotion, as compared to those with weak emotion-food associations as well as to those in the neutral condition. Participants who scored high on both the positive and negative ST-IATs ate more during a positive mood induction than during a negative mood induction. This effect did not extend to milkshake consumption after the mood induction procedure. In addition, IAT-positive emotional eaters consumed more food than IAT-non-emotional eaters. No effects of the DEBQ on milkshake consumption were found. It is concluded that the ST-IAT has potential as a measure of emotional eating. © 2013 Elsevier Ltd. All rights reserved.

  13. Nuclear IGF-1R predicts chemotherapy and targeted therapy resistance in metastatic colorectal cancer.

    Science.gov (United States)

    Codony-Servat, Jordi; Cuatrecasas, Miriam; Asensio, Elena; Montironi, Carla; Martínez-Cardús, Anna; Marín-Aguilera, Mercedes; Horndler, Carlos; Martínez-Balibrea, Eva; Rubini, Michele; Jares, Pedro; Reig, Oscar; Victoria, Iván; Gaba, Lydia; Martín-Richard, Marta; Alonso, Vicente; Escudero, Pilar; Fernández-Martos, Carlos; Feliu, Jaime; Méndez, Jose Carlos; Méndez, Miguel; Gallego, Javier; Salud, Antonieta; Rojo, Federico; Castells, Antoni; Prat, Aleix; Rosell, Rafael; García-Albéniz, Xabier; Camps, Jordi; Maurel, Joan

    2017-12-05

    Although chemotherapy is the cornerstone treatment for patients with metastatic colorectal cancer (mCRC), acquired chemoresistance is common and constitutes the main reason for treatment failure. Monoclonal antibodies against insulin-like growth factor-1 receptor (IGF-1R) have been tested in pre-treated mCRC patients, but results have been largely deceiving. We analysed time to progression, overall survival, and the mutational status of RAS, BRAF and nuclear p-IGF-1R expression by immunohistochemistry, in 470 metastatic CRC patients. The effect of IGF-1R activation and distribution was also assessed using cellular models of CRC and RNAi for functional validation. Nuclear IGF-1R increased in metastatic tumours compared to paired untreated primary tumours, and significantly correlated with poor overall survival in mCRC patients. In vitro, chemo-resistant cell lines presented significantly higher levels of IGF-1R expression within the nuclear compartment, and PIAS3, a protein implicated also in the sumoylation process of intranuclear proteins, contributed to IGF-1R nuclear sequestration, highlighting the essential role of PIAS3 in this process. Intriguingly, we observed that ganitumab, an IGF-1R blocking-antibody used in several clinical trials, and dasatinib, an SRC inhibitor, increased the nuclear localisation of IGF-1R. Our study demonstrates that IGF-1R nuclear location might lead to chemotherapy and targeted agent resistance.

  14. In silico models for predicting vector control chemicals targeting Aedes aegypti

    Science.gov (United States)

    Devillers, J.; Lagneau, C.; Lattes, A.; Garrigues, J.C.; Clémenté, M.M.; Yébakima, A.

    2014-01-01

    Human arboviral diseases have emerged or re-emerged in numerous countries worldwide due to a number of factors including the lack of progress in vaccine development, lack of drugs, insecticide resistance in mosquitoes, climate changes, societal behaviours, and economical constraints. Thus, Aedes aegypti is the main vector of the yellow fever and dengue fever flaviviruses and is also responsible for several recent outbreaks of the chikungunya alphavirus. As for the other mosquito species, the A. aegypti control relies heavily on the use of insecticides. However, because of increasing resistance to the different families of insecticides, reduction of Aedes populations is becoming increasingly difficult. Despite the unquestionable utility of insecticides in fighting mosquito populations, there are very few new insecticides developed and commercialized for vector control. This is because the high cost of the discovery of an insecticide is not counterbalanced by the ‘low profitability’ of the vector control market. Fortunately, the use of quantitative structure–activity relationship (QSAR) modelling allows the reduction of time and cost in the discovery of new chemical structures potentially active against mosquitoes. In this context, the goal of the present study was to review all the existing QSAR models on A. aegypti. The homology and pharmacophore models were also reviewed. Specific attention was paid to show the variety of targets investigated in Aedes in relation to the physiology and ecology of the mosquito as well as the diversity of the chemical structures which have been proposed, encompassing man-made and natural substances. PMID:25275884

  15. Study of a Terrain-Based Motion Estimation Model to Predict the Position of a Moving Target to Enhance Weapon Probability of Kill

    Science.gov (United States)

    2017-09-01

    the operational level. The goal of this thesis is to develop a realistic model characterizing the most probable paths 2 of interest for specific...TERRAIN-BASED MOTION ESTIMATION MODEL TO PREDICT THE POSITION OF A MOVING TARGET TO ENHANCE WEAPON PROBABILITY OF KILL by Chin Beng Ang...ESTIMATION MODEL TO PREDICT THE POSITION OF A MOVING TARGET TO ENHANCE WEAPON PROBABILITY OF KILL 5. FUNDING NUMBERS 6. AUTHOR(S) Chin Beng Ang 7

  16. Secretome Prediction of Two M. tuberculosis Clinical Isolates Reveals Their High Antigenic Density and Potential Drug Targets

    Science.gov (United States)

    Cornejo-Granados, Fernanda; Zatarain-Barrón, Zyanya L.; Cantu-Robles, Vito A.; Mendoza-Vargas, Alfredo; Molina-Romero, Camilo; Sánchez, Filiberto; Del Pozo-Yauner, Luis; Hernández-Pando, Rogelio; Ochoa-Leyva, Adrián

    2017-01-01

    The Excreted/Secreted (ES) proteins play important roles during Mycobacterium tuberculosis invasion, virulence, and survival inside the host and they are a major source of immunogenic proteins. However, the molecular complexity of the bacillus cell wall has made difficult the experimental isolation of the total bacterial ES proteins. Here, we reported the genomes of two Beijing genotype M. tuberculosis clinical isolates obtained from patients from Vietnam (isolate 46) and South Africa (isolate 48). We developed a bioinformatics pipeline to predict their secretomes and observed that ~12% of the genome-encoded proteins are ES, being PE, PE-PGRS, and PPE the most abundant protein domains. Additionally, the Gene Ontology, KEGG pathways and Enzyme Classes annotations supported the expected functions for the secretomes. The ~70% of an experimental secretome compiled from literature was contained in our predicted secretomes, while only the 34–41% of the experimental secretome was contained in the two previously reported secretomes for H37Rv. These results suggest that our bioinformatics pipeline is better to predict a more complete set of ES proteins in M. tuberculosis genomes. The predicted ES proteins showed a significant higher antigenic density measured by Abundance of Antigenic Regions (AAR) value than the non-ES proteins and also compared to random constructed secretomes. Additionally, we predicted the secretomes for H37Rv, H37Ra, and two M. bovis BCG genomes. The antigenic density for BGG and for isolates 46 and 48 was higher than the observed for H37Rv and H37Ra secretomes. In addition, two sets of immunogenic proteins previously reported in patients with tuberculosis also showed a high antigenic density. Interestingly, mice infected with isolate 46 showed a significant lower survival rate than the ones infected with isolate 48 and both survival rates were lower than the one previously reported for the H37Rv in the same murine model. Finally, after a

  17. Predicting ground contact events for a continuum of gait types: An application of targeted machine learning using principal component analysis.

    Science.gov (United States)

    Osis, Sean T; Hettinga, Blayne A; Ferber, Reed

    2016-05-01

    An ongoing challenge in the application of gait analysis to clinical settings is the standardized detection of temporal events, with unobtrusive and cost-effective equipment, for a wide range of gait types. The purpose of the current study was to investigate a targeted machine learning approach for the prediction of timing for foot strike (or initial contact) and toe-off, using only kinematics for walking, forefoot running, and heel-toe running. Data were categorized by gait type and split into a training set (∼30%) and a validation set (∼70%). A principal component analysis was performed, and separate linear models were trained and validated for foot strike and toe-off, using ground reaction force data as a gold-standard for event timing. Results indicate the model predicted both foot strike and toe-off timing to within 20ms of the gold-standard for more than 95% of cases in walking and running gaits. The machine learning approach continues to provide robust timing predictions for clinical use, and may offer a flexible methodology to handle new events and gait types. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Microinvasion of liver metastases from colorectal cancer: predictive factors and application for determining clinical target volume

    International Nuclear Information System (INIS)

    Qian, Yang; Zeng, Zhao-Chong; Ji, Yuan; Xiao, Yin-Ping

    2015-01-01

    This study evaluates the microscopic characteristics of liver metastases from colorectal cancer (LMCRC) invasion and provides a reference for expansion from gross tumor volume (GTV) to clinical targeting volume (CTV). Data from 129 LMCRC patients treated by surgical resection at our hospital between January 2008 and September 2009 were collected for study. Tissue sections used for pathology and clinical data were reviewed. Patient information used for the study included gender, age, original tumor site, number of tumors, tumor size, levels of carcinoembryonic antigen (CEA) and carbohydrate antigen 199 (CA199), synchronous or metachronous liver metastases, and whether patients received chemotherapy. The distance of liver microinvasion from the tumor boundary was measured microscopically by two senior pathologists. Of 129 patients evaluated, 81 (62.8 %) presented microinvasion distances from the tumor boundary ranging between 1.0 − 7.0 mm. A GTV-to-CTV expansion of 5, 6.7, or 7.0 mm was required to provide a 95, 99, or 100 % probability, respectively, of obtaining clear resection margins by microscopic observation. The extent of invasion was not related to gender, age, synchronous or metachronous liver metastases, tumor size, CA199 level, or chemotherapy. The extent of invasion was related to original tumor site, CEA level, and number of tumors. A scoring system was established based on the latter three positive predictors. Using this system, an invasion distance less than 3 mm was measured in 93.4 % of patients with a score of ≤1 point, but in only 85.7 % of patients with a score of ≤2 points. The extent of tumor invasion in our LMCRC patient cohort correlated with original tumor site, CEA level, and number of tumors. These positive predictors may potentially be used as a scoring system for determining GTV-to-CTV expansion

  19. Peripheral blood transcriptome sequencing reveals rejection-relevant genes in long-term heart transplantation.

    Science.gov (United States)

    Chen, Yan; Zhang, Haibo; Xiao, Xue; Jia, Yixin; Wu, Weili; Liu, Licheng; Jiang, Jun; Zhu, Baoli; Meng, Xu; Chen, Weijun

    2013-10-03

    Peripheral blood-based gene expression patterns have been investigated as biomarkers to monitor the immune system and rule out rejection after heart transplantation. Recent advances in the high-throughput deep sequencing (HTS) technologies provide new leads in transcriptome analysis. By performing Solexa/Illumina's digital gene expression (DGE) profiling, we analyzed gene expression profiles of PBMCs from 6 quiescent (grade 0) and 6 rejection (grade 2R&3R) heart transplant recipients at more than 6 months after transplantation. Subsequently, quantitative real-time polymerase chain reaction (qRT-PCR) was carried out in an independent validation cohort of 47 individuals from three rejection groups (ISHLT, grade 0,1R, 2R&3R). Through DGE sequencing and qPCR validation, 10 genes were identified as informative genes for detection of cardiac transplant rejection. A further clustering analysis showed that the 10 genes were not only effective for distinguishing patients with acute cardiac allograft rejection, but also informative for discriminating patients with renal allograft rejection based on both blood and biopsy samples. Moreover, PPI network analysis revealed that the 10 genes were connected to each other within a short interaction distance. We proposed a 10-gene signature for heart transplant patients at high-risk of developing severe rejection, which was found to be effective as well in other organ transplant. Moreover, we supposed that these genes function systematically as biomarkers in long-time allograft rejection. Further validation in broad transplant population would be required before the non-invasive biomarkers can be generally utilized to predict the risk of transplant rejection. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  20. Unpacking the psychological weight of weight stigma: A rejection-expectation pathway

    Science.gov (United States)

    Blodorn, Alison; Major, Brenda; Hunger, Jeffrey; Miller, Carol

    2015-01-01

    The present research tested the hypothesis that the negative effects of weight stigma among higher body-weight individuals are mediated by expectations of social rejection. Women and men who varied in objective body-weight (body mass index; BMI) gave a speech describing why they would make a good date. Half believed that a potential dating partner would see a videotape of their speech (weight seen) and half believed that a potential dating partner would listen to an audiotape of their speech (weight unseen). Among women, but not men, higher body-weight predicted increased expectations of social rejection, decreased executive control resources, decreased self-esteem, increased self-conscious emotions and behavioral displays of self-consciousness when weight was seen but not when weight was unseen. As predicted, higher body-weight women reported increased expectations of social rejection when weight was seen (versus unseen), which in turn predicted decreased self-esteem, increased self-conscious emotions, and increased stress. In contrast, lower body-weight women reported decreased expectations of social rejection when weight was seen (versus unseen), which in turn predicted increased self-esteem, decreased self-conscious emotions, and decreased stress. Men’s responses were largely unaffected by body-weight or visibility, suggesting that a dating context may not be identity threatening for higher body-weight men. Overall, the present research illuminates a rejection-expectation pathway by which weight stigma undermines higher body-weight women’s health. PMID:26752792

  1. Predicting the establishment success of introduced target species in grassland restoration by functional traits.

    Science.gov (United States)

    Engst, Karina; Baasch, Annett; Bruelheide, Helge

    2017-09-01

    potential of functional trait analysis to predict success in restoration projects.

  2. Postprandial regulation of hepatic microRNAs predicted to target the insulin pathway in rainbow trout.

    Directory of Open Access Journals (Sweden)

    Jan A Mennigen

    Full Text Available Rainbow trout are carnivorous fish and poor metabolizers of carbohydrates, which established this species as a model organism to study the comparative physiology of insulin. Following the recent characterisation of key roles of several miRNAs in the insulin action on hepatic intermediary metabolism in mammalian models, we investigated the hypothesis that hepatic miRNA expression is postprandially regulated in the rainbow trout and temporally coordinated in the context of insulin-mediated regulation of metabolic gene expression in the liver. To address this hypothesis, we used a time-course experiment in which rainbow trout were fed a commercial diet after short-term fasting. We investigated hepatic miRNA expression, activation of the insulin pathway, and insulin regulated metabolic target genes at several time points. Several miRNAs which negatively regulate hepatic insulin signaling in mammalian model organisms were transiently increased 4 h after the meal, consistent with a potential role in acute postprandial negative feed-back regulation of the insulin pathway and attenuation of gluconeogenic gene expression. We equally observed a transient increase in omy- miRNA-33 and omy-miRNA-122b 4 h after feeding, whose homologues have potent lipogenic roles in the liver of mammalian model systems. A concurrent increase in the activity of the hepatic insulin signaling pathway and the expression of lipogenic genes (srebp1c, fas, acly was equally observed, while lipolytic gene expression (cpt1a and cpt1b decreased significantly 4 h after the meal. This suggests lipogenic roles of omy-miRNA-33 and omy-miRNA-122b may be conserved between rainbow trout and mammals and that these miRNAs may furthermore contribute to acute postprandial regulation of de novo hepatic lipid synthesis in rainbow trout. These findings provide a framework for future research of miRNA regulation of hepatic metabolism in trout and will help to further elucidate the metabolic

  3. Predicting target vessel location on robot-assisted coronary artery bypass graft using CT to ultrasound registration

    International Nuclear Information System (INIS)

    Cho, Daniel S.; Linte, Cristian; Chen, Elvis C. S.; Bainbridge, Daniel; Wedlake, Chris; Moore, John; Barron, John; Patel, Rajni; Peters, Terry

    2012-01-01

    Purpose: Although robot-assisted coronary artery bypass grafting (RA-CABG) has gained more acceptance worldwide, its success still depends on the surgeon's experience and expertise, and the conversion rate to full sternotomy is in the order of 15%-25%. One of the reasons for conversion is poor pre-operative planning, which is based solely on pre-operative computed tomography (CT) images. In this paper, the authors propose a technique to estimate the global peri-operative displacement of the heart and to predict the intra-operative target vessel location, validated via both an in vitro and a clinical study. Methods: As the peri-operative heart migration during RA-CABG has never been reported in the literatures, a simple in vitro validation study was conducted using a heart phantom. To mimic the clinical workflow, a pre-operative CT as well as peri-operative ultrasound images at three different stages in the procedure (Stage 0 --following intubation; Stage 1 --following lung deflation; and Stage 2 --following thoracic insufflation) were acquired during the experiment. Following image acquisition, a rigid-body registration using iterative closest point algorithm with the robust estimator was employed to map the pre-operative stage to each of the peri-operative ones, to estimate the heart migration and predict the peri-operative target vessel location. Moreover, a clinical validation of this technique was conducted using offline patient data, where a Monte Carlo simulation was used to overcome the limitations arising due to the invisibility of the target vessel in the peri-operative ultrasound images. Results: For the in vitro study, the computed target registration error (TRE) at Stage 0 , Stage 1 , and Stage 2 was 2.1, 3.3, and 2.6 mm, respectively. According to the offline clinical validation study, the maximum TRE at the left anterior descending (LAD) coronary artery was 4.1 mm at Stage 0 , 5.1 mm at Stage 1 , and 3.4 mm at Stage 2 . Conclusions: The authors

  4. Lung allograft rejection in the rat. I. Accelerated rejection caused by graft lymphocytes

    International Nuclear Information System (INIS)

    Prop, J.; Nieuwenhuis, P.; Wildevuur, C.R.

    1985-01-01

    To find out to what extent rejection of lungs differs from that of other organs, functional rejection of lung allografts was studied in five combinations of inbred rat strains. Rejection could be monitored accurately by perfusion scintigraphy, and equally well by chest roentgenography. The rejection of lung grafts was found to proceed remarkably fast, when compared with heart grafts, in combinations with strong RT1-incompatibilities. This accelerated rejection pattern could be converted into rejection at a normal pace by pretreatment of the donor with 10 Gy roentgen irradiation one day before transplantation. Donor pretreatment depleted the lung graft's bronchus-associated lymphoid tissue (BALT) of lymphocytes. When grafts were depleted of all other passenger cells as well--by retransplantation from a cyclosporine-treated intermediate host--they showed an even more reduced immunogenicity, probably because of the loss of donor-type dendritic cells. These results indicate that lymphocytes from the BALT of lung grafts are capable of accelerating the rejection response

  5. Increased circulating follicular helper T cells with decreased programmed death-1 in chronic renal allograft rejection.

    Science.gov (United States)

    Shi, Jian; Luo, Fengbao; Shi, Qianqian; Xu, Xianlin; He, Xiaozhou; Xia, Ying

    2015-11-03

    Chronic antibody-mediated rejection is a major issue that affects long-term renal allograft survival. Since follicular helper T (Tfh) cells promote the development of antigen-specific B cells in alloimmune responses, we investigated the potential roles of Tfh cells, B cells and their alloimmune-regulating molecules in the pathogenesis of chronic renal allograft rejection in this study. The frequency of Tfh, B cells and the levels of their alloimmune-regulating molecules including chemokine receptor type 5 (CXCR5), inducible T cell co-stimulator (ICOS), programmed death-1 (PD-1), ICOSL, PDL-1 and interleukin-21 (IL-21), of peripheral blood were comparatively measured in 42 primary renal allograft recipients within 1-3 years after transplantation. Among them, 24 patients had definite chronic rejection, while other 18 patients had normal renal function. Tfh-cell ratio was significantly increased with PD-1 down-regulation in the patients with chronic renal allograft rejection, while B cells and the alloimmune-regulating molecules studied did not show any appreciable change in parallel. The patients with chronic renal allograft rejection have a characteristic increase in circulating Tfh cells with a decrease in PD-1 expression. These pathological changes may be a therapeutic target for the treatment of chronic renal allograft rejection and can be useful as a clinical index for monitoring conditions of renal transplant.

  6. Resilience and rejection sensitivity mediate long-term outcomes of parental divorce.

    Science.gov (United States)

    Schaan, Violetta K; Vögele, Claus

    2016-11-01

    Increasing divorce rates leave more and more children to deal with the separation of their parents. Recent research suggests that children of divorced parents more often experience psychological and physical symptoms than children of non-divorced parents. The processes that mediate the relationship between parental divorce and ill-health, however, are still elusive. This study investigated the mediating role of psychological factors such as resilience and rejection sensitivity on the long-term consequences of parental divorce in young adults. One hundred and ninety-nine participants (mean age 22.3 years) completed an online survey, including measures of mental health, childhood trauma, resilience, and rejection sensitivity. Participants with divorced parents (33 %) reported increased levels of psychological symptoms, childhood trauma, rejection sensitivity, and lower levels of resilience. The association between parental divorce and mental health was fully mediated by resilience, rejection sensitivity, and childhood trauma. The mediation model explained up to 44 % of the total variance in mental health symptoms. Resilience and rejection sensitivity are crucial factors for successful coping with the experience of parental separation. Prevention programs that help to boost children's resilience might help to reduce the long-term effects of parental divorce on their attachment style (e.g., rejection sensitivity), thereby improving their mental health on the long run. Furthermore, the results call for parental awareness and counseling to target and reduce the observed increased level of childhood trauma. Limitations concern the cross-sectional and retrospective design of the study.

  7. Ferrite grade iron oxides from ore rejects

    Indian Academy of Sciences (India)

    Iron oxyhydroxides and hydroxides were synthesized from chemically beneficiated high SiO2/Al2O3 low-grade iron ore (57.49% Fe2O3) rejects and heated to get iron oxides of 96–99.73% purity. The infrared band positions, isothermal weight loss and thermogravimetric and chemical analysis established the chemical ...

  8. Development of enhanced sulfur rejection processes

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, R.H.; Luttrell, G.H.; Adel, G.T.; Richardson, P.E.

    1996-03-01

    Research at Virginia Tech led to the development of two complementary concepts for improving the removal of inorganic sulfur from many eastern U.S. coals. These concepts are referred to as Electrochemically Enhanced Sulfur Rejection (EESR) and Polymer Enhanced Sulfur Rejection (PESR) processes. The EESR process uses electrochemical techniques to suppress the formation of hydrophobic oxidation products believed to be responsible for the floatability of coal pyrite. The PESR process uses polymeric reagents that react with pyrite and convert floatable middlings, i.e., composite particles composed of pyrite with coal inclusions, into hydrophilic particles. These new pyritic-sulfur rejection processes do not require significant modifications to existing coal preparation facilities, thereby enhancing their adoptability by the coal industry. It is believed that these processes can be used simultaneously to maximize the rejection of both well-liberated pyrite and composite coal-pyrite particles. The project was initiated on October 1, 1992 and all technical work has been completed. This report is based on the research carried out under Tasks 2-7 described in the project proposal. These tasks include Characterization, Electrochemical Studies, In Situ Monitoring of Reagent Adsorption on Pyrite, Bench Scale Testing of the EESR Process, Bench Scale Testing of the PESR Process, and Modeling and Simulation.

  9. Waste heat rejection from geothermal power stations

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, R.C.

    1978-12-01

    This study of waste heat rejection from geothermal power stations is concerned only with the heat rejected from the power cycle. The heat contained in reinjected or otherwise discharged geothermal fluids is not included with the waste heat considered here. The heat contained in the underflow from the flashtanks in such systems is not considered as part of the heat rejected from the power cycle. By following this definition of the waste heat to be rejected, various methods of waste heat dissipation are discussed without regard for the particular arrangement to obtain heat from the geothermal source. Recent conceptual design studies made for 50-MW(e) geothermal power stations at Heber and Niland, California, are of particular interst. The former uses a flashed-steam system and the latter a binary cycle that uses isopentane. In last-quarter 1976 dollars, the total estimated capital costs were about $750/kW and production costs about 50 mills/kWhr. If wet/dry towers were used to conserve 50% of the water evaporation at Heber, production costs would be about 65 mills/kWhr.

  10. Music genre recognition with risk and rejection

    DEFF Research Database (Denmark)

    Sturm, Bob L.

    2013-01-01

    We explore risk and rejection for music genre recognition (MGR) within the minimum risk framework of Bayesian classification. In this way, we attempt to give an MGR system knowledge that some misclassifications are worse than others, and that deferring classification to an expert may be a better...

  11. Antimyosin imaging in cardiac transplant rejection

    International Nuclear Information System (INIS)

    Johnson, L.L.; Cannon, P.J.

    1991-01-01

    Fab fragments of antibodies specific for cardiac myosin have been labeled with indium-111 and injected intravenously into animals and into patients with heart transplants. The antibodies, developed by Khaw, Haber, and co-workers, localize in cardiac myocytes that have been damaged irreversibly by ischemia, myocarditis, or the rejection process. After clearance of the labeled antibody from the cardiac blood pool, planar imaging or single photon emission computed tomography is performed. Scintigrams reveal the uptake of the labeled antimyosin in areas of myocardium undergoing transplant rejection. In animal studies, the degree of antimyosin uptake appears to correlate significantly with the degree of rejection assessed at necropsy. In patients, the correlation between scans and pathologic findings from endomyocardial biopsy is not as good, possibly because of sampling error in the endomyocardial biopsy technique. The scan results at 1 year correlate with either late complications (positive) or benign course (negative). Current limitations of the method include slow blood clearance, long half-life of indium-111, and hepatic uptake. Overcoming these limitations represents a direction for current research. It is possible that from these efforts a noninvasive approach to the diagnosis and evaluation of cardiac transplantation may evolve that will decrease the number of endomyocardial biopsies required to evaluate rejection. This would be particularly useful in infants and children. 31 references

  12. Accept & Reject Statement-Based Uncertainty Models

    NARCIS (Netherlands)

    E. Quaeghebeur (Erik); G. de Cooman; F. Hermans (Felienne)

    2015-01-01

    textabstractWe develop a framework for modelling and reasoning with uncertainty based on accept and reject statements about gambles. It generalises the frameworks found in the literature based on statements of acceptability, desirability, or favourability and clarifies their relative position. Next

  13. Neural Mechanisms of the Rejection-Aggression Link.

    Science.gov (United States)

    Chester, David S; Lynam, Donald R; Milich, Richard; DeWall, C Nathan

    2018-03-28

    Social rejection is a painful event that often increases aggression. However, the neural mechanisms of this rejection-aggression link remain unclear. A potential clue may be that rejected people often recruit the ventrolateral prefrontal cortex's (VLPFC) self-regulatory processes to manage the pain of rejection. Using functional MRI, we replicated previous links between rejection and activity in the brain's mentalizing network, social pain network, and VLPFC. VLPFC recruitment during rejection was associated with greater activity in the brain's reward network (i.e., the ventral striatum) when individuals were given an opportunity to retaliate. This retaliation-related striatal response was associated with greater levels of retaliatory aggression. Dispositionally aggressive individuals exhibited less functional connectivity between the ventral striatum and the right VLPFC during aggression. This connectivity exerted a suppressing effect on dispositionally aggressive individuals' greater aggressive responses to rejection. These results help explain how the pain of rejection and reward of revenge motivate rejected people to behave aggressively.

  14. Self-organizing molecular fingerprints: a ligand-based view on drug-like chemical space and off-target prediction.

    Science.gov (United States)

    Schneider, Gisbert; Tanrikulu, Yusuf; Schneider, Petra

    2009-04-01

    Reliable prediction of multiple ligand-receptor interactions for a given bioactive compound helps recognize and understand off-target effects, and enables drug re-purposing and scaffold-hopping in lead discovery. We developed a ligand-based computational method for drug-target prediction that is independent from protein structural analysis. The idea is to infer drug targets from the pharmacophoric feature similarity of known ligands, and define functional target similarity from a ligand perspective, which also provides access to targets with unknown structures. First, known ligands were represented by topological pharmacophoric features. Then, the self-organizing map technique was used to generate fingerprint patterns for similarity analysis, where each resulting fingerprint represents a drug target. Target fingerprints were clustered and analyzed for correlations. Well-structured dendrograms were obtained presenting interpretable and meaningful relationships between drug targets. Self-organization of fingerprints reduces noise from molecular pharmacophore descriptors, captures their essential features, and reveals potential cross-activities of ligand classes and off-target effects of bioactive compounds.

  15. Cellular basis for accumulation of In-111-labeled leukocytes and platelets in rejecting cardiac allografts: concise communication

    International Nuclear Information System (INIS)

    Wang, T.S.T.; Oluwole, S.; Fawwaz, R.A.; Wolff, M.; Kuromoto, N.; Satake, K.; Hardy, M.A.; Alderson, P.O.

    1982-01-01

    Biodistribution and imaging studies in rats showed that In-111-labeled leukocytes and platelets accumulate progressively with time after transplantation in cardiac allografts undergoing rejection, but do not accumulate in normal syngeneic heart grafts. Maximum heart allograft-to-blood ratios of 9:1 were obtained, and allograft-to-native heart ratios of 17:1. Microscopic studies of the rejecting cardiac allografts showed that histologic findings paralleled the cellular changes predicted by the radionuclide studies. Intravenously administered Ga-67 citrate and Tc-99m sulfur colloid failed to show significant accumulation in rejecting grafts. The findings suggest that cellular rejection, rather than nonspecific inflammatory changes, is the primary basis for accumulation of In-111 leukocytes and platelets in rejecting cardiac allografts

  16. Cellular basis for accumulation of 111In-labeled leukocytes and platelets in rejecting cardiac allografts: concise communication

    International Nuclear Information System (INIS)

    Wang, T.S.; Oluwole, S.; Fawwaz, R.A.; Wolff, M.; Kuromoto, N.; Satake, K.; Hardy, M.A.; Alderson, P.O.

    1982-01-01

    Biodistribution and imaging studies in rats showed that 111 In-labeled leukocytes and platelets accumulate progressively with time after transplantation in cardiac allografts undergoing rejection, but do not accumulate in normal syngeneic heart grafts. Maximum heart allograft-to-blood ratios of 9:1 were obtained, and allograft-to-native heart ratios of 17:1. Microscopic studies of the rejecting cardiac allografts showed that histologic findings paralleled the cellular changes predicted by the radionuclide studies. Intravenously administered 67 Ga citrate and /sup 99m/Tc sulfur colloid failed to show significant accumulation in rejecting grafts. The findings suggest that cellular rejection, rather than nonspecific inflammatory changes, is the primary basis for accumulation of 111 In leukocytes and platelets in rejecting cardiac allografts

  17. To Accept or Reject? The Impact of Adolescent Rejection Sensitivity on Early Adult Romantic Relationships.

    Science.gov (United States)

    Hafen, Christopher A; Spilker, Ann; Chango, Joanna; Marston, Emily S; Allen, Joseph P

    2014-03-01

    Successfully navigating entry into romantic relationships is a key task in adolescence, which sensitivity to rejection can make difficult to accomplish. This study uses multi-informant data from a community sample of 180 adolescents assessed repeatedly from age 16 to 22. Individuals with elevated levels of rejection sensitivity at age 16 were less likely to have a romantic partner at age 22, reported more anxiety and avoidance when they did have relationships, and were observed to be more negative in their interactions with romantic partners. In addition, females whose rejection sensitivity increased during late adolescence were more likely to adopt a submissive pattern within adult romantic relationships, further suggesting a pattern in which rejection sensitivity forecasts difficulties.

  18. Immune response and histology of humoral rejection in kidney transplantation.

    Science.gov (United States)

    González-Molina, Miguel; Ruiz-Esteban, Pedro; Caballero, Abelardo; Burgos, Dolores; Cabello, Mercedes; Leon, Miriam; Fuentes, Laura; Hernandez, Domingo

    2016-01-01

    The adaptive immune response forms the basis of allograft rejection. Its weapons are direct cellular cytotoxicity, identified from the beginning of organ transplantation, and/or antibodies, limited to hyperacute rejection by preformed antibodies and not as an allogenic response. This resulted in allogenic response being thought for decades to have just a cellular origin. But the experimental studies by Gorer demonstrating tissue damage in allografts due to antibodies secreted by B lymphocytes activated against polymorphic molecules were disregarded. The special coexistence of binding and unbinding between antibodies and antigens of the endothelial cell membranes has been the cause of the delay in demonstrating the humoral allogenic response. The endothelium, the target tissue of antibodies, has a high turnover, and antigen-antibody binding is non-covalent. If endothelial cells are attacked by the humoral response, immunoglobulins are rapidly removed from their surface by shedding and/or internalization, as well as degrading the components of the complement system by the action of MCP, DAF and CD59. Thus, the presence of complement proteins in the membrane of endothelial cells is transient. In fact, the acute form of antibody-mediated rejection was not demonstrated until C4d complement fragment deposition was identified, which is the only component that binds covalently to endothelial cells. This review examines the relationship between humoral immune response and the types of acute and chronic histological lesion shown on biopsy of the transplanted organ. Copyright © 2016 Sociedad Española de Nefrología. Published by Elsevier España, S.L.U. All rights reserved.

  19. Rejection of stable cultured allografts by active or passive (adoptive) immunization.

    OpenAIRE

    Vesole, D H; Dart, G A; Talmage, D W

    1982-01-01

    Injection of live lymphoid cells of donor strain or immune cells of recipient strain resulted in rejection of previously stable cultured mouse thyroid allografts. The results are interpreted to indicate that a cultured graft is relatively ineffective in activating recipient lymphocytes but is capable of maintaining them in an activated state and serving as a target for them once they are activated.

  20. Predicting target vessel location on robot-assisted coronary artery bypass graft using CT to ultrasound registration

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Daniel S.; Linte, Cristian; Chen, Elvis C. S.; Bainbridge, Daniel; Wedlake, Chris; Moore, John; Barron, John; Patel, Rajni; Peters, Terry [Imaging Research Laboratories, Robarts Research Institute and Biomedical Engineering Graduate Program, University of Western Ontario, Ontario N6A 5K8 (Canada); Imaging Research Laboratories, Robarts Research Institute and Biomedical Imaging Resource, Mayo Clinic, Rochester, Minnesota 55905 (United States); Imaging Research Laboratories, Robarts Research Institute, University of Western Ontario, Ontario N6A 5K8 (Canada); Canadian Surgical Technologies and Advanced Robotics, London, Ontario N6A 5A5 (Canada); Imaging Research Laboratories, Robarts Research Institute, University of Western Ontario, Ontario N6A 5K8 (Canada); Department of Computer Science, University of Western Ontario, Ontario N6A 5B7 (Canada); Canadian Surgical Technologies and Advanced Robotics, London, Ontario N6A 5A5 (Canada); Imaging Research Laboratories, Robarts Research Institute, Biomedical Engineering Graduate Program, University of Western Ontario N6A 5K8 (Canada); and Canadian Surgical Technologies and Advanced Robotics, London, Ontario N6A 5A5 (Canada)

    2012-03-15

    Purpose: Although robot-assisted coronary artery bypass grafting (RA-CABG) has gained more acceptance worldwide, its success still depends on the surgeon's experience and expertise, and the conversion rate to full sternotomy is in the order of 15%-25%. One of the reasons for conversion is poor pre-operative planning, which is based solely on pre-operative computed tomography (CT) images. In this paper, the authors propose a technique to estimate the global peri-operative displacement of the heart and to predict the intra-operative target vessel location, validated via both an in vitro and a clinical study. Methods: As the peri-operative heart migration during RA-CABG has never been reported in the literatures, a simple in vitro validation study was conducted using a heart phantom. To mimic the clinical workflow, a pre-operative CT as well as peri-operative ultrasound images at three different stages in the procedure (Stage{sub 0}--following intubation; Stage{sub 1}--following lung deflation; and Stage{sub 2}--following thoracic insufflation) were acquired during the experiment. Following image acquisition, a rigid-body registration using iterative closest point algorithm with the robust estimator was employed to map the pre-operative stage to each of the peri-operative ones, to estimate the heart migration and predict the peri-operative target vessel location. Moreover, a clinical validation of this technique was conducted using offline patient data, where a Monte Carlo simulation was used to overcome the limitations arising due to the invisibility of the target vessel in the peri-operative ultrasound images. Results: For the in vitro study, the computed target registration error (TRE) at Stage{sub 0}, Stage{sub 1}, and Stage{sub 2} was 2.1, 3.3, and 2.6 mm, respectively. According to the offline clinical validation study, the maximum TRE at the left anterior descending (LAD) coronary artery was 4.1 mm at Stage{sub 0}, 5.1 mm at Stage{sub 1}, and 3.4 mm at

  1. Significance and suppression of redundant IL17 responses in acute allograft rejection by bioinformatics based drug repositioning of fenofibrate.

    Directory of Open Access Journals (Sweden)

    Silke Roedder

    Full Text Available Despite advanced immunosuppression, redundancy in the molecular diversity of acute rejection (AR often results in incomplete resolution of the injury response. We present a bioinformatics based approach for identification of these redundant molecular pathways in AR and a drug repositioning approach to suppress these using FDA approved drugs currently available for non-transplant indications. Two independent microarray data-sets from human renal allograft biopsies (n = 101 from patients on majorly Th1/IFN-y immune response targeted immunosuppression, with and without AR, were profiled. Using gene-set analysis across 3305 biological pathways, significant enrichment was found for the IL17 pathway in AR in both data-sets. Recent evidence suggests IL17 pathway as an important escape mechanism when Th1/IFN-y mediated responses are suppressed. As current immunosuppressions do not specifically target the IL17 axis, 7200 molecular compounds were interrogated for FDA approved drugs with specific inhibition of this axis. A combined IL17/IFN-y suppressive role was predicted for the antilipidemic drug Fenofibrate. To assess the immunregulatory action of Fenofibrate, we conducted in-vitro treatment of anti-CD3/CD28 stimulated human peripheral blood cells (PBMC, and, as predicted, Fenofibrate reduced IL17 and IFN-γ gene expression in stimulated PMBC. In-vivo Fenofibrate treatment of an experimental rodent model of cardiac AR reduced infiltration of total leukocytes, reduced expression of IL17/IFN-y and their pathway related genes in allografts and recipients' spleens, and extended graft survival by 21 days (p<0.007. In conclusion, this study provides important proof of concept that meta-analyses of genomic data and drug databases can provide new insights into the redundancy of the rejection response and presents an economic methodology to reposition FDA approved drugs in organ transplantation.

  2. Neurokinin3 receptor as a target to predict and improve learning and memory in the aged organism.

    Science.gov (United States)

    de Souza Silva, Maria A; Lenz, Bernd; Rotter, Andrea; Biermann, Teresa; Peters, Oliver; Ramirez, Alfredo; Jessen, Frank; Maier, Wolfgang; Hüll, Michael; Schröder, Johannes; Frölich, Lutz; Teipel, Stefan; Gruber, Oliver; Kornhuber, Johannes; Huston, Joseph P; Müller, Christian P; Schäble, Sandra

    2013-09-10

    Impaired learning and memory performance is often found in aging as an early sign of dementia. It is associated with neuronal loss and reduced functioning of cholinergic networks. Here we present evidence that the neurokinin3 receptors (NK3-R) and their influence on acetylcholine (ACh) release may represent a crucial mechanism that underlies age-related deficits in learning and memory. Repeated pharmacological stimulation of NK3-R in aged rats was found to improve learning in the water maze and in object-place recognition. This treatment also enhanced in vivo acetylcholinergic activity in the frontal cortex, hippocampus, and amygdala but reduced NK3-R mRNA expression in the hippocampus. Furthermore, NK3-R agonism incurred a significantly higher increase in ACh levels in aged animals that showed superior learning than in those that were most deficient in learning. Our findings suggest that the induced activation of ACh, rather than basal ACh activity, is associated with superior learning in the aged. To test whether natural variation in NK3-R function also determines learning and memory performance in aged humans, we investigated 209 elderly patients with cognitive impairments. We found that of the 15 analyzed single single-nucleotide ploymorphism (SNPs) of the NK3-R-coding gene, TACR3, the rs2765 SNP predicted the degree of impairment of learning and memory in these patients. This relationship could be partially explained by a reduced right hippocampus volume in a subsample of 111 tested dementia patients. These data indicate the NK3-R as an important target to predict and improve learning and memory performance in the aged organism.

  3. A Two-Step Model of Acute CD4 T-Cell Mediated Cardiac Allograft Rejection1

    OpenAIRE

    Grazia, Todd J.; Pietra, Biagio A.; Johnson, Zachary A.; Kelly, Brian P.; Plenter, Robert J.; Gill, Ronald G.

    2004-01-01

    CD4 T cells are both necessary and sufficient to mediate acute cardiac allograft rejection in mice. This process requires “direct” engagement of donor MHC class II molecules. That is, acute rejection by CD4+ T cells requires target MHC class II expression by the donor and not by the host. However, it is unclear whether CD4+ T cell rejection requires MHC class II expression on donor hemopoietic cells, nonhemopoietic cells, or both. To address this issue, bone marrow transplantation in mice was...

  4. Partial interference subspace rejection in CDMA systems

    DEFF Research Database (Denmark)

    Hansen, Henrik; Affes, Sofiene; Mewelstein, Paul

    2001-01-01

    Previously presented interference subspace rejection (ISR) proposed a family of new efficient multiuser detectors for CDMA. We reconsider in this paper the modes of ISR using decision feedback (DF). DF modes share similarities with parallel interference cancellation (PIC) but attempt to cancel...... interference by nulling rather than subtraction. However like the PIC they are prone to wrong tentative decisions. We propose a modification to DF modes that performs partial ISR instead of complete interference cancellation. When tentative decisions are correct, interference is therefore not perfectly...... rejected anymore. This drawback is compensated by improved robustness to wrong tentative decisions. We show that in hard handoff systems, partial ISR can only provide negligible performance improvements in high loaded systems outside the region of interest due to out-sector interference. In situations...

  5. Background Rejection in the ARA Experiment

    Directory of Open Access Journals (Sweden)

    Pfendner Carl

    2017-01-01

    Full Text Available The Askaryan Radio Array (ARA is a radio frequency observatory under construction at the South Pole that is searching for ultrahigh energy neutrinos via the Askaryan effect. Thermal fluctuations currently dominate the trigger-level background for the observatory and anthropogenic sources also introduce a significant source of noise. By taking advantage of the observatory’s regular geometry and the expected coincident nature of the RF signals arriving from neutrino-induced events, this background can be filtered efficiently. This contribution will discuss techniques developed for the ARA analyses to reject these thermal signals, to reject anthropogenic backgrounds, and to search for neutrino-induced particle showers in the Antarctic ice. The results of a search for neutrinos from GRBs using the prototype station using some of these techniques will be presented.

  6. Parametric Adaptive Radar Detector with Enhanced Mismatched Signals Rejection Capabilities

    Directory of Open Access Journals (Sweden)

    Liu Bin

    2010-01-01

    Full Text Available We consider the problem of adaptive signal detection in the presence of Gaussian noise with unknown covariance matrix. We propose a parametric radar detector by introducing a design parameter to trade off the target sensitivity with sidelobes energy rejection. The resulting detector merges the statistics of Kelly's GLRT and of the Rao test and so covers Kelly's GLRT and the Rao test as special cases. Both invariance properties and constant false alarm rate (CFAR behavior for this detector are studied. At the analysis stage, the performance of the new receiver is assessed and compared with several traditional adaptive detectors. The results highlight better rejection capabilities of this proposed detector for mismatched signals. Further, we develop two two-stage detectors, one of which consists of an adaptive matched filter (AMF followed by the aforementioned detector, and the other is obtained by cascading a GLRT-based Subspace Detector (SD and the proposed adaptive detector. We show that the former two-stage detector outperforms traditional two-stage detectors in terms of selectivity, and the latter yields more robustness.

  7. Magnetic Nanoparticles in-vivo Detection of Transplant Rejection

    Science.gov (United States)

    Flynn, E. R.; Bryant, H. C.; Larson, R. S.; Sergatskov, D. A.

    2006-03-01

    Superparamagnetic nanoparticles are being used to develop methodology for the in-vivo detection and imaging of immune system attacks on transplanted organs. The signature for impending rejection of a transplant is enhanced presence of T-cells. Magnetic nanoparticles coated with specific antibodies (CD-2 and CD-3) will target and attach to these T-cells. Approximately 3 .10^5 nanoparticles can attach to each cell. When a pulsed external magnetic field is applied to the decorated cells for a fraction of a second, magnetic moments of the nanoparticles aligned with the field. After the pulse is switched off, the net magnetic moment decays over several seconds by the Nèel mechanism. The resulting magnetic remanence field (typically 10-11 T) is measured using a multi-channel SQUID array. We present the data from live T-cells placed in realistic kidney phantom. The detection sensitivity was ˜2.10^3 T-cells - a small fraction of the number actually invading the rejected transplant. The 7-channel SQUID array allows us to image the cell clusters with a few millimeters resolution.

  8. Antibody-Mediated Rejection: Pathogenesis, Prevention, Treatment, and Outcomes

    Directory of Open Access Journals (Sweden)

    Olivia R. Blume

    2012-01-01

    Full Text Available Antibody-mediated rejection (AMR is a major cause of late kidney transplant failure. It is important to have an understanding of human-leukocyte antigen (HLA typing including well-designed studies to determine anti-MHC-class-I-related chain A (MICA and antibody rejection pathogenesis. This can allow for more specific diagnosis and treatment which may improve long-term graft function. HLA-specific antibody detection prior to transplantation allows one to help determine the risk for AMR while detection of DSA along with a biopsy confirms it. It is now appreciated that biopsy for AMR does not have to include diffuse C4d, but does require a closer look at peritubular capillary microvasculature. Although plasmapheresis (PP is effective in removing alloantibodies (DSAs from the circulation, rebound synthesis of alloantibodies can occur. Splenectomy is used in desensitization protocols for ABO incompatible transplants as well as being found to treat AMR refractory to conventional treatment. Also used are agents targeted for plasma cells, B cells, and the complement cascade which are bortezomib rituximab and eculizumab, respectively.

  9. Ferrite grade iron oxides from ore rejects

    Indian Academy of Sciences (India)

    Unknown

    Ferrite grade iron oxides from ore rejects. 333. S 250 MK III were used to find out the particle size distributions in the final oxide products. 3. Results and discussion. 3.1 Phase identification. The dhkl values of all oxide products were compared with the JCPDS files: 24–81 and 25–1402. All were found to be mainly γ-Fe2O3 ...

  10. Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm

    Science.gov (United States)

    Öhrmalm, Christina; Jobs, Magnus; Eriksson, Ronnie; Golbob, Sultan; Elfaitouri, Amal; Benachenhou, Farid; Strømme, Maria; Blomberg, Jonas

    2010-01-01

    One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes. PMID:20864443

  11. High energy density physics effects predicted in simulations of the CERN HiRadMat beam-target interaction experiments

    Science.gov (United States)

    Tahir, N. A.; Burkart, F.; Schmidt, R.; Shutov, A.; Wollmann, D.; Piriz, A. R.

    2016-12-01

    Experiments have been done at the CERN HiRadMat (High Radiation to Materials) facility in which large cylindrical copper targets were irradiated with 440 GeV proton beam generated by the Super Proton Synchrotron (SPS). The primary purpose of these experiments was to confirm the existence of hydrodynamic tunneling of ultra-relativistic protons and their hadronic shower in solid materials, that was predicted by previous numerical simulations. The experimental measurements have shown very good agreement with the simulation results. This provides confidence in our simulations of the interaction of the 7 TeV LHC (Large Hadron Collider) protons and the 50 TeV Future Circular Collider (FCC) protons with solid materials, respectively. This work is important from the machine protection point of view. The numerical simulations have also shown that in the HiRadMat experiments, a significant part of thetarget material is be converted into different phases of High Energy Density (HED) matter, including two-phase solid-liquid mixture, expanded as well as compressed hot liquid phases, two-phase liquid-gas mixture and gaseous state. The HiRadMat facility is therefore a unique ion beam facility worldwide that is currently available for studying the thermophysical properties of HED matter. In the present paper we discuss the numerical simulation results and present a comparison with the experimental measurements.

  12. Neural Responses to Peer Rejection in Anxious Adolescents: Contributions from the Amygdala-Hippocampal Complex

    Science.gov (United States)

    Lau, Jennifer Y. F.; Guyer, Amanda E.; Tone, Erin B.; Jenness, Jessica; Parrish, Jessica M.; Pine, Daniel S.; Nelson, Eric E.

    2012-01-01

    Peer rejection powerfully predicts adolescent anxiety. While cognitive differences influence anxious responses to social feedback, little is known about neural contributions. Twelve anxious and twelve age-, gender- and IQ-matched, psychiatrically healthy adolescents received "not interested" and "interested" feedback from unknown peers during a…

  13. Active disturbance rejection controller for chemical reactor

    International Nuclear Information System (INIS)

    Both, Roxana; Dulf, Eva H.; Muresan, Cristina I.

    2015-01-01

    In the petrochemical industry, the synthesis of 2 ethyl-hexanol-oxo-alcohols (plasticizers alcohol) is of high importance, being achieved through hydrogenation of 2 ethyl-hexenal inside catalytic trickle bed three-phase reactors. For this type of processes the use of advanced control strategies is suitable due to their nonlinear behavior and extreme sensitivity to load changes and other disturbances. Due to the complexity of the mathematical model an approach was to use a simple linear model of the process in combination with an advanced control algorithm which takes into account the model uncertainties, the disturbances and command signal limitations like robust control. However the resulting controller is complex, involving cost effective hardware. This paper proposes a simple integer-order control scheme using a linear model of the process, based on active disturbance rejection method. By treating the model dynamics as a common disturbance and actively rejecting it, active disturbance rejection control (ADRC) can achieve the desired response. Simulation results are provided to demonstrate the effectiveness of the proposed method

  14. Mesenchymal stem cells avoid allogeneic rejection

    Directory of Open Access Journals (Sweden)

    Murphy J Mary

    2005-07-01

    Full Text Available Abstract Adult bone marrow derived mesenchymal stem cells offer the potential to open a new frontier in medicine. Regenerative medicine aims to replace effete cells in a broad range of conditions associated with damaged cartilage, bone, muscle, tendon and ligament. However the normal process of immune rejection of mismatched allogeneic tissue would appear to prevent the realisation of such ambitions. In fact mesenchymal stem cells avoid allogeneic rejection in humans and in animal models. These finding are supported by in vitro co-culture studies. Three broad mechanisms contribute to this effect. Firstly, mesenchymal stem cells are hypoimmunogenic, often lacking MHC-II and costimulatory molecule expression. Secondly, these stem cells prevent T cell responses indirectly through modulation of dendritic cells and directly by disrupting NK as well as CD8+ and CD4+ T cell function. Thirdly, mesenchymal stem cells induce a suppressive local microenvironment through the production of prostaglandins and interleukin-10 as well as by the expression of indoleamine 2,3,-dioxygenase, which depletes the local milieu of tryptophan. Comparison is made to maternal tolerance of the fetal allograft, and contrasted with the immune evasion mechanisms of tumor cells. Mesenchymal stem cells are a highly regulated self-renewing population of cells with potent mechanisms to avoid allogeneic rejection.

  15. Rejection Sensitivity in Late Adolescence: Social and Emotional Sequelae

    OpenAIRE

    Marston, Emily G.; Hare, Amanda; Allen, Joseph P.

    2010-01-01

    This study used longitudinal, multi-reporter data, in a community sample, to examine the role of rejection sensitivity in late adolescents’ social and emotional development. Rejection sensitivity was linked to a relative increase in adolescent depressive and anxiety symptoms over a three-year period, even after accounting for teens’ baseline level of social competence. Additionally, reciprocal relationships emerged between rejection sensitivity and internalizing symptoms. Rejection sensitivit...

  16. Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs.

    Science.gov (United States)

    Le, Duc-Hau; Verbeke, Lieven; Son, Le Hoang; Chu, Dinh-Toi; Pham, Van-Huy

    2017-11-14

    MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes. Although such homogeneous networks can predict potential disease-associated miRNAs, they do not consider the roles of the target genes of the miRNAs. Here, we introduce a novel method based on a heterogeneous network that not only considers miRNAs but also the corresponding target genes in the network model. Instead of constructing homogeneous miRNA networks, we built heterogeneous miRNA networks consisting of both miRNAs and their target genes, using databases of known miRNA-target gene interactions. In addition, as recent studies demonstrated reciprocal regulatory relations between miRNAs and their target genes, we considered these heterogeneous miRNA networks to be undirected, assuming mutual miRNA-target interactions. Next, we introduced a novel method (RWRMTN) operating on these mutual heterogeneous miRNA networks to rank candidate disease-related miRNAs using a random walk with restart (RWR) based algorithm. Using both known disease-associated miRNAs and their target genes as seed nodes, the method can identify additional miRNAs involved in the disease phenotype. Experiments indicated that RWRMTN outperformed two existing state-of-the-art methods: RWRMDA, a network-based method that also uses a RWR on homogeneous (rather than heterogeneous) miRNA networks, and RLSMDA, a machine learning-based method. Interestingly, we could relate this performance gain to the emergence of "disease modules" in the heterogeneous miRNA networks used as input for the algorithm. Moreover, we could demonstrate that RWRMTN is stable

  17. Alteration of Cardiac Deformation in Acute Rejection in Pediatric Heart Transplant Recipients.

    Science.gov (United States)

    Chanana, Nitin; Van Dorn, Charlotte S; Everitt, Melanie D; Weng, Hsin Yi; Miller, Dylan V; Menon, Shaji C

    2017-04-01

    The objective of this study is to assess changes in cardiac deformation during acute cellular- and antibody-mediated rejection in pediatric HT recipients. Pediatric HT recipients aged ≤18 years with at least one episode of biopsy-diagnosed rejection from 2006 to 2013 were included. Left ventricular systolic S (SS) and SR (SSr) data were acquired using 2D speckle tracking on echocardiograms obtained within 12 h of right ventricular endomyocardial biopsy. A mixed effect model was used to compare cardiac deformation during CR (Grade ≥ 1R), AMR (pAMR ≥ 2), and mixed rejection (CR and AMR positive) versus no rejection (Grade 0R and pAMR 0 or 1). A total of 20 subjects (10 males, 50%) with 71 rejection events (CR 35, 49%; AMR 21, 30% and mixed 15, 21%) met inclusion criteria. The median time from HT to first biopsy used for analysis was 5 months (IQR 0.25-192 months). Average LV longitudinal SS and SSr were reduced significantly during rejection (SS: -17.2 ± 3.4% vs. -10.7 ± 4.5%, p < 0.001 and SSr: -1.2 ± 0.2 s - 1 vs. -0.9 ± 0.3 s - 1 ; p < 0.001) and in all rejection types. Average LV short-axis radial SS was reduced only in CR compared to no rejection (p = 0.04), while average LV circumferential SS and SSr were reduced significantly in AMR compared to CR (SS: 18.9 ± 4.2% vs. 20.8 ± 8.8%, p = 0.03 and SSr: 1.35 ± 0.8 s - 1 vs. 1.54 ± 0.9 s - 1 ; p = 0.03). In pediatric HT recipients, LV longitudinal SS and SSr were reduced in all rejection types, while LV radial SS was reduced only in CR. LV circumferential SS and SSr further differentiated between CR and AMR with a significant reduction seen in AMR as compared to CR. This novel finding suggests mechanistic differences between AMR- and CR-induced myocardial injury which may be useful in non-invasively predicting the type of rejection in pediatric HT recipients.

  18. Analyses of Potential Predictive Markers and Response to Targeted Therapy in Patients with Advanced Clear-cell Renal Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Yan Song

    2015-01-01

    Full Text Available Background: Vascular endothelial growth factor-targeted agents are standard treatments in advanced clear-cell renal cell carcinoma (ccRCC, but biomarkers of activity are lacking. The aim of this study was to investigate the association of Von Hippel-Lindau (VHL gene status, vascular endothelial growth factor receptor (VEGFR or stem cell factor receptor (KIT expression, and their relationships with characteristics and clinical outcome of advanced ccRCC. Methods: A total of 59 patients who received targeted treatment with sunitinib or pazopanib were evaluated for determination at Cancer Hospital and Institute, Chinese Academy of Medical Sciences between January 2010 and November 2012. Paraffin-embedded tumor samples were collected and status of the VHL gene and expression of VEGFR and KIT were determined by VHL sequence analysis and immunohistochemistry. Clinical-pathological features were collected and efficacy such as response rate and Median progression-free survival (PFS and overall survival (OS were calculated and then compared based on expression status. The Chi-square test, the Kaplan-Meier method, and the Lon-rank test were used for statistical analyses. Results: Of 59 patients, objective responses were observed in 28 patients (47.5%. The median PFS was 13.8 months and median OS was 39.9 months. There was an improved PFS in patients with the following clinical features: Male gender, number of metastatic sites 2 or less, VEGFR-2 positive or KIT positive. Eleven patients (18.6% had evidence of VHL mutation, with an objective response rate of 45.5%, which showed no difference with patients with no VHL mutation (47.9%. VHL mutation status did not correlate with either overall response rate (P = 0.938 or PFS (P = 0.277. The PFS was 17.6 months and 22.2 months in VEGFR-2 positive patients and KIT positive patients, respectively, which was significantly longer than that of VEGFR-2 or KIT negative patients (P = 0.026 and P = 0.043. Conclusion

  19. Real-Time PCR Targeting thepenAMosaic XXXIV Type for Prediction of Extended-Spectrum-Cephalosporin Susceptibility in Clinical Neisseria gonorrhoeae Isolates.

    Science.gov (United States)

    Wong, L K; Hemarajata, P; Soge, O O; Humphries, R M; Klausner, J D

    2017-11-01

    Neisseria gonorrhoeae isolates with decreased susceptibility to extended-spectrum cephalosporins (ESCs) are increasing. We developed an assay to predict N. gonorrhoeae susceptibility to ESCs by targeting penA mosaic XXXIV, an allele prevalent among U.S. isolates with elevated ESC MICs. The assay was 97% sensitive and 100% specific for predicting at least one ESC MIC above the CDC alert value among clinical isolates, and it could be multiplexed with a previously validated gyrA PCR to predict ciprofloxacin susceptibility. Copyright © 2017 American Society for Microbiology.

  20. A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation.

    Science.gov (United States)

    Khatri, Purvesh; Roedder, Silke; Kimura, Naoyuki; De Vusser, Katrien; Morgan, Alexander A; Gong, Yongquan; Fischbein, Michael P; Robbins, Robert C; Naesens, Maarten; Butte, Atul J; Sarwal, Minnie M

    2013-10-21

    Using meta-analysis of eight independent transplant datasets (236 graft biopsy samples) from four organs, we identified a common rejection module (CRM) consisting of 11 genes that were significantly overexpressed in acute rejection (AR) across all transplanted organs. The CRM genes could diagnose AR with high specificity and sensitivity in three additional independent cohorts (794 samples). In another two independent cohorts (151 renal transplant biopsies), the CRM genes correlated with the extent of graft injury and predicted future injury to a graft using protocol biopsies. Inferred drug mechanisms from the literature suggested that two FDA-approved drugs (atorvastatin and dasatinib), approved for nontransplant indications, could regulate specific CRM genes and reduce the number of graft-infiltrating cells during AR. We treated mice with HLA-mismatched mouse cardiac transplant with atorvastatin and dasatinib and showed reduction of the CRM genes, significant reduction of graft-infiltrating cells, and extended graft survival. We further validated the beneficial effect of atorvastatin on graft survival by retrospective analysis of electronic medical records of a single-center cohort of 2,515 renal transplant patients followed for up to 22 yr. In conclusion, we identified a CRM in transplantation that provides new opportunities for diagnosis, drug repositioning, and rational drug design.

  1. A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation

    Science.gov (United States)

    Khatri, Purvesh; Roedder, Silke; Kimura, Naoyuki; De Vusser, Katrien; Morgan, Alexander A.; Gong, Yongquan; Fischbein, Michael P.; Robbins, Robert C.; Naesens, Maarten

    2013-01-01

    Using meta-analysis of eight independent transplant datasets (236 graft biopsy samples) from four organs, we identified a common rejection module (CRM) consisting of 11 genes that were significantly overexpressed in acute rejection (AR) across all transplanted organs. The CRM genes could diagnose AR with high specificity and sensitivity in three additional independent cohorts (794 samples). In another two independent cohorts (151 renal transplant biopsies), the CRM genes correlated with the extent of graft injury and predicted future injury to a graft using protocol biopsies. Inferred drug mechanisms from the literature suggested that two FDA-approved drugs (atorvastatin and dasatinib), approved for nontransplant indications, could regulate specific CRM genes and reduce the number of graft-infiltrating cells during AR. We treated mice with HLA-mismatched mouse cardiac transplant with atorvastatin and dasatinib and showed reduction of the CRM genes, significant reduction of graft-infiltrating cells, and extended graft survival. We further validated the beneficial effect of atorvastatin on graft survival by retrospective analysis of electronic medical records of a single-center cohort of 2,515 renal transplant patients followed for up to 22 yr. In conclusion, we identified a CRM in transplantation that provides new opportunities for diagnosis, drug repositioning, and rational drug design. PMID:24127489

  2. Relationship between platelet serotonin content and rejections of unfair offers in the ultimatum game.

    Science.gov (United States)

    Emanuele, Enzo; Brondino, Natascia; Bertona, Marco; Re, Simona; Geroldi, Diego

    2008-05-30

    The ultimatum game (UG), a well-studied decision task used in experimental neuroeconomics, represents a simple two-person bargaining between a proposer and a responder. The proposer offers the responder how to split a sum of money. The responder decides whether to accept or reject the offer. When the responder accepts it, each player earns money according to the proposer's offer. If the offer is rejected, neither player gets anything. Rejections of "free" money in the UG represent a deviation from the standard economic model of rationality. This behaviour could be linked to adverse psychological reactions to unfair offers, including anger, hostility and impulsiveness. Currently, it is believed that the most plausible biological system related to anger and impulsivity is the serotonergic system. We hypothesize that serotonergic activity, as measured by platelet serotonin levels, will differentiate subjects who either reject or accept low UG offers. A sample of 60 economy students (31 males and 29 females, mean age: 24.4+/-2.3 years) was investigated. As predicted, the mean platelet serotonin level was significantly lower in participants who reject unfair offers (euro 1 out of euro 10) than in those who accept (2.86+/-0.13 versus 3.48+/-0.11 nmol/10(9) platelets, respectively, p<0.001). We conclude that low platelet serotonin may serve as a reliable biomarker to identify people who are more likely to reject unfair ultimatum offers in an experimental neuroeconomic setting. Our pilot data seem to indicate that the serotonergic system may play an important role in the UG rejection behaviour.

  3. CD28 Family and Chronic Rejection: “To Belatacept...and Beyond!”

    Directory of Open Access Journals (Sweden)

    Marcos V. Silva

    2012-01-01

    Full Text Available Kidneys are one of the most frequently transplanted human organs. Immunosuppressive agents may prevent or reverse most acute rejection episodes; however, the graft may still succumb to chronic rejection. The immunological response involved in the chronic rejection process depends on both innate and adaptive immune response. T lymphocytes have a pivotal role in chronic rejection in adaptive immune response. Meanwhile, we aim to present a general overview on the state-of-the-art knowledge of the strategies used for manipulating the lymphocyte activation mechanisms involved in allografts, with emphasis on T-lymphocyte costimulatory and coinhibitory molecules of the B7-CD28 superfamily. A deeper understanding of the structure and function of these molecules improves both the knowledge of the immune system itself and their potential action as rejection inducers or tolerance promoters. In this context, the central role played by CD28 family, especially the relationship between CD28 and CTLA-4, becomes an interesting target for the development of immune-based therapies aiming to increase the survival rate of allografts and to decrease autoimmune phenomena. Good results obtained by the recent development of abatacept and belatacept with potential clinical use aroused better expectations concerning the outcome of transplanted patients.

  4. Nitration and Inactivation of Manganese Superoxide Dismutase in Chronic Rejection of Human Renal Allografts

    Science.gov (United States)

    MacMillan-Crow, L. A.; Crow, John P.; Kerby, Jeffrey D.; Beckman, Joseph S.; Thompson, John A.

    1996-10-01

    Inflammatory processes in chronic rejection remain a serious clinical problem in organ transplantation. Activated cellular infiltrate produces high levels of both superoxide and nitric oxide. These reactive oxygen species interact to form peroxynitrite, a potent oxidant that can modify proteins to form 3-nitrotyrosine. We identified enhanced immunostaining for nitrotyrosine localized to tubular epithelium of chronically rejected human renal allografts. Western blot analysis of rejected tissue demonstrated that tyrosine nitration was restricted to a few specific polypeptides. Immunoprecipitation and amino acid sequencing techniques identified manganese superoxide dismutase, the major antioxidant enzyme in mitochondria, as one of the targets of tyrosine nitration. Total manganese superoxide dismutase protein was increased in rejected kidney, particularly in the tubular epithelium; however, enzymatic activity was significantly decreased. Exposure of recombinant human manganese superoxide dismutase to peroxynitrite resulted in a dose-dependent (IC50 = 10 μ M) decrease in enzymatic activity and concomitant increase in tyrosine nitration. Collectively, these observations suggest a role for peroxynitrite during development and progression of chronic rejection in human renal allografts. In addition, inactivation of manganese superoxide dismutase by peroxynitrite may represent a general mechanism that progressively increases the production of peroxynitrite, leading to irreversible oxidative injury to mitochondria.

  5. A comparison of the predictive performance of three pharmacokinetic models for propofol using measured values obtained during target-controlled infusion

    NARCIS (Netherlands)

    Glen, J. B.; White, M.

    2014-01-01

    We compared the predictive performance of the existing Diprifusor and Schnider models, used for target-controlled infusion of propofol, with a new modification of the Diprifusor model (White) incorporating age and sex covariates. The bias and inaccuracy (precision) of each model were determined

  6. Network pharmacology-based prediction of the active ingredients and potential targets of Mahuang Fuzi Xixin decoction for application to allergic rhinitis.

    Science.gov (United States)

    Tang, Feng; Tang, Qingfa; Tian, Yuanxin; Fan, Qin; Huang, Yao; Tan, Xiaomei

    2015-12-24

    Certain herbal formulae from Traditional Chinese Medicine (TCM) are effective for treating and preventing diseases in clinical practice. Mahuang fuzi Xixin Decoction (MFXD) is a TCM that is used to treat allergic rhinitis (AR); however, the active ingredients and potential targets of its action against AR remain unclear. Therefore, further investigation is required. A network pharmacology approach comprising drug-likeness evaluation, oral bioavailability prediction, multiple drug target prediction, and network analysis has been used in this study. The comprehensive systematic approach was successfully to indentify 41 bioactive ingredients in MFXD, while 37 potential targets hit by these ingredients related to AR. Moreover, wherein four predicted ingredients possess anti-inflammatory effects were found by this technique. Our works successfully predict the active ingredients and potential targets of MFXD for application to allergic rhinitis and helps to illustrate mechanism of action on a systematic level. This study not only provides new insights into the chemical basis and pharmacology of MFXD but also demonstrates a feasible method for discovering potential drugs from herbal medicine. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  7. Computational prediction of MicroRNAs targeting GABA receptors and experimental verification of miR-181, miR-216 and miR-203 targets in GABA-A receptor

    Directory of Open Access Journals (Sweden)

    Zhao Chunling

    2012-02-01

    Full Text Available Abstract Background GABA receptors are well known as the inhibitory receptors in the central nervous system and are also found in peripheral tissues. We have previously shown that GABA receptors are involved in lung development and fluid homeostasis. However, the microRNAs that regulate GABA receptors have not yet been identified. Results In this study, we used the online software, TargetScan and miRanda, to query the microRNAs that directly target GABA receptors and then selected some of them to verify experimentally using 3'-UTR reporter assays. Computational approaches predict many microRNA binding sites on the 3'-UTR of GABAA receptors, but not on GABAC receptors. 3'-UTR reporter assays only verified miR-181, miR-216, and miR-203 as the microRNAs that target GABA receptor α1-subunit among 10 microRNAs tested. Conclusions Our studies reinforce that microRNA target prediction needs to be verified experimentally. The identification of microRNAs that target GABA receptors provides a basis for further studies of post-transcriptional regulation of GABA receptors.

  8. Rejection in Bargaining Situations: An Event-Related Potential Study in Adolescents and Adults.

    Directory of Open Access Journals (Sweden)

    Kiki Zanolie

    Full Text Available The neural correlates of rejection in bargaining situations when proposing a fair or unfair offer are not yet well understood. We measured neural responses to rejection and acceptance of monetary offers with event-related potentials (ERPs in mid-adolescents (14-17 years and early adults (19-24 years. Participants played multiple rounds of the Ultimatum Game as proposers, dividing coins between themselves and a second player (responder by making a choice between an unfair distribution (7 coins for proposer and 3 for responder; 7/3 and one of two alternatives: a fair distribution (5/5 or a hyperfair distribution (3/7. Participants mostly made fair offers (5/5 when the alternative was unfair (7/3, but made mostly unfair offers (7/3 when the alternative was hyperfair (3/7. When participants' fair offers (5/5; alternative was 7/3 were rejected this was associated with a larger Medial Frontal Negativity (MFN compared to acceptance of fair offers and rejection of unfair offers (7/3; alternative was 3/7. Also, the MFN was smaller after acceptance of unfair offers (7/3 compared to rejection. These neural responses did not differ between adults and mid-adolescents, suggesting that the MFN reacts as a neural alarm system to social prediction errors which is already prevalent during adolescence.

  9. Changing Paradigms in the Management of Rejection in Kidney Transplantation

    Directory of Open Access Journals (Sweden)

    Mirela Maier

    2017-01-01

    Full Text Available Purpose of review: P4 medicine denotes an evolving field of medicine encompassing predictive, preventive, personalized, and participatory medicine. Using the example of kidney allograft rejection because of donor-recipient incompatibility in human leukocyte antigens, this review outlines P4 medicine’s relevance to the various stages of the kidney transplant cycle. Sources of information: A search for English articles was conducted in Medline via OvidSP (up to August 18, 2016 using a combination of subject headings (MeSH and free text in titles, abstracts, and author keywords for the concepts kidney transplantation and P4 medicine. The electronic database search was expanded further on particular subject headings. Findings: Available histocompatibility methods exemplify current applications of the predictive and preventive domains of P4 medicine in kidney transplant recipients’ care. Pharmacogenomics are discussed as means to facilitate personalized immunosuppression regimens and promotion of active patient participation as a means to improve adherence. Limitations: For simplicity, this review focuses on rejection. P4 medicine, however, should more broadly address health concerns in kidney transplant recipients, including competing outcomes such as infections, malignancies, and cardiovascular disease. This review highlights how biomarkers to evaluate these competing outcomes warrant validation and standardization prior to their incorporation into clinical practice. Implications: Consideration of all 4 domains of the P4 medicine framework when caring for and/or studying kidney transplant recipients has the potential of increasing therapeutic efficiency, minimizing adverse effects, decreasing health care costs, and maximizing wellness. Technologies to gauge immune competency, immunosuppression requirements, and early/reversible immune-mediated injuries are required to optimize kidney transplant care.

  10. Changing Paradigms in the Management of Rejection in Kidney Transplantation

    Science.gov (United States)

    Maier, Mirela; Takano, Tomoko; Sapir-Pichhadze, Ruth

    2017-01-01

    Purpose of review: P4 medicine denotes an evolving field of medicine encompassing predictive, preventive, personalized, and participatory medicine. Using the example of kidney allograft rejection because of donor-recipient incompatibility in human leukocyte antigens, this review outlines P4 medicine’s relevance to the various stages of the kidney transplant cycle. Sources of information: A search for English articles was conducted in Medline via OvidSP (up to August 18, 2016) using a combination of subject headings (MeSH) and free text in titles, abstracts, and author keywords for the concepts kidney transplantation and P4 medicine. The electronic database search was expanded further on particular subject headings. Findings: Available histocompatibility methods exemplify current applications of the predictive and preventive domains of P4 medicine in kidney transplant recipients’ care. Pharmacogenomics are discussed as means to facilitate personalized immunosuppression regimens and promotion of active patient participation as a means to improve adherence. Limitations: For simplicity, this review focuses on rejection. P4 medicine, however, should more broadly address health concerns in kidney transplant recipients, including competing outcomes such as infections, malignancies, and cardiovascular disease. This review highlights how biomarkers to evaluate these competing outcomes warrant validation and standardization prior to their incorporation into clinical practice. Implications: Consideration of all 4 domains of the P4 medicine framework when caring for and/or studying kidney transplant recipients has the potential of increasing therapeutic efficiency, minimizing adverse effects, decreasing health care costs, and maximizing wellness. Technologies to gauge immune competency, immunosuppression requirements, and early/reversible immune-mediated injuries are required to optimize kidney transplant care. PMID:28270929

  11. Thermoelectric air conditioning with water heat rejection

    International Nuclear Information System (INIS)

    Buffet, J.P.

    1984-01-01

    A brief review of thermoelectric air conditioning with water heat rejection is given. Water vapour condensation can produce water droplet carry over which considerably reduces cooling performance. A model to calculate condensation is described, calculations are presented in graphic form that give water film thickness on heat exchange surfaces and influence on cooling performances. A new industrial design is presented that has two important features: a continuous water tube that is grounded and air heat exchangers that eliminate water as it condensates. Performances and specific volumes of subunits are given

  12. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

    LENUS (Irish Health Repository)

    Browne, Patrick

    2010-11-25

    Abstract Background Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5\\' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate

  13. A simple, fast and accurate thermodynamic-based approach for transfer and prediction of GC retention times between columns and instruments Part III: Retention time prediction on target column.

    Science.gov (United States)

    Hou, Siyuan; Stevenson, Keisean A J M; Harynuk, James J

    2018-03-27

    This is the third part of a three-part series of papers. In Part I we presented a method for determining the actual effective geometry of a reference column as well as the thermodynamic-based parameters of a set of probe compounds in an in-house mixture. Part II introduced an approach for estimating the actual effective geometry of a target column by collecting retention data of the same mixture of probe compounds on the target column and using their thermodynamic parameters, acquired on the reference column, as a bridge between both systems. Part III, presented here, demonstrates the retention time transfer and prediction from the reference column to the target column using experimental data for a separate mixture of compounds. To predict the retention time of a new compound we first estimate its thermodynamic-based parameters on the reference column (using geometric parameters determined previously). The compound's retention time on a second column (of previously determined geometry) is then predicted. The models and the associated optimization algorithms were tested using simulated and experimental data. The accuracy of predicted retention times shows that the proposed approach is simple, fast and accurate for retention time transfer and prediction between gas chromatography columns. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  14. Time-dependent changes in B-type natriuretic peptide after heart transplantation: correlation with allograft rejection and function.

    Science.gov (United States)

    Bader, Feras M; Rogers, R Kevin; Kfoury, Abdallah G; Gilbert, Edward M; Horne, Ben D; Stehlik, Josef; Renlund, Dale G

    2009-01-01

    Endomyocardial biopsy is the gold standard to diagnose cardiac allograft rejection, although a noninvasive modality such as brain natriuretic peptide (BNP) is attractive. The authors examined the correlation of BNP levels with rejection patterns and allograft function in cardiac allograft recipients followed up to 8 years. One hundred forty-four consecutive patients underwent endomyocardial biopsy, right heart catheterization, and blood sampling. BNP levels decreased during the first 6 months after transplant but then reached a plateau. Time-dependent correlations were made between BNP levels and allograft rejection, left ventricular ejection fraction, pulmonary capillary wedge pressure, right atrial pressure, and serum creatinine. BNP levels were not different between patients with any rejection pattern and no rejection prior to or after 6 months following transplant. BNP levels did not correlate with ejection fraction, pulmonary capillary wedge pressure, right atrial pressure, or creatinine in the first 6 months after transplant. Statistically significant correlations existed between BNP and these parameters after 6 months following transplant. In cardiac transplant recipients, BNP levels decrease in the first 6 months following transplant and then reach a plateau regardless of the presence, type, or severity of allograft rejection. BNP levels do predict allograft rejection but correlate with allograft function after 6 months following transplant.

  15. CARDIAC TRANSPLANT REJECTION AND NON-INVASIVE COMON CAROTID ARTERY WALL FUNCTIONAL INDICES

    Directory of Open Access Journals (Sweden)

    A. O. Shevchenko

    2015-01-01

    Full Text Available Allograft rejection would entail an increase in certain blood biomarkers and active substances derived from activated inflammatory cells which could influence entire vascular endothelial function and deteriorate arterial wall stiffness. We propose that carotid wall functional indices measured with non-invasive ultrasound could we valuable markers of the subclinical cardiac allograft rejection. Aim. Our goal was to analyze the clinical utility of functional common carotid wall (CCW variables measured with high-resolution Doppler ultrasound as a non-invasive screening tool for allograft rejection in cardiac transplant patients (pts. Methods. One hundred and seventy one pts included 93 cardiac recipients, 30 dilated cardiomyopathy waiting list pts, and 48 stable coronary artery disease (SCAD pts without decompensated heart failure were included. Along with resistive index (Ri, pulsative index (Pi, and CCW intima-media thickness (IMT, CCW rigidity index (iRIG was estimated using empirical equation. Non-invasive evaluation was performed in cardiac transplant recipients prior the endomyo- cardial biopsy. Results. Neither of Ri, Pi, or CCW IMT were different in studied subgroups. iRIG was signifi- cantly lower in SCAD pts when compared to the dilated cardiomyopathy subgroup. The later had similar values with cardiac transplant recipients without rejection. Antibody-mediated and cellular rejection were found in 22 (23.7% and 17 (18.3% cardiac recipients, respectively. Mean iRIG in pts without rejection was significantly lower in comparison to antibody-mediated rejection and cell-mediated (5514.7 ± 2404.0 vs 11856.1 ± 6643.5 and 16071.9 ± 10029.1 cm/sec2, respectively, p = 0.001. Area under ROC for iRIG was 0.90 ± 0.03 units2. Analysis showed that iRIG values above estimated treshold 7172 cm/sec2 suggested relative risk of any type of rejection 17.7 (95%CI = 6.3–49.9 sensitivity 80.5%, specificity – 81.1%, negative predictive value – 84

  16. In Silico Identification of Proteins Associated with Drug-induced Liver Injury Based on the Prediction of Drug-target Interactions.

    Science.gov (United States)

    Ivanov, Sergey; Semin, Maxim; Lagunin, Alexey; Filimonov, Dmitry; Poroikov, Vladimir

    2017-07-01

    Drug-induced liver injury (DILI) is the leading cause of acute liver failure as well as one of the major reasons for drug withdrawal from clinical trials and the market. Elucidation of molecular interactions associated with DILI may help to detect potentially hazardous pharmacological agents at the early stages of drug development. The purpose of our study is to investigate which interactions with specific human protein targets may cause DILI. Prediction of interactions with 1534 human proteins was performed for the dataset with information about 699 drugs, which were divided into three categories of DILI: severe (178 drugs), moderate (310 drugs) and without DILI (211 drugs). Based on the comparison of drug-target interactions predicted for different drugs' categories and interpretation of those results using clustering, Gene Ontology, pathway and gene expression analysis, we identified 61 protein targets associated with DILI. Most of the revealed proteins were linked with hepatocytes' death caused by disruption of vital cellular processes, as well as the emergence of inflammation in the liver. It was found that interaction of a drug with the identified targets is the essential molecular mechanism of the severe DILI for the most of the considered pharmaceuticals. Thus, pharmaceutical agents interacting with many of the identified targets may be considered as candidates for filtering out at the early stages of drug research. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Experimental validation of plant peroxisomal targeting prediction algorithms by systematic comparison of in vivo import efficiency and in vitro PTS1 binding affinity.

    Science.gov (United States)

    Skoulding, Nicola S; Chowdhary, Gopal; Deus, Mara J; Baker, Alison; Reumann, Sigrun; Warriner, Stuart L

    2015-03-13

    Most peroxisomal matrix proteins possess a C-terminal targeting signal type 1 (PTS1). Accurate prediction of functional PTS1 sequences and their relative strength by computational methods is essential for determination of peroxisomal proteomes in silico but has proved challenging due to high levels of sequence variability of non-canonical targeting signals, particularly in higher plants, and low levels of availability of experimentally validated non-canonical examples. In this study, in silico predictions were compared with in vivo targeting analyses and in vitro thermodynamic binding of mutated variants within the context of one model targeting sequence. There was broad agreement between the methods for entire PTS1 domains and position-specific single amino acid residues, including residues upstream of the PTS1 tripeptide. The hierarchy Leu>Met>Ile>Val at the C-terminal position was determined for all methods but both experimental approaches suggest that Tyr is underweighted in the prediction algorithm due to the absence of this residue in the positive training dataset. A combination of methods better defines the score range that discriminates a functional PTS1. In vitro binding to the PEX5 receptor could discriminate among strong targeting signals while in vivo targeting assays were more sensitive, allowing detection of weak functional import signals that were below the limit of detection in the binding assay. Together, the data provide a comprehensive assessment of the factors driving PTS1 efficacy and provide a framework for the more quantitative assessment of the protein import pathway in higher plants. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Comparing the Suitability of Autodock, Gold and Glide for the Docking and Predicting the Possible Targets of Ru(II-Based Complexes as Anticancer Agents

    Directory of Open Access Journals (Sweden)

    Adebayo A. Adeniyi

    2013-03-01

    Full Text Available In cancer chemotherapy, metal-based complexes have been recognized as the most promising means of inhibiting cancer growth due to the successful application of cis-platin and its derivatives above many of the existing organic anticancer agents. The limitations in their rational design can be traced to the complexity of the mechanism of their operations, lack of proper knowledge of their targets and lack of force fields in docking packages to appropriately define the metal centre of the organometallic complexes. In this paper, some of the promising anticancer complexes of Ru(II such as the rapta-based complexes formulated as [Ru(η6-p-cymeneL2(pta] and those with unusual ligands are considered. CatB and kinases which have been experimentally confirmed as possible targets of the complexes are also predicted by the three methods as one of the most targeted receptors while TopII and HDAC7 are predicted by two and one of the methods as best targets. The interesting features of the binding of the complexes show that some of the complexes preferentially target specific macromolecules than the others, which is an indication of their specificity and possibility of their therapeutic combination without severe side effects that may come from competition for the same target. Also, introduction of unusual ligands is found to significantly improve the activities of most of the complexes studied. Strong correlations are observed for the predicted binding sites and the orientation of the complexes within the binding site by the three methods of docking. However there are disparities in the ranking of the complexes by the three method of docking, especially that of Glide.

  19. Factors Related to Rejection of Care and Behaviors Directed towards Others: A Longitudinal Study in Nursing Home Residents with Dementia

    Directory of Open Access Journals (Sweden)

    Francisca Galindo-Garre

    2015-04-01

    Full Text Available Aims: The aim of this study was to analyze factors related to rejection of care and behaviors directed towards others in nursing home residents with dementia. Methods: The relationship of lack of understanding, depression, psychosis and pain with rejection of care and behaviors directed towards others was explored using four assessments from the Minimum Data Set (MDS within a period of 15 months on 1,101 residents with dementia in Dutch nursing homes. Presence of depressive symptoms was ascertained using a validated MDS scale, and presence of lack of understanding, rejection of care, psychosis and pain through the individual MDS items. A structural equation modeling approach and latent growth models were used to investigate the longitudinal relationship between changes in rejection of care and physical or verbal behaviors directed towards others, and changes in lack of understanding, pain, depression and psychotic symptoms. Results: Changes in lack of understanding predicted changes in rejection of care, and there was also a relationship between changes in depression and rejection of care. Changes of behaviors directed towards others were related to changes in lack of understanding and depression. Pain and behaviors directed towards others were unrelated, and psychosis was rather stable throughout. A mediation model suggested that the relationship of lack of understanding with behaviors directed towards others was mediated by rejection of care. Conclusion: These results indicate that lack of understanding and depression are important factors in development of rejection of care and behaviors directed towards others. The relationship between lack of understanding and behaviors directed towards others is mediated by rejection of care. Improvement in communication between residents and caregivers, and perhaps also effective treatment of depression may prevent or ameliorate these behaviors directed towards others.

  20. Drugs in development for prophylaxis of rejection in kidney-transplant recipients

    Directory of Open Access Journals (Sweden)

    Sanders ML

    2015-08-01

    Full Text Available Marion Lee Sanders,1 Anthony James Langone2 1Department of Medicine, Division of Nephrology and Hypertension, University of Iowa, Iowa City, IA, 2Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA Abstract: Transplantation is the preferred treatment option for individuals with end-stage renal disease. Individuals who undergo transplantation must chronically be maintained on an immunosuppression regimen for rejection prophylaxis to help ensure graft survival. Current rejection prophylaxis consists of using a combination of calcineurin inhibitors, mTOR inhibitors, antimetabolite agents, and/or corticosteroids. These agents have collectively improved the short-term outcomes of renal transplantation, but improvements in late/chronic graft loss and recipient survival have lagged significantly behind challenging the field of transplantation to develop novel prophylactic agents. There have been several clinical trials conducted within the last 5 years in an attempt to bring such novel agents to the commercial market. These trials have resulted in the US Food and Drug Administration (FDA approval of extended-release tacrolimus, as well as belatacept, which has the potential to replace calcineurin inhibitors for rejection prophylaxis. Other trials have focused on the development of novel calcineurin inhibitors (voclosporin, costimulation blockade (ASKP1240 and alefacept, kinase inhibitors (tofacitinib and sotrastaurin, and inhibitors of leukocyte migration (efalizumab. While these later agents have not been FDA-approved for use in transplantation, they remain noteworthy, as these agents explore pathways not previously targeted for allograft-rejection prophylaxis. The purpose of this review was to consolidate available clinical trial data with regard to the recent developments in rejection prophylaxis in kidney transplantation. Keywords: rejection, prophylaxis, immunosuppression

  1. Insecure attachment and maladaptive schema in disordered eating: The mediating role of rejection sensitivity.

    Science.gov (United States)

    De Paoli, Tara; Fuller-Tyszkiewicz, Matthew; Krug, Isabel

    2017-11-01

    The current study aimed to assess insecure attachment and the disconnection and rejection domain of maladaptive schema in the context of disordered eating. Rejection sensitivity (RS) was proposed as a mediator between maladaptive schema and disordered eating. The sample consisted of 108 female participants with a lifetime eating disorder diagnosis and 508 female control participants. Participants were asked to complete a number of self-report measures related to insecure attachment (anxious and avoidant), maladaptive schema (emotional deprivation, abandonment, mistrust, social isolation, and defectiveness), RS (interpersonal and appearance-based), and disordered eating. Path analysis indicated that anxious attachment was associated with disordered eating through multiple pathways involving emotional deprivation, abandonment, interpersonal RS, and appearance-based RS. Avoidant attachment was not related to disordered eating behaviours. The results indicate that both interpersonal and appearance-based RS are important mediators for the relationships between insecure attachment, maladaptive schema, and disordered eating. The results from the current study suggest that insecure attachment leads to maladaptive schema, which in turn leads to sensitivity to rejection and subsequent disordered eating behaviour. Attachment anxiety, but not attachment avoidance, was related to greater endorsement of all five schemas in the disconnection and rejection domain. Path analysis revealed that, of the schema in the disconnection and rejection domain, only emotional deprivation and abandonment were related to disordered eating. Interpersonal and appearance-based rejection sensitivity were significant mediators of the relationship between emotional deprivation and disordered eating as well as the relationship between abandonment and disordered eating. Differentiating between schemas within schema domains has clinical value in further understanding the pathway to disordered eating. The

  2. Changes in left ventricular function and wall thickness in heart transplant recipients and their relation to acute rejection: an assessment by digitised M mode echocardiography

    NARCIS (Netherlands)

    Mannaerts, H. F.; Balk, A. H.; Simoons, M. L.; Tijssen, J.; van der Borden, S. G.; Zondervan, P.; Sutherland, G. R.; Roelandt, J. R.

    1992-01-01

    OBJECTIVE: Assessment of changes in left ventricular diastolic function and wall thickness after heart transplantation to verify whether these changes predicted acute rejection assessed by endomyocardial biopsy. DESIGN: Follow up according to a predefined protocol of consecutive patients from the

  3. Improved coincidence rejection for silicon drift detectors

    Science.gov (United States)

    Mott, Richard B.

    2010-12-01

    The high count rates possible with silicon drift detectors (SDDs) raise the importance of coincidence ("pile-up") rejection in the pulse processor. Detection efficiency for close coincidence is energy dependent, with resolving times increasing sharply when at least one X-ray of the pair is below 1 keV. Traditional pile-up detection for low energies is done by applying a width test to the output of a shaping filter. SDDs have varying rise times at the preamplifier output due to the expansion of the charge cloud with drift path length, which limits the effectiveness of pulse width testing. Novel digital methods have been developed, which are largely immune to variations in rise time and significantly improve pulse-pair resolving times. Digital pulse processor filter parameters must take resolving times into account to achieve good sum peak position and shape for optimum software removal of sum peak artifacts during spectrum post-processing.

  4. The rejection-rage contingency in borderline personality disorder.

    Science.gov (United States)

    Berenson, Kathy R; Downey, Geraldine; Rafaeli, Eshkol; Coifman, Karin G; Paquin, Nina Leventhal

    2011-08-01

    Though long-standing clinical observation reflected in the Diagnostic and Statistical Manual of Mental Disorders (4th ed., text rev.) suggests that the rage characteristic of borderline personality disorder (BPD) often appears in response to perceived rejection, the role of perceived rejection in triggering rage in BPD has never been empirically tested. Extending basic personality research on rejection sensitivity to a clinical sample, a priming-pronunciation experiment and a 21-day experience-sampling diary examined the contingent relationship between perceived rejection and rage in participants diagnosed with BPD compared with healthy controls. Despite the differences in these 2 assessment methods, the indices of rejection-contingent rage that they both produced were elevated in the BPD group and were strongly interrelated. They provide corroborating evidence that reactions to perceived rejection significantly explain the rage seen in BPD. © 2011 American Psychological Association

  5. Effects of brief mindfulness and loving-kindness meditation inductions on emotional and behavioral responses to social rejection among individuals with high borderline personality traits.

    Science.gov (United States)

    Keng, Shian-Ling; Tan, Hui Han

    2018-01-01

    Borderline personality disorder (BPD) is characterized by an enduring pattern of instability across affective, behavioral, cognitive, and interpersonal domains. Individuals with BPD are known to be particularly vulnerable to experiences of social rejection, but little work has examined strategies that may moderate their reactivity to social rejection. Using a laboratory experimental approach, this study investigated the effects of brief mindfulness and loving-kindness meditation (LKM) inductions on emotional and behavioral responses to social rejection in a sample of adults with high BPD traits. One hundred and eighteen participants were randomly assigned to receive 10 min of mindful breathing practice, LKM, or a no-instruction control condition, prior to exposure to a social rejection manipulation. Participants rated their emotions and completed a competitive reaction time task, which provided a proxy measure of aggression. Compared to the control condition, the mindfulness group demonstrated significantly quicker recovery in negative affect and feelings of rejection after social rejection. The mindfulness group also reported significantly quicker recovery in negative affect compared to the LKM group. Whereas baseline trait mindfulness negatively predicted aggressive behaviors across all participants, groups did not differ in immediate emotional reactivity or aggressive behavior following social rejection. The findings suggest that mindfulness training may be a promising strategy in alleviating negative emotional effects of social rejection among individuals with high borderline personality traits, and highlight the limited utility of brief LKM practice in buffering the effects of social rejection. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Experimental Evaluation of Interference Rejection Combining for 5G small cells,

    DEFF Research Database (Denmark)

    Assefa, Dereje; Berardinelli, Gilberto; Tavares, Fernando Menezes Leitão

    2015-01-01

    The Interference Rejection Combining (IRC) receiver can significantly boost the network throughput in scenarios characterized by dense uncoordinated deployment of small cells, as targeted by future 5th generation (5G) radio access technology. This paper presents an experimental study on the poten......The Interference Rejection Combining (IRC) receiver can significantly boost the network throughput in scenarios characterized by dense uncoordinated deployment of small cells, as targeted by future 5th generation (5G) radio access technology. This paper presents an experimental study...... scenarios, respectively. In each scenario, the cells were arranged to characterize the propagation in different spatial configurations. Using the obtained propagation data, we analysed the cases of closed and open subscriber group for the respective scenarios, to compare the achievable throughput with IRC...

  7. Host intra-clutch variation, cuckoo egg matching and egg rejection by great reed warblers.

    Science.gov (United States)

    Cherry, Michael I; Bennett, Andrew T D; Moskát, Csaba

    2007-06-01

    Prevailing theory predicts that lower levels of intra-clutch variation in host eggs facilitate the detection of brood parasitism. We assessed egg matching using both human vision and UV-VIS spectrophotometry and then followed the nest fate of great reed warblers naturally parasitised by European cuckoos. Rejection was predicted by the following three variables: matching between cuckoo and host eggs on the main chromatic variable defined by principal components analysis of the egg spectra (which has a strong loading in the UV); the number of host eggs in the nest; and human estimates of intra-clutch variation. The first variable is not correlated to human estimates of matching, which do not predict rejection. In line with another recent study, rejection rates were predicted by higher levels of intra-clutch variation in the host eggs, suggesting that higher rather than lower levels of intra-clutch variation can facilitate the discrimination of cuckoo eggs by hosts. We suggest that the importance of intra-clutch variation is context dependent, with intra-clutch variation being important when there is good matching between the host and the cuckoo eggs. Our results also suggest that both spectrometric and human visual assessments of egg matching and intra-clutch variation are prudent: the former provide the best method of estimating reflectance variation, whereas the latter include some assessment of patterns of maculation.

  8. Docking analysis targeted to the whole enzyme: an application to the prediction of inhibition of PTP1B by thiomorpholine and thiazolyl derivatives.

    Science.gov (United States)

    Ganou, C A; Eleftheriou, P Th; Theodosis-Nobelos, P; Fesatidou, M; Geronikaki, A A; Lialiaris, T; Rekka, E A

    2018-02-01

    PTP1b is a protein tyrosine phosphatase involved in the inactivation of insulin receptor. Since inhibition of PTP1b may prolong the action of the receptor, PTP1b has become a drug target for the treatment of type II diabetes. In the present study, prediction of inhibition using docking analysis targeted specifically to the active or allosteric site was performed on 87 compounds structurally belonging to 10 different groups. Two groups, consisting of 15 thiomorpholine and 10 thiazolyl derivatives exhibiting the best prediction results, were selected for in vitro evaluation. All thiomorpholines showed inhibitory action (with IC 50 = 4-45 μΜ, Ki = 2-23 μM), while only three thiazolyl derivatives showed low inhibition (best IC 50 = 18 μΜ, Ki = 9 μΜ). However, free binding energy (E) was in accordance with the IC 50 values only for some compounds. Docking analysis targeted to the whole enzyme revealed that the compounds exhibiting IC 50 values higher than expected could bind to other peripheral sites with lower free energy, E o , than when bound to the active/allosteric site. A prediction factor, E- (Σ Eo × 0.16), which takes into account lower energy binding to peripheral sites, was proposed and was found to correlate well with the IC 50 values following an asymmetrical sigmoidal equation with r 2 = 0.9692.

  9. Patterns of oil-sediment rejection in corals

    Energy Technology Data Exchange (ETDEWEB)

    Bak, R.P.M.; Elgershuizen, J.H.B.W.

    1976-01-01

    The patterns of oil-sediment rejection of 19 Caribbean hermatypic corals are identical to their patterns of rejection of clean sediments. The rejection pattern is typical for coral species, and displays maximum and minimum rates dependent on the size and density of the oil-sediment particles. A coral's efficiency of rejection of sediment depends on the size and amount of the sediment particles. Oil drops less than or equal to 0.06 mm are removed by the coral's tissues. Physical contact with oil-sediment particles appears to be less harmful to corals than the toxic effects of oils.

  10. Novel Techniques for Background / Foreground Rejection in Particle Instruments

    Data.gov (United States)

    National Aeronautics and Space Administration — The Novel Techniques for Background / Foreground Rejection in Particle Instruments project addresses the need for signal contamination and background signal...

  11. Prediction of Multi-Target Networks of Neuroprotective Compounds with Entropy Indices and Synthesis, Assay, and Theoretical Study of New Asymmetric 1,2-Rasagiline Carbamates

    Science.gov (United States)

    Romero Durán, Francisco J.; Alonso, Nerea; Caamaño, Olga; García-Mera, Xerardo; Yañez, Matilde; Prado-Prado, Francisco J.; González-Díaz, Humberto

    2014-01-01

    In a multi-target complex network, the links (Lij) represent the interactions between the drug (di) and the target (tj), characterized by different experimental measures (Ki, Km, IC50, etc.) obtained in pharmacological assays under diverse boundary conditions (cj). In this work, we handle Shannon entropy measures for developing a model encompassing a multi-target network of neuroprotective/neurotoxic compounds reported in the CHEMBL database. The model predicts correctly >8300 experimental outcomes with Accuracy, Specificity, and Sensitivity above 80%–90% on training and external validation series. Indeed, the model can calculate different outcomes for >30 experimental measures in >400 different experimental protocolsin relation with >150 molecular and cellular targets on 11 different organisms (including human). Hereafter, we reported by the first time the synthesis, characterization, and experimental assays of a new series of chiral 1,2-rasagiline carbamate derivatives not reported in previous works. The experimental tests included: (1) assay in absence of neurotoxic agents; (2) in the presence of glutamate; and (3) in the presence of H2O2. Lastly, we used the new Assessing Links with Moving Averages (ALMA)-entropy model to predict possible outcomes for the new compounds in a high number of pharmacological tests not carried out experimentally. PMID:25255029

  12. Prediction of Multi-Target Networks of Neuroprotective Compounds with Entropy Indices and Synthesis, Assay, and Theoretical Study of New Asymmetric 1,2-Rasagiline Carbamates

    Directory of Open Access Journals (Sweden)

    Francisco J. Romero Durán

    2014-09-01

    Full Text Available In a multi-target complex network, the links (Lij represent the interactions between the drug (di and the target (tj, characterized by different experimental measures (Ki, Km, IC50, etc. obtained in pharmacological assays under diverse boundary conditions (cj. In this work, we handle Shannon entropy measures for developing a model encompassing a multi-target network of neuroprotective/neurotoxic compounds reported in the CHEMBL database. The model predicts correctly >8300 experimental outcomes with Accuracy, Specificity, and Sensitivity above 80%–90% on training and external validation series. Indeed, the model can calculate different outcomes for >30 experimental measures in >400 different experimental protocolsin relation with >150 molecular and cellular targets on 11 different organisms (including human. Hereafter, we reported by the first time the synthesis, characterization, and experimental assays of a new series of chiral 1,2-rasagiline carbamate derivatives not reported in previous works. The experimental tests included: (1 assay in absence of neurotoxic agents; (2 in the presence of glutamate; and (3 in the presence of H2O2. Lastly, we used the new Assessing Links with Moving Averages (ALMA-entropy model to predict possible outcomes for the new compounds in a high number of pharmacological tests not carried out experimentally.

  13. Prediction of multi-target networks of neuroprotective compounds with entropy indices and synthesis, assay, and theoretical study of new asymmetric 1,2-rasagiline carbamates.

    Science.gov (United States)

    Romero Durán, Francisco J; Alonso, Nerea; Caamaño, Olga; García-Mera, Xerardo; Yañez, Matilde; Prado-Prado, Francisco J; González-Díaz, Humberto

    2014-09-24

    In a multi-target complex network, the links (L(ij)) represent the interactions between the drug (d(i)) and the target (t(j)), characterized by different experimental measures (K(i), K(m), IC50, etc.) obtained in pharmacological assays under diverse boundary conditions (c(j)). In this work, we handle Shannon entropy measures for developing a model encompassing a multi-target network of neuroprotective/neurotoxic compounds reported in the CHEMBL database. The model predicts correctly >8300 experimental outcomes with Accuracy, Specificity, and Sensitivity above 80%-90% on training and external validation series. Indeed, the model can calculate different outcomes for >30 experimental measures in >400 different experimental protocolsin relation with >150 molecular and cellular targets on 11 different organisms (including human). Hereafter, we reported by the first time the synthesis, characterization, and experimental assays of a new series of chiral 1,2-rasagiline carbamate derivatives not reported in previous works. The experimental tests included: (1) assay in absence of neurotoxic agents; (2) in the presence of glutamate; and (3) in the presence of H2O2. Lastly, we used the new Assessing Links with Moving Averages (ALMA)-entropy model to predict possible outcomes for the new compounds in a high number of pharmacological tests not carried out experimentally.

  14. Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast.

    Science.gov (United States)

    Schlecht, Ulrich; Erb, Ionas; Demougin, Philippe; Robine, Nicolas; Borde, Valérie; van Nimwegen, Erik; Nicolas, Alain; Primig, Michael

    2008-05-01

    The autonomously replicating sequence binding factor 1 (Abf1) was initially identified as an essential DNA replication factor and later shown to be a component of the regulatory network controlling mitotic and meiotic cell cycle progression in budding yeast. The protein is thought to exert its functions via specific interaction with its target site as part of distinct protein complexes, but its roles during mitotic growth and meiotic development are only partially understood. Here, we report a comprehensive approach aiming at the identification of direct Abf1-target genes expressed during fermentation, respiration, and sporulation. Computational prediction of the protein's target sites was integrated with a genome-wide DNA binding assay in growing and sporulating cells. The resulting data were combined with the output of expression profiling studies using wild-type versus temperature-sensitive alleles. This work identified 434 protein-coding loci as being transcriptionally dependent on Abf1. More than 60% of their putative promoter regions contained a computationally predicted Abf1 binding site and/or were bound by Abf1 in vivo, identifying them as direct targets. The present study revealed numerous loci previously unknown to be under Abf1 control, and it yielded evidence for the protein's variable DNA binding pattern during mitotic growth and meiotic development.

  15. IMPRESS YOUR FRIENDS AND PREDICT THE FINAL SCORE: An analysis of the psychic ability of four target resetting methods used in One-Day International Cricket

    Directory of Open Access Journals (Sweden)

    Barbara J. O'Riley

    2006-12-01

    Full Text Available One-Day cricket's eternal problem is how to fairly account for an interruption that occurs during a team's innings. Several methods have been applied in the past, some more successfully than others. Numerous articles have been written about different target resetting methods applicable in one-day international cricket and how they "favour" one team over another. In this paper we use an alternative approach looking at the psychic ability of four target resetting methods and compare how well they predict the final score based on the present state of the first innings. We attempt to convert each of methods we investigate into a ball-by-ball predictive tool. We introduce a terminal interruption to the first innings at every ball and compute the predicted final score. We ascribe a nominal value to the difference between the final achieved score and the prediction given by each method. We compute our own 'Psychic Metric' to enable a comparison between the four methods. We also develop a computer package to manipulate the data from matches in which the first innings was completed

  16. Pain Catastrophizing and Fear of Pain Predict the Experience of Pain in Body Parts Not Targeted by a Delayed-Onset Muscle Soreness Procedure.

    Science.gov (United States)

    Niederstrasser, Nils Georg; Meulders, Ann; Meulders, Michel; Slepian, P Maxwell; Vlaeyen, Johan W S; Sullivan, Michael J L

    2015-11-01

    The present study examined whether pain catastrophizing and pain-related fear predict the experience of pain in body regions that are not targeted by an experimental muscle injury protocol. A delayed-onset muscle soreness (DOMS) protocol was used to induce pain unilaterally in the pectoralis, serratus, trapezius, latissimus dorsi, and deltoid muscles. The day after the DOMS protocol, participants were asked to rate their pain as they lifted weighted canisters with their targeted (ie, injured) arm and their nontargeted arm. The lifting task is a nonnoxious stimulus unless participants are already experiencing musculoskeletal pain. Therefore, reports of pain on the nontargeted arm were operationalized as pain in response to a nonnoxious stimulus. Eighty-two healthy university students (54 men, 28 women) completed questionnaires on pain catastrophizing and fear of pain and went through the DOMS protocol. The analyses revealed that catastrophizing and pain-related fear prospectively predicted pain experience in response to a nonnoxious stimulus. The possible mechanisms underlying this effect and clinical implications are discussed. Pain catastrophizing and fear of pain prospectively predict the pain experience in response to a nonnoxious stimulus. The pattern of findings is consistent with the predictions of current models of generalization of pain-related fear. Copyright © 2015 American Pain Society. Published by Elsevier Inc. All rights reserved.

  17. Metabonomic analysis of rats with acute heart rejection.

    Science.gov (United States)

    Tao, M; Xiu, D R

    2013-03-01

    Organs transplantation is an effective treatment for end-stage organ failure. Despite the use of modern immunosuppressants to decrease its incidence, acute rejection episodes (ARE), still present a problem for diagnosis, resolution, and prediction of long-term outcomes due to the absence of sufficiently robust biomarkers. Using an heterotopic heart transplantation model using Dark Agouti to Lewis rats, and sirolimus (rapamycin, Rapa) treatment by gavage, we divided recipients into four groups: controls, ARE, Rapa-14, and Rapa-7. We evaluated recipients by hematoxylin and eosin staining of grafts and reverse transcription polymerase chain reactions. Levels of plasma metabolites were quantified using gas chromatography/time-of-flight mass spectrometry. Data were evaluated employing partial least-squares discriminant analysis (PLS-DA), the area under the receiver operating characteristic curves with negative predictive values (NPV) and positive predictive values (PPV). The graft survival was prolonged by Rapa. Plasma levels of 10 metabolites differed significantly between the ARE and the Rapa-14 groups as illustrated by the total ion current. According to PLS-DA, proline, glycine, serine, phenylalanine, and isocitrate showed the greatest effects with areas under the curve of 0.944, 0.917, 1.0, 0.861, and 0.944 respectively. The NPV values were 85.7%, 85.7%, 100%, 83.3%, and 85.7% and PPV values, 100%, 100%, 100%, 83.3%, and 100% respectively. Therefore, these metabolites may be used to predict the occurrence and progression of ARE. The trend of changes suggested that plasma metabolites correlated with the immune state of recipients. Therefore, metabonomics may provide new biomarkers for graft injury in the early phases of ARE. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

  18. NASA faked the moon landing--therefore, (climate) science is a hoax: an anatomy of the motivated rejection of science.

    Science.gov (United States)

    Lewandowsky, Stephan; Oberauer, Klaus; Gignac, Gilles E

    2013-05-01

    Although nearly all domain experts agree that carbon dioxide emissions are altering the world's climate, segments of the public remain unconvinced by the scientific evidence. Internet blogs have become a platform for denial of climate change, and bloggers have taken a prominent role in questioning climate science. We report a survey of climate-blog visitors to identify the variables underlying acceptance and rejection of climate science. Our findings parallel those of previous work and show that endorsement of free-market economics predicted rejection of climate science. Endorsement of free markets also predicted the rejection of other established scientific findings, such as the facts that HIV causes AIDS and that smoking causes lung cancer. We additionally show that, above and beyond endorsement of free markets, endorsement of a cluster of conspiracy theories (e.g., that the Federal Bureau of Investigation killed Martin Luther King, Jr.) predicted rejection of climate science as well as other scientific findings. Our results provide empirical support for previous suggestions that conspiratorial thinking contributes to the rejection of science. Acceptance of science, by contrast, was strongly associated with the perception of a consensus among scientists.

  19. Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines.

    Science.gov (United States)

    LaBute, Montiago X; Zhang, Xiaohua; Lenderman, Jason; Bennion, Brian J; Wong, Sergio E; Lightstone, Felice C

    2014-01-01

    Late-stage or post-market identification of adverse drug reactions (ADRs) is a significant public health issue and a source of major economic liability for drug development. Thus, reliable in silico screening of drug candidates for possible ADRs would be advantageous. In this work, we introduce a computational approach that predicts ADRs by combining the results of molecular docking and leverages known ADR information from DrugBank and SIDER. We employed a recently parallelized version of AutoDock Vina (VinaLC) to dock 906 small molecule drugs to a virtual panel of 409 DrugBank protein targets. L1-regularized logistic regression models were trained on the resulting docking scores of a 560 compound subset from the initial 906 compounds to predict 85 side effects, grouped into 10 ADR phenotype groups. Only 21% (87 out of 409) of the drug-protein binding features involve known targets of the drug subset, providing a significant probe of off-target effects. As a control, associations of this drug subset with the 555 annotated targets of these compounds, as reported in DrugBank, were used as features to train a separate group of models. The Vina off-target models and the DrugBank on-target models yielded comparable median area-under-the-receiver-operating-characteristic-curves (AUCs) during 10-fold cross-validation (0.60-0.69 and 0.61-0.74, respectively). Evidence was found in the PubMed literature to support several putative ADR-protein associations identified by our analysis. Among them, several associations between neoplasm-related ADRs and known tumor suppressor and tumor invasiveness marker proteins were found. A dual role for interstitial collagenase in both neoplasms and aneurysm formation was also identified. These associations all involve off-target proteins and could not have been found using available drug/on-target interaction data. This study illustrates a path forward to comprehensive ADR virtual screening that can potentially scale with increasing number

  20. Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines.

    Directory of Open Access Journals (Sweden)

    Montiago X LaBute

    Full Text Available Late-stage or post-market identification of adverse drug reactions (ADRs is a significant public health issue and a source of major economic liability for drug development. Thus, reliable in silico screening of drug candidates for possible ADRs would be advantageous. In this work, we introduce a computational approach that predicts ADRs by combining the results of molecular docking and leverages known ADR information from DrugBank and SIDER. We employed a recently parallelized version of AutoDock Vina (VinaLC to dock 906 small molecule drugs to a virtual panel of 409 DrugBank protein targets. L1-regularized logistic regression models were trained on the resulting docking scores of a 560 compound subset from the initial 906 compounds to predict 85 side effects, grouped into 10 ADR phenotype groups. Only 21% (87 out of 409 of the drug-protein binding features involve known targets of the drug subset, providing a significant probe of off-target effects. As a control, associations of this drug subset with the 555 annotated targets of these compounds, as reported in DrugBank, were used as features to train a separate group of models. The Vina off-target models and the DrugBank on-target models yielded comparable median area-under-the-receiver-operating-characteristic-curves (AUCs during 10-fold cross-validation (0.60-0.69 and 0.61-0.74, respectively. Evidence was found in the PubMed literature to support several putative ADR-protein associations identified by our analysis. Among them, several associations between neoplasm-related ADRs and known tumor suppressor and tumor invasiveness marker proteins were found. A dual role for interstitial collagenase in both neoplasms and aneurysm formation was also identified. These associations all involve off-target proteins and could not have been found using available drug/on-target interaction data. This study illustrates a path forward to comprehensive ADR virtual screening that can potentially scale with

  1. Naturally acquired antibodies target the glutamate-rich protein on intact merozoites and predict protection against febrile malaria

    DEFF Research Database (Denmark)

    Kana, Ikhlaq Hussain; Adu, Bright; Tiendrebeogo, Régis Wendpayangde

    2017-01-01

    Background.: Plasmodium species antigens accessible at the time of merozoite release are likely targets of biologically functional antibodies. Methods.: Immunoglobulin G (IgG) antibodies against intact merozoites were quantified in the plasma of Ghanaian children from a longitudinal cohort using...... support previous studies that found OP of merozoites to be associated with protection against malaria and further shows IgG3 and GLURP antibodies are key in the OP mechanism, thus giving further impetus for the development of malaria vaccines targeting GLURP....

  2. Corneal allograft rejection: Risk factors, diagnosis, prevention, and treatment

    Directory of Open Access Journals (Sweden)

    Dua Harminder

    1999-01-01

    Full Text Available Recent advances in corneal graft technology, including donor tissue retrieval, storage and surgical techniques, have greatly improved the clinical outcome of corneal grafts. Despite these advances, immune mediated corneal graft rejection remains the single most important cause of corneal graft failure. Several host factors have been identified as conferring a "high risk" status to the host. These include: more than two quadrant vascularisation, with associated lymphatics, which augment the afferent and efferent arc of the immune response; herpes simplex keratitis; uveitis; silicone oil keratopathy; previous failed (rejected grafts; "hot eyes"; young recipient age; and multiple surgical procedures at the time of grafting. Large grafts, by virtue of being closer to the host limbus, with its complement of vessels and antigen-presenting Langerhans cells, also are more susceptible to rejection. The diagnosis of graft rejection is entirely clinical and in its early stages the clinical signs could be subtle. Graft rejection is largely mediated by the major histocompatibility antigens, minor antigens and perhaps blood group ABO antigens and some cornea-specific antigens. Just as rejection is mediated by active immune mediated events, the lack of rejection (tolerance is also sustained by active immune regulatory mechanisms. The anterior chamber associated immune deviation (ACAID and probably, conjunctiva associated lymphoid tissue (CALT induced mucosal tolerance, besides others, play an important role. Although graft rejection can lead to graft failure, most rejections can be readily controlled if appropriate management is commenced at the proper time. Topical steroids are the mainstay of graft rejection management. In the high-risk situations however, systemic steroids, and other immunosuppressive drugs such as cyclosporin and tacrolimus (FK506 are of proven benefit, both for treatment and prevention of rejection.

  3. shRNA target prediction informed by comprehensive enquiry (SPICE): a supporting system for high-throughput screening of shRNA library.

    Science.gov (United States)

    Kamatuka, Kenta; Hattori, Masahiro; Sugiyama, Tomoyasu

    2016-12-01

    RNA interference (RNAi) screening is extensively used in the field of reverse genetics. RNAi libraries constructed using random oligonucleotides have made this technology affordable. However, the new methodology requires exploration of the RNAi target gene information after screening because the RNAi library includes non-natural sequences that are not found in genes. Here, we developed a web-based tool to support RNAi screening. The system performs short hairpin RNA (shRNA) target prediction that is informed by comprehensive enquiry (SPICE). SPICE automates several tasks that are laborious but indispensable to evaluate the shRNAs obtained by RNAi screening. SPICE has four main functions: (i) sequence identification of shRNA in the input sequence (the sequence might be obtained by sequencing clones in the RNAi library), (ii) searching the target genes in the database, (iii) demonstrating biological information obtained from the database, and (iv) preparation of search result files that can be utilized in a local personal computer (PC). Using this system, we demonstrated that genes targeted by random oligonucleotide-derived shRNAs were not different from those targeted by organism-specific shRNA. The system facilitates RNAi screening, which requires sequence analysis after screening. The SPICE web application is available at http://www.spice.sugysun.org/.

  4. Evaluation of load rejection to house load test at 50% power for UCN 3

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Chang Gyun; Sohn, Suk Whun; Sohn, Jong Joo; Seo, Jong Tae; Lee, Sang Keun [KOPEC, Yongin (Korea, Republic of); Kim, Yong Sung; Nam, Kyu Won; Jung, Yang Mook; Chae, Kyeong Sik; Koh, Bum Jae; Oh, Chul Sung; Park, Hee Chool [KEPCO, Seoul (Korea, Republic of)

    1998-05-01

    The Load Rejection to House Load test at 50% power was successfully performed during the UCN 3 PAT period. In this test, all plant control systems automatically controlled the plant from 50% power to house load operation mode. The KISPAC code, which was used in the performance analysis during the design process of UCN 3 and 4, predictions of the test agreed with the measured data demonstrating the validity of the code as well as completeness of the plant design.

  5. Analysis of chronic lung transplant rejection by MALDI-TOF profiles of bronchoalveolar lavage fluid.

    Science.gov (United States)

    Zhang, Yan; Wroblewski, Matthew; Hertz, Marshall I; Wendt, Christine H; Cervenka, Tereza M; Nelsestuen, Gary L

    2006-02-01

    While lung transplant is an effective therapy for advanced lung disease, chronic allograph rejection remains a primary basis for lower survival rates than those for other solid organ transplants. This study used carefully controlled Zip-Tip extraction of bronchoalveolar lavage fluid (BALF) followed by MALDI-TOF MS to identify biomarkers of chronic lung transplant rejection. Many differences were observed between controls, those who did not develop chronic rejection within 100 months, and patients who had developed chronic rejection, diagnosed as bronchiolitis obliterans syndrome (BOS). Intensity ratios of peaks within the same MALDI-TOF profile were used to quantify the result. One of the best identifiers of BOS was a lowered ratio of clara cell protein (CCP m/z = 15,835) to lysozyme (m/z = 14,700), which gave 94% specificity and 74% sensitivity for diagnosis. Furthermore, low values for CCP/Lysozyme (<0.3) were observed in 66% of samples taken at 1 to 15 months prior to the diagnosis of BOS. Many other components of the profile gave similar or better outcomes for diagnosis but tended to be less valuable for the prediction of future disease. Overall, this study demonstrated the feasibility of this approach for the detection of disease biomarkers.

  6. Perceptions of intragroup rejection and coping strategies: malleable factors affecting Hispanic adolescents’ emotional and academic outcomes.

    Science.gov (United States)

    Basáñez, Tatiana; Warren, Michael T; Crano, William D; Unger, Jennifer B

    2014-08-01

    Understanding psychosocial factors that affect the academic achievement of Hispanic adolescents remains a nationwide priority in the United States. Extending previous studies of the stressful effects of perceived discrimination, this year-long longitudinal study examined the correlates of perceived ethnic in-group rejection, coping strategies and fatalistic beliefs, on depressive symptoms, grades, and college aspirations of 2,214 Hispanic adolescents (54% female) in Southern California. Based on the transactional model of stress and coping and on self-perception theory, structural equation models revealed that high perceived intragroup rejection (10th grade) and low levels of active coping (11th grade) were associated with depressive symptoms in 11th grade. Also, depressive symptoms partially mediated the link between intragroup rejection and both academic outcomes. Avoidant coping strategies (e.g., watching TV) also predicted depressive symptoms and were positively related to fatalism. In addition, fatalism was negatively related to grades and aspiration to attend college. The findings suggest the need to help adolescents find adequate outlets for communication and to create awareness about the potential effects of intragroup rejection.

  7. Perceptions of Intragroup Rejection and Coping Strategies: Malleable Factors Affecting Hispanic Adolescents’ Emotional and Academic Outcomes

    Science.gov (United States)

    Warren, Michael T.; Crano, William D.; Unger, Jennifer B.

    2015-01-01

    Understanding psychosocial factors that affect the academic achievement of Hispanic adolescents remains a nationwide priority in the United States. Extending previous studies of the stressful effects of perceived discrimination, this year-long longitudinal study examined the correlates of perceived ethnic in-group rejection, coping strategies and fatalistic beliefs, on depressive symptoms, grades, and college aspirations of 2,214 Hispanic adolescents (54 % female) in Southern California. Based on the transactional model of stress and coping and on self-perception theory, structural equation models revealed that high perceived intragroup rejection (10th grade) and low levels of active coping (11th grade) were associated with depressive symptoms in 11th grade. Also, depressive symptoms partially mediated the link between intragroup rejection and both academic outcomes. Avoidant coping strategies (e.g., watching TV) also predicted depressive symptoms and were positively related to fatalism. In addition, fatalism was negatively related to grades and aspiration to attend college. The findings suggest the need to help adolescents find adequate outlets for communication and to create awareness about the potential effects of intragroup rejection. PMID:24234042

  8. Speeding up Monte Carlo molecular simulation by a non-conservative early rejection scheme

    KAUST Repository

    Kadoura, Ahmad Salim

    2015-04-23

    Monte Carlo (MC) molecular simulation describes fluid systems with rich information, and it is capable of predicting many fluid properties of engineering interest. In general, it is more accurate and representative than equations of state. On the other hand, it requires much more computational effort and simulation time. For that purpose, several techniques have been developed in order to speed up MC molecular simulations while preserving their precision. In particular, early rejection schemes are capable of reducing computational cost by reaching the rejection decision for the undesired MC trials at an earlier stage in comparison to the conventional scheme. In a recent work, we have introduced a ‘conservative’ early rejection scheme as a method to accelerate MC simulations while producing exactly the same results as the conventional algorithm. In this paper, we introduce a ‘non-conservative’ early rejection scheme, which is much faster than the conservative scheme, yet it preserves the precision of the method. The proposed scheme is tested for systems of structureless Lennard-Jones particles in both canonical and NVT-Gibbs ensembles. Numerical experiments were conducted at several thermodynamic conditions for different number of particles. Results show that at certain thermodynamic conditions, the non-conservative method is capable of doubling the speed of the MC molecular simulations in both canonical and NVT-Gibbs ensembles. © 2015 Taylor & Francis

  9. Context-Specific Associations Between Harsh Parenting and Peer Rejection on Child Conduct Problems at Home and School.

    Science.gov (United States)

    Tung, Irene; Lee, Steve S

    2016-02-06

    Although harsh parenting and peer rejection are independently associated with childhood conduct problems (CP), these patterns are often informant specific, suggesting that their associations across contexts (i.e., home and school) should be considered. In a sample of 142 children with and without attention-deficit/hyperactivity disorder (ADHD; ages 5-10; 66% male), we used structural equation modeling to evaluate the structure of multi-informant (parent, teacher) and multimethod (semi-structured interview, questionnaire) rated aggressive, rule-breaking, and oppositional behavior. Next, we explored context-specific associations by modeling harsh parenting and peer rejection as simultaneous and independent predictors of home and school CP. We observed several key findings: (a) the structure of parent- and teacher-reported CP was best accounted by context-specific CP (i.e., home vs. school) and a second-order general CP factor; (b) harsh punishment and peer rejection each independently predicted the second-order general CP factor; and (c) peer rejection was uniquely associated with school CP, whereas harsh punishment was associated only with the second-order general CP factor and did not exhibit specificity with home CP. Whereas harsh parenting and peer rejection were each independently associated with generalized CP, peer rejection showed an additional, unique context-specific association with CP exclusively expressed at school. We discuss potential explanatory mechanisms underlying context-specific associations of CP, as well as address etiological and clinical implications for understanding informant-discrepancies in CP.

  10. MicroRNAs and their predicted target messenger RNAs are deregulated by exposure to a carcinogenic dose of comfrey in rat liver.

    Science.gov (United States)

    Li, Zhiguang; Fuscoe, James C; Chen, Tao

    2011-07-01

    MicroRNAs (MiRNAs) are small noncoding RNAs that function as regulators of gene expression to control cell growth and differentiation. In this study, we analyzed miRNA and mRNA expression in the livers of rats treated with a carcinogenic dose of comfrey (Symphytum officinale) for 12 weeks. Groups of six rats were fed a normal diet or a diet containing 8% comfrey root. The animals were sacrificed 1 day after the last treatment and the livers were isolated for miRNA expression analysis using LC Sciences miRNA microarrays and for mRNA expression analysis using Affymetrix rat genome microarrays. MiRNA expression levels were significantly changed by comfrey treatment. The treated samples were separated clearly from the control samples in both principal component analysis (PCA) and hierarchical clustering analysis (HCA). Quantitative measurements of seven miRNAs using TaqMan real-time PCR were consistent with the microarray results in terms of fold-change and the direction of the change in expression. Forty-five miRNAs (P comfrey treatment. Using a target prediction algorithm, 434 differentially expressed genes (DEGs) were predicted to be targeted by the differentially expressed miRNAs (DEMs). The DEM-targeted DEGs were more likely to be involved in carcinogenesis than the DEGs that were not targeted by the DEMs. The nontargeted DEGs were enriched in noncancer-related biological processes. Our data suggest that comfrey may exert its carcinogenic effects by disturbing miRNA expression resulting in altered mRNA levels of the DEM-targeted genes that are functionally associated with carcinogenesis. Copyright © 2011 Wiley-Liss, Inc.

  11. Rejection Sensitivity in Late Adolescence: Social and Emotional Sequelae

    Science.gov (United States)

    Marston, Emily G.; Hare, Amanda; Allen, Joseph P.

    2010-01-01

    This study used longitudinal, multireporter data, in a community sample, to examine the role of rejection sensitivity in late adolescents' social and emotional development. Rejection sensitivity was linked to a relative increase in adolescent depressive and anxiety symptoms over a 3-year period, even after accounting for teens' baseline level of…

  12. Refusals and Rejections: Designing Messages to Serve Multiple Goals.

    Science.gov (United States)

    Saeki, Mimako; O'Keefe, Barbara J.

    1994-01-01

    Tests a rational model of the elaboration of themes found in rejection messages, using Japanese and American participants. Finds partial support for the initial rational model but notes two key revisions: identifies two new themes in rejection messages and suggests substantial differences in the way Americans and Japanese elaborate themes to serve…

  13. A protocol for arguing about rejections in negotiation

    NARCIS (Netherlands)

    Prakken, Henry; van Veenen, J.; Parsons, S; Maudet, N; Moraitis, P; Rahwan,

    2006-01-01

    One form of argument-based negotiation is when agents argue about why an offer was rejected. If an agent can state a reason for a rejection of an offer, the negotiation process may become more efficient since the other agent can take this reason into account when making new offers. Also, if a reason

  14. Development crisis of rejection transplant on a background of leucopenia

    Directory of Open Access Journals (Sweden)

    A. A. Korzenewsky

    2014-01-01

    Full Text Available The patient in the remote period after cadaveric kidney allotransplantation developed leukopenia, which required a dose reduction of immunosuppressive drugs. The transplant rejection crisis developed against this background. Thus, the presence of leukopenia in a patient after cadaveric kidney allograft transplantation requires detecting early signs ofnot only infectious complications, but also a crisis of rejection.

  15. Indium-labeled platelet uptake in rejecting renal transplants

    International Nuclear Information System (INIS)

    Chandler, S.T.; Buckels, J.; Hawker, R.J.; Smith, N.; Barnes, A.D.; McCollum, C.N.

    1983-01-01

    The uptake of 111 In autologous platelets in transplanted kidneys was measured in 16 patients shortly after operation. Each patient was then observed for two years. When transplant radioactivity had increased, despite treatment for acute rejection, the kidney was ultimately lost because of rejection

  16. Perception of Parental Acceptance and Rejection among Swedish University Students.

    Science.gov (United States)

    Kitahara, Michio

    1987-01-01

    Results of administering the Parental Acceptance-Rejection and Personality Assessment Questionnaires to 71 Swedish university students showed significant relationships between various forms of parental rejection in childhood and negative personality assessment of the self as an adult. Females showed more dependence and emotional instability than…

  17. 48 CFR 2919.505 - Rejecting Small Business Administration recommendations.

    Science.gov (United States)

    2010-10-01

    ... Small Business 2919.505 Rejecting Small Business Administration recommendations. When the SBA...) and (c), the appeal must be referred to the Assistant Secretary for Administration and Management who... 48 Federal Acquisition Regulations System 7 2010-10-01 2010-10-01 false Rejecting Small Business...

  18. Effects of composite mango ( Mangifera indica ) fruit reject meal on ...

    African Journals Online (AJOL)

    The experiment was conducted to determine the effect of mango fruit reject meal on growth performance, digestibility and economics of production of growing rabbits. Mango fruit rejects were sliced such that the peel and pulp were together and the seed discarded, sun dried until it attained about 10% moisture and milled to ...

  19. 48 CFR 619.505 - Rejecting Small Business Administration recommendations.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Rejecting Small Business Administration recommendations. 619.505 Section 619.505 Federal Acquisition Regulations System DEPARTMENT OF STATE SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 619.505 Rejecting Small Business Administration...

  20. 48 CFR 19.505 - Rejecting Small Business Administration recommendations.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Rejecting Small Business Administration recommendations. 19.505 Section 19.505 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 19.505 Rejecting Small Business Administration...

  1. 48 CFR 1319.505 - Rejecting Small Business Administration recommendations.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Rejecting Small Business Administration recommendations. 1319.505 Section 1319.505 Federal Acquisition Regulations System DEPARTMENT OF COMMERCE SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 1319.505 Rejecting Small Business Administration...

  2. 48 CFR 1419.505 - Rejecting Small Business Administration recommendations.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Rejecting Small Business Administration recommendations. 1419.505 Section 1419.505 Federal Acquisition Regulations System DEPARTMENT OF THE INTERIOR SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 1419.505 Rejecting Small Business Administration...

  3. Heterosexual Rejection and Mate Choice: A Sociometer Perspective

    Directory of Open Access Journals (Sweden)

    Lin eZHANG

    2015-12-01

    Full Text Available Previous studies about the effects of social rejection on individuals’ social behaviors have produced mixed results and tend to study mating behaviors from a static point of view. However, mate selection in essence is a dynamic process, and therefore sociometer theory opens up a new perspective for studying mating and its underlying practices. Based on this theory and using self-perceived mate value in the relationship between heterosexual rejection and mate choice as a mediating role, this current study examined the effects of heterosexual rejection on mate choice in two experiments. Results showed that heterosexual rejection significantly reduced self-perceived mate value, expectation, and behavioral tendencies, while heterosexual acceptance indistinctively increased these measures. Self-perceived mate value did not serve as a mediator in the relationship between heterosexual rejection and mate expectation, but it mediated the relationship between heterosexual rejection and mating behavior tendencies towards potential objects. Moreover, individuals evaded both rejection and irrelevant people when suffering from rejection.

  4. Perceived parental rejection mediates the effects of previous ...

    African Journals Online (AJOL)

    Results: The study found that perceived maternal rejection partially mediated the association between abuse and internalising behaviours in the male cohort, whereas perceived father's rejection partially mediated this association in the female cohort. However, mental illness had no moderating effect on these relationships.

  5. Quantum Communication Using Coherent Rejection Sampling

    Science.gov (United States)

    Anshu, Anurag; Devabathini, Vamsi Krishna; Jain, Rahul

    2017-09-01

    Compression of a message up to the information it carries is key to many tasks involved in classical and quantum information theory. Schumacher [B. Schumacher, Phys. Rev. A 51, 2738 (1995), 10.1103/PhysRevA.51.2738] provided one of the first quantum compression schemes and several more general schemes have been developed ever since [M. Horodecki, J. Oppenheim, and A. Winter, Commun. Math. Phys. 269, 107 (2007); , 10.1007/s00220-006-0118-xI. Devetak and J. Yard, Phys. Rev. Lett. 100, 230501 (2008); , 10.1103/PhysRevLett.100.230501A. Abeyesinghe, I. Devetak, P. Hayden, and A. Winter, Proc. R. Soc. A 465, 2537 (2009), 10.1098/rspa.2009.0202]. However, the one-shot characterization of these quantum tasks is still under development, and often lacks a direct connection with analogous classical tasks. Here we show a new technique for the compression of quantum messages with the aid of entanglement. We devise a new tool that we call the convex split lemma, which is a coherent quantum analogue of the widely used rejection sampling procedure in classical communication protocols. As a consequence, we exhibit new explicit protocols with tight communication cost for quantum state merging, quantum state splitting, and quantum state redistribution (up to a certain optimization in the latter case). We also present a port-based teleportation scheme which uses a fewer number of ports in the presence of information about input.

  6. Expression of miR-142-5p in peripheral blood mononuclear cells from renal transplant patients with chronic antibody-mediated rejection.

    Directory of Open Access Journals (Sweden)

    Richard Danger

    Full Text Available In renal transplantation, the unresponsiveness of patients undergoing chronic antibody mediated rejection (CAMR to classical treatment stress on the need for accurate biomarkers to improve its diagnosis. We aim to determine whether microRNA expression patterns may be associated with a diagnosis of CAMR. We performed expression profiling of miRNAs in peripheral blood mononuclear cells (PBMC of kidney transplant recipients with CAMR or stable graft function. Among 257 expressed miRNAs, 10 miRNAs associated with CAMR were selected. Among them, miR-142-5p was increased in PBMC and biopsies of patients with CAMR as well as in a rodent model of CAMR. The lack of modulation of miR-142-5p in PBMC of patients with renal failure, suggests that its over-expression in CAMR was associated with immunological disorders rather than renal dysfunction. A ROC curve analysis performed on independent samples showed that miR-142-5p is a potential biomarker of CAMR allowing a very good discrimination of the patients with CAMR (AUC = 0.74; p = 0.0056. Moreover, its expression was decreased in PHA-activated blood cells and was not modulated in PBMC from patients with acute rejection, excluding a non-specific T cell activation expression. The absence of modulation of this miRNA in immunosuppressed patients suggests that its expression was not influenced by treatment. Finally, the analysis of miR-142-5p predicted targets under-expressed in CAMR PBMC in a published microarray dataset revealed an enrichment of immune-related genes. Altogether, these data suggest that miR-142-5p could be used as a biomarker in CAMR and these finding may improve our understanding of chronic rejection mechanisms.

  7. Multi-output Model with Box-Jenkins Operators of Quadratic Indices for Prediction of Malaria and Cancer Inhibitors Targeting Ubiquitin- Proteasome Pathway (UPP) Proteins.

    Science.gov (United States)

    Casañola-Martin, Gerardo M; Le-Thi-Thu, Huong; Pérez-Giménez, Facundo; Marrero-Ponce, Yovani; Merino-Sanjuán, Matilde; Abad, Concepción; González-Díaz, Humberto

    2016-01-01

    The ubiquitin-proteasome pathway (UPP) is the primary degradation system of short-lived regulatory proteins. Cellular processes such as the cell cycle, signal transduction, gene expression, DNA repair and apoptosis are regulated by this UPP and dysfunctions in this system have important implications in the development of cancer, neurodegenerative, cardiac and other human pathologies. UPP seems also to be very important in the function of eukaryote cells of the human parasites like Plasmodium falciparum, the causal agent of the neglected disease Malaria. Hence, the UPP could be considered as an attractive target for the development of compounds with Anti-Malarial or Anti-cancer properties. Recent online databases like ChEMBL contains a larger quantity of information in terms of pharmacological assay protocols and compounds tested as UPP inhibitors under many different conditions. This large amount of data give new openings for the computer-aided identification of UPP inhibitors, but the intrinsic data diversity is an obstacle for the development of successful classifiers. To solve this problem here we used the Bob-Jenkins moving average operators and the atom-based quadratic molecular indices calculated with the software TOMOCOMD-CARDD (TC) to develop a quantitative model for the prediction of the multiple outputs in this complex dataset. Our multi-target model can predict results for drugs against 22 molecular or cellular targets of different organisms with accuracies above 70% in both training and validation sets.

  8. Prediction of production of {sup 22}Na in a gas-cell target irradiated by protons using Monte Carlo tracking

    Energy Technology Data Exchange (ETDEWEB)

    Eslami, M., E-mail: mohammad.eslami25@yahoo.com [Department of Physics, Faculty of Science, University of Zanjan, Zengan (Zanjan) (Iran, Islamic Republic of); Kakavand, T. [Department of Physics, Faculty of Science, University of Zanjan, Zengan (Zanjan) (Iran, Islamic Republic of); Department of Physics, Faculty of Science, Imam Khomeini International University, Qazvin (Iran, Islamic Republic of); Mirzaii, M.; Rajabifar, S. [Agricultural, Medical and Industrial Research School, Nuclear Science and Technology Research Institute, AEOI, Karaj (Iran, Islamic Republic of)

    2015-01-01

    Highlights: • Angular distribution of the proton beam in a gaseous environment. • Particle energy distribution profile and proton flux within gas-cell target with MCNPX. • Detection of the residual nuclei during the nuclear reactions. • Estimation of production yield for {sup 22,nat}Ne(p,x){sup 22}Na reactions. - Abstract: The {sup 22}Ne(p,n){sup 22}Na is an optimal reaction for the cyclotron production of {sup 22}Na. This work tends to monitor the proton induced production of {sup 22}Na in a gas-cell target, containing natural and enriched neon gas, using Monte Carlo method. The excitation functions of reactions are calculated by both TALYS-1.6 and ALICE/ASH codes and then the optimum energy range of projectile for the high yield production is selected. A free gaseous environment of neon at a particular pressure and temperature is prearranged and the proton beam is transported within it using Monte Carlo codes MCNPX and SRIM. The beam monitoring performed by each of these codes indicates that the gas-cell has to be designed as conical frustum to reach desired interactions. The MCNPX is also employed to calculate the energy distribution of proton in the designed target and estimation of the residual nuclei during irradiation. The production yield of {sup 22}Na in {sup 22}Ne(p,n){sup 22}Na and {sup nat}Ne(p,x){sup 22}Na reactions are estimated and it shows a good agreement with the experimental results. The results demonstrate that Monte Carlo makes available a beneficial manner to design and optimize the gas targets as well as calibration of detectors, which can be used for the radionuclide production purposes.

  9. Predictive microbiology combined with metagenomic analysis targeted on the 16S rDNA : A new approach for food quality

    OpenAIRE

    Delhalle, Laurent; Taminiau, Bernard; Ellouze, Mariem; Nezer, Carine; Daube, Georges

    2013-01-01

    OBJECTIVES The food spoilage process is mainly caused by alteration micro-organisms and classical culture-based methods have therefore been used to assess the microbiological quality of food. These techniques are simple to implement but may not be relevant to understand the modifications of the microbial ecology which occur in the food product in response to different changes in the environmental conditions. Metagenomic analysis targeted on 16S ribosomal DNA can bring about a solution to t...

  10. A theoretical study on predicted protein targets of apple polyphenols and possible mechanisms of chemoprevention in colorectal cancer

    OpenAIRE

    Bernardina Scafuri; Anna Marabotti; Virginia Carbone; Paola Minasi; Serena Dotolo; Angelo Facchiano

    2016-01-01

    We investigated the potential role of apple phenolic compounds in human pathologies by integrating chemical characterization of phenolic compounds in three apple varieties, computational approaches to identify potential protein targets of the compounds, bioinformatics analyses on data from public archive of gene expression data, and functional analyses to hypothesize the effects of the selected compounds in molecular pathways. Starting by the analytic characterization of phenolic compounds in...

  11. Nighttime assaults: using a national emergency department monitoring system to predict occurrence, target prevention and plan services

    Directory of Open Access Journals (Sweden)

    Bellis Mark A

    2012-09-01

    Full Text Available Abstract Background Emergency department (ED data have the potential to provide critical intelligence on when violence is most likely to occur and the characteristics of those who suffer the greatest health impacts. We use a national experimental ED monitoring system to examine how it could target violence prevention interventions towards at risk communities and optimise acute responses to calendar, holiday and other celebration-related changes in nighttime assaults. Methods A cross-sectional examination of nighttime assault presentations (6.01 pm to 6.00 am; n = 330,172 over a three-year period (31st March 2008 to 30th March 2011 to English EDs analysing changes by weekday, month, holidays, major sporting events, and demographics of those presenting. Results Males are at greater risk of assault presentation (adjusted odds ratio [AOR] 3.14, 95% confidence intervals [CIs] 3.11-3.16; P 2 = 0.918; P  Conclusions To date, the role of ED data has focused on helping target nightlife police activity. Its utility is much greater; capable of targeting and evaluating multi-agency life course approaches to violence prevention and optimising frontline resources. National ED data are critical for fully engaging health services in the prevention of violence.

  12. Collaborative targeted maximum likelihood estimation for variable importance measure: Illustration for functional outcome prediction in mild traumatic brain injuries.

    Science.gov (United States)

    Pirracchio, Romain; Yue, John K; Manley, Geoffrey T; van der Laan, Mark J; Hubbard, Alan E

    2018-01-01

    Standard statistical practice used for determining the relative importance of competing causes of disease typically relies on ad hoc methods, often byproducts of machine learning procedures (stepwise regression, random forest, etc.). Causal inference framework and data-adaptive methods may help to tailor parameters to match the clinical question and free one from arbitrary modeling assumptions. Our focus is on implementations of such semiparametric methods for a variable importance measure (VIM). We propose a fully automated procedure for VIM based on collaborative targeted maximum likelihood estimation (cTMLE), a method that optimizes the estimate of an association in the presence of potentially numerous competing causes. We applied the approach to data collected from traumatic brain injury patients, specifically a prospective, observational study including three US Level-1 trauma centers. The primary outcome was a disability score (Glasgow Outcome Scale - Extended (GOSE)) collected three months post-injury. We identified clinically important predictors among a set of risk factors using a variable importance analysis based on targeted maximum likelihood estimators (TMLE) and on cTMLE. Via a parametric bootstrap, we demonstrate that the latter procedure has the potential for robust automated estimation of variable importance measures based upon machine-learning algorithms. The cTMLE estimator was associated with substantially less positivity bias as compared to TMLE and larger coverage of the 95% CI. This study confirms the power of an automated cTMLE procedure that can target model selection via machine learning to estimate VIMs in complicated, high-dimensional data.

  13. Specimen rejection in laboratory medicine: Necessary for patient safety?

    Science.gov (United States)

    Dikmen, Zeliha Gunnur; Pinar, Asli; Akbiyik, Filiz

    2015-01-01

    The emergency laboratory in Hacettepe University Hospitals receives specimens from emergency departments (EDs), inpatient services and intensive care units (ICUs). The samples are accepted according to the rejection criteria of the laboratory. In this study, we aimed to evaluate the sample rejection ratios according to the types of pre-preanalytical errors and collection areas. The samples sent to the emergency laboratory were recorded during 12 months between January to December, 2013 in which 453,171 samples were received and 27,067 specimens were rejected. Rejection ratios was 2.5% for biochemistry tests, 3.2% for complete blood count (CBC), 9.8% for blood gases, 9.2% for urine analysis, 13.3% for coagulation tests, 12.8% for therapeutic drug monitoring, 3.5% for cardiac markers and 12% for hormone tests. The most frequent rejection reasons were fibrin clots (28%) and inadequate volume (9%) for biochemical tests. Clotted samples (35%) and inadequate volume (13%) were the major causes for coagulation tests, blood gas analyses and CBC. The ratio of rejected specimens was higher in the EDs (40%) compared to ICUs (30%) and inpatient services (28%). The highest rejection ratio was observed in neurology ICU (14%) among the ICUs and internal medicine inpatient service (10%) within inpatient clinics. We detected an overall specimen rejection rate of 6% in emergency laboratory. By documentation of rejected samples and periodic training of healthcare personnel, we expect to decrease sample rejection ratios below 2%, improve total quality management of the emergency laboratory and promote patient safety.

  14. Rejection of micropollutants by clean and fouled forward osmosis membrane

    KAUST Repository

    Valladares Linares, Rodrigo

    2011-12-01

    As forward osmosis (FO) gains attention as an efficient technology to improve wastewater reclamation processes, it is fundamental to determine the influence of fouling in the rejection of emerging contaminants (micropollutants). This study focuses on the rejection of 13 selected micropollutants, spiked in a secondary wastewater effluent, by a FO membrane, using Red Sea water as draw solution (DS), differentiating the effects on the rejection caused by a clean and fouled membrane. The resulting effluent was then desalinated at low pressure with a reverse osmosis (RO) membrane, to produce a high quality permeate and determine the rejection with a coupled forward osmosis - low pressure reverse osmosis (FO-LPRO) system. When considering only FO with a clean membrane, the rejection of the hydrophilic neutral compounds was between 48.6% and 84.7%, for the hydrophobic neutrals the rejection ranged from 40.0% to 87.5%, and for the ionic compounds the rejections were between 92.9% and 96.5%. With a fouled membrane, the rejections were between 44.6% and 95.2%, 48.7%-91.5% and 96.9%-98.6%, respectively. These results suggest that, except for the hydrophilic neutral compounds, the rejection of the micropollutants is increased by the presence of a fouling layer, possibly due to the higher hydrophilicity of the FO fouled membrane compared to the clean one, the increased adsorption capacity of hydrophilic compounds and reduced mass transport capacity, membrane swelling, and the higher negative charge of the membrane surface, related to the foulants composition, mainly NOM acids (carboxylic radicals) and polysaccharides or polysaccharide-like substances. However, when coupled with RO, the rejections in both cases increased above 96%. The coupled FO-LPRO system was an effective double barrier against the selected micropollutants. © 2011 Elsevier Ltd.

  15. Eosinophil count, allergies, and rejection in pediatric heart transplant recipients.

    Science.gov (United States)

    Arbon, Kate S; Albers, Erin; Kemna, Mariska; Law, Sabrina; Law, Yuk

    2015-08-01

    Allograft rejection and long-term immunosuppression remain significant challenges in pediatric heart transplantation. Pediatric recipients are known to have fewer rejection episodes and to develop more allergic conditions than adults. A T-helper 2 cell dominant phenotype, manifested clinically by allergies and an elevated eosinophil count, may be associated with immunologic quiescence in transplant recipients. This study assessed whether the longitudinal eosinophil count and an allergic phenotype were associated with freedom from rejection. This single-center, longitudinal, observational study included 86 heart transplant patients monitored from 1994 to 2011. Post-transplant biannual complete blood counts, allergic conditions, and clinical characteristics related to rejection risk were examined. At least 1 episode of acute cellular rejection (ACR) occurred in 38 patients (44%), antibody-mediated rejection (AMR) occurred in 11 (13%), and 49 patients (57%) were diagnosed with an allergic condition. Patients with ACR or AMR had a lower eosinophil count compared with non-rejectors (p = 0.011 and p = 0.022, respectively). In the multivariable regression analysis, the presence of panel reactive antibodies to human leukocyte antigen I (p = 0.014) and the median eosinophil count (p = 0.011) were the only independent covariates associated with AMR. Eosinophil count (p = 0.010) and female sex (p = 0.009) were independent risk factors for ACR. Allergic conditions or young age at transplant were not protective from rejection. This study demonstrates a novel association between a high eosinophil count and freedom from rejection. Identifying a biomarker for low rejection risk may allow a reduction in immunosuppression. Further investigation into the role of the T-helper 2 cell phenotype and eosinophils in rejection quiescence is warranted. Copyright © 2015 International Society for Heart and Lung Transplantation. Published by Elsevier Inc. All rights reserved.

  16. Cognitive distortions mediate depression and affective response to social acceptance and rejection.

    Science.gov (United States)

    Caouette, Justin D; Guyer, Amanda E

    2016-01-15

    The emotional context insensitivity (ECI) hypothesis suggests individuals with depression have blunted affective responses to both positive and negative events. We tested ECI in a social context to examine how depression relates to affective responses to social acceptance and rejection outcomes. Furthermore, we aimed to identify cognitive mechanisms linking depression with affective response to social feedback. Finally, we tested whether these processes are similar for social anxiety. 90 participants (age 18-26 years; 53 women) completed the two-visit Chatroom task. At Visit 1 they rated their expectations about being liked by 60 peers. At Visit 2 they completed self-reports of depressive and social anxiety symptoms, and of cognitive flexibility, then received acceptance or rejection feedback from each peer and rated their affective response. Greater depressive symptoms related to negative expectancy bias, lower cognitive flexibility, and less positive affective response to acceptance, but did not relate to rejection. Negative expectations and cognitive flexibility mediated the relationship between depressive symptoms and affective response for acceptance; only negative expectations mediated rejection responses. These cognitive mechanisms were not related to social anxiety. A community sample was used to assess depression. Rumination and current mood state were omitted as potential predictors of affective response. Findings support the ECI framework. Depression but not social anxiety interferes with positive and negative affect through cognitively mediated dampening of emotional response to social acceptance and rejection. Emotion regulation strategies in depression therapy can target social flexibility to improve alignment of affective reactions to social outcomes. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Comparison of Sociometrically High Visibility Rejected and Low Visibility Rejected Children on Teacher, Parent, and Self-Rating Measures.

    Science.gov (United States)

    Neighbor, Jonelle C.

    The study looked at differences between groups of children identified as high visibility rejected (HVR) and low visibility rejected (LVR) on a sociometric measure with 952 fourth, fifth, and sixth grade students. Questionnaires were analyzed to determine the number of positive and negative nominations from peers received by each child. HVR…

  18. Rejected by Peers--Attracted to Antisocial Media Content: Rejection-Based Anger Impairs Moral Judgment among Adolescents

    Science.gov (United States)

    Plaisier, Xanthe S.; Konijn, Elly A.

    2013-01-01

    Adolescence is an important developmental stage during which both peers and the media have a strong influence. Both peer rejection and the use of morally adverse media are associated with negative developmental outcomes. This study examines processes by which peer rejection might drive adolescents to select antisocial media content by tying…

  19. Performance of CT ASPECTS and Collateral Score in Risk Stratification: Can Target Perfusion Profiles Be Predicted without Perfusion Imaging?

    Science.gov (United States)

    Dehkharghani, S; Bammer, R; Straka, M; Bowen, M; Allen, J W; Rangaraju, S; Kang, J; Gleason, T; Brasher, C; Nahab, F

    2016-08-01

    Endovascular trials suggest that revascularization benefits a subset of acute ischemic stroke patients with large-artery occlusion and small-core infarct volumes. The objective of our study was to identify thresholds of noncontrast CT-ASPECTS and collateral scores on CT angiography that best predict ischemic core volume thresholds quantified by CT perfusion among patients with acute ischemic stroke. Fifty-four patients with acute ischemic stroke (collateral score of 3 had 100% specificity for identifying patients with a CBF core volume of ≤50 mL. NCCT-ASPECTS of ≤6 had 100% specificity for identifying patients with a CBF core volume of >50 mL. In our cohort, 44 (81%) patients had an NCCT-ASPECTS of ≥9, a CTA collateral score of 3, or an NCCT-ASPECTS of ≤6. Using an NCCT-ASPECTS of ≥9 or a CTA collateral score of 3 best predicts CBF core volume infarct of ≤50 mL, while an NCCT-ASPECTS of ≤6 best predicts a CBF core volume infarct of >50 mL. Together these thresholds suggest that a specific population of patients with acute ischemic stroke not meeting such profiles may benefit most from CTP imaging to determine candidacy for revascularization. © 2016 by American Journal of Neuroradiology.

  20. In-Flight Performance of the TES Loop Heat Pipe Rejection System: Seven Years in Space

    Science.gov (United States)

    Rodriguez, Jose I.; Na-Nakornpanom, Arthur

    2012-01-01

    The Tropospheric Emission Spectrometer (TES) instrument heat rejection system has been operating in space for nearly 8 years since launched on NASA's EOS Aura Spacecraft. The instrument is an infrared imaging fourier transform spectrometer with spectral coverage of 3.2 to 15.4 microns. The loop heat pipe (LHP) based heat rejection system manages all of the instrument components waste heat including the two mechanical cryocoolers and their drive electronics. Five propylene LHPs collect and transport the instrument waste heat to the near room temperature nadir viewing radiators. During the early months of the mission, ice contamination of the cryogenic surfaces including the focal planes led to increased cryocooler loads and the need for periodic decontamination cycles. Focal plane decontamination cycles require power cycling both cryocoolers which also requires the two cryocooler LHPs to turn off and on during each cycle. To date, the cryocooler LHPs have undergone 24 start-ups in orbit successfully. This paper reports on the TES cryocooler loop heat pipe based heat rejection system performance. After a brief overview of the instrument thermal design, the paper presents detailed data on the highly successful space operation of the loop heat pipes since instrument turn-on in 2004. The data shows that the steady-state and transient operation of the LHPs has not changed since 2004 and shows consistent and predictable performance. The LHP based heat rejection system has provided a nearly constant heat rejection heat sink for all of its equipment which has led to exceptional overall instrument performance with world class science.

  1. Multi-output model with Box-Jenkins operators of linear indices to predict multi-target inhibitors of ubiquitin-proteasome pathway.

    Science.gov (United States)

    Casañola-Martin, Gerardo M; Le-Thi-Thu, Huong; Pérez-Giménez, Facundo; Marrero-Ponce, Yovani; Merino-Sanjuán, Matilde; Abad, Concepción; González-Díaz, Humberto

    2015-05-01

    The ubiquitin-proteasome pathway (UPP) plays an important role in the degradation of cellular proteins and regulation of different cellular processes that include cell cycle control, proliferation, differentiation, and apoptosis. In this sense, the disruption of proteasome activity leads to different pathological states linked to clinical disorders such as inflammation, neurodegeneration, and cancer. The use of UPP inhibitors is one of the proposed approaches to manage these alterations. On other hand, the ChEMBL database contains >5,000 experimental outcomes for >2,000 compounds tested as possible proteasome inhibitors using a large number of pharmacological assay protocols. All these assays report a large number of experimental parameters of biological activity like EC50, IC50 percent of inhibition, and many others that have been determined under many different conditions, targets, organisms, etc. Although this large amount of data offers new opportunities for the computational discovery of proteasome inhibitors, the complexity of these data represents a bottleneck for the development of predictive models. In this work, we used linear molecular indices calculated with the software TOMOCOMD-CARDD and Box-Jenkins moving average operators to develop a multi-output model that can predict outcomes for 20 experimental parameters in >450 assays carried out under different conditions. This generated multi-output model showed values of accuracy, sensitivity, and specificity above 70% for training and validation series. Finally, this model is considered multi-target and multi-scale, because it predicts the inhibition of the UPP for drugs against 22 molecular or cellular targets of different organisms contained in the ChEMBL database.

  2. Enhancing predicted efficacy of tumor treating fields therapy of glioblastoma using targeted surgical craniectomy: A computer modeling study

    DEFF Research Database (Denmark)

    Korshoej, Anders Rosendal; Saturnino, Guilherme Bicalho; Rasmussen, Line Kirkegaard

    2016-01-01

    Objective: The present work proposes a new clinical approach to TTFields therapy of glioblastoma. The approach combines targeted surgical skull removal (craniectomy) with TTFields therapy to enhance the induced electrical field in the underlying tumor tissue. Using computer simulations, we explore...... the potential of the intervention to improve the clinical efficacy of TTFields therapy of brain cancer. Methods: We used finite element analysis to calculate the electrical field distribution in realistic head models based on MRI data from two patients: One with left cortical/subcortical glioblastoma and one...

  3. Quantum Communication Using Coherent Rejection Sampling.

    Science.gov (United States)

    Anshu, Anurag; Devabathini, Vamsi Krishna; Jain, Rahul

    2017-09-22

    Compression of a message up to the information it carries is key to many tasks involved in classical and quantum information theory. Schumacher [B. Schumacher, Phys. Rev. A 51, 2738 (1995)PLRAAN1050-294710.1103/PhysRevA.51.2738] provided one of the first quantum compression schemes and several more general schemes have been developed ever since [M. Horodecki, J. Oppenheim, and A. Winter, Commun. Math. Phys. 269, 107 (2007); CMPHAY0010-361610.1007/s00220-006-0118-xI. Devetak and J. Yard, Phys. Rev. Lett. 100, 230501 (2008); PRLTAO0031-900710.1103/PhysRevLett.100.230501A. Abeyesinghe, I. Devetak, P. Hayden, and A. Winter, Proc. R. Soc. A 465, 2537 (2009)PRLAAZ1364-502110.1098/rspa.2009.0202]. However, the one-shot characterization of these quantum tasks is still under development, and often lacks a direct connection with analogous classical tasks. Here we show a new technique for the compression of quantum messages with the aid of entanglement. We devise a new tool that we call the convex split lemma, which is a coherent quantum analogue of the widely used rejection sampling procedure in classical communication protocols. As a consequence, we exhibit new explicit protocols with tight communication cost for quantum state merging, quantum state splitting, and quantum state redistribution (up to a certain optimization in the latter case). We also present a port-based teleportation scheme which uses a fewer number of ports in the presence of information about input.

  4. Acute rejection episodes after kidney transplantation

    Directory of Open Access Journals (Sweden)

    Hamida Fethi

    2009-01-01

    Full Text Available Acute rejection episodes (AREs are a major determinant of renal allograft survival. The incorporation of new immunosuppressive agents explains, at least partially, the improvement seen in the results of transplantation in recent years. The objectives of this study are to analyze the incidence and severity of AREs, their risk factors and their influence on graft and patient survival. We retrospectively studied 280 kidney transplants performed in adults at the Charles Nicolle Hospital, Tunis, between 1986 and 2004. The diagnosis of ARE was based on clinical data and response to treatment. Allograft biopsies were performed in ten cases. The treatment of AREs consisted of pulse methylprednisolone and anti-thymocyte globulin. There were 186 males (66.4% and 94 females (33.6%, and their mean age was 31 ± 8.9 years. Overall, the 280 study patients experienced a total of 113 AREs. Of them, 85 had only one ARE, 28 had two to three and none had more than three AREs. A total of 68 AREs were completely re-versible, 42 were partially reversible while three could not be reversed with treatment. The mean inci-dence of AREs was 40.4%. The incidence was > 45% between 1986 and 1997, decreased to 20.5% between 1998 and 2000 and to 9% between 2001 and 2004. Graft survival rates in patients with and without AREs were respectively 91% and 93% at three years, 82% and 90% at five years and 73% and 83% at 10 years. We found a decrease in the incidence of AREs in recent years in our study patients, and this was related to the introduction of sensitized cross-match and the newer immunosuppressive agents, particularly MMF. Additionally, AREs had a deleterious impact on late graft survival in our study population.

  5. Prediction of Significant Prostate Cancer at Prostate Biopsy and Per Core Detection Rate of Targeted and Systematic Biopsies Using Real-Time Shear Wave Elastography.

    Science.gov (United States)

    Boehm, Katharina; Budäus, Lars; Tennstedt, Pierre; Beyer, Burkhard; Schiffmann, Jonas; Larcher, Alessandro; Simonis, Kathrin; Graefen, Markus; Beyersdorff, Dirk; Salomon, Georg

    2015-01-01

    Prostate cancer (PCa) detection is accompanied by overdiagnosis and mischaracterization of PCa. Therefore, new imaging modalities like shear wave elastography (SWE) are required. The aim of this study was to evaluate per-core detection rates (DRs) of targeted biopsies and systematic biopsies and to test if SWE findings can predict presence of clinically significant PCa (csPCa) at biopsy. Overall, 95 patients scheduled for prostate biopsy in our center underwent SWE. SWE findings were classified into suspicious or normal. Targeted biopsies were taken in up to 3 SWE-suspicious areas. csPCa was defined as the presence of Gleason pattern ≥4, level of prostate-specific antigen ≥10 ng/ml or >2 positive cores. Overall DR for csPCa in our study cohort was 40%. Per-core DR for exclusively SWE-targeted cores versus systematic samples cores was 10.5 vs. 8.6% (p = 0.3). In the logistic regression models, individuals with suspicious SWE findings are at 6.4-fold higher risk of harboring csPCa (p = 0.03). Gain in predictive accuracy was 2.3% (0.82 vs. 0.84, p = 0.01). Presence of suspicious SWE findings is an independent predictor of csPCa. Therefore, SWE may be helpful in selecting patients for biopsy. Nonetheless, per-core DR for SWE-targeted cores was not statistically significant higher than DR of systematic sampled cores. Therefore, additional systematic biopsy is mandatory. © 2015 S. Karger AG, Basel.

  6. Indirect Effects of Emotion Regulation on Peer Acceptance and Rejection: The Roles of Positive and Negative Social Behaviors

    Science.gov (United States)

    Blair, Bethany L.; Gangel, Meghan J.; Perry, Nicole B.; O'Brien, Marion; Calkins, Susan D.; Keane, Susan P.; Shanahan, Lilly

    2016-01-01

    A growing body of literature indicates that childhood emotion regulation predicts later success with peers, yet little is known about the processes through which this association occurs. The current study examined mechanisms through which emotion regulation was associated with later peer acceptance and peer rejection, controlling for earlier…

  7. Organ transplant tissue rejection: detection and staging by fluorescence spectroscopy

    Science.gov (United States)

    MacAulay, Calum E.; Whitehead, Peter D.; McManus, Bruce; Zeng, Haishan; Wilson-McManus, Janet; MacKinnon, Nick; Morgan, David C.; Dong, Chunming; Gerla, Paul; Kenyon, Jennifer

    1998-07-01

    Patients receiving heart or other organ transplants usually require some level of anti-rejection drug therapy, most commonly cyclosporine. The rejection status of the organ must be monitored to determine the optimal anti-rejection drug therapy. The current method for monitoring post-transplant rejection status of heart transplant patients consists of taking biopsies from the right ventricle. In this work we have developed a system employing optical and signal-processing techniques that will allow a cardiologist to measure spectral changes associated with tissue rejection using an optical catheter probe. The system employs time gated illumination and detection systems to deal with the dynamic signal acquisition problems associated with in vivo measurements of a beating heart. Spectral data processing software evaluates and processes the data to produce a simple numerical score. Results of measurements made on 100 excised transplanted isograft and allograft rat hearts have demonstrated the ability of the system to detect the presence of rejection and to accurately correlate the spectroscopic results with the ISHLT (International Society for Heart and Lung Transplantation) stage of rejection determined by histopathology. In vivo measurements using a pig transplant model are now in process.

  8. Detection of cardiac transplant rejection with radiolabeled lymphocytes

    International Nuclear Information System (INIS)

    Bergmann, S.R.; Lerch, R.A.; Carlson, E.M.; Saffitz, J.E.; Sobel, B.E.

    1982-01-01

    To determine whether rejections of cardiac transplants could be detected specifically and non-invasively by lymphocytes labeled with indium-111 (111In), we studied 36 allogeneic and 14 isogeneic heterotopic cardiac transplants in rats. Allogeneic grafts accumulated autologous 111In-lymphocytes, detectable scintigraphically 24 hours after i.v. injection of the labeled cells. At the time of peak histologic rejection, the allogeneic grafts accumulated 92. +/- 4.8 times more activity than the native hearts (determined by well counting). The tissue-to-blood ratio in the rejecting transplants was 3.7 +/- 2.2; total uptake by the graft was 2.9 +/- 2.1% of the injected dose. Autoradiography confirmed that graft radioactivity was associated with labeled lymphocytes. In contrast, isogeneic grafts showed no signs of rejection and did not accumulate radioactivity. Because conventionally isolated and labeled lymphocytes are often contaminated with platelets, we prepared both 111In-platelets and purified 111In-lymphocytes for use in additional experiments. Allogeneic grafts accumulated platelets and purified lymphocytes independently. Thus, deposition of immunologically active cells in the rejecting graft representing specific pathophysiologic events can be detected. The results suggest that rejection of cardiac transplants can be detected noninvasively, potentially facilitating objective early clinical detection of rejection and titration of antirejection therapy

  9. Building and validating a prediction model for paediatric type 1 diabetes risk using next generation targeted sequencing of class II HLA genes.

    Science.gov (United States)

    Zhao, Lue Ping; Carlsson, Annelie; Larsson, Helena Elding; Forsander, Gun; Ivarsson, Sten A; Kockum, Ingrid; Ludvigsson, Johnny; Marcus, Claude; Persson, Martina; Samuelsson, Ulf; Örtqvist, Eva; Pyo, Chul-Woo; Bolouri, Hamid; Zhao, Michael; Nelson, Wyatt C; Geraghty, Daniel E; Lernmark, Åke

    2017-11-01

    It is of interest to predict possible lifetime risk of type 1 diabetes (T1D) in young children for recruiting high-risk subjects into longitudinal studies of effective prevention strategies. Utilizing a case-control study in Sweden, we applied a recently developed next generation targeted sequencing technology to genotype class II genes and applied an object-oriented regression to build and validate a prediction model for T1D. In the training set, estimated risk scores were significantly different between patients and controls (P = 8.12 × 10 -92 ), and the area under the curve (AUC) from the receiver operating characteristic (ROC) analysis was 0.917. Using the validation data set, we validated the result with AUC of 0.886. Combining both training and validation data resulted in a predictive model with AUC of 0.903. Further, we performed a "biological validation" by correlating risk scores with 6 islet autoantibodies, and found that the risk score was significantly correlated with IA-2A (Z-score = 3.628, P prediction model to the Swedish population, where the lifetime T1D risk ranges from 0.5% to 2%, we anticipate identifying approximately 20 000 high-risk subjects after testing all newborns, and this calculation would identify approximately 80% of all patients expected to develop T1D in their lifetime. Through both empirical and biological validation, we have established a prediction model for estimating lifetime T1D risk, using class II HLA. This prediction model should prove useful for future investigations to identify high-risk subjects for prevention research in high-risk populations. Copyright © 2017 John Wiley & Sons, Ltd.

  10. The prognostic and predictive value of sstr{sub 2}-immunohistochemistry and sstr{sub 2}-targeted imaging in neuroendocrine tumors

    Energy Technology Data Exchange (ETDEWEB)

    Brunner, Philippe [University Hospital Basel, Institute of Pathology (Switzerland); University Hospital Basel, Institute of Nuclear Medicine (Switzerland); Joerg, Ann-Catherine; Mueller-Brand, Jan [University Hospital Basel, Institute of Nuclear Medicine (Switzerland); Glatz, Katharina; Bubendorf, Lukas [University Hospital Basel, Institute of Pathology (Switzerland); Radojewski, Piotr; Umlauft, Maria; Spanjol, Petar-Marko; Krause, Thomas; Dumont, Rebecca A.; Walter, Martin A. [University Hospital Bern, Institute of Nuclear Medicine (Switzerland); Marincek, Nicolas [University Hospital Basel, Institute of Nuclear Medicine (Switzerland); University Hospital Bern, Institute of Nuclear Medicine (Switzerland); Maecke, Helmut R. [University Hospital Basel, Division of Radiological Chemistry (Switzerland); Briel, Matthias [University Hospital Basel, Basel Institute for Clinical Epidemiology and Biostatistics (Switzerland); McMaster University, Department of Clinical Epidemiology and Biostatistics, Hamilton (Canada); Schmitt, Anja; Perren, Aurel [University Bern, Institute of Pathology, Bern (Switzerland)

    2017-03-15

    Our aim was to assess the prognostic and predictive value of somatostatin receptor 2 (sstr{sub 2}) in neuroendocrine tumors (NETs). We established a tissue microarray and imaging database from NET patients that received sstr{sub 2}-targeted radiopeptide therapy with yttrium-90-DOTATOC, lutetium-177-DOTATOC or alternative treatment. We used univariate and multivariate analyses to identify prognostic and predictive markers for overall survival, including sstr{sub 2}-imaging and sstr{sub 2}-immunohistochemistry. We included a total of 279 patients. In these patients, sstr{sub 2}-immunohistochemistry was an independent prognostic marker for overall survival (HR: 0.82, 95 % CI: 0.67 - 0.99, n = 279, p = 0.037). In DOTATOC patients, sstr{sub 2}-expression on immunohistochemistry correlated with tumor uptake on sstr{sub 2}-imaging (n = 170, p < 0.001); however, sstr{sub 2}-imaging showed a higher prognostic accuracy (positive predictive value: +27 %, 95 % CI: 3 - 56 %, p = 0.025). Sstr{sub 2}-expression did not predict a benefit of DOTATOC over alternative treatment (p = 0.93). Our results suggest sstr{sub 2} as an independent prognostic marker in NETs. Sstr{sub 2}-immunohistochemistry correlates with sstr{sub 2}-imaging; however, sstr{sub 2}-imaging is more accurate for determining the individual prognosis. (orig.)

  11. Intramyocardial impedance measurements for diagnosis of acute cardiac allograft rejection.

    Science.gov (United States)

    Pfitzmann, R; Müller, J; Grauhan, O; Hetzer, R

    2000-08-01

    Measurements of intramyocardial impedance at high frequencies can indicate alterations in cell membranes and intracellular spaces during acute cardiac allograft rejection. Fifteen beagle dogs underwent heterotopic heart transplantation and were immunosuppressed with cyclosporine and methyl prednisolone (MP). Impedance was determined twice daily by means of four screw-in electrodes in the right and left ventricle. Transmyocardial biopsies and the intramyocardial electrogram (IMEG) were performed as reference methods. A total of 23 rejection episodes were induced. When acute rejection was recognized histologically and through IMEG readings, the animals were treated with a bolus of 125 mg of methyl prednisolone over 5 consecutive days. Treatment of rejection was controlled by biopsy and IMEG. All hearts showed a uniform decrease in impedance of about 28.3%+/-5.5% immediately after transplantation, which subsequently reached a stable plateau after 7 to 8 days. Impedance values then remained unchanged as long as rejection was absent. Biopsy findings of grades 1A to 1B (ISHLT) were accompanied by a statistically significant increase in impedance of 12.2%+/-2.5%; of grades 2 to 3A of 19.2%+/-3.2% and of grades 3B to 4 of 27.0%+/-2.9%. Sensitivity was 96%, specificity 91%. Successful treatment of rejection led to a decrease of impedance to the initial levels. The amount of increase in impedance of high frequencies is a method to stratify acute cardiac allograft rejection into grades like histologically grading. The effectiveness of rejection treatment can also be monitored through impedance measurement. The method is also applicable for telemetric rejection monitoring by means of an implantable device.

  12. Generativity and Interaction Between the Old and Young: The Role of Perceived Respect and Perceived Rejection.

    Science.gov (United States)

    Tabuchi, Megumi; Nakagawa, Takeshi; Miura, Asako; Gondo, Yasuyuki

    2015-08-01

    We examined the relationships among development of generativity, generative acts, and psychological well-being in old age and the possible mediating effects of perceived rejection and respect from younger generations. We hypothesized that generative action would not lead to well-being unless responding elders perceived respect from younger generations, and, further, that perceived respect would predict the development of generativity. In Study 1, we sampled 252 older persons to verify our hypothetical model in a cross-sectional survey. We assessed generative concern, generative action, perceived rejection from younger people, and psychological well-being. In Study 2, the same measures and a new scale to measure perceived respect from younger people were administered in a longitudinal survey. Four hundred older adults responded at 2 time points, 12 months apart. Path analysis showed that the effect of generative action on ill-being was mediated by perceived rejection and respect from younger generations. Perceived respect from younger generations at baseline predicted an increase in generative concern 12 months later. The results suggest that positive intergenerational interaction leads to generativity development and better well-being in old age. © The Author 2013. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Identity fusion predicts endorsement of pro-group behaviours targeting nationality, religion, or football in Brazilian samples.

    Science.gov (United States)

    Bortolini, Tiago; Newson, Martha; Natividade, Jean Carlos; Vázquez, Alexandra; Gómez, Ángel

    2018-04-01

    A visceral feeling of oneness with a group - identity fusion - has proven to be a stronger predictor of pro-group behaviours than other measures of group bonding, such as group identification. However, the relationship between identity fusion, other group alignment measures and their different roles in predicting pro-group behaviour is still controversial. Here, we test whether identity fusion is related to, but different from, unidimensional and multidimensional measures of group identification. We also show that identity fusion explains further variance of the endorsement of pro-group behaviour than these alternative measures and examine the structural and discriminant properties of identity fusion and group identification measures in three different contexts: nationality, religion, and football fandom. Finally, we extend the fusion literature to a new culture: Brazil. To the best of our knowledge, this is the first research explicitly addressing a comparison between these two forms of group alignment, identity fusion and identification with a group, and their role in predicting pro-group behaviours. © 2018 The British Psychological Society.

  14. Donor-specific rejection: Clinical and scan correlation

    International Nuclear Information System (INIS)

    Wilson, M.A.; Mehta, R.C.; Perlman, S.B.; Servilla, K.; Sollinger, H.W.; Deierhoi, M.H.; Belzer, F.O.

    1986-01-01

    All 470 scans on 132 consecutive renal transplantation patients were reviewed. Scan patterns identified included acute tubular necrosis and conventional rejection. A new pattern, donor specific rejection (DSR), was identified in 24 of 42 patients on the living related donor specific transfusion (DST) protocol. This was characterized by good perfusion and extraction but significant renal stasis of tracer. This pattern was unique to the DST recipients and improved with antirejection therapy. The clinical features (incidence, temporal onset) and severity (duration, serum creatinines) are compared in these patient populations. DSR occurs more frequently than conventional rejection but is a milder process

  15. Changes in heparin dose response slope during cardiac surgery: possible result in inaccuracy in predicting heparin bolus dose requirement to achieve target ACT.

    Science.gov (United States)

    Ichikawa, Junko; Mori, Tetsu; Kodaka, Mitsuharu; Nishiyama, Keiko; Ozaki, Makoto; Komori, Makiko

    2017-09-01

    The substantial interpatient variability in heparin requirement has led to the use of a heparin dose response (HDR) technique. The accuracy of Hepcon-based heparin administration in achieving a target activated clotting time (ACT) using an HDR slope remains controversial. We prospectively studied 86 adult patients scheduled for cardiac surgery requiring cardiopulmonary bypass. The total dose of calculated heparin required for patient and pump priming was administered simultaneously to achieve a target ACT of 450 s for HDR on the Hepcon HMS system. Blood samples were obtained after the induction of anesthesia, at 3 min after heparin administration and after the initiation of CPB to measure kaolin ACT, HDR slope, whole-blood heparin concentration based on the HDR slope and anti-Xa heparin concentration, antithrombin and complete blood count. The target ACT of 450 s was not achieved in 68.6% of patients. Compared with patients who achieved the target ACT, those who failed to achieve their target ACT had a significantly higher platelet count at baseline. Correlation between the HDR slope and heparin sensitivity was poor. Projected heparin concentration and anti-Xa heparin concentration are not interchangeable based on the Bland-Altman analysis. It can be hypothesized that the wide discrepancy in HDR slope versus heparin sensitivity may be explained by an inaccurate prediction of the plasma heparin level and/or the change in HDR of individual patients, depending on in vivo factors such as extravascular sequestration of heparin, decreased intrinsic antithrombin activity level and platelet count and/or activity.

  16. Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis.

    Science.gov (United States)

    Kumar, Dhananjay; Dutta, Summi; Singh, Dharmendra; Prabhu, Kumble Vinod; Kumar, Manish; Mukhopadhyay, Kunal

    2017-01-01

    Deep sequencing identified 497 conserved and 559 novel miRNAs in wheat, while degradome analysis revealed 701 targets genes. QRT-PCR demonstrated differential expression of miRNAs during stages of leaf rust progression. Bread wheat (Triticum aestivum L.) is an important cereal food crop feeding 30 % of the world population. Major threat to wheat production is the rust epidemics. This study was targeted towards identification and functional characterizations of micro(mi)RNAs and their target genes in wheat in response to leaf rust ingression. High-throughput sequencing was used for transcriptome-wide identification of miRNAs and their expression profiling in retort to leaf rust using mock and pathogen-inoculated resistant and susceptible near-isogenic wheat plants. A total of 1056 mature miRNAs were identified, of which 497 miRNAs were conserved and 559 miRNAs were novel. The pathogen-inoculated resistant plants manifested more miRNAs compared with the pathogen infected susceptible plants. The miRNA counts increased in susceptible isoline due to leaf rust, conversely, the counts decreased in the resistant isoline in response to pathogenesis illustrating precise spatial tuning of miRNAs during compatible and incompatible interaction. Stem-loop quantitative real-time PCR was used to profile 10 highly differentially expressed miRNAs obtained from high-throughput sequencing data. The spatio-temporal profiling validated the differential expression of miRNAs between the isolines as well as in retort to pathogen infection. Degradome analysis provided 701 predicted target genes associated with defense response, signal transduction, development, metabolism, and transcriptional regulation. The obtained results indicate that wheat isolines employ diverse arrays of miRNAs that modulate their target genes during compatible and incompatible interaction. Our findings contribute to increase knowledge on roles of microRNA in wheat-leaf rust interactions and could help in rust

  17. MicroRNA-10b downregulation mediates acute rejection of renal allografts by derepressing BCL2L11

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xiaoyou [Department of Organ Transplantation, Zhujiang Hospital, Guangzhou 510282 (China); Dong, Changgui [Institute of Molecular Ecology and Evolution, East China Normal University, Shanghai 200062 (China); Jiang, Zhengyao [Department of Organ Transplantation, Zhujiang Hospital, Guangzhou 510282 (China); Wu, William K.K. [Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, NT, Hong Kong (China); State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong (China); Chan, Matthew T.V. [Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, NT, Hong Kong (China); Zhang, Jie [Department of Organ Transplantation, Zhujiang Hospital, Guangzhou 510282 (China); Li, Haibin; Qin, Ke [Guangxi Key Laboratory for Transplantation Medicine Department of Organ Transplantation in Guangzhou Military Region, Institute of Transplant Medicine, 303 Hospital of People' s Liberation Army, Nanning, Guangxi 530021 (China); Sun, Xuyong, E-mail: sunxuyong0528@163.com [Guangxi Key Laboratory for Transplantation Medicine Department of Organ Transplantation in Guangzhou Military Region, Institute of Transplant Medicine, 303 Hospital of People' s Liberation Army, Nanning, Guangxi 530021 (China)

    2015-04-10

    Kidney transplantation is the major therapeutic option for end-stage kidney diseases. However, acute rejection could cause allograft loss in some of these patients. Emerging evidence supports that microRNA (miRNA) dysregulation is implicated in acute allograft rejection. In this study, we used next-generation sequencing to profile miRNA expression in normal and acutely rejected kidney allografts. Among 75 identified dysregulated miRNAs, miR-10b was the most significantly downregulated miRNAs in rejected allografts. Transfecting miR-10b inhibitor into human renal glomerular endothelial cells recapitulated key features of acute allograft rejection, including endothelial cell apoptosis, release of pro-inflammatory cytokines (interleukin-6, tumor necrosis factor α, interferon-γ, and chemokine (C–C motif) ligand 2) and chemotaxis of macrophages whereas transfection of miR-10b mimics had opposite effects. Downregulation of miR-10b directly derepressed the expression of BCL2L11 (an apoptosis inducer) as revealed by luciferase reporter assay. Taken together, miR-10b downregulation mediates many aspects of disease pathogenicity of acute kidney allograft rejection. Restoring miR-10b expression in glomerular endothelial cells could be a novel therapeutic approach to reduce acute renal allograft loss. - Highlights: • miR-10b was the most downregulated microRNAs in acutely rejected renal allografts. • miR-10b downregulation triggered glomerular endothelial cell apoptosis. • miR-10b downregulation induced release of pro-inflammatory cytokines. • miR-10b downregulation derepressed its pro-apoptotic target BCL2L11.

  18. Using intramyocardial electrograms combined with other noninvasive methods for monitoring acute rejection following human heart transplantation.

    Science.gov (United States)

    Jia, Yi-xin; Meng, Xu; Sun, Ling-bo; Han, Jie; Chen, Yang-tian

    2009-01-20

    Acute allograft rejection in heart transplantation remains as one of the major complications. Obligatory graft surveillance is still achieved with the invasive and expensive endomyocardial biopsy (EMB). Our study aimed to study the use of intramyocardial electrograms combined with other noninvasive methods for the monitoring of acute rejection after human heart transplantation. Permanent pacemakers were implanted in 58 patients undergoing heart transplantations. Intramyocardial electrograms (IMEG) were recorded periodically and the results were compared with those from EMBs. The R wave amplitude of the IMEG was used as the index value, the average R wave amplitude at the third week following transplantation was considered as the baseline, and a reduction of > 20% compared with the baseline was regarded as a positive result. EMB was performed in cases of positive IMEG results and also at other times. Other noninvasive methods were used to help the diagnosis. Acute rejection (AR) was defined as International Society of Heart-Lung Transplantation grade IIIA or higher. We obtained 1231 IMEG records and 127 EMBs. Of the total 127 EMBs, 53 were positive, in which there were 42 IMEG positive results and 11 negative, while in the rest 74 negative EMBs, there were 9 IMEG positive results and 65 negative. The sensitivity of IMEG for the diagnosis of AR was 79.2%, and the specificity was 87.8%. The positive predictive value was 82.4% and the negative predictive value was 85.5%. Of the total of 1231 IMEG records, 51 were positive and 1180 were negative. Excluding 11 proved by EMB to be false negative, if the other 1169 were considered as no evidence of rejection, through the other noninvasive methods, AR diagnosed by this noninvasive monitoring strategy, the sensitivity was 79.2%, and the specificity was 99.2%. The positive predictive value was 82.4% and the negative predictive value was 99.1%. IMEG can be used as a noninvasive method for monitoring AR following heart

  19. Laughter as a social rejection cue: Influence of prior explicit experience of social rejection on cardiac signs of "freezing".

    Science.gov (United States)

    Lackner, Helmut K; Reiter-Scheidl, Katharina; Aydin, Nilüfer; Perchtold, Corinna M; Weiss, Elisabeth M; Papousek, Ilona

    2018-03-28

    The study aimed at investigating the immediate cardiac effect of the sudden perception of other people's laughter after experimentally manipulating healthy participants' proneness to experience laughter as a cue of social threat. We expected that participants would show cardiac signs of freezing (i.e., sustained heart rate deceleration immediately after perception of the laughter) after prior social rejection but not or less so after prior acceptance, due to an increased bias to perceive the ambiguous social signal as a cue of social threat and rejection after rejection had been primed. Contrary to expectations, the perception of other people's laughter elicited a decelerative (freezing) response regardless of whether it was preceded by the experience of social rejection or acceptance. The response was prolonged in participants who had been accepted beforehand compared to those who had been rejected. The findings indicate that, given a relevant social context, other people's laughter can be a powerful cue of social threat and rejection also in healthy individuals. Prolonged heart rate deceleration after an ambiguous social signal may facilitate the processing of significant social information in the socially threatening situation. The study adds to the literature rendering the course of the immediate transient heart rate response a useful tool in social rejection research. Additionally, the findings suggested that in some cases the further progress of transient heart rate changes in more extended time-windows (about 30 s) may provide additional relevant information about the processing of social cues. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Use of a SQUID array to detect T-cells with magnetic nanoparticles in determining transplant rejection

    Science.gov (United States)

    Flynn, Edward R.; Bryant, H. C.; Bergemann, Christian; Larson, Richard S.; Lovato, Debbie; Sergatskov, Dmitri A.

    2007-04-01

    Acute rejection in organ transplant is signaled by the proliferation of T-cells that target and kill the donor cells requiring painful biopsies to detect rejection onset. An alternative non-invasive technique is proposed using a multi-channel superconducting quantum interference device (SQUID) magnetometer to detect T-cell lymphocytes in the transplanted organ labeled with magnetic nanoparticles conjugated to antibodies specifically attached to lymphocytic ligand receptors. After a magnetic field pulse, the T-cells produce a decaying magnetic signal with a characteristic time of the order of a second. The extreme sensitivity of this technique, 10 5 cells, can provide early warning of impending transplant rejection and monitor immune-suppressive chemotherapy.

  1. Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets.

    Science.gov (United States)

    Gazi, Md Amran; Kibria, Mohammad Golam; Mahfuz, Mustafa; Islam, Md Rezaul; Ghosh, Prakash; Afsar, Md Nure Alam; Khan, Md Arif; Ahmed, Tahmeed

    2016-10-15

    The global control of tuberculosis (TB) remains a great challenge from the standpoint of diagnosis, detection of drug resistance, and treatment. Major serodiagnostic limitations include low sensitivity and high cost in detecting TB. On the other hand, treatment measures are often hindered by low efficacies of commonly used drugs and resistance developed by the bacteria. Hence, there is a need to look into newer diagnostic and therapeutic targets. The proteome information available suggests that among the 3906 proteins in Mycobacterium tuberculosis H37Rv, about quarter remain classified as hypothetical uncharacterized set. This study involves a combination of a number of bioinformatics tools to analyze those hypothetical proteins (HPs). An entire set of 999 proteins was primarily screened for protein sequences having conserved domains with high confidence using a combination of the latest versions of protein family databases. Subsequently, 98 of such potential target proteins were extensively analyzed by means of physicochemical characteristics, protein-protein interaction, sub-cellular localization, structural similarity and functional classification. Next, we predicted antigenic proteins from the entire set and identified B and T cell epitopes of these proteins in M. tuberculosis H37Rv. We predicted the function of these HPs belong to various classes of proteins such as enzymes, transporters, receptors, structural proteins, transcription regulators and other proteins. However, the structural similarity prediction of the annotated proteins substantiated the functional classification of those proteins. Consequently, based on higher antigenicity score and sub-cellular localization, we choose two (NP_216420.1, NP_216903.1) of the antigenic proteins to exemplify B and T cell epitope prediction approach. Finally we found 15 epitopes those located partially or fully in the linear epitope region. We found 21 conformational epitopes by using Ellipro server as well. In

  2. Associations between rejection sensitivity and mental health outcomes : A meta-analytic review

    NARCIS (Netherlands)

    Gao, S.; Assink, M.; Cipriani, A.; Lin, K.

    2017-01-01

    Rejection sensitivity is a personality disposition characterized by oversensitivity to social rejection. Using a three-level meta-analytic model, 75 studies were reviewed that examined associations between rejection sensitivity and five mental health outcomes: depression, anxiety, loneliness,

  3. Nonlinear Optimization-Based Device-Free Localization with Outlier Link Rejection

    Directory of Open Access Journals (Sweden)

    Wendong Xiao

    2015-04-01

    Full Text Available Device-free localization (DFL is an emerging wireless technique for estimating the location of target that does not have any attached electronic device. It has found extensive use in Smart City applications such as healthcare at home and hospitals, location-based services at smart spaces, city emergency response and infrastructure security. In DFL, wireless devices are used as sensors that can sense the target by transmitting and receiving wireless signals collaboratively. Many DFL systems are implemented based on received signal strength (RSS measurements and the location of the target is estimated by detecting the changes of the RSS measurements of the wireless links. Due to the uncertainty of the wireless channel, certain links may be seriously polluted and result in erroneous detection. In this paper, we propose a novel nonlinear optimization approach with outlier link rejection (NOOLR for RSS-based DFL. It consists of three key strategies, including: (1 affected link identification by differential RSS detection; (2 outlier link rejection via geometrical positional relationship among links; (3 target location estimation by formulating and solving a nonlinear optimization problem. Experimental results demonstrate that NOOLR is robust to the fluctuation of the wireless signals with superior localization accuracy compared with the existing Radio Tomographic Imaging (RTI approach.

  4. Increased Expression of Peripheral Blood Leukocyte Genes Implicate CD14+ Tissue Macrophages in Cellular Intestine Allograft Rejection

    Science.gov (United States)

    Ashokkumar, Chethan; Ningappa, Mylarappa; Ranganathan, Sarangarajan; Higgs, Brandon W.; Sun, Qing; Schmitt, Lori; Snyder, Sara; Dobberstein, Jennifer; Branca, Maria; Jaffe, Ronald; Zeevi, Adriana; Squires, Robert; Alissa, Feras; Shneider, Benjamin; Soltys, Kyle; Bond, Geoffrey; Abu-Elmagd, Kareem; Humar, Abhinav; Mazariegos, George; Hakonarson, Hakon; Sindhi, Rakesh

    2011-01-01

    Recurrent rejection shortens graft survival after intestinal transplantation (ITx) in children, most of whom also experience early acute cellular rejection (rejectors). To elucidate mechanisms common to early and recurrent rejection, we used a test cohort of 20 recipients to test the hypothesis that candidate peripheral blood leukocyte genes that trigger rejection episodes would be evident late after ITx during quiescent periods in genome-wide gene expression analysis and would achieve quantitative real-time PCR replication pre-ITx (another quiescent period) and in the early post-ITx period during first rejection episodes. Eight genes were significantly up-regulated among rejectors in the late post-ITx and pre-ITx periods, compared with nonrejectors: TBX21, CCL5, GNLY, SLAMF7, TGFBR3, NKG7, SYNE1, and GK5. Only CCL5 was also up-regulated in the early post-ITx period. Among resting peripheral blood leukocyte subsets in randomly sampled nonrejectors, CD14+ monocytes expressed the CCL5 protein maximally. Compared with nonrejectors, rejectors demonstrated higher counts of both circulating CCL5+CD14+ monocytes and intragraft CD14+ monocyte-derived macrophages in immunohistochemistry of postperfusion and early post-ITx biopsies from the test and an independent replication cohort. Donor-specific alloreactivity measured with CD154+ T-cytotoxic memory cells correlated with the CCL5 gene and intragraft CD14+ monocyte-derived macrophages at graft reperfusion and early post-ITx. CCL5 gene up-regulation and CD14+ macrophages likely prime cellular ITx rejection. Infiltration of reperfused intestine allografts with CD14+ macrophages may predict rejection events. PMID:21854741

  5. Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Jianfeng Zhu

    2016-12-01

    Full Text Available MicroRNAs (miRNAs are a class of endogenous small RNAs with important roles in plant growth, development, and environmental stress responses. Ulmus pumila L., a deciduous broadleaved tree species of northern temperate regions, is widely distributed in central and northern Asia and has important economic and ecological value. With the spread and aggravation of soil salinization, salt stress has become a major abiotic stress affecting the normal growth and development of U. pumila. However, the influence of salt stress on U. pumila miRNA expression has not been investigated. To identify miRNAs and predict their target mRNA genes under salt stress, three small RNA libraries were generated and sequenced from roots of U. pumila seedlings treated with various concentrations of NaCl corresponding to no salt stress, light short-term salt stress, and medium-heavy long-term salt stress. Integrative analysis identified 254 conserved miRNAs representing 29 families and 49 novel miRNAs; 232 potential targets of the miRNAs were also predicted. Expression profiling of miRNAs between libraries was performed, and the expression of six miRNAs was validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR. Our findings provide an overview of potential miRNAs and corresponding targets involved in regulating U. pumila salt defense responses. These results lay the foundation for further research into molecular mechanisms involved in salt stress resistance in U. pumila and other Ulmaceae species.

  6. The prediction of the optical contrast of air-borne targets against the night-sky background for Photopic and NVG sensors

    Science.gov (United States)

    Havemann, Stephan; Wong, Gerald

    2016-10-01

    The Havemann-Taylor Fast Radiative Transfer Code (HT-FRTC) represents transmittances, radiances and fluxes by principal components that cover the spectra at very high resolution, allowing fast highly-resolved pseudo line-by-line, hyperspectral and broadband simulations across the electromagnetic spectrum form the microwave to the ultraviolet for satellite-based, airborne and ground-based sensors. HT-FRTC models clear atmospheres and those containing clouds and aerosols, as well as any surface (land/sea/man-made). The HT-FRTC has been used operationally in the NEON Tactical Decision Aid (TDA) since 2008. The TDA combines the HT-FRTC with a thermal contrast model and an NWP model forecast data feed to predict the apparent thermal contrast between different surfaces and ground-based targets in the thermal and short-wave IR. The new objective here is to predict the optical contrast of air-borne targets under realistic night-time scenarios in the Photopic and NVG parts of the spectrum. This requires the inclusion of all the relevant radiation sources, which include twilight, moonlight, starlight, airglow and cultural light. A completely new exact scattering code has been developed which allows the straight-forward addition of any number of direct and diffuse sources anywhere in the atmosphere. The new code solves the radiative transfer equation iteratively and is faster than the previous solution. Simulations of scenarios with different light levels, from situations during a full moon to a moonless night with very low light levels and a situation with cultural light from a town are presented. The impact of surface reflectance and target reflectance is investigated.

  7. Kernel number as a positive target trait for prediction of hybrid performance under low-nitrogen stress as revealed by diallel analysis under contrasting nitrogen conditions.

    Science.gov (United States)

    Li, Xiuxiu; Sun, Zhen; Xu, Xiaojie; Li, Wen-Xue; Zou, Cheng; Wang, Shanhong; Xu, Yunbi; Xie, Chuanxiao

    2014-12-01

    Environmental sustainability concerns make improving yield under lower N input a desirable breeding goal. To evaluate genetic variation and heterosis for low-N tolerance breeding, 28 F1 hybrids from a diallel scheme, along with their eight parental lines, were tested for agronomic traits including kernel number per ear (KNE) and grain yield per plant (GY), in replicated plots over two years under low-nitrogen (LN, without nitrogen application) and normal-nitrogen (NN, 220 kg N ha(-1)) conditions. Taken together the heritability in this and our previous studies, the correlation with grain yield, and the sensitivity to the stress for target trait selection, KNE was a good secondary target trait for LN selection in maize breeding. KNE also showed much higher mid-parent heterosis than hundred-kernel weight under both nitrogen levels, particularly under LN, indicating that KNE contributed the majority of GY heterosis, particularly under LN. Therefore, KNE can be used as a positive target trait for hybrid performance prediction in LN tolerance breeding. Our results also suggest that breeding hybrids for LN tolerance largely relies on phenotypic evaluation of hybrids under LN condition and yield under LN might be improved more by selection for KNE than by direct selection for GY per se.

  8. Immunosuppression in cardiac graft rejection: A human in vitro model to study the potential use of new immunomodulatory drugs

    International Nuclear Information System (INIS)

    Crescioli, Clara; Squecco, Roberta; Cosmi, Lorenzo; Sottili, Mariangela; Gelmini, Stefania; Borgogni, Elisa; Sarchielli, Erica; Scolletta, Sabino; Francini, Fabio; Annunziato, Francesco; Vannelli, Gabriella Barbara; Serio, Mario

    2008-01-01

    CXCL10-CXCR3 axis plays a pivotal role in cardiac allograft rejection, so that targeting CXCL10 without inducing generalized immunosuppression may be of therapeutic significance in allotransplantation. Since the role of resident cells in cardiac rejection is still unclear, we aimed to establish reliable human cardiomyocyte cultures to investigate Th1 cytokine-mediated response in allograft rejection. We used human fetal cardiomyocytes (Hfcm) isolated from fetal hearts, obtained after legal abortions. Hfcm expressed specific cardiac lineage markers, specific cardiac structural proteins, typical cardiac currents and generated ventricular action potentials. Thus, Hfcm represent a reliable in vitro tool for allograft rejection research, since they resemble the features of mature cells. Hfcm secreted CXCL10 in response to IFNγ and TNFαα; this effect was magnified by cytokine combination. Cytokine synergy was associated to a significant TNFα-induced up-regulation of IFNγR. The response of Hfcm to some currently used immunosuppressive drugs compared to rosiglitazone, a peroxisome proliferator-activated receptor γ agonist and Th1-mediated response inhibitor, was also evaluated. Only micophenolic acid and rosiglitazone halved CXCL10 secretion by Hfcm. Given the pivotal role of IFNγ-induced chemokines in Th1-mediated allograft rejection, these preliminary results suggest that the combined effects of immunosuppressive agents and rosiglitazone could be potentially beneficial to patients receiving heart transplants

  9. A simple method to optimize the HSCCC two-phase solvent system by predicting the partition coefficient for target compound.

    Science.gov (United States)

    Han, Quan-Bin; Wong, Lina; Yang, Nian-Yun; Song, Jing-Zheng; Qiao, Chun-Feng; Yiu, Hillary; Ito, Yoichiro; Xu, Hong-Xi

    2008-04-01

    A simple method was developed to optimize the solvent ratio of the two-phase solvent system used in the high-speed counter-current chromatography (HSCCC) separation. Some mathematic equations, such as the exponential and the power equations, were established to describe the relationship between the solvent ratio and the partition coefficient. Using this new method, the two-phase solvent system was easily optimized to obtain a proper partition coefficient for the CCC separation of the target compound. Furthermore, this method was satisfactorily applied in determining the two-phase solvent system for the HSCCC preparation of pseudolaric acid B from the Chinese herb Pseudolarix kaempferi Gordon (Pinaceae). The two-phase solvent system of n-hexane/EtOAc/MeOH/H(2)O (5:5:5:5 by volume) was used with a good partition coefficient K = 1.08. As a result, 232.05 mg of pseudolaric acid B was yielded from 0.5 g of the crude extract with a purity of 97.26% by HPLC analysis.

  10. High-sensitivity C-reactive protein predicts target organ damage in Chinese patients with metabolic syndrome

    DEFF Research Database (Denmark)

    Zhao, Zhigang; Nie, Hai; He, Hongbo

    2007-01-01

    with metabolic syndrome. A total of 1082 consecutive patients of Chinese origin were screened for the presence of metabolic syndrome according to the National Cholesterol Education Program's Adult Treatment Panel III. High-sensitivity C-reactive protein and target organ damage, including cardiac hypertrophy......, carotid intima-media thickness, and renal impairment, were investigated. The median (25th and 75th percentiles) of high-sensitivity C-reactive protein in 619 patients with metabolic syndrome was 2.42 mg/L (0.75 and 3.66 mg/L) compared with 1.13 mg/L (0.51 and 2.46 mg/L) among 463 control subjects (P ...). There was a progressive increase in high-sensitivity C-reactive protein level with the number of components of the metabolic syndrome. Stratification of patients with metabolic syndrome into 3 groups according to their high-sensitivity C-reactive protein concentrations (3.0 mg/L) showed that the subjects...

  11. Differences in the expression of microRNAs and their predicted gene targets between cauda epididymal and ejaculated boar sperm.

    Science.gov (United States)

    Chang, Yu; Dai, Ding-Hui; Li, Yuan; Zhang, Yan; Zhang, Ming; Zhou, Guang-Bin; Zeng, Chang-Jun

    2016-12-01

    Mammalian spermatozoa gradually mature and acquire fertility during the transition from the testis to the caput and cauda epididymis, after which they are stored at the tail of the epididymis and the ampulla of vas deferens. During ejaculation, mixing of spermatozoa with the secretions of accessory sex glands leads to their dilution and changes in their function. Although remarkable progress has been made toward the understanding of changes in spermatozoa biochemistry and function before and after ejaculation, it is unknown whether microRNAs (miRNAs) are involved in regulating the function of spermatozoa during the transition between the cauda epididymis and ejaculation. In this study, 48 miRNAs were selected for analysis on the basis of their potential involvement in spermatogenesis, sperm maturation, and quality parameters markers. The differential expression levels of these 48 miRNAs between the caudal epididymis and fresh ejaculates of boar spermatozoa were determined. We found that 15 miRNAs were significantly differentially expressed (eight downregulated and seven upregulated) between boar cauda epididymal and fresh spermatozoa. Five miRNAs hypothesized to be involved in sperm apoptosis were further tested to demonstrate their influence over the expression of their target mRNAs using quantitative reverse-transcription polymerase chain reaction. Together, our findings suggest that these differentially expressed miRNAs are associated with the functional regulation of spermatozoa between cauda epididymis and ejaculation. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Community rejection following sexual assault as ‘forced migration’

    Directory of Open Access Journals (Sweden)

    AJ Morgen

    2013-09-01

    Full Text Available When women are banished from their communities following sexual assault, this rejection should be considered an act of forced migration by the administrators of truth commission reparations programmes.

  13. Hyperacute Rejection of a Living Unrelated Kidney Graft

    Directory of Open Access Journals (Sweden)

    Dietlind Tittelbach-Helmrich

    2014-01-01

    Full Text Available We present a case report of a 59-year-old man, who received a blood group identical living unrelated kidney graft. This was his second kidney transplantation. Pretransplant T-cell crossmatch resulted negative. B-cell crossmatch, which is not considered a strict contraindication for transplantation, resulted positive. During surgery no abnormalities occurred. Four hours after the transplantation diuresis suddenly decreased. In an immediately performed relaparotomy the transplanted kidney showed signs of hyperacute rejection and had to be removed. Pathological examination was consistent with hyperacute rejection. Depositions of IgM or IgG antibodies were not present in pathologic evaluation of the rejected kidney, suggesting that no irregular endothelial specific antibodies had been involved in the rejection. We recommend examining more closely recipients of second allografts, considering not only a positive T-cell crossmatch but also a positive B-cell crossmatch as exclusion criteria for transplantation.

  14. Reliability and construct validity for scale of rejection of Christianity.

    Science.gov (United States)

    Robbins, Mandy; Francis, Leslie J; Bradford, Amanda

    2003-02-01

    A sample of 16 male and 30 female undergraduates completed the Greer and Francis Scale of Rejection of Christianity. The data support the internal consistency reliability and construct validity of the scale for this sample.

  15. Asymmetric Frontal Brain Activity and Parental Rejection

    NARCIS (Netherlands)

    Huffmeijer, R.; Alink, L.R.A.; Tops, M.; Bakermans-Kranenburg, M.J.; van IJzendoorn, M.H.

    2013-01-01

    Asymmetric frontal brain activity has been widely implicated in reactions to emotional stimuli and is thought to reflect individual differences in approach-withdrawal motivation. Here, we investigate whether asymmetric frontal activity, as a measure of approach-withdrawal motivation, also predicts

  16. SU-E-T-170: Characterization of the Location, Extent, and Proximity to Critical Structures of Target Volumes Provides Detail for Improved Outcome Predictions Among Pancreatic Cancer Patients

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Z; Moore, J; Rosati, L; Mian, O; Narang, A; Herman, J; McNutt, T [Johns Hopkins University, Baltimore, MD (United States)

    2015-06-15

    Purpose: In radiotherapy, size, location and proximity of the target to critical structures influence treatment decisions. It has been shown that proximity of the target predicts dosimetric sparing of critical structures. In addition to dosimetry, precise location of disease has further implications such as tumor invasion, or proximity to major arteries that inhibit surgery. Knowledge of which patients can be converted to surgical candidates by radiation may have high impact on future treat/no-treat decisions. We propose a method to improve our characterization of the location of pancreatic cancer and treatment volume extent with respect to nearby arteries with the goal of developing features to improve clinical predictions and decisions. Methods: Oncospace is a local learning health system that systematically captures clinical outcomes and all aspects of radiotherapy treatment plans, including overlap volume histograms (OVH) – a measure of spatial relationships between two structures. Minimum and maximum distances of PTV and OARs based on OVH, PTV volume, anatomic location by ICD-9 code, and surgical outcome were queried. Normalized distance to center from the left and right kidney was calculated to indicate tumor location and laterality. Distance to critical arteries (celiac, superior mesenteric, common hepatic) is validated by surgical status (borderline resectable, locally advanced converted to resectable). Results: There were 205 pancreas stereotactic body radiotherapy patients treated from 2009–2015 queried. Location/laterality of tumor based on kidney OVH show strong trends between location by OVH and by ICD-9. Compared to the locally advanced group, the borderline resectable group showed larger geometrical distance from critical arteries (p=0.03). Conclusion: Our platform enabled analysis of shape/size-location relationships. These data suggest that PTV volume and attention to distance between PTVs and surrounding OARs and major arteries may be

  17. SU-E-T-170: Characterization of the Location, Extent, and Proximity to Critical Structures of Target Volumes Provides Detail for Improved Outcome Predictions Among Pancreatic Cancer Patients

    International Nuclear Information System (INIS)

    Cheng, Z; Moore, J; Rosati, L; Mian, O; Narang, A; Herman, J; McNutt, T

    2015-01-01

    Purpose: In radiotherapy, size, location and proximity of the target to critical structures influence treatment decisions. It has been shown that proximity of the target predicts dosimetric sparing of critical structures. In addition to dosimetry, precise location of disease has further implications such as tumor invasion, or proximity to major arteries that inhibit surgery. Knowledge of which patients can be converted to surgical candidates by radiation may have high impact on future treat/no-treat decisions. We propose a method to improve our characterization of the location of pancreatic cancer and treatment volume extent with respect to nearby arteries with the goal of developing features to improve clinical predictions and decisions. Methods: Oncospace is a local learning health system that systematically captures clinical outcomes and all aspects of radiotherapy treatment plans, including overlap volume histograms (OVH) – a measure of spatial relationships between two structures. Minimum and maximum distances of PTV and OARs based on OVH, PTV volume, anatomic location by ICD-9 code, and surgical outcome were queried. Normalized distance to center from the left and right kidney was calculated to indicate tumor location and laterality. Distance to critical arteries (celiac, superior mesenteric, common hepatic) is validated by surgical status (borderline resectable, locally advanced converted to resectable). Results: There were 205 pancreas stereotactic body radiotherapy patients treated from 2009–2015 queried. Location/laterality of tumor based on kidney OVH show strong trends between location by OVH and by ICD-9. Compared to the locally advanced group, the borderline resectable group showed larger geometrical distance from critical arteries (p=0.03). Conclusion: Our platform enabled analysis of shape/size-location relationships. These data suggest that PTV volume and attention to distance between PTVs and surrounding OARs and major arteries may be

  18. EEG Asymmetry in Borderline Personality Disorder and Depression Following Rejection

    OpenAIRE

    Beeney, Joseph E.; Levy, Kenneth N.; Gatzke-Kopp, Lisa M.; Hallquist, Michael N.

    2013-01-01

    Borderline personality disorder (BPD) and major depressive disorder (MDD) share numerous features including dysphoric affect, irritability, suicidality, and a heightened sensitivity to perceived interpersonal rejection. However, these disorders are associated with divergent profiles of reactivity to rejection; individuals with MDD are more likely to respond with withdrawal and isolation, and those with BPD appear to respond with increased approach behaviors and greater hostility. Potential me...

  19. Acute Hepatic Allograft Rejection in Pediatric Recipients: Independent Factors

    OpenAIRE

    Dehghani, S. M.; Shahramian, I.; Afshari, M.; Bahmanyar, M.; Ataollahi, M.; Sargazi, A.

    2017-01-01

    Background: Acute cellular rejection (ACR) has a reversible effect on graft and its survival. Objective: To evaluate the relation between ACR and clinical factors in recipients of liver transplant allografts. Methods: 47 consecutive liver recipients were retrospectively studied. Their data were extracted from records and analyzed. Results: 38 (81%) of the 47 recipients experienced ACR during a 24-month follow-up. The rate of rejection was associated with none of the studied factors—recipient’...

  20. Brain Region-Dependent Rejection of Neural Precursor Cell Transplants

    Directory of Open Access Journals (Sweden)

    Nina Fainstein

    2018-04-01

    Full Text Available The concept of CNS as an immune-privileged site has been challenged by the occurrence of immune surveillance and allogeneic graft rejection in the brain. Here we examined whether the immune response to allogeneic neural grafts is determined by the site of implantation in the CNS. Dramatic regional differences were observed between immune responses to allogeneic neural precursor/stem cell (NPC grafts in the striatum vs. the hippocampus. Striatal grafts were heavily infiltrated with IBA-1+ microglia/macrophages and CD3+ T cells and completely rejected. In contrast, hippocampal grafts exhibited milder IBA-1+ cell infiltration, were not penetrated efficiently by CD3+ cells, and survived efficiently for at least 2 months. To evaluate whether the hippocampal protective effect is universal, astrocytes were then transplanted. Allogeneic astrocyte grafts elicited a vigorous rejection process from the hippocampus. CD200, a major immune-inhibitory signal, plays an important role in protecting grafts from rejection. Indeed, CD200 knock out NPC grafts were rejected more efficiently than wild type NPCs from the striatum. However, lack of CD200 expression did not elicit NPC graft rejection from the hippocampus. In conclusion, the hippocampus has partial immune-privilege properties that are restricted to NPCs and are CD200-independent. The unique hippocampal milieu may be protective for allogeneic NPC grafts, through host-graft interactions enabling sustained immune-regulatory properties of transplanted NPCs. These findings have implications for providing adequate immunosuppression in clinical translation of cell therapy.

  1. Autoantibodies to vimentin cause accelerated rejection of cardiac allografts.

    Science.gov (United States)

    Mahesh, Balakrishnan; Leong, Hon-Sing; McCormack, Ann; Sarathchandra, Padmini; Holder, Angela; Rose, Marlene L

    2007-04-01

    Autoimmune responses to vimentin occur after solid organ transplantation, but their pathogenic effects are unclear. The aim of these studies was to investigate the effects of vimentin preimmunization on allogeneic and isografted hearts in a murine transplant model. Immunization of C57BL/6 mice with murine vimentin in complete Freund's adjuvant resulted in anti-vimentin antibodies and vimentin-reactive Th-1 cells. Transplantation of 129/sv hearts into vimentin-immunized C57BL/6 recipients resulted in accelerated rejection (8.4 +/- 1.5 days; n = 18), compared with hen egg lysozyme-immunized C57BL/6 (13.3 +/- 2.2 days; n = 10; P rejection, shown by the fact that vimentin-immunized B-cell-deficient IgH6 mice did not show accelerated rejection of 129/sv allografts, but rejection was restored by adoptive transfer of serum containing anti-vimentin antibodies. Eluates from donor hearts placed in vimentin/complete Freund's adjuvant recipients contained anti-vimentin antibodies, shown by Western blotting. Confocal imaging of rejected hearts de-monstrated presence of vimentin and C3d on apoptosed leukocytes, endothelial cells, and platelet/leukocyte conjugates. These results demonstrate that autoantibodies to vimentin, in conjunction with the alloimmune response, have a pathogenic role in allograft rejection.

  2. Higher boron rejection with a new TFC forward osmosis membrane

    KAUST Repository

    Valladares Linares, Rodrigo

    2014-07-17

    Due to the stringent limits for boron in drinking and irrigation water, water treatment facilities have to incur additional treatment to remove boron down to a safe concentration. Forward osmosis (FO) is a membrane technology that may reduce the energy required to remove boron present in seawater. In direct FO desalination hybrid systems, fresh water is recovered from seawater using a recoverable draw solution, FO membranes are expected to show high boron rejection. This study focuses on determining the boron rejection capabilities of a new generation thin-film composite (TFC) FO membrane compared to a first generation cellulose triacetate (CTA) FO membrane. The effects of water permeate flux, membrane structure, draw solute charge, and reverse solute flux on boron rejection were determined. For TFC and CTA FO membranes, experiments showed that when similar operating conditions are applied (e.g. membrane type and draw solute type) boron rejection decreases with increase in permeate flux. Reverse draw solute flux and membrane fouling have no significant impact on boron rejection. Compared to the first generation CTA FO membrane operated at the same conditions, the TFC FO membrane showed a 40% higher boron rejection capability and a 20% higher water flux. This demonstrates the potential for boron removal for new generation TFC FO membranes. © 2014 © 2014 Balaban Desalination Publications. All rights reserved.

  3. The effect of parental rejection on the emotional eating behaviour of youngsters: A laboratory-based study.

    Science.gov (United States)

    Vandewalle, Julie; Moens, Ellen; Bosmans, Guy; Braet, Caroline

    2017-01-01

    Results from survey studies demonstrate a relationship between parental rejection and self-reported emotional eating of youngsters. The aim of the current study was to build on this research by examining the relationship between parental rejection and actual emotional eating, using an experimental laboratory paradigm. Participants were 46 youngsters between the ages of 10 and 17 years old. Participants first completed online questionnaires at home, measuring parental rejection and emotional eating style. At the laboratory, participants were randomly assigned to a neutral condition or negative mood condition, followed by a multi-item snack buffet. The interaction effect maternal rejection × condition on energy intake from savoury food was significant. More maternal rejection predicted more energy intake from savoury food in the negative mood condition, but not in the neutral condition. The results highlight the importance of assessing, and if mandatory, improving the emotional bond between parent and child in the prevention and intervention of emotional eating. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. The role of interleukin-1β as a predictive biomarker and potential therapeutic target during clinical ex vivo lung perfusion.

    Science.gov (United States)

    Andreasson, Anders S I; Borthwick, Lee A; Gillespie, Colin; Jiwa, Kasim; Scott, Jonathan; Henderson, Paul; Mayes, Jonny; Romano, Rosalba; Roman, Marius; Ali, Simi; Fildes, James E; Marczin, Nandor; Dark, John H; Fisher, Andrew J

    2017-09-01

    Extended criteria donor lungs deemed unsuitable for immediate transplantation can be reconditioned using ex vivo lung perfusion (EVLP). Objective identification of which donor lungs can be successfully reconditioned and will function well post-operatively has not been established. This study assessed the predictive value of markers of inflammation and tissue injury in donor lungs undergoing EVLP as part of the DEVELOP-UK study. Longitudinal samples of perfusate, bronchoalveolar lavage, and tissue from 42 human donor lungs undergoing clinical EVLP assessments were analyzed for markers of inflammation and tissue injury. Levels were compared according to EVLP success and post-transplant outcomes. Neutrophil adhesion to human pulmonary microvascular endothelial cells (HPMECs) conditioned with perfusates from EVLP assessments was investigated on a microfluidic platform. The most effective markers to differentiate between in-hospital survival and non-survival post-transplant were perfusate interleukin (IL)-1β (area under the curve = 1.00, p = 0.002) and tumor necrosis factor-α (area under the curve = 0.95, p = 0.006) after 30 minutes of EVLP. IL-1β levels in perfusate correlated with upregulation of intracellular adhesion molecule-1 in donor lung vasculature (R 2 = 0.68, p < 0.001) and to a lesser degree upregulation of intracellular adhesion molecule-1 (R 2 = 0.30, p = 0.001) and E-selectin (R 2 = 0.29, p = 0.001) in conditioned HPMECs and neutrophil adhesion to conditioned HPMECs (R 2 = 0.33, p < 0.001). Neutralization of IL-1β in perfusate effectively inhibited neutrophil adhesion to conditioned HPMECs (91% reduction, p = 0.002). Donor lungs develop a detectable and discriminatory pro-inflammatory signature in perfusate during EVLP. Blocking the IL-1β pathway during EVLP may reduce endothelial activation and subsequent neutrophil adhesion on reperfusion; this requires further investigation in vivo. Copyright © 2017 The Authors. Published by Elsevier Inc. All

  5. Does visual working memory represent the predicted locations of future target objects? An event-related brain potential study.

    Science.gov (United States)

    Grubert, Anna; Eimer, Martin

    2015-11-11

    During the maintenance of task-relevant objects in visual working memory, the contralateral delay activity (CDA) is elicited over the hemisphere opposite to the visual field where these objects are presented. The presence of this lateralised CDA component demonstrates the existence of position-dependent object representations in working memory. We employed a change detection task to investigate whether the represented object locations in visual working memory are shifted in preparation for the known location of upcoming comparison stimuli. On each trial, bilateral memory displays were followed after a delay period by bilateral test displays. Participants had to encode and maintain three visual objects on one side of the memory display, and to judge whether they were identical or different to three objects in the test display. Task-relevant memory and test stimuli were located in the same visual hemifield in the no-shift task, and on opposite sides in the horizontal shift task. CDA components of similar size were triggered contralateral to the memorized objects in both tasks. The absence of a polarity reversal of the CDA in the horizontal shift task demonstrated that there was no preparatory shift of memorized object location towards the side of the upcoming comparison stimuli. These results suggest that visual working memory represents the locations of visual objects during encoding, and that the matching of memorized and test objects at different locations is based on a comparison process that can bridge spatial translations between these objects. This article is part of a Special Issue entitled SI: Prediction and Attention. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Current and future challenges in therapy for antibody-mediated rejection.

    Science.gov (United States)

    Nair, Nandini; Ball, Timothy; Uber, Patricia A; Mehra, Mandeep R

    2011-06-01

    Antibody-mediated rejection (AMR) continues to present a challenge for the survival of the cardiac allograft. AMR appears to be on the rise, likely secondary to changing trends in clinical practice, including selection of patients for transplantation on mechanical circulatory support and development of more effective combinations of immunosuppressive drugs against acute cellular rejection. Most current strategies are aimed at treating acute AMR, but the treatment of chronic AMR is still not well defined. Clinically, AMR can often be more severe than cellular rejection and more difficult to treat, often not responding to typical protocols of increased immunosuppression. Complex steps involved in the antibody response allows for several potential targets for therapeutic intervention, including suppression of T and B cells, elimination of circulating antibodies, and inhibition of residual antibodies. Existing evidence suggests a multiregimen approach is the best option. Sustenance of accommodation and induction of tolerance could be viewed as viable options if adequate immune surveillance can be achieved in this setting. This review discusses the challenges in treating AMR and provides a critical analysis of current and possible future therapies. Copyright © 2011 International Society for Heart and Lung Transplantation. Published by Elsevier Inc. All rights reserved.

  7. Factors Influencing the Cure Rate in the Corneal Graft Rejection with Survival Analysis

    Directory of Open Access Journals (Sweden)

    Feizi S.

    2009-11-01

    Full Text Available AbstractBackground and Objectives: Immunologic rejection of the transplanted cornea is the major cause of human allograft failure with several risk factors contributing to it. Since in the corneal graft, most individuals do not reject the graft, we used the survival analysis with cure rate for the assessment of the factors influencing the cure rate at the time of data analysis. The main aim of this study was to evaluate the cure rate and assess the risk factors for corneal graft rejection in the keratoconus disease in Labafinejad Hospital, Tehran, Iran. Methods: This was a routine data base study in which the data were gathered from keratoconus patients’ files that had undergone penetrating keratoplasty operation. In the survival analysis, individuals who didn’t reject corneal were considered cured. To study the factors influencing the cure rate, we used the Weibull distribution for survival function and the logistic link function for the cure rate because of their tractability and accuracy.Results: Out of 119 patients 31 patients (26% rejected grafts. Among the factors influencing cure rate, only in vascularization and in persons older than 25 years of age was ameaningful effect on decreasing cure rate. With this cure model, the expected cure rate in the non-vascularization and less than 25 year- old patients was 81, in non-vascularization and more than 25 year- olds it is 64, in the vascularization and less than 25 year- olds, the cure rate is 19 and in the vascularization and more than 25 years of age, the cure rate is 9 percent and the observed cure rate for Kaplan-Meier product limit estimator was 79, 61, 27 and 0 percent, respectively. The results showed that the estimate of cure rate in the survival analysis was near the Kaplan-Meier product-limits estimator.Conclusion: One of the benefits of modeling is its ability to generalize the results; using them in the prediction. According to the results obtained from the fitting cure model

  8. 111-Indium-labelled platelets for diagnosis of acute kidney transplant rejection and monitoring of prostacyclin anti-rejection treatment

    International Nuclear Information System (INIS)

    Leithner, C.; Pohanka, E.; Schwarz, M.; Sinzinger, H.; Syre, G.

    1984-01-01

    33 patients were examined daily under a gamma camera after weekly injections of 111-In-labelled autologous platelets over a period of at least 4 weeks after transplantation. A group of 33 patients with long-term stable and well-functioning grafts served as controls. By means of a computerized recording technique, platelet trapping in the graft was measured and expressed as platelet-uptake index (PUI). The method worked well for the early diagnosis of acute rejection signified by an increase in PUI, accompanied by a shortening of platelet half life (t/2). 6 patients suffering from acute rejection received infusions of prostacyclin in addition to conventional high-dose methylprednisolone therapy. In 4 cases the PUI decreased again and an improvement in graft function was observed. Prostacyclin infusion treatment was applied also in 12 patients with histologically-proven chronic transplant rejection. Decreased platelet consumption by the graft and a temporary improvement in transplant function were achieved. We suggest that prostacyclin could enrich the possibilities of anti-rejection treatment by providing a tool for the suppression of platelet trapping in the graft. The platelet scan served as a useful method for the early detection of acute rejection, as well as the monitoring of prostacyclin anti-rejection treatment. (Autor)

  9. Diagonal rejection-based minimum variance distortionless response for fiber underwater acoustic array

    Science.gov (United States)

    Chen, Yang; Zou, Ling; Zhou, Bin

    2017-07-01

    The high mounting precision of the fiber underwater acoustic array leads to an array manifold without perturbation. Besides, the targets are either static or slowly moving in azimuth in underwater acoustic array signal processing. Therefore, the covariance matrix can be estimated accurately by prolonging the observation time. However, this processing is limited to poor bearing resolution due to small aperture, low SNR and strong interferences. In this paper, diagonal rejection (DR) technology for Minimum Variance Distortionless Response (MVDR) was developed to enhance the resolution performance. The core idea of DR is rejecting the main diagonal elements of the covariance matrix to improve the output signal to interference and noise ratio (SINR). The definition of SINR here implicitly assumes independence between the spatial filter and the received observations at which the SINR is measured. The power of noise converges on the diagonal line in the covariance matrix and then it is integrated into the output beams. With the diagonal noise rejected by a factor smaller than 1, the array weights of MVDR will concentrate on interference suppression, leading to a better resolution capability. The algorithm was theoretically proved with optimal rejecting coefficient derived under both infinite and finite snapshots scenarios. Numerical simulations were conducted with an example of a linear array with eight elements half-wavelength spaced. Both resolution and Direction-of-Arrival (DOA) performances of MVDR and DR-based MVDR (DR-MVDR) were compared under different SNR and snapshot numbers. A conclusion can be drawn that with the covariance matrix accurately estimated, DR-MVDR can provide a lower sidelobe output level and a better bearing resolution capacity than MVDR without harming the DOA performance.

  10. Feedback model predictive control by randomized algorithms

    NARCIS (Netherlands)

    Batina, Ivo; Stoorvogel, Antonie Arij; Weiland, Siep

    2001-01-01

    In this paper we present a further development of an algorithm for stochastic disturbance rejection in model predictive control with input constraints based on randomized algorithms. The algorithm presented in our work can solve the problem of stochastic disturbance rejection approximately but with

  11. Pan-Genome Analysis of Human Gastric Pathogen H. pylori: Comparative Genomics and Pathogenomics Approaches to Identify Regions Associated with Pathogenicity and Prediction of Potential Core Therapeutic Targets

    DEFF Research Database (Denmark)

    Ali, Amjad; Naz, Anam; Soares, Siomar C.

    2015-01-01

    Helicobacter pylori is a human gastric pathogen implicated as the major cause of peptic ulcer and second leading cause of gastric cancer (similar to 70%) around the world. Conversely, an increased resistance to antibiotics and hindrances in the development of vaccines against H. pylori are observed......-genome approach; the predicted conserved gene families (1,193) constitute similar to 77% of the average H. pylori genome and 45% of the global gene repertoire of the species. Reverse vaccinology strategies have been adopted to identify and narrow down the potential core-immunogenic candidates. Total of 28 nonhost...... homolog proteins were characterized as universal therapeutic targets against H. pylori based on their functional annotation and protein-protein interaction. Finally, pathogenomics and genome plasticity analysis revealed 3 highly conserved and 2 highly variable putative pathogenicity islands in all...

  12. Delayed allogeneic skin graft rejection in CD26-deficient mice.

    Science.gov (United States)

    Zhao, Xiangli; Zhang, Kai; Daniel, Peter; Wisbrun, Natali; Fuchs, Hendrik; Fan, Hua

    2018-03-23

    Organ transplantation is an effective therapeutic tool for treating many terminal diseases. However, one of the biggest challenges of transplantation is determining how to achieve the long-term survival of the allogeneic or xenogeneic transplant by, for example, preventing transplant rejection. In the current study, CD26 gene-knockout mice were used to investigate the potential role of CD26/dipeptidyl peptidase-4 (DPPIV) in allogeneic skin graft rejection by tail-skin transplantation. Compared with wild-type (CD26 +/+ ) counterparts, CD26 -/- mice showed reduced necrosis of grafts and delayed graft rejection after skin transplantation. Concentrations of serum IgG, including its subclasses IgG1 and IgG2a, were significantly reduced in CD26 -/- mice during graft rejection. Moreover, after allogeneic skin transplantation, the secretion levels of the cytokines IFN-γ, IL-2, IL-6, IL-4, and IL-13 were significantly reduced, whereas the level of the cytokine IL-10 was increased in the serum of CD26 -/- mice compared with that in the serum of CD26 +/+ mice. Additionally, the concentration of IL-17 in serum and the percentage of cells secreting IL-17 in mouse peripheral blood lymphocytes (MPBLs) were both significantly lower, while the percentage of regulatory T cells (Tregs) was significantly higher in MPBLs of CD26 -/- mice than in those of CD26 +/+ mice. Furthermore, a lower percentage of CD8 + T cells in MPBLs and fewer infiltrated macrophages and T cells in graft tissues of CD26 -/- mice were detected during graft rejection. These results indicate that CD26 is involved in allogeneic skin graft rejection and provides another hint that CD26 deficiency leads to less rejection due to lower activation and proliferation of host immune cells.

  13. Response Versus Nonresponse to Self-Regulatory Treatment Targets Is Not Discriminated by Personal Characteristics but Predicts Physical Activity, Eating Behavior, and Weight Changes in Women With Obesity.

    Science.gov (United States)

    Annesi, James J

    2018-01-01

    Background Results of behavioral weight-loss treatments vary widely, with mostly unsuccessful outcomes beyond the short term. Women with obesity participating in a new cognitive-behavioral weight-loss treatment were assessed on their responses to psychological targets. Methods Groups of responders ( n = 43) and nonresponders ( n = 48) were established post hoc. Results Age, race/ethnicity, education, income, body composition, physical activity, and eating behaviors at baseline were not discriminated between responders and nonresponders. Over both 6 and 24 months, responders improved significantly more in physical activity and fruit/vegetable consumption but not sweets intake. Weight loss over 6 and 24 months was significantly greater for the responder group at 8.1% and 8.6% versus nonresponders at 4.7% and 3.8%, respectively. Self-regulation change significantly predicted all behavioral changes, with mood change improving the predictive strength for only sweets intake. Discussion Although further research is required to determine the etiology of, and to maximize, positive responses, findings suggested prospects for treatment improvements.

  14. Comparative proteomics of cerebrospinal fluid reveals a predictive model for differential diagnosis of pneumococcal, meningococcal, and enteroviral meningitis, and novel putative therapeutic targets

    Science.gov (United States)

    2015-01-01

    Background Meningitis is the inflammation of the meninges in response to infection or chemical agents. While aseptic meningitis, most frequently caused by enteroviruses, is usually benign with a self-limiting course, bacterial meningitis remains associated with high morbidity and mortality rates, despite advances in antimicrobial therapy and intensive care. Fast and accurate differential diagnosis is crucial for assertive choice of the appropriate therapeutic approach for each form of meningitis. Methods We used 2D-PAGE and mass spectrometry to identify the cerebrospinal fluid proteome specifically related to the host response to pneumococcal, meningococcal, and enteroviral meningitis. The disease-specific proteome signatures were inspected by pathway analysis. Results Unique cerebrospinal fluid proteome signatures were found to the three aetiological forms of meningitis investigated, and a qualitative predictive model with four protein markers was developed for the differential diagnosis of these diseases. Nevertheless, pathway analysis of the disease-specific proteomes unveiled that Kallikrein-kinin system may play a crucial role in the pathophysiological mechanisms leading to brain damage in bacterial meningitis. Proteins taking part in this cellular process are proposed as putative targets to novel adjunctive therapies. Conclusions Comparative proteomics of cerebrospinal fluid disclosed candidate biomarkers, which were combined in a qualitative and sequential predictive model with potential to improve the differential diagnosis of pneumococcal, meningococcal and enteroviral meningitis. Moreover, we present the first evidence of the possible implication of Kallikrein-kinin system in the pathophysiology of bacterial meningitis. PMID:26040285

  15. EEG asymmetry in borderline personality disorder and depression following rejection.

    Science.gov (United States)

    Beeney, Joseph E; Levy, Kenneth N; Gatzke-Kopp, Lisa M; Hallquist, Michael N

    2014-04-01

    Borderline personality disorder (BPD) and major depressive disorder (MDD) share numerous features, including dysphoric affect, irritability, suicidality, and a heightened sensitivity to perceived interpersonal rejection. However, these disorders are associated with divergent profiles of reactivity to rejection: Individuals with MDD are more likely to respond with withdrawal and isolation, and those with BPD appear to respond with increased approach behaviors and greater hostility. Potential mechanisms underlying these divergent patterns of response have not been elaborated. The goal of the present study was to assess whether prefrontal cortical asymmetry is associated with these behavioral profiles. EEG alpha activity was recorded at baseline and after individuals with BPD, MDD and healthy controls (HCs) participated in a rejection task. Although no differences were found at baseline, results demonstrated that following rejection, individuals with BPD showed greater left cortical activation, consistent with approach motivation, whereas those with MDD showed greater right cortical activation, consistent with withdrawal motivation. HCs evidenced a more balanced cortical profile, as hypothesized. Although BPD and MDD are highly comorbid, are easily confused, and are phenomenologically similar in a number of ways, individuals with these two disorders respond in very different ways to perceived rejection. PsycINFO Database Record (c) 2014 APA, all rights reserved

  16. The influence of structural stigma and rejection sensitivity on young sexual minority men's daily tobacco and alcohol use

    Science.gov (United States)

    Pachankis, John E.; Hatzenbuehler, Mark L.; Starks, Tyrel J.

    2018-01-01

    Stigma occurs at both individual and structural levels, but existing research tends to examine the effect of individual and structural forms of stigma in isolation, rather than considering potential synergistic effects. To address this gap, our study examined whether stigma at the individual level, namely gay-related rejection sensitivity, interacts with structural stigma to predict substance use among young sexual minority men. Sexual minority (n = 119) participants completed online measures of our constructs (e.g., rejection sensitivity). Participants currently resided across a broad array of geographic areas (i.e., 24 U.S. states), and had attended high school in 28 states, allowing us to capture sufficient variance in current and past forms of structural stigma, defined as (1) a lack of state-level policies providing equal opportunities for heterosexual and sexual minority individuals and (2) negative state-aggregated attitudes toward sexual minorities. To measure daily substance use, we utilized a daily diary approach, whereby all participants were asked to indicate whether they used tobacco or alcohol on nine consecutive days. Results indicated that structural stigma interacted with rejection sensitivity to predict tobacco and alcohol use, and that this relationship depended on the developmental timing of exposure to structural stigma. In contrast, rejection sensitivity did not mediate the relationship between structural stigma and substance use. These results suggest that psychological predispositions, such as rejection sensitivity, interact with features of the social environment, such as structural stigma, to predict important health behaviors among young sexual minority men. These results add to a growing body of research documenting the multiple levels through which stigma interacts to produce negative health outcomes among sexual minority individuals. PMID:24507912

  17. Evaluation of Load Rejection to house load test at 50% power for UCN 3

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Chang Gyun; Sohn, Suk Whun; Sohn, Jong Joo; Seo, Jong Tae; Lee, Sang Keun [Korea Power Engineering Company, Inc., Seoul (Korea, Republic of); Kim, Yong Sung; Nam, Kyu Won; Jung, Yang Mook; Chae, Kyeong Sik; Koh, Bum Jae; Oh, Chul Sung; Park, Hee Chool [Korea Electric Power Corporation, Taejon (Korea, Republic of)

    1998-12-31

    The Load Rejection to House Load test at 50% power was successfully performed during the UCN 3 PAT period. In this test, all plant control systems automatically controlled the plant from 50% power to house load operation mode. The KISPAC code, which was used in the performance analysis during the design process of UCN 3 and 4, predictions of the test agreed with the measured data demonstrating the validity of the code as well as the completeness of the plant design. 3 refs., 8 figs., 1 tab. (Author)

  18. Relational Victimization and Rejection Sensitivity: The Long-Term Impact of Social Hurt

    Science.gov (United States)

    Mellin, Elizabeth A.

    2012-01-01

    The Rejection Sensitivity Model is used to examine the social antecedents to expectations of rejection among adults. College students (N = 314) completed measures of relational victimization and rejection sensitivity. Results indicate that relational victimization is significantly related to rejection sensitivity for women. Implications for…

  19. Active disturbance rejection control for fractional-order system.

    Science.gov (United States)

    Li, Mingda; Li, Donghai; Wang, Jing; Zhao, Chunzhe

    2013-05-01

    Fractional-order proportional-integral (PI) and proportional-integral-derivative (PID) controllers are the most commonly used controllers in fractional-order systems. However, this paper proposes a simple integer-order control scheme for fractional-order system based on active disturbance rejection method. By treating the fractional-order dynamics as a common disturbance and actively rejecting it, active disturbance rejection control (ADRC) can achieve the desired response. External disturbance, sensor noise, and parameter disturbance are also estimated using extended state observer. The ADRC stability of rational-order model is analyzed. Simulation results on three typical fractional-order systems are provided to demonstrate the effectiveness of the proposed method. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

  20. Marginality and Social Rejection in Amiri Baraka's Slave Ship

    Directory of Open Access Journals (Sweden)

    Hamid Hammad Abed

    2016-11-01

    Full Text Available Marginality and social rejection are the most influential matters exploited by Baraka to intentionally criticize the American society.  More often than not, these two matters have become the scenes of major or minor acts of humiliation and dehumanization that threaten to violate the ethical rules of living. This paper aims at investigating the impact of marginality and social rejection on a number of black characters in Baraka's Slave Ship who are brought to America to be sold as commodities. It is divided into two sections and conclusion. Section one deals with Amiri Baraka’s dramatic thought and experience of marginality within the American society. The textual analysis of Slave Ship is investigated in section two. The significance of the study lies in its textual exploration of the impact of marginality and social rejection in subverting the American dream of democracy, freedom, and equality in Baraka’s Slave Ship.

  1. Acute Hepatic Allograft Rejection in Pediatric Recipients: Effective Factors.

    Science.gov (United States)

    Dehghani, S M; Shahramian, I; Afshari, M; Bahmanyar, M; Ataollahi, M; Sargazi, A

    2018-01-01

    Acute cellular rejection (ACR), a reversible process, can affect the graft survival. To evaluate the relation between ACR and clinical factors in recipients of allograft liver transplantation. 47 recipients of liver were consecutively enrolled in a retrospective study. Their information were retrieved from their medical records and analyzed. Of the 47 recipients, 38 (81%) experienced acute rejection during 24 months of the transplantation. None of the studied factors for occurring transplant rejection, i.e ., blood groups, sex, age, familial history of disease, receiving drugs and blood products, type of donor, Child score, and Child class, was not found to be significant. During a limited follow-up period, we did not find any association between ACR and suspected risk factors.

  2. T-regulatory cells in chronic rejection versus stable grafts.

    Science.gov (United States)

    Al-Wedaie, Fatima; Farid, Eman; Tabbara, Khaled; El-Agroudy, Amgad E; Al-Ghareeb, Sumaya M

    2015-04-01

    Studying regulatory T cells in kidney allograft acceptance versus chronic rejection may help in the understanding of more mechanisms of immune tolerance and, in the future, may enable clinicians to induce immune tolerance and decrease the use of immunosuppressive drugs. The aim of the current study was to evaluate regulatory T cells in kidney transplant patients with stable graft versus transplant with biopsy-proven chronic rejection. The 3 groups that were studied included: kidney transplanted patients with no rejection episodes (n = 43); transplanted patients with biopsy-proven renal rejection (n = 27); and healthy age-matched nontransplanted individuals as controls (n = 42).The percentage of regulatory T cells (CD4+CD25+Foxp3+) in blood was determined by flow cytometry. The regulatory T cell percentage was significantly lower in chronic rejection patients than control or stable graft groups. No significant difference was observed in regulatory T cell percentage between the stable graft and control groups. In the stable graft group, patients on rapamycin had a significantly higher regulatory T cell percentage than patients on cyclosporine. No effect of donor type, infection, or duration after transplant was observed on regulatory T cell percentage. The results of the current study are consistent with previous studies addressing the function of regulatory T cells in inducing immunotolerance after kidney transplant. Considering the established role of regulatory T cells in graft maintenance and our observation of high regulatory T cell percentage in patients receiving rapamycin than cyclosporine, we recommend including rapamycin when possible in immunosuppressive protocols. The findings from the current study on the chronic rejection group support ongoing research of having treatment with regulatory T cells, which may constitute a novel, efficient antirejection therapy in the future.

  3. High Frequency Target Strength Predictions

    Science.gov (United States)

    2007-02-01

    Quest. Aux fins de la prévision de l’indice de réflexion acoustique , ces modèles comprennent suffisamment de détails pour permettre des prévisions à 50...jusqu’à environ 50 Hz) dû à une source acoustique théorique simulant une hélice en régime de cavitation. L’entrepreneur a examiné les écarts entre...Sommaire Introduction Des méthodes de calcul perfectionnées permettant de prévoir le rayonnement acoustique et la diffusion du rayonnement par

  4. Synthesis of unsymmetrical dimethylhydrazine oxalate from rejected liquid rocket propellant

    Science.gov (United States)

    Mu, Xiaogang; Yang, Jingjing; Zhang, Youzhi

    2018-02-01

    The rejected liquid propellant unsymmetrical dimethylhydrazine (UDMH) was converted to UDMH oxalate, which has commercial value. The UDMH oxalate structure and stability were investigated by the Fourier transform infrared spectroscopy, nuclear magnetic resonance spectroscopy, differential scanning calorimetry, and ultraviolet-visible spectrophotometric analysis. The results indicate that UDMH oxalate has good thermal and aqueous solution stability, a melting point of 144 °C, an initial decomposition temperature of 180 °C, and a peak wavelength of UV in aqueous solution at λ = 204 nm. This disposal method of rejected UDMH is highly efficient and environmentally safe.

  5. A Timing Single Channel Analyzer with pileup rejection

    International Nuclear Information System (INIS)

    Lauch, J.; Nachbar, H.U.

    1981-07-01

    A Timing Single Channel Analyzer is described as normally used in nuclear physics applications for measuring certain ranges of energy spectra. The unit accepts unipolar or bipolar gaussian shaped or rectangular pulses and includes a special pileup rejection circuit. Because of its good timing performance high resolution timing and coincidence measurements are possible. The differential analyzer, trigger and timing modes and the function of external strobe and gate signals are explained. Parts of the circuit are illustrated by help of block diagrams and pulse schematics. An essential part of the unit is the pileup rejection circuit. Following theoretical reflections the circuit is described and some measurement results are reported. (orig.) [de

  6. Active Disturbance Rejection Control of a Heat Integrated Distillation Column

    DEFF Research Database (Denmark)

    Al-Kalbani, Fahad; Zhang, Jie; Bisgaard, Thomas

    2016-01-01

    -toluene mixture. The efficiency of the ADRC technique is demonstrated by comparing with the conventional PI controller in terms of set-point trackingand external disturbance rejection capability. The results show that the ADRC gives much improved control performance than the PID control....... pressure. However, the control of some HiDC processesis generally difficult due to the strong control loop interaction, high purity of the components and undesired disturbances. Active disturbance rejection control (ADRC) is used in this paperto control a simulated HiDC for separating benzene...

  7. What next after the rejection of Swiss electricity market legislation?

    International Nuclear Information System (INIS)

    Miolo, A.; Rechsteiner, S.

    2002-01-01

    This article discusses the situation in Switzerland after the rejection of new legislation on the liberalisation of the Swiss electricity market (Electricity Market Law, EMG) in a public vote in September 2002. The problems thus posed and the possibilities for further action available to those involved and affected are discussed. The legal situation after the rejection of the EMG is discussed with respect to Swiss regional structures and cantonal regulations. Three possible scenarios are discussed - the status quo, a solution to be provided by the electricity business or a Federal decree. The possibilities open to electricity enterprises for optimisation and the realisation of synergies to increase efficiency and competitiveness are discussed

  8. Kidney graft rejection studies with labeled platelets and lymphocytes

    International Nuclear Information System (INIS)

    Martin-Comin, J.

    1986-01-01

    The usefulness of In-111-labelled platelets and lymphocyte scintigraphy in acute kidney graft rejection is evaluated in 155 patients. Blood cells were labelled with 100-150 uCi of In-111-oxine and reinjected. Subsequently patients were scanned once daily from 2 hours post-reinjection up to a week. The graft/contralateral area activity ratio was calculated in all scans. It is concluded that In-111-labelled platelets scintigraphy is nowadays the method of choice for acute kidney graft rejection diagnosis, especially in patients under cyclosporine immunosuppression. (author)

  9. Causes of rejection of beef bulls in breeding soundness evaluation

    Directory of Open Access Journals (Sweden)

    Silvio Renato Oliveira Menegassi

    2012-07-01

    Full Text Available The objective of this study was to analyze the rates of rejection in the different steps of the breeding soundness evaluation of beef bulls in the state of Rio Grande do Sul, Brazil. The breeding soundness of 22,113 young and mature bulls of 14 beef breeds, participating in the Program of Reproductive Evaluation (PARTO was evaluated in the experiment. Data concerning to the causes of rejection in the four steps of the breeding soundness evaluation (general physical examination, genital tract examination, semen evaluation and sexual behavior assessment were analyzed by the Chi-square test and univariate regression analysis. According to year, general physical examination, genital tract examination and semen evaluation determined the rejection of 0.9% to 2.5%, 5.1% to 7.7%, 1.8% to 5.3%; and 4.2% to 6.7%, 7.3 to 9.3%, and 2.5% to 5.5% of young and mature bulls, respectively. Mature bulls presented higher chances of rejection than young bulls in the general physical examination in every year evaluated; as to the genital tract examination, their chances of rejection were higher in years I and II, but not in year III. In the semen evaluation, there was no difference between the ages assessed in any of the three years evaluated. Sexual behavior assessment accounted for the rejection of 1.9 to 6.0% of the young bulls and 2.9% to 3.9% of mature bulls, in accordance with the years evaluated; in years I and II, mature bulls presented higher rejection rates than young bulls. These results confirm the importance of performing all steps of the breeding soundness evaluation, including the sexual behavior assessment as a work routine, rather than an additional, optional stage of the evaluation, which should be carried out before the breeding season. The results indicate the relationship between bull age and rejection rate in the breeding soundness evaluation.

  10. Multiquadrant Subtenon Triamcinolone Injection for Acute Corneal Graft Rejection: A Case Report

    Directory of Open Access Journals (Sweden)

    Sunali Goyal

    2017-05-01

    Full Text Available Background: We report a case of reversal of an acute corneal graft rejection following multiquadrant subtenon triamcinolone injection. Case Presentation: A 19-year-old woman who had acute corneal graft rejection failed to show resolution of the graft rejection after standard treatment with systemic, intravenous, and topical steroids. The graft rejection, however, responded to injection of triamcinolone in multiple subtenon quadrants. Conclusions: For corneal graft rejection, multiquadrant subtenon triamcinolone injections may be a safe adjunct to systemic treatment.

  11. Crossmatch testing in kidney transplantation: Patterns of practice and associations with rejection and graft survival

    International Nuclear Information System (INIS)

    Salvalaggio, Paolo R; Graff, Ralph J; Pinsky, Brett; Schnitzler, Mark A; Takemoto, Steven K; Burroughs, Thomas E; Santos, Luiz S; Lentine Krista L

    2009-01-01

    Methods of crossmatch testing prior to kidney transplantation are not standardized and there are limited large-scale data on the use and outcomes implications of crossmatch modality. Data describing the most sensitive crossmatch modality for crossmatch-negative kidney transplants were drawn from the Organ Procurement and Transplant Network Registry. Within the cohort transplanted in 1999-2005, we identified patient and transplant characteristics predictive of each testing modality by multivariate logistic regression. We assessed associations of crossmatch modality with rejection risk by logistic regression and with graft survival by Cox's hazards analysis. Among 230,995 transplants, use of flow cytometry with T-and B-lymphocytes (T and B FC) increased progressively in 1987-2005. Among the recent transplants performed in 1999-2005 (n=64,320), negative T and B FC crossmatch was associated with 15% lower relative risk of first-year acute rejection (adjusted HR 0.85, 95% CI 0.80-0.89) compared to negative T-antihuman-globulin and B-National Institutes of Health/Wash (T AHG and B) crossmatch. Five-year graft survival after transplant with negative T and B FC (82.6%) was modestly better than after negative T AHG and B (81.4%, P0.008) or T AHG crossmatch (81.1%, P 60 years. Many subgroups for whom negative T and B FC crossmatch predicted lower rejection risk (Caucasians, deceased donor recipients, re-transplants) were not more likely to be crossmatched by this method. We conclude that current practice patterns have not aligned utilization of T and B FC crossmatch with associated benefits. Prospective evaluation of the relationship of crossmatch modality with outcomes is warranted. (author)

  12. CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems.

    Directory of Open Access Journals (Sweden)

    Md Khaledur Rahman

    Full Text Available The CRISPR/Cas9-sgRNA system has recently become a popular tool for genome editing and a very hot topic in the field of medical research. In this system, Cas9 protein is directed to a desired location for gene engineering and cleaves target DNA sequence which is complementary to a 20-nucleotide guide sequence found within the sgRNA. A lot of experimental efforts, ranging from in vivo selection to in silico modeling, have been made for efficient designing of sgRNAs in CRISPR/Cas9 system. In this article, we present a novel tool, called CRISPRpred, for efficient in silico prediction of sgRNAs on-target activity which is based on the applications of Support Vector Machine (SVM model. To conduct experiments, we have used a benchmark dataset of 17 genes and 5310 guide sequences where there are only 20% true values. CRISPRpred achieves Area Under Receiver Operating Characteristics Curve (AUROC-Curve, Area Under Precision Recall Curve (AUPR-Curve and maximum Matthews Correlation Coefficient (MCC as 0.85, 0.56 and 0.48, respectively. Our tool shows approximately 5% improvement in AUPR-Curve and after analyzing all evaluation metrics, we find that CRISPRpred is better than the current state-of-the-art. CRISPRpred is enough flexible to extract relevant features and use them in a learning algorithm. The source code of our entire software with relevant dataset can be found in the following link: https://github.com/khaled-buet/CRISPRpred.

  13. Muon identification and pion rejection in the 4th concept

    Indian Academy of Sciences (India)

    The ATLAS detector at the LHC has avoided this limit with air-core toroids both around the cylindrical detector providing a largely azimuthal field, and separate toroids to cover the end cap regions of the detector. 2. Two essential features. Momentum resolution for background pion rejection. On the 4th concept we also.

  14. Facility for electrochemical dissolution of rejected fuel elements

    International Nuclear Information System (INIS)

    Deniskin, V.P.; Filatov, O.N.; Konovalov, E.A.; Kolesnikov, B.P.; Bukharin, A.D.

    2003-01-01

    A facility for electrochemical dissolution of rejected fuel elements with the stainless steel can and uranium of 90% enrichment is described. The start-adjustment works and trial-commercial tests of the facility are carried out. A s a result its technological parameters are determined [ru

  15. Mutual Antipathies during Early Adolescence: More than Just Rejection

    Science.gov (United States)

    Witkow, Melissa R.; Bellmore, Amy D.; Nishina, Adrienne; Juvonen, Jaana; Graham, Sandra

    2005-01-01

    Recent research suggests that having a mutual antipathy, in comparison to not having an antipathy, is associated with a host of negative outcomes. However, the methods used may not have adequately controlled for rejection and therefore may have provided an incomplete description of the psychosocial correlates of having a mutual antipathy. With a…

  16. Sonar waveforms for reverberation rejection, Part IV: Adaptive processing.

    NARCIS (Netherlands)

    IJsselmuide, S.P. van; Deruaz, L.; Been, R.; Doisy, Y.; Beerens, S.P.

    2002-01-01

    For littoral ASW, reverberation is a big problem and rejection of reverberation is of utmost importance. The influence of the transmitted signal on the signal to reverberation ratio has been presented in three preceding papers. In this paper, the influence of improved signal processing on the

  17. Dimensions of self-appraisal and perceived peer rejection among ...

    African Journals Online (AJOL)

    Accordingly, the main aim of this study is to explore influence of skin colour satisfaction, self-esteem and self-attractiveness on perceived peer rejection among entry ... on an individual and societal level to decrease the incongruent feeling not espoused by our culture in order to reduce self and body image disparagement.

  18. Maternal Predictors of Rejecting Parenting and Early Adolescent Antisocial Behavior

    Science.gov (United States)

    Trentacosta, Christopher J.; Shaw, Daniel S.

    2008-01-01

    The present study examined relations among maternal psychological resources, rejecting parenting, and early adolescent antisocial behavior in a sample of 231 low-income mothers and their sons with longitudinal assessments from age 18 months to 12 years. The maternal resources examined were age at first birth, aggressive personality, and empathy.…

  19. Compact filtering monopole patch antenna with dual-band rejection.

    Science.gov (United States)

    Kim, Sun-Woong; Choi, Dong-You

    2016-01-01

    In this paper, a compact ultra-wideband patch antenna with dual-band rejection is proposed. The proposed antenna filters 3.3-3.8 GHz WiMAX and 5.15-5.85 GHz WLAN by respectively rejecting these bands through a C-shaped slit and a λg/4 resonator. The λg/4 resonator is positioned as a pair, centered around the microstrip line, and a C-type slit is inserted into an elliptical patch. The impedance bandwidth of the proposed antenna is 2.9-9.3 GHz, which satisfies the bandwidth for ultra-wideband communication systems. Further, the proposed antenna provides dual-band rejection at two bands: 3.2-3.85 and 4.7-6.03 GHz. The radiation pattern of the antenna is omnidirectional, and antenna gain is maintained constantly while showing -8.4 and -1.5 dBi at the two rejected bands, respectively.

  20. Shape Morphing Adaptive Radiator Technology (SMART) for Variable Heat Rejection

    Science.gov (United States)

    Erickson, Lisa

    2016-01-01

    The proposed technology leverages the temperature dependent phase change of shape memory alloys (SMAs) to drive the shape of a flexible radiator panel. The opening/closing of the radiator panel, as a function of temperature, passively adapts the radiator's rate of heat rejection in response to a vehicle's needs.

  1. Bone marrow-derived T lymphocytes responsible for allograft rejection

    International Nuclear Information System (INIS)

    Senjanovic, M.; Marusic, M.

    1984-01-01

    Lethally irradiated mice reconstituted with syngeneic bone marrow cells were grafted with allogeneic skin grafts 6-7 weeks after irradiation and reconstitution. Mice with intact thymuses rejected the grafts whereas the mice thymectomized before irradiation and reconstitution did not. Thymectomized irradiated mice (TIR mice) reconstituted with bone marrow cells from donors immune to the allografts rejected the grafts. Bone marrow cells from immunized donors, pretreated with Thy 1.2 antibody and C', did not confer immunity to TIR recipients. To determine the number of T lymphocytes necessary for the transfer of immunity by bone marrow cells from immunized donors, thymectomized irradiated mice were reconstituted with nonimmune bone marrow cells treated with Thy 1.2 antibody and C' and with various numbers of splenic T lymphocytes from nonimmune and immune donors. Allogeneic skin graft rejection was obtained with 10(6) nonimmune or 10(4) immune T cells. The effect of immune T cells was specific: i.e., immune T cells accelerated only rejection of the relevant skin grafts whereas against a third-party skin grafts acted as normal T lymphocytes

  2. Tracking and disturbance rejection for fully actuated mechanical systems

    NARCIS (Netherlands)

    Jayawardhana, Bayu; Weiss, George

    2008-01-01

    In this paper, we solve the tracking and disturbance rejection problem for fully actuated passive mechanical systems. We assume that the reference signal r and its first two derivatives r, r are available to the controller and the disturbance signal d can be decomposed into a finite superposition of

  3. Immediate autogenous cartilage grafts in rhinoplasty after alloplastic implant rejection.

    Science.gov (United States)

    Raghavan, Ullas; Jones, Nick S; Romo, Thomas

    2004-01-01

    It is accepted in rhinoplasty that complications are more common with alloplastic implants than with autografts. There is little guidance in the literature on how to deal with the cosmetic and/or functional problems that follow alloplastic implant rejection. The conventional advice has been to remove the allograft and not place any graft at the same time. The present article presents our experience treating allograft rejection and immediately repairing any structural defect with autografts. To demonstrate that immediate nasal reconstruction using autogenous cartilage is a good technique when an alloplastic material has to be removed because of rejection, inflammation, or infection. A retrospective analysis of outcome for a case series. A retrospective review of the management of 8 patients who presented to 2 tertiary referral centers with alloplastic implant rejection following rhinoplasty. In 7 cases, the alloplastic implant had to be removed because it had migrated and caused a foreign body reaction; in 1 case, the implant had caused a bacterial infection. In all 8 cases, the nasal deformity that followed the removal of the allograft was so marked that the nose was immediately reconstructed with autogenous cartilage. The patients all made a good recovery after immediate reconstruction, although skin changes associated with the alloplastic implant remained after a mean follow-up of 3 years 3 months. The use of autogenous cartilage is a good option for nasal augmentation immediately after the removal of an alloplastic implant.

  4. Veto cell suppression mechanisms in the prevention of allograft rejection

    DEFF Research Database (Denmark)

    Jacobsen, I M; Claesson, Mogens Helweg

    1998-01-01

    on the surface of the veto-active cell. Data from a large number of experimental and clinical studies strongly indicate that veto-active cells function in vivo and are capable of preventing allograft rejection. Thus, donor-cell-mediated veto activity is the most likely explanation for the well-known graft...

  5. 48 CFR 814.404-2 - Rejection of individual bids.

    Science.gov (United States)

    2010-10-01

    ... that the bid as submitted is in such a form that acceptance would create a valid and binding contract... CONTRACTING METHODS AND CONTRACT TYPES SEALED BIDDING Opening of Bids and Award of Contract 814.404-2 Rejection of individual bids. (a) When a contracting officer finds a bid that is being considered for an...

  6. Increased neural response to social rejection in major depression

    NARCIS (Netherlands)

    Kumar, Poornima; Waiter, Gordon D.; Dubois, Magda; Milders, Maarten; Reid, Ian; Steele, J. Douglas

    2017-01-01

    Background: Being a part of community is critical for survival and individuals with major depressive disorder (MDD) have a greater sensitivity to interpersonal stress that makes them vulnerable to future episodes. Social rejection is a critical risk factor for depression and it is said to increase

  7. 48 CFR 219.505 - Rejecting Small Business Administration recommendations.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Rejecting Small Business Administration recommendations. 219.505 Section 219.505 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Set-Asides for Small Business 219.505 Rejectin...

  8. Evolution of silvicultural thinning: from rejection to transcendence

    Science.gov (United States)

    Boris Zeide

    2006-01-01

    Our views on a main tool of forestry, silvicultural thinning, have changed greatly since the beginning of forestry over 200 years ago. At first, thinning was rejected as something unnatural and destructive. It was believed that the densest stands were the most productive and any thinning only detracted from maximum growth produced by nature. This philosophy was still...

  9. Rejected Manuscripts in Publishers' Archives: Legal Rights and Access

    Science.gov (United States)

    Hamburger, Susan

    2011-01-01

    This article focuses on an analysis of how various archival repositories deal with rejected manuscripts in publishers' archives as part of existing collections and as potential donations, and includes suggestions for ways to provide access while maintaining the author's legal rights. Viewpoints from the journal editor, author, archivist, and…

  10. Information about radiographic films rejects of dental x-rays

    International Nuclear Information System (INIS)

    Cezimbra, M.R.; Bernarsiuk, M.E.; Bauer V, E.

    1996-01-01

    The purpose of this research was to qualify and quantify the number of dental x-ray films rejected in a Porto Alegre clinic. As we analyzed the captured data, it was concluded that, our of 1066 peri-apical films, we had a total percentage of 4.5% in relation to the total of the exams made. This 4.5% consists of the following rejects: placement, patient movement, technical errors, diaphragm, too much clarity in the result, double exposure, prolongation, shortness, darkened for not have been shot, superposed film. Because of that, the rejection, due to the bad placement of the film, is the one with the larger percentage value, i.e., 1.22% of the 4.5%. With the knowledge of the types of rejects and their causes, it was possible to correct some sources of systematic errors minimizing the repetition of the exams, saving costs, time and diminishing the ionizing radiation exposure for the patient, odontologist and his technical staff, which will be proved. (authors). 4 refs., 1 tab

  11. 25 CFR 81.24 - Approval, disapproval, or rejection action.

    Science.gov (United States)

    2010-04-01

    ... proposed constitution or charter action is rejected by the voters, the authorizing officer shall indicate... Indian Affairs in Washington, DC, copies of the communication, the Certificate of Results of Election and... Commissioner of Indian Affairs in Washington, DC, a copy of the communication along with the Certificate of...

  12. Examining Appearance-Based Rejection Sensitivity during Early Adolescence

    Science.gov (United States)

    Bowker, Julie C.; Thomas, Katelyn K.; Spencer, Sarah V.; Park, Lora E.

    2013-01-01

    The present study of 150 adolescents ("M" age = 13.05 years) examined the associations between appearance-based rejection sensitivity (Appearance-RS) and psychological adjustment during early adolescence, and evaluated three types of other-gender peer experiences (other-gender friendship, peer acceptance, and romantic relationships) as…

  13. Muon identification and pion rejection in the 4th concept

    Indian Academy of Sciences (India)

    Abstract. We describe a completely new way to reconstruct and identify muons with high efficiency and very high pion rejection in the 4th concept detector. The dual-solenoid magnetic field allows the reconstruction and precision momentum measurement of muons down to a few GeV (just the energy loss in the 10-λint ...

  14. Fate of Manuscripts Rejected From the Red Journal

    International Nuclear Information System (INIS)

    Holliday, Emma B.; Yang, George; Jagsi, Reshma; Hoffman, Karen E.; Bennett, Katherine Egan; Grace, Calley; Zietman, Anthony L.

    2015-01-01

    Purpose: To evaluate characteristics associated with higher rates of acceptance for original manuscripts submitted for publication to the International Journal of Radiation Oncology • Biology • Physics (IJROBP) and describe the fate of rejected manuscripts. Methods and Materials: Manuscripts submitted to the IJROBP from May 1, 2010, to August 31, 2010, and May 1, 2012, to August 31, 2012, were evaluated for author demographics and acceptance status. A PubMed search was performed for each IJROBP-rejected manuscript to ascertain whether the manuscript was ultimately published elsewhere. The Impact Factor of the accepting journal and the number of citations of the published manuscript were also collected. Results: Of the 500 included manuscripts, 172 (34.4%) were accepted and 328 (65.6%) were rejected. There was no significant difference in acceptance rates according to gender or degree of the submitting author, but there were significant differences seen based on the submitting author's country,