Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding

PubMed Central

Koenig, Patrick; Lee, Chingwei V.; Walters, Benjamin T.; Janakiraman, Vasantharajan; Stinson, Jeremy; Patapoff, Thomas W.; Fuh, Germaine

2017-01-01

Somatic mutations within the antibody variable domains are critical to the immense capacity of the immune repertoire. Here, via a deep mutational scan, we dissect how mutations at all positions of the variable domains of a high-affinity anti-VEGF antibody G6.31 impact its antigen-binding function. The resulting mutational landscape demonstrates that large portions of antibody variable domain positions are open to mutation, and that beneficial mutations can be found throughout the variable domains. We determine the role of one antigen-distal light chain position 83, demonstrating that mutation at this site optimizes both antigen affinity and thermostability by modulating the interdomain conformational dynamics of the antigen-binding fragment. Furthermore, by analyzing a large number of human antibody sequences and structures, we demonstrate that somatic mutations occur frequently at position 83, with corresponding domain conformations observed for G6.31. Therefore, the modulation of interdomain dynamics represents an important mechanism during antibody maturation in vivo. PMID:28057863

Modular Construction of Large Non-Immune Human Antibody Phage-Display Libraries from Variable Heavy and Light Chain Gene Cassettes.

PubMed

Lee, Nam-Kyung; Bidlingmaier, Scott; Su, Yang; Liu, Bin

2018-01-01

Monoclonal antibodies and antibody-derived therapeutics have emerged as a rapidly growing class of biological drugs for the treatment of cancer, autoimmunity, infection, and neurological diseases. To support the development of human antibodies, various display techniques based on antibody gene repertoires have been constructed over the last two decades. In particular, scFv-antibody phage display has been extensively utilized to select lead antibodies against a variety of target antigens. To construct a scFv phage display that enables efficient antibody discovery, and optimization, it is desirable to develop a system that allows modular assembly of highly diverse variable heavy chain and light chain (Vκ and Vλ) repertoires. Here, we describe modular construction of large non-immune human antibody phage-display libraries built on variable gene cassettes from heavy chain and light chain repertoires (Vκ- and Vλ-light can be made into independent cassettes). We describe utility of such libraries in antibody discovery and optimization through chain shuffling.

Expansion of the Preimmune Antibody Repertoire by Junctional Diversity in Bos taurus

PubMed Central

Liljavirta, Jenni; Niku, Mikael; Pessa-Morikawa, Tiina; Ekman, Anna; Iivanainen, Antti

2014-01-01

Cattle have a limited range of immunoglobulin genes which are further diversified by antigen independent somatic hypermutation in fetuses. Junctional diversity generated during somatic recombination contributes to antibody diversity but its relative significance has not been comprehensively studied. We have investigated the importance of terminal deoxynucleotidyl transferase (TdT) -mediated junctional diversity to the bovine immunoglobulin repertoire. We also searched for new bovine heavy chain diversity (IGHD) genes as the information of the germline sequences is essential to define the junctional boundaries between gene segments. New heavy chain variable genes (IGHV) were explored to address the gene usage in the fetal recombinations. Our bioinformatics search revealed five new IGHD genes, which included the longest IGHD reported so far, 154 bp. By genomic sequencing we found 26 new IGHV sequences that represent potentially new IGHV genes or allelic variants. Sequence analysis of immunoglobulin heavy chain cDNA libraries of fetal bone marrow, ileum and spleen showed 0 to 36 nontemplated N-nucleotide additions between variable, diversity and joining genes. A maximum of 8 N nucleotides were also identified in the light chains. The junctional base profile was biased towards A and T nucleotide additions (64% in heavy chain VD, 52% in heavy chain DJ and 61% in light chain VJ junctions) in contrast to the high G/C content which is usually observed in mice. Sequence analysis also revealed extensive exonuclease activity, providing additional diversity. B-lymphocyte specific TdT expression was detected in bovine fetal bone marrow by reverse transcription-qPCR and immunofluorescence. These results suggest that TdT-mediated junctional diversity and exonuclease activity contribute significantly to the size of the cattle preimmune antibody repertoire already in the fetal period. PMID:24926997

Using collective variables to drive molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme

2013-12-01

A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.

Detection of specific antibody responses to vaccination in variable flying foxes (Pteropus hypomelanus).

PubMed

Wellehan, James F X; Green, Linda G; Duke, Diane G; Bootorabi, Shadi; Heard, Darryl J; Klein, Paul A; Jacobson, Elliott R

2009-09-01

Megachiropteran bats are biologically important both as endangered species and reservoirs for emerging human pathogens. Reliable detection of antibodies to specific pathogens in bats is thus epidemiologically critical. Eight variable flying foxes (Pteropus hypomelanus) were immunized with 2,4-dinitrophenylated bovine serum albumin (DNP-BSA). Each bat received monthly inoculations for 2 months. Affinity-purified IgG was used for production of polyclonal and monoclonal anti-variable flying fox IgG antibodies. ELISA and western blot analysis were used to monitor immune responses and for assessment of polyclonal and monoclonal antibody species cross-reactivity. Protein G, polyclonal antibodies, and monoclonal antibodies detected specific anti-DNP antibody responses in immunized variable flying foxes, with protein G being the most sensitive, followed by monoclonal antibodies and then polyclonal antibodies. While the polyclonal antibody was found to cross-react well against IgG of all bat species tested, some non-specific background was observed. The monoclonal antibody was found to cross-react well against IgG of six other species in the genus Pteropus and to cross-react less strongly against IgG from Eidolon helvum or Phyllostomus hastatus. Protein G distinguished best between vaccinated and unvaccinated bats, and these results validate the use of protein G for detection of bat IgG. Monoclonal antibodies developed in this study recognized immunoglobulins from other members of the genus Pteropus well, and may be useful in applications where specific detection of Pteropus IgG is needed.

Causal Inference and Omitted Variable Bias in Financial Aid Research: Assessing Solutions

ERIC Educational Resources Information Center

Riegg, Stephanie K.

2008-01-01

This article highlights the problem of omitted variable bias in research on the causal effect of financial aid on college-going. I first describe the problem of self-selection and the resulting bias from omitted variables. I then assess and explore the strengths and weaknesses of random assignment, multivariate regression, proxy variables, fixed…

Relationship of health-related variables to levels of anti-polyribosylribitol phosphate antibodies in adults.

PubMed Central

McDonnell, W M; Gilsdorf, J R; Kent, J B; Sheagren, J N

1988-01-01

To identify adults who may be at risk for Haemophilus influenzae type b disease by virtue of low levels of antibody against the H. influenzae b capsule and who may thus benefit from receiving H. influenzae b vaccine, we correlated serum anticapsular antibody levels of 388 adult patients with 26 health-related variables, including 3 personal characteristics, 10 laboratory values, 4 drug use categories, and 8 disease categories. Steroid use was consistently associated with low levels of anticapsular antibody; associations were also found between low antibody levels and both non-Caucasian race and increasing age. However, less than 4% of the antibody variability could be attributed to these factors, and they were not predictive of low antibody levels. Thus, although H. influenzae b infections are seen in adults with predisposing medical conditions, on the basis of the present findings, use of the H. influenzae b vaccine in adults cannot be recommended. PMID:3260243

Selection of cholera toxin specific IgNAR single-domain antibodies from a naïve shark library.

PubMed

Liu, Jinny L; Anderson, George P; Delehanty, James B; Baumann, Richard; Hayhurst, Andrew; Goldman, Ellen R

2007-03-01

Shark immunoglobulin new antigen receptor (IgNAR, also referred to as NAR) variable domains (Vs) are single-domain antibody (sdAb) fragments containing only two hypervariable loop structures forming 3D topologies for a wide range of antigen recognition and binding. Their small size ( approximately 12kDa) and high solubility, thermostability and binding specificity make IgNARs an exceptional alternative source of engineered antibodies for sensor applications. Here, two new shark NAR V display libraries containing >10(7) unique clones from non-immunized (naïve) adult spiny dogfish (Squalus acanthias) and smooth dogfish (Mustelus canis) sharks were constructed. The most conserved consensus sequences derived from random clone sequence were compared with published nurse shark (Ginglymostoma cirratum) sequences. Cholera toxin (CT) was chosen for panning one of the naïve display libraries due to its severe pathogenicity and commercial availability. Three very similar CT binders were selected and purified soluble monomeric anti-CT sdAbs were characterized using Luminex(100) and traditional ELISA assays. These novel anti-CT sdAbs selected from our newly constructed shark NAR V sdAb library specifically bound to soluble antigen, without cross reacting with other irrelevant antigens. They also showed superior heat stability, exhibiting slow loss of activity over the course of one hour at high temperature (95 degrees C), while conventional antibodies lost all activity in the first 5-10min. The successful isolation of target specific sdAbs from one of our non-biased NAR libraries, demonstrate their ability to provide binders against an unacquainted antigen of interest.

Reducing Cognitive Biases in Probabilistic Reasoning by the Use of Logarithm Formats

ERIC Educational Resources Information Center

Juslin, Peter; Nilsson, Hakan; Winman, Anders; Lindskog, Marcus

2011-01-01

Research on probability judgment has traditionally emphasized that people are susceptible to biases because they rely on "variable substitution": the assessment of normative variables is replaced by assessment of heuristic, subjective variables. A recent proposal is that many of these biases may rather derive from constraints on cognitive…

Simultaneous Estimation of Model State Variables and Observation and Forecast Biases Using a Two-Stage Hybrid Kalman Filter

NASA Technical Reports Server (NTRS)

Pauwels, V. R. N.; DeLannoy, G. J. M.; Hendricks Franssen, H.-J.; Vereecken, H.

2013-01-01

In this paper, we present a two-stage hybrid Kalman filter to estimate both observation and forecast bias in hydrologic models, in addition to state variables. The biases are estimated using the discrete Kalman filter, and the state variables using the ensemble Kalman filter. A key issue in this multi-component assimilation scheme is the exact partitioning of the difference between observation and forecasts into state, forecast bias and observation bias updates. Here, the error covariances of the forecast bias and the unbiased states are calculated as constant fractions of the biased state error covariance, and the observation bias error covariance is a function of the observation prediction error covariance. In a series of synthetic experiments, focusing on the assimilation of discharge into a rainfall-runoff model, it is shown that both static and dynamic observation and forecast biases can be successfully estimated. The results indicate a strong improvement in the estimation of the state variables and resulting discharge as opposed to the use of a bias-unaware ensemble Kalman filter. Furthermore, minimal code modification in existing data assimilation software is needed to implement the method. The results suggest that a better performance of data assimilation methods should be possible if both forecast and observation biases are taken into account.

Identification and verification of hybridoma-derived monoclonal antibody variable region sequences using recombinant DNA technology and mass spectrometry

USDA-ARS?s Scientific Manuscript database

Antibody engineering requires the identification of antigen binding domains or variable regions (VR) unique to each antibody. It is the VR that define the unique antigen binding properties and proper sequence identification is essential for functional evaluation and performance of recombinant antibo...

Using a combined computational-experimental approach to predict antibody-specific B cell epitopes.

PubMed

Sela-Culang, Inbal; Benhnia, Mohammed Rafii-El-Idrissi; Matho, Michael H; Kaever, Thomas; Maybeno, Matt; Schlossman, Andrew; Nimrod, Guy; Li, Sheng; Xiang, Yan; Zajonc, Dirk; Crotty, Shane; Ofran, Yanay; Peters, Bjoern

2014-04-08

Antibody epitope mapping is crucial for understanding B cell-mediated immunity and required for characterizing therapeutic antibodies. In contrast to T cell epitope mapping, no computational tools are in widespread use for prediction of B cell epitopes. Here, we show that, utilizing the sequence of an antibody, it is possible to identify discontinuous epitopes on its cognate antigen. The predictions are based on residue-pairing preferences and other interface characteristics. We combined these antibody-specific predictions with results of cross-blocking experiments that identify groups of antibodies with overlapping epitopes to improve the predictions. We validate the high performance of this approach by mapping the epitopes of a set of antibodies against the previously uncharacterized D8 antigen, using complementary techniques to reduce method-specific biases (X-ray crystallography, peptide ELISA, deuterium exchange, and site-directed mutagenesis). These results suggest that antibody-specific computational predictions and simple cross-blocking experiments allow for accurate prediction of residues in conformational B cell epitopes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Using ERA-Interim reanalysis for creating datasets of energy-relevant climate variables

NASA Astrophysics Data System (ADS)

Jones, Philip D.; Harpham, Colin; Troccoli, Alberto; Gschwind, Benoit; Ranchin, Thierry; Wald, Lucien; Goodess, Clare M.; Dorling, Stephen

2017-07-01

The construction of a bias-adjusted dataset of climate variables at the near surface using ERA-Interim reanalysis is presented. A number of different, variable-dependent, bias-adjustment approaches have been proposed. Here we modify the parameters of different distributions (depending on the variable), adjusting ERA-Interim based on gridded station or direct station observations. The variables are air temperature, dewpoint temperature, precipitation (daily only), solar radiation, wind speed, and relative humidity. These are available on either 3 or 6 h timescales over the period 1979-2016. The resulting bias-adjusted dataset is available through the Climate Data Store (CDS) of the Copernicus Climate Change Data Store (C3S) and can be accessed at present from ftp://ecem.climate.copernicus.eu. The benefit of performing bias adjustment is demonstrated by comparing initial and bias-adjusted ERA-Interim data against gridded observational fields.

Eliminating Survivor Bias in Two-stage Instrumental Variable Estimators.

PubMed

Vansteelandt, Stijn; Walter, Stefan; Tchetgen Tchetgen, Eric

2018-07-01

Mendelian randomization studies commonly focus on elderly populations. This makes the instrumental variables analysis of such studies sensitive to survivor bias, a type of selection bias. A particular concern is that the instrumental variable conditions, even when valid for the source population, may be violated for the selective population of individuals who survive the onset of the study. This is potentially very damaging because Mendelian randomization studies are known to be sensitive to bias due to even minor violations of the instrumental variable conditions. Interestingly, the instrumental variable conditions continue to hold within certain risk sets of individuals who are still alive at a given age when the instrument and unmeasured confounders exert additive effects on the exposure, and moreover, the exposure and unmeasured confounders exert additive effects on the hazard of death. In this article, we will exploit this property to derive a two-stage instrumental variable estimator for the effect of exposure on mortality, which is insulated against the above described selection bias under these additivity assumptions.

Characterization of the immune response to canine parvovirus induced by vaccination with chimaeric plant viruses.

PubMed

Nicholas, Benjamin L; Brennan, F R; Martinez-Torrecuadrada, J L; Casal, J I; Hamilton, W D; Wakelin, D

2002-06-21

NIH mice were vaccinated subcutaneously or intranasally with chimaeric cow pea mosaic virus (CPMV) constructs expressing a 17-mer peptide sequence from canine parvovirus (CPV) as monomers or dimers on the small or large protein surface subunits. Responses to the chimaeric virus particles (CVPs) were compared with those of mice immunized with the native virus or with parvovirus peptide conjugated to keyhole limpet haemocyanin (KLH). The characteristics of the immune response to vaccination were examined by measuring serum and mucosal antibody responses in ELISA, in vitro antigen-induced spleen cell proliferation and cytokine responses. Mice made strong antibody responses to the native plant virus and peptide-specific responses to two of the four CVP constructs tested which were approximately 10-fold lower than responses to native plant virus. The immune response generated by the CVP constructs showed a marked TH1 bias, as determined by a predominantly IgG(2a) isotype peptide-specific antibody response and the release of IFN-gamma but not IL-4 or IL-5 from lymphocytes exposed to antigen in vitro. In comparison, parvovirus peptide conjugated to KLH generated an IgG(1)-biased (TH2) response. These data indicate that the presentation of peptides on viral particles could be used to bias the immune response in favor of a TH1 response.Anti-viral and anti-peptide IgA were detected in intestinal and bronchial lavage fluid of immunized mice, demonstrating that a mucosal immune response to CPV can be generated by systemic and mucosal immunization with CVP vaccines. Serum antibody from both subcutaneously-vaccinated and intranasally-vaccinated mice showed neutralizing activity against CPV in vitro.

Adsorption of Toll-Like Receptor 4 Agonist to Alum-Based Tetanus Toxoid Vaccine Dampens Pro-T Helper 2 Activities and Enhances Antibody Responses.

PubMed

Bortolatto, Juliana; Mirotti, Luciana; Rodriguez, Dunia; Gomes, Eliane; Russo, Momtchilo

2015-01-01

Aluminum salts gels (alum) are TLR-independent adjuvants and have been used to boost antibody responses in alum-based vaccines such as diphtheria, pertussis, and tetanus toxoid (DPT) triple vaccine. However, the pro-Th2 activity of alum-based vaccine formulations has not been fully appreciated. Here we found that alum-based tetanus toxoid (TT) vaccine was biased toward a Th-2 profile as shown by TT-induced airway eosinophilic inflammation, type 2 cytokine production, and high levels of IgE anaphylactic antibodies. The adsorption into alum of prototypic TLR4 agonists such as lipopolysaccharides (LPS) derived from Escherichia coli consistently dampened TT-induced Th2 activities without inducing IFNγ or Th1-like responses in the lung. Conversely, adsorption of monophosphoryl lipid A (MPLA) extracted from Salmonella minnesota, which is a TIR-domain-containing adapter-inducing interferon-β- (TRIF-) biased TLR4 agonist, was less effective in decreasing Th-2 responses. Importantly, in a situation with antigenic competition (OVA plus TT), TT-specific IgG1 or IgG2a was decreased compared with TT sensitization. Notably, LPS increased the production of IgG1 and IgG2a TT-specific antibodies. In conclusion, the addition of LPS induces a more robust IgG1 and IgG2a TT-specific antibody production and concomitantly decreases Th2-cellular and humoral responses, indicating a potential use of alum/TLR-based vaccines.

Decoupling global biases and local interactions between cell biological variables

PubMed Central

Zaritsky, Assaf; Obolski, Uri; Gan, Zhuo; Reis, Carlos R; Kadlecova, Zuzana; Du, Yi; Schmid, Sandra L; Danuser, Gaudenz

2017-01-01

Analysis of coupled variables is a core concept of cell biological inference, with co-localization of two molecules as a proxy for protein interaction being a ubiquitous example. However, external effectors may influence the observed co-localization independently from the local interaction of two proteins. Such global bias, although biologically meaningful, is often neglected when interpreting co-localization. Here, we describe DeBias, a computational method to quantify and decouple global bias from local interactions between variables by modeling the observed co-localization as the cumulative contribution of a global and a local component. We showcase four applications of DeBias in different areas of cell biology, and demonstrate that the global bias encapsulates fundamental mechanistic insight into cellular behavior. The DeBias software package is freely accessible online via a web-server at https://debias.biohpc.swmed.edu. DOI: http://dx.doi.org/10.7554/eLife.22323.001 PMID:28287393

Fundamental characteristics of the expressed immunoglobulin VH and VL repertoire in different canine breeds in comparison with those of humans and mice.

PubMed

Steiniger, Sebastian C J; Dunkle, William E; Bammert, Gary F; Wilson, Thomas L; Krishnan, Abhiram; Dunham, Steven A; Ippolito, Gregory C; Bainbridge, Graeme

2014-05-01

Complementarity determining regions (CDR) are responsible for binding antigen and provide substantial diversity to the antibody repertoire, with VH CDR3 of the immunoglobulin variable heavy (VH) domain playing a dominant role. In this study, we examined 1200 unique canine VH and 500 unique variable light (VL) sequences of large and small canine breeds derived from peripheral B cells. Unlike the human and murine repertoire, the canine repertoire is heavily dominated by the Canis lupus familiaris IGHV1 subgroup, evolutionarily closest to the human IGHV3 subgroup. Our studies clearly show that the productive canine repertoire of all analyzed breeds shows similarities to both human and mouse; however, there are distinct differences in terms of VH CDR3 length and amino acid paratope composition. In comparison with the human and murine antibody repertoire, canine VH CDR3 regions are shorter in length than the human counterparts, but longer than the murine VH CDR3. Similar to corresponding human and mouse VH CDR3, the amino acids at the base of the VH CDR3 loop are strictly conserved. For identical CDR positions, there were significant changes in chemical paratope composition. Similar to human and mouse repertoires, the neutral amino acids tyrosine, glycine and serine dominate the canine VH CDR3 interval (comprising 35%) although the interval is nonetheless relatively depleted of tyrosine when compared to human and mouse. Furthermore, canine VH CDR3 displays an overrepresentation of the neutral amino acid threonine and the negatively charged aspartic acid while proline content is similar to that in the human repertoire. In general, the canine repertoire shows a bias towards small, negatively charged amino acids. Overall, this analysis suggests that functional canine therapeutic antibodies can be obtained from human and mouse sequences by methods of speciation and affinity maturation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Toward Effective HIV Vaccination INDUCTION OF BINARY EPITOPE REACTIVE ANTIBODIES WITH BROAD HIV NEUTRALIZING ACTIVITY

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

Nishiyama, Yasuhiro; Planque, Stephanie; Mitsuda, Yukie

2009-11-23

We describe murine monoclonal antibodies (mAbs) raised by immunization with an electrophilic gp120 analog (E-gp120) expressing the rare ability to neutralize genetically heterologous human immunodeficiency virus (HIV) strains. Unlike gp120, E-gp120 formed covalent oligomers. The reactivity of gp120 and E-gp120 with mAbs to reference neutralizing epitopes was markedly different, indicating their divergent structures. Epitope mapping with synthetic peptides and electrophilic peptide analogs indicated binary recognition of two distinct gp120 regions by anti-E-gp120 mAbs, the 421-433 and 288-306 peptide regions. Univalent Fab and single chain Fv fragments expressed the ability to recognize both peptides. X-ray crystallography of an anti-E-gp120 Fab fragmentmore » revealed two neighboring cavities, the typical antigen-binding cavity formed by the complementarity determining regions (CDRs) and another cavity dominated by antibody heavy chain variable (VH) domain framework (FR) residues. Substitution of the FR cavity VH Lys-19 residue by an Ala residue resulted in attenuated binding of the 421-433 region peptide probe. The CDRs and VH FR replacement/silent mutation ratios exceeded the ratio for a random mutation process, suggesting adaptive development of both putative binding sites. All mAbs studied were derived from VH1 family genes, suggesting biased recruitment of the V gene germ line repertoire by E-gp120. The conserved 421-433 region of gp120 is essential for HIV binding to host CD4 receptors. This region is recognized weakly by the FR of antibodies produced without exposure to HIV, but it usually fails to induce adaptive synthesis of neutralizing antibodies. We present models accounting for improved CD4-binding site recognition and broad HIV neutralizing activity of the mAbs, long sought goals in HIV vaccine development.« less

A Cautious Note on Auxiliary Variables That Can Increase Bias in Missing Data Problems.

PubMed

Thoemmes, Felix; Rose, Norman

2014-01-01

The treatment of missing data in the social sciences has changed tremendously during the last decade. Modern missing data techniques such as multiple imputation and full-information maximum likelihood are used much more frequently. These methods assume that data are missing at random. One very common approach to increase the likelihood that missing at random is achieved consists of including many covariates as so-called auxiliary variables. These variables are either included based on data considerations or in an inclusive fashion; that is, taking all available auxiliary variables. In this article, we point out that there are some instances in which auxiliary variables exhibit the surprising property of increasing bias in missing data problems. In a series of focused simulation studies, we highlight some situations in which this type of biasing behavior can occur. We briefly discuss possible ways how one can avoid selecting bias-inducing covariates as auxiliary variables.

Mismeasurement and the resonance of strong confounders: uncorrelated errors.

PubMed

Marshall, J R; Hastrup, J L

1996-05-15

Greenland first documented (Am J Epidemiol 1980; 112:564-9) that error in the measurement of a confounder could resonate--that it could bias estimates of other study variables, and that the bias could persist even with statistical adjustment for the confounder as measured. An important question is raised by this finding: can such bias be more than trivial within the bounds of realistic data configurations? The authors examine several situations involving dichotomous and continuous data in which a confounder and a null variable are measured with error, and they assess the extent of resultant bias in estimates of the effect of the null variable. They show that, with continuous variables, measurement error amounting to 40% of observed variance in the confounder could cause the observed impact of the null study variable to appear to alter risk by as much as 30%. Similarly, they show, with dichotomous independent variables, that 15% measurement error in the form of misclassification could lead the null study variable to appear to alter risk by as much as 50%. Such bias would result only from strong confounding. Measurement error would obscure the evidence that strong confounding is a likely problem. These results support the need for every epidemiologic inquiry to include evaluations of measurement error in each variable considered.

Generation of “LYmph Node Derived Antibody Libraries” (LYNDAL) for selecting fully human antibody fragments with therapeutic potential

PubMed Central

Diebolder, Philipp; Keller, Armin; Haase, Stephanie; Schlegelmilch, Anne; Kiefer, Jonathan D; Karimi, Tamana; Weber, Tobias; Moldenhauer, Gerhard; Kehm, Roland; Eis-Hübinger, Anna M; Jäger, Dirk; Federspil, Philippe A; Herold-Mende, Christel; Dyckhoff, Gerhard; Kontermann, Roland E; Arndt, Michaela AE; Krauss, Jürgen

2014-01-01

The development of efficient strategies for generating fully human monoclonal antibodies with unique functional properties that are exploitable for tailored therapeutic interventions remains a major challenge in the antibody technology field. Here, we present a methodology for recovering such antibodies from antigen-encountered human B cell repertoires. As the source for variable antibody genes, we cloned immunoglobulin G (IgG)-derived B cell repertoires from lymph nodes of 20 individuals undergoing surgery for head and neck cancer. Sequence analysis of unselected “LYmph Node Derived Antibody Libraries” (LYNDAL) revealed a naturally occurring distribution pattern of rearranged antibody sequences, representing all known variable gene families and most functional germline sequences. To demonstrate the feasibility for selecting antibodies with therapeutic potential from these repertoires, seven LYNDAL from donors with high serum titers against herpes simplex virus (HSV) were panned on recombinant glycoprotein B of HSV-1. Screening for specific binders delivered 34 single-chain variable fragments (scFvs) with unique sequences. Sequence analysis revealed extensive somatic hypermutation of enriched clones as a result of affinity maturation. Binding of scFvs to common glycoprotein B variants from HSV-1 and HSV-2 strains was highly specific, and the majority of analyzed antibody fragments bound to the target antigen with nanomolar affinity. From eight scFvs with HSV-neutralizing capacity in vitro, the most potent antibody neutralized 50% HSV-2 at 4.5 nM as a dimeric (scFv)2. We anticipate our approach to be useful for recovering fully human antibodies with therapeutic potential. PMID:24256717

Generation of “LYmph Node Derived Antibody Libraries” (LYNDAL) for selecting fully human antibody fragments with therapeutic potential.

PubMed

Diebolder, Philipp; Keller, Armin; Haase, Stephanie; Schlegelmilch, Anne; Kiefer, Jonathan D; Karimi, Tamana; Weber, Tobias; Moldenhauer, Gerhard; Kehm, Roland; Eis-Hübinger, Anna M; Jäger, Dirk; Federspil, Philippe A; Herold-Mende, Christel; Dyckhoff, Gerhard; Kontermann, Roland E; Arndt, Michaela A E; Krauss, Jürgen

2014-01-01

The development of efficient strategies for generating fully human monoclonal antibodies with unique functional properties that are exploitable for tailored therapeutic interventions remains a major challenge in the antibody technology field. Here, we present a methodology for recovering such antibodies from antigen-encountered human B cell repertoires. As the source for variable antibody genes, we cloned immunoglobulin G (IgG)-derived B cell repertoires from lymph nodes of 20 individuals undergoing surgery for head and neck cancer. Sequence analysis of unselected “LYmph Node Derived Antibody Libraries” (LYNDAL) revealed a naturally occurring distribution pattern of rearranged antibody sequences, representing all known variable gene families and most functional germline sequences. To demonstrate the feasibility for selecting antibodies with therapeutic potential from these repertoires, seven LYNDAL from donors with high serum titers against herpes simplex virus (HSV) were panned on recombinant glycoprotein B of HSV-1. Screening for specific binders delivered 34 single-chain variable fragments (scFvs) with unique sequences. Sequence analysis revealed extensive somatic hypermutation of enriched clones as a result of affinity maturation. Binding of scFvs to common glycoprotein B variants from HSV-1 and HSV-2 strains was highly specific, and the majority of analyzed antibody fragments bound to the target antigen with nanomolar affinity. From eight scFvs with HSV-neutralizing capacity in vitro,the most potent antibody neutralized 50% HSV-2 at 4.5 nM as a dimeric (scFv)2. We anticipate our approach to be useful for recovering fully human antibodies with therapeutic potential.

Modeling Antibody Diversity.

ERIC Educational Resources Information Center

Baker, William P.; Moore, Cathy Ronstadt

1998-01-01

Understanding antibody structure and function is difficult for many students. The rearrangement of constant and variable regions during antibody differentiation can be effectively simulated using a paper model. Describes a hands-on laboratory exercise which allows students to model antibody diversity using readily available resources. (PVD)

Bias, Confounding, and Interaction: Lions and Tigers, and Bears, Oh My!

PubMed

Vetter, Thomas R; Mascha, Edward J

2017-09-01

Epidemiologists seek to make a valid inference about the causal effect between an exposure and a disease in a specific population, using representative sample data from a specific population. Clinical researchers likewise seek to make a valid inference about the association between an intervention and outcome(s) in a specific population, based upon their randomly collected, representative sample data. Both do so by using the available data about the sample variable to make a valid estimate about its corresponding or underlying, but unknown population parameter. Random error in an experiment can be due to the natural, periodic fluctuation or variation in the accuracy or precision of virtually any data sampling technique or health measurement tool or scale. In a clinical research study, random error can be due to not only innate human variability but also purely chance. Systematic error in an experiment arises from an innate flaw in the data sampling technique or measurement instrument. In the clinical research setting, systematic error is more commonly referred to as systematic bias. The most commonly encountered types of bias in anesthesia, perioperative, critical care, and pain medicine research include recall bias, observational bias (Hawthorne effect), attrition bias, misclassification or informational bias, and selection bias. A confounding variable is a factor associated with both the exposure of interest and the outcome of interest. A confounding variable (confounding factor or confounder) is a variable that correlates (positively or negatively) with both the exposure and outcome. Confounding is typically not an issue in a randomized trial because the randomized groups are sufficiently balanced on all potential confounding variables, both observed and nonobserved. However, confounding can be a major problem with any observational (nonrandomized) study. Ignoring confounding in an observational study will often result in a "distorted" or incorrect estimate of the association or treatment effect. Interaction among variables, also known as effect modification, exists when the effect of 1 explanatory variable on the outcome depends on the particular level or value of another explanatory variable. Bias and confounding are common potential explanations for statistically significant associations between exposure and outcome when the true relationship is noncausal. Understanding interactions is vital to proper interpretation of treatment effects. These complex concepts should be consistently and appropriately considered whenever one is not only designing but also analyzing and interpreting data from a randomized trial or observational study.

Antibody incubation at 37°C improves fluorescent immunolabeling in free-floating thick tissue sections.

PubMed

Xiao, Xia; Feng, Ya-Ping; Du, Bin; Sun, Han-Ru; Ding, You-Quan; Qi, Jian-Guo

2017-03-01

Fluorescent immunolabeling and imaging in free-floating thick (50-60 μm) tissue sections is relatively simple in practice and enables design-based non-biased stereology, or 3-D reconstruction and analysis. This method is widely used for 3-D in situ quantitative biology in many areas of biological research. However, the labeling quality and efficiency of standard protocols for fluorescent immunolabeling of these tissue sections are not always satisfactory. Here, we systematically evaluate the effects of raising the conventional antibody incubation temperatures (4°C or 21°C) to mammalian body temperature (37°C) in these protocols. Our modification significantly enhances the quality (labeling sensitivity, specificity, and homogeneity) and efficiency (antibody concentration and antibody incubation duration) of fluorescent immunolabeling of free-floating thick tissue sections.

Structural classification of CDR-H3 revisited: a lesson in antibody modeling.

PubMed

Kuroda, Daisuke; Shirai, Hiroki; Kobori, Masato; Nakamura, Haruki

2008-11-15

Among the six complementarity-determining regions (CDRs) in the variable domains of an antibody, the third CDR of the heavy chain (CDR-H3), which lies in the center of the antigen-binding site, plays a particularly important role in antigen recognition. CDR-H3 shows significant variability in its length, sequence, and structure. Although difficult, model building of this segment is the most critical step in antibody modeling. Since our first proposal of the "H3-rules," which classify CDR-H3 structure based on amino acid sequence, the number of experimentally determined antibody structures has increased. Here, we revise these H3-rules and propose an improved classification scheme for CDR-H3 structure modeling. In addition, we determine the common features of CDR-H3 in antibody drugs as well as discuss the concept of "antibody druggability," which can be applied as an indicator of antibody evaluation during drug discovery.

LES study of microphysical variability bias in shallow cumulus

NASA Astrophysics Data System (ADS)

Kogan, Yefim

2017-05-01

Subgrid-scale (SGS) variability of cloud microphysical variables over the mesoscale numerical weather prediction (NWP) model has been evaluated by means of joint probability distribution functions (JPDFs). The latter were obtained using dynamically balanced Large Eddy Simulation (LES) model dataset from a case of marine trade cumulus initialized with soundings from Rain in Cumulus Over the Ocean (RICO) field project. Bias in autoconversion and accretion rates from different formulations of the JPDFs was analyzed. Approximating the 2-D PDF using a generic (fixed-in-time), but variable-in-height JPDFs give an acceptable level of accuracy, whereas neglecting the SGS variability altogether results in a substantial underestimate of the grid-mean total conversion rate and producing negative bias in rain water. Nevertheless the total effect on rain formation may be uncertain in the long run due to the fact that the negative bias in rain water may be counterbalanced by the positive bias in cloud water. Consequently, the overall effect of SGS neglect needs to be investigated in direct simulations with a NWP model.

Community-Based Seroepidemiological Survey of Hepatitis E Virus Infection in Catalonia, Spain▿

PubMed Central

Buti, Maria; Domínguez, Àngela; Plans, Pere; Jardí, Rossend; Schaper, Mélani; Espuñes, Jordi; Cardeñosa, Neus; Rodríguez-Frías, Francisco; Esteban, Rafael; Plasència, Antoni; Salleras, Luis

2006-01-01

The objective of the study was to investigate the prevalence of immunoglobulin G (IgG) antibodies to hepatitis E virus (HEV) infection in a population sample from Catalonia and to analyze the demographic and clinical variables associated with the presence of these antibodies. A total of 1,280 subjects between 15 and 74 years of age were selected randomly from urban and rural areas. Data for sociodemographic and clinical variables were collected by using a questionnaire. IgG antibodies to HEV were determined by an immunoenzymatic method. The odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated for studied variables. Multiple logistic regression analysis was used to determine which variables were independently associated with the prevalence of HEV infection. Anti-HEV antibodies were detected in 96 (7.3%) of the 1,280 samples analyzed. The prevalence of antibodies was greater among males (7.8%) than among women (7%) and increased with age for both sexes, from 3% among subjects 15 to 24 years of age to 12% among subjects ≥65 years of age. Bivariate analysis of the sociodemographic and clinical variables showed an association between the prevalence of hepatitis E virus infection and minor surgery (OR, 1.96; 95% CI, 1.24 to 3.11), abdominal surgery (OR, 1.74; 95% CI, 1.12 to 2.73), and, for women, being uniparous or multiparous (OR, 2.84; 95% CI, 1.19 to 6.79). The multivariate analysis showed an association with minor surgery only (OR, 1.68; 95% CI, 1.03 to 2.70). In conclusion, anti-HEV antibodies were detected in 7.3% of the Catalan population. The seroprevalence of anti-HEV antibodies increased with age and was associated with previous minor surgery. PMID:17050741

Measuring Variability in the Presence of Noise

NASA Astrophysics Data System (ADS)

Welsh, W. F.

Quantitative measurements of a variable signal in the presence of noise requires very careful attention to subtle affects which can easily bias the measurements. This is not limited to the low-count rate regime, nor is the bias error necessarily small. In this talk I will mention some of the dangers in applying standard techniques which are appropriate for high signal to noise data but fail in the cases where the S/N is low. I will discuss methods for correcting the bias in the these cases, both for periodic and non-periodic variability, and will introduce the concept of the ``filtered de-biased RMS''. I will also illustrate some common abuses of power spectrum interpretation. All of these points will be illustrated with examples from recent work on CV and AGN variability.

The antigenic evolution of influenza: drift or thrift?

PubMed Central

Wikramaratna, Paul S.; Sandeman, Michi; Recker, Mario; Gupta, Sunetra

2013-01-01

It is commonly assumed that antibody responses against the influenza virus are polarized in the following manner: strong antibody responses are directed at highly variable antigenic epitopes, which consequently undergo ‘antigenic drift’, while weak antibody responses develop against conserved epitopes. As the highly variable epitopes are in a constant state of flux, current antibody-based vaccine strategies are focused on the conserved epitopes in the expectation that they will provide some level of clinical protection after appropriate boosting. Here, we use a theoretical model to suggest the existence of epitopes of low variability, which elicit a high degree of both clinical and transmission-blocking immunity. We show that several epidemiological features of influenza and its serological and molecular profiles are consistent with this model of ‘antigenic thrift’, and that identifying the protective epitopes of low variability predicted by this model could offer a more viable alternative to regularly update the influenza vaccine than exploiting responses to weakly immunogenic conserved regions. PMID:23382423

Larger differences in utilization of rarely requested tests in primary care in Spain.

PubMed

Salinas, Maria; López-Garrigós, Maite; Flores, Emilio; Uris, Joaquín; Leiva-Salinas, Carlos

2015-01-01

The study was performed to compare and analyze the inter-departmental variability in the request of rarely requested laboratory tests in primary care, as opposed to other more common and highly requested tests. Data from production statistics for the year 2012 from 76 Spanish laboratories was used. The number of antinuclear antibodies, antistreptolysin O, creatinine, cyclic citrullinated peptide antibodies, deaminated peptide gliadine IgA antibodies, glucose, protein electrophoresis, rheumatoid factor, transglutaminase IgA antibodies, urinalysis and uric acid tests requested was collected. The number of test requests per 1000 inhabitants was calculated. In order to explore the variability the coefficient of quartile dispersion was calculated. The smallest variation was seen for creatinine, glucose, uric acid and urinalysis; the most requested tests. The tests that were least requested showed the greatest variability. Our study shows through a very simplified approach, in a population close to twenty million inhabitants, how in primary care, the variability in the request of laboratory tests is inversely proportional to the request rate.

Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains.

PubMed

Fera, Daniela; Schmidt, Aaron G; Haynes, Barton F; Gao, Feng; Liao, Hua-Xin; Kepler, Thomas B; Harrison, Stephen C

2014-07-15

Rapidly evolving pathogens, such as human immunodeficiency and influenza viruses, escape immune defenses provided by most vaccine-induced antibodies. Proposed strategies to elicit broadly neutralizing antibodies require a deeper understanding of antibody affinity maturation and evolution of the immune response to vaccination or infection. In HIV-infected individuals, viruses and B cells evolve together, creating a virus-antibody "arms race." Analysis of samples from an individual designated CH505 has illustrated the interplay between an antibody lineage, CH103, and autologous viruses at various time points. The CH103 antibodies, relatively broad in their neutralization spectrum, interact with the CD4 binding site of gp120, with a contact dominated by CDRH3. We show by analyzing structures of progenitor and intermediate antibodies and by correlating them with measurements of binding to various gp120s that there was a shift in the relative orientation of the light- and heavy-chain variable domains during evolution of the CH103 lineage. We further show that mutations leading to this conformational shift probably occurred in response to insertions in variable loop 5 (V5) of the HIV envelope. The shift displaced the tips of the light chain away from contact with V5, making room for the inserted residues, which had allowed escape from neutralization by the progenitor antibody. These results, which document the selective mechanism underlying this example of a virus-antibody arms race, illustrate the functional significance of affinity maturation by mutation outside the complementarity determining region surface of the antibody molecule.

¹⁵N, ¹³C and ¹H resonance assignments and secondary structure determination of a variable heavy domain of a heavy chain antibody.

PubMed

Prosser, Christine E; Waters, Lorna C; Muskett, Frederick W; Veverka, Vaclav; Addis, Philip W; Griffin, Laura M; Baker, Terry S; Lawson, Alastair D G; Wernery, Ulrich; Kinne, Jorg; Henry, Alistair J; Taylor, Richard J; Carr, Mark D

2014-04-01

Heavy chain antibodies differ in structure to conventional antibodies lacking both the light chain and the first heavy chain constant domain (CH1). Characteristics of the antigen-binding variable heavy domain of the heavy chain antibody (VHH) including the smaller size, high solubility and stability make them an attractive alternative to more traditional antibody fragments for detailed NMR-based structural analysis. Here we report essentially complete backbone and side chain (15)N, (13)C and (1)H assignments for a free VHH. Analysis of the backbone chemical shift data obtained indicates that the VHH is comprised predominantly of β-sheets corresponding to nearly 60% of the protein backbone.

Model-Based Control of Observer Bias for the Analysis of Presence-Only Data in Ecology

PubMed Central

Warton, David I.; Renner, Ian W.; Ramp, Daniel

2013-01-01

Presence-only data, where information is available concerning species presence but not species absence, are subject to bias due to observers being more likely to visit and record sightings at some locations than others (hereafter “observer bias”). In this paper, we describe and evaluate a model-based approach to accounting for observer bias directly – by modelling presence locations as a function of known observer bias variables (such as accessibility variables) in addition to environmental variables, then conditioning on a common level of bias to make predictions of species occurrence free of such observer bias. We implement this idea using point process models with a LASSO penalty, a new presence-only method related to maximum entropy modelling, that implicitly addresses the “pseudo-absence problem” of where to locate pseudo-absences (and how many). The proposed method of bias-correction is evaluated using systematically collected presence/absence data for 62 plant species endemic to the Blue Mountains near Sydney, Australia. It is shown that modelling and controlling for observer bias significantly improves the accuracy of predictions made using presence-only data, and usually improves predictions as compared to pseudo-absence or “inventory” methods of bias correction based on absences from non-target species. Future research will consider the potential for improving the proposed bias-correction approach by estimating the observer bias simultaneously across multiple species. PMID:24260167

Expression and assembly of a fully active antibody in algae

NASA Astrophysics Data System (ADS)

Mayfield, Stephen P.; Franklin, Scott E.; Lerner, Richard A.

2003-01-01

Although combinatorial antibody libraries have solved the problem of access to large immunological repertoires, efficient production of these complex molecules remains a problem. Here we demonstrate the efficient expression of a unique large single-chain (lsc) antibody in the chloroplast of the unicellular, green alga, Chlamydomonas reinhardtii. We achieved high levels of protein accumulation by synthesizing the lsc gene in chloroplast codon bias and by driving expression of the chimeric gene using either of two C. reinhardtii chloroplast promoters and 5' and 3' RNA elements. This lsc antibody, directed against glycoprotein D of the herpes simplex virus, is produced in a soluble form by the alga and assembles into higher order complexes in vivo. Aside from dimerization by disulfide bond formation, the antibody undergoes no detectable posttranslational modification. We further demonstrate that accumulation of the antibody can be modulated by the specific growth regime used to culture the alga, and by the choice of 5' and 3' elements used to drive expression of the antibody gene. These results demonstrate the utility of alga as an expression platform for recombinant proteins, and describe a new type of single chain antibody containing the entire heavy chain protein, including the Fc domain.

Impact of Uniform Methods on Interlaboratory Antibody Titration Variability: Antibody Titration and Uniform Methods.

PubMed

Bachegowda, Lohith S; Cheng, Yan H; Long, Thomas; Shaz, Beth H

2017-01-01

-Substantial variability between different antibody titration methods prompted development and introduction of uniform methods in 2008. -To determine whether uniform methods consistently decrease interlaboratory variation in proficiency testing. -Proficiency testing data for antibody titration between 2009 and 2013 were obtained from the College of American Pathologists. Each laboratory was supplied plasma and red cells to determine anti-A and anti-D antibody titers by their standard method: gel or tube by uniform or other methods at different testing phases (immediate spin and/or room temperature [anti-A], and/or anti-human globulin [AHG: anti-A and anti-D]) with different additives. Interlaboratory variations were compared by analyzing the distribution of titer results by method and phase. -A median of 574 and 1100 responses were reported for anti-A and anti-D antibody titers, respectively, during a 5-year period. The 3 most frequent (median) methods performed for anti-A antibody were uniform tube room temperature (147.5; range, 119-159), uniform tube AHG (143.5; range, 134-150), and other tube AHG (97; range, 82-116); for anti-D antibody, the methods were other tube (451; range, 431-465), uniform tube (404; range, 382-462), and uniform gel (137; range, 121-153). Of the larger reported methods, uniform gel AHG phase for anti-A and anti-D antibodies had the most participants with the same result (mode). For anti-A antibody, 0 of 8 (uniform versus other tube room temperature) and 1 of 8 (uniform versus other tube AHG), and for anti-D antibody, 0 of 8 (uniform versus other tube) and 0 of 8 (uniform versus other gel) proficiency tests showed significant titer variability reduction. -Uniform methods harmonize laboratory techniques but rarely reduce interlaboratory titer variance in comparison with other methods.

Bias and Bias Correction in Multi-Site Instrumental Variables Analysis of Heterogeneous Mediator Effects

ERIC Educational Resources Information Center

Reardon, Sean F.; Unlu, Faith; Zhu, Pei; Bloom, Howard

2013-01-01

We explore the use of instrumental variables (IV) analysis with a multi-site randomized trial to estimate the effect of a mediating variable on an outcome in cases where it can be assumed that the observed mediator is the only mechanism linking treatment assignment to outcomes, as assumption known in the instrumental variables literature as the…

Method for altering antibody light chain interactions

DOEpatents

Stevens, Fred J.; Stevens, Priscilla Wilkins; Raffen, Rosemarie; Schiffer, Marianne

2002-01-01

A method for recombinant antibody subunit dimerization including modifying at least one codon of a nucleic acid sequence to replace an amino acid occurring naturally in the antibody with a charged amino acid at a position in the interface segment of the light polypeptide variable region, the charged amino acid having a first polarity; and modifying at least one codon of the nucleic acid sequence to replace an amino acid occurring naturally in the antibody with a charged amino acid at a position in an interface segment of the heavy polypeptide variable region corresponding to a position in the light polypeptide variable region, the charged amino acid having a second polarity opposite the first polarity. Nucleic acid sequences which code for novel light chain proteins, the latter of which are used in conjunction with the inventive method, are also provided.

The role of cognitive biases and personality variables in subclinical delusional ideation.

PubMed

Menon, Mahesh; Quilty, Lena Catherine; Zawadzki, John Anthony; Woodward, Todd Stephen; Sokolowski, Helen Moriah; Boon, Heather Shirley; Wong, Albert Hung Choy

2013-05-01

A number of cognitive biases, most notably a data gathering bias characterised by "jumping to conclusions" (JTC), and the "bias against disconfirmatory evidence" (BADE), have been shown to be associated with delusions and subclinical delusional ideation. Certain personality variables, particularly "openness to experience", are thought to be associated with schizotypy. Using structural equation modelling, we examined the association between two higher order subfactors ("aspects") of "openness to experience" (labelled "openness" and "intellect"), these cognitive biases, and their relationship to subclinical delusional ideation in 121 healthy, nonpsychiatric controls. Our results suggest that cognitive biases (specifically the data gathering bias and BADE) and the "openness" aspect are independently associated with subclinical delusional ideation, and the data gathering bias is weakly associated with "positive schizotypy". "Intellect" is negatively associated with delusional ideation and might play a potential protective role. Cognitive biases and personality are likely to be independent risk factors for the development of delusions.

Comparisons of estimates of annual exceedance-probability discharges for small drainage basins in Iowa, based on data through water year 2013

USGS Publications Warehouse

Eash, David A.

2015-01-01

An examination was conducted to understand why the 1987 single-variable RREs seem to provide better accuracy and less bias than either of the 2013 multi- or single-variable RREs. A comparison of 1-percent annual exceedance-probability regression lines for hydrologic regions 1-4 from the 1987 single-variable RREs and for flood regions 1-3 from the 2013 single-variable RREs indicates that the 1987 single-variable regional-regression lines generally have steeper slopes and lower discharges when compared to 2013 single-variable regional-regression lines for corresponding areas of Iowa. The combination of the definition of hydrologic regions, the lower discharges, and the steeper slopes of regression lines associated with the 1987 single-variable RREs seem to provide better accuracy and less bias when compared to the 2013 multi- or single-variable RREs; better accuracy and less bias was determined particularly for drainage areas less than 2 mi2, and also for some drainage areas between 2 and 20 mi2. The 2013 multi- and single-variable RREs are considered to provide better accuracy and less bias for larger drainage areas. Results of this study indicate that additional research is needed to address the curvilinear relation between drainage area and AEPDs for areas of Iowa.

Human toxocariasis: frequency of anti-Toxocara antibodies in children and adolescents from an outpatient clinic for lymphatic filariasis in Recife, Northeast Brazil.

PubMed

Aguiar-Santos, Ana Maria; Andrade, Luiz D; Medeiros, Zulma; Chieffi, Pedro Paulo; Lescano, Suzana Z; Perez, Emília P

2004-01-01

In a transversal study on a sample of 386 children and adolescents from an outpatient clinic for filariasis in Recife, Northeast Brazil, the frequency of anti-Toxocara antibodies and its relation to age, gender, number of peripheral eosinophils, Wuchereria bancrofti microfilariae and intestinal helminths was determined. The total anti-Toxocara IgG antibody frequency was 39.4%, by ELISA technique. The difference in frequency between males (40.1%) and females (37.6%) was not statistically significant. The 6 to 10-year-old subset presented the highest frequency of anti-Toxocara antibodies (60%), and within this age group there was a statistically significant male bias. There was also a significant association between the number of eosinophils and the presence of anti-Toxocara antibodies. Intestinal parasite frequency was 52.1%, but no association was found between this data and the presence of anti-Toxocara antibodies. In the present sample, 42.2% of the patients were Wuchereria bancrofti carriers, however, again this was not associated with the presence of anti-Toxocara antibodies. In conclusion, anti-Toxocara antibodies were highly prevalent in this sample. The present data show that there is no cross correlation between anti-Toxocara IgG antibody and the presence of intestinal helminths and filariasis.

Potential diagnostic value of serum p53 antibody for detecting colorectal cancer: A meta-analysis.

PubMed

Meng, Rongqin; Wang, Yang; He, Liang; He, Yuanqing; Du, Zedong

2018-04-01

Numerous studies have assessed the diagnostic value of serum p53 (s-p53) antibody in patients with colorectal cancer (CRC); however, results remain controversial. The present study aimed to comprehensively and quantitatively summarize the potential diagnostic value of s-p53 antibody in CRC. The present study utilized databases, including PubMed and EmBase, systematically regarding s-p53 antibody diagnosis in CRC, accessed on and prior to 31 July 2016. The quality of all the included studies was assessed using quality assessment of studies of diagnostic accuracy (QUADAS). The result of pooled sensitivity, pooled specificity, positive likelihood ratio (PLR) and negative likelihood ratio (NLR) were analyzed and compared with overall accuracy measures using diagnostic odds ratios (DORs) and area under the curve (AUC) analysis. Publication bias and heterogeneity were also assessed. A total of 11 trials that enrolled a combined 3,392 participants were included in the meta-analysis. Approximately 72.73% (8/11) of the included studies were of high quality (QUADAS score >7), and all were retrospective case-control studies. The pooled sensitivity was 0.19 [95% confidence interval (CI), 0.18-0.21] and pooled specificity was 0.93 (95% CI, 0.92-0.94). Results also demonstrated a PLR of 4.56 (95% CI, 3.27-6.34), NLR of 0.78 (95% CI, 0.71-0.85) and DOR of 6.70 (95% CI, 4.59-9.76). The symmetrical summary receiver operating characteristic curve was 0.73. Furthermore, no evidence of publication bias or heterogeneity was observed in the meta-analysis. Meta-analysis data indicated that s-p53 antibody possesses potential diagnostic value for CRC. However, discrimination power was somewhat limited due to the low sensitivity.

DISTINCT ANTIBODY SPECIES: STRUCTURAL DIFFERENCES CREATING THERAPEUTIC OPPORTUNITIES

PubMed Central

Muyldermans, Serge; Smider, Vaughn V.

2016-01-01

Antibodies have been a remarkably successful class of molecules for binding a large number of antigens in therapeutic, diagnostic, and research applications. Typical antibodies derived from mouse or human sources use the surface formed by complementarity determining regions (CDRs) on the variable regions of the heavy chain/light chain heterodimer, which typically forms a relatively flat binding surface. Alternative species, particularly camelids and bovines, provide a unique paradigm for antigen recognition through novel domains which form the antigen binding paratope. For camelids, heavy chain antibodies bind antigen with only a single heavy chain variable region, in the absence of light chains. In bovines, ultralong CDR-H3 regions form an independently folding minidomain, which protrudes from the surface of the antibody and is diverse in both its sequence and disulfide patterns. The atypical paratopes of camelids and bovines potentially provide the ability to interact with different epitopes, particularly recessed or concave surfaces, compared to traditional antibodies. PMID:26922135

A method for estimation of bias and variability of continuous gas monitor data: application to carbon monoxide monitor accuracy.

PubMed

Shulman, Stanley A; Smith, Jerome P

2002-01-01

A method is presented for the evaluation of the bias, variability, and accuracy of gas monitors. This method is based on using the parameters for the fitted response curves of the monitors. Thereby, variability between calibrations, between dates within each calibration period, and between different units can be evaluated at several different standard concentrations. By combining variability information with bias information, accuracy can be assessed. An example using carbon monoxide monitor data is provided. Although the most general statistical software required for these tasks is not available on a spreadsheet, when the same number of dates in a calibration period are evaluated for each monitor unit, the calculations can be done on a spreadsheet. An example of such calculations, together with the formulas needed for their implementation, is provided. In addition, the methods can be extended by use of appropriate statistical models and software to evaluate monitor trends within calibration periods, as well as consider the effects of other variables, such as humidity and temperature, on monitor variability and bias.

Constructing a multidimensional free energy surface like a spider weaving a web.

PubMed

Chen, Changjun

2017-10-15

Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials. Fast-growing biasing potential accelerates the sampling speed but decreases the accuracy of the free energy result. Slow-growing biasing potential gives an optimized result but needs more simulation time. In this article, we propose an alternative method. It adds the biasing potential to a representative point of the molecule in the collective variable space to improve the conformational sampling. And the free energy surface is calculated from the free energy gradient in the constrained simulation, not given by the negative of the biasing potential as previous methods. So the presented method does not require the biasing potential to remove all the barriers and basins on the free energy surface exactly. Practical applications show that the method in this work is able to produce the accurate free energy surfaces for different molecules in a short time period. The free energy errors are small in the cases of various biasing potentials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation.

PubMed

Sheng, Zizhang; Schramm, Chaim A; Kong, Rui; Mullikin, James C; Mascola, John R; Kwong, Peter D; Shapiro, Lawrence

2017-01-01

Somatic hypermutation (SHM) plays a critical role in the maturation of antibodies, optimizing recognition initiated by recombination of V(D)J genes. Previous studies have shown that the propensity to mutate is modulated by the context of surrounding nucleotides and that SHM machinery generates biased substitutions. To investigate the intrinsic mutation frequency and substitution bias of SHMs at the amino acid level, we analyzed functional human antibody repertoires and developed mGSSP (method for gene-specific substitution profile), a method to construct amino acid substitution profiles from next-generation sequencing-determined B cell transcripts. We demonstrated that these gene-specific substitution profiles (GSSPs) are unique to each V gene and highly consistent between donors. We also showed that the GSSPs constructed from functional antibody repertoires are highly similar to those constructed from antibody sequences amplified from non-productively rearranged passenger alleles, which do not undergo functional selection. This suggests the types and frequencies, or mutational space, of a majority of amino acid changes sampled by the SHM machinery to be well captured by GSSPs. We further observed the rates of mutational exchange between some amino acids to be both asymmetric and context dependent and to correlate weakly with their biochemical properties. GSSPs provide an improved, position-dependent alternative to standard substitution matrices, and can be utilized to developing software for accurately modeling the SHM process. GSSPs can also be used for predicting the amino acid mutational space available for antigen-driven selection and for understanding factors modulating the maturation pathways of antibody lineages in a gene-specific context. The mGSSP method can be used to build, compare, and plot GSSPs; we report the GSSPs constructed for 69 common human V genes (DOI: 10.6084/m9.figshare.3511083) and provide high-resolution logo plots for each (DOI: 10.6084/m9.figshare.3511085).

An analysis of input errors in precipitation-runoff models using regression with errors in the independent variables

USGS Publications Warehouse

Troutman, Brent M.

1982-01-01

Errors in runoff prediction caused by input data errors are analyzed by treating precipitation-runoff models as regression (conditional expectation) models. Independent variables of the regression consist of precipitation and other input measurements; the dependent variable is runoff. In models using erroneous input data, prediction errors are inflated and estimates of expected storm runoff for given observed input variables are biased. This bias in expected runoff estimation results in biased parameter estimates if these parameter estimates are obtained by a least squares fit of predicted to observed runoff values. The problems of error inflation and bias are examined in detail for a simple linear regression of runoff on rainfall and for a nonlinear U.S. Geological Survey precipitation-runoff model. Some implications for flood frequency analysis are considered. A case study using a set of data from Turtle Creek near Dallas, Texas illustrates the problems of model input errors.

Adaptive Variable Bias Magnetic Bearing Control

NASA Technical Reports Server (NTRS)

Johnson, Dexter; Brown, Gerald V.; Inman, Daniel J.

1998-01-01

Most magnetic bearing control schemes use a bias current with a superimposed control current to linearize the relationship between the control current and the force it delivers. With the existence of the bias current, even in no load conditions, there is always some power consumption. In aerospace applications, power consumption becomes an important concern. In response to this concern, an alternative magnetic bearing control method, called Adaptive Variable Bias Control (AVBC), has been developed and its performance examined. The AVBC operates primarily as a proportional-derivative controller with a relatively slow, bias current dependent, time-varying gain. The AVBC is shown to reduce electrical power loss, be nominally stable, and provide control performance similar to conventional bias control. Analytical, computer simulation, and experimental results are presented in this paper.

Development of anti-bovine IgA single chain variable fragment and its application in diagnosis of foot-and-mouth disease

PubMed Central

Sridevi, N. V.; Shukra, A. M.; Neelakantam, B.; Anilkumar, J.; Madhanmohan, M.; Rajan, S.; Dev Chandran

2014-01-01

Recombinant antibody fragments like single chain variable fragments (scFvs) represent an attractive yet powerful alternative to immunoglobulins and hold great potential in the development of clinical diagnostic/therapeutic reagents. Structurally, scFvs are the smallest antibody fragments capable of retaining the antigen-binding capacity of whole antibodies and are composed of an immunoglobulin (Ig) variable light (VL) and variable heavy (VH) chain joined by a flexible polypeptide linker. In the present study, we constructed a scFv against bovine IgA from a hybridoma cell line IL-A71 that secretes a monoclonal antibody against bovine IgA using recombinant DNA technology. The scFv was expressed in Escherichia coli and purified using immobilized metal affinity chromatography (IMAC). The binding activity and specificity of the scFv was established by its non-reactivity toward other classes of immunoglobulins as determined by enzyme-linked immunosorbent assay (ELISA) and immunoblot analysis. Kinetic measurement of the scFv indicated that the recombinant antibody fragment had an affinity in picomolar range toward purified IgA. Furthermore, the scFv was used to develop a sensitive ELISA for the detection of foot and mouth disease virus (FMDV) carrier animals. PMID:24678404

Production of Recombinant Human scFv Against Tetanus Toxin Heavy Chain by Phage Display Technology.

PubMed

Khalili, Ehsan; Lakzaei, Mostafa; Rasaee, Mohhamad Javad; Aminian, Mahdi

2015-10-01

Tetanus, as a major cause of death in developing countries, is caused by tetanus neurotoxin. Recombinant antibodies against tetanus neurotoxin can be useful in tetanus management. Phage display of antibody fragments from immune human antibody libraries with single chain constructs combining the variable fragments (scFv) has been one of the most prominent technologies in antibody engineering. The aim of this study was the generation of a single chain fragment of variable region (scFv) library and selection of specific antibodies with high affinity against tetanus toxin. Immune human single chain fragment variable (HuscFv) antibody phagemid library was displayed on pIII of filamentous bacteriophage. Selection of scFv clones was performed against tetanus toxin antigens after three rounds of panning. The selected scFv clones were analyzed for inhibition of tetanus toxin binding to ganglioside GT1b. After the third round of panning, over 35 HuscFv phages specific for tetanus toxin were isolated from this library of which 15 clones were found to bind specifically to tetanus toxin. The selected HuscFv phages expressed as a soluble HuscFv peptide and some clones showed positive signals against tetanus toxin. We found that six HuscFv clones inhibit toxin binding to ganglioside GT1b. These selected antibodies can be used in the management of tetanus.

Production and characterization of a single chain variable fragment (scFv) for the mycotoxin deoxynivalenol

USDA-ARS?s Scientific Manuscript database

Deoxynivalenol (DON)is a mycotoxin produced by certain fungi that infest cereal grains worldwide. A hybridoma cell line producing a monoclonal antibody (Mab) recognizing DON was used as the starting point in the development of a recombinant single chain variable fragment (scFv) antibody. The scFv wa...

Associations between Mycobacterium paratuberculosis sero-status, milk quality parameters, and reproduction in dairy cows.

PubMed

Pesqueira, María N; Factor, Camino; Mato, Ivan; Sanjuán, María L; Macias, Laura; Eiras, Carmen; Arnaiz, Ignacio; Camino, Fernando; Yus, Eduardo; Diéguez, Francisco J

2015-01-01

The objective of this study was to investigate the influence of Mycobocterium avium subsp. paratuberculosis (MAP) sero-status of dairy cows on different milk production variables and reproductive traits. The study was carried out on 40 herds from the region of Galicia (North-West Spain). These herds were randomly selected from a larger group that had taken part in a voluntary paratuberculosis control program since 2005, which involves regular serum sampling of every adult animal to run antibody-ELISA tests. Milk production and reproductive data were obtained from the "Dairy Herd Improvement Program (DHIP) of Galicia". All the gathered data were processed following a linear regression model. Results indicated that there was no significant effect of MAP sero-status on individual milk production variables. However, a significant difference was observed at the calving-to-first-insemination interval, with an average increase of 14 days in positive animals compared to negatives. It has to be taken into consideration that the paratuberculosis status was only defined by the serological status. Since para tb-infected animals may have antbodies or may not, para tb-positive animals can also be included in the sero-negative group of animals, which may bias the results.

Population entropies estimates of proteins

NASA Astrophysics Data System (ADS)

Low, Wai Yee

2017-05-01

The Shannon entropy equation provides a way to estimate variability of amino acids sequences in a multiple sequence alignment of proteins. Knowledge of protein variability is useful in many areas such as vaccine design, identification of antibody binding sites, and exploration of protein 3D structural properties. In cases where the population entropies of a protein are of interest but only a small sample size can be obtained, a method based on linear regression and random subsampling can be used to estimate the population entropy. This method is useful for comparisons of entropies where the actual sequence counts differ and thus, correction for alignment size bias is needed. In the current work, an R based package named EntropyCorrect that enables estimation of population entropy is presented and an empirical study on how well this new algorithm performs on simulated dataset of various combinations of population and sample sizes is discussed. The package is available at https://github.com/lloydlow/EntropyCorrect. This article, which was originally published online on 12 May 2017, contained an error in Eq. (1), where the summation sign was missing. The corrected equation appears in the Corrigendum attached to the pdf.

DARPA Antibody Technology Program Standardized Test Bed for Antibody Characterization: Characterization of an MS2 ScFv Antibody

DTIC Science & Technology

2016-03-01

performance in an enzyme-linked immunosorbent assay ( ELISA ), with little regard for quantification of the full spectrum of variables affecting antibody...Program (ATP) Quality MS2 coat protein (MS2CP) Enzyme-linked immunosorbent assay ( ELISA ) 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT...5 2.7 ELISA ................................................................................................................5

Reducing bias and analyzing variability in the time-left procedure.

PubMed

Trujano, R Emmanuel; Orduña, Vladimir

2015-04-01

The time-left procedure was designed to evaluate the psychophysical function for time. Although previous results indicated a linear relationship, it is not clear what role the observed bias toward the time-left option plays in this procedure and there are no reports of how variability changes with predicted indifference. The purposes of this experiment were to reduce bias experimentally, and to contrast the difference limen (a measure of variability around indifference) with predictions from scalar expectancy theory (linear timing) and behavioral economic model (logarithmic timing). A control group of 6 rats performed the original time-left procedure with C=60 s and S=5, 10,…, 50, 55 s, whereas a no-bias group of 6 rats performed the same conditions in a modified time-left procedure in which only a single response per choice trial was allowed. Results showed that bias was reduced for the no-bias group, observed indifference grew linearly with predicted indifference for both groups, and difference limen and Weber ratios decreased as expected indifference increased for the control group, which is consistent with linear timing, whereas for the no-bias group they remained constant, consistent with logarithmic timing. Therefore, the time-left procedure generates results consistent with logarithmic perceived time once bias is experimentally reduced. Copyright © 2015 Elsevier B.V. All rights reserved.

B cell epitopes on infliximab identified by oligopeptide microarray with unprocessed patient sera.

PubMed

Homann, Arne; Röckendorf, Niels; Kromminga, Arno; Frey, Andreas; Jappe, Uta

2015-10-29

Autoimmune diseases like rheumatoid arthritis and inflammatory bowel disease are treated with TNF-alpha-blocking antibodies such as infliximab and adalimumab. A common side effect of therapeutic antibodies is the induction of anti-drug antibodies, which may reduce therapeutic efficacy. In order to reveal immunogenic epitopes on infliximab which are responsible for the adverse effects, sera from patients treated with infliximab were screened by ELISA for anti-infliximab antibodies. Sera containing high levels of anti-drug-antibodies (>1.25 µg/ml) were analyzed in an oligopeptide microarray system containing immobilized 15-meric oligopeptides from the infliximab amino acid sequence. Immunogenic infliximab IgG-epitopes were identified by infrared fluorescence scanning and comparison of infliximab-treated patients versus untreated controls. Six relevant epitopes on infliximab were recognized by the majority of all patient sera: 4 in the variable and 2 in the constant region. Three of the epitopes in the variable region are located in the TNF-alpha binding region of infliximab. The fourth epitope of the variable part of infliximab is located close to the TNF-alpha binding region and contains an N-glycosylation sequon. The sera positive for anti-infliximab antibodies do not contain antibodies against adalimumab as determined by ELISA. Thus, there is no infliximab-adalimumab cross-reactivity as determined by these systems. Our data shall contribute to a knowledge-based recommendation for a potentially necessary therapy switch from infliximab to another type of TNF-alpha-blocker. The characterization of immunogenic epitopes on therapeutic monoclonal antibodies using unprocessed patient sera shall lead to direct translational aspects for the development of less immunogenic therapeutic antibodies. Patients benefit from less adverse events and longer lasting drug effects.

Bias and Bias Correction in Multisite Instrumental Variables Analysis of Heterogeneous Mediator Effects

ERIC Educational Resources Information Center

Reardon, Sean F.; Unlu, Fatih; Zhu, Pei; Bloom, Howard S.

2014-01-01

We explore the use of instrumental variables (IV) analysis with a multisite randomized trial to estimate the effect of a mediating variable on an outcome in cases where it can be assumed that the observed mediator is the only mechanism linking treatment assignment to outcomes, an assumption known in the IV literature as the exclusion restriction.…

Dance and Essence: Reflections on Morality and Education.

ERIC Educational Resources Information Center

Hodes, Stuart

1995-01-01

Asserts that the self-actualizing and expressive nature of dance contributes to an intuitive sense of morality. Criticizes the body versus mind dualism and antibody bias implicit in the Western intellectual tradition. Contrasts the aggressive nature of sports with the expressive character of dance. (MJP)

Development of single chain variable fragment (scFv) antibodies against surface proteins of ‘Ca. Liberibacter asiaticus’

USDA-ARS?s Scientific Manuscript database

‘Ca. Liberibacter asiaticus’ is the causal agent of citrus huanglongbing, the most serious disease of citrus worldwide. We have developed and applied immunization and affinity screening methods to develop a primary library of recombinant single chain variable fragment (scFv) antibodies in an M13 vec...

Study of Bias in 2012-Placement Test through Rasch Model in Terms of Gender Variable

ERIC Educational Resources Information Center

Turkan, Azmi; Cetin, Bayram

2017-01-01

Validity and reliability are among the most crucial characteristics of a test. One of the steps to make sure that a test is valid and reliable is to examine the bias in test items. The purpose of this study was to examine the bias in 2012 Placement Test items in terms of gender variable using Rasch Model in Turkey. The sample of this study was…

Sources of Biased Inference in Alcohol and Drug Services Research: An Instrumental Variable Approach

PubMed Central

Schmidt, Laura A.; Tam, Tammy W.; Larson, Mary Jo

2012-01-01

Objective: This study examined the potential for biased inference due to endogeneity when using standard approaches for modeling the utilization of alcohol and drug treatment. Method: Results from standard regression analysis were compared with those that controlled for endogeneity using instrumental variables estimation. Comparable models predicted the likelihood of receiving alcohol treatment based on the widely used Aday and Andersen medical care–seeking model. Data were from the National Epidemiologic Survey on Alcohol and Related Conditions and included a representative sample of adults in households and group quarters throughout the contiguous United States. Results: Findings suggested that standard approaches for modeling treatment utilization are prone to bias because of uncontrolled reverse causation and omitted variables. Compared with instrumental variables estimation, standard regression analyses produced downwardly biased estimates of the impact of alcohol problem severity on the likelihood of receiving care. Conclusions: Standard approaches for modeling service utilization are prone to underestimating the true effects of problem severity on service use. Biased inference could lead to inaccurate policy recommendations, for example, by suggesting that people with milder forms of substance use disorder are more likely to receive care than is actually the case. PMID:22152672

ScaffoldSeq: Software for characterization of directed evolution populations.

PubMed

Woldring, Daniel R; Holec, Patrick V; Hackel, Benjamin J

2016-07-01

ScaffoldSeq is software designed for the numerous applications-including directed evolution analysis-in which a user generates a population of DNA sequences encoding for partially diverse proteins with related functions and would like to characterize the single site and pairwise amino acid frequencies across the population. A common scenario for enzyme maturation, antibody screening, and alternative scaffold engineering involves naïve and evolved populations that contain diversified regions, varying in both sequence and length, within a conserved framework. Analyzing the diversified regions of such populations is facilitated by high-throughput sequencing platforms; however, length variability within these regions (e.g., antibody CDRs) encumbers the alignment process. To overcome this challenge, the ScaffoldSeq algorithm takes advantage of conserved framework sequences to quickly identify diverse regions. Beyond this, unintended biases in sequence frequency are generated throughout the experimental workflow required to evolve and isolate clones of interest prior to DNA sequencing. ScaffoldSeq software uniquely handles this issue by providing tools to quantify and remove background sequences, cluster similar protein families, and dampen the impact of dominant clones. The software produces graphical and tabular summaries for each region of interest, allowing users to evaluate diversity in a site-specific manner as well as identify epistatic pairwise interactions. The code and detailed information are freely available at http://research.cems.umn.edu/hackel. Proteins 2016; 84:869-874. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Creation of a Ligand-Dependent Enzyme by Fusing Circularly Permuted Antibody Variable Region Domains.

PubMed

Iwai, Hiroto; Kojima-Misaizu, Miki; Dong, Jinhua; Ueda, Hiroshi

2016-04-20

Allosteric control of enzyme activity with exogenous substances has been hard to achieve, especially using antibody domains that potentially allow control by any antigens of choice. Here, in order to attain this goal, we developed a novel antibody variable region format introduced with circular permutations, called Clampbody. The two variable-region domains of the antibone Gla protein (BGP) antibody were each circularly permutated to have novel termini at the loops near their domain interface. Through their attachment to the N- and C-termini of a circularly permutated TEM-1 β-lactamase (cpBLA), we created a molecular switch that responds to the antigen peptide. The fusion protein specifically recognized the antigen, and in the presence of some detergent or denaturant, its catalytic activity was enhanced up to 4.7-fold in an antigen-dependent manner, due to increased resistance to these reagents. Hence, Clampbody will be a powerful tool for the allosteric regulation of enzyme and other protein activities and especially useful to design robust biosensors.

DNA double-strand break response factors influence end-joining features of IgH class switch and general translocation junctions.

PubMed

Panchakshari, Rohit A; Zhang, Xuefei; Kumar, Vipul; Du, Zhou; Wei, Pei-Chi; Kao, Jennifer; Dong, Junchao; Alt, Frederick W

2018-01-23

Ig heavy chain (IgH) class switch recombination (CSR) in B lymphocytes switches IgH constant regions to change antibody functions. CSR is initiated by DNA double-strand breaks (DSBs) within a donor IgH switch (S) region and a downstream acceptor S region. CSR is completed by fusing donor and acceptor S region DSB ends by classical nonhomologous end-joining (C-NHEJ) and, in its absence, by alternative end-joining that is more biased to use longer junctional microhomologies (MHs). Deficiency for DSB response (DSBR) factors, including ataxia telangiectasia-mutated (ATM) and 53BP1, variably impair CSR end-joining, with 53BP1 deficiency having the greatest impact. However, studies of potential impact of DSBR factor deficiencies on MH-mediated CSR end-joining have been technically limited. We now use a robust DSB joining assay to elucidate impacts of deficiencies for DSBR factors on CSR and chromosomal translocation junctions in primary mouse B cells and CH12F3 B-lymphoma cells. Compared with wild-type, CSR and c-myc to S region translocation junctions in the absence of 53BP1, and, to a lesser extent, other DSBR factors, have increased MH utilization; indeed, 53BP1-deficient MH profiles resemble those associated with C-NHEJ deficiency. However, translocation junctions between c-myc DSB and general DSBs genome-wide are not MH-biased in ATM-deficient versus wild-type CH12F3 cells and are less biased in 53BP1- and C-NHEJ-deficient cells than CSR junctions or c-myc to S region translocation junctions. We discuss potential roles of DSBR factors in suppressing increased MH-mediated DSB end-joining and features of S regions that may render their DSBs prone to MH-biased end-joining in the absence of DSBR factors.

Duration of serum antibody responses following vaccination and revaccination of cattle with non-living commercial Pasteurella haemolytica vaccines.

PubMed

Confer, A W; Fulton, R W; Clinkenbeard, K D; Driskel, B A

1998-12-01

This study was designed to determine the duration of serum antibody responses to Pasteurella haemolytica whole cells (WC) and leukotoxin (LKT) in weanling beef cattle vaccinated with various non-living P. haemolytica vaccines. Serum antibodies to P. haemolytica antigens were determined periodically through day 140 by enzyme-linked immunosorbent assays. At day 140, cattle were revaccinated, and antibody responses periodically determined through day 196. Three vaccines were used in two experiments (A and B), OneShot, Presponse HP/tK, and Septimune PH-K. In general, all three vaccines between 7 and 14 days induced antibody responses to WC after vaccination. Antibodies to LKT were induced with OneShot and Presponse. Revaccination at days 28 and 140 usually stimulated anamnestic responses. Serum antibodies to the various antigens remained significantly increased for up to 84 days after vaccination or revaccination. The intensity and duration of antibody responses were variable depending on the experiment and vaccines used. Vaccination with OneShot usually stimulated the greatest responses to WC. Vaccination with OneShot or Presponse resulted in equivalent primary anti-LKT responses. In experiment B, spontaneous seroconversion was found in numerous calves on day 112. Revaccination of those cattle at day 140 resulted in markedly variable antibody responses such that several groups had no increase in antibody responses.

A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties

PubMed Central

Tiller, Thomas; Schuster, Ingrid; Deppe, Dorothée; Siegers, Katja; Strohner, Ralf; Herrmann, Tanja; Berenguer, Marion; Poujol, Dominique; Stehle, Jennifer; Stark, Yvonne; Heßling, Martin; Daubert, Daniela; Felderer, Karin; Kaden, Stefan; Kölln, Johanna; Enzelberger, Markus; Urlinger, Stefanie

2013-01-01

This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds. PMID:23571156

An improved standardization procedure to remove systematic low frequency variability biases in GCM simulations

NASA Astrophysics Data System (ADS)

Mehrotra, Rajeshwar; Sharma, Ashish

2012-12-01

The quality of the absolute estimates of general circulation models (GCMs) calls into question the direct use of GCM outputs for climate change impact assessment studies, particularly at regional scales. Statistical correction of GCM output is often necessary when significant systematic biasesoccur between the modeled output and observations. A common procedure is to correct the GCM output by removing the systematic biases in low-order moments relative to observations or to reanalysis data at daily, monthly, or seasonal timescales. In this paper, we present an extension of a recently published nested bias correction (NBC) technique to correct for the low- as well as higher-order moments biases in the GCM-derived variables across selected multiple time-scales. The proposed recursive nested bias correction (RNBC) approach offers an improved basis for applying bias correction at multiple timescales over the original NBC procedure. The method ensures that the bias-corrected series exhibits improvements that are consistently spread over all of the timescales considered. Different variations of the approach starting from the standard NBC to the more complex recursive alternatives are tested to assess their impacts on a range of GCM-simulated atmospheric variables of interest in downscaling applications related to hydrology and water resources. Results of the study suggest that three to five iteration RNBCs are the most effective in removing distributional and persistence related biases across the timescales considered.

Regression dilution bias: tools for correction methods and sample size calculation.

PubMed

Berglund, Lars

2012-08-01

Random errors in measurement of a risk factor will introduce downward bias of an estimated association to a disease or a disease marker. This phenomenon is called regression dilution bias. A bias correction may be made with data from a validity study or a reliability study. In this article we give a non-technical description of designs of reliability studies with emphasis on selection of individuals for a repeated measurement, assumptions of measurement error models, and correction methods for the slope in a simple linear regression model where the dependent variable is a continuous variable. Also, we describe situations where correction for regression dilution bias is not appropriate. The methods are illustrated with the association between insulin sensitivity measured with the euglycaemic insulin clamp technique and fasting insulin, where measurement of the latter variable carries noticeable random error. We provide software tools for estimation of a corrected slope in a simple linear regression model assuming data for a continuous dependent variable and a continuous risk factor from a main study and an additional measurement of the risk factor in a reliability study. Also, we supply programs for estimation of the number of individuals needed in the reliability study and for choice of its design. Our conclusion is that correction for regression dilution bias is seldom applied in epidemiological studies. This may cause important effects of risk factors with large measurement errors to be neglected.

Detection and Attribution of Simulated Climatic Extreme Events and Impacts: High Sensitivity to Bias Correction

NASA Astrophysics Data System (ADS)

Sippel, S.; Otto, F. E. L.; Forkel, M.; Allen, M. R.; Guillod, B. P.; Heimann, M.; Reichstein, M.; Seneviratne, S. I.; Kirsten, T.; Mahecha, M. D.

2015-12-01

Understanding, quantifying and attributing the impacts of climatic extreme events and variability is crucial for societal adaptation in a changing climate. However, climate model simulations generated for this purpose typically exhibit pronounced biases in their output that hinders any straightforward assessment of impacts. To overcome this issue, various bias correction strategies are routinely used to alleviate climate model deficiencies most of which have been criticized for physical inconsistency and the non-preservation of the multivariate correlation structure. We assess how biases and their correction affect the quantification and attribution of simulated extremes and variability in i) climatological variables and ii) impacts on ecosystem functioning as simulated by a terrestrial biosphere model. Our study demonstrates that assessments of simulated climatic extreme events and impacts in the terrestrial biosphere are highly sensitive to bias correction schemes with major implications for the detection and attribution of these events. We introduce a novel ensemble-based resampling scheme based on a large regional climate model ensemble generated by the distributed weather@home setup[1], which fully preserves the physical consistency and multivariate correlation structure of the model output. We use extreme value statistics to show that this procedure considerably improves the representation of climatic extremes and variability. Subsequently, biosphere-atmosphere carbon fluxes are simulated using a terrestrial ecosystem model (LPJ-GSI) to further demonstrate the sensitivity of ecosystem impacts to the methodology of bias correcting climate model output. We find that uncertainties arising from bias correction schemes are comparable in magnitude to model structural and parameter uncertainties. The present study consists of a first attempt to alleviate climate model biases in a physically consistent way and demonstrates that this yields improved simulations of climate extremes and associated impacts. [1] http://www.climateprediction.net/weatherathome/

Bias estimation for the Landsat 8 operational land imager

USGS Publications Warehouse

Morfitt, Ron; Vanderwerff, Kelly

2011-01-01

The Operational Land Imager (OLI) is a pushbroom sensor that will be a part of the Landsat Data Continuity Mission (LDCM). This instrument is the latest in the line of Landsat imagers, and will continue to expand the archive of calibrated earth imagery. An important step in producing a calibrated image from instrument data is accurately accounting for the bias of the imaging detectors. Bias variability is one factor that contributes to error in bias estimation for OLI. Typically, the bias is simply estimated by averaging dark data on a per-detector basis. However, data acquired during OLI pre-launch testing exhibited bias variation that correlated well with the variation in concurrently collected data from a special set of detectors on the focal plane. These detectors are sensitive to certain electronic effects but not directly to incoming electromagnetic radiation. A method of using data from these special detectors to estimate the bias of the imaging detectors was developed, but found not to be beneficial at typical radiance levels as the detectors respond slightly when the focal plane is illuminated. In addition to bias variability, a systematic bias error is introduced by the truncation performed by the spacecraft of the 14-bit instrument data to 12-bit integers. This systematic error can be estimated and removed on average, but the per pixel quantization error remains. This paper describes the variability of the bias, the effectiveness of a new approach to estimate and compensate for it, as well as the errors due to truncation and how they are reduced.

Impacts of correcting the inter-variable correlation of climate model outputs on hydrological modeling

NASA Astrophysics Data System (ADS)

Chen, Jie; Li, Chao; Brissette, François P.; Chen, Hua; Wang, Mingna; Essou, Gilles R. C.

2018-05-01

Bias correction is usually implemented prior to using climate model outputs for impact studies. However, bias correction methods that are commonly used treat climate variables independently and often ignore inter-variable dependencies. The effects of ignoring such dependencies on impact studies need to be investigated. This study aims to assess the impacts of correcting the inter-variable correlation of climate model outputs on hydrological modeling. To this end, a joint bias correction (JBC) method which corrects the joint distribution of two variables as a whole is compared with an independent bias correction (IBC) method; this is considered in terms of correcting simulations of precipitation and temperature from 26 climate models for hydrological modeling over 12 watersheds located in various climate regimes. The results show that the simulated precipitation and temperature are considerably biased not only in the individual distributions, but also in their correlations, which in turn result in biased hydrological simulations. In addition to reducing the biases of the individual characteristics of precipitation and temperature, the JBC method can also reduce the bias in precipitation-temperature (P-T) correlations. In terms of hydrological modeling, the JBC method performs significantly better than the IBC method for 11 out of the 12 watersheds over the calibration period. For the validation period, the advantages of the JBC method are greatly reduced as the performance becomes dependent on the watershed, GCM and hydrological metric considered. For arid/tropical and snowfall-rainfall-mixed watersheds, JBC performs better than IBC. For snowfall- or rainfall-dominated watersheds, however, the two methods behave similarly, with IBC performing somewhat better than JBC. Overall, the results emphasize the advantages of correcting the P-T correlation when using climate model-simulated precipitation and temperature to assess the impact of climate change on watershed hydrology. However, a thorough validation and a comparison with other methods are recommended before using the JBC method, since it may perform worse than the IBC method for some cases due to bias nonstationarity of climate model outputs.

Non-equilibrium Green's functions study of discrete dopants variability on an ultra-scaled FinFET

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

Valin, R., E-mail: r.valinferreiro@swansea.ac.uk; Martinez, A., E-mail: a.e.Martinez@swansea.ac.uk; Barker, J. R., E-mail: john.barker@glasgow.ac.uk

In this paper, we study the effect of random discrete dopants on the performance of a 6.6 nm channel length silicon FinFET. The discrete dopants have been distributed randomly in the source/drain region of the device. Due to the small dimensions of the FinFET, a quantum transport formalism based on the non-equilibrium Green's functions has been deployed. The transfer characteristics for several devices that differ in location and number of dopants have been calculated. Our results demonstrate that discrete dopants modify the effective channel length and the height of the source/drain barrier, consequently changing the channel control of the charge. Thismore » effect becomes more significant at high drain bias. As a consequence, there is a strong effect on the variability of the on-current, off-current, sub-threshold slope, and threshold voltage. Finally, we have also calculated the mean and standard deviation of these parameters to quantify their variability. The obtained results show that the variability at high drain bias is 1.75 larger than at low drain bias. However, the variability of the on-current, off-current, and sub-threshold slope remains independent of the drain bias. In addition, we have found that a large source to drain current by tunnelling current occurs at low gate bias.« less

Model selection bias and Freedman's paradox

USGS Publications Warehouse

Lukacs, P.M.; Burnham, K.P.; Anderson, D.R.

2010-01-01

In situations where limited knowledge of a system exists and the ratio of data points to variables is small, variable selection methods can often be misleading. Freedman (Am Stat 37:152-155, 1983) demonstrated how common it is to select completely unrelated variables as highly "significant" when the number of data points is similar in magnitude to the number of variables. A new type of model averaging estimator based on model selection with Akaike's AIC is used with linear regression to investigate the problems of likely inclusion of spurious effects and model selection bias, the bias introduced while using the data to select a single seemingly "best" model from a (often large) set of models employing many predictor variables. The new model averaging estimator helps reduce these problems and provides confidence interval coverage at the nominal level while traditional stepwise selection has poor inferential properties. ?? The Institute of Statistical Mathematics, Tokyo 2009.

Role Appropriateness of Educational Fields: Bias in Selection.

ERIC Educational Resources Information Center

Smith, Elizabeth P.; And Others

Bias towards women exists in the selection of applicants to professional and other positions. This research investigated the effects of two rater variables--sex and attitude toward women--and three applicant variables--sex, field (engineering-dietetics), and attributes--(feminine-masculine) upon ratings of competency and personal charm. Analyses…

Overcoming codon-usage bias in heterologous protein expression in Streptococcus gordonii.

PubMed

Lee, Song F; Li, Yi-Jing; Halperin, Scott A

2009-11-01

One of the limitations facing the development of Streptococcus gordonii into a successful vaccine vector is the inability of this bacterium to express high levels of heterologous proteins. In the present study, we have identified 12 codons deemed as rare codons in S. gordonii and seven other streptococcal species. tRNA genes encoding 10 of the 12 rare codons were cloned into a plasmid. The plasmid was transformed into strains of S. gordonii expressing the fusion protein SpaP/S1, the anti-complement receptor 1 (CR1) single-chain variable fragment (scFv) antibody, or the Toxoplasma gondii cyclophilin C18 protein. These three heterologous proteins contained high percentages of amino acids encoded by rare codons. The results showed that the production of SpaP/S1, anti-CR1 scFv and C18 increased by 2.7-, 120- and 10-fold, respectively, over the control strains. In contrast, the production of the streptococcal SpaP protein without the pertussis toxin S1 fragment was not affected by tRNA gene supplementation, indicating that the increased production of SpaP/S1 protein was due to the ability to overcome the limitation caused by rare codons required for the S1 fragment. The increase in anti-CR1 scFv production was also observed in Streptococcus mutans following tRNA gene supplementation. Collectively, the findings in the present study demonstrate for the first time, to the best of our knowledge, that codon-usage bias exists in Streptococcus spp. and the limitation of heterologous protein expression caused by codon-usage bias can be overcome by tRNA supplementation.

Evaluating the Bias of Alternative Cost Progress Models: Tests Using Aerospace Industry Acquisition Programs

DTIC Science & Technology

1992-12-01

suspect :mat, -n2 extent predict:.on cas jas ccsiziveiv crrei:=e amonc e v:arious models, :he fandom *.;aik, learn ha r ur e, i;<ea- variable and Bemis...Functions, Production Rate Adjustment Model, Learning Curve Model. Random Walk Model. Bemis Model. Evaluating Model Bias, Cost Prediction Bias. Cost...of four cost progress models--a random walk model, the tradiuonai learning curve model, a production rate model Ifixed-variable model). and a model

Myeloma-Derived Light Chain Paired with a Diagnostic Monoclonal Antibody Hinders Immunoassay Performance.

PubMed

Tu, Bailin; Tieman, Bryan; Moore, Jeffrey; Pan, You; Muerhoff, A Scott

2017-06-01

Monoclonal antibodies are widely used as the capture and detection reagents in diagnostic immunoassays. In the past, myeloma fusion partners expressing endogenous heavy and/or light chains were often used to generate hybridoma cell lines. As a result, mixed populations of antibodies were produced that can cause inaccurate test results, poor antibody stability, and significant lot-to-lot variability. We describe one such scenario where the P3U1 (P3X63Ag8U.1) myeloma fusion partner was used in the generation of a hybridoma producing protein induced vitamin K absence/antagonist-II (PIVKA II) antibody. The hybridoma produces three subpopulations of immunoglobulin as determined by ion exchange (IEx) chromatography that exhibit varying degrees of immunoreactivity (0%, 50%, or 100%) to the target antigen as determined by Surface Plasmon Resonance. To produce an antibody with the highest possible sensitivity and specificity, the antigen-specific heavy and light chain variable domains (VH and VL) were cloned from the hybridoma and tethered to murine IgG1 and kappa scaffolds. The resulting recombinant antibody was expressed in Chinese hamster ovary cells and is compatible for use in a diagnostic immunoassay.

Enzyme-linked immunosorbent assay with monoclonal and single-chain variable fragment antibodies selective to coplanar polychlorinated biphenyls.

PubMed

Inui, Hideyuki; Takeuchi, Tetsuya; Uesugi, Akari; Doi, Fumito; Takai, Mikio; Nishi, Kosuke; Miyake, Shiro; Ohkawa, Hideo

2012-02-22

Coplanar polychlorinated biphenyls (Co-PCBs) consisting of non-ortho and mono-ortho-chlorinated PCBs are dioxin-like compounds and cause wide contamination in the environment. To monitor Co-PCB residues, it was attempted to establish an enzyme-linked immunosorbent assay (ELISA) with monoclonal and recombinant antibodies selective to Co-PCBs. When 3,3',5,5'-tetrachlorobiphenoxybutyric acid (PCBH)-keyhole limpet hemocyanin conjugate was immunized into mice, two monoclonal antibodies, Mab-0217 and Mab-4444, were obtained. 3,3',5,5'-Tetrachlorobiphenyl (PCB80) was determined with an IC(50) value of 2.6 and 0.46 ng mL(-1) in ELISA based on Mab-0217 and Mab-4444, respectively. Mab-4444 cross-reacted with Co-PCB congeners, except for PCB77 and PCB81. Mab-0217 reacted with PCB80 and cross-reacted with PCB111. A single-chain variable fragment (scFv) antibody derived from Mab-4444 was produced in recombinant Escherichia coli cells. The scFv antibody showed nearly the same sensitivity toward PCBH as the parent monoclonal antibody in ELISA. These results clearly suggested that Mab-4444 and its scFv antibodies were suitable for monitoring the representative congeners of Co-PCBs.

Mice with megabase humanization of their immunoglobulin genes generate antibodies as efficiently as normal mice.

PubMed

Murphy, Andrew J; Macdonald, Lynn E; Stevens, Sean; Karow, Margaret; Dore, Anthony T; Pobursky, Kevin; Huang, Tammy T; Poueymirou, William T; Esau, Lakeisha; Meola, Melissa; Mikulka, Warren; Krueger, Pamela; Fairhurst, Jeanette; Valenzuela, David M; Papadopoulos, Nicholas; Yancopoulos, George D

2014-04-08

Mice genetically engineered to be humanized for their Ig genes allow for human antibody responses within a mouse background (HumAb mice), providing a valuable platform for the generation of fully human therapeutic antibodies. Unfortunately, existing HumAb mice do not have fully functional immune systems, perhaps because of the manner in which their genetic humanization was carried out. Heretofore, HumAb mice have been generated by disrupting the endogenous mouse Ig genes and simultaneously introducing human Ig transgenes at a different and random location; KO-plus-transgenic humanization. As we describe in the companion paper, we attempted to make mice that more efficiently use human variable region segments in their humoral responses by precisely replacing 6 Mb of mouse Ig heavy and kappa light variable region germ-line gene segments with their human counterparts while leaving the mouse constant regions intact, using a unique in situ humanization approach. We reasoned the introduced human variable region gene segments would function indistinguishably in their new genetic location, whereas the retained mouse constant regions would allow for optimal interactions and selection of the resulting antibodies within the mouse environment. We show that these mice, termed VelocImmune mice because they were generated using VelociGene technology, efficiently produce human:mouse hybrid antibodies (that are rapidly convertible to fully human antibodies) and have fully functional humoral immune systems indistinguishable from those of WT mice. The efficiency of the VelocImmune approach is confirmed by the rapid progression of 10 different fully human antibodies into human clinical trials.

Sensitivity of HER-2/neu antibodies in archival tissue samples: potential source of error in immunohistochemical studies of oncogene expression.

PubMed

Press, M F; Hung, G; Godolphin, W; Slamon, D J

1994-05-15

HER-2/neu oncogene amplification and overexpression of breast cancer tissue has been correlated with poor prognosis in women with both node-positive and node-negative disease. However, several studies have not confirmed this association. Review of these studies reveals the presence of considerable methodological variability including differences in study size, follow-up time, techniques and reagents. The majority of papers with clinical follow-up information are immunohistochemical studies using archival, paraffin-embedded breast cancers, and a variety of HER-2/neu antibodies have been used in these studies. Very little information, however, is available about the ability of the antibodies to detect overexpression following tissue processing for paraffin-embedding. Therefore, a series of antibodies, reported in the literature or commercially available, were evaluated to assess their sensitivity and specificity as immunohistochemical reagents. Paraffin-embedded samples of 187 breast cancers, previously characterized as frozen specimens for HER-2/neu amplification by Southern blot and for overexpression by Northern blot, Western blot, and immunohistochemistry, were used. Two multitumor paraffin-embedded tissue blocks were prepared from the previously analyzed breast cancers as a panel of cases to test a series of previously studied and/or commercially available anti-HER-2/neu antibodies. Immunohistochemical staining results obtained with 7 polyclonal and 21 monoclonal antibodies in sections from paraffin-embedded blocks of these breast cancers were compared. The ability of these antibodies to detect overexpression was extremely variable, providing an important explantation for the variable overexpression rate reported in the literature.

What is the contribution of different cognitive biases and stressful childhood events to the presence and number of previous depressive episodes?

PubMed

Vrijsen, Janna N; Becker, Eni S; Arias-Vásquez, Alejandro; van Dijk, Maarten K; Speckens, Anne; Oostrom, Iris van

2014-07-30

Negative cognitive biases as well as stressful childhood events are well-known risk factors for depression. Few studies have compared the association of different types of biases and events with depression. The current study examined whether different cognitive biases and stressful childhood events variables were associated with depression and recurrence. Three types of childhood events were assessed in 83 never-depressed and 337 formerly depressed individuals: trauma within the family, trauma outside the family, and adverse events. Furthermore, after a sad mood induction procedure, participants executed a Dot Probe task (selective attentional bias), an Emotional Stroop task (attentional interference bias) and an incidental learning task (memory bias). The association of these measures with case status and recurrence status (one or multiple past episodes) was examined. Negative memory bias and traumatic childhood events within the family were associated with case status, whereas none of the bias measures or childhood events variables were associated with recurrence status. The results indicate that memory bias as well as the experience of aggression and/or abuse within the family during childhood are independently associated with depression. Biases and stressful childhood events did not offer differentiation between individuals with one or multiple past episodes. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Young Age at Diagnosis of Type 1 Diabetes Is Associated with the Development of Celiac Disease-Associated Antibodies in Children Living in Newfoundland and Labrador, Canada.

PubMed

Pall, Harpreet; Newhook, Leigh A; Aaron, Hillary; Curtis, Joseph; Randell, Ed

2015-10-14

The objectives of this study were to establish the prevalence of positive antibodies to endomysium (EMA) and tissue transglutaminase (tTG) in children with type 1 diabetes living in Newfoundland and Labrador (NL), and to examine clinical features associated with positive antibodies. Patients were recruited from the pediatric diabetes clinic. One hundred sixty-seven children with type 1 diabetes from the 280 children followed at the clinic were prospectively screened for celiac disease using EMA and tTG. The variables of Irish descent, age at onset of diabetes, duration of diabetes, sex, family history of celiac disease, hemoglobin A1C (A1C), ferritin, gastrointestinal symptoms, and body mass index were compiled for all patients. The group of patients with positive antibodies to EMA and/or tTG was compared to the group with negative antibodies. The prevalence of patients with positive antibodies to EMA and/or tTG was 16.8% (n = 28). One patient had also been previously diagnosed with symptomatic celiac disease. The two statistically significant variables with positive antibodies were an earlier age at onset of diabetes (Mann-Whitney U two-tailed test: mean difference 3.2 years, 95% CI 1.7-4.8 years, p < 0.0001) and longer duration of diabetes (Mann-Whitney U two-tailed test: mean difference 2.9 years, 95% CI 1.3-4.4 years, p < 0.0001). Irish descent was associated with positive antibodies but did not reach statistical significance. On logistic regression analysis performed with these three variables together, only age at onset of diabetes remained significant. There is a high prevalence of celiac disease-associated antibodies in children living in NL with type 1 diabetes. Unlike other clinical features, an earlier age at onset of diabetes was predictive for positive antibodies. As the majority of children with positive antibodies did not have signs or symptoms of celiac disease, routine screening for celiac disease in type 1 diabetes is recommended.

Biasogram: Visualization of Confounding Technical Bias in Gene Expression Data

PubMed Central

Krzystanek, Marcin; Szallasi, Zoltan; Eklund, Aron C.

2013-01-01

Gene expression profiles of clinical cohorts can be used to identify genes that are correlated with a clinical variable of interest such as patient outcome or response to a particular drug. However, expression measurements are susceptible to technical bias caused by variation in extraneous factors such as RNA quality and array hybridization conditions. If such technical bias is correlated with the clinical variable of interest, the likelihood of identifying false positive genes is increased. Here we describe a method to visualize an expression matrix as a projection of all genes onto a plane defined by a clinical variable and a technical nuisance variable. The resulting plot indicates the extent to which each gene is correlated with the clinical variable or the technical variable. We demonstrate this method by applying it to three clinical trial microarray data sets, one of which identified genes that may have been driven by a confounding technical variable. This approach can be used as a quality control step to identify data sets that are likely to yield false positive results. PMID:23613961

The contribution of natural variability to GCM bias: Can we effectively bias-correct climate projections?

NASA Astrophysics Data System (ADS)

McAfee, S. A.; DeLaFrance, A.

2017-12-01

Investigating the impacts of climate change often entails using projections from inherently imperfect general circulation models (GCMs) to drive models that simulate biophysical or societal systems in great detail. Error or bias in the GCM output is often assessed in relation to observations, and the projections are adjusted so that the output from impacts models can be compared to historical or observed conditions. Uncertainty in the projections is typically accommodated by running more than one future climate trajectory to account for differing emissions scenarios, model simulations, and natural variability. The current methods for dealing with error and uncertainty treat them as separate problems. In places where observed and/or simulated natural variability is large, however, it may not be possible to identify a consistent degree of bias in mean climate, blurring the lines between model error and projection uncertainty. Here we demonstrate substantial instability in mean monthly temperature bias across a suite of GCMs used in CMIP5. This instability is greatest in the highest latitudes during the cool season, where shifts from average temperatures below to above freezing could have profound impacts. In models with the greatest degree of bias instability, the timing of regional shifts from below to above average normal temperatures in a single climate projection can vary by about three decades, depending solely on the degree of bias assessed. This suggests that current bias correction methods based on comparison to 20- or 30-year normals may be inappropriate, particularly in the polar regions.

Neutralisation and binding of VHS virus by monovalent antibody fragments.

PubMed

Cupit, P M; Lorenzen, N; Strachan, G; Kemp, G J; Secombes, C J; Cunningham, C

2001-12-04

We have previously reported the cloning and characterisation of the heavy and light chain variable domain genes encoding three monoclonal antibodies (Mabs) that bind viral haemorrhagic septicaemia virus (VHSV). Two of these antibodies, 3F1H10 and 3F1A2 both neutralised the virus though 3F1A2 appeared to recognise a broader range of virus isolates. The variable domains of these two antibodies differ by only four residues (Lorenzen et al., 2000a. Fish Shellfish Immunol. 10, 129-142). To further study the mechanism of neutralisation, Fab fragments as well as a series of recombinant bacterial single chain antibody (scAb) fragments were generated from the three anti-VHSV Mabs and their variable domain genes, respectively. Fabs and scAbs derived from the neutralising Mabs were both able to neutralise the VHSV type 1 isolate DK-F1. In addition, a series of scAb fragments were produced using the 3F1H10 variable heavy (VH) chain and variable light (Vkappa) chain domains but containing, either alone or in dual combination, each of the four different residues present in 3F1A2. The dissociation constants of Mabs 3F1H10 and 3F1A2 and their respective Fab and scAb fragments were measured by BIAcore analysis and found to correlate with the capacity of each molecule to neutralise DK-F1. These investigations, together with computer assisted molecular analysis of the theoretical influence of each mutation on antigen binding, led to the identification of a single mutation at position 35a in the VH domain as having the most marked impact on viral neutralisation.

Estimating the price elasticity of beer: meta-analysis of data with heterogeneity, dependence, and publication bias.

PubMed

Nelson, Jon P

2014-01-01

Precise estimates of price elasticities are important for alcohol tax policy. Using meta-analysis, this paper corrects average beer elasticities for heterogeneity, dependence, and publication selection bias. A sample of 191 estimates is obtained from 114 primary studies. Simple and weighted means are reported. Dependence is addressed by restricting number of estimates per study, author-restricted samples, and author-specific variables. Publication bias is addressed using funnel graph, trim-and-fill, and Egger's intercept model. Heterogeneity and selection bias are examined jointly in meta-regressions containing moderator variables for econometric methodology, primary data, and precision of estimates. Results for fixed- and random-effects regressions are reported. Country-specific effects and sample time periods are unimportant, but several methodology variables help explain the dispersion of estimates. In models that correct for selection bias and heterogeneity, the average beer price elasticity is about -0.20, which is less elastic by 50% compared to values commonly used in alcohol tax policy simulations. Copyright © 2013 Elsevier B.V. All rights reserved.

Microarray image analysis: background estimation using quantile and morphological filters.

PubMed

Bengtsson, Anders; Bengtsson, Henrik

2006-02-28

In a microarray experiment the difference in expression between genes on the same slide is up to 103 fold or more. At low expression, even a small error in the estimate will have great influence on the final test and reference ratios. In addition to the true spot intensity the scanned signal consists of different kinds of noise referred to as background. In order to assess the true spot intensity background must be subtracted. The standard approach to estimate background intensities is to assume they are equal to the intensity levels between spots. In the literature, morphological opening is suggested to be one of the best methods for estimating background this way. This paper examines fundamental properties of rank and quantile filters, which include morphological filters at the extremes, with focus on their ability to estimate between-spot intensity levels. The bias and variance of these filter estimates are driven by the number of background pixels used and their distributions. A new rank-filter algorithm is implemented and compared to methods available in Spot by CSIRO and GenePix Pro by Axon Instruments. Spot's morphological opening has a mean bias between -47 and -248 compared to a bias between 2 and -2 for the rank filter and the variability of the morphological opening estimate is 3 times higher than for the rank filter. The mean bias of Spot's second method, morph.close.open, is between -5 and -16 and the variability is approximately the same as for morphological opening. The variability of GenePix Pro's region-based estimate is more than ten times higher than the variability of the rank-filter estimate and with slightly more bias. The large variability is because the size of the background window changes with spot size. To overcome this, a non-adaptive region-based method is implemented. Its bias and variability are comparable to that of the rank filter. The performance of more advanced rank filters is equal to the best region-based methods. However, in order to get unbiased estimates these filters have to be implemented with great care. The performance of morphological opening is in general poor with a substantial spatial-dependent bias.

Direct estimation and correction of bias from temporally variable non-stationary noise in a channelized Hotelling model observer.

PubMed

Fetterly, Kenneth A; Favazza, Christopher P

2016-08-07

Channelized Hotelling model observer (CHO) methods were developed to assess performance of an x-ray angiography system. The analytical methods included correction for known bias error due to finite sampling. Detectability indices ([Formula: see text]) corresponding to disk-shaped objects with diameters in the range 0.5-4 mm were calculated. Application of the CHO for variable detector target dose (DTD) in the range 6-240 nGy frame(-1) resulted in [Formula: see text] estimates which were as much as 2.9×  greater than expected of a quantum limited system. Over-estimation of [Formula: see text] was presumed to be a result of bias error due to temporally variable non-stationary noise. Statistical theory which allows for independent contributions of 'signal' from a test object (o) and temporally variable non-stationary noise (ns) was developed. The theory demonstrates that the biased [Formula: see text] is the sum of the detectability indices associated with the test object [Formula: see text] and non-stationary noise ([Formula: see text]). Given the nature of the imaging system and the experimental methods, [Formula: see text] cannot be directly determined independent of [Formula: see text]. However, methods to estimate [Formula: see text] independent of [Formula: see text] were developed. In accordance with the theory, [Formula: see text] was subtracted from experimental estimates of [Formula: see text], providing an unbiased estimate of [Formula: see text]. Estimates of [Formula: see text] exhibited trends consistent with expectations of an angiography system that is quantum limited for high DTD and compromised by detector electronic readout noise for low DTD conditions. Results suggest that these methods provide [Formula: see text] estimates which are accurate and precise for [Formula: see text]. Further, results demonstrated that the source of bias was detector electronic readout noise. In summary, this work presents theory and methods to test for the presence of bias in Hotelling model observers due to temporally variable non-stationary noise and correct this bias when the temporally variable non-stationary noise is independent and additive with respect to the test object signal.

Efficient generation of monoclonal antibodies from single rhesus macaque antibody secreting cells.

PubMed

Meng, Weixu; Li, Leike; Xiong, Wei; Fan, Xuejun; Deng, Hui; Bett, Andrew J; Chen, Zhifeng; Tang, Aimin; Cox, Kara S; Joyce, Joseph G; Freed, Daniel C; Thoryk, Elizabeth; Fu, Tong-Ming; Casimiro, Danilo R; Zhang, Ningyan; A Vora, Kalpit; An, Zhiqiang

2015-01-01

Nonhuman primates (NHPs) are used as a preclinical model for vaccine development, and the antibody profiles to experimental vaccines in NHPs can provide critical information for both vaccine design and translation to clinical efficacy. However, an efficient protocol for generating monoclonal antibodies from single antibody secreting cells of NHPs is currently lacking. In this study we established a robust protocol for cloning immunoglobulin (IG) variable domain genes from single rhesus macaque (Macaca mulatta) antibody secreting cells. A sorting strategy was developed using a panel of molecular markers (CD3, CD19, CD20, surface IgG, intracellular IgG, CD27, Ki67 and CD38) to identify the kinetics of B cell response after vaccination. Specific primers for the rhesus macaque IG genes were designed and validated using cDNA isolated from macaque peripheral blood mononuclear cells. Cloning efficiency was averaged at 90% for variable heavy (VH) and light (VL) domains, and 78.5% of the clones (n = 335) were matched VH and VL pairs. Sequence analysis revealed that diverse IGHV subgroups (for VH) and IGKV and IGLV subgroups (for VL) were represented in the cloned antibodies. The protocol was tested in a study using an experimental dengue vaccine candidate. About 26.6% of the monoclonal antibodies cloned from the vaccinated rhesus macaques react with the dengue vaccine antigens. These results validate the protocol for cloning monoclonal antibodies in response to vaccination from single macaque antibody secreting cells, which have general applicability for determining monoclonal antibody profiles in response to other immunogens or vaccine studies of interest in NHPs.

Effect of priming/booster immunisation protocols on immune response to canine parvovirus peptide induced by vaccination with a chimaeric plant virus construct.

PubMed

Nicholas, B L; Brennan, F R; Hamilton, W D O; Wakelin, D

2003-06-02

Expression of a 17-mer peptide sequence from canine parvovirus expressed on cowpea mosaic virus (CPMV) to form chimaeric virus particles (CVPs) creates vaccine antigens that elicit strong anti-peptide immune responses in mice. Systemic (subcutaneous, s.c.) immunisation and boosting with such CVP constructs produces IgG(2a) serum antibody responses, while mucosal (intranasal, i.n.) immunisation and boosting elicits intestinal IgA responses. Combinations of systemic and mucosal routes for priming and boosting immunisations were used to examine their influence on the level, type and location of immune response generated to one of these constructs (CVP-1). In all cases, s.c. administration, whether for immunisation or boosting, generated a Th1-biased response, reflected in a predominantly IgG(2a) serum antibody isotype and secretion of IFN-gamma from in vitro-stimulated lymphocytes. Serum antibody responses were greatest in animals primed and boosted subcutaneously, and least in mucosally vaccinated mice. The i.n. exposure also led to IFN-gamma release from in vitro-stimulated cells, but serum IgG(2a) was significantly elevated only in mice primed intranasally and boosted subcutaneously. Peptide- and wild-type CPMV-specific IgA responses in gut lavage fluid were greatest in animals exposed mucosally and least in those primed and boosted subcutaneously or primed subcutaneously and boosted orally. Lymphocytes from immunised mice proliferated in response to in vitro stimulation with CPMV but not with peptide. The predominant secretion of IFN-gamma from all immunising/boosting combinations indicates that the route of vaccination and challenge does not alter the Th1 bias of the response to CVP constructs. However, optimal serum and intestinal antibody responses were achieved by combining s.c. and i.n. administration.

Biases associated with genotype and sex in prediction of fat-free lean mass and carcass value in hogs.

PubMed

Hicks, C; Schinckel, A P; Forrest, J C; Akridge, J T; Wagner, J R; Chen, W

1998-09-01

Carcass and live measurements of 165 market hogs that represented seven genotypes were used to investigate genotype and sex biases associated with the prediction of fat-free lean mass (FFLM) and carcass value. Carcass value was determined as the sum of the product of weight of individual cuts and their average unit prices adjusted for slaughter and processing costs. Independent variables used in the prediction equations included carcass measurements, such as optical probe, midline ruler, ribbed carcass measurements, and electromagnetic scanning (EMSCAN), and live animal ultrasonic scanning. The effect of including subpopulation mean values of independent variables in the prediction equations for FFLM and carcass value was also investigated. Genotype and sex biases were found in equations in which midline backfat, ribbed carcass, EMSCAN, and live ultrasonic scanning were used as single technology sets of measurements. The prediction equations generally undervalued genotypes with above-average carcass value. Biases were reduced when measurements of combined technologies and mean adjusted variables were used. The FFLM and carcass value of gilts were underestimated, and they were overestimated of barrows. Equations that combined OP and EMSCAN technologies were the most accurate and least biased for both FFLM and carcass value. Equations that included carcass weight and midline last-rib backfat thickness measurements were the least accurate and most biased. Genotype and sex biases must be considered when predicting FFLM and carcass value.

Rater variables associated with ITER ratings.

PubMed

Paget, Michael; Wu, Caren; McIlwrick, Joann; Woloschuk, Wayne; Wright, Bruce; McLaughlin, Kevin

2013-10-01

Advocates of holistic assessment consider the ITER a more authentic way to assess performance. But this assessment format is subjective and, therefore, susceptible to rater bias. Here our objective was to study the association between rater variables and ITER ratings. In this observational study our participants were clerks at the University of Calgary and preceptors who completed online ITERs between February 2008 and July 2009. Our outcome variable was global rating on the ITER (rated 1-5), and we used a generalized estimating equation model to identify variables associated with this rating. Students were rated "above expected level" or "outstanding" on 66.4 % of 1050 online ITERs completed during the study period. Two rater variables attenuated ITER ratings: the log transformed time taken to complete the ITER [β = -0.06, 95 % confidence interval (-0.10, -0.02), p = 0.002], and the number of ITERs that a preceptor completed over the time period of the study [β = -0.008 (-0.02, -0.001), p = 0.02]. In this study we found evidence of leniency bias that resulted in two thirds of students being rated above expected level of performance. This leniency bias appeared to be attenuated by delay in ITER completion, and was also blunted in preceptors who rated more students. As all biases threaten the internal validity of the assessment process, further research is needed to confirm these and other sources of rater bias in ITER ratings, and to explore ways of limiting their impact.

Bias correction by use of errors-in-variables regression models in studies with K-X-ray fluorescence bone lead measurements.

PubMed

Lamadrid-Figueroa, Héctor; Téllez-Rojo, Martha M; Angeles, Gustavo; Hernández-Ávila, Mauricio; Hu, Howard

2011-01-01

In-vivo measurement of bone lead by means of K-X-ray fluorescence (KXRF) is the preferred biological marker of chronic exposure to lead. Unfortunately, considerable measurement error associated with KXRF estimations can introduce bias in estimates of the effect of bone lead when this variable is included as the exposure in a regression model. Estimates of uncertainty reported by the KXRF instrument reflect the variance of the measurement error and, although they can be used to correct the measurement error bias, they are seldom used in epidemiological statistical analyzes. Errors-in-variables regression (EIV) allows for correction of bias caused by measurement error in predictor variables, based on the knowledge of the reliability of such variables. The authors propose a way to obtain reliability coefficients for bone lead measurements from uncertainty data reported by the KXRF instrument and compare, by the use of Monte Carlo simulations, results obtained using EIV regression models vs. those obtained by the standard procedures. Results of the simulations show that Ordinary Least Square (OLS) regression models provide severely biased estimates of effect, and that EIV provides nearly unbiased estimates. Although EIV effect estimates are more imprecise, their mean squared error is much smaller than that of OLS estimates. In conclusion, EIV is a better alternative than OLS to estimate the effect of bone lead when measured by KXRF. Copyright © 2010 Elsevier Inc. All rights reserved.

Characterization of antibodies directed against the immunoglobulin light kappa chain variable chain region (VK) of hepatitis C virus-related type-II mixed cryoglobulinemia and B-cell proliferations.

PubMed

de Re, Valli; Simula, Maria Paola; Pavan, Alessandro; Garziera, Marica; Marin, Dolores; Dolcetti, Riccardo; de Vita, Salvatore; Sansonno, Domenico; Geremia, Silvano; Toffoli, Giuseppe

2009-09-01

Autoimmune type-II cryoglobulinemia (II-MC) is sustained by hepatitis C virus (HCV) infection and B-cell (oligo)clones. This is the reason why the disease may be considered an "indolent B-cell lymphoma (NHL)." B clones show a restricted use of immunoglobulin variable genes (BCR), in particular in the use of the variable kappa (VK)3-20/15 light chain, and show a homology between their BCR functional regions and those of autoimmune rheumatoid factors. We underlined the BCR unique repertoire with frequent rheumatoid factor activity also observed in other autoimmune disorders associated with NHL. The immunoglobulin idiotype is a clonal B-cell marker and an ideal target for immunotherapy. Five monoclonal antibodies were produced in our laboratory toward the VK3-20 of a subject with HCV infection and a II-MC-associated NHL. Epitope determination was performed using the epitope excision approach. Monoclonal antibody reactivity was tested in vitro in ELISA, Western blot, and cytofluorimetry. Data confirmed that a panel of antibodies, reactive against shared idiotypes, can be produced from patients with HCV-associated B-cell lymphoproliferative diseases, thus obviating the need to produce an anti-idiotype antibody for each patient.

Multivariate quantile mapping bias correction: an N-dimensional probability density function transform for climate model simulations of multiple variables

NASA Astrophysics Data System (ADS)

Cannon, Alex J.

2018-01-01

Most bias correction algorithms used in climatology, for example quantile mapping, are applied to univariate time series. They neglect the dependence between different variables. Those that are multivariate often correct only limited measures of joint dependence, such as Pearson or Spearman rank correlation. Here, an image processing technique designed to transfer colour information from one image to another—the N-dimensional probability density function transform—is adapted for use as a multivariate bias correction algorithm (MBCn) for climate model projections/predictions of multiple climate variables. MBCn is a multivariate generalization of quantile mapping that transfers all aspects of an observed continuous multivariate distribution to the corresponding multivariate distribution of variables from a climate model. When applied to climate model projections, changes in quantiles of each variable between the historical and projection period are also preserved. The MBCn algorithm is demonstrated on three case studies. First, the method is applied to an image processing example with characteristics that mimic a climate projection problem. Second, MBCn is used to correct a suite of 3-hourly surface meteorological variables from the Canadian Centre for Climate Modelling and Analysis Regional Climate Model (CanRCM4) across a North American domain. Components of the Canadian Forest Fire Weather Index (FWI) System, a complicated set of multivariate indices that characterizes the risk of wildfire, are then calculated and verified against observed values. Third, MBCn is used to correct biases in the spatial dependence structure of CanRCM4 precipitation fields. Results are compared against a univariate quantile mapping algorithm, which neglects the dependence between variables, and two multivariate bias correction algorithms, each of which corrects a different form of inter-variable correlation structure. MBCn outperforms these alternatives, often by a large margin, particularly for annual maxima of the FWI distribution and spatiotemporal autocorrelation of precipitation fields.

Identification of antigen-specific human monoclonal antibodies using high-throughput sequencing of the antibody repertoire.

PubMed

Liu, Ju; Li, Ruihua; Liu, Kun; Li, Liangliang; Zai, Xiaodong; Chi, Xiangyang; Fu, Ling; Xu, Junjie; Chen, Wei

2016-04-22

High-throughput sequencing of the antibody repertoire provides a large number of antibody variable region sequences that can be used to generate human monoclonal antibodies. However, current screening methods for identifying antigen-specific antibodies are inefficient. In the present study, we developed an antibody clone screening strategy based on clone dynamics and relative frequency, and used it to identify antigen-specific human monoclonal antibodies. Enzyme-linked immunosorbent assay showed that at least 52% of putative positive immunoglobulin heavy chains composed antigen-specific antibodies. Combining information on dynamics and relative frequency improved identification of positive clones and elimination of negative clones. and increase the credibility of putative positive clones. Therefore the screening strategy could simplify the subsequent experimental screening and may facilitate the generation of antigen-specific antibodies. Copyright © 2016 Elsevier Inc. All rights reserved.

Anti-neutrophil cytoplasmic antibodies in new-onset systemic lupus erythematosus.

PubMed

Su, Fang; Xiao, Weiguo; Yang, Pingting; Chen, Qingyan; Sun, Xiaojie; Li, Tienan

2017-01-01

The clinical significance of anti-neutrophil cytoplasmic antibodies in patients with new-onset systemic lupus erythematosus, especially in systemic disease accompanied by interstitial lung disease remains to be elucidated. This study was designed to investigate the role of anti-neutrophil cytoplasmic antibodies in new-onset systemic lupus erythematosus patients. A hundred and seven patients with new-onset SLE were enrolled. Presence of anti-neutrophil cytoplasmic antibodies in the sera was assessed by indirect immunofluorescence as well as enzyme linked immunosorbent assay against proteinase-3 and myeloperoxidase. Clinical features and laboratory parameters of patients were also recorded. All patients were subjected to chest X-ray, chest high-resolution computed tomography and pulmonary function test. Forty-five systemic lupus erythematosus patients (45/107, 42%) were seropositive for anti-neutrophil cytoplasmic antibodies. Compared with anti-neutrophil cytoplasmic antibodies-negative patients, the anti-neutrophil cytoplasmic antibodies-positive patients had significantly higher incidence of renal involvement, anemia, and Raynaud's phenomenon as well as decreased serum level of complement 3/complement 4 and elevated erythrocyte sedimentation rate. In addition, there was a positive correlation between serum anti-neutrophil cytoplasmic antibodies level and disease activity of systemic lupus erythematosus. Furthermore, prevalence of interstitial lung disease in the anti-neutrophil cytoplasmic antibodies -positive patients (25/45, 55.6%) was obviously higher than that in the anti-neutrophil cytoplasmic antibodies-negative patients (15/62, 24.2%). The sample size was limited and the criteria for screening new-onset systemic lupus erythematosus patients might produce bias. The level of anti-neutrophil cytoplasmic antibodies in new-onset systemic lupus erythematosus patients correlates positively with the disease activity and the prevalence of interstitial lung disease.

Gender Bias in the College Classroom: A Critical Review of the Literature and Implications for Future Research.

ERIC Educational Resources Information Center

Brady, Kristine L.; Eisler, Richard M.

1995-01-01

Summarizes eight studies on gender bias in college classrooms, examining the range of variables assessed and adequacy of evidence supporting the existence of bias. Inconsistent findings and significant methodological flaws in existing literature suggest that more empirical research is needed to investigate the existence of gender bias in college…

Decadal evaluation of regional climate, air quality, and their interactions over the continental US and their interactions using WRF/Chem version 3.6.1

NASA Astrophysics Data System (ADS)

Yahya, Khairunnisa; Wang, Kai; Campbell, Patrick; Glotfelty, Timothy; He, Jian; Zhang, Yang

2016-02-01

The Weather Research and Forecasting model with Chemistry (WRF/Chem) v3.6.1 with the Carbon Bond 2005 (CB05) gas-phase mechanism is evaluated for its first decadal application during 2001-2010 using the Representative Concentration Pathway 8.5 (RCP 8.5) emissions to assess its capability and appropriateness for long-term climatological simulations. The initial and boundary conditions are downscaled from the modified Community Earth System Model/Community Atmosphere Model (CESM/CAM5) v1.2.2. The meteorological initial and boundary conditions are bias-corrected using the National Center for Environmental Protection's Final (FNL) Operational Global Analysis data. Climatological evaluations are carried out for meteorological, chemical, and aerosol-cloud-radiation variables against data from surface networks and satellite retrievals. The model performs very well for the 2 m temperature (T2) for the 10-year period, with only a small cold bias of -0.3 °C. Biases in other meteorological variables including relative humidity at 2 m, wind speed at 10 m, and precipitation tend to be site- and season-specific; however, with the exception of T2, consistent annual biases exist for most of the years from 2001 to 2010. Ozone mixing ratios are slightly overpredicted at both urban and rural locations with a normalized mean bias (NMB) of 9.7 % but underpredicted at rural locations with an NMB of -8.8 %. PM2.5 concentrations are moderately overpredicted with an NMB of 23.3 % at rural sites but slightly underpredicted with an NMB of -10.8 % at urban/suburban sites. In general, the model performs relatively well for chemical and meteorological variables, and not as well for aerosol-cloud-radiation variables. Cloud-aerosol variables including aerosol optical depth, cloud water path, cloud optical thickness, and cloud droplet number concentration are generally underpredicted on average across the continental US. Overpredictions of several cloud variables over the eastern US result in underpredictions of radiation variables (such as net shortwave radiation - GSW - with a mean bias - MB - of -5.7 W m-2) and overpredictions of shortwave and longwave cloud forcing (MBs of ˜ 7 to 8 W m-2), which are important climate variables. While the current performance is deemed to be acceptable, improvements to the bias-correction method for CESM downscaling and the model parameterizations of cloud dynamics and thermodynamics, as well as aerosol-cloud interactions, can potentially improve model performance for long-term climate simulations.

Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies.

PubMed

Pfeifer, Nico; Walter, Hauke; Lengauer, Thomas

2014-10-01

Recently discovered broadly neutralizing antibodies have revitalized hopes of developing a universal vaccine against HIV-1. Mainly responsible for new infections are variants only using CCR5 for cell entry, whereas CXCR4-using variants can become dominant in later infection stages. We performed a statistical analysis on two different previously published data sets. The first data set was a panel of 199 diverse HIV-1 isolates for which IC50 neutralization titers were determined for the broadly neutralizing antibodies VRC01, VRC-PG04, PG9, and PG16. The second data set contained env sequences of viral variants extracted from HIV-1-infected humanized mice treated with the antibody PGT128 and from untreated control mice. For the panel of 199 diverse HIV-1 isolates, we found a statistically significant association between viral resistance to PG9 and PG16 and CXCR4 coreceptor usage (P = 0.0011 and P = 0.0010, respectively). Our analysis of viral variants from HIV-1-infected humanized mice under treatment with the broadly neutralizing antibody PGT128 indicated that certain antibodies might drive a viral population toward developing CXCR4 coreceptor usage capability (P = 0.0011 for the comparison between PGT128 and control measurement). These analyses highlight the importance of accounting for a possible coreceptor usage bias pertaining to the effectiveness of an HIV vaccine and to passive antibody transfer as therapeutic approach.

Design, analysis, and interpretation of field quality-control data for water-sampling projects

USGS Publications Warehouse

Mueller, David K.; Schertz, Terry L.; Martin, Jeffrey D.; Sandstrom, Mark W.

2015-01-01

The report provides extensive information about statistical methods used to analyze quality-control data in order to estimate potential bias and variability in environmental data. These methods include construction of confidence intervals on various statistical measures, such as the mean, percentiles and percentages, and standard deviation. The methods are used to compare quality-control results with the larger set of environmental data in order to determine whether the effects of bias and variability might interfere with interpretation of these data. Examples from published reports are presented to illustrate how the methods are applied, how bias and variability are reported, and how the interpretation of environmental data can be qualified based on the quality-control analysis.

Construction and characterization of a highly reactive chicken-derived single-chain variable fragment (scFv) antibody against Staphylococcus aureus developed with the T7 phage display system.

PubMed

Li, Jingquan; Xu, Yongping; Wang, Xitao; Li, Yuan; Wang, Lili; Li, Xiaoyu

2016-06-01

The purpose of this study was to construct a single-chain variable fragment (scFv) antibody from chicken egg yolk immunoglobulin (IgY) by means of genetic engineering and subsequent panning for a specific antibody against Staphylococcus aureus. We amplified the scFv using blood and spleen obtained from 100-day-old Roman chickens immunized with inactivated S. aureus and subsequently constructed a T7 phage display antibody library using phage display technology. Four non-repeated blood scFv and 6 spleen scFv were obtained following 3 rounds of panning of the T7 phage display antibody library, enzyme-linked immunosorbent assay and sequencing. These 10 scFv were cloned into the prokaryotic expression vector pCold I with expression induced at a low temperature. Four soluble proteins were obtained. Among them, soluble protein SFV6 derived from the spleen showed good reactivity against S. aureus using indirect ELISA and produced a particularly strong antibacterial effect in vitro. We were successful in isolating a highly specific scFv antibody against S. aureus from the spleen phage display library. This study provides a simple and rapid method for the quick preparation of a large number of antibodies against S. aureus and provides the foundation for the positioning of antibodies in the organism and the study of the antibacterial mechanism through which the antibody functions. Copyright © 2016 Elsevier B.V. All rights reserved.

Cloning, bacterial expression and crystallization of Fv antibody fragments

NASA Astrophysics Data System (ADS)

E´, Jean-Luc; Boulot, Ginette; Chitarra, V´ronique; Riottot, Marie-Madeleine; Souchon, H´le`ne; Houdusse, Anne; Bentley, Graham A.; Narayana Bhat, T.; Spinelli, Silvia; Poljak, Roberto J.

1992-08-01

The variable Fv fragments of antibodies, cloned in recombinant plasmids, can be expressed in bacteria as functional proteins having immunochemical properties which are very similar or identical with those of the corresponding parts of the parent eukaryotic antibodies. They offer new possibilities for the study of antibody-antigen interactions since the crystals of Fv fragments and of their complexes with antigen reported here diffract X-rays to a higher resolution that those obtained with the cognate Fab fragments. The Fv approach should facilitate the structural study of the combining site of antibodies and the further characterization of antigen-antibody interactions by site-directed mutagenesis experiments.

Increased Antibody Affinity Confers Broad In Vitro Protection against Escape Mutants of Severe Acute Respiratory Syndrome Coronavirus

PubMed Central

Rani, Mridula; Bolles, Meagan; Donaldson, Eric F.; Van Blarcom, Thomas; Baric, Ralph; Iverson, Brent

2012-01-01

Even though the effect of antibody affinity on neutralization potency is well documented, surprisingly, its impact on neutralization breadth and escape has not been systematically determined. Here, random mutagenesis and DNA shuffling of the single-chain variable fragment of the neutralizing antibody 80R followed by bacterial display screening using anchored periplasmic expression (APEx) were used to generate a number of higher-affinity variants of the severe acute respiratory syndrome coronavirus (SARS-CoV)-neutralizing antibody 80R with equilibrium dissociation constants (KD) as low as 37 pM, a >270-fold improvement relative to that of the parental 80R single-chain variable fragment (scFv). As expected, antigen affinity was shown to correlate directly with neutralization potency toward the icUrbani strain of SARS-CoV. Additionally, the highest-affinity antibody fragment displayed 10-fold-increased broad neutralization in vitro and completely protected against several SARS-CoV strains containing substitutions associated with antibody escape. Importantly, higher affinity also led to the suppression of viral escape mutants in vitro. Escape from the highest-affinity variant required reduced selective pressure and multiple substitutions in the binding epitope. Collectively, these results support the hypothesis that engineered antibodies with picomolar dissociation constants for a neutralizing epitope can confer escape-resistant protection. PMID:22696652

Detection of Pituitary Antibodies by Immunofluorescence: Approach and Results in Patients With Pituitary Diseases

PubMed Central

Ricciuti, Adriana; De Remigis, Alessandra; Landek-Salgado, Melissa A.; De Vincentiis, Ludovica; Guaraldi, Federica; Lupi, Isabella; Iwama, Shintaro; Wand, Gary S.; Salvatori, Roberto

2014-01-01

Context: Pituitary antibodies have been measured mainly to identify patients whose disease is caused or sustained by pituitary-specific autoimmunity. Although reported in over 100 publications, they have yielded variable results and are thus considered of limited clinical utility. Objectives: Our objectives were to analyze all publications reporting pituitary antibodies by immunofluorescence for detecting the major sources of variability, to experimentally test these sources and devise an optimized immunofluorescence protocol, and to assess prevalence and significance of pituitary antibodies in patients with pituitary diseases. Study Design and Outcome Measures: We first evaluated the effect of pituitary gland species, section fixation, autofluorescence quenching, blockade of unwanted antibody binding, and use of purified IgG on the performance of this antibody assay. We then measured cross-sectionally the prevalence of pituitary antibodies in 390 pituitary cases and 60 healthy controls, expressing results as present or absent and according to the (granular, diffuse, perinuclear, or mixed) staining pattern. Results: Human pituitary was the best substrate to detect pituitary antibodies and yielded an optimal signal-to-noise ratio when treated with Sudan black B to reduce autofluorescence. Pituitary antibodies were more common in cases (95 of 390, 24%) than controls (3 of 60, 5%, P = .001) but did not discriminate among pituitary diseases when reported dichotomously. However, when expressed according to their cytosolic staining, a granular pattern was highly predictive of pituitary autoimmunity (P < .0001). Conclusion: We report a comprehensive study of pituitary antibodies by immunofluorescence and provide a method and an interpretation scheme that should be useful for identifying and monitoring patients with pituitary autoimmunity. PMID:24606106

Vaccine induced antibodies to the first variable loop of human immunodeficiency virus type 1 gp120, mediate antibody-dependent virus inhibition in macaques.

PubMed

Bialuk, Izabela; Whitney, Stephen; Andresen, Vibeke; Florese, Ruth H; Nacsa, Janos; Cecchinato, Valentina; Valeri, Valerio W; Heraud, Jean-Michel; Gordon, Shari; Parks, Robyn Washington; Montefiori, David C; Venzon, David; Demberg, Thorsten; Guroff, Marjorie Robert-; Landucci, Gary; Forthal, Donald N; Franchini, Genoveffa

2011-12-09

The role of antibodies directed against the hyper variable envelope region V1 of human immunodeficiency virus type 1 (HIV-1), has not been thoroughly studied. We show that a vaccine able to elicit strain-specific non-neutralizing antibodies to this region of gp120 is associated with control of highly pathogenic chimeric SHIV(89.6P) replication in rhesus macaques. The vaccinated animal that had the highest titers of antibodies to the amino terminus portion of V1, prior to challenge, had secondary antibody responses that mediated cell killing by antibody-dependent cellular cytotoxicity (ADCC), as early as 2 weeks after infection and inhibited viral replication by antibody-dependent cell-mediated virus inhibition (ADCVI), by 4 weeks after infection. There was a significant inverse correlation between virus level and binding antibody titers to the envelope protein, (R=-0.83, p=0.015), and ADCVI (R=-0.84 p=0.044). Genotyping of plasma virus demonstrated in vivo selection of three SHIV(89.6P) variants with changes in potential N-linked glycosylation sites in V1. We found a significant inverse correlation between virus levels and titers of antibodies that mediated ADCVI against all the identified V1 virus variants. A significant inverse correlation was also found between neutralizing antibody titers to SHIV(89.6) and virus levels (R=-0.72 p=0.0050). However, passive inoculation of purified immunoglobulin from animal M316, the macaque that best controlled virus, to a naïve macaque, resulted in a low serum neutralizing antibodies and low ADCVI activity that failed to protect from SHIV(89.6P) challenge. Collectively, while our data suggest that anti-envelope antibodies with neutralizing and non-neutralizing Fc(R-dependent activities may be important in the control of SHIV replication, they also demonstrate that low levels of these antibodies alone are not sufficient to protect from infection. Published by Elsevier Ltd.

Vaccine Induced Antibodies to the First Variable Loop of Human Immunodeficiency Virus Type 1 gp120, Mediate Antibody-Dependent Virus Inhibition in Macaques

PubMed Central

Bialuk, Izabela; Whitney, Stephen; Andresen, Vibeke; Florese, Ruth H.; Nacsa, Janos; Cecchinato, Valentina; Valeri, Valerio W.; Heraud, Jean-Michel; Gordon, Shari; Parks, Robyn Washington; Montefiori, David C.; Venzon, David; Demberg, Thorsten; Guroff, Marjorie Robert; Landucci, Gary; Forthal, Donald N.; Franchini, Genoveffa

2011-01-01

The role of antibodies directed against the hyper variable envelope region V1 of human immunodeficiency virus type 1 (HIV-1), has not been thoroughly studied. We show that a vaccine able to elicit strain-specific non-neutralizing antibodies to this region of gp120 is associated with control of highly pathogenic chimeric SHIV89.6P replication in rhesus macaques. The vaccinated animal that had the highest titers of antibodies to the amino terminus portion of V1, prior to challenge, had secondary antibody responses that mediated cell killing by antibody-dependent cellular cytotoxicity (ADCC), as early as two weeks after infection and inhibited viral replication by antibody-dependent cell-mediated virus inhibition (ADCVI), by four weeks after infection. There was a significant inverse correlation between virus level and binding antibody titers to the envelope protein, (R = -0.83, p 0.015), and ADCVI (R = -0.84 p=0.044). Genotyping of plasma virus demonstrated in vivo selection of three SHIV89.6P variants with changes in potential N-linked glycosylation sites in V1. We found a significant inverse correlation between virus levels and titers of antibodies that mediated ADCVI against all the identified V1 virus variants. A significant inverse correlation was also found between neutralizing antibody titers to SHIV89.6 and virus levels (R = -0.72 p =0.0050). However, passive inoculation of purified immunoglobulin from animal M316, the macaque that best controlled virus, to a naïve macaque, resulted in a low serum neutralizing antibodies and low ADCVI activity that failed to protect from SHIV89.6P challenge. Collectively, while our data suggest that anti-envelope antibodies with neutralizing and non-neutralizing FcγR-dependent activities may be important in the control of SHIV replication, they also demonstrate that low levels of these antibodies alone are not sufficient to protect from infection. PMID:22037204

Measuring temporal stability of positron emission tomography standardized uptake value bias using long-lived sources in a multicenter network.

PubMed

Byrd, Darrin; Christopfel, Rebecca; Arabasz, Grae; Catana, Ciprian; Karp, Joel; Lodge, Martin A; Laymon, Charles; Moros, Eduardo G; Budzevich, Mikalai; Nehmeh, Sadek; Scheuermann, Joshua; Sunderland, John; Zhang, Jun; Kinahan, Paul

2018-01-01

Positron emission tomography (PET) is a quantitative imaging modality, but the computation of standardized uptake values (SUVs) requires several instruments to be correctly calibrated. Variability in the calibration process may lead to unreliable quantitation. Sealed source kits containing traceable amounts of [Formula: see text] were used to measure signal stability for 19 PET scanners at nine hospitals in the National Cancer Institute's Quantitative Imaging Network. Repeated measurements of the sources were performed on PET scanners and in dose calibrators. The measured scanner and dose calibrator signal biases were used to compute the bias in SUVs at multiple time points for each site over a 14-month period. Estimation of absolute SUV accuracy was confounded by bias from the solid phantoms' physical properties. On average, the intrascanner coefficient of variation for SUV measurements was 3.5%. Over the entire length of the study, single-scanner SUV values varied over a range of 11%. Dose calibrator bias was not correlated with scanner bias. Calibration factors from the image metadata were nearly as variable as scanner signal, and were correlated with signal for many scanners. SUVs often showed low intrascanner variability between successive measurements but were also prone to shifts in apparent bias, possibly in part due to scanner recalibrations that are part of regular scanner quality control. Biases of key factors in the computation of SUVs were not correlated and their temporal variations did not cancel out of the computation. Long-lived sources and image metadata may provide a check on the recalibration process.

Quantitative bioanalysis of antibody-conjugated payload in monkey plasma using a hybrid immuno-capture LC-MS/MS approach: Assay development, validation, and a case study.

PubMed

Liu, Ang; Kozhich, Alexander; Passmore, David; Gu, Huidong; Wong, Richard; Zambito, Frank; Rangan, Vangipuram S; Myler, Heather; Aubry, Anne-Françoise; Arnold, Mark E; Wang, Jian

2015-10-01

Antibody drug conjugates (ADCs) are complex molecules composed of two pharmacologically distinct components, the cytotoxic payload and the antibody. The measurement of the payload molecules that are attached to the antibody in vivo is important for the evaluation of the safety and efficacy of ADCs, and can also provide distinct information compared to the antibody-related analytes. However, analyzing the antibody-conjugated payload is challenging and in some cases may not be feasible. The in vivo change in drug antibody ratio (DAR), due to deconjugation, biotransformation or other clearance phenomena, generates unique and additional challenges for ADC analysis in biological samples. Here, we report a novel hybrid approach with immuno-capture of the ADC, payload cleavage by specific enzyme, and LC-MS/MS of the cleaved payload to quantitatively measure the concentration of payload molecules still attached to the antibody via linker in plasma. The ADC reference material used for the calibration curve is not likely to be identical to the ADC measured in study samples due to the change in DAR distribution over the PK time course. The assay clearly demonstrated that there was no bias in the measurement of antibody-conjugated payload for ADC with varying DAR, which thus allowed accurate quantification even when the DAR distribution dynamically changes in vivo. This hybrid assay was fully validated based on a combination of requirements for both chromatographic and ligand binding methods, and was successfully applied to support a GLP safety study in monkeys. Copyright © 2015 Elsevier B.V. All rights reserved.

Intrapersonal Variability in Negative Affect as a Moderator of Accuracy and Bias in Interpersonal Perception.

PubMed

Sadikaj, Gentiana; Moskowitz, D S; Zuroff, David C

2015-08-01

High intrapersonal variability has frequently been found to be related to poor personal and interpersonal outcomes. Little research has examined processes by which intrapersonal variability influences outcomes. This study explored the relation of intrapersonal variability in negative affect (negative affect flux) to accuracy and bias in the perception of a romantic partner's quarrelsome behavior. A sample of 93 cohabiting couples participated in a study using an event-contingent recording (ECR) methodology in which they reported their negative affect, quarrelsome behavior, and perception of their partner's quarrelsome behavior in interactions with each other during a 20-day period. Negative affect flux was operationalized as the within-person standard deviation of negative affect scores across couple interactions. Findings suggested that participants were both accurate in tracking changes in their partner's quarrelsome behavior and biased in assuming their partner's quarrelsome behavior mirrored their own quarrelsome behavior. Negative affect flux moderated both accuracy and bias of assumed similarity such that participants with higher flux manifested both greater tracking accuracy and larger bias of assumed similarity. Negative affect flux may be related to enhanced vigilance to close others' negative behavior, which may explain higher tracking accuracy and propensity to rely on a person's own negative behavior as a means of judging others' negative behavior. These processes may augment these individuals' negative interpersonal behavior, enhance cycles of negative social interactions, and lead to poor intrapersonal and interpersonal outcomes.

Studies of thermostability in Camelus bactrianus (Bactrian camel) single-domain antibody specific for the mutant epidermal-growth-factor receptor expressed by Pichia.

PubMed

Omidfar, Kobra; Rasaee, Mohhamad Javad; Kashanian, Soheila; Paknejad, Malieheh; Bathaie, Zahra

2007-01-01

Camelids have a unique immune system capable of producing heavy-chain antibodies lacking the light chains and CH1 (constant heavy-chain domain 1). It has been shown that, in contrast with conventional antibody fragments, the variable domains of these heavy-chain antibodies are functional at or after exposure to high temperatures. In the present study, the VHH (variable domain of heavy-chain antibody) camel antibody was subcloned into vector Ppiczc and expressed in Pichia pastoris. ORB1-83 VHH antibody recognizes the external domain of the mutant EGFR [EGF (epidermal growth factor) receptor], EGFR VIII. This tumour-specific antigen is ligand-independent, contains a constitutively active tyrosine kinase domain and has been shown to be present in a number of human malignancies. We report here that, although expression from P. pastoris resulted in a significantly increased level of expression of the anti-EGFR VIII VHH antibodies compared with Escherichia coli [Omidfar, Rasaee, Modjtahedi, Forouzandeh, Taghikhani, Bakhtiari, Paknejad and Kashanian (2004) Tumor Biol. 25, 179-187; Omidfar, Rasaee, Modjtahedi, Forouzandeh, Taghikhani and Golmakany (2004) Tumor Biol. 25, 296-305], this antibody selectively bound to the EGFR VIII peptide and reacted specifically with the immunoaffinity-purified antigen from non-small-cell lung cancer. Furthermore, thermal denaturation stability and CD spectra analysis of the Camelus bactrianus (Bactrian camel) VHH and heavy-chain antibodies at different temperature proved reversibility and binding activity after heat denaturation. Our results indicate that the P. pastoris expression system may be useful for the expression of camel single domain antibody and the ability of the expressed protein to reversibly melt without aggregation, allowing it to regain binding activity after heat denaturation.

Estimating loss of Brucella abortus antibodies from age-specific serological data in elk

USGS Publications Warehouse

Benavides, J. A.; Caillaud, D.; Scurlock, B. M.; Maichak, E. J.; Edwards, W.H.; Cross, Paul C.

2017-01-01

Serological data are one of the primary sources of information for disease monitoring in wildlife. However, the duration of the seropositive status of exposed individuals is almost always unknown for many free-ranging host species. Directly estimating rates of antibody loss typically requires difficult longitudinal sampling of individuals following seroconversion. Instead, we propose a Bayesian statistical approach linking age and serological data to a mechanistic epidemiological model to infer brucellosis infection, the probability of antibody loss, and recovery rates of elk (Cervus canadensis) in the Greater Yellowstone Ecosystem. We found that seroprevalence declined above the age of ten, with no evidence of disease-induced mortality. The probability of antibody loss was estimated to be 0.70 per year after a five-year period of seropositivity and the basic reproduction number for brucellosis to 2.13. Our results suggest that individuals are unlikely to become re-infected because models with this mechanism were unable to reproduce a significant decline in seroprevalence in older individuals. This study highlights the possible implications of antibody loss, which could bias our estimation of critical epidemiological parameters for wildlife disease management based on serological data.

Dual-color Proteomic Profiling of Complex Samples with a Microarray of 810 Cancer-related Antibodies*

PubMed Central

Schröder, Christoph; Jacob, Anette; Tonack, Sarah; Radon, Tomasz P.; Sill, Martin; Zucknick, Manuela; Rüffer, Sven; Costello, Eithne; Neoptolemos, John P.; Crnogorac-Jurcevic, Tatjana; Bauer, Andrea; Fellenberg, Kurt; Hoheisel, Jörg D.

2010-01-01

Antibody microarrays have the potential to enable comprehensive proteomic analysis of small amounts of sample material. Here, protocols are presented for the production, quality assessment, and reproducible application of antibody microarrays in a two-color mode with an array of 1,800 features, representing 810 antibodies that were directed at 741 cancer-related proteins. In addition to measures of array quality, we implemented indicators for the accuracy and significance of dual-color detection. Dual-color measurements outperform a single-color approach concerning assay reproducibility and discriminative power. In the analysis of serum samples, depletion of high-abundance proteins did not improve technical assay quality. On the contrary, depletion introduced a strong bias in protein representation. In an initial study, we demonstrated the applicability of the protocols to proteins derived from urine samples. We identified differences between urine samples from pancreatic cancer patients and healthy subjects and between sexes. This study demonstrates that biomedically relevant data can be produced. As demonstrated by the thorough quality analysis, the dual-color antibody array approach proved to be competitive with other proteomic techniques and comparable in performance to transcriptional microarray analyses. PMID:20164060

Experimental Rhodococcus equi and equine infectious anemia virus DNA vaccination in adult and neonatal horses: Effect of IL-12, dose, and route

PubMed Central

Mealey, R.H.; Stone, D.M.; Hines, M.T.; Alperin, D.C.; Littke, M.H.; Leib, S.R.; Leach, S.E.; Hines, S.A.

2012-01-01

Improving the ability of DNA-based vaccines to induce potent Type1/Th1 responses against intracellular pathogens in large outbred species is essential. Rhodoccocus equi and equine infectious anemia virus (EIAV) are two naturally occurring equine pathogens that also serve as important large animal models of neonatal immunity and lentiviral immune control. Neonates present a unique challenge for immunization due to their diminished immunologic capabilities and apparent Th2 bias. In an effort to augment R. equi- and EIAV-specific Th1 responses induced by DNA vaccination, we hypothesized that a dual promoter plasmid encoding recombinant equine IL-12 (rEqIL-12) would function as a molecular adjuvant. In adult horses, DNA vaccines induced R. equi- and EIAV-specific antibody and lymphoproliferative responses, and EIAV-specific CTL and tetramer-positive CD8+ T lymphocytes. These responses were not enhanced by the rEqIL-12 plasmid. In neonatal foals, DNA immunization induced EIAV-specific antibody and lymphoproliferative responses, but not CTL. The R. equi vapA vaccine was poorly immunogenic in foals even when co-administered with the IL-12 plasmid. It was concluded that DNA immunization was capable of inducing Th1 responses in horses; dose and route were significant variables, but rEqIL-12 was not an effective molecular adjuvant. Additional work is needed to optimize DNA vaccine-induced Th1 responses in horses, especially in neonates. PMID:17889970

Dynamic modulation of decision biases by brainstem arousal systems.

PubMed

de Gee, Jan Willem; Colizoli, Olympia; Kloosterman, Niels A; Knapen, Tomas; Nieuwenhuis, Sander; Donner, Tobias H

2017-04-11

Decision-makers often arrive at different choices when faced with repeated presentations of the same evidence. Variability of behavior is commonly attributed to noise in the brain's decision-making machinery. We hypothesized that phasic responses of brainstem arousal systems are a significant source of this variability. We tracked pupil responses (a proxy of phasic arousal) during sensory-motor decisions in humans, across different sensory modalities and task protocols. Large pupil responses generally predicted a reduction in decision bias. Using fMRI, we showed that the pupil-linked bias reduction was (i) accompanied by a modulation of choice-encoding pattern signals in parietal and prefrontal cortex and (ii) predicted by phasic, pupil-linked responses of a number of neuromodulatory brainstem centers involved in the control of cortical arousal state, including the noradrenergic locus coeruleus. We conclude that phasic arousal suppresses decision bias on a trial-by-trial basis, thus accounting for a significant component of the variability of choice behavior.

Dynamic modulation of decision biases by brainstem arousal systems

PubMed Central

de Gee, Jan Willem; Colizoli, Olympia; Kloosterman, Niels A; Knapen, Tomas; Nieuwenhuis, Sander; Donner, Tobias H

2017-01-01

Decision-makers often arrive at different choices when faced with repeated presentations of the same evidence. Variability of behavior is commonly attributed to noise in the brain’s decision-making machinery. We hypothesized that phasic responses of brainstem arousal systems are a significant source of this variability. We tracked pupil responses (a proxy of phasic arousal) during sensory-motor decisions in humans, across different sensory modalities and task protocols. Large pupil responses generally predicted a reduction in decision bias. Using fMRI, we showed that the pupil-linked bias reduction was (i) accompanied by a modulation of choice-encoding pattern signals in parietal and prefrontal cortex and (ii) predicted by phasic, pupil-linked responses of a number of neuromodulatory brainstem centers involved in the control of cortical arousal state, including the noradrenergic locus coeruleus. We conclude that phasic arousal suppresses decision bias on a trial-by-trial basis, thus accounting for a significant component of the variability of choice behavior. DOI: http://dx.doi.org/10.7554/eLife.23232.001 PMID:28383284

Predictive Inference Using Latent Variables with Covariates*

PubMed Central

Schofield, Lynne Steuerle; Junker, Brian; Taylor, Lowell J.; Black, Dan A.

2014-01-01

Plausible Values (PVs) are a standard multiple imputation tool for analysis of large education survey data that measures latent proficiency variables. When latent proficiency is the dependent variable, we reconsider the standard institutionally-generated PV methodology and find it applies with greater generality than shown previously. When latent proficiency is an independent variable, we show that the standard institutional PV methodology produces biased inference because the institutional conditioning model places restrictions on the form of the secondary analysts’ model. We offer an alternative approach that avoids these biases based on the mixed effects structural equations (MESE) model of Schofield (2008). PMID:25231627

Performance of nonlinear mixed effects models in the presence of informative dropout.

PubMed

Björnsson, Marcus A; Friberg, Lena E; Simonsson, Ulrika S H

2015-01-01

Informative dropout can lead to bias in statistical analyses if not handled appropriately. The objective of this simulation study was to investigate the performance of nonlinear mixed effects models with regard to bias and precision, with and without handling informative dropout. An efficacy variable and dropout depending on that efficacy variable were simulated and model parameters were reestimated, with or without including a dropout model. The Laplace and FOCE-I estimation methods in NONMEM 7, and the stochastic simulations and estimations (SSE) functionality in PsN, were used in the analysis. For the base scenario, bias was low, less than 5% for all fixed effects parameters, when a dropout model was used in the estimations. When a dropout model was not included, bias increased up to 8% for the Laplace method and up to 21% if the FOCE-I estimation method was applied. The bias increased with decreasing number of observations per subject, increasing placebo effect and increasing dropout rate, but was relatively unaffected by the number of subjects in the study. This study illustrates that ignoring informative dropout can lead to biased parameters in nonlinear mixed effects modeling, but even in cases with few observations or high dropout rate, the bias is relatively low and only translates into small effects on predictions of the underlying effect variable. A dropout model is, however, crucial in the presence of informative dropout in order to make realistic simulations of trial outcomes.

Comparative Evaluation of Accuracy of Pulse Oximeters and Factors Affecting Their Performance in a Tertiary Intensive Care Unit

PubMed Central

Sahi, Malvinder Singh; Mahawar, Bablesh; Rajpurohit, Sajjan

2017-01-01

Introduction Pulse oximetry is a widely used tool, unfortunately there is a paucity of data investigating its accuracy in Intensive Care Units (ICU) and if they are able to meet mandated FDA criteria as claimed by them in critically ill patients. Aim To assess bias, precision and accuracy of pulse oximeters used in ICU and factors affecting them. Materials and Methods A prospective cohort study, including 129 patients admitted to the ICU of a tertiary referral centre. Pulse oximetry and blood gas were done simultaneously. Pulse oximetry was done using two pulse oximetres: Nonin and Philips. All physiological variables like haemoglobin, lactate, use of vasopressors and blood pressure were recorded. Bland Altman curves were constructed to determine bias and limits of agreement. Effect of physiological variables on bias and difference between performance characteristics of bias was determined using SPSS. Results Pulse oximetry overestimated arterial oxygen saturation (SaO2) by 1.44%. There was negative correlation between bias and SaO2 (r=-0.32) and positive correlation with lactate (r=0.16). The Philips pulse oximeter had significant higher bias and variability than Nonin pulse oximeter. (2.49±2.99 versus 0.46±1.68, mean difference = 1.98, 95% C.I. = 1.53 – 2.43, p-value <0.001). Conclusion Pulse oximetry overestimates SaO2. Bias tends to increase with rising lactate and hypoxia. There is heterogeneity in performance of various pulse oximetry devices in ICU. PMID:28764215

Comparative Evaluation of Accuracy of Pulse Oximeters and Factors Affecting Their Performance in a Tertiary Intensive Care Unit.

PubMed

Singh, Anupam Kumar; Sahi, Malvinder Singh; Mahawar, Bablesh; Rajpurohit, Sajjan

2017-06-01

Pulse oximetry is a widely used tool, unfortunately there is a paucity of data investigating its accuracy in Intensive Care Units (ICU) and if they are able to meet mandated FDA criteria as claimed by them in critically ill patients. To assess bias, precision and accuracy of pulse oximeters used in ICU and factors affecting them. A prospective cohort study, including 129 patients admitted to the ICU of a tertiary referral centre. Pulse oximetry and blood gas were done simultaneously. Pulse oximetry was done using two pulse oximetres: Nonin and Philips. All physiological variables like haemoglobin, lactate, use of vasopressors and blood pressure were recorded. Bland Altman curves were constructed to determine bias and limits of agreement. Effect of physiological variables on bias and difference between performance characteristics of bias was determined using SPSS. Pulse oximetry overestimated arterial oxygen saturation (SaO 2 ) by 1.44%. There was negative correlation between bias and SaO 2 (r=-0.32) and positive correlation with lactate (r=0.16). The Philips pulse oximeter had significant higher bias and variability than Nonin pulse oximeter. (2.49±2.99 versus 0.46±1.68, mean difference = 1.98, 95% C.I. = 1.53 - 2.43, p-value <0.001). Pulse oximetry overestimates SaO 2 . Bias tends to increase with rising lactate and hypoxia. There is heterogeneity in performance of various pulse oximetry devices in ICU.

Generation and analysis of the improved human HAL9/10 antibody phage display libraries.

PubMed

Kügler, Jonas; Wilke, Sonja; Meier, Doris; Tomszak, Florian; Frenzel, André; Schirrmann, Thomas; Dübel, Stefan; Garritsen, Henk; Hock, Björn; Toleikis, Lars; Schütte, Mark; Hust, Michael

2015-02-19

Antibody phage display is a proven key technology that allows the generation of human antibodies for diagnostics and therapy. From naive antibody gene libraries - in theory - antibodies against any target can be selected. Here we describe the design, construction and characterization of an optimized antibody phage display library. The naive antibody gene libraries HAL9 and HAL10, with a combined theoretical diversity of 1.5×10(10) independent clones, were constructed from 98 healthy donors using improved phage display vectors. In detail, most common phagemids employed for antibody phage display are using a combined His/Myc tag for detection and purification. We show that changing the tag order to Myc/His improved the production of soluble antibodies, but did not affect antibody phage display. For several published antibody libraries, the selected number of kappa scFvs were lower compared to lambda scFvs, probably due to a lower kappa scFv or Fab expression rate. Deletion of a phenylalanine at the end of the CL linker sequence in our new phagemid design increased scFv production rate and frequency of selected kappa antibodies significantly. The HAL libraries and 834 antibodies selected against 121 targets were analyzed regarding the used germline V-genes, used V-gene combinations and CDR-H3/-L3 length and composition. The amino acid diversity and distribution in the CDR-H3 of the initial library was retrieved in the CDR-H3 of selected antibodies showing that all CDR-H3 amino acids occurring in the human antibody repertoire can be functionally used and is not biased by E. coli expression or phage selection. Further, the data underline the importance of CDR length variations. The highly diverse universal antibody gene libraries HAL9/10 were constructed using an optimized scFv phagemid vector design. Analysis of selected antibodies revealed that the complete amino acid diversity in the CDR-H3 was also found in selected scFvs showing the functionality of the naive CDR-H3 diversity.

Single- and Dual-Process Models of Biased Contingency Detection.

PubMed

Vadillo, Miguel A; Blanco, Fernando; Yarritu, Ion; Matute, Helena

2016-01-01

Decades of research in causal and contingency learning show that people's estimations of the degree of contingency between two events are easily biased by the relative probabilities of those two events. If two events co-occur frequently, then people tend to overestimate the strength of the contingency between them. Traditionally, these biases have been explained in terms of relatively simple single-process models of learning and reasoning. However, more recently some authors have found that these biases do not appear in all dependent variables and have proposed dual-process models to explain these dissociations between variables. In the present paper we review the evidence for dissociations supporting dual-process models and we point out important shortcomings of this literature. Some dissociations seem to be difficult to replicate or poorly generalizable and others can be attributed to methodological artifacts. Overall, we conclude that support for dual-process models of biased contingency detection is scarce and inconclusive.

Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses

PubMed Central

Schein, Catherine H; Zhou, Bin; Braun, Werner

2005-01-01

Background Flaviviruses, which include Dengue (DV) and West Nile (WN), mutate in response to immune system pressure. Identifying escape mutants, variant progeny that replicate in the presence of neutralizing antibodies, is a common way to identify functionally important residues of viral proteins. However, the mutations typically occur at variable positions on the viral surface that are not essential for viral replication. Methods are needed to determine the true targets of the neutralizing antibodies. Results Stereophysicochemical variability plots (SVPs), 3-D images of protein structures colored according to variability, as determined by our PCPMer program, were used to visualize residues conserved in their physical chemical properties (PCPs) near escape mutant positions. The analysis showed 1) that escape mutations in the flavivirus envelope protein are variable residues by our criteria and 2) two escape mutants found at the same position in many flaviviruses sit above clusters of conserved residues from different regions of the linear sequence. Conservation patterns in T-cell epitopes in the NS3- protease suggest a similar mechanism of immune system evasion. Conclusion The SVPs add another dimension to structurally defining the binding sites of neutralizing antibodies. They provide a useful aid for determining antigenically important regions and designing vaccines. PMID:15845145

The short-term culture of lymphoid tissue from immunized guinea-pigs

PubMed Central

Dresser, Ann M.

1965-01-01

Lymph node tissue from guinea-pigs immunized against one of several antigens was cultured in different media in order to determine conditions under which maximal amounts of antibody are formed in vitro. The amounts of antibody formed were variable and bore no relation to the level of serum antibody in the tissue donor. Heterologous sera of several origins, when included in the culture medium, varied very markedly in their capacity to support antibody production in vitro. PMID:5847427

Generation of human Fab antibody libraries: PCR amplification and assembly of light- and heavy-chain coding sequences.

PubMed

Andris-Widhopf, Jennifer; Steinberger, Peter; Fuller, Roberta; Rader, Christoph; Barbas, Carlos F

2011-09-01

The development of therapeutic antibodies for use in the treatment of human diseases has long been a goal for many researchers in the antibody field. One way to obtain these antibodies is through phage-display libraries constructed from human lymphocytes. This protocol describes the construction of human Fab (fragment antigen binding) antibody libraries. In this method, the individual rearranged heavy- and light-chain variable regions are amplified separately and are linked through a series of overlap polymerase chain reaction (PCR) steps to give the final Fab products that are used for cloning.

A non-parametric postprocessor for bias-correcting multi-model ensemble forecasts of hydrometeorological and hydrologic variables

NASA Astrophysics Data System (ADS)

Brown, James; Seo, Dong-Jun

2010-05-01

Operational forecasts of hydrometeorological and hydrologic variables often contain large uncertainties, for which ensemble techniques are increasingly used. However, the utility of ensemble forecasts depends on the unbiasedness of the forecast probabilities. We describe a technique for quantifying and removing biases from ensemble forecasts of hydrometeorological and hydrologic variables, intended for use in operational forecasting. The technique makes no a priori assumptions about the distributional form of the variables, which is often unknown or difficult to model parametrically. The aim is to estimate the conditional cumulative distribution function (ccdf) of the observed variable given a (possibly biased) real-time ensemble forecast from one or several forecasting systems (multi-model ensembles). The technique is based on Bayesian optimal linear estimation of indicator variables, and is analogous to indicator cokriging (ICK) in geostatistics. By developing linear estimators for the conditional expectation of the observed variable at many thresholds, ICK provides a discrete approximation of the full ccdf. Since ICK minimizes the conditional error variance of the indicator expectation at each threshold, it effectively minimizes the Continuous Ranked Probability Score (CRPS) when infinitely many thresholds are employed. However, the ensemble members used as predictors in ICK, and other bias-correction techniques, are often highly cross-correlated, both within and between models. Thus, we propose an orthogonal transform of the predictors used in ICK, which is analogous to using their principal components in the linear system of equations. This leads to a well-posed problem in which a minimum number of predictors are used to provide maximum information content in terms of the total variance explained. The technique is used to bias-correct precipitation ensemble forecasts from the NCEP Global Ensemble Forecast System (GEFS), for which independent validation results are presented. Extension to multimodel ensembles from the NCEP GFS and Short Range Ensemble Forecast (SREF) systems is also proposed.

How can we reduce costs of solid-phase multiplex-bead assays used to determine anti-HLA antibodies?

PubMed

Kamburova, E G; Wisse, B W; Joosten, I; Allebes, W A; van der Meer, A; Hilbrands, L B; Baas, M C; Spierings, E; Hack, C E; van Reekum, F E; van Zuilen, A D; Verhaar, M; Bots, M L; Drop, A C A D; Plaisier, L; Seelen, M A J; Sanders, J S F; Hepkema, B G; Lambeck, A J; Bungener, L B; Roozendaal, C; Tilanus, M G J; Vanderlocht, J; Voorter, C E; Wieten, L; van Duijnhoven, E M; Gelens, M; Christiaans, M H L; van Ittersum, F J; Nurmohamed, A; Lardy, N M; Swelsen, W; van der Pant, K A; van der Weerd, N C; Ten Berge, I J M; Bemelman, F J; Hoitsma, A; van der Boog, P J M; de Fijter, J W; Betjes, M G H; Heidt, S; Roelen, D L; Claas, F H; Otten, H G

2016-09-01

Solid-phase multiplex-bead assays are widely used in transplantation to detect anti-human leukocyte antigen (HLA) antibodies. These assays enable high resolution detection of low levels of HLA antibodies. However, multiplex-bead assays are costly and yield variable measurements that limit the comparison of results between laboratories. In the context of a Dutch national Consortium study we aimed to determine the inter-assay and inter-machine variability of multiplex-bead assays, and we assessed how to reduce the assay reagents costs. Fifteen sera containing a variety of HLA antibodies were used yielding in total 7092 median fluorescence intensities (MFI) values. The inter-assay and inter-machine mean absolute relative differences (MARD) of the screening assay were 12% and 13%, respectively. The single antigen bead (SAB) inter-assay MARD was comparable, but showed a higher lot-to-lot variability. Reduction of screening assay reagents to 50% or 40% of manufacturers' recommendations resulted in MFI values comparable to 100% of the reagents, with an MARD of 12% or 14%, respectively. The MARD of the 50% and 40% SAB assay reagent reductions were 11% and 22%, respectively. From this study, we conclude that the reagents can be reliably reduced at least to 50% of manufacturers' recommendations with virtually no differences in HLA antibody assignments. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A novel gamma-fitting statistical method for anti-drug antibody assays to establish assay cut points for data with non-normal distribution.

PubMed

Schlain, Brian; Amaravadi, Lakshmi; Donley, Jean; Wickramasekera, Ananda; Bennett, Donald; Subramanyam, Meena

2010-01-31

In recent years there has been growing recognition of the impact of anti-drug or anti-therapeutic antibodies (ADAs, ATAs) on the pharmacokinetic and pharmacodynamic behavior of the drug, which ultimately affects drug exposure and activity. These anti-drug antibodies can also impact safety of the therapeutic by inducing a range of reactions from hypersensitivity to neutralization of the activity of an endogenous protein. Assessments of immunogenicity, therefore, are critically dependent on the bioanalytical method used to test samples, in which a positive versus negative reactivity is determined by a statistically derived cut point based on the distribution of drug naïve samples. For non-normally distributed data, a novel gamma-fitting method for obtaining assay cut points is presented. Non-normal immunogenicity data distributions, which tend to be unimodal and positively skewed, can often be modeled by 3-parameter gamma fits. Under a gamma regime, gamma based cut points were found to be more accurate (closer to their targeted false positive rates) compared to normal or log-normal methods and more precise (smaller standard errors of cut point estimators) compared with the nonparametric percentile method. Under a gamma regime, normal theory based methods for estimating cut points targeting a 5% false positive rate were found in computer simulation experiments to have, on average, false positive rates ranging from 6.2 to 8.3% (or positive biases between +1.2 and +3.3%) with bias decreasing with the magnitude of the gamma shape parameter. The log-normal fits tended, on average, to underestimate false positive rates with negative biases as large a -2.3% with absolute bias decreasing with the shape parameter. These results were consistent with the well known fact that gamma distributions become less skewed and closer to a normal distribution as their shape parameters increase. Inflated false positive rates, especially in a screening assay, shifts the emphasis to confirm test results in a subsequent test (confirmatory assay). On the other hand, deflated false positive rates in the case of screening immunogenicity assays will not meet the minimum 5% false positive target as proposed in the immunogenicity assay guidance white papers. Copyright 2009 Elsevier B.V. All rights reserved.

Expression and Functional Properties of an Anti-Triazophos High-Affinity Single-Chain Variable Fragment Antibody with Specific Lambda Light Chain

PubMed Central

Liu, Rui; Liang, Xiao; Xiang, Dandan; Guo, Yirong; Liu, Yihua; Zhu, Guonian

2016-01-01

Triazophos is a widely used organophosphorous insecticide that has potentially adverse effects to organisms. In the present study, a high-affinity single-chain variable fragment (scFv) antibody with specific lambda light chain was developed for residue monitoring. First, the specific variable regions were correctly amplified from a hybridoma cell line 8C10 that secreted monoclonal antibody (mAb) against triazophos. The regions were then assembled as scFv via splicing by overlap extension polymerase chain reaction. Subsequently, the recombinant anti-triazophos scFv-8C10 was successfully expressed in Escherichia coli strain HB2151 in soluble form, purified through immobilized metal ion affinity chromatography, and verified via Western blot and peptide mass fingerprinting analyses. Afterward, an indirect competitive enzyme-linked immunosorbent assay was established based on the purified anti-triazophos scFv-8C10 antibody. The assay exhibited properties similar to those based on the parent mAb, with a high sensitivity (IC50 of 1.73 ng/mL) to triazophos and no cross reaction for other organophosphorus pesticides; it was reliable in detecting triazophos residues in spiked water samples. Moreover, kinetic measurement using a surface plasmon resonance biosensor indicated that the purified scFv-8C10 antibody had a high affinity of 1.8 × 10−10 M and exhibited good binding stability. Results indicated that the recombinant high-affinity scFv-8C10 antibody was an effective detection material that would be promising for monitoring triazophos residues in environment samples. PMID:27338340

Chemical & Biological Point Detection Decontamination

DTIC Science & Technology

2002-04-01

high priority in biological defense. Research on multivalent assays is also ongoing. Biased libraries, generated from immunized animals, or unbiased ...2003 TBD decontamination and modeling and simulation I I The Chem-Bio Point Detection Roadmap The summary level updated and expanded Bio Point... Molecular Imprinted Polymer Sensor, Dendrimer-based Antibody Assays, Pyrolysis-GC-ion mobility spectrometry, and surface enhanced Raman spectroscopy. Data

Selection of single chain antibody fragments binding to the extracellular domain of 4-1BB receptor by phage display technology.

PubMed

Bagheri, Salman; Yousefi, Mehdi; Safaie Qamsari, Elmira; Riazi-Rad, Farhad; Abolhassani, Mohsen; Younesi, Vahid; Dorostkar, Ruhollah; Movassaghpour, Ali Akbar; Sharifzadeh, Zahra

2017-03-01

The 4-1BB is a surface glycoprotein that pertains to the tumor necrosis factor-receptor family. There is compelling evidence suggesting important roles for 4-1BB in the immune response, including cell activation and proliferation and also cytokine induction. Because of encouraging results of different agonistic monoclonal antibodies against 4-1BB in the treatment of cancer, infectious, and autoimmune diseases, 4-1BB has been suggested as an attractive target for immunotherapy. In this study, single chain variable fragment phage display libraries, Tomlinson I+J, were screened against specific synthetic oligopeptides (peptides I and II) designed from 4-1BB extracellular domain. Five rounds of panning led to selection of four 4-1BB specific single chain variable fragments (PI.12, PI.42, PII.16, and PII.29) which showed specific reaction to relevant peptides in phage enzyme-linked immunosorbent assay. The selected clones were successfully expressed in Escherichia coli Rosetta-gami 2, and their expression was confirmed by western blot analysis. Enzyme-linked immunosorbent assay experiments indicated that these antibodies were able to specifically recognize 4-1BB without any cross-reactivity with other antigens. Flow cytometry analysis demonstrated an acceptable specific binding of the single chain variable fragments to 4-1BB expressed on CCRF-CEM cells, while no binding was observed with an irrelevant antibody. Anti-4-1BB single chain variable fragments enhanced surface CD69 expression and interleukin-2 production in stimulated CCRF-CEM cells which confirmed the agonistic effect of the selected single chain variable fragments. The data from this study have provided a rationale for further experiments involving the biological functions of anti-4-1BB single chain variable fragments in future studies.

Variability and bias between magnetoencephalography systems in non-invasive localization of the primary somatosensory cortex.

PubMed

Bardouille, Timothy; Power, Lindsey; Lalancette, Marc; Bishop, Ronald; Beyea, Steven; Taylor, Margot J; Dunkley, Benjamin T

2018-05-26

Magnetoencephalography (MEG) provides functional neuroimaging data for pre-surgical planning in patients with epilepsy or brain tumour. For mapping the primary somatosensory cortex (S1), MEG data are acquired while a patient undergoes median nerve stimulation (MNS) to localize components of the somatosensory evoked field (SEF). In clinical settings, only one MEG imaging session is usually possible due to limited resources. As such, it is important to have an a priori estimate of the expected variability in localization. Variability in S1 localization between mapping sessions using the same MEG system has been previously measured as 8 mm. There are different types of MEG systems available with varied hardware and software, and it is not known how using a different MEG system will impact on S1 localization. In our study, healthy participants underwent the MNS procedure with two different MEG systems (Vector View and CTF). We compared the location, amplitude and latency of SEF components between data from each system to quantify variability and bias between MEG systems. We found 8-11 mm variability in S1 localization between the two MEG systems, and no evidence for a systematic bias in location, amplitude or latency between the two systems. These findings suggest that S1 localization is not biased by the type of MEG system used, and that differences between the two systems are not a major contributor to variability in localization. Copyright © 2018. Published by Elsevier B.V.

Personal Variables and Bias in Educational Decision-Making.

ERIC Educational Resources Information Center

Huebner, E. Scott; And Others

1984-01-01

Findings regarding the influence of four potential sources of bias (sex, socioeconimic status, race, physical attractiveness) upon decision-making stages of the assessment process are selectively reviewed. It is concluded that, though further research is needed, convincing evidence of bias in later stages of decision making has yet to be…

Estimation and correction of different flavors of surface observation biases in ensemble Kalman filter

NASA Astrophysics Data System (ADS)

Lorente-Plazas, Raquel; Hacker, Josua P.; Collins, Nancy; Lee, Jared A.

2017-04-01

The impact of assimilating surface observations has been shown in several publications, for improving weather prediction inside of the boundary layer as well as the flow aloft. However, the assimilation of surface observations is often far from optimal due to the presence of both model and observation biases. The sources of these biases can be diverse: an instrumental offset, errors associated to the comparison of point-based observations and grid-cell average, etc. To overcome this challenge, a method was developed using the ensemble Kalman filter. The approach consists on representing each observation bias as a parameter. These bias parameters are added to the forward operator and they extend the state vector. As opposed to the observation bias estimation approaches most common in operational systems (e.g. for satellite radiances), the state vector and parameters are simultaneously updated by applying the Kalman filter equations to the augmented state. The method to estimate and correct the observation bias is evaluated using observing system simulation experiments (OSSEs) with the Weather Research and Forecasting (WRF) model. OSSEs are constructed for the conventional observation network including radiosondes, aircraft observations, atmospheric motion vectors, and surface observations. Three different kinds of biases are added to 2-meter temperature for synthetic METARs. From the simplest to more sophisticated, imposed biases are: (1) a spatially invariant bias, (2) a spatially varying bias proportional to topographic height differences between the model and the observations, and (3) bias that is proportional to the temperature. The target region characterized by complex terrain is the western U.S. on a domain with 30-km grid spacing. Observations are assimilated every 3 hours using an 80-member ensemble during September 2012. Results demonstrate that the approach is able to estimate and correct the bias when it is spatially invariant (experiment 1). More complex bias structure in experiments (2) and (3) are more difficult to estimate, but still possible. Estimated the parameter in experiments with unbiased observations results in spatial and temporal parameter variability about zero, and establishes a threshold on the accuracy of the parameter in further experiments. When the observations are biased, the mean parameter value is close to the true bias, but temporal and spatial variability in the parameter estimates is similar to the parameters used when estimating a zero bias in the observations. The distributions are related to other errors in the forecasts, indicating that the parameters are absorbing some of the forecast error from other sources. In this presentation we elucidate the reasons for the resulting parameter estimates, and their variability.

Serosurvey of selected viruses in captive giant pandas (Ailuropoda melanoleuca) in China.

PubMed

Qin, Qin; Li, Desheng; Zhang, Hemin; Hou, Rong; Zhang, Zhihe; Zhang, Chenglin; Zhang, Jinguo; Wei, Fuwen

2010-05-19

Serum samples from 92 giant pandas in three captive facilities were tested for antibodies against five viruses of carnivores. Antibody titers against canine distemper virus (CDV) in two facilities in which giant pandas were vaccinated were variable. The canine adenovirus (CAV-1) and canine parvovirus (CPV) titers in vaccinated group were both positive, but titers were not high and varied among individual except one vaccinated panda had extremely high CAV-1 titer, indicating infection with the field virus following vaccination. Our results suggest that the vaccines used for these giant pandas do not elicit consistent antibody titers. Antibody titers against CDV, CPV and CAV-1 in unvaccinated giant pandas were highly variable, especially CPV titer. Almost half of sera were CPV antibody positive, and CPV titers were high enough to suggest infection with the virus. Canine coronavirus (CCV) and canine parainfluenza virus (CPIV) titers were not detected in all serum samples. The results of this study emphasize the need for research on infectious diseases of giant pandas and development of suitable vaccines for the species. Copyright 2009 Elsevier B.V. All rights reserved.

Antibody Light-Chain-Restricted Recognition of the Site of Immune Pressure in the RV144 HIV-1 Vaccine Trial Is Phylogenetically Conserved

DOE PAGES

Wiehe, Kevin; Easterhoff, David; Luo, Kan; ...

2014-11-29

In HIV-1, the ability to mount antibody responses to conserved, neutralizing epitopes is critical for protection. Here we have studied the light chain usage of human and rhesus macaque antibodies targeted to a dominant region of the HIV-1 envelope second variable (V2) region involving lysine (K) 169, the site of immune pressure in the RV144 vaccine efficacy trial. We found that humans and rhesus macaques used orthologous lambda variable gene segments encoding a glutamic acid-aspartic acid (ED) motif for K169 recognition. Structure determination of an unmutated ancestor antibody demonstrated that the V2 binding site was preconfigured for ED motif-mediated recognitionmore » prior to maturation. Thus, light chain usage for recognition of the site of immune pressure in the RV144 trial is highly conserved across species. In conclusion, these data indicate that the HIV-1 K169-recognizing ED motif has persisted over the diversification between rhesus macaques and humans, suggesting an evolutionary advantage of this antibody recognition mode.« less

Antibody Light-Chain-Restricted Recognition of the Site of Immune Pressure in the RV144 HIV-1 Vaccine Trial Is Phylogenetically Conserved

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

Wiehe, Kevin; Easterhoff, David; Luo, Kan

In HIV-1, the ability to mount antibody responses to conserved, neutralizing epitopes is critical for protection. Here we have studied the light chain usage of human and rhesus macaque antibodies targeted to a dominant region of the HIV-1 envelope second variable (V2) region involving lysine (K) 169, the site of immune pressure in the RV144 vaccine efficacy trial. We found that humans and rhesus macaques used orthologous lambda variable gene segments encoding a glutamic acid-aspartic acid (ED) motif for K169 recognition. Structure determination of an unmutated ancestor antibody demonstrated that the V2 binding site was preconfigured for ED motif-mediated recognitionmore » prior to maturation. Thus, light chain usage for recognition of the site of immune pressure in the RV144 trial is highly conserved across species. In conclusion, these data indicate that the HIV-1 K169-recognizing ED motif has persisted over the diversification between rhesus macaques and humans, suggesting an evolutionary advantage of this antibody recognition mode.« less

Generation, Diversity Determination, and Application to Antibody Selection of a Human Naïve Fab Library

PubMed Central

Kim, Sangkyu; Park, Insoo; Park, Seung Gu; Cho, Seulki; Kim, Jin Hong; Ipper, Nagesh S.; Choi, Sun Shim; Lee, Eung Suk; Hong, Hyo Jeong

2017-01-01

We constructed a large naïve human Fab library (3 × 1010 colonies) from the lymphocytes of 809 human donors, assessed available diversities of the heavy-chain variable (VH) and κ light-chain variable (VK) domain repertoires, and validated the library by selecting Fabs against 10 therapeutically relevant antigens by phage display. We obtained a database of unique 7,373 VH and 41,804 VK sequences by 454 pyrosequencing, and analyzed the repertoires. The distribution of VH and VK subfamilies and germline genes in our antibody repertoires slightly differed from those in earlier published natural antibody libraries. The frequency of somatic hypermutations (SHMs) in heavy-chain complementarity determining region (HCDR)1 and HCDR2 are higher compared with the natural IgM repertoire. Analysis of position-specific SHMs in CDRs indicates that asparagine, threonine, arginine, aspartate and phenylalanine are the most frequent non-germline residues on the antibody-antigen interface and are converted mostly from the germline residues, which are highly represented in germline SHM hotspots. The amino acid composition and length-dependent changes in amino acid frequencies of HCDR3 are similar to those in previous reports, except that frequencies of aspartate and phenylalanine are a little higher in our repertoire. Taken together, the results show that this antibody library shares common features of natural antibody repertoires and also has unique features. The antibody library will be useful in the generation of human antibodies against diverse antigens, and the information about the diversity of natural antibody repertoires will be valuable in the future design of synthetic human antibody libraries with high functional diversity. PMID:28927259

Generation, Diversity Determination, and Application to Antibody Selection of a Human Naïve Fab Library.

PubMed

Kim, Sangkyu; Park, Insoo; Park, Seung Gu; Cho, Seulki; Kim, Jin Hong; Ipper, Nagesh S; Choi, Sun Shim; Lee, Eung Suk; Hong, Hyo Jeong

2017-09-30

We constructed a large naïve human Fab library (3 × 10 10 colonies) from the lymphocytes of 809 human donors, assessed available diversities of the heavy-chain variable (VH) and κ light-chain variable (VK) domain repertoires, and validated the library by selecting Fabs against 10 therapeutically relevant antigens by phage display. We obtained a database of unique 7,373 VH and 41,804 VK sequences by 454 pyrosequencing, and analyzed the repertoires. The distribution of VH and VK subfamilies and germline genes in our antibody repertoires slightly differed from those in earlier published natural antibody libraries. The frequency of somatic hypermutations (SHMs) in heavy-chain complementarity determining region (HCDR)1 and HCDR2 are higher compared with the natural IgM repertoire. Analysis of position-specific SHMs in CDRs indicates that asparagine, threonine, arginine, aspartate and phenylalanine are the most frequent non-germline residues on the antibody-antigen interface and are converted mostly from the germline residues, which are highly represented in germline SHM hotspots. The amino acid composition and length-dependent changes in amino acid frequencies of HCDR3 are similar to those in previous reports, except that frequencies of aspartate and phenylalanine are a little higher in our repertoire. Taken together, the results show that this antibody library shares common features of natural antibody repertoires and also has unique features. The antibody library will be useful in the generation of human antibodies against diverse antigens, and the information about the diversity of natural antibody repertoires will be valuable in the future design of synthetic human antibody libraries with high functional diversity.

Diagnosing GCM errors over West Africa using relaxation experiments. Part I: summer monsoon climatology and interannual variability

NASA Astrophysics Data System (ADS)

Pohl, Benjamin; Douville, Hervé

2011-10-01

The CNRM atmospheric general circulation model Arpege-Climat is relaxed towards atmospheric reanalyses outside the 10°S-32°N 30°W-50°E domain in order to disentangle the regional versus large-scale sources of climatological biases and interannual variability of the West African monsoon (WAM). On the one hand, the main climatological features of the monsoon, including the spatial distribution of summer precipitation, are only weakly improved by the nudging, thereby suggesting the regional origin of the Arpege-Climat biases. On the other hand, the nudging technique is relatively efficient to control the interannual variability of the WAM dynamics, though the impact on rainfall variability is less clear. Additional sensitivity experiments focusing on the strong 1994 summer monsoon suggest that the weak sensitivity of the model biases is not an artifact of the nudging design, but the evidence that regional physical processes are the main limiting factors for a realistic simulation of monsoon circulation and precipitation in the Arpege-Climat model. Sensitivity experiments to soil moisture boundary conditions are also conducted and highlight the relevance of land-atmosphere coupling for the amplification of precipitation biases. Nevertheless, the land surface hydrology is not the main explanation for the model errors that are rather due to deficiencies in the atmospheric physics. The intraseasonal timescale and the model internal variability are discussed in a companion paper.

Confounding, causality, and confusion: the role of intermediate variables in interpreting observational studies in obstetrics.

PubMed

Ananth, Cande V; Schisterman, Enrique F

2017-08-01

Prospective and retrospective cohorts and case-control studies are some of the most important study designs in epidemiology because, under certain assumptions, they can mimic a randomized trial when done well. These assumptions include, but are not limited to, properly accounting for 2 important sources of bias: confounding and selection bias. While not adjusting the causal association for an intermediate variable will yield an unbiased estimate of the exposure-outcome's total causal effect, it is often that obstetricians will want to adjust for an intermediate variable to assess if the intermediate is the underlying driver of the association. Such a practice must be weighed in light of the underlying research question and whether such an adjustment is necessary should be carefully considered. Gestational age is, by far, the most commonly encountered variable in obstetrics that is often mislabeled as a confounder when, in fact, it may be an intermediate. If, indeed, gestational age is an intermediate but if mistakenly labeled as a confounding variable and consequently adjusted in an analysis, the conclusions can be unexpected. The implications of this overadjustment of an intermediate as though it were a confounder can render an otherwise persuasive study downright meaningless. This commentary provides an exposition of confounding bias, collider stratification, and selection biases, with applications in obstetrics and perinatal epidemiology. Copyright © 2017 Elsevier Inc. All rights reserved.

Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire.

PubMed

Yeung, Yik Andy; Foletti, Davide; Deng, Xiaodi; Abdiche, Yasmina; Strop, Pavel; Glanville, Jacob; Pitts, Steven; Lindquist, Kevin; Sundar, Purnima D; Sirota, Marina; Hasa-Moreno, Adela; Pham, Amber; Melton Witt, Jody; Ni, Irene; Pons, Jaume; Shelton, David; Rajpal, Arvind; Chaparro-Riggers, Javier

2016-11-18

Staphylococcus aureus is both an important pathogen and a human commensal. To explore this ambivalent relationship between host and microbe, we analysed the memory humoral response against IsdB, a protein involved in iron acquisition, in four healthy donors. Here we show that in all donors a heavily biased use of two immunoglobulin heavy chain germlines generated high affinity (pM) antibodies that neutralize the two IsdB NEAT domains, IGHV4-39 for NEAT1 and IGHV1-69 for NEAT2. In contrast to the typical antibody/antigen interactions, the binding is primarily driven by the germline-encoded hydrophobic CDRH-2 motifs of IGHV1-69 and IGHV4-39, with a binding mechanism nearly identical for each antibody derived from different donors. Our results suggest that IGHV1-69 and IGHV4-39, while part of the adaptive immune system, may have evolved under selection pressure to encode a binding motif innately capable of recognizing and neutralizing a structurally conserved protein domain involved in pathogen iron acquisition.

Decadal evaluation of regional climate, air quality, and their interactions using WRF/Chem Version 3.6.1

NASA Astrophysics Data System (ADS)

Yahya, K.; Wang, K.; Campbell, P.; Glotfelty, T.; He, J.; Zhang, Y.

2015-08-01

The Weather Research and Forecasting model with Chemistry (WRF/Chem) v3.6.1 with the Carbon Bond 2005 (CB05) gas-phase mechanism is evaluated for its first decadal application during 2001-2010 using the Representative Concentration Pathway (RCP 8.5) emissions to assess its capability and appropriateness for long-term climatological simulations. The initial and boundary conditions are downscaled from the modified Community Earth System Model/Community Atmosphere Model (CESM/CAM5) v1.2.2. The meteorological initial and boundary conditions are bias-corrected using the National Center for Environmental Protection's Final (FNL) Operational Global Analysis data. Climatological evaluations are carried out for meteorological, chemical, and aerosol-cloud-radiation variables against data from surface networks and satellite retrievals. The model performs very well for the 2 m temperature (T2) for the 10 year period with only a small cold bias of -0.3 °C. Biases in other meteorological variables including relative humidity at 2 m, wind speed at 10 m, and precipitation tend to be site- and season-specific; however, with the exception of T2, consistent annual biases exist for most of the years from 2001 to 2010. Ozone mixing ratios are slightly overpredicted at both urban and rural locations but underpredicted at rural locations. PM2.5 concentrations are slightly overpredicted at rural sites, but slightly underpredicted at urban/suburban sites. In general, the model performs relatively well for chemical and meteorological variables, and not as well for aerosol-cloud-radiation variables. Cloud-aerosol variables including aerosol optical depth, cloud water path, cloud optical thickness, and cloud droplet number concentration are generally underpredicted on average across the continental US. Overpredictions of several cloud variables over eastern US result in underpredictions of radiation variables and overpredictions of shortwave and longwave cloud forcing which are important climate variables. While the current performance is deemed to be acceptable, improvements to the bias-correction method for CESM downscaling and the model parameterizations of cloud dynamics and thermodynamics, as well as aerosol-cloud interactions can potentially improve model performance for long-term climate simulations.

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

PubMed

Bonomi, M; Barducci, A; Parrinello, M

2009-08-01

Metadynamics is a widely used and successful method for reconstructing the free-energy surface of complex systems as a function of a small number of suitably chosen collective variables. This is achieved by biasing the dynamics of the system. The bias acting on the collective variables distorts the probability distribution of the other variables. Here we present a simple reweighting algorithm for recovering the unbiased probability distribution of any variable from a well-tempered metadynamics simulation. We show the efficiency of the reweighting procedure by reconstructing the distribution of the four backbone dihedral angles of alanine dipeptide from two and even one dimensional metadynamics simulation. 2009 Wiley Periodicals, Inc.

The association of serum anti-ribosomal P antibody with clinical and serological disorders in systemic lupus erythematosus: a systematic review and meta-analysis.

PubMed

Shi, Z-R; Cao, C-X; Tan, G-Z; Wang, L

2015-05-01

Anti-ribosomal P (anti-P) antibody is a serological specific marker of systemic lupus erythematosus (SLE). The aim of this study is to investigate the association of this antibody with clinical and serological disorders in SLE. All relevant literature was retrieved from PubMed, EMBASE, Web of Science and CNKI databases. The qualities of these studies were evaluated using a modified version of the Newcastle-Ottawa scale. The associations of anti-P antibody with clinical and serological disorders were determined by the pooled odds ratio (OR) and the confidence interval (CI) calculated using meta-analysis with the Mantel-Haenszel method. Sixteen cohort studies with 2355 patients were included in this study. Malar rash, oral ulcer and photosensitivity were strongly associated with serum anti-P antibody, with OR (95% CI) values of 2.05 (1.42-2.92), 1.49 (1.05-2.13) and 1.44 (1.08-1.91), respectively. Arthritis and renal involvement were not associated with anti-P antibody, whereas a high heterogeneity was observed due to ethnicity and publication bias, respectively. Neuropsychiatric SLE (NPSLE), hepatic involvement, anti-dsDNA, anti-Sm and anti-cardiolipin antibodies (aCL) were observed more frequently in anti-P positive patients than in negative patients. Studies on hepatic involvement showed a low precision with substantially broad CI (2.56-11.2). A high heterogeneity presented among studies on NPSLE, anti-Sm and aCL. Anti-P antibody is significantly associated with malar rash, oral ulcer, photosensitivity and serum anti-dsDNA antibody, and potentially associated with NPSLE, hepatic damage, serum anti-Sm and aCL. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Alleviating tropical Atlantic sector biases in the Kiel climate model by enhancing horizontal and vertical atmosphere model resolution: climatology and interannual variability

NASA Astrophysics Data System (ADS)

Harlaß, Jan; Latif, Mojib; Park, Wonsun

2018-04-01

We investigate the quality of simulating tropical Atlantic (TA) sector climatology and interannual variability in integrations of the Kiel climate model (KCM) with varying atmosphere model resolution. The ocean model resolution is kept fixed. A reasonable simulation of TA sector annual-mean climate, seasonal cycle and interannual variability can only be achieved at sufficiently high horizontal and vertical atmospheric resolution. Two major reasons for the improvements are identified. First, the western equatorial Atlantic westerly surface wind bias in spring can be largely eliminated, which is explained by a better representation of meridional and especially vertical zonal momentum transport. The enhanced atmospheric circulation along the equator in turn greatly improves the thermal structure of the upper equatorial Atlantic with much reduced warm sea surface temperature (SST) biases. Second, the coastline in the southeastern TA and steep orography are better resolved at high resolution, which improves wind structure and in turn reduces warm SST biases in the Benguela upwelling region. The strongly diminished wind and SST biases at high atmosphere model resolution allow for a more realistic latitudinal position of the intertropical convergence zone. Resulting stronger cross-equatorial winds, in conjunction with a shallower thermocline, enable a rapid cold tongue development in the eastern TA in boreal spring. This enables simulation of realistic interannual SST variability and its seasonal phase locking in the KCM, which primarily is the result of a stronger thermocline feedback. Our findings suggest that enhanced atmospheric resolution, both vertical and horizontal, could be a key to achieving more realistic simulation of TA climatology and interannual variability in climate models.

The second Southern African Bird Atlas Project: Causes and consequences of geographical sampling bias.

PubMed

Hugo, Sanet; Altwegg, Res

2017-09-01

Using the Southern African Bird Atlas Project (SABAP2) as a case study, we examine the possible determinants of spatial bias in volunteer sampling effort and how well such biased data represent environmental gradients across the area covered by the atlas. For each province in South Africa, we used generalized linear mixed models to determine the combination of variables that explain spatial variation in sampling effort (number of visits per 5' × 5' grid cell, or "pentad"). The explanatory variables were distance to major road and exceptional birding locations or "sampling hubs," percentage cover of protected, urban, and cultivated area, and the climate variables mean annual precipitation, winter temperatures, and summer temperatures. Further, we used the climate variables and plant biomes to define subsets of pentads representing environmental zones across South Africa, Lesotho, and Swaziland. For each environmental zone, we quantified sampling intensity, and we assessed sampling completeness with species accumulation curves fitted to the asymptotic Lomolino model. Sampling effort was highest close to sampling hubs, major roads, urban areas, and protected areas. Cultivated area and the climate variables were less important. Further, environmental zones were not evenly represented by current data and the zones varied in the amount of sampling required representing the species that are present. SABAP2 volunteers' preferences in birding locations cause spatial bias in the dataset that should be taken into account when analyzing these data. Large parts of South Africa remain underrepresented, which may restrict the kind of ecological questions that may be addressed. However, sampling bias may be improved by directing volunteers toward undersampled regions while taking into account volunteer preferences.

Problems and Progress regarding Sex Bias and Omission in Neuroscience Research

PubMed Central

Will, Tyler R.; Proaño, Stephanie B.; Thomas, Anly M.; Kunz, Lindsey M.; Thompson, Kelly C.; Ginnari, Laura A.; Jones, Clay H.; Lucas, Sarah-Catherine; Reavis, Elizabeth M.

2017-01-01

Neuroscience research has historically ignored female animals. This neglect comes in two general forms. The first is sex bias, defined as favoring one sex over another; in this case, male over female. The second is sex omission, which is the lack of reporting sex. The recognition of this phenomenon has generated fierce debate across the sciences. Here we test whether sex bias and omission are still present in the neuroscience literature, whether studies employing both males and females neglect sex as an experimental variable, and whether sex bias and omission differs between animal models and journals. To accomplish this, we analyzed the largest-ever number of neuroscience articles for sex bias and omission: 6636 articles using mice or rats in 6 journals published from 2010 to 2014. Sex omission is declining, as increasing numbers of articles report sex. Sex bias remains present, as increasing numbers of articles report the sole use of males. Articles using both males and females are also increasing, but few report assessing sex as an experimental variable. Sex bias and omission varies substantially by animal model and journal. These findings are essential for understanding the complex status of sex bias and omission in neuroscience research and may inform effective decisions regarding policy action. PMID:29134192

Errors in causal inference: an organizational schema for systematic error and random error.

PubMed

Suzuki, Etsuji; Tsuda, Toshihide; Mitsuhashi, Toshiharu; Mansournia, Mohammad Ali; Yamamoto, Eiji

2016-11-01

To provide an organizational schema for systematic error and random error in estimating causal measures, aimed at clarifying the concept of errors from the perspective of causal inference. We propose to divide systematic error into structural error and analytic error. With regard to random error, our schema shows its four major sources: nondeterministic counterfactuals, sampling variability, a mechanism that generates exposure events and measurement variability. Structural error is defined from the perspective of counterfactual reasoning and divided into nonexchangeability bias (which comprises confounding bias and selection bias) and measurement bias. Directed acyclic graphs are useful to illustrate this kind of error. Nonexchangeability bias implies a lack of "exchangeability" between the selected exposed and unexposed groups. A lack of exchangeability is not a primary concern of measurement bias, justifying its separation from confounding bias and selection bias. Many forms of analytic errors result from the small-sample properties of the estimator used and vanish asymptotically. Analytic error also results from wrong (misspecified) statistical models and inappropriate statistical methods. Our organizational schema is helpful for understanding the relationship between systematic error and random error from a previously less investigated aspect, enabling us to better understand the relationship between accuracy, validity, and precision. Copyright © 2016 Elsevier Inc. All rights reserved.

Towards process-informed bias correction of climate change simulations

NASA Astrophysics Data System (ADS)

Maraun, Douglas; Shepherd, Theodore G.; Widmann, Martin; Zappa, Giuseppe; Walton, Daniel; Gutiérrez, José M.; Hagemann, Stefan; Richter, Ingo; Soares, Pedro M. M.; Hall, Alex; Mearns, Linda O.

2017-11-01

Biases in climate model simulations introduce biases in subsequent impact simulations. Therefore, bias correction methods are operationally used to post-process regional climate projections. However, many problems have been identified, and some researchers question the very basis of the approach. Here we demonstrate that a typical cross-validation is unable to identify improper use of bias correction. Several examples show the limited ability of bias correction to correct and to downscale variability, and demonstrate that bias correction can cause implausible climate change signals. Bias correction cannot overcome major model errors, and naive application might result in ill-informed adaptation decisions. We conclude with a list of recommendations and suggestions for future research to reduce, post-process, and cope with climate model biases.

A comparative study of monoclonal antibodies. 1. Phase behavior and protein-protein interactions

PubMed Central

Lewus, Rachael A.; Levy, Nicholas E.; Lenhoff, Abraham M.; Sandler, Stanley I.

2018-01-01

Protein phase behavior is involved in numerous aspects of downstream processing, either by design as in crystallization or precipitation processes, or as an undesired effect, such as aggregation. This work explores the phase behavior of eight monoclonal antibodies (mAbs) that exhibit liquid-liquid separation, aggregation, gelation, and crystallization. The phase behavior has been studied systematically as a function of a number of factors, including solution composition and pH, in order to explore the degree of variability among different antibodies. Comparisons of the locations of phase boundaries show consistent trends as a function of solution composition; however, changing the solution pH has different effects on each of the antibodies studied. Furthermore, the types of dense phases formed varied among the antibodies. Protein-protein interactions, as reflected by values of the osmotic second virial coefficient, are used to correlate the phase behavior. The primary findings are that values of the osmotic second virial coefficient are useful for correlating phase boundary locations, though there is appreciable variability among the antibodies in the apparent strengths of the intrinsic protein-protein attraction manifested. However, the osmotic second virial coefficient does not provide a clear basis to predict the type of dense phase likely to result under a given set of solution conditions. PMID:25378269

Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability

PubMed Central

Julian, Mark C.; Li, Lijuan; Garde, Shekhar; Wilen, Rebecca; Tessier, Peter M.

2017-01-01

The ability of antibodies to accumulate affinity-enhancing mutations in their complementarity-determining regions (CDRs) without compromising thermodynamic stability is critical to their natural function. However, it is unclear if affinity mutations in the hypervariable CDRs generally impact antibody stability and to what extent additional compensatory mutations are required to maintain stability during affinity maturation. Here we have experimentally and computationally evaluated the functional contributions of mutations acquired by a human variable (VH) domain that was evolved using strong selections for enhanced stability and affinity for the Alzheimer’s Aβ42 peptide. Interestingly, half of the key affinity mutations in the CDRs were destabilizing. Moreover, the destabilizing effects of these mutations were compensated for by a subset of the affinity mutations that were also stabilizing. Our findings demonstrate that the accumulation of both affinity and stability mutations is necessary to maintain thermodynamic stability during extensive mutagenesis and affinity maturation in vitro, which is similar to findings for natural antibodies that are subjected to somatic hypermutation in vivo. These findings for diverse antibodies and antibody fragments specific for unrelated antigens suggest that the formation of the antigen-binding site is generally a destabilizing process and that co-enrichment for compensatory mutations is critical for maintaining thermodynamic stability. PMID:28349921

Another Piece of the Antibody Puzzle: Observations from the HALT study\\.

PubMed

Snyder, Laurie D; Tinckam, Kathryn J

2018-06-04

In the rapidly evolving domain of clinical transplantation immunobiology, the interrogation and interpretation of HLA antibodies and their associated clinical consequences are in the spotlight. In lung transplant, HLA antibodies, in particular donor specific antibodies (DSA), are a determining component of the lung transplant antibody mediated rejection (AMR) definition (1). DSA after lung transplant are widely regarded as poor prognosticator, though sparse data to date necessitate ongoing discourse and continued investigation into incidence, timing and treatment. Prior studies reported a wide range of DSA incidence with differing consequences on a background of highly variable timing, methods, antibody analytic strategies and clinical definitions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Food-related attentional bias. Word versus pictorial stimuli and the importance of stimuli calorific value in the dot probe task.

PubMed

Freijy, Tanya; Mullan, Barbara; Sharpe, Louise

2014-12-01

The primary aim of this study was to extend previous research on food-related attentional biases by examining biases towards pictorial versus word stimuli, and foods of high versus low calorific value. It was expected that participants would demonstrate greater biases to pictures over words, and to high-calorie over low-calorie foods. A secondary aim was to examine associations between BMI, dietary restraint, external eating and attentional biases. It was expected that high scores on these individual difference variables would be associated with a bias towards high-calorie stimuli. Undergraduates (N = 99) completed a dot probe task including matched word and pictorial food stimuli in a controlled setting. Questionnaires assessing eating behaviour were administered, and height and weight were measured. Contrary to predictions, there were no main effects for stimuli type (pictures vs words) or calorific value (high vs low). There was, however, a significant interaction effect suggesting a bias towards high-calorie pictures, but away from high-calorie words; and a bias towards low-calorie words, but away from low-calorie pictures. No associations between attentional bias and any of the individual difference variables were found. The presence of a stimulus type by calorific value interaction demonstrates the importance of stimuli type in the dot probe task, and may help to explain inconsistencies in prior research. Further research is needed to clarify associations between attentional bias and BMI, restraint, and external eating. Copyright © 2014 Elsevier Ltd. All rights reserved.

On-chip optical phase locking of single growth monolithically integrated Slotted Fabry Perot lasers.

PubMed

Morrissey, P E; Cotter, W; Goulding, D; Kelleher, B; Osborne, S; Yang, H; O'Callaghan, J; Roycroft, B; Corbett, B; Peters, F H

2013-07-15

This work investigates the optical phase locking performance of Slotted Fabry Perot (SFP) lasers and develops an integrated variable phase locked system on chip for the first time to our knowledge using these lasers. Stable phase locking is demonstrated between two SFP lasers coupled on chip via a variable gain waveguide section. The two lasers are biased differently, one just above the threshold current of the device with the other at three times this value. The coupling between the lasers can be controlled using the variable gain section which can act as a variable optical attenuator or amplifier depending on bias. Using this, the width of the stable phase locking region on chip is shown to be variable.

Synonymous deoptimization of the foot-and-mouth disease virus P1 coding region causes attenuation in vivo while inducing a strong neutralizing antibody response

USDA-ARS?s Scientific Manuscript database

Codon bias deoptimization has been previously used to successfully attenuate human pathogens including polio, respiratory syncytial and influenza viruses. We have applied a similar technology to deoptimize the capsid coding region (P1 region) of the cDNA infectious clone of foot-and-mouth disease vi...

Collinear Latent Variables in Multilevel Confirmatory Factor Analysis

PubMed Central

van de Schoot, Rens; Hox, Joop

2014-01-01

Because variables may be correlated in the social and behavioral sciences, multicollinearity might be problematic. This study investigates the effect of collinearity manipulated in within and between levels of a two-level confirmatory factor analysis by Monte Carlo simulation. Furthermore, the influence of the size of the intraclass correlation coefficient (ICC) and estimation method; maximum likelihood estimation with robust chi-squares and standard errors and Bayesian estimation, on the convergence rate are investigated. The other variables of interest were rate of inadmissible solutions and the relative parameter and standard error bias on the between level. The results showed that inadmissible solutions were obtained when there was between level collinearity and the estimation method was maximum likelihood. In the within level multicollinearity condition, all of the solutions were admissible but the bias values were higher compared with the between level collinearity condition. Bayesian estimation appeared to be robust in obtaining admissible parameters but the relative bias was higher than for maximum likelihood estimation. Finally, as expected, high ICC produced less biased results compared to medium ICC conditions. PMID:29795827

Collinear Latent Variables in Multilevel Confirmatory Factor Analysis: A Comparison of Maximum Likelihood and Bayesian Estimations.

PubMed

Can, Seda; van de Schoot, Rens; Hox, Joop

2015-06-01

Because variables may be correlated in the social and behavioral sciences, multicollinearity might be problematic. This study investigates the effect of collinearity manipulated in within and between levels of a two-level confirmatory factor analysis by Monte Carlo simulation. Furthermore, the influence of the size of the intraclass correlation coefficient (ICC) and estimation method; maximum likelihood estimation with robust chi-squares and standard errors and Bayesian estimation, on the convergence rate are investigated. The other variables of interest were rate of inadmissible solutions and the relative parameter and standard error bias on the between level. The results showed that inadmissible solutions were obtained when there was between level collinearity and the estimation method was maximum likelihood. In the within level multicollinearity condition, all of the solutions were admissible but the bias values were higher compared with the between level collinearity condition. Bayesian estimation appeared to be robust in obtaining admissible parameters but the relative bias was higher than for maximum likelihood estimation. Finally, as expected, high ICC produced less biased results compared to medium ICC conditions.

Inferring Master Painters' Esthetic Biases from the Statistics of Portraits

PubMed Central

Aleem, Hassan; Correa-Herran, Ivan; Grzywacz, Norberto M.

2017-01-01

The Processing Fluency Theory posits that the ease of sensory information processing in the brain facilitates esthetic pleasure. Accordingly, the theory would predict that master painters should display biases toward visual properties such as symmetry, balance, and moderate complexity. Have these biases been occurring and if so, have painters been optimizing these properties (fluency variables)? Here, we address these questions with statistics of portrait paintings from the Early Renaissance period. To do this, we first developed different computational measures for each of the aforementioned fluency variables. Then, we measured their statistics in 153 portraits from 26 master painters, in 27 photographs of people in three controlled poses, and in 38 quickly snapped photographs of individual persons. A statistical comparison between Early Renaissance portraits and quickly snapped photographs revealed that painters showed a bias toward balance, symmetry, and moderate complexity. However, a comparison between portraits and controlled-pose photographs showed that painters did not optimize each of these properties. Instead, different painters presented biases toward different, narrow ranges of fluency variables. Further analysis suggested that the painters' individuality stemmed in part from having to resolve the tension between complexity vs. symmetry and balance. We additionally found that constraints on the use of different painting materials by distinct painters modulated these fluency variables systematically. In conclusion, the Processing Fluency Theory of Esthetic Pleasure would need expansion if we were to apply it to the history of visual art since it cannot explain the lack of optimization of each fluency variables. To expand the theory, we propose the existence of a Neuroesthetic Space, which encompasses the possible values that each of the fluency variables can reach in any given art period. We discuss the neural mechanisms of this Space and propose that it has a distributed representation in the human brain. We further propose that different artists reside in different, small sub-regions of the Space. This Neuroesthetic-Space hypothesis raises the question of how painters and their paintings evolve across art periods. PMID:28337133

Reliable cloning of functional antibody variable domains from hybridomas and spleen cell repertoires employing a reengineered phage display system.

PubMed

Krebber, A; Bornhauser, S; Burmester, J; Honegger, A; Willuda, J; Bosshard, H R; Plückthun, A

1997-02-14

A prerequisite for the use of recombinant antibody technologies starting from hybridomas or immune repertoires is the reliable cloning of functional immunoglobulin genes. For this purpose, a standard phage display system was optimized for robustness, vector stability, tight control of scFv-delta geneIII expression, primer usage for PCR amplification of variable region genes, scFv assembly strategy and subsequent directional cloning using a single rare cutting restriction enzyme. This integrated cloning, screening and selection system allowed us to rapidly obtain antigen binding scFvs derived from spleen-cell repertoires of mice immunized with ampicillin as well as from all hybridoma cell lines tested to date. As representative examples, cloning of monoclonal antibodies against a his tag, leucine zippers, the tumor marker EGP-2 and the insecticide DDT is presented. Several hybridomas whose genes could not be cloned in previous experimental setups, but were successfully obtained with the present system, expressed high amounts of aberrant heavy and light chain mRNAs, which were amplified by PCR and greatly exceeded the amount of binding antibody sequences. These contaminating variable region genes were successfully eliminated by employing the optimized phage display system, thus avoiding time consuming sequencing of non-binding scFv genes. To maximize soluble expression of functional scFvs subsequent to cloning, a compatible vector series to simplify modification, detection, multimerization and rapid purification of recombinant antibody fragments was constructed.

Examining the influence of link function misspecification in conventional regression models for developing crash modification factors.

PubMed

Wu, Lingtao; Lord, Dominique

2017-05-01

This study further examined the use of regression models for developing crash modification factors (CMFs), specifically focusing on the misspecification in the link function. The primary objectives were to validate the accuracy of CMFs derived from the commonly used regression models (i.e., generalized linear models or GLMs with additive linear link functions) when some of the variables have nonlinear relationships and quantify the amount of bias as a function of the nonlinearity. Using the concept of artificial realistic data, various linear and nonlinear crash modification functions (CM-Functions) were assumed for three variables. Crash counts were randomly generated based on these CM-Functions. CMFs were then derived from regression models for three different scenarios. The results were compared with the assumed true values. The main findings are summarized as follows: (1) when some variables have nonlinear relationships with crash risk, the CMFs for these variables derived from the commonly used GLMs are all biased, especially around areas away from the baseline conditions (e.g., boundary areas); (2) with the increase in nonlinearity (i.e., nonlinear relationship becomes stronger), the bias becomes more significant; (3) the quality of CMFs for other variables having linear relationships can be influenced when mixed with those having nonlinear relationships, but the accuracy may still be acceptable; and (4) the misuse of the link function for one or more variables can also lead to biased estimates for other parameters. This study raised the importance of the link function when using regression models for developing CMFs. Copyright © 2017 Elsevier Ltd. All rights reserved.

The dynamics of motivated perception: Effects of control and status on the perception of ambivalent stimuli.

PubMed

Voss, Andreas; Schwieren, Christiane

2015-01-01

Previous studies on attentional biases often show contradictory results. This suggests that important moderating variables have been neglected so far. We suggest that (1) control over potential consequences and (2) satisfaction with the current status are important factors that need to be considered. We explored the influence of these variables using a colour classification task, where colours are associated with financial gains and losses. Data were analysed with hierarchical logistic regression models and with stochastic diffusion models. The latter approach has the special advantage that it allows separating perceptual and judgemental biases. Results show an overall positive judgemental bias. In the absence of control, this positivity bias increases with the amount of money that has been gained, whereas the opposite pattern is present when dangers can be controlled. In the second experiment, no general feedback was given, which led to an increasing negativity bias. Results are discussed within an action theoretic framework.

Single- and Dual-Process Models of Biased Contingency Detection

PubMed Central

2016-01-01

Abstract. Decades of research in causal and contingency learning show that people’s estimations of the degree of contingency between two events are easily biased by the relative probabilities of those two events. If two events co-occur frequently, then people tend to overestimate the strength of the contingency between them. Traditionally, these biases have been explained in terms of relatively simple single-process models of learning and reasoning. However, more recently some authors have found that these biases do not appear in all dependent variables and have proposed dual-process models to explain these dissociations between variables. In the present paper we review the evidence for dissociations supporting dual-process models and we point out important shortcomings of this literature. Some dissociations seem to be difficult to replicate or poorly generalizable and others can be attributed to methodological artifacts. Overall, we conclude that support for dual-process models of biased contingency detection is scarce and inconclusive. PMID:27025532

A large population-based association study between HLA and KIR genotypes and measles vaccine antibody responses.

PubMed

Ovsyannikova, Inna G; Schaid, Daniel J; Larrabee, Beth R; Haralambieva, Iana H; Kennedy, Richard B; Poland, Gregory A

2017-01-01

Human antibody response to measles vaccine is highly variable in the population. Host genes contribute to inter-individual antibody response variation. The killer cell immunoglobulin-like receptors (KIR) are recognized to interact with HLA molecules and possibly influence humoral immune response to viral antigens. To expand on and improve our previous work with HLA genes, and to explore the genetic contribution of KIR genes to the inter-individual variability in measles vaccine-induced antibody responses, we performed a large population-based study in 2,506 healthy immunized subjects (ages 11 to 41 years) to identify HLA and KIR associations with measles vaccine-induced neutralizing antibodies. After correcting for the large number of statistical tests of allele effects on measles-specific neutralizing antibody titers, no statistically significant associations were found for either HLA or KIR loci. However, suggestive associations worthy of follow-up in other cohorts include B*57:01, DQB1*06:02, and DRB1*15:05 alleles. Specifically, the B*57:01 allele (1,040 mIU/mL; p = 0.0002) was suggestive of an association with lower measles antibody titer. In contrast, the DQB1*06:02 (1,349 mIU/mL; p = 0.0004) and DRB1*15:05 (2,547 mIU/mL; p = 0.0004) alleles were suggestive of an association with higher measles antibodies. Notably, the associations with KIR genotypes were strongly nonsignificant, suggesting that KIR loci in terms of copy number and haplotypes are not likely to play a major role in antibody response to measles vaccination. These findings refine our knowledge of the role of HLA and KIR alleles in measles vaccine-induced immunity.

Generation of a rabbit single-chain fragment variable (scFv) antibody for specific detection of Bradyrhizobium sp. DOA9 in both free-living and bacteroid forms

PubMed Central

Srila, Witsanu; Yuttavanichakul, Watcharin; Teamtisong, Kamonluck; Teaumroong, Neung; Boonkerd, Nantakorn; Tittabutr, Panlada

2017-01-01

A simple and reliable method for the detection of specific nitrogen-fixing bacteria in both free-living and bacteroid forms is essential for the development and application of biofertilizer. Traditionally, a polyclonal antibody generated from an immunized rabbit was used for detection. However, the disadvantages of using a polyclonal antibody include limited supply and cross-reactivity to related bacterial strains. This is the first report on the application of phage display technology for the generation of a rabbit recombinant monoclonal antibody for specific detection and monitoring of nitrogen-fixing bacteria in both free-living form and in plant nodules. Bradyrhizobium sp. DOA9, a broad host range soil bacteria, originally isolated from the root nodules of Aeschynomene americana in Thailand was used as a model in this study. A recombinant single-chain fragment variable (scFv) antibody library was constructed from the spleen of a rabbit immunized with DOA9. After three rounds of biopanning, one specific phage-displayed scFv antibody, designated bDOA9rb8, was identified. Specific binding of this antibody was confirmed by phage enzyme-linked immunosorbent assay (phage ELISA). The phage antibody could bind specifically to DOA9 in both free-living cells (pure culture) and bacteroids inside plant nodules. In addition to phage ELISA, specific and robust immunofluorescence staining of both free-living and bacteroid forms could also be observed by confocal-immunofluorescence imaging, without cross-reactivity with other tested bradyrhizobial strains. Moreover, specific binding of free scFv to DOA9 was also demonstrated by ELISA. This recombinant antibody can also be used for the study of the molecular mechanism of plant–microbe interactions in the future. PMID:28654662

Generation of a rabbit single-chain fragment variable (scFv) antibody for specific detection of Bradyrhizobium sp. DOA9 in both free-living and bacteroid forms.

PubMed

Vu, Nguyen Xuan; Pruksametanan, Natcha; Srila, Witsanu; Yuttavanichakul, Watcharin; Teamtisong, Kamonluck; Teaumroong, Neung; Boonkerd, Nantakorn; Tittabutr, Panlada; Yamabhai, Montarop

2017-01-01

A simple and reliable method for the detection of specific nitrogen-fixing bacteria in both free-living and bacteroid forms is essential for the development and application of biofertilizer. Traditionally, a polyclonal antibody generated from an immunized rabbit was used for detection. However, the disadvantages of using a polyclonal antibody include limited supply and cross-reactivity to related bacterial strains. This is the first report on the application of phage display technology for the generation of a rabbit recombinant monoclonal antibody for specific detection and monitoring of nitrogen-fixing bacteria in both free-living form and in plant nodules. Bradyrhizobium sp. DOA9, a broad host range soil bacteria, originally isolated from the root nodules of Aeschynomene americana in Thailand was used as a model in this study. A recombinant single-chain fragment variable (scFv) antibody library was constructed from the spleen of a rabbit immunized with DOA9. After three rounds of biopanning, one specific phage-displayed scFv antibody, designated bDOA9rb8, was identified. Specific binding of this antibody was confirmed by phage enzyme-linked immunosorbent assay (phage ELISA). The phage antibody could bind specifically to DOA9 in both free-living cells (pure culture) and bacteroids inside plant nodules. In addition to phage ELISA, specific and robust immunofluorescence staining of both free-living and bacteroid forms could also be observed by confocal-immunofluorescence imaging, without cross-reactivity with other tested bradyrhizobial strains. Moreover, specific binding of free scFv to DOA9 was also demonstrated by ELISA. This recombinant antibody can also be used for the study of the molecular mechanism of plant-microbe interactions in the future.

Development of cell-penetrating bispecific antibodies targeting the N-terminal domain of androgen receptor for prostate cancer therapy.

PubMed

Goicochea, Nancy L; Garnovskaya, Maria; Blanton, Mary G; Chan, Grace; Weisbart, Richard; Lilly, Michael B

2017-12-01

Castration-resistant prostate cancer cells exhibit continued androgen receptor signaling in spite of low levels of ligand. Current therapies to block androgen receptor signaling act by inhibiting ligand production or binding. We developed bispecific antibodies capable of penetrating cells and binding androgen receptor outside of the ligand-binding domain. Half of the bispecific antibody molecule consists of a single-chain variable fragment of 3E10, an anti-DNA antibody that enters cells. The other half is a single-chain variable fragment version of AR441, an anti-AR antibody. The resulting 3E10-AR441 bispecific antibody enters human LNCaP prostate cells and accumulates in the nucleus. The antibody binds to wild-type, mutant and splice variant androgen receptor. Binding affinity of 3E10-AR441 to androgen receptor (284 nM) was lower than that of the parental AR441 mAb (4.6 nM), but could be improved (45 nM) through alternative placement of the affinity tags, and ordering of the VH and VK domains. The 3E10-AR441 bispecific antibody blocked genomic signaling by wild-type or splice variant androgen receptor in LNCaP cells. It also blocked non-genomic signaling by the wild-type receptor. Furthermore, bispecific antibody inhibited the growth of C4-2 prostate cancer cells under androgen-stimulated conditions. The 3E10-AR441 biAb can enter prostate cancer cells and inhibits androgen receptor function in a ligand-independent manner. It may be an attractive prototype agent for prostate cancer therapy. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

[Prevalence of antibodies to hepatitis A virus in healthcare workers and associated variables].

PubMed

Carreras-Valls, Rosa; Valverde-Lozano, Judit; Benito-Carreras, Dolors; Inglés-Torruella, Joan; Vilardell-Ynaraja, Miquel; Garre-Olmo, Josep; Gil-Soto, Rosa; Escalé-Roca, Margarita

2013-01-01

Vaccination against hepatitis A is recommended in risk groups, including healthcare workers. The objective of this study was to determine the prevalence of antibodies to HAV (IgG) among workers in the healthcare setting in order to establish criteria for vaccination. A cross-sectional, analytic, observational study of 4,864 employees was undertaken in four healthcare companies in Catalonia (Spain). The variables gathered included personal data, professional category, location of employment, and serology. The overall prevalence of antibodies to HAV was 52.7%. The prevalence significantly increased with greater age. The mean age of seropositive workers was 41.5 years compared with 34.3 in workers with negative serology. The highest prevalence of antibodies was found in cleaning employees (74.2%) and catering staff (75.3%). Given the high prevalence of seronegative adults susceptible to infection and the characteristics of their professional activities, vaccination of all staff working in health institutions should be considered. Copyright © 2012 SESPAS. Published by Elsevier Espana. All rights reserved.

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies.

PubMed

Yamashita, Kazuo; Ikeda, Kazuyoshi; Amada, Karlou; Liang, Shide; Tsuchiya, Yuko; Nakamura, Haruki; Shirai, Hiroki; Standley, Daron M

2014-11-15

Kotai Antibody Builder is a Web service for tertiary structural modeling of antibody variable regions. It consists of three main steps: hybrid template selection by sequence alignment and canonical rules, 3D rendering of alignments and CDR-H3 loop modeling. For the last step, in addition to rule-based heuristics used to build the initial model, a refinement option is available that uses fragment assembly followed by knowledge-based scoring. Using targets from the Second Antibody Modeling Assessment, we demonstrate that Kotai Antibody Builder generates models with an overall accuracy equal to that of the best-performing semi-automated predictors using expert knowledge. Kotai Antibody Builder is available at http://kotaiab.org standley@ifrec.osaka-u.ac.jp. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Single-Domain Antibodies and the Promise of Modular Targeting in Cancer Imaging and Treatment.

PubMed

Iezzi, María Elena; Policastro, Lucía; Werbajh, Santiago; Podhajcer, Osvaldo; Canziani, Gabriela Alicia

2018-01-01

Monoclonal antibodies and their fragments have significantly changed the outcome of cancer in the clinic, effectively inhibiting tumor cell proliferation, triggering antibody-dependent immune effector cell activation and complement mediated cell death. Along with a continued expansion in number, diversity, and complexity of validated tumor targets there is an increasing focus on engineering recombinant antibody fragments for lead development. Single-domain antibodies (sdAbs), in particular those engineered from the variable heavy-chain fragment (VHH gene) found in Camelidae heavy-chain antibodies (or IgG2 and IgG3), are the smallest fragments that retain the full antigen-binding capacity of the antibody with advantageous properties as drugs. For similar reasons, growing attention is being paid to the yet smaller variable heavy chain new antigen receptor (VNAR) fragments found in Squalidae. sdAbs have been selected, mostly from immune VHH libraries, to inhibit or modulate enzyme activity, bind soluble factors, internalize cell membrane receptors, or block cytoplasmic targets. This succinct review is a compilation of recent data documenting the application of engineered, recombinant sdAb in the clinic as epitope recognition "modules" to build monomeric, dimeric and multimeric ligands that target, tag and stall solid tumor growth in vivo . Size, affinity, specificity, and the development profile of sdAbs drugs are seemingly consistent with desirable clinical efficacy and safety requirements. But the hepatotoxicity of the tetrameric anti-DR5-VHH drug in patients with pre-existing anti-drug antibodies halted the phase I clinical trial and called for a thorough pre-screening of the immune and poly-specific reactivities of the sdAb leads.

Generation of a Highly Reactive Chicken-Derived Single-Chain Variable Fragment against Fusarium verticillioides by Phage Display

PubMed Central

Hu, Zu-Quan; Liu, Jin-Long; Li, He-Ping; Xing, Shu; Xue, Sheng; Zhang, Jing-Bo; Wang, Jian-Hua; Nölke, Greta; Liao, Yu-Cai

2012-01-01

Fusarium verticillioides is the primary causal agent of Fusarium ear and kernel rot in maize, producing fumonisin mycotoxins that are toxic to humans and domestic animals. Rapid detection and monitoring of fumonisin-producing fungi are pivotally important for the prevention of mycotoxins from entering into food/feed products. Chicken-derived single-chain variable fragments (scFvs) against cell wall-bound proteins from F. verticillioides were isolated from an immunocompetent phage display library. Comparative phage enzyme-linked immunosorbant assays (ELISAs) and sequencing analyses identified four different scFv antibodies with high sensitivity. Soluble antibody ELISAs identified two highly sensitive scFv antibodies, FvCA3 and FvCA4, with the latter being slightly more sensitive. Three-dimensional modeling revealed that the FvCA4 may hold a better overall structure with CDRH3, CDRL1 and CDRL3 centered in the core region of antibody surface compared with that of other scFvs. Immunofluorescence labeling revealed that the binding of FvCA4 antibody was localized to the cell walls of conidiospores and hyphae of F. verticillioides, confirming the specificity of this antibody for a surface target. This scFv antibody was able to detect the fungal mycelium as low as 10−2 μg/mL and contaminating mycelium at a quantity of 10−2 mg/g maize. This is the first report that scFv antibodies derived from phage display have a wide application for rapid and accurate detection and monitoring of fumonisin-producing pathogens in agricultural samples. PMID:22837678

Sequence-Based Discovery Demonstrates That Fixed Light Chain Human Transgenic Rats Produce a Diverse Repertoire of Antigen-Specific Antibodies.

PubMed

Harris, Katherine E; Aldred, Shelley Force; Davison, Laura M; Ogana, Heather Anne N; Boudreau, Andrew; Brüggemann, Marianne; Osborn, Michael; Ma, Biao; Buelow, Benjamin; Clarke, Starlynn C; Dang, Kevin H; Iyer, Suhasini; Jorgensen, Brett; Pham, Duy T; Pratap, Payal P; Rangaswamy, Udaya S; Schellenberger, Ute; van Schooten, Wim C; Ugamraj, Harshad S; Vafa, Omid; Buelow, Roland; Trinklein, Nathan D

2018-01-01

We created a novel transgenic rat that expresses human antibodies comprising a diverse repertoire of heavy chains with a single common rearranged kappa light chain (IgKV3-15-JK1). This fixed light chain animal, called OmniFlic, presents a unique system for human therapeutic antibody discovery and a model to study heavy chain repertoire diversity in the context of a constant light chain. The purpose of this study was to analyze heavy chain variable gene usage, clonotype diversity, and to describe the sequence characteristics of antigen-specific monoclonal antibodies (mAbs) isolated from immunized OmniFlic animals. Using next-generation sequencing antibody repertoire analysis, we measured heavy chain variable gene usage and the diversity of clonotypes present in the lymph node germinal centers of 75 OmniFlic rats immunized with 9 different protein antigens. Furthermore, we expressed 2,560 unique heavy chain sequences sampled from a diverse set of clonotypes as fixed light chain antibody proteins and measured their binding to antigen by ELISA. Finally, we measured patterns and overall levels of somatic hypermutation in the full B-cell repertoire and in the 2,560 mAbs tested for binding. The results demonstrate that OmniFlic animals produce an abundance of antigen-specific antibodies with heavy chain clonotype diversity that is similar to what has been described with unrestricted light chain use in mammals. In addition, we show that sequence-based discovery is a highly effective and efficient way to identify a large number of diverse monoclonal antibodies to a protein target of interest.

Gender Bias in the Diagnosis of a Geriatric Standardized Patient: A Potential Confounding Variable

ERIC Educational Resources Information Center

Lewis, Roya; Lamdan, Ruth M.; Wald, David; Curtis, Michael

2006-01-01

Background: Gender bias has been reported in the diagnosis and treatment of patients with a variety of illnesses. In the context of our 10-station fourth year Objective Structured Clinical Evaluation, we queried whether this could influence diagnosis in a geriatric case. Case writers hypothesized that, due to this bias, the female standardized…

IgG4 subclass antibodies impair antitumor immunity in melanoma

PubMed Central

Karagiannis, Panagiotis; Gilbert, Amy E.; Josephs, Debra H.; Ali, Niwa; Dodev, Tihomir; Saul, Louise; Correa, Isabel; Roberts, Luke; Beddowes, Emma; Koers, Alexander; Hobbs, Carl; Ferreira, Silvia; Geh, Jenny L.C.; Healy, Ciaran; Harries, Mark; Acland, Katharine M.; Blower, Philip J.; Mitchell, Tracey; Fear, David J.; Spicer, James F.; Lacy, Katie E.; Nestle, Frank O.; Karagiannis, Sophia N.

2013-01-01

Host-induced antibodies and their contributions to cancer inflammation are largely unexplored. IgG4 subclass antibodies are present in IL-10–driven Th2 immune responses in some inflammatory conditions. Since Th2-biased inflammation is a hallmark of tumor microenvironments, we investigated the presence and functional implications of IgG4 in malignant melanoma. Consistent with Th2 inflammation, CD22+ B cells and IgG4+-infiltrating cells accumulated in tumors, and IL-10, IL-4, and tumor-reactive IgG4 were expressed in situ. When compared with B cells from patient lymph nodes and blood, tumor-associated B cells were polarized to produce IgG4. Secreted B cells increased VEGF and IgG4, and tumor cells enhanced IL-10 secretion in cocultures. Unlike IgG1, an engineered tumor antigen-specific IgG4 was ineffective in triggering effector cell–mediated tumor killing in vitro. Antigen-specific and nonspecific IgG4 inhibited IgG1-mediated tumoricidal functions. IgG4 blockade was mediated through reduction of FcγRI activation. Additionally, IgG4 significantly impaired the potency of tumoricidal IgG1 in a human melanoma xenograft mouse model. Furthermore, serum IgG4 was inversely correlated with patient survival. These findings suggest that IgG4 promoted by tumor-induced Th2-biased inflammation may restrict effector cell functions against tumors, providing a previously unexplored aspect of tumor-induced immune escape and a basis for biomarker development and patient-specific therapeutic approaches. PMID:23454746

Production of anti-amoxicillin ScFv antibody and simulation studying its molecular recognition mechanism for penicillins.

PubMed

Liu, Jing; Zhang, Hui C; Duan, Chang F; Dong, Jun; Zhao, Guo X; Wang, Jian P; Li, Nan; Liu, Jin Z; Li, Yu W

2016-11-01

The molecular recognition mechanism of an antibody for its hapten is very interesting. The objective of this research was to study the intermolecular interactions of an anti-amoxicillin antibody with penicillin drugs. The single chain variable fragment (ScFv) antibody was generated from a hybridoma cell strain excreting the monoclonal antibody for amoxicillin. The recombinant ScFv antibody showed similar recognition ability for penicillins to its parental monoclonal antibody: simultaneous recognizing 11 penicillins with cross-reactivities of 18-107%. The three-dimensional structure of the ScFv antibody was simulated by using homology modeling, and its intermolecular interactions with 11 penicillins were studied by using molecular docking. Results showed that three CDRs are involved in antibody recognition; CDR L3 Arg 100, CDR H3 Tyr226, and CDR H3 Arg 228 were the key contact amino acid residues; hydrogen bonding was the main antibody-drug intermolecular force; and the core structure of penicillin drugs was the main antibody binding position. These results could explain the recognition mechanism of anti-amoxicillin antibody for amoxicillin and its analogs. This is the first study reporting the production of ScFv antibody for penicillins and stimulation studying its recognition mechanism.

Recombinant scFv antibodies against infectious pancreatic necrosis virus isolated by flow cytometry.

PubMed

Xu, Li-Ming; Zhao, Jing-Zhuang; Liu, Miao; Cao, Yong-Sheng; Yin, Jia-Sheng; Liu, Hong-Bai; Lu, Tongyan

2016-11-01

Infectious pancreatic necrosis is a significant disease of farmed salmonids in China. In this study, a single chain variable fragment (scFv) antibody library derived from rainbow trout (Oncorhynchus mykiss) and viral protein VP2 of a Chinese infectious pancreatic necrosis virus (IPNV) isolate ChRtm213 were co-expressed by a bacterial display technology. The library was subjected to three rounds of screening by flow cytometry (FCM) to select IPNV specific antibodies. Six antibody clones with different mean fluorescence intensities (MFI) were obtained by picking colonies at random. The antibody clones were expressed and purified. The purified IPNV-specific scFv antibodies were used successfully in Western blotting, enzyme linked immunosorbent assay (ELISA) and an immunofluorescence antibody test (IFAT). This method provides a high throughput means to screen an antibody library by flow cytometry, and isolate a panel of antibody that can be used as potential reagents for the detection and study of IPNV that are prevalent in China. Copyright © 2016 Elsevier B.V. All rights reserved.

Single Domain Antibodies as New Biomarker Detectors

PubMed Central

Fischer, Katja; Leow, Chiuan Yee; Chuah, Candy; McCarthy, James

2017-01-01

Biomarkers are defined as indicators of biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. Biomarkers have been widely used for early detection, prediction of response after treatment, and for monitoring the progression of diseases. Antibodies represent promising tools for recognition of biomarkers, and are widely deployed as analytical tools in clinical settings. For immunodiagnostics, antibodies are now exploited as binders for antigens of interest across a range of platforms. More recently, the discovery of antibody surface display and combinatorial chemistry techniques has allowed the exploration of new binders from a range of animals, for instance variable domains of new antigen receptors (VNAR) from shark and variable heavy chain domains (VHH) or nanobodies from camelids. These single domain antibodies (sdAbs) have some advantages over conventional murine immunoglobulin owing to the lack of a light chain, making them the smallest natural biomarker binders thus far identified. In this review, we will discuss several biomarkers used as a means to validate diseases progress. The potential functionality of modern singe domain antigen binders derived from phylogenetically early animals as new biomarker detectors for current diagnostic and research platforms development will be described. PMID:29039819

Somatic diversification in the heavy chain variable region genes expressed by human autoantibodies bearing a lupus-associated nephritogenic anti-DNA idiotype

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

Demaison, C.; Chastagner, P.; Theze, J.

1994-01-18

Monoclonal anti-DNA antibodies bearing a lupus nephritis-associated idiotype were derived from five patients with systemic lupus erythematosus (SLE). Genes encoding their heavy (H)-chain variable (V[sub H]) regions were cloned and sequenced. When compared with their closest V[sub h] germ-line gene relatives, these sequences exhibit a number of silent (S) and replacement (R) substitutions. The ratios of R/S mutations were much higher in the complementarity-determining regions (CDRs) of the antibodies than in the framework regions. Molecular amplification of genomic V[sub H] genes and Southern hybridization with somatic CDR2-specific oligonucleotide probes showed that the configuration of the V[sub H] genes corresponding tomore » V[sub H] sequences in the nephritogenic antibodies is not present in the patient's own germ-line DNA, implying that the B-cell clones underwent somatic mutation in vivo. These findings, together with the characteristics of the diversity and junctional gene elements utilized to form the antibody, indicate that these autoantibodies have been driven through somatic selection processes reminiscent of those that govern antibody responses triggered by exogenous stimuli.« less

Generation of human scFv antibody libraries: PCR amplification and assembly of light- and heavy-chain coding sequences.

PubMed

Andris-Widhopf, Jennifer; Steinberger, Peter; Fuller, Roberta; Rader, Christoph; Barbas, Carlos F

2011-09-01

The development of therapeutic antibodies for use in the treatment of human diseases has long been a goal for many researchers in the antibody field. One way to obtain these antibodies is through phage-display libraries constructed from human lymphocytes. This protocol describes the construction of human scFv (single chain antibody fragment) libraries using a short linker (GGSSRSS) or a long linker (GGSSRSSSSGGGGSGGGG). In this method, the individual rearranged heavy- and light-chain variable regions are amplified separately and are linked through a series of overlap polymerase chain reaction (PCR) steps to give the final scFv products that are used for cloning.

Potential fitting biases resulting from grouping data into variable width bins

NASA Astrophysics Data System (ADS)

Towers, S.

2014-07-01

When reading peer-reviewed scientific literature describing any analysis of empirical data, it is natural and correct to proceed with the underlying assumption that experiments have made good faith efforts to ensure that their analyses yield unbiased results. However, particle physics experiments are expensive and time consuming to carry out, thus if an analysis has inherent bias (even if unintentional), much money and effort can be wasted trying to replicate or understand the results, particularly if the analysis is fundamental to our understanding of the universe. In this note we discuss the significant biases that can result from data binning schemes. As we will show, if data are binned such that they provide the best comparison to a particular (but incorrect) model, the resulting model parameter estimates when fitting to the binned data can be significantly biased, leading us to too often accept the model hypothesis when it is not in fact true. When using binned likelihood or least squares methods there is of course no a priori requirement that data bin sizes need to be constant, but we show that fitting to data grouped into variable width bins is particularly prone to produce biased results if the bin boundaries are chosen to optimize the comparison of the binned data to a wrong model. The degree of bias that can be achieved simply with variable binning can be surprisingly large. Fitting the data with an unbinned likelihood method, when possible to do so, is the best way for researchers to show that their analyses are not biased by binning effects. Failing that, equal bin widths should be employed as a cross-check of the fitting analysis whenever possible.

Intercomparison of Downscaling Methods on Hydrological Impact for Earth System Model of NE United States

NASA Astrophysics Data System (ADS)

Yang, P.; Fekete, B. M.; Rosenzweig, B.; Lengyel, F.; Vorosmarty, C. J.

2012-12-01

Atmospheric dynamics are essential inputs to Regional-scale Earth System Models (RESMs). Variables including surface air temperature, total precipitation, solar radiation, wind speed and humidity must be downscaled from coarse-resolution, global General Circulation Models (GCMs) to the high temporal and spatial resolution required for regional modeling. However, this downscaling procedure can be challenging due to the need to correct for bias from the GCM and to capture the spatiotemporal heterogeneity of the regional dynamics. In this study, the results obtained using several downscaling techniques and observational datasets were compared for a RESM of the Northeast Corridor of the United States. Previous efforts have enhanced GCM model outputs through bias correction using novel techniques. For example, the Climate Impact Research at Potsdam Institute developed a series of bias-corrected GCMs towards the next generation climate change scenarios (Schiermeier, 2012; Moss et al., 2010). Techniques to better represent the heterogeneity of climate variables have also been improved using statistical approaches (Maurer, 2008; Abatzoglou, 2011). For this study, four downscaling approaches to transform bias-corrected HADGEM2-ES Model output (daily at .5 x .5 degree) to the 3'*3'(longitude*latitude) daily and monthly resolution required for the Northeast RESM were compared: 1) Bilinear Interpolation, 2) Daily bias-corrected spatial downscaling (D-BCSD) with Gridded Meteorological Datasets (developed by Abazoglou 2011), 3) Monthly bias-corrected spatial disaggregation (M-BCSD) with CRU(Climate Research Unit) and 4) Dynamic Downscaling based on Weather Research and Forecast (WRF) model. Spatio-temporal analysis of the variability in precipitation was conducted over the study domain. Validation of the variables of different downscaling methods against observational datasets was carried out for assessment of the downscaled climate model outputs. The effects of using the different approaches to downscale atmospheric variables (specifically air temperature and precipitation) for use as inputs to the Water Balance Model (WBMPlus, Vorosmarty et al., 1998;Wisser et al., 2008) for simulation of daily discharge and monthly stream flow in the Northeast US for a 100-year period in the 21st century were also assessed. Statistical techniques especially monthly bias-corrected spatial disaggregation (M-BCSD) showed potential advantage among other methods for the daily discharge and monthly stream flow simulation. However, Dynamic Downscaling will provide important complements to the statistical approaches tested.

Persistent states in vision break universality and time invariance

PubMed Central

Wexler, Mark; Duyck, Marianne; Mamassian, Pascal

2015-01-01

Studies of perception usually emphasize processes that are largely universal across observers and—except for short-term fluctuations—stationary over time. Here we test the universality and stationarity assumptions with two families of ambiguous visual stimuli. Each stimulus can be perceived in two different ways, parameterized by two opposite directions from a continuous circular variable. A large-sample study showed that almost all observers have preferred directions or biases, with directions lying within 90 degrees of the bias direction nearly always perceived and opposite directions almost never perceived. The biases differ dramatically from one observer to the next, and although nearly every bias direction occurs in the population, the population distributions of the biases are nonuniform, featuring asymmetric peaks in the cardinal directions. The biases for the two families of stimuli are independent and have distinct population distributions. Following external perturbations and spontaneous fluctuations, the biases decay over tens of seconds toward their initial values. Persistent changes in the biases are found on time scales of several minutes to 1 hour. On scales of days to months, the biases undergo a variety of dynamical processes such as drifts, jumps, and oscillations. The global statistics of a majority of these long-term time series are well modeled as random walk processes. The measurable fluctuations of these hitherto unknown degrees of freedom show that the assumptions of universality and stationarity in perception may be unwarranted and that models of perception must include both directly observable variables as well as covert, persistent states. PMID:26627250

SAbPred: a structure-based antibody prediction server

PubMed Central

Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo; Marks, Claire; Nowak, Jaroslaw; Regep, Cristian; Georges, Guy; Kelm, Sebastian; Popovic, Bojana; Deane, Charlotte M.

2016-01-01

SAbPred is a server that makes predictions of the properties of antibodies focusing on their structures. Antibody informatics tools can help improve our understanding of immune responses to disease and aid in the design and engineering of therapeutic molecules. SAbPred is a single platform containing multiple applications which can: number and align sequences; automatically generate antibody variable fragment homology models; annotate such models with estimated accuracy alongside sequence and structural properties including potential developability issues; predict paratope residues; and predict epitope patches on protein antigens. The server is available at http://opig.stats.ox.ac.uk/webapps/sabpred. PMID:27131379

Reshaping Human Antibodies: Grafting an Antilysozyme Activity

NASA Astrophysics Data System (ADS)

Verhoeyen, Martine; Milstein, Cesar; Winter, Greg

1988-03-01

The production of therapeutic human monoclonal antibodies by hybridoma technology has proved difficult, and this has prompted the ``humanizing'' of mouse monoclonal antibodies by recombinant DNA techniques. It was shown previously that the binding site for a small hapten could be grafted from the heavy-chain variable domain of a mouse antibody to that of a human myeloma protein by transplanting the hypervariable loops. It is now shown that a large binding site for a protein antigen (lysozyme) can also be transplanted from mouse to human heavy chain. The success of such constructions may be facilitated by an induced-fit mechanism.

Detection of antibodies against classical swine fever virus in fecal samples from wild boar.

PubMed

Seo, Sang won; Sunwoo, Sun young; Hyun, Bang hoon; Lyoo, Young S

2012-12-28

Classical swine fever (CSF) is a contagious viral disease that affects pigs. Wild boars can play an important epidemiological role in CSF outbreaks. In the past decades, studies conducted in many countries have reported that the CSF virus (CSFV) may persist in wild boar populations. The existence of CSFV in the free-ranging wild boar populations was indirectly confirmed by determining the prevalence of antibodies against CSFV in the serum of hunted wild boars. However, analyzing sero-prevalence in hunted wild boars to study the risk of CSF outbreaks is difficult due to insufficient number of samples, limitation of hunting area and biased age distribution of hunted wild boars. To improve this survey method, we collected feces of wild boars from their habitat and tested them using CSFV antibody enzyme-linked immunosorbent assay (ELISA) and CSF virus neutralization (VN) test. In this study, ELISA was found to be highly sensitive for detecting antibodies against CSFV in fecal samples. Most of doubtful or positive results obtained in CSFV ELISA were confirmed by VN tests. Despite the high coincidence rate of antibody-positive samples between CSFV ELISA and VN test, the possibility of false positive reaction should be considered. In the regional distribution, a fact that antibody-positive fecal and serum samples were found in geographically close area was shown. Hence, presence of antibodies in fecal samples may provide vital information regarding the risk of CSF outbreaks in wild boar groups in geographical proximity. Copyright © 2012 Elsevier B.V. All rights reserved.

An assessment of change in risk perception and optimistic bias for hurricanes among Gulf Coast residents.

PubMed

Trumbo, Craig; Meyer, Michelle A; Marlatt, Holly; Peek, Lori; Morrissey, Bridget

2014-06-01

This study focuses on levels of concern for hurricanes among individuals living along the Gulf Coast during the quiescent two-year period following the exceptionally destructive 2005 hurricane season. A small study of risk perception and optimistic bias was conducted immediately following Hurricanes Katrina and Rita. Two years later, a follow-up was done in which respondents were recontacted. This provided an opportunity to examine changes, and potential causal ordering, in risk perception and optimistic bias. The analysis uses 201 panel respondents who were matched across the two mail surveys. Measures included hurricane risk perception, optimistic bias for hurricane evacuation, past hurricane experience, and a small set of demographic variables (age, sex, income, and education). Paired t-tests were used to compare scores across time. Hurricane risk perception declined and optimistic bias increased. Cross-lagged correlations were used to test the potential causal ordering between risk perception and optimistic bias, with a weak effect suggesting the former affects the latter. Additional cross-lagged analysis using structural equation modeling was used to look more closely at the components of optimistic bias (risk to self vs. risk to others). A significant and stronger potentially causal effect from risk perception to optimistic bias was found. Analysis of the experience and demographic variables' effects on risk perception and optimistic bias, and their change, provided mixed results. The lessening of risk perception and increase in optimistic bias over the period of quiescence suggest that risk communicators and emergency managers should direct attention toward reversing these trends to increase disaster preparedness. © 2013 Society for Risk Analysis.

Serum VacA antibody is associated with risks of peptic ulcer and gastric cancer: A meta-analysis.

PubMed

Li, Qiuping; Liu, Jingwei; Gong, Yuehua; Yuan, Yuan

2016-10-01

Increasing studies have investigated the relationship between the status of H. pylori vacA antibody and risks of peptic ulcer disease (PUD) and gastric cancer (GC). However, the results were controversial. The aim of this meta-analysis is to clarify whether serum vacA antibody is associated with risks of PUD and GC. Databases including PubMed, Embase, Web of knowledge, Wanfang, Chinese National Knowledge Infrastructure (CNKI), OVID, Karger and Scopus were systematically searched for potentially eligible literature. Odds ratios (OR) and their 95% confidence interval (CI) were adopted to assess the strength of association. Serum VacA antibody was associated with increased risk of PUD compared with gastritis/functional dyspepsia (FD) (OR = 1.96, 95%CI = 1.56-2.46, P < 0.001). Serum VacA antibody was significantly associated with increased risk of gastric ulcer (GU) and duodenal ulcer (DU) compared with gastritis/FD (GU: OR = 1.64, 95%CI = 1.02-2.62, P = 0.042; DU: OR = 2.06, 95%CI = 1.50-2.84, P < 0.001, respectively). Significant increased risk of GC was found in serum VacA antibody positive subjects compared with serum VacA antibody negative individuals (OR = 2.78, 95%CI = 1.98-3.89, P < 0.001). There was no significant publication bias in all of the comparisons. Serum VacA antibody was significantly associated with increased risks of peptic ulcer disease, gastric ulcer and duodenal ulcer compared with gastritis and functional dyspepsia controls. Significant association was also found between serum VacA antibody and gastric cancer risk. Serum VacA antibody might be a potential biomarker for the prediction of risks of PUD and GC. Copyright © 2016 Elsevier Ltd. All rights reserved.

Combinatorial Libraries of Arrayable Single-Chain Antibodies

NASA Astrophysics Data System (ADS)

Benhar, Itai

Antibodies that bind their respective targets with high affinity and specificity have proven to be essential reagents for biological research. Antibody phage display has become the leading tool for the rapid isolation of single-chain variable fragment (scFv) antibodies in vitro for research applications, but there is usually a gap between scFv isolation and its application in an array format suitable for high-throughput proteomics. In this chapter, we present our antibody phage display system where antibody isolation and scFv immobilization are facilitated by the design of the phagemid vector used as platform. In our system, the scFvs are fused at their C-termini to a cellulose-binding domain (CBD) and can be immobilized onto cellulose-based filters. This made it possible to develop a unique filter lift screen that allowed the efficient screen for multiple binding specificities, and to directly apply library-derived scFvs in an antibody spotted microarray.

Molecular Simulation of Receptor Occupancy and Tumor Penetration of an Antibody and Smaller Scaffolds: Application to Molecular Imaging.

PubMed

Orcutt, Kelly D; Adams, Gregory P; Wu, Anna M; Silva, Matthew D; Harwell, Catey; Hoppin, Jack; Matsumura, Manabu; Kotsuma, Masakatsu; Greenberg, Jonathan; Scott, Andrew M; Beckman, Robert A

2017-10-01

Competitive radiolabeled antibody imaging can determine the unlabeled intact antibody dose that fully blocks target binding but may be confounded by heterogeneous tumor penetration. We evaluated the hypothesis that smaller radiolabeled constructs can be used to more accurately evaluate tumor expressed receptors. The Krogh cylinder distributed model, including bivalent binding and variable intervessel distances, simulated distribution of smaller constructs in the presence of increasing doses of labeled antibody forms. Smaller constructs <25 kDa accessed binding sites more uniformly at large distances from blood vessels compared with larger constructs and intact antibody. These observations were consistent for different affinity and internalization characteristics of constructs. As predicted, a higher dose of unlabeled intact antibody was required to block binding to these distant receptor sites. Small radiolabeled constructs provide more accurate information on total receptor expression in tumors and reveal the need for higher antibody doses for target receptor blockade.

Development of Spatiotemporal Bias-Correction Techniques for Downscaling GCM Predictions

NASA Astrophysics Data System (ADS)

Hwang, S.; Graham, W. D.; Geurink, J.; Adams, A.; Martinez, C. J.

2010-12-01

Accurately representing the spatial variability of precipitation is an important factor for predicting watershed response to climatic forcing, particularly in small, low-relief watersheds affected by convective storm systems. Although Global Circulation Models (GCMs) generally preserve spatial relationships between large-scale and local-scale mean precipitation trends, most GCM downscaling techniques focus on preserving only observed temporal variability on point by point basis, not spatial patterns of events. Downscaled GCM results (e.g., CMIP3 ensembles) have been widely used to predict hydrologic implications of climate variability and climate change in large snow-dominated river basins in the western United States (Diffenbaugh et al., 2008; Adam et al., 2009). However fewer applications to smaller rain-driven river basins in the southeastern US (where preserving spatial variability of rainfall patterns may be more important) have been reported. In this study a new method was developed to bias-correct GCMs to preserve both the long term temporal mean and variance of the precipitation data, and the spatial structure of daily precipitation fields. Forty-year retrospective simulations (1960-1999) from 16 GCMs were collected (IPCC, 2007; WCRP CMIP3 multi-model database: https://esg.llnl.gov:8443/), and the daily precipitation data at coarse resolution (i.e., 280km) were interpolated to 12km spatial resolution and bias corrected using gridded observations over the state of Florida (Maurer et al., 2002; Wood et al, 2002; Wood et al, 2004). In this method spatial random fields which preserved the observed spatial correlation structure of the historic gridded observations and the spatial mean corresponding to the coarse scale GCM daily rainfall were generated. The spatiotemporal variability of the spatio-temporally bias-corrected GCMs were evaluated against gridded observations, and compared to the original temporally bias-corrected and downscaled CMIP3 data for the central Florida. The hydrologic response of two southwest Florida watersheds to the gridded observation data, the original bias corrected CMIP3 data, and the new spatiotemporally corrected CMIP3 predictions was compared using an integrated surface-subsurface hydrologic model developed by Tampa Bay Water.

The challenges of modelling antibody repertoire dynamics in HIV infection

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

Luo, Shishi; Perelson, Alan S.

Antibody affinity maturation by somatic hypermutation of B-cell immunoglobulin variable region genes has been studied for decades in various model systems using well-defined antigens. While much is known about the molecular details of the process, our understanding of the selective forces that generate affinity maturation are less well developed, particularly in the case of a co-evolving pathogen such as HIV. Despite this gap in understanding, high-throughput antibody sequence data are increasingly being collected to investigate the evolutionary trajectories of antibody lineages in HIV-infected individuals. Here, we review what is known in controlled experimental systems about the mechanisms underlying antibody selectionmore » and compare this to the observed temporal patterns of antibody evolution in HIV infection. In addition, we describe how our current understanding of antibody selection mechanisms leaves questions about antibody dynamics in HIV infection unanswered. Without a mechanistic understanding of antibody selection in the context of a co-evolving viral population, modelling and analysis of antibody sequences in HIV-infected individuals will be limited in their interpretation and predictive ability.« less

The challenges of modelling antibody repertoire dynamics in HIV infection

DOE PAGES

Luo, Shishi; Perelson, Alan S.

2015-07-20

Antibody affinity maturation by somatic hypermutation of B-cell immunoglobulin variable region genes has been studied for decades in various model systems using well-defined antigens. While much is known about the molecular details of the process, our understanding of the selective forces that generate affinity maturation are less well developed, particularly in the case of a co-evolving pathogen such as HIV. Despite this gap in understanding, high-throughput antibody sequence data are increasingly being collected to investigate the evolutionary trajectories of antibody lineages in HIV-infected individuals. Here, we review what is known in controlled experimental systems about the mechanisms underlying antibody selectionmore » and compare this to the observed temporal patterns of antibody evolution in HIV infection. In addition, we describe how our current understanding of antibody selection mechanisms leaves questions about antibody dynamics in HIV infection unanswered. Without a mechanistic understanding of antibody selection in the context of a co-evolving viral population, modelling and analysis of antibody sequences in HIV-infected individuals will be limited in their interpretation and predictive ability.« less

North Atlantic climate model bias influence on multiyear predictability

NASA Astrophysics Data System (ADS)

Wu, Y.; Park, T.; Park, W.; Latif, M.

2018-01-01

The influences of North Atlantic biases on multiyear predictability of unforced surface air temperature (SAT) variability are examined in the Kiel Climate Model (KCM). By employing a freshwater flux correction over the North Atlantic to the model, which strongly alleviates both North Atlantic sea surface salinity (SSS) and sea surface temperature (SST) biases, the freshwater flux-corrected integration depicts significantly enhanced multiyear SAT predictability in the North Atlantic sector in comparison to the uncorrected one. The enhanced SAT predictability in the corrected integration is due to a stronger and more variable Atlantic Meridional Overturning Circulation (AMOC) and its enhanced influence on North Atlantic SST. Results obtained from preindustrial control integrations of models participating in the Coupled Model Intercomparison Project Phase 5 (CMIP5) support the findings obtained from the KCM: models with large North Atlantic biases tend to have a weak AMOC influence on SAT and exhibit a smaller SAT predictability over the North Atlantic sector.

Steady-State Density Functional Theory for Finite Bias Conductances.

PubMed

Stefanucci, G; Kurth, S

2015-12-09

In the framework of density functional theory, a formalism to describe electronic transport in the steady state is proposed which uses the density on the junction and the steady current as basic variables. We prove that, in a finite window around zero bias, there is a one-to-one map between the basic variables and both local potential on as well as bias across the junction. The resulting Kohn-Sham system features two exchange-correlation (xc) potentials, a local xc potential, and an xc contribution to the bias. For weakly coupled junctions the xc potentials exhibit steps in the density-current plane which are shown to be crucial to describe the Coulomb blockade diamonds. At small currents these steps emerge as the equilibrium xc discontinuity bifurcates. The formalism is applied to a model benzene junction, finding perfect agreement with the orthodox theory of Coulomb blockade.

Inference for binomial probability based on dependent Bernoulli random variables with applications to meta-analysis and group level studies.

PubMed

Bakbergenuly, Ilyas; Kulinskaya, Elena; Morgenthaler, Stephan

2016-07-01

We study bias arising as a result of nonlinear transformations of random variables in random or mixed effects models and its effect on inference in group-level studies or in meta-analysis. The findings are illustrated on the example of overdispersed binomial distributions, where we demonstrate considerable biases arising from standard log-odds and arcsine transformations of the estimated probability p̂, both for single-group studies and in combining results from several groups or studies in meta-analysis. Our simulations confirm that these biases are linear in ρ, for small values of ρ, the intracluster correlation coefficient. These biases do not depend on the sample sizes or the number of studies K in a meta-analysis and result in abysmal coverage of the combined effect for large K. We also propose bias-correction for the arcsine transformation. Our simulations demonstrate that this bias-correction works well for small values of the intraclass correlation. The methods are applied to two examples of meta-analyses of prevalence. © 2016 The Authors. Biometrical Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Antibody responses to the chlamydial heat shock proteins hsp60 and hsp70 are H-2 linked.

PubMed Central

Zhong, G; Brunham, R C

1992-01-01

The effects of both H-2 and non-H-2 genes on antibody responses to two Chlamydia trachomatis heat shock proteins (hsp60 and hsp70) were investigated. These chlamydial proteins are homologs of Escherichia coli GroEL (hsp60) and DnaK (hsp70) and are highly sequence conserved between bacterial and mammalian sources. Antibody responses among 17 different strains of mice immunized with C. trachomatis serovar B and serovar C elementary bodies were evaluated by immunoblot, radioimmunoprecipitation and enzyme-linked immunosorbent assay. Antibody responses to the two proteins displayed host genetic restriction. Of six distinctive H-2 haplotypes, only H-2d generated high antibody responses to hsp70. Five of the six H-2 haplotypes, i.e., H-2a, H-2d, H-2k, H-2q, and H-2s, produced high antibody responses to hsp60. Only the H-2b-bearing strain had low antibody responses to hsp60. By using congenic and H-2 recombinant strains, the genes responsible for regulating antibody responses to hsp70 and hsp60 were mapped to the K-IA region of the H-2 locus. In F1 hybrid crosses between high and low responders, high responses to hsp60 and hsp70 were dominant traits. Other genes outside the H-2 locus also influenced antibody responses to hsp60 and hsp70, since inbred strains of identical H-2 but different background genes displayed variable antibody responses to the proteins. The genetic control of murine immune responses to C. trachomatis hsp60, a putative chlamydial immunopathologic antigen, suggests that a similar genetic mechanism may also exist in humans, and this observation may help to explain the observed variability in the spectrum of chlamydial diseases seen in humans. Images PMID:1639484

Facile Affinity Maturation of Antibody Variable Domains Using Natural Diversity Mutagenesis

PubMed Central

Tiller, Kathryn E.; Chowdhury, Ratul; Li, Tong; Ludwig, Seth D.; Sen, Sabyasachi; Maranas, Costas D.; Tessier, Peter M.

2017-01-01

The identification of mutations that enhance antibody affinity while maintaining high antibody specificity and stability is a time-consuming and laborious process. Here, we report an efficient methodology for systematically and rapidly enhancing the affinity of antibody variable domains while maximizing specificity and stability using novel synthetic antibody libraries. Our approach first uses computational and experimental alanine scanning mutagenesis to identify sites in the complementarity-determining regions (CDRs) that are permissive to mutagenesis while maintaining antigen binding. Next, we mutagenize the most permissive CDR positions using degenerate codons to encode wild-type residues and a small number of the most frequently occurring residues at each CDR position based on natural antibody diversity. This mutagenesis approach results in antibody libraries with variants that have a wide range of numbers of CDR mutations, including antibody domains with single mutations and others with tens of mutations. Finally, we sort the modest size libraries (~10 million variants) displayed on the surface of yeast to identify CDR mutations with the greatest increases in affinity. Importantly, we find that single-domain (VHH) antibodies specific for the α-synuclein protein (whose aggregation is associated with Parkinson’s disease) with the greatest gains in affinity (>5-fold) have several (four to six) CDR mutations. This finding highlights the importance of sampling combinations of CDR mutations during the first step of affinity maturation to maximize the efficiency of the process. Interestingly, we find that some natural diversity mutations simultaneously enhance all three key antibody properties (affinity, specificity, and stability) while other mutations enhance some of these properties (e.g., increased specificity) and display trade-offs in others (e.g., reduced affinity and/or stability). Computational modeling reveals that improvements in affinity are generally not due to direct interactions involving CDR mutations but rather due to indirect effects that enhance existing interactions and/or promote new interactions between the antigen and wild-type CDR residues. We expect that natural diversity mutagenesis will be useful for efficient affinity maturation of a wide range of antibody fragments and full-length antibodies. PMID:28928732

Validation of satellite-based rainfall in Kalahari

NASA Astrophysics Data System (ADS)

Lekula, Moiteela; Lubczynski, Maciek W.; Shemang, Elisha M.; Verhoef, Wouter

2018-06-01

Water resources management in arid and semi-arid areas is hampered by insufficient rainfall data, typically obtained from sparsely distributed rain gauges. Satellite-based rainfall estimates (SREs) are alternative sources of such data in these areas. In this study, daily rainfall estimates from FEWS-RFE∼11 km, TRMM-3B42∼27 km, CMOPRH∼27 km and CMORPH∼8 km were evaluated against nine, daily rain gauge records in Central Kalahari Basin (CKB), over a five-year period, 01/01/2001-31/12/2005. The aims were to evaluate the daily rainfall detection capabilities of the four SRE algorithms, analyze the spatio-temporal variability of rainfall in the CKB and perform bias-correction of the four SREs. Evaluation methods included scatter plot analysis, descriptive statistics, categorical statistics and bias decomposition. The spatio-temporal variability of rainfall, was assessed using the SREs' mean annual rainfall, standard deviation, coefficient of variation and spatial correlation functions. Bias correction of the four SREs was conducted using a Time-Varying Space-Fixed bias-correction scheme. The results underlined the importance of validating daily SREs, as they had different rainfall detection capabilities in the CKB. The FEWS-RFE∼11 km performed best, providing better results of descriptive and categorical statistics than the other three SREs, although bias decomposition showed that all SREs underestimated rainfall. The analysis showed that the most reliable SREs performance analysis indicator were the frequency of "miss" rainfall events and the "miss-bias", as they directly indicated SREs' sensitivity and bias of rainfall detection, respectively. The Time Varying and Space Fixed (TVSF) bias-correction scheme, improved some error measures but resulted in the reduction of the spatial correlation distance, thus increased, already high, spatial rainfall variability of all the four SREs. This study highlighted SREs as valuable source of daily rainfall data providing good spatio-temporal data coverage especially suitable for areas with limited rain gauges, such as the CKB, but also emphasized SREs' drawbacks, creating avenue for follow up research.

Subseasonal forecast skills and biases of global summer monsoons in the NCEP Climate Forecast System version 2

NASA Astrophysics Data System (ADS)

Liu, Xiangwen; Yang, Song; Li, Qiaoping; Kumar, Arun; Weaver, Scott; Liu, Shi

2014-03-01

Subseasonal forecast skills and biases of global summer monsoons are diagnosed using daily data from the hindcasts of 45-day integrations by the NCEP Climate Forecast System version 2. Predictions for subseasonal variability of zonal wind and precipitation are generally more skillful over the Asian and Australian monsoon regions than other monsoon regions. Climatologically, forecasts for the variations of dynamical monsoon indices have high skills at leads of about 2 weeks. However, apparent interannual differences exist, with high skills up to 5 weeks in exceptional cases. Comparisons for the relationships of monsoon indices with atmospheric circulation and precipitation patterns between skillful and unskillful forecasts indicate that skills for subseasonal variability of a monsoon index depend partially on the degree to which the observed variability of the index attributes to the variation of large-scale circulation. Thus, predictions are often more skillful when the index is closely linked to atmospheric circulation over a broad region than over a regional and narrow range. It is also revealed that, the subseasonal variations of biases of winds, precipitation, and surface temperature over various monsoon regions are captured by a first mode with seasonally independent biases and a second mode with apparent phase transition of biases during summer. The first mode indicates the dominance of overall weaker-than-observed summer monsoons over major monsoon regions. However, at certain stages of monsoon evolution, these underestimations are regionally offset or intensified by the time evolving biases portrayed by the second mode. This feature may be partially related to factors such as the shifts of subtropical highs and intertropical convergence zones, the reversal of biases of surface temperature over some monsoon regions, and the transition of regional circulation system. The significant geographical differences in bias growth with increasing lead time reflect the distinctions of initial memory capability of the climate system over different monsoon regions.

Impacts of Model Bias on the Climate Change Signal and Effects of Weighted Ensembles of Regional Climate Model Simulations: A Case Study over Southern Québec, Canada

DOE PAGES

Eum, Hyung-Il; Gachon, Philippe; Laprise, René

2016-01-01

This study examined the impact of model biases on climate change signals for daily precipitation and for minimum and maximum temperatures. Through the use of multiple climate scenarios from 12 regional climate model simulations, the ensemble mean, and three synthetic simulations generated by a weighting procedure, we investigated intermodel seasonal climate change signals between current and future periods, for both median and extreme precipitation/temperature values. A significant dependence of seasonal climate change signals on the model biases over southern Québec in Canada was detected for temperatures, but not for precipitation. This suggests that the regional temperature change signal is affectedmore » by local processes. Seasonally, model bias affects future mean and extreme values in winter and summer. In addition, potentially large increases in future extremes of temperature and precipitation values were projected. For three synthetic scenarios, systematically less bias and a narrow range of mean change for all variables were projected compared to those of climate model simulations. In addition, synthetic scenarios were found to better capture the spatial variability of extreme cold temperatures than the ensemble mean scenario. Finally, these results indicate that the synthetic scenarios have greater potential to reduce the uncertainty of future climate projections and capture the spatial variability of extreme climate events.« less

Impacts of Model Bias on the Climate Change Signal and Effects of Weighted Ensembles of Regional Climate Model Simulations: A Case Study over Southern Québec, Canada

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

Eum, Hyung-Il; Gachon, Philippe; Laprise, René

This study examined the impact of model biases on climate change signals for daily precipitation and for minimum and maximum temperatures. Through the use of multiple climate scenarios from 12 regional climate model simulations, the ensemble mean, and three synthetic simulations generated by a weighting procedure, we investigated intermodel seasonal climate change signals between current and future periods, for both median and extreme precipitation/temperature values. A significant dependence of seasonal climate change signals on the model biases over southern Québec in Canada was detected for temperatures, but not for precipitation. This suggests that the regional temperature change signal is affectedmore » by local processes. Seasonally, model bias affects future mean and extreme values in winter and summer. In addition, potentially large increases in future extremes of temperature and precipitation values were projected. For three synthetic scenarios, systematically less bias and a narrow range of mean change for all variables were projected compared to those of climate model simulations. In addition, synthetic scenarios were found to better capture the spatial variability of extreme cold temperatures than the ensemble mean scenario. Finally, these results indicate that the synthetic scenarios have greater potential to reduce the uncertainty of future climate projections and capture the spatial variability of extreme climate events.« less

An efficient method for variable region assembly in the construction of scFv phage display libraries using independent strand amplification

PubMed Central

Sotelo, Pablo H.; Collazo, Noberto; Zuñiga, Roberto; Gutiérrez-González, Matías; Catalán, Diego; Ribeiro, Carolina Hager; Aguillón, Juan Carlos; Molina, María Carmen

2012-01-01

Phage display library technology is a common method to produce human antibodies. In this technique, the immunoglobulin variable regions are displayed in a bacteriophage in a way that each filamentous virus displays the product of a single antibody gene on its surface. From the collection of different phages, it is possible to isolate the virus that recognizes specific targets. The most common form in which to display antibody variable regions in the phage is the single chain variable fragment format (scFv), which requires assembly of the heavy and light immunoglobulin variable regions in a single gene. In this work, we describe a simple and efficient method for the assembly of immunoglobulin heavy and light chain variable regions in a scFv format. This procedure involves a two-step reaction: (1) DNA amplification to produce the single strand form of the heavy or light chain gene required for the fusion; and (2) mixture of both single strand products followed by an assembly reaction to construct a complete scFv gene. Using this method, we produced 6-fold more scFv encoding DNA than the commonly used splicing by overlap extension PCR (SOE-PCR) approach. The scFv gene produced by this method also proved to be efficient in generating a diverse scFv phage display library. From this scFv library, we obtained phages that bound several non-related antigens, including recombinant proteins and rotavirus particles. PMID:22692130

Development of single chain variable fragment (scFv) antibodies against Xylella fastidiosa subsp. pauca by phage display.

PubMed

Yuan, Qing; Jordan, Ramon; Brlansky, Ronald H; Istomina, Olga; Hartung, John

2015-10-01

Xylella fastidiosa is a member of the gamma proteobacteria. It is fastidious, insect-vectored and xylem-limited and causes a variety of diseases, some severe, on a wide range of economically important perennial crops, including grape and citrus. Antibody based detection assays are commercially available for X. fastidiosa, and are effective at the species, but not at the subspecies level. We have made a library of scFv antibody fragments directed against X. fastidiosa subsp. pauca strain 9a5c (citrus) by using phage display technology. Antibody gene repertoires were PCR-amplified using 23 primers for the heavy chain variable region (V(H)) and 21 primers for the light chain variable region (V(L)). The V(H) and V(L) were joined by overlap extension PCR, and then the genes of the scFv library were ligated into the phage vector pKM19. The library contained 1.2×10(7) independent clones with full-length scFv inserts. In each of 3cycles of affinity-selection with 9a5c, about 1.0×10(12) phage were used for panning with 4.1×10(6), 7.1×10(6), 2.1×10(7) phage recovered after the first, second and third cycles, respectively. Sixty-six percent of clones from the final library bound X. fastidiosa 9a5c in an ELISA. Some of these scFv antibodies recognized strain 9a5c and did not recognize X. fastidiosa strains that cause Pierce's disease of grapevine. Published by Elsevier B.V.

Fab-based bispecific antibody formats with robust biophysical properties and biological activity.

PubMed

Wu, Xiufeng; Sereno, Arlene J; Huang, Flora; Lewis, Steven M; Lieu, Ricky L; Weldon, Caroline; Torres, Carina; Fine, Cody; Batt, Micheal A; Fitchett, Jonathan R; Glasebrook, Andrew L; Kuhlman, Brian; Demarest, Stephen J

2015-01-01

A myriad of innovative bispecific antibody (BsAb) platforms have been reported. Most require significant protein engineering to be viable from a development and manufacturing perspective. Single-chain variable fragments (scFvs) and diabodies that consist only of antibody variable domains have been used as building blocks for making BsAbs for decades. The drawback with Fv-only moieties is that they lack the native-like interactions with CH1/CL domains that make antibody Fab regions stable and soluble. Here, we utilize a redesigned Fab interface to explore 2 novel Fab-based BsAbs platforms. The redesigned Fab interface designs limit heavy and light chain mixing when 2 Fabs are co-expressed simultaneously, thus allowing the use of 2 different Fabs within a BsAb construct without the requirement of one or more scFvs. We describe the stability and activity of a HER2×HER2 IgG-Fab BsAb, and compare its biophysical and activity properties with those of an IgG-scFv that utilizes the variable domains of the same parental antibodies. We also generated an EGFR × CD3 tandem Fab protein with a similar format to a tandem scFv (otherwise known as a bispecific T cell engager or BiTE). We show that the Fab-based BsAbs have superior biophysical properties compared to the scFv-based BsAbs. Additionally, the Fab-based BsAbs do not simply recapitulate the activity of their scFv counterparts, but are shown to possess unique biological activity.

Fab-based bispecific antibody formats with robust biophysical properties and biological activity

PubMed Central

Wu, Xiufeng; Sereno, Arlene J; Huang, Flora; Lewis, Steven M; Lieu, Ricky L; Weldon, Caroline; Torres, Carina; Fine, Cody; Batt, Micheal A; Fitchett, Jonathan R; Glasebrook, Andrew L; Kuhlman, Brian; Demarest, Stephen J

2015-01-01

A myriad of innovative bispecific antibody (BsAb) platforms have been reported. Most require significant protein engineering to be viable from a development and manufacturing perspective. Single-chain variable fragments (scFvs) and diabodies that consist only of antibody variable domains have been used as building blocks for making BsAbs for decades. The drawback with Fv-only moieties is that they lack the native-like interactions with CH1/CL domains that make antibody Fab regions stable and soluble. Here, we utilize a redesigned Fab interface to explore 2 novel Fab-based BsAbs platforms. The redesigned Fab interface designs limit heavy and light chain mixing when 2 Fabs are co-expressed simultaneously, thus allowing the use of 2 different Fabs within a BsAb construct without the requirement of one or more scFvs. We describe the stability and activity of a HER2×HER2 IgG-Fab BsAb, and compare its biophysical and activity properties with those of an IgG-scFv that utilizes the variable domains of the same parental antibodies. We also generated an EGFR × CD3 tandem Fab protein with a similar format to a tandem scFv (otherwise known as a bispecific T cell engager or BiTE). We show that the Fab-based BsAbs have superior biophysical properties compared to the scFv-based BsAbs. Additionally, the Fab-based BsAbs do not simply recapitulate the activity of their scFv counterparts, but are shown to possess unique biological activity. PMID:25774965

Evaluation and optimization of a commercial blocking ELISA for detecting antibodies to influenza A virus for research and surveillance of mallards.

PubMed

Shriner, Susan A; VanDalen, Kaci K; Root, J Jeffrey; Sullivan, Heather J

2016-02-01

The availability of a validated commercial assay is an asset for any wildlife investigation. However, commercial products are often developed for use in livestock and are not optimized for wildlife. Consequently, it is incumbent upon researchers and managers to apply commercial products appropriately to optimize program outcomes. We tested more than 800 serum samples from mallards for antibodies to influenza A virus with the IDEXX AI MultiS-Screen Ab test to evaluate assay performance. Applying the test per manufacturer's recommendations resulted in good performance with 84% sensitivity and 100% specificity. However, performance was improved to 98% sensitivity and 98% specificity by increasing the recommended cut-off. Using this alternative threshold for identifying positive and negative samples would greatly improve sample classification, especially for field samples collected months after infection when antibody titers have waned from the initial primary immune response. Furthermore, a threshold that balances sensitivity and specificity reduces estimation bias in seroprevalence estimates. Published by Elsevier B.V.

Spatial scaling of net primary productivity using subpixel landcover information

NASA Astrophysics Data System (ADS)

Chen, X. F.; Chen, Jing M.; Ju, Wei M.; Ren, L. L.

2008-10-01

Gridding the land surface into coarse homogeneous pixels may cause important biases on ecosystem model estimations of carbon budget components at local, regional and global scales. These biases result from overlooking subpixel variability of land surface characteristics. Vegetation heterogeneity is an important factor introducing biases in regional ecological modeling, especially when the modeling is made on large grids. This study suggests a simple algorithm that uses subpixel information on the spatial variability of land cover type to correct net primary productivity (NPP) estimates, made at coarse spatial resolutions where the land surface is considered as homogeneous within each pixel. The algorithm operates in such a way that NPP obtained from calculations made at coarse spatial resolutions are multiplied by simple functions that attempt to reproduce the effects of subpixel variability of land cover type on NPP. Its application to a carbon-hydrology coupled model(BEPS-TerrainLab model) estimates made at a 1-km resolution over a watershed (named Baohe River Basin) located in the southwestern part of Qinling Mountains, Shaanxi Province, China, improved estimates of average NPP as well as its spatial variability.

HIV-1 Gag p17 presented as virus-like particles on the E2 scaffold from Geobacillus stearothermophilus induces sustained humoral and cellular immune responses in the absence of IFN{gamma} production by CD4+ T cells

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

Caivano, Antonella; Doria-Rose, Nicole A.; Dept. of Molecular and Cell Biology, University of Washington, Seattle, WA 98124-6108

2010-11-25

We have constructed stable virus-like particles displaying the HIV-1 Gag(p17) protein as an N-terminal fusion with an engineered protein domain from the Geobacillus stearothermophilus pyruvate dehydrogenase subunit E2. Mice immunized with the Gag(p17)-E2 60-mer scaffold particles mounted a strong and sustained antibody response. Antibodies directed to Gag(p17) were boosted significantly with additional immunizations, while anti-E2 responses reached a plateau. The isotype of the induced antibodies was biased towards IgG1, and the E2-primed CD4+ T cells did not secrete IFN{gamma}. Using transgenic mouse model systems, we demonstrated that CD8+ T cells primed with E2 particles were able to exert lytic activitymore » and produce IFN{gamma}. These results show that the E2 scaffold represents a powerful vaccine delivery system for whole antigenic proteins or polyepitope engineered proteins, evoking antibody production and antigen specific CTL activity even in the absence of IFN{gamma}-producing CD4+ T cells.« less

Antibody quality and protection from lethal Ebola virus challenge in nonhuman primates immunized with rabies virus based bivalent vaccine.

PubMed

Blaney, Joseph E; Marzi, Andrea; Willet, Mallory; Papaneri, Amy B; Wirblich, Christoph; Feldmann, Friederike; Holbrook, Michael; Jahrling, Peter; Feldmann, Heinz; Schnell, Matthias J

2013-01-01

We have previously described the generation of a novel Ebola virus (EBOV) vaccine platform based on (a) replication-competent rabies virus (RABV), (b) replication-deficient RABV, or (c) chemically inactivated RABV expressing EBOV glycoprotein (GP). Mouse studies demonstrated safety, immunogenicity, and protective efficacy of these live or inactivated RABV/EBOV vaccines. Here, we evaluated these vaccines in nonhuman primates. Our results indicate that all three vaccines do induce potent immune responses against both RABV and EBOV, while the protection of immunized animals against EBOV was largely dependent on the quality of humoral immune response against EBOV GP. We also determined if the induced antibodies against EBOV GP differ in their target, affinity, or the isotype. Our results show that IgG1-biased humoral responses as well as high levels of GP-specific antibodies were beneficial for the control of EBOV infection after immunization. These results further support the concept that a successful EBOV vaccine needs to induce strong antibodies against EBOV. We also showed that a dual vaccine against RABV and filoviruses is achievable; therefore addressing concerns for the marketability of this urgently needed vaccine.

Single-Domain Antibodies and the Promise of Modular Targeting in Cancer Imaging and Treatment

PubMed Central

Iezzi, María Elena; Policastro, Lucía; Werbajh, Santiago; Podhajcer, Osvaldo; Canziani, Gabriela Alicia

2018-01-01

Monoclonal antibodies and their fragments have significantly changed the outcome of cancer in the clinic, effectively inhibiting tumor cell proliferation, triggering antibody-dependent immune effector cell activation and complement mediated cell death. Along with a continued expansion in number, diversity, and complexity of validated tumor targets there is an increasing focus on engineering recombinant antibody fragments for lead development. Single-domain antibodies (sdAbs), in particular those engineered from the variable heavy-chain fragment (VHH gene) found in Camelidae heavy-chain antibodies (or IgG2 and IgG3), are the smallest fragments that retain the full antigen-binding capacity of the antibody with advantageous properties as drugs. For similar reasons, growing attention is being paid to the yet smaller variable heavy chain new antigen receptor (VNAR) fragments found in Squalidae. sdAbs have been selected, mostly from immune VHH libraries, to inhibit or modulate enzyme activity, bind soluble factors, internalize cell membrane receptors, or block cytoplasmic targets. This succinct review is a compilation of recent data documenting the application of engineered, recombinant sdAb in the clinic as epitope recognition “modules” to build monomeric, dimeric and multimeric ligands that target, tag and stall solid tumor growth in vivo. Size, affinity, specificity, and the development profile of sdAbs drugs are seemingly consistent with desirable clinical efficacy and safety requirements. But the hepatotoxicity of the tetrameric anti-DR5-VHH drug in patients with pre-existing anti-drug antibodies halted the phase I clinical trial and called for a thorough pre-screening of the immune and poly-specific reactivities of the sdAb leads. PMID:29520274

Evaluating the Use of Antibody Variable Region (Fv) Charge as a Risk Assessment Tool for Predicting Typical Cynomolgus Monkey Pharmacokinetics*

PubMed Central

Bumbaca Yadav, Daniela; Sharma, Vikas K.; Boswell, Charles Andrew; Hotzel, Isidro; Tesar, Devin; Shang, Yonglei; Ying, Yong; Fischer, Saloumeh K.; Grogan, Jane L.; Chiang, Eugene Y.; Urban, Konnie; Ulufatu, Sheila; Khawli, Leslie A.; Prabhu, Saileta; Joseph, Sean; Kelley, Robert F.

2015-01-01

The pharmacokinetic (PK) behavior of monoclonal antibodies in cynomolgus monkeys (cynos) is generally translatable to that in humans. Unfortunately, about 39% of the antibodies evaluated for PKs in cynos have fast nonspecific (or non-target-mediated) clearance (in-house data). An empirical model relating variable region (Fv) charge and hydrophobicity to cyno nonspecific clearance was developed to gauge the risk an antibody would have for fast nonspecific clearance in the monkey. The purpose of this study was to evaluate the predictability of this empirical model on cyno nonspecific clearance with antibodies specifically engineered to have either high or low Fv charge. These amino acid changes were made in the Fv region of two test antibodies, humAb4D5-8 and anti-lymphotoxin α. The humAb4D5-8 has a typical nonspecific clearance in cynos, and by making it more positively charged, the antibody acquires fast nonspecific clearance, and making it less positively charged did not impact its clearance. Anti-lymphotoxin α has fast nonspecific clearance in cynos, and making it more positively charged caused it to clear even faster, whereas making it less positively charged caused it to clear slower and within the typical range. These trends in clearance were also observed in two other preclinical species, mice and rats. The effect of modifying Fv charge on subcutaneous bioavailability was also examined, and in general bioavailability was inversely related to the direction of the Fv charge change. Thus, modifying Fv charge appears to impact antibody PKs, and the changes tended to correlate with those predicted by the empirical model. PMID:26491012

Treatment Effect Estimation Using Nonlinear Two-Stage Instrumental Variable Estimators: Another Cautionary Note.

PubMed

Chapman, Cole G; Brooks, John M

2016-12-01

To examine the settings of simulation evidence supporting use of nonlinear two-stage residual inclusion (2SRI) instrumental variable (IV) methods for estimating average treatment effects (ATE) using observational data and investigate potential bias of 2SRI across alternative scenarios of essential heterogeneity and uniqueness of marginal patients. Potential bias of linear and nonlinear IV methods for ATE and local average treatment effects (LATE) is assessed using simulation models with a binary outcome and binary endogenous treatment across settings varying by the relationship between treatment effectiveness and treatment choice. Results show that nonlinear 2SRI models produce estimates of ATE and LATE that are substantially biased when the relationships between treatment and outcome for marginal patients are unique from relationships for the full population. Bias of linear IV estimates for LATE was low across all scenarios. Researchers are increasingly opting for nonlinear 2SRI to estimate treatment effects in models with binary and otherwise inherently nonlinear dependent variables, believing that it produces generally unbiased and consistent estimates. This research shows that positive properties of nonlinear 2SRI rely on assumptions about the relationships between treatment effect heterogeneity and choice. © Health Research and Educational Trust.

Towards identification of relevant variables in the observed aerosol optical depth bias between MODIS and AERONET observations

NASA Astrophysics Data System (ADS)

Malakar, N. K.; Lary, D. J.; Gencaga, D.; Albayrak, A.; Wei, J.

2013-08-01

Measurements made by satellite remote sensing, Moderate Resolution Imaging Spectroradiometer (MODIS), and globally distributed Aerosol Robotic Network (AERONET) are compared. Comparison of the two datasets measurements for aerosol optical depth values show that there are biases between the two data products. In this paper, we present a general framework towards identifying relevant set of variables responsible for the observed bias. We present a general framework to identify the possible factors influencing the bias, which might be associated with the measurement conditions such as the solar and sensor zenith angles, the solar and sensor azimuth, scattering angles, and surface reflectivity at the various measured wavelengths, etc. Specifically, we performed analysis for remote sensing Aqua-Land data set, and used machine learning technique, neural network in this case, to perform multivariate regression between the ground-truth and the training data sets. Finally, we used mutual information between the observed and the predicted values as the measure of similarity to identify the most relevant set of variables. The search is brute force method as we have to consider all possible combinations. The computations involves a huge number crunching exercise, and we implemented it by writing a job-parallel program.

Measurement error in epidemiologic studies of air pollution based on land-use regression models.

PubMed

Basagaña, Xavier; Aguilera, Inmaculada; Rivera, Marcela; Agis, David; Foraster, Maria; Marrugat, Jaume; Elosua, Roberto; Künzli, Nino

2013-10-15

Land-use regression (LUR) models are increasingly used to estimate air pollution exposure in epidemiologic studies. These models use air pollution measurements taken at a small set of locations and modeling based on geographical covariates for which data are available at all study participant locations. The process of LUR model development commonly includes a variable selection procedure. When LUR model predictions are used as explanatory variables in a model for a health outcome, measurement error can lead to bias of the regression coefficients and to inflation of their variance. In previous studies dealing with spatial predictions of air pollution, bias was shown to be small while most of the effect of measurement error was on the variance. In this study, we show that in realistic cases where LUR models are applied to health data, bias in health-effect estimates can be substantial. This bias depends on the number of air pollution measurement sites, the number of available predictors for model selection, and the amount of explainable variability in the true exposure. These results should be taken into account when interpreting health effects from studies that used LUR models.

Bias in Prediction: A Test of Three Models with Elementary School Children

ERIC Educational Resources Information Center

Frazer, William G.; And Others

1975-01-01

Explores the differences among the traditional single-equation prediction model of test bias, the Cleary and the Thorndike model in a situation involving typical educational variables with young female and male children. (Author/DEP)

A murine monoclonal antibody based enzyme-linked immunosorbent assay for almond (Prunus dulcis L.) detection.

PubMed

Su, Mengna; Venkatachalam, Mahesh; Liu, Changqi; Zhang, Ying; Roux, Kenneth H; Sathe, Shridhar K

2013-11-13

A sandwich enzyme-linked immunosorbent assay (ELISA) using anti-almond soluble protein rabbit polyclonal antibodies as capture antibodies and murine monoclonal antibody 4C10 as the detection antibodies was developed. The assay is specific and sensitive (3-200 ng almond protein/mL) for almond detection. The standardized assay is accurate (<15% CV) and reproducible (intra- and inter assay variability <15% CV). The assay did not register any cross-reactivity with the tested food matrices, suggesting the assay to be almond amandin specific. The assay could detect the presence of declared almond in the tested matched commercial samples. Further, the assay reliably detected the presence of almonds in the laboratory prepared food samples spiked with almond flour.

Immunological aspects of Giardia infections

PubMed Central

Heyworth, Martin F.

2014-01-01

Immunodeficiency, particularly antibody deficiency, predisposes to increased intensity and persistence of Giardia infections. Giardia-infected immunocompetent hosts produce serum and intestinal antibodies against Giardia trophozoites. The number of Giardia muris trophozoites, in mice with G. muris infection, is reduced by intra-duodenal administration of anti-G. muris antibody. Giardia intestinalis antigens that are recognised by human anti-trophozoite antibodies include variable (variant-specific) and invariant proteins. Nitric oxide (NO) appears to contribute to host clearance of Giardia trophozoites. Arginine is a precursor of NO and is metabolised by Giardia trophozoites, possibly reducing its availability for generation of NO by the host. Work with mice suggests that T lymphocytes and interleukin-6 (IL-6) contribute to clearance of Giardia infection via mechanisms independent of antibodies. PMID:25347704

Theoretic criteria for antibody penetration into solid tumors and micrometastases.

PubMed

Thurber, Greg M; Zajic, Stefan C; Wittrup, K Dane

2007-06-01

Targeting tumors with antibody-based therapeutics is a complex task presenting multiple kinetic barriers. Antibody internalization and clearance inhibit uptake both in solid tumors, limited by tumor vascular permeability, and in micrometastases, limited by diffusion. A modeling exercise is used to introduce 2 simple criteria that must be less than unity for saturation of both tumors and micrometastases. The clearance modulus and the Thiele modulus are ratios of the plasma clearance rate and antibody catabolism, respectively, to the tumor tissue penetration rate. Even low rates of antigen internalization from constitutive membrane turnover can significantly retard antibody penetration. Rapid clearance of single-chain variable fragments also hinders uptake, often more than counterbalancing their more rapid extravasation and diffusion. The model illustrates that with the large resistance from the tumor capillary, antibodies may be more suitable for targeting micrometastases than vascularized tumors.

Genetic instrumental variable regression: Explaining socioeconomic and health outcomes in nonexperimental data

PubMed Central

DiPrete, Thomas A.; Burik, Casper A. P.; Koellinger, Philipp D.

2018-01-01

Identifying causal effects in nonexperimental data is an enduring challenge. One proposed solution that recently gained popularity is the idea to use genes as instrumental variables [i.e., Mendelian randomization (MR)]. However, this approach is problematic because many variables of interest are genetically correlated, which implies the possibility that many genes could affect both the exposure and the outcome directly or via unobserved confounding factors. Thus, pleiotropic effects of genes are themselves a source of bias in nonexperimental data that would also undermine the ability of MR to correct for endogeneity bias from nongenetic sources. Here, we propose an alternative approach, genetic instrumental variable (GIV) regression, that provides estimates for the effect of an exposure on an outcome in the presence of pleiotropy. As a valuable byproduct, GIV regression also provides accurate estimates of the chip heritability of the outcome variable. GIV regression uses polygenic scores (PGSs) for the outcome of interest which can be constructed from genome-wide association study (GWAS) results. By splitting the GWAS sample for the outcome into nonoverlapping subsamples, we obtain multiple indicators of the outcome PGSs that can be used as instruments for each other and, in combination with other methods such as sibling fixed effects, can address endogeneity bias from both pleiotropy and the environment. In two empirical applications, we demonstrate that our approach produces reasonable estimates of the chip heritability of educational attainment (EA) and show that standard regression and MR provide upwardly biased estimates of the effect of body height on EA. PMID:29686100

Genetic instrumental variable regression: Explaining socioeconomic and health outcomes in nonexperimental data.

PubMed

DiPrete, Thomas A; Burik, Casper A P; Koellinger, Philipp D

2018-05-29

Identifying causal effects in nonexperimental data is an enduring challenge. One proposed solution that recently gained popularity is the idea to use genes as instrumental variables [i.e., Mendelian randomization (MR)]. However, this approach is problematic because many variables of interest are genetically correlated, which implies the possibility that many genes could affect both the exposure and the outcome directly or via unobserved confounding factors. Thus, pleiotropic effects of genes are themselves a source of bias in nonexperimental data that would also undermine the ability of MR to correct for endogeneity bias from nongenetic sources. Here, we propose an alternative approach, genetic instrumental variable (GIV) regression, that provides estimates for the effect of an exposure on an outcome in the presence of pleiotropy. As a valuable byproduct, GIV regression also provides accurate estimates of the chip heritability of the outcome variable. GIV regression uses polygenic scores (PGSs) for the outcome of interest which can be constructed from genome-wide association study (GWAS) results. By splitting the GWAS sample for the outcome into nonoverlapping subsamples, we obtain multiple indicators of the outcome PGSs that can be used as instruments for each other and, in combination with other methods such as sibling fixed effects, can address endogeneity bias from both pleiotropy and the environment. In two empirical applications, we demonstrate that our approach produces reasonable estimates of the chip heritability of educational attainment (EA) and show that standard regression and MR provide upwardly biased estimates of the effect of body height on EA. Copyright © 2018 the Author(s). Published by PNAS.

Detecting and correcting the bias of unmeasured factors using perturbation analysis: a data-mining approach.

PubMed

Lee, Wen-Chung

2014-02-05

The randomized controlled study is the gold-standard research method in biomedicine. In contrast, the validity of a (nonrandomized) observational study is often questioned because of unknown/unmeasured factors, which may have confounding and/or effect-modifying potential. In this paper, the author proposes a perturbation test to detect the bias of unmeasured factors and a perturbation adjustment to correct for such bias. The proposed method circumvents the problem of measuring unknowns by collecting the perturbations of unmeasured factors instead. Specifically, a perturbation is a variable that is readily available (or can be measured easily) and is potentially associated, though perhaps only very weakly, with unmeasured factors. The author conducted extensive computer simulations to provide a proof of concept. Computer simulations show that, as the number of perturbation variables increases from data mining, the power of the perturbation test increased progressively, up to nearly 100%. In addition, after the perturbation adjustment, the bias decreased progressively, down to nearly 0%. The data-mining perturbation analysis described here is recommended for use in detecting and correcting the bias of unmeasured factors in observational studies.

Memory bias for threatening information in anxiety and anxiety disorders: a meta-analytic review.

PubMed

Mitte, Kristin

2008-11-01

Although some theories suggest that anxious individuals selectively remember threatening stimuli, findings remain contradictory despite a considerable amount of research. A quantitative integration of 165 studies with 9,046 participants (clinical and nonclinical samples) examined whether a memory bias exists and which moderator variables influence its magnitude. Implicit memory bias was investigated in lexical decision/stimulus identification and word-stem completion paradigms; explicit memory bias was investigated in recognition and recall paradigms. Overall, effect sizes showed no significant impact of anxiety on implicit memory and recognition. Analyses indicated a memory bias for recall, whose magnitude depended on experimental study procedures like the encoding procedure or retention interval. Anxiety influenced recollection of previous experiences; anxious individuals favored threat-related information. Across all paradigms, clinical status was not significantly linked to effect sizes, indicating no qualitative difference in information processing between anxiety patients and high-anxious persons. The large discrepancy between study effects in recall and recognition indicates that future research is needed to identify moderator variables for avoidant and preferred remembering.

Investigation of within- and between-herd variability of bovine leukaemia virus bulk tank milk antibody levels over different sampling intervals in the Canadian Maritimes.

PubMed

John, Emily E; Nekouei, Omid; McClure, J T; Cameron, Marguerite; Keefe, Greg; Stryhn, Henrik

2018-06-01

Bulk tank milk (BTM) samples are used to determine the infection status and estimate dairy herd prevalence for bovine leukaemia virus (BLV) using an antibody ELISA assay. BLV ELISA variability between samples from the same herd or from different herds has not been investigated over long time periods. The main objective of this study was to determine the within-herd and between-herd variability of a BTM BLV ELISA assay over 1-month, 3-month, and 3-year sampling intervals. All of the Canadian Maritime region dairy herds (n = 523) that were active in 2013 and 2016 were included (83.9% and 86.9% of total herds in 2013 and 2016, respectively). BLV antibody levels were measured in three BTM samples collected at 1-month intervals in early 2013 as well as two BTM samples collected over a 3-month interval in early 2016. Random-effects models, with fixed effects for sample replicate and province and random effects for herd, were used to estimate the variability between BTM samples from the same herd and between herds for 1-month, 3-month, and 3-year sampling intervals. The majority of variability of BTM BLV ELISA results was seen between herds (1-month, 6.792 ± 0.533; 3-month, 7.806 ± 0.652; 3-year, 6.222 ± 0.528). Unexplained variance between samples from the same herd, on square-root scale, was greatest for the 3-year (0.976 ± 0.104), followed by the 1-month (0.611 ± 0.035) then the 3-month (0.557 ± 0.071) intervals. Variability of BTM antibody levels within the same herd was present but was much smaller than the variability between herds, and was greatest for the 3-year sampling interval. The 3-month sampling interval resulted in the least variability and is appropriate to use for estimating the baseline level of within-herd prevalence for BLV control programs. Knowledge of the baseline variability and within-herd prevalence can help to determine effectiveness of control programs when BTM sampling is repeated at longer intervals. Copyright © 2018 Elsevier B.V. All rights reserved.

Aging and the Immune Response to the Haemophilus influenzae Type b Capsular Polysaccharide: Retention of the Dominant Idiotype and Antibody Function in the Elderly

PubMed Central

Lucas, Alexander H.; Reason, Donald C.

1998-01-01

Anti-Haemophilus influenzae b polysaccharide (Hib PS) antibodies elicited in elderly subjects following conjugate vaccination expressed a light-chain variable-region (VL)-associated idiotype and had functional activities similar to those previously observed in children and younger adults. These findings indicate that advanced age is not accompanied by shifts in the major VL component of the Hib PS-specific repertoire or by diminution of the protective function of antibodies. PMID:9529108

An Investigation of Gender, Income, and Special Education Status Bias on Curriculum-Based Measurement Slope in Reading

ERIC Educational Resources Information Center

Yeo, Seungsoo; Fearrington, Jamie; Christ, Theodore J.

2011-01-01

This study investigated slope bias on student background variables for both Curriculum Based Measurement of Oral Reading (CBM-R) and Curriculum Based Measurement Maze Reading (Maze). Benchmark scores from 1,738 students in Grades 3 through 8 were used to examine potential slope bias in CBM-R and Maze. Latent growth modeling was used to both…

Simplifying complex sequence information: a PCP-consensus protein binds antibodies against all four Dengue serotypes.

PubMed

Bowen, David M; Lewis, Jessica A; Lu, Wenzhe; Schein, Catherine H

2012-09-14

Designing proteins that reflect the natural variability of a pathogen is essential for developing novel vaccines and drugs. Flaviviruses, including Dengue (DENV) and West Nile (WNV), evolve rapidly and can "escape" neutralizing monoclonal antibodies by mutation. Designing antigens that represent many distinct strains is important for DENV, where infection with a strain from one of the four serotypes may lead to severe hemorrhagic disease on subsequent infection with a strain from another serotype. Here, a DENV physicochemical property (PCP)-consensus sequence was derived from 671 unique sequences from the Flavitrack database. PCP-consensus proteins for domain 3 of the envelope protein (EdomIII) were expressed from synthetic genes in Escherichia coli. The ability of the purified consensus proteins to bind polyclonal antibodies generated in response to infection with strains from each of the four DENV serotypes was determined. The initial consensus protein bound antibodies from DENV-1-3 in ELISA and Western blot assays. This sequence was altered in 3 steps to incorporate regions of maximum variability, identified as significant changes in the PCPs, characteristic of DENV-4 strains. The final protein was recognized by antibodies against all four serotypes. Two amino acids essential for efficient binding to all DENV antibodies are part of a discontinuous epitope previously defined for a neutralizing monoclonal antibody. The PCP-consensus method can significantly reduce the number of experiments required to define a multivalent antigen, which is particularly important when dealing with pathogens that must be tested at higher biosafety levels. Copyright © 2012 Elsevier Ltd. All rights reserved.

Combining phage display with de novo protein sequencing for reverse engineering of monoclonal antibodies.

PubMed

Rickert, Keith W; Grinberg, Luba; Woods, Robert M; Wilson, Susan; Bowen, Michael A; Baca, Manuel

2016-01-01

The enormous diversity created by gene recombination and somatic hypermutation makes de novo protein sequencing of monoclonal antibodies a uniquely challenging problem. Modern mass spectrometry-based sequencing will rarely, if ever, provide a single unambiguous sequence for the variable domains. A more likely outcome is computation of an ensemble of highly similar sequences that can satisfy the experimental data. This outcome can result in the need for empirical testing of many candidate sequences, sometimes iteratively, to identity one which can replicate the activity of the parental antibody. Here we describe an improved approach to antibody protein sequencing by using phage display technology to generate a combinatorial library of sequences that satisfy the mass spectrometry data, and selecting for functional candidates that bind antigen. This approach was used to reverse engineer 2 commercially-obtained monoclonal antibodies against murine CD137. Proteomic data enabled us to assign the majority of the variable domain sequences, with the exception of 3-5% of the sequence located within or adjacent to complementarity-determining regions. To efficiently resolve the sequence in these regions, small phage-displayed libraries were generated and subjected to antigen binding selection. Following enrichment of antigen-binding clones, 2 clones were selected for each antibody and recombinantly expressed as antigen-binding fragments (Fabs). In both cases, the reverse-engineered Fabs exhibited identical antigen binding affinity, within error, as Fabs produced from the commercial IgGs. This combination of proteomic and protein engineering techniques provides a useful approach to simplifying the technically challenging process of reverse engineering monoclonal antibodies from protein material.

Combining phage display with de novo protein sequencing for reverse engineering of monoclonal antibodies

PubMed Central

Rickert, Keith W.; Grinberg, Luba; Woods, Robert M.; Wilson, Susan; Bowen, Michael A.; Baca, Manuel

2016-01-01

ABSTRACT The enormous diversity created by gene recombination and somatic hypermutation makes de novo protein sequencing of monoclonal antibodies a uniquely challenging problem. Modern mass spectrometry-based sequencing will rarely, if ever, provide a single unambiguous sequence for the variable domains. A more likely outcome is computation of an ensemble of highly similar sequences that can satisfy the experimental data. This outcome can result in the need for empirical testing of many candidate sequences, sometimes iteratively, to identity one which can replicate the activity of the parental antibody. Here we describe an improved approach to antibody protein sequencing by using phage display technology to generate a combinatorial library of sequences that satisfy the mass spectrometry data, and selecting for functional candidates that bind antigen. This approach was used to reverse engineer 2 commercially-obtained monoclonal antibodies against murine CD137. Proteomic data enabled us to assign the majority of the variable domain sequences, with the exception of 3–5% of the sequence located within or adjacent to complementarity-determining regions. To efficiently resolve the sequence in these regions, small phage-displayed libraries were generated and subjected to antigen binding selection. Following enrichment of antigen-binding clones, 2 clones were selected for each antibody and recombinantly expressed as antigen-binding fragments (Fabs). In both cases, the reverse-engineered Fabs exhibited identical antigen binding affinity, within error, as Fabs produced from the commercial IgGs. This combination of proteomic and protein engineering techniques provides a useful approach to simplifying the technically challenging process of reverse engineering monoclonal antibodies from protein material. PMID:26852694

Proteomic Identification of Monoclonal Antibodies from Serum

PubMed Central

2015-01-01

Characterizing the in vivo dynamics of the polyclonal antibody repertoire in serum, such as that which might arise in response to stimulation with an antigen, is difficult due to the presence of many highly similar immunoglobulin proteins, each specified by distinct B lymphocytes. These challenges have precluded the use of conventional mass spectrometry for antibody identification based on peptide mass spectral matches to a genomic reference database. Recently, progress has been made using bottom-up analysis of serum antibodies by nanoflow liquid chromatography/high-resolution tandem mass spectrometry combined with a sample-specific antibody sequence database generated by high-throughput sequencing of individual B cell immunoglobulin variable domains (V genes). Here, we describe how intrinsic features of antibody primary structure, most notably the interspersed segments of variable and conserved amino acid sequences, generate recurring patterns in the corresponding peptide mass spectra of V gene peptides, greatly complicating the assignment of correct sequences to mass spectral data. We show that the standard method of decoy-based error modeling fails to account for the error introduced by these highly similar sequences, leading to a significant underestimation of the false discovery rate. Because of these effects, antibody-derived peptide mass spectra require increased stringency in their interpretation. The use of filters based on the mean precursor ion mass accuracy of peptide-spectrum matches is shown to be particularly effective in distinguishing between “true” and “false” identifications. These findings highlight important caveats associated with the use of standard database search and error-modeling methods with nonstandard data sets and custom sequence databases. PMID:24684310

A Diverse Repertoire of Human Immunoglobulin Variable Genes in a Chicken B Cell Line is Generated by Both Gene Conversion and Somatic Hypermutation.

PubMed

Leighton, Philip A; Schusser, Benjamin; Yi, Henry; Glanville, Jacob; Harriman, William

2015-01-01

Chicken immune responses to human proteins are often more robust than rodent responses because of the phylogenetic relationship between the different species. For discovery of a diverse panel of unique therapeutic antibody candidates, chickens therefore represent an attractive host for human-derived targets. Recent advances in monoclonal antibody technology, specifically new methods for the molecular cloning of antibody genes directly from primary B cells, has ushered in a new era of generating monoclonal antibodies from non-traditional host animals that were previously inaccessible through hybridoma technology. However, such monoclonals still require post-discovery humanization in order to be developed as therapeutics. To obviate the need for humanization, a modified strain of chickens could be engineered to express a human-sequence immunoglobulin variable region repertoire. Here, human variable genes introduced into the chicken immunoglobulin loci through gene targeting were evaluated for their ability to be recognized and diversified by the native chicken recombination machinery that is present in the B-lineage cell line DT40. After expansion in culture the DT40 population accumulated genetic mutants that were detected via deep sequencing. Bioinformatic analysis revealed that the human targeted constructs are performing as expected in the cell culture system, and provide a measure of confidence that they will be functional in transgenic animals.

Cloning and molecular characterization of the cDNAs encoding the variable regions of an anti-CD20 monoclonal antibody.

PubMed

Shanehbandi, Dariush; Majidi, Jafar; Kazemi, Tohid; Baradaran, Behzad; Aghebati-Maleki, Leili

2017-01-01

CD20-based targeting of B-cells in hematologic malignancies and autoimmune disorders is associated with outstanding clinical outcomes. Isolation and characterization of VH and VL cDNAs encoding the variable regions of the heavy and light chains of monoclonal antibodies (MAb) is necessary to produce next generation MAbs and their derivatives such as bispecific antibodies (bsAb) and single-chain variable fragments (scFv). This study was aimed at cloning and characterization of the VH and VL cDNAs from a hybridoma cell line producing an anti-CD20 MAb. VH and VL fragments were amplified, cloned and characterized. Furthermore, amino acid sequences of VH, VL and corresponding complementarity-determining regions (CDR) were determined and compared with those of four approved MAbs including Rituximab (RTX), Ibritumomab tiuxetan, Ofatumumab and GA101. The cloned VH and VL cDNAs were found to be functional and follow a consensus pattern. Amino acid sequences corresponding to the VH and VL fragments also indicated noticeable homologies to those of RTX and Ibritumomab. Furthermore, amino acid sequences of the relating CDRs had remarkable similarities to their counterparts in RTX and Ibritumomab. Successful recovery of VH and VL fragments encourages the development of novel CD20 targeting bsAbs, scFvs, antibody conjugates and T-cells armed with chimeric antigen receptors.

Kinetics of anti-carcinoembryonic antigen antibody internalization: effects of affinity, bivalency, and stability

PubMed Central

Schmidt, Michael M.; Thurber, Greg M.

2010-01-01

Theoretical analyses suggest that the cellular internalization and catabolism of bound antibodies contribute significantly to poor penetration into tumors. Here we quantitatively assess the internalization of antibodies and antibody fragments against the commonly targeted antigen carcinoembryonic antigen (CEA). Although CEA is often referred to as a non-internalizing or shed antigen, anti-CEA antibodies and antibody fragments are shown to be slowly endocytosed by LS174T cells with a half-time of 10–16 h, a time scale consistent with the metabolic turnover rate of CEA in the absence of antibody. Anti-CEA single chain variable fragments (scFvs) with significant differences in affinity, stability against protease digestion, and valency exhibit similar uptake rates of bound antibody. In contrast, one anti-CEA IgG exhibits unique binding and trafficking properties with twice as many molecules bound per cell at saturation and significantly faster cellular internalization after binding. The internalization rates measured herein can be used in simple computational models to predict the microdistribution of these antibodies in tumor spheroids. PMID:18408925

Nonconscious attention bias to threat is correlated with anterior cingulate cortex gray matter volume: a voxel-based morphometry result and replication.

PubMed

Carlson, Joshua M; Beacher, Felix; Reinke, Karen S; Habib, Reza; Harmon-Jones, Eddie; Mujica-Parodi, Lilianne R; Hajcak, Greg

2012-01-16

An important aspect of the fear response is the allocation of spatial attention toward threatening stimuli. This response is so powerful that modulations in spatial attention can occur automatically without conscious awareness. Functional neuroimaging research suggests that the amygdala and anterior cingulate cortex (ACC) form a network involved in the rapid orienting of attention to threat. A hyper-responsive attention bias to threat is a common component of anxiety disorders. Yet, little is known of how individual differences in underlying brain morphometry relate to variability in attention bias to threat. Here, we performed two experiments using dot-probe tasks that measured individuals' attention bias to backward masked fearful faces. We collected whole-brain structural magnetic resonance images and used voxel-based morphometry to measure brain morphometry. We tested the hypothesis that reduced gray matter within the amygdala and ACC would be associated with reduced attention bias to threat. In Experiment 1, we found that backward masked fearful faces captured spatial attention and that elevated attention bias to masked threat was associated with greater ACC gray matter volumes. In Experiment 2, this association was replicated in a separate sample. Thus, we provide initial and replicating evidence that ACC gray matter volume is correlated with biased attention to threat. Importantly, we demonstrate that variability in affective attention bias within the healthy population is associated with ACC morphometry. This result opens the door for future research into the underlying brain morphometry associated with attention bias in clinically anxious populations. Copyright © 2011 Elsevier Inc. All rights reserved.

The Observed Behavior of the Bias in MODIS-retrieved Cloud Droplet Effective Radius through MISR-MODIS Data Fusion

NASA Astrophysics Data System (ADS)

Fu, D.; Di Girolamo, L.; Liang, L.; Zhao, G.

2017-12-01

Listed as one of the Essential Climate Variables by the Global Climate Observing System, the effective radius (Re) of the cloud drop size distribution plays an important role in the energy and water cycles of the Earth system. Re is retrieved from several passive sensors, such as the Moderate Resolution Imaging Spectroradiometer (MODIS), based on a visible and near-infrared bi-spectral technique that had its foundation more than a quarter century ago. This technique makes a wide range of assumptions, including 1-D radiative transfer, assumed single-mode drop size distribution, and cloud horizontal and vertical homogeneity. It is well known that deviations from these assumptions lead to bias in the retrieved Re. Recently, an effort to characterize the bias in MODIS-retrieved Re through MISR-MODIS data fusion revealed biases in the zonal-mean values of MODIS-retrieved Re that varied from 2 to 11 µm, depending on latitude (Liang et al., 2015). Here, in a push towards bias-correction of MODIS-retrieved Re, we further examine the bias with MISR-MODIS data fusion as it relates to other observed cloud properties, such as cloud-top height and the spatial variability of the radiance field, sun-view geometry, and the driving meteorology had from reanalysis data. Our results show interesting relationships in Re bias behavior with these observed properties, revealing that while Re bias do show a certain degree of dependence on some properties, no single property dominates the behavior in MODIS-retrieved Re bias.

A new dynamical downscaling approach with GCM bias corrections and spectral nudging

NASA Astrophysics Data System (ADS)

Xu, Zhongfeng; Yang, Zong-Liang

2015-04-01

To improve confidence in regional projections of future climate, a new dynamical downscaling (NDD) approach with both general circulation model (GCM) bias corrections and spectral nudging is developed and assessed over North America. GCM biases are corrected by adjusting GCM climatological means and variances based on reanalysis data before the GCM output is used to drive a regional climate model (RCM). Spectral nudging is also applied to constrain RCM-based biases. Three sets of RCM experiments are integrated over a 31 year period. In the first set of experiments, the model configurations are identical except that the initial and lateral boundary conditions are derived from either the original GCM output, the bias-corrected GCM output, or the reanalysis data. The second set of experiments is the same as the first set except spectral nudging is applied. The third set of experiments includes two sensitivity runs with both GCM bias corrections and nudging where the nudging strength is progressively reduced. All RCM simulations are assessed against North American Regional Reanalysis. The results show that NDD significantly improves the downscaled mean climate and climate variability relative to other GCM-driven RCM downscaling approach in terms of climatological mean air temperature, geopotential height, wind vectors, and surface air temperature variability. In the NDD approach, spectral nudging introduces the effects of GCM bias corrections throughout the RCM domain rather than just limiting them to the initial and lateral boundary conditions, thereby minimizing climate drifts resulting from both the GCM and RCM biases.

Genetic relationships of antibody response, viremia level and weight gain in pigs experimentally infected with porcine reproductive and respiratory syndrome virus

USDA-ARS?s Scientific Manuscript database

Genetic and antigenic variability between Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) isolates has encumbered the development of effective vaccines. Therefore, the potential of genetic selection on PRRSV antibody response to improve resistance to PRRSV infection was assessed using da...

Array-Based Rational Design of Short Peptide Probe-Derived from an Anti-TNT Monoclonal Antibody.

PubMed

Okochi, Mina; Muto, Masaki; Yanai, Kentaro; Tanaka, Masayoshi; Onodera, Takeshi; Wang, Jin; Ueda, Hiroshi; Toko, Kiyoshi

2017-10-09

Complementarity-determining regions (CDRs) are sites on the variable chains of antibodies responsible for binding to specific antigens. In this study, a short peptide probe for recognition of 2,4,6-trinitrotoluene (TNT), was identified by testing sequences derived from the CDRs of an anti-TNT monoclonal antibody. The major TNT-binding site in this antibody was identified in the heavy chain CDR3 by antigen docking simulation and confirmed by an immunoassay using a spot-synthesis based peptide array comprising amino acid sequences of six CDRs in the variable region. A peptide derived from heavy chain CDR3 (RGYSSFIYWF) bound to TNT with a dissociation constant of 1.3 μM measured by surface plasmon resonance. Substitution of selected amino acids with basic residues increased TNT binding while substitution with acidic amino acids decreased affinity, an isoleucine to arginine change showed the greatest improvement of 1.8-fold. The ability to create simple peptide binders of volatile organic compounds from sequence information provided by the immune system in the creation of an immune response will be beneficial for sensor developments in the future.

Amino acid sequence of the Fv region of a human monoclonal IgM (protein WEA) with antibody activity against 3,4-pyruvylated galactose in Klebsiella polysaccharides K30 and K33.

PubMed Central

Goñi, F; Frangione, B

1983-01-01

We have determined the amino acid sequence of the Fv [variable heavy (VH) and variable light (VL)] region of a human monoclonal IgM-kappa with antibody activity against 3,4-pyruvylated galactose, isolated from the plasma of patient WEA with Waldenström macroglobulinemia. The VH region has 114 residues, belongs to subgroup III, and has a very short third complementarity-determining region (CDR3), probably due to a small D segment/or an unusual D-J rearrangement (D, diversity; J, joining). The VL region has 108 residues and belongs to subgroup V kappa I. Compared to other members of the human VHIII and V kappa I families, WEA Fv does not appear to have significant differences within the framework residues but has unique CDRs that might be responsible for the particular antibody activity. Another IgM-kappa (GAL), which has an as-yet-undetermined antibody activity, shares a striking homology in V kappa with WEA, including an identical CDR1. PMID:6410398

Molecular imprint of enzyme active site by camel nanobodies: rapid and efficient approach to produce abzymes with alliinase activity.

PubMed

Li, Jiang-Wei; Xia, Lijie; Su, Youhong; Liu, Hongchun; Xia, Xueqing; Lu, Qinxia; Yang, Chunjin; Reheman, Kalbinur

2012-04-20

Screening of inhibitory Ab1 antibodies is a critical step for producing catalytic antibodies in the anti-idiotypic approach. However, the incompatible surface of the active site of the enzyme and the antigen-binding site of heterotetrameric conventional antibodies become the limiting step. Because camelid-derived nanobodies possess the potential to preferentially bind to the active site of enzymes due to their small size and long CDR3, we have developed a novel approach to produce antibodies with alliinase activities by exploiting the molecular mimicry of camel nanobodies. By screening the camelid-derived variable region of the heavy chain cDNA phage display library with alliinase, we obtained an inhibitory nanobody VHHA4 that recognizes the active site. Further screening with VHHA4 from the same variable domain of the heavy chain of a heavy-chain antibody library led to a higher incidence of anti-idiotypic Ab2 abzymes with alliinase activities. One of the abzymes, VHHC10, showed the highest activity that can be inhibited by Ab1 VHHA4 and alliinase competitive inhibitor penicillamine and significantly suppressed the B16 tumor cell growth in the presence of alliin in vitro. The results highlight the feasibility of producing abzymes via anti-idiotypic nanobody approach.

Molluskan Hemocyanins Activate the Classical Pathway of the Human Complement System through Natural Antibodies

PubMed Central

Pizarro-Bauerle, Javier; Maldonado, Ismael; Sosoniuk-Roche, Eduardo; Vallejos, Gerardo; López, Mercedes N.; Salazar-Onfray, Flavio; Aguilar-Guzmán, Lorena; Valck, Carolina; Ferreira, Arturo; Becker, María Inés

2017-01-01

Molluskan hemocyanins are enormous oxygen-carrier glycoproteins that show remarkable immunostimulatory properties when inoculated in mammals, such as the generation of high levels of antibodies, a strong cellular reaction, and generation of non-specific antitumor immune responses in some types of cancer, particularly for superficial bladder cancer. These proteins have the ability to bias the immune response toward a Th1 phenotype. However, despite all their current uses with beneficial clinical outcomes, a clear mechanism explaining these properties is not available. Taking into account reports of natural antibodies against the hemocyanin of the gastropod Megathura crenulata [keyhole limpet hemocyanin (KLH)] in humans as well as other vertebrate species, we report here for the first time, the presence, in sera from unimmunized healthy donors, of antibodies recognizing, in addition to KLH, two other hemocyanins from gastropods with documented immunomodulatory capacities: Fisurella latimarginata hemocyanin (FLH) and Concholepas concholepas hemocyanin (CCH). Through an ELISA screening, we found IgM and IgG antibodies reactive with these hemocyanins. When the capacity of these antibodies to bind deglycosylated hemocyanins was studied, no decreased interaction was detected. Moreover, in the case of FLH, deglycosylation increased antibody binding. We evaluated through an in vitro complement deposition assay whether these antibodies activated the classical pathway of the human complement system. The results showed that all three hemocyanins and their deglycosylated counterparts elicited this activation, mediated by C1 binding to immunoglobulins. Thus, this work contributes to the understanding on how the complement system could participate in the immunostimulatory properties of hemocyanins, through natural, complement-activating antibodies reacting with these proteins. Although a role for carbohydrates cannot be completely ruled out, in our experimental setting, glycosylation status had a limited effect. Finally, our data open possibilities for further studies leading to the design of improved hemocyanin-based research tools for diagnosis and immunotherapy. PMID:28286504

Molluskan Hemocyanins Activate the Classical Pathway of the Human Complement System through Natural Antibodies.

PubMed

Pizarro-Bauerle, Javier; Maldonado, Ismael; Sosoniuk-Roche, Eduardo; Vallejos, Gerardo; López, Mercedes N; Salazar-Onfray, Flavio; Aguilar-Guzmán, Lorena; Valck, Carolina; Ferreira, Arturo; Becker, María Inés

2017-01-01

Molluskan hemocyanins are enormous oxygen-carrier glycoproteins that show remarkable immunostimulatory properties when inoculated in mammals, such as the generation of high levels of antibodies, a strong cellular reaction, and generation of non-specific antitumor immune responses in some types of cancer, particularly for superficial bladder cancer. These proteins have the ability to bias the immune response toward a T h 1 phenotype. However, despite all their current uses with beneficial clinical outcomes, a clear mechanism explaining these properties is not available. Taking into account reports of natural antibodies against the hemocyanin of the gastropod Megathura crenulata [keyhole limpet hemocyanin (KLH)] in humans as well as other vertebrate species, we report here for the first time, the presence, in sera from unimmunized healthy donors, of antibodies recognizing, in addition to KLH, two other hemocyanins from gastropods with documented immunomodulatory capacities: Fisurella latimarginata hemocyanin (FLH) and Concholepas concholepas hemocyanin (CCH). Through an ELISA screening, we found IgM and IgG antibodies reactive with these hemocyanins. When the capacity of these antibodies to bind deglycosylated hemocyanins was studied, no decreased interaction was detected. Moreover, in the case of FLH, deglycosylation increased antibody binding. We evaluated through an in vitro complement deposition assay whether these antibodies activated the classical pathway of the human complement system. The results showed that all three hemocyanins and their deglycosylated counterparts elicited this activation, mediated by C1 binding to immunoglobulins. Thus, this work contributes to the understanding on how the complement system could participate in the immunostimulatory properties of hemocyanins, through natural, complement-activating antibodies reacting with these proteins. Although a role for carbohydrates cannot be completely ruled out, in our experimental setting, glycosylation status had a limited effect. Finally, our data open possibilities for further studies leading to the design of improved hemocyanin-based research tools for diagnosis and immunotherapy.

Human anti-CD30 recombinant antibodies by guided phage antibody selection using cell panning

PubMed Central

Klimka, A; Matthey, B; Roovers, R C; Barth, S; Arends, J-W; Engert, A; Hoogenboom, H R

2000-01-01

In various clinical studies, Hodgkin’s patients have been treated with anti-CD30 immunotherapeutic agents and have shown promising responses. One of the problems that appeared from these studies is the development of an immune response against the non-human therapeutics, which limits repeated administration and reduces efficacy. We have set out to make a recombinant, human anti-CD30 single-chain variable fragment (scFv) antibody, which may serve as a targeting moiety with reduced immunogenicity and more rapid tumour penetration in similar clinical applications. Rather than selecting a naive phage antibody library on recombinant CD30 antigen, we used guided selection of a murine antibody in combination with panning on the CD30-positive cell line L540. The murine monoclonal antibody Ki-4 was chosen as starting antibody, because it inhibits the shedding of the extracellular part of the CD30 antigen. This makes the antibody better suited for CD30-targeting than most other anti-CD30 antibodies. We have previously isolated the murine Ki-4 scFv by selecting a mini-library of hybridoma-derived phage scFv-antibodies via panning on L540 cells. Here, we report that phage display technology was successfully used to obtain a human Ki-4 scFv version by guided selection. The murine variable heavy (VH) and light (VL) chain genes of the Ki-4 scFv were sequentially replaced by human V gene repertoires, while retaining only the major determinant for epitope-specificity: the heavy-chain complementarity determining region 3 (CDR3) of murine Ki-4. After two rounds of chain shuffling and selection by panning on L540 cells, a fully human anti-CD30 scFv was selected. It competes with the parental monoclonal antibody Ki-4 for binding to CD30, inhibits the shedding of the extracellular part of the CD30 receptor from L540 cells and is thus a promising candidate for the generation of anti-CD30 immunotherapeutics. © 2000 Cancer Research Campaign PMID:10901379

Effect of study design on the reported effect of cardiac resynchronization therapy (CRT) on quantitative physiological measures: stratified meta-analysis in narrow-QRS heart failure and implications for planning future studies.

PubMed

Jabbour, Richard J; Shun-Shin, Matthew J; Finegold, Judith A; Afzal Sohaib, S M; Cook, Christopher; Nijjer, Sukhjinder S; Whinnett, Zachary I; Manisty, Charlotte H; Brugada, Josep; Francis, Darrel P

2015-01-06

Biventricular pacing (CRT) shows clear benefits in heart failure with wide QRS, but results in narrow QRS have appeared conflicting. We tested the hypothesis that study design might have influenced findings. We identified all reports of CRT-P/D therapy in subjects with narrow QRS reporting effects on continuous physiological variables. Twelve studies (2074 patients) met these criteria. Studies were stratified by presence of bias-resistance steps: the presence of a randomized control arm over a single arm, and blinded outcome measurement. Change in each endpoint was quantified using a standardized effect size (Cohen's d). We conducted separate meta-analyses for each variable in turn, stratified by trial quality. In non-randomized, non-blinded studies, the majority of variables (10 of 12, 83%) showed significant improvement, ranging from a standardized mean effect size of +1.57 (95%CI +0.43 to +2.7) for ejection fraction to +2.87 (+1.78 to +3.95) for NYHA class. In the randomized, non-blinded study, only 3 out of 6 variables (50%) showed improvement. For the randomized blinded studies, 0 out of 9 variables (0%) showed benefit, ranging from -0.04 (-0.31 to +0.22) for ejection fraction to -0.1 (-0.73 to +0.53) for 6-minute walk test. Differences in degrees of resistance to bias, rather than choice of endpoint, explain the variation between studies of CRT in narrow-QRS heart failure addressing physiological variables. When bias-resistance features are implemented, it becomes clear that these patients do not improve in any tested physiological variable. Guidance from studies without careful planning to resist bias may be far less useful than commonly perceived. © 2015 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Seroincidence of non-typhoid Salmonella infections: convenience vs. random community-based sampling.

PubMed

Emborg, H-D; Simonsen, J; Jørgensen, C S; Harritshøj, L H; Krogfelt, K A; Linneberg, A; Mølbak, K

2016-01-01

The incidence of reported infections of non-typhoid Salmonella is affected by biases inherent to passive laboratory surveillance, whereas analysis of blood sera may provide a less biased alternative to estimate the force of Salmonella transmission in humans. We developed a mathematical model that enabled a back-calculation of the annual seroincidence of Salmonella based on measurements of specific antibodies. The aim of the present study was to determine the seroincidence in two convenience samples from 2012 (Danish blood donors, n = 500, and pregnant women, n = 637) and a community-based sample of healthy individuals from 2006 to 2007 (n = 1780). The lowest antibody levels were measured in the samples from the community cohort and the highest in pregnant women. The annual Salmonella seroincidences were 319 infections/1000 pregnant women [90% credibility interval (CrI) 210-441], 182/1000 in blood donors (90% CrI 85-298) and 77/1000 in the community cohort (90% CrI 45-114). Although the differences between study populations decreased when accounting for different age distributions the estimates depend on the study population. It is important to be aware of this issue and define a certain population under surveillance in order to obtain consistent results in an application of serological measures for public health purposes.

C3d enhanced DNA vaccination induced humoral immune response to glycoprotein C of pseudorabies virus

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

Tong Tiezhu; Provincial Key Laboratory of Preventive Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070; Fan Huiying

2006-09-08

Murine C3d were utilized to enhance immunogenicity of pseudorabies virus (PrV) gC DNA vaccination. Three copies of C3d and four copies of CR2-binding domain M28{sub 4} were fused, respectively, to truncated gC gene encoding soluble glycoprotein C (sgC) in pcDNA3.1. BALB/c mice were, respectively, immunized with recombinant plasmids, blank vector, and inactivated vaccine. The antibody ELISA titer for sgC-C3d{sub 3} DNA was 49-fold more than that for sgC DNA, and the neutralizing antibody obtained 8-fold rise. Protection of mice from death after lethal PrV (316 LD{sub 5}) challenge was augmented from 25% to 100%. Furthermore, C3d fusion increased Th2-biased immunemore » response by inducing IL-4 production. The IL-4 level for sgC-C3d{sub 3} DNA immunization approached that for the inactivated vaccine. Compared to C3d, M28 enhanced sgC DNA immunogenicity to a lesser extent. In conclusion, we demonstrated that murine C3d fusion significantly enhanced gC DNA immunity by directing Th1-biased to a balanced and more effective Th1/Th2 response.« less

Serum antibody titers following routine rabies vaccination in African elephants.

PubMed

Miller, Michele A; Olea-Popelka, Francisco

2009-10-15

To evaluate serum antibody titers in captive African elephants (Loxodonta africana) following routine vaccination with a commercially available, inactivated rabies vaccine. Seroepidemiologic study. 14 captive African elephants from a single herd. Elephants were vaccinated as part of a routine preventive health program. Initially, elephants were vaccinated annually (2 mL, IM), and blood was collected every 4 or 6 months for measurement of rabies virus-neutralizing antibody titer by means of the rapid fluorescent focus inhibition test. Individual elephants were later switched to an intermittent vaccination schedule to allow duration of the antibody response to be determined. All elephants had detectable antibody responses following rabies vaccination, although there was great variability among individual animals in regard to antibody titers, and antibody titers could be detected as long as 24 months after vaccine administration. Young animals were found to develop an antibody titer following administration of a single dose of the rabies vaccine. Age and time since vaccination had significant effects on measured antibody titers. Results indicated that African elephants developed detectable antibody titers in response to inoculation with a standard large animal dose of a commercially available, inactivated rabies vaccine. The persistence of detectable antibody titers in some animals suggested that vaccination could be performed less frequently than once a year if antibody titers were routinely monitored.

Construction and characterization of VL-VH tail-parallel genetically engineered antibodies against staphylococcal enterotoxins.

PubMed

He, Xianzhi; Zhang, Lei; Liu, Pengchong; Liu, Li; Deng, Hui; Huang, Jinhai

2015-03-01

Staphylococcal enterotoxins (SEs) produced by Staphylococcus aureus have increasingly given rise to human health and food safety. Genetically engineered small molecular antibody is a useful tool in immuno-detection and treatment for clinical illness caused by SEs. In this study, we constructed the V(L)-V(H) tail-parallel genetically engineered antibody against SEs by using the repertoire of rearranged germ-line immunoglobulin variable region genes. Total RNA were extracted from six hybridoma cell lines that stably express anti-SEs antibodies. The variable region genes of light chain (V(L)) and heavy chain (V(H)) were cloned by reverse transcription PCR, and their classical murine antibody structure and functional V(D)J gene rearrangement were analyzed. To construct the eukaryotic V(H)-V(L) tail-parallel co-expression vectors based on the "5'-V(H)-ivs-IRES-V(L)-3'" mode, the ivs-IRES fragment and V(L) genes were spliced by two-step overlap extension PCR, and then, the recombined gene fragment and V(H) genes were inserted into the pcDNA3.1(+) expression vector sequentially. And then the constructed eukaryotic expression clones termed as p2C2HILO and p5C12HILO were transfected into baby hamster kidney 21 cell line, respectively. Two clonal cell lines stably expressing V(L)-V(H) tail-parallel antibodies against SEs were obtained, and the antibodies that expressed intracytoplasma were evaluated by enzyme-linked immunosorbent assay, immunofluorescence assay, and flow cytometry. SEs can stimulate the expression of some chemokines and chemokine receptors in porcine IPEC-J2 cells; mRNA transcription level of four chemokines and chemokine receptors can be blocked by the recombinant SE antibody prepared in this study. Our results showed that it is possible to get functional V(L)-V(H) tail-parallel genetically engineered antibodies in same vector using eukaryotic expression system.

Social desirability bias in dietary self-report may compromise the validity of dietary intake measures.

PubMed

Hebert, J R; Clemow, L; Pbert, L; Ockene, I S; Ockene, J K

1995-04-01

Self-report of dietary intake could be biased by social desirability or social approval thus affecting risk estimates in epidemiological studies. These constructs produce response set biases, which are evident when testing in domains characterized by easily recognizable correct or desirable responses. Given the social and psychological value ascribed to diet, assessment methodologies used most commonly in epidemiological studies are particularly vulnerable to these biases. Social desirability and social approval biases were tested by comparing nutrient scores derived from multiple 24-hour diet recalls (24HR) on seven randomly assigned days with those from two 7-day diet recalls (7DDR) (similar in some respects to commonly used food frequency questionnaires), one administered at the beginning of the test period (pre) and one at the end (post). Statistical analysis included correlation and multiple linear regression. Cross-sectionally, no relationships between social approval score and the nutritional variables existed. Social desirability score was negatively correlated with most nutritional variables. In linear regression analysis, social desirability score produced a large downward bias in nutrient estimation in the 7DDR relative to the 24HR. For total energy, this bias equalled about 50 kcal/point on the social desirability scale or about 450 kcal over its interquartile range. The bias was approximately twice as large for women as for men and only about half as large in the post measures. Individuals having the highest 24HR-derived fat and total energy intake scores had the largest downward bias due to social desirability. We observed a large downward bias in reporting food intake related to social desirability score. These results are consistent with the theoretical constructs on which the hypothesis is based. The effect of social desirability bias is discussed in terms of its influence on epidemiological estimates of effect. Suggestions are made for future work aimed at improving dietary assessment methodologies and adjusting risk estimates for this bias.

Effect of transmission intensity and age on subclass antibody responses to Plasmodium falciparum pre-erythrocytic and blood-stage antigens.

PubMed

Noland, Gregory S; Jansen, Paul; Vulule, John M; Park, Gregory S; Ondigo, Bartholomew N; Kazura, James W; Moormann, Ann M; John, Chandy C

2015-02-01

Cytophilic immunoglobulin (IgG) subclass responses (IgG1 and IgG3) to Plasmodium falciparum antigens have been associated with protection from malaria, yet the relative importance of transmission intensity and age in generation of subclass responses to pre-erythrocytic and blood-stage antigens have not been clearly defined. We analyzed IgG subclass responses to the pre-erythrocytic antigens CSP, LSA-1, and TRAP and the blood-stage antigens AMA-1, EBA-175, and MSP-1 in asymptomatic residents age 2 years or older in stable (n=116) and unstable (n=96) transmission areas in Western Kenya. In the area of stable malaria transmission, a high prevalence of cytophilic (IgG1 and IgG3) antibodies to each antigen was seen in all age groups. Prevalence and levels of cytophilic antibodies to pre-erythrocytic and blood-stage P. falciparum antigens increased with age in the unstable transmission area, yet IgG1 and IgG3 responses to most antigens for all ages in the unstable transmission area were less prevalent and lower in magnitude than even the youngest age group from the stable transmission area. The dominance of cytophilic responses over non-cytophilic (IgG2 and IgG4) was more pronounced in the stable transmission area, and the ratio of IgG3 over IgG1 generally increased with age. In the unstable transmission area, the ratio of cytophilic to non-cytophilic antibodies did not increase with age, and tended to be IgG3-biased for pre-erythrocytic antigens yet IgG1-biased for blood-stage antigens. The differences between areas could not be attributed to active parasitemia status, as there were minimal differences in antibody responses between those positive and negative for Plasmodium infection by microscopy in the stable transmission area. Individuals in areas of unstable transmission have low cytophilic to non-cytophilic IgG subclass ratios and low IgG3:IgG1 ratios to P. falciparum antigens. These imbalances could contribute to the persistent risk of clinical malaria in these areas and serve as population-level, age-specific biomarkers of transmission. Copyright © 2014 Elsevier B.V. All rights reserved.

Inadequate Reference Datasets Biased toward Short Non-epitopes Confound B-cell Epitope Prediction*

PubMed Central

Rahman, Kh. Shamsur; Chowdhury, Erfan Ullah; Sachse, Konrad; Kaltenboeck, Bernhard

2016-01-01

X-ray crystallography has shown that an antibody paratope typically binds 15–22 amino acids (aa) of an epitope, of which 2–5 randomly distributed amino acids contribute most of the binding energy. In contrast, researchers typically choose for B-cell epitope mapping short peptide antigens in antibody binding assays. Furthermore, short 6–11-aa epitopes, and in particular non-epitopes, are over-represented in published B-cell epitope datasets that are commonly used for development of B-cell epitope prediction approaches from protein antigen sequences. We hypothesized that such suboptimal length peptides result in weak antibody binding and cause false-negative results. We tested the influence of peptide antigen length on antibody binding by analyzing data on more than 900 peptides used for B-cell epitope mapping of immunodominant proteins of Chlamydia spp. We demonstrate that short 7–12-aa peptides of B-cell epitopes bind antibodies poorly; thus, epitope mapping with short peptide antigens falsely classifies many B-cell epitopes as non-epitopes. We also show in published datasets of confirmed epitopes and non-epitopes a direct correlation between length of peptide antigens and antibody binding. Elimination of short, ≤11-aa epitope/non-epitope sequences improved datasets for evaluation of in silico B-cell epitope prediction. Achieving up to 86% accuracy, protein disorder tendency is the best indicator of B-cell epitope regions for chlamydial and published datasets. For B-cell epitope prediction, the most effective approach is plotting disorder of protein sequences with the IUPred-L scale, followed by antibody reactivity testing of 16–30-aa peptides from peak regions. This strategy overcomes the well known inaccuracy of in silico B-cell epitope prediction from primary protein sequences. PMID:27189949

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

Conroy, W.G.

Structural relatedness between the variable region of anti-ligand antibodies and opioid binding sites allowed the generation of anti-idiotypic antibodies which recognized opioid receptors. The IgG{sub 3}k antibodies which bound to opioid receptors were obtained when an anti-morphine antiserum was the idiotype. Both antibodies bound to opioid receptors, but only one of these blocked the binding of ({sup 3}H)naloxone. The antibody which did not inhibit the binding of ({sup 3}H)naloxone was itself displaced from the receptor by opioid ligands. The unique binding properties displayed by this antibody indicated that anti-idiotypic antibodies are not always a perfect image of the original ligand,more » and therefore may be more useful than typical ligands as probes for the receptor. An auto-anti-idiotypic technique was successfully used to obtain anti-opioid receptor antibodies. Another IgG{sub 3}k antibody that blocked the binding of ({sup 3}H)naloxone to rat brain opioid receptors was obtained when a mouse was immunized with naloxone conjugated to bovine serum albumin. These data confirmed that an idiotype-anti-idiotype network which can generate an anti-receptor antibody normally functions when an opioid ligand is introduced into an animal in an immunogenic form.« less

Mechanisms of monoclonal antibody stabilization and release from silk biomaterials

PubMed Central

Guziewicz, Nicholas A.; Massetti, Andrew J.; Perez-Ramirez, Bernardo J.; Kaplan, David L.

2013-01-01

The availability of stabilization and sustained delivery systems for antibody therapeutics remains a major clinical challenge, despite the growing development of antibodies for a wide range of therapeutic applications due to their specificity and efficacy. A mechanistic understanding of protein-matrix interactions is critical for the development of such systems and is currently lacking as a mode to guide the field. We report mechanistic insight to address this need by using well-defined matrices based on silk gels, in combination with a monoclonal antibody. Variables including antibody loading, matrix density, charge interactions, hydrophobicity and water access were assessed to clarify mechanisms involved in the release of antibody from the biomaterial matrix. The results indicate that antibody release is primarily governed by hydrophobic interactions and hydration resistance, which are controlled by silk matrix chemistry, peptide domain distribution and protein density. Secondary ionic repulsions are also critical in antibody stabilization and release. Matrix modification by free methionine incorporation was found to be an effective strategy for mitigating encapsulation induced antibody oxidation. Additionally, these studies highlight a characterization approach to improve the understanding and development of other protein sustained delivery systems, with broad applicability to the rapidly developing monoclonal antibody field. PMID:23859659

Generation of a chickenized catalytic anti-nucleic acid antibody by complementarity-determining region grafting.

PubMed

Roh, Jooho; Byun, Sung June; Seo, Youngsil; KIm, Minjae; Lee, Jae-Ho; Kim, Songmi; Lee, Yuno; Lee, Keun Woo; Kim, Jin-Kyoo; Kwon, Myung-Hee

2015-02-01

In contrast to a number of studies on the humanization of non-human antibodies, the reshaping of a non-human antibody into a chicken antibody has never been attempted. Therefore, nothing is known about the animal species-dependent compatibility of the framework regions (FRs) that sustain the appropriate conformation of the complementarity-determining regions (CDRs). In this study, we attempted the reshaping of the variable domains of the mouse catalytic anti-nucleic acid antibody 3D8 (m3D8) into the FRs of a chicken antibody (“chickenization”) by CDR grafting, which is a common method for the humanization of antibodies. CDRs of the acceptor chicken antibody that showed a high homology to the FRs of m3D8 were replaced with those of m3D8, resulting in the chickenized antibody (ck3D8). ck3D8 retained the biochemical properties (DNA binding, DNA hydrolysis, and cellular internalizing activities) and three-dimensional structure of m3D8 and showed reduced immunogenicity in chickens. Our study demonstrates that CDR grafting can be applied to the chickenization of a mouse antibody, probably due to the interspecies compatibility of the FRs.

Development of VHH antibodies against dengue virus type 2 NS1 and comparison with monoclonal antibodies for use in immunological diagnosis.

PubMed

Fatima, Aneela; Wang, Haiying; Kang, Keren; Xia, Liliang; Wang, Ying; Ye, Wei; Wang, Jufang; Wang, Xiaoning

2014-01-01

The possibility of using variable domain heavy-chain antibodies (VHH antibodies) as diagnostic tools for dengue virus (DENV) type 2 NS1 protein was investigated and compared with the use of conventional monoclonal antibodies. After successful expression of DENV type 2 NS1 protein, the genes of VHH antibodies against NS1 protein were biopanned from a non-immune llama library by phage display. VHH antibodies were then expressed and purified from Escherichia coli. Simultaneously, monoclonal antibodies were obtained by the conventional route. Sequence analysis of the VHH antibodies revealed novel and long complementarity determining regions 3 (CDR3). Epitope mapping was performed via a phage display peptide library using purified VHH and monoclonal antibodies as targets. Interestingly, the same region of NS1, which comprises amino acids 224HWPKPHTLW232, was conserved for both kinds of antibodies displaying the consensus motif histidine-tryptophan-tryptophan or tryptophan-proline-tryptophan. The two types of antibodies were used to prepare rapid diagnostic kits based on immunochromatographic assay. The VHH antibody immobilized rapid diagnostic kit showed better sensitivity and specificity than the monoclonal antibody immobilized rapid diagnostic kit, which might be due to the long CDR3 regions of the VHH antibodies and their ability to bind to the pocket and cleft of the targeted antigen. This demonstrates that VHH antibodies are likely to be an option for developing point-of-care tests against DENV infection.

Development of VHH Antibodies against Dengue Virus Type 2 NS1 and Comparison with Monoclonal Antibodies for Use in Immunological Diagnosis

PubMed Central

Fatima, Aneela; Wang, Haiying; Kang, Keren; Xia, Liliang; Wang, Ying; Ye, Wei; Wang, Jufang; Wang, Xiaoning

2014-01-01

The possibility of using variable domain heavy-chain antibodies (VHH antibodies) as diagnostic tools for dengue virus (DENV) type 2 NS1 protein was investigated and compared with the use of conventional monoclonal antibodies. After successful expression of DENV type 2 NS1 protein, the genes of VHH antibodies against NS1 protein were biopanned from a non-immune llama library by phage display. VHH antibodies were then expressed and purified from Escherichia coli. Simultaneously, monoclonal antibodies were obtained by the conventional route. Sequence analysis of the VHH antibodies revealed novel and long complementarity determining regions 3 (CDR3). Epitope mapping was performed via a phage display peptide library using purified VHH and monoclonal antibodies as targets. Interestingly, the same region of NS1, which comprises amino acids 224HWPKPHTLW232, was conserved for both kinds of antibodies displaying the consensus motif histidine-tryptophan-tryptophan or tryptophan-proline-tryptophan. The two types of antibodies were used to prepare rapid diagnostic kits based on immunochromatographic assay. The VHH antibody immobilized rapid diagnostic kit showed better sensitivity and specificity than the monoclonal antibody immobilized rapid diagnostic kit, which might be due to the long CDR3 regions of the VHH antibodies and their ability to bind to the pocket and cleft of the targeted antigen. This demonstrates that VHH antibodies are likely to be an option for developing point-of-care tests against DENV infection. PMID:24751715

We Know the Yin—But Where Is the Yang? Toward a Balanced Approach on Common Source Bias in Public Administration Scholarship

PubMed Central

George, Bert; Pandey, Sanjay K.

2017-01-01

Surveys have long been a dominant instrument for data collection in public administration. However, it has become widely accepted in the last decade that the usage of a self-reported instrument to measure both the independent and dependent variables results in common source bias (CSB). In turn, CSB is argued to inflate correlations between variables, resulting in biased findings. Subsequently, a narrow blinkered approach on the usage of surveys as single data source has emerged. In this article, we argue that this approach has resulted in an unbalanced perspective on CSB. We argue that claims on CSB are exaggerated, draw upon selective evidence, and project what should be tentative inferences as certainty over large domains of inquiry. We also discuss the perceptual nature of some variables and measurement validity concerns in using archival data. In conclusion, we present a flowchart that public administration scholars can use to analyze CSB concerns. PMID:29046599

We Know the Yin-But Where Is the Yang? Toward a Balanced Approach on Common Source Bias in Public Administration Scholarship.

PubMed

George, Bert; Pandey, Sanjay K

2017-06-01

Surveys have long been a dominant instrument for data collection in public administration. However, it has become widely accepted in the last decade that the usage of a self-reported instrument to measure both the independent and dependent variables results in common source bias (CSB). In turn, CSB is argued to inflate correlations between variables, resulting in biased findings. Subsequently, a narrow blinkered approach on the usage of surveys as single data source has emerged. In this article, we argue that this approach has resulted in an unbalanced perspective on CSB. We argue that claims on CSB are exaggerated, draw upon selective evidence, and project what should be tentative inferences as certainty over large domains of inquiry. We also discuss the perceptual nature of some variables and measurement validity concerns in using archival data. In conclusion, we present a flowchart that public administration scholars can use to analyze CSB concerns.

Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater

EPA Science Inventory

Metagenomics is a powerful tool for characterizing viral composition within environmental samples, but sample and molecular processing steps can bias the estimation of viral community structure. The objective of this study is to understand the inherent variability introduced when...

External quality-assurance results for the National Atmospheric Deposition Program / National Trends Network and Mercury Deposition Network, 2004

USGS Publications Warehouse

Wetherbee, Gregory A.; Latysh, Natalie E.; Greene, Shannon M.

2006-01-01

The U.S. Geological Survey (USGS) used five programs to provide external quality-assurance monitoring for the National Atmospheric Deposition Program/National Trends Network (NADP/NTN) and two programs to provide external quality-assurance monitoring for the NADP/Mercury Deposition Network (NADP/MDN) during 2004. An intersite-comparison program was used to estimate accuracy and precision of field-measured pH and specific-conductance. The variability and bias of NADP/NTN data attributed to field exposure, sample handling and shipping, and laboratory chemical analysis were estimated using the sample-handling evaluation (SHE), field-audit, and interlaboratory-comparison programs. Overall variability of NADP/NTN data was estimated using a collocated-sampler program. Variability and bias of NADP/MDN data attributed to field exposure, sample handling and shipping, and laboratory chemical analysis were estimated using a system-blank program and an interlaboratory-comparison program. In two intersite-comparison studies, approximately 89 percent of NADP/NTN site operators met the pH measurement accuracy goals, and 94.7 to 97.1 percent of NADP/NTN site operators met the accuracy goals for specific conductance. Field chemistry measurements were discontinued by NADP at the end of 2004. As a result, the USGS intersite-comparison program also was discontinued at the end of 2004. Variability and bias in NADP/NTN data due to sample handling and shipping were estimated from paired-sample concentration differences and specific conductance differences obtained for the SHE program. Median absolute errors (MAEs) equal to less than 3 percent were indicated for all measured analytes except potassium and hydrogen ion. Positive bias was indicated for most of the measured analytes except for calcium, hydrogen ion and specific conductance. Negative bias for hydrogen ion and specific conductance indicated loss of hydrogen ion and decreased specific conductance from contact of the sample with the collector bucket. Field-audit results for 2004 indicate dissolved analyte loss in more than one-half of NADP/NTN wet-deposition samples for all analytes except chloride. Concentrations of contaminants also were estimated from field-audit data. On the basis of 2004 field-audit results, at least 25 percent of the 2004 NADP/NTN concentrations for sodium, potassium, and chloride were lower than the maximum sodium, potassium, and chloride contamination likely to be found in 90 percent of the samples with 90-percent confidence. Variability and bias in NADP/NTN data attributed to chemical analysis by the NADP Central Analytical Laboratory (CAL) were comparable to the variability and bias estimated for other laboratories participating in the interlaboratory-comparison program for all analytes. Variability in NADP/NTN ammonium data evident in 2002-03 was reduced substantially during 2004. Sulfate, hydrogen-ion, and specific conductance data reported by CAL during 2004 were positively biased. A significant (a = 0.05) bias was identified for CAL sodium, potassium, ammonium, and nitrate data, but the absolute values of the median differences for these analytes were less than the method detection limits. No detections were reported for CAL analyses of deionized-water samples, indicating that contamination was not a problem for CAL. Control charts show that CAL data were within statistical control during at least 90 percent of 2004. Most 2004 CAL interlaboratory-comparison results for synthetic wet-deposition solutions were within ?10 percent of the most probable values (MPVs) for solution concentrations except for chloride, nitrate, sulfate, and specific conductance results from one sample in November and one specific conductance result in December. Overall variability of NADP/NTN wet-deposition measurements was estimated during water year 2004 by the median absolute errors for weekly wet-deposition sample concentrations and precipitation measurements for tw

Adaptive History Biases Result from Confidence-Weighted Accumulation of past Choices

PubMed Central

2018-01-01

Perceptual decision-making is biased by previous events, including the history of preceding choices: observers tend to repeat (or alternate) their judgments of the sensory environment more often than expected by chance. Computational models postulate that these so-called choice history biases result from the accumulation of internal decision signals across trials. Here, we provide psychophysical evidence for such a mechanism and its adaptive utility. Male and female human observers performed different variants of a challenging visual motion discrimination task near psychophysical threshold. In a first experiment, we decoupled categorical perceptual choices and motor responses on a trial-by-trial basis. Choice history bias was explained by previous perceptual choices, not motor responses, highlighting the importance of internal decision signals in action-independent formats. In a second experiment, observers performed the task in stimulus environments containing different levels of autocorrelation and providing no external feedback about choice correctness. Despite performing under overall high levels of uncertainty, observers adjusted both the strength and the sign of their choice history biases to these environments. When stimulus sequences were dominated by either repetitions or alternations, the individual degree of this adjustment of history bias was about as good a predictor of individual performance as individual perceptual sensitivity. The history bias adjustment scaled with two proxies for observers' confidence about their previous choices (accuracy and reaction time). Together, our results are consistent with the idea that action-independent, confidence-modulated decision variables are accumulated across choices in a flexible manner that depends on decision-makers' model of their environment. SIGNIFICANCE STATEMENT Decisions based on sensory input are often influenced by the history of one's preceding choices, manifesting as a bias to systematically repeat (or alternate) choices. We here provide support for the idea that such choice history biases arise from the context-dependent accumulation of a quantity referred to as the decision variable: the variable's sign dictates the choice and its magnitude the confidence about choice correctness. We show that choices are accumulated in an action-independent format and a context-dependent manner, weighted by the confidence about their correctness. This confidence-weighted accumulation of choices enables decision-makers to flexibly adjust their behavior to different sensory environments. The bias adjustment can be as important for optimizing performance as one's sensitivity to the momentary sensory input. PMID:29371318

Adaptive History Biases Result from Confidence-weighted Accumulation of Past Choices.

PubMed

Braun, Anke; Urai, Anne E; Donner, Tobias H

2018-01-25

Perceptual decision-making is biased by previous events, including the history of preceding choices: Observers tend to repeat (or alternate) their judgments of the sensory environment more often than expected by chance. Computational models postulate that these so-called choice history biases result from the accumulation of internal decision signals across trials. Here, we provide psychophysical evidence for such a mechanism and its adaptive utility. Male and female human observers performed different variants of a challenging visual motion discrimination task near psychophysical threshold. In a first experiment, we decoupled categorical perceptual choices and motor responses on a trial-by-trial basis. Choice history bias was explained by previous perceptual choices, not motor responses, highlighting the importance of internal decision signals in action-independent formats. In a second experiment, observers performed the task in stimulus environments containing different levels of auto-correlation and providing no external feedback about choice correctness. Despite performing under overall high levels of uncertainty, observers adjusted both the strength and the sign of their choice history biases to these environments. When stimulus sequences were dominated by either repetitions or alternations, the individual degree of this adjustment of history bias was about as good a predictor of individual performance as individual perceptual sensitivity. The history bias adjustment scaled with two proxies for observers' confidence about their previous choices (accuracy and reaction time). Taken together, our results are consistent with the idea that action-independent, confidence-modulated decision variables are accumulated across choices in a flexible manner that depends on decision-makers' model of their environment. Significance statement: Decisions based on sensory input are often influenced by the history of one's preceding choices, manifesting as a bias to systematically repeat (or alternate) choices. We here provide support for the idea that such choice history biases arise from the context-dependent accumulation of a quantity referred to as the decision variable: the variable's sign dictates the choice and its magnitude the confidence about choice correctness. We show that choices are accumulated in an action-independent format and a context-dependent manner, weighted by the confidence about their correctness. This confidence-weighted accumulation of choices enables decision-makers to flexibly adjust their behavior to different sensory environments. The bias adjustment can be as important for optimizing performance as one's sensitivity to the momentary sensory input. Copyright © 2018 Braun et al.

Single-dose Universal Hepatitis A Immunization in One-year-old Children in Argentina: High Prevalence of Protective Antibodies up to 9 Years After Vaccination.

PubMed

Urueña, Analía; González, Jorge E; Rearte, Analía; Pérez Carrega, María E; Calli, Rogelio; Pagani, María F; Uboldi, Andrea; Vicentín, Rosalía; Caglio, Patricia; Cañero-Velasco, María C; Gentile, Angela; Ramonet, Margarita; Vizzotti, Carla

2016-12-01

Single-dose hepatitis A virus (HAV) vaccination was implemented in all Argentinean children 12 months of age in 2005. Previous studies demonstrated high prevalence of protective antibody response 4 years after single-dose vaccination. This study assessed long-term seroprotection against HAV after vaccination. Children who received 1 dose of HAV vaccine at 1 year of age at least 6 years before enrollment were included at 5 centers in Argentina between 2013 and 2014. Demographic and socioeconomic characteristics were collected through a questionnaire. Blood samples were tested for anti-HAV antibodies. Antibody values ≥10 mIU/mL were considered seroprotective. Logistic regression analysis was performed to evaluate the association between demographic and socioeconomic variables and seroprotection. A total of 1088 children were included, with a median postvaccination interval of 7.7 years (range 6.3-9.2 years). Of these children, 97.4% (95% confidence interval: 96.3%-98.3%) had protective antibodies against HAV. No association between demographic or socioeconomic variables and seroprotection was found. Geometric mean concentration of antibody levels against HAV was 170.5 mUI/mL (95% confidence interval: 163.2-178.2 mUI/mL). Single-dose universal hepatitis A immunization in 1-year-old children resulted in sustained immunologic protection for up to 9 years in Argentina. These findings, along with the low current disease burden, confirm the success of the intervention.

Usefulness of thyrogastric immune features as predictors of pernicious anaemia that lacks intrinsic factor antibody.

PubMed

Chan, J; Chan, H Y F

2011-08-01

The study aims to evaluate the diagnostic utility of thyrogastric immune features in the identification of intrinsic factor antibody negative (IFA -ve) pernicious anaemia (PA) patients. Clinico-pathological features of 'intrinsic factor antibody positive (IFA +ve) PA' and 'IFA -ve presumed PA' Chinese patients in a single hospital (2001-2009) were studied. Coefficients of independent variables identified were used as weighted scores. The result was validated by patients (1994-2000) with Schilling test done. Comparison of 127 'IFA +ve PA' and 130 'IFA -ve presumed PA' patients showed four independent variables, namely (+) gastric parietal cell (GPC) antibody (OR, 2.907, 95%; CI, 2.346-3.468; P < 0.001), (+) antithyroid antibodies (OR, 3.098, 95%; CI, 2.496-3.70; P < 0.001), (+) gastric atrophy (OR, 3.827, 95%; CI, 3.041-4.64; P = 0.001), and (-) Helicobacter pylori (HP) organisms (OR, 0.134, 95%; CI, -1.60-1.869; P = 0.023). The respective scores were 1.067, 1.131, 1.342 and -2.012. Total scores for each patient ranged from 3.54 to -2.012. When the cut-off score 1.528 was applied to the validation sample (n = 75), the specificity of identifying IFA -ve PA was 100%, sensitivity 53%, positive predictive value 100%, and negative predictive value 36%. Patients with two out of three features, GPC, antithyroid antibodies, gastric atrophy, but without HP organisms; or three features with HP organisms, can be predicted to have PA. © 2011 Blackwell Publishing Ltd.

Clinical and Serological Predictors of Suicide in Schizophrenia and Major Mood Disorders.

PubMed

Dickerson, Faith; Origoni, Andrea; Schweinfurth, Lucy A B; Stallings, Cassie; Savage, Christina L G; Sweeney, Kevin; Katsafanas, Emily; Wilcox, Holly C; Khushalani, Sunil; Yolken, Robert

2018-03-01

Persons with serious mental illness are at high risk for suicide, but this outcome is difficult to predict. Serological markers may help to identify suicide risk. We prospectively assessed 733 persons with a schizophrenia spectrum disorder, 483 with bipolar disorder, and 76 with major depressive disorder for an average of 8.15 years. The initial evaluation consisted of clinical and demographic data as well as a blood samples from which immunoglobulin G antibodies to herpes viruses and Toxoplasma gondii were measured. Suicide was determined using data from the National Death Index. Cox proportional hazard regression models examined the role of baseline variables on suicide outcomes. Suicide was associated with male sex, divorced/separated status, Caucasian race, and elevated levels of antibodies to Cytomegalovirus (CMV). Increasing levels of CMV antibodies were associated with increasing hazard ratios for suicide. The identification of serological variables associated with suicide might provide more personalized methods for suicide prevention.

Conserved Structural Elements in the V3 Crown of HIV-1 gp120

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

Jiang, X.; Burke, V; Totrov, M

2010-01-01

Binding of the third variable region (V3) of the HIV-1 envelope glycoprotein gp120 to the cell-surface coreceptors CCR5 or CXCR4 during viral entry suggests that there are conserved structural elements in this sequence-variable region. These conserved elements could serve as epitopes to be targeted by a vaccine against HIV-1. Here we perform a systematic structural analysis of representative human anti-V3 monoclonal antibodies in complex with V3 peptides, revealing that the crown of V3 has four conserved structural elements: an arch, a band, a hydrophobic core and the peptide backbone. These are either unaffected by or are subject to minimal sequencemore » variation. As these regions are targeted by cross-clade neutralizing human antibodies, they provide a blueprint for the design of vaccine immunogens that could elicit broadly cross-reactive protective antibodies.« less

Epigallocatechin-3-gallate preferentially induces aggregation of amyloidogenic immunoglobulin light chains

PubMed Central

Hora, Manuel; Carballo-Pacheco, Martin; Weber, Benedikt; Morris, Vanessa K.; Wittkopf, Antje; Buchner, Johannes; Strodel, Birgit; Reif, Bernd

2017-01-01

Antibody light chain amyloidosis is a rare disease caused by fibril formation of secreted immunoglobulin light chains (LCs). The huge variety of antibody sequences puts a serious challenge to drug discovery. The green tea polyphenol epigallocatechin-3-gallate (EGCG) is known to interfere with fibril formation in general. Here we present solution- and solid-state NMR studies as well as MD simulations to characterise the interaction of EGCG with LC variable domains. We identified two distinct EGCG binding sites, both of which include a proline as an important recognition element. The binding sites were confirmed by site-directed mutagenesis and solid-state NMR analysis. The EGCG-induced protein complexes are unstructured. We propose a general mechanistic model for EGCG binding to a conserved site in LCs. We find that EGCG reacts selectively with amyloidogenic mutants. This makes this compound a promising lead structure, that can handle the immense sequence variability of antibody LCs. PMID:28128355

High Titers ofChlamydia trachomatis Antibodies in Brazilian Women with Tubal Occlusion or Previous Ectopic Pregnancy

PubMed Central

Machado, A. C. S.; Guimarães, E. M. B.; Sakurai, E.; Fioravante, F. C. R.; Amaral, W. N.; Alves, M. F. C.

2007-01-01

Objective. To evaluate serum chlamydia antibody titers (CATs) in tubal occlusion or previous ectopic pregnancy and the associated risk factors.Methods. The study population consisted of 55 women wih tubal damage and 55 parous women. CAT was measured using the whole-cell inclusion immunofluorescence test and cervical chlamydial DNA detected by PCR. Odds ratios were calculated to assess variables associated withC. trachomatis infection.Results. The prevalence of chlamydial antibodies and antibody titers in women with tubal occlusion or previous ectopic pregnancy was significantly higher (P < .01) than in parous women. Stepwise logistic regression analysis showed that chlamydia IgG antibodies were associated with tubal damage and with a larger number of lifetime sexual partners.Conclusions. Chlamydia antibody titers were associated with tubal occlusion, prior ectopic pregnancy, and with sexual behavior, suggesting that a chlamydia infection was the major contributor to the tubal damage in these women. PMID:17541464

Homologous and heterologous antibody responses of mice immunized with purified feline herpesvirus type 1 and canine herpesvirus glycoproteins.

PubMed

Limcumpao, J A; Horimoto, T; Xuan, X N; Tohya, Y; Azetaka, M; Takahashi, E; Mikami, T

1991-06-01

The three glycoproteins each of feline herpesvirus type 1 (FHV-1) and canine herpesvirus (CHV) were purified by affinity chromatography using glycoprotein-specific monoclonal antibodies and used individually or in combination in immunizing mice to determine their relative immunogenicity. All the glycoproteins induced detectable virus neutralizing antibodies to the homologous virus but FHV-1 gp143/108 and its cross-reacting counterpart, CHV gp145/112, elicited the highest titers not only to the homologous virus but to the heterologous virus as well. The production of ELISA antibodies after glycoprotein immunization was variable, while hemagglutination-inhibiting antibodies were produced by only 1 out of 10 FHV-1 gp60-inoculated mice. In general, the antibody titers induced by CHV glycoproteins were lower than those by FHV-1 glycoproteins. These results indicate that these glycoproteins may be useful as subunit vaccines against FHV-1 and CHV infections.

Correlation between sonography and antibody activity in patients with Hashimoto thyroiditis.

PubMed

Willms, Arnulf; Bieler, Dan; Wieler, Helmut; Willms, Diana; Kaiser, Klaus P; Schwab, Robert

2013-11-01

Patients with Hashimoto thyroiditis show structural changes of the thyroid that can be identified by a variety of sonographic criteria. We conducted this study to investigate whether there is a correlation between sonography and antibody activity and to assess the role of sonography in the diagnosis and follow-up of Hashimoto thyroiditis. In addition, we present a new classification system (termed the VESINC system [volume, echogenicity, sonographic texture, pseudonodular hypoechoic infiltration, nodules, and cysts]), which helps improve the clarity of sonographic findings. The study included 223 consecutive patients with previously diagnosed Hashimoto autoimmune thyroiditis who attended the thyroid clinic of the German Armed Forces Central Hospital in Koblenz for follow-up examinations between 2006 and 2008. Laboratory tests were performed to measure the levels of free triiodothyronine, free thyroxine, thyrotropin, anti-thyroglobulin antibodies (TgAbs), and antithyroid peroxidase antibodies (TPOAbs). Sonography was performed according to a strict protocol. We then assessed whether a correlation existed between antibody activity and the 6 sonographic variables of the VESINC system. Hypoechogenicity, heterogeneity, and pseudonodular hypoechoic infiltration were associated with significantly higher TPOAb activity (P < .001). There were no significant correlations between the other sonographic variables examined (cysts, nodules, and volume) or the biometric data with the TPOAb and TgAb levels. In addition, an assessment of TgAb levels did not show significant differences in correlations with any of the sonographic variables. Sonography is a noninvasive diagnostic imaging modality that provides information about the level of inflammatory activity. Markedly decreased echogenicity, heterogeneity, and multifocal pseudoinodular hypoechoic infiltration are indicative of a high level of inflammatory activity. The sonographic classification system presented here (VESINC system) can be a useful tool for comparing sonographic findings in a rapid and objective manner during follow-up of Hashimoto thyroiditis.

Development of an affinity-matured humanized anti-epidermal growth factor receptor antibody for cancer immunotherapy.

PubMed

Nakanishi, Takeshi; Maru, Takamitsu; Tahara, Kazuhiro; Sanada, Hideaki; Umetsu, Mitsuo; Asano, Ryutaro; Kumagai, Izumi

2013-02-01

We showed previously that humanization of 528, a murine anti-epidermal growth factor receptor (EGFR) antibody, causes reduced affinity for its target. Here, to improve the affinity of the humanized antibody for use in cancer immunotherapy, we constructed phage display libraries focused on the complementarity-determining regions (CDRs) of the antibody and carried out affinity selection. Two-step selections using libraries constructed in a stepwise manner enabled a 32-fold affinity enhancement of humanized 528 (h528). Thermodynamic analysis of the interactions between the variable domain fragment of h528 (h528Fv) mutants and the soluble extracellular domain of EGFR indicated that the h528Fv mutants obtained from the first selection showed a large increase in negative enthalpy change due to binding, resulting in affinity enhancement. Furthermore, mutants from the second selection showed a decrease in entropy loss, which led to further affinity maturation. These results suggest that a single mutation in the heavy chain variable domain (i.e. Tyr(52) to Trp) enthalpically contributed for overcoming the energetic barrier to the antigen-antibody interaction, which was a major hurdle for the in vitro affinity maturation of h528. We reported previously that the humanized bispecific diabody hEx3 Db, which targets EGFR and CD3, shows strong anti-tumor activity. hEx3 Db mutants, in which the variable domains of h528 were replaced with those of the affinity-enhanced mutants, were prepared and characterized. In a growth inhibition assay of tumor cells, the hEx3 Db mutants showed stronger anti-tumor activity than that of hEx3 Db, suggesting that affinity enhancement of h528Fv enhances the anti-tumor activity of the bispecific diabody.

High-frequency expression of a conserved kappa light-chain variable-region gene in chronic lymphocytic leukemia

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

Kipps, T.J.; Fong, S.; Tomhave, E.

Malignant B lymphocytes from several patients with chronic lymphocytic leukemia (CLL) were examined for reactivity with murine monoclonal antibody 17.109. This antibody, prepared against the rheumatoid factor (RF) paraprotein Sie, recognizes a cross reactive idiotype on 48% of human IgM RF paraproteins, but does not react with IgM paraproteins without RF activity or substantially with normal pooled immunoglobulin. The 17.109-reactive idiotype is a marker for a kappa III variable-region gene, designated V/sub kappa/RF, that is conserved in outbred human populations. In a limited study of 31 CLL patients, the leukemic cells from 5 of 20 patients with kappa light chain-expressingmore » CLL were recognized by the 17.109 monoclonal antibody. Despite having malignant cells specifically reactive with this antibody, patients with 17.109-positive CLL did not have elevated serum levels of circulating antibody bearing 17.109-reactive determinants. Total RNAs isolated from the CLL B lymphocytes, or from hybridomas produced by fusing the CLL cells with the WI-L2-729-HF/sub 2/ cell line, were fractionated electrophoretically and examined by blot hybridization. Under stringent hybridization conditions capable of discerning a single base-pair mismatch, RNA from the 17.109-idiotype-positive CLL cells hybridized to synthetic oligonucleotide probes corresponding to framework and complementary-determining regions in the V/sub kappa/RF gene. The high frequency of the 17.109-associated idiotype and the V/sub kappa/RF gene in CLL suggests that the disease may arise from B lymphocytes that express a restricted set of inherited immunoglobulin variable-region genes with little or no somatic mutation.« less

Implication of observed cloud variability for parameterizations of microphysical and radiative transfer processes in climate models

NASA Astrophysics Data System (ADS)

Huang, D.; Liu, Y.

2014-12-01

The effects of subgrid cloud variability on grid-average microphysical rates and radiative fluxes are examined by use of long-term retrieval products at the Tropical West Pacific (TWP), Southern Great Plains (SGP), and North Slope of Alaska (NSA) sites of the Department of Energy's Atmospheric Radiation Measurement (ARM) Program. Four commonly used distribution functions, the truncated Gaussian, Gamma, lognormal, and Weibull distributions, are constrained to have the same mean and standard deviation as observed cloud liquid water content. The PDFs are then used to upscale relevant physical processes to obtain grid-average process rates. It is found that the truncated Gaussian representation results in up to 30% mean bias in autoconversion rate whereas the mean bias for the lognormal representation is about 10%. The Gamma and Weibull distribution function performs the best for the grid-average autoconversion rate with the mean relative bias less than 5%. For radiative fluxes, the lognormal and truncated Gaussian representations perform better than the Gamma and Weibull representations. The results show that the optimal choice of subgrid cloud distribution function depends on the nonlinearity of the process of interest and thus there is no single distribution function that works best for all parameterizations. Examination of the scale (window size) dependence of the mean bias indicates that the bias in grid-average process rates monotonically increases with increasing window sizes, suggesting the increasing importance of subgrid variability with increasing grid sizes.

Characterizing energy budget variability at a Sahelian site: a test of NWP model behaviour

NASA Astrophysics Data System (ADS)

Mackie, Anna; Palmer, Paul I.; Brindley, Helen

2017-12-01

We use observations of surface and top-of-the-atmosphere (TOA) broadband radiation fluxes determined from the Atmospheric Radiation Measurement programme mobile facility, the Geostationary Earth Radiation Budget (GERB) and Spinning Enhanced Visible and Infrared Imager (SEVIRI) instruments and a range of meteorological variables at a site in the Sahel to test the ability of the ECMWF Integrated Forecasting System cycle 43r1 to describe energy budget variability. The model has daily average biases of -12 and 18 W m-2 for outgoing longwave and reflected shortwave TOA radiation fluxes, respectively. At the surface, the daily average bias is 12(13) W m-2 for the longwave downwelling (upwelling) radiation flux and -21(-13) W m-2 for the shortwave downwelling (upwelling) radiation flux. Using multivariate linear models of observation-model differences, we attribute radiation flux discrepancies to physical processes, and link surface and TOA fluxes. We find that model biases in surface radiation fluxes are mainly due to a low bias in ice water path (IWP), poor description of surface albedo and model-observation differences in surface temperature. We also attribute observed discrepancies in the radiation fluxes, particularly during the dry season, to the misrepresentation of aerosol fields in the model from use of a climatology instead of a dynamic approach. At the TOA, the low IWP impacts the amount of reflected shortwave radiation while biases in outgoing longwave radiation are additionally coupled to discrepancies in the surface upwelling longwave flux and atmospheric humidity.

Investigating Uncertainty in Predicting Carbon Dynamics in North American Biomes: Putting Support-Effect Bias in Perspective

NASA Technical Reports Server (NTRS)

Dungan, Jennifer L.; Brass, Jim (Technical Monitor)

2001-01-01

A fundamental strategy in NASA's Earth Observing System's (EOS) monitoring of vegetation and its contribution to the global carbon cycle is to rely on deterministic, process-based ecosystem models to make predictions of carbon flux over large regions. These models are parameterized (that is, the input variables are derived) using remotely sensed images such as those from the Moderate Resolution Imaging Spectroradiometer (MODIS), ground measurements and interpolated maps. Since early applications of these models, investigators have noted that results depend partly on the spatial support of the input variables. In general, the larger the support of the input data, the greater the chance that the effects of important components of the ecosystem will be averaged out. A review of previous work shows that using large supports can cause either positive or negative bias in carbon flux predictions. To put the magnitude and direction of these biases in perspective, we must quantify the range of uncertainty on our best measurements of carbon-related variables made on equivalent areas. In other words, support-effect bias should be placed in the context of prediction uncertainty from other sources. If the range of uncertainty at the smallest support is less than the support-effect bias, more research emphasis should probably be placed on support sizes that are intermediate between those of field measurements and MODIS. If the uncertainty range at the smallest support is larger than the support-effect bias, the accuracy of MODIS-based predictions will be difficult to quantify and more emphasis should be placed on field-scale characterization and sampling. This talk will describe methods to address these issues using a field measurement campaign in North America and "upscaling" using geostatistical estimation and simulation.

Variation of the Specificity of the Human Antibody Responses after Tick-Borne Encephalitis Virus Infection and Vaccination

PubMed Central

Jarmer, Johanna; Zlatkovic, Jürgen; Tsouchnikas, Georgios; Vratskikh, Oksana; Strauß, Judith; Aberle, Judith H.; Chmelik, Vaclav; Kundi, Michael; Stiasny, Karin

2014-01-01

ABSTRACT Tick-borne encephalitis (TBE) virus is an important human-pathogenic flavivirus endemic in large parts of Europe and Central and Eastern Asia. Neutralizing antibodies specific for the viral envelope protein E are believed to mediate long-lasting protection after natural infection and vaccination. To study the specificity and individual variation of human antibody responses, we developed immunoassays with recombinant antigens representing viral surface protein domains and domain combinations. These allowed us to dissect and quantify antibody populations of different fine specificities in sera of TBE patients and vaccinees. Postinfection and postvaccination sera both displayed strong individual variation of antibody titers as well as the relative proportions of antibodies to different domains of E, indicating that the immunodominance patterns observed were strongly influenced by individual-specific factors. The contributions of these antibody populations to virus neutralization were quantified by serum depletion analyses and revealed a significantly biased pattern. Antibodies to domain III, in contrast to what was found in mouse immunization studies with TBE and other flaviviruses, did not play any role in the human neutralizing antibody response, which was dominated by antibodies to domains I and II. Importantly, most of the neutralizing activity could be depleted from sera by a dimeric soluble form of the E protein, which is the building block of the icosahedral herringbone-like shell of flaviviruses, suggesting that antibodies to more complex quaternary epitopes involving residues from adjacent dimers play only a minor role in the total response to natural infection and vaccination in humans. IMPORTANCE Tick-borne encephalitis (TBE) virus is a close relative of yellow fever, dengue, Japanese encephalitis, and West Nile viruses and distributed in large parts of Europe and Central and Eastern Asia. Antibodies to the viral envelope protein E prevent viral attachment and entry into cells and thus mediate virus neutralization and protection from disease. However, the fine specificity and individual variation of neutralizing antibody responses are currently not known. We have therefore developed new in vitro assays for dissecting the antibody populations present in blood serum and determining their contribution to virus neutralization. In our analysis of human postinfection and postvaccination sera, we found an extensive variation of the antibody populations present in sera, indicating substantial influences of individual-specific factors that control the specificity of the antibody response. Our study provides new insights into the immune response to an important human pathogen that is of relevance for the design of novel vaccines. PMID:25253341

Variation of the specificity of the human antibody responses after tick-borne encephalitis virus infection and vaccination.

PubMed

Jarmer, Johanna; Zlatkovic, Jürgen; Tsouchnikas, Georgios; Vratskikh, Oksana; Strauß, Judith; Aberle, Judith H; Chmelik, Vaclav; Kundi, Michael; Stiasny, Karin; Heinz, Franz X

2014-12-01

Tick-borne encephalitis (TBE) virus is an important human-pathogenic flavivirus endemic in large parts of Europe and Central and Eastern Asia. Neutralizing antibodies specific for the viral envelope protein E are believed to mediate long-lasting protection after natural infection and vaccination. To study the specificity and individual variation of human antibody responses, we developed immunoassays with recombinant antigens representing viral surface protein domains and domain combinations. These allowed us to dissect and quantify antibody populations of different fine specificities in sera of TBE patients and vaccinees. Postinfection and postvaccination sera both displayed strong individual variation of antibody titers as well as the relative proportions of antibodies to different domains of E, indicating that the immunodominance patterns observed were strongly influenced by individual-specific factors. The contributions of these antibody populations to virus neutralization were quantified by serum depletion analyses and revealed a significantly biased pattern. Antibodies to domain III, in contrast to what was found in mouse immunization studies with TBE and other flaviviruses, did not play any role in the human neutralizing antibody response, which was dominated by antibodies to domains I and II. Importantly, most of the neutralizing activity could be depleted from sera by a dimeric soluble form of the E protein, which is the building block of the icosahedral herringbone-like shell of flaviviruses, suggesting that antibodies to more complex quaternary epitopes involving residues from adjacent dimers play only a minor role in the total response to natural infection and vaccination in humans. Tick-borne encephalitis (TBE) virus is a close relative of yellow fever, dengue, Japanese encephalitis, and West Nile viruses and distributed in large parts of Europe and Central and Eastern Asia. Antibodies to the viral envelope protein E prevent viral attachment and entry into cells and thus mediate virus neutralization and protection from disease. However, the fine specificity and individual variation of neutralizing antibody responses are currently not known. We have therefore developed new in vitro assays for dissecting the antibody populations present in blood serum and determining their contribution to virus neutralization. In our analysis of human postinfection and postvaccination sera, we found an extensive variation of the antibody populations present in sera, indicating substantial influences of individual-specific factors that control the specificity of the antibody response. Our study provides new insights into the immune response to an important human pathogen that is of relevance for the design of novel vaccines. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

INDUCTION OF RABBIT ANTIBODY WITH MOLECULAR UNIFORMITY AFTER IMMUNIZATION WITH GROUP C STREPTOCOCCI

PubMed Central

Eichmann, Klaus; Lackland, Henry; Hood, Leroy; Krause, Richard M.

1970-01-01

Antibodies with uniform properties may occur in rabbits after immunization with Group C streptococci. These precipitating antibodies possess specificity for the group-specific carbohydrate. Not uncommonly, their concentration is between 20 and 40 mg/ml of antiserum. Evidence for molecular uniformity in the case of one of these antibodies, described in detail here, includes: individual antigenic specificity; monodisperse distribution of the light chains by alkaline urea polyacrylamide disc electrophoresis; and a single amino acid in each of the first three N-terminal positions of the light chains. When the amino acid sequence of rabbit antibody b+ light chains (κ type) are aligned against their human κ counterparts, a definite homology is observed between the N-terminus of the human and the rabbit variable region. PMID:5409946

Immunological aspects of Giardia infections.

PubMed

Heyworth, Martin F

2014-01-01

Immunodeficiency, particularly antibody deficiency, predisposes to increased intensity and persistence of Giardia infections. Giardia-infected immunocompetent hosts produce serum and intestinal antibodies against Giardia trophozoites. The number of Giardia muris trophozoites, in mice with G. muris infection, is reduced by intra-duodenal administration of anti-G. muris antibody. Giardia intestinalis antigens that are recognised by human anti-trophozoite antibodies include variable (variant-specific) and invariant proteins. Nitric oxide (NO) appears to contribute to host clearance of Giardia trophozoites. Arginine is a precursor of NO and is metabolised by Giardia trophozoites, possibly reducing its availability for generation of NO by the host. Work with mice suggests that T lymphocytes and interleukin-6 (IL-6) contribute to clearance of Giardia infection via mechanisms independent of antibodies. © M.F. Heyworth, published by EDP Sciences, 2014.

Inter-Annual Variability of Fledgling Sex Ratio in King Penguins.

PubMed

Bordier, Célia; Saraux, Claire; Viblanc, Vincent A; Gachot-Neveu, Hélène; Beaugey, Magali; Le Maho, Yvon; Le Bohec, Céline

2014-01-01

As the number of breeding pairs depends on the adult sex ratio in a monogamous species with biparental care, investigating sex-ratio variability in natural populations is essential to understand population dynamics. Using 10 years of data (2000-2009) in a seasonally monogamous seabird, the king penguin (Aptenodytes patagonicus), we investigated the annual sex ratio at fledging, and the potential environmental causes for its variation. Over more than 4000 birds, the annual sex ratio at fledging was highly variable (ranging from 44.4% to 58.3% of males), and on average slightly biased towards males (51.6%). Yearly variation in sex-ratio bias was neither related to density within the colony, nor to global or local oceanographic conditions known to affect both the productivity and accessibility of penguin foraging areas. However, rising sea surface temperature coincided with an increase in fledging sex-ratio variability. Fledging sex ratio was also correlated with difference in body condition between male and female fledglings. When more males were produced in a given year, their body condition was higher (and reciprocally), suggesting that parents might adopt a sex-biased allocation strategy depending on yearly environmental conditions and/or that the effect of environmental parameters on chick condition and survival may be sex-dependent. The initial bias in sex ratio observed at the juvenile stage tended to return to 1∶1 equilibrium upon first breeding attempts, as would be expected from Fisher's classic theory of offspring sex-ratio variation.

A semi high-throughput method for screening small bispecific antibodies with high cytotoxicity.

PubMed

Sugiyama, Aruto; Umetsu, Mitsuo; Nakazawa, Hikaru; Niide, Teppei; Onodera, Tomoko; Hosokawa, Katsuhiro; Hattori, Shuhei; Asano, Ryutaro; Kumagai, Izumi

2017-06-06

Small bispecific antibodies that induce T-cell-mediated cytotoxicity have the potential to damage late-stage tumor masses to a clinically relevant degree, but their cytotoxicity is critically dependent on their structural and functional properties. Here, we constructed an optimized procedure for identifying highly cytotoxic antibodies from a variety of the T-cell-recruiting antibodies engineered from a series of antibodies against cancer antigens of epidermal growth factor receptor family and T-cell receptors. By developing and applying a set of rapid operations for expression vector construction and protein preparation, we screened the cytotoxicity of 104 small antibodies with diabody format and identified some with 10 3 -times higher cytotoxicity than that of previously reported active diabody. The results demonstrate that cytotoxicity is enhanced by synergistic effects between the target, epitope, binding affinity, and the order of heavy-chain and light-chain variable domains. We demonstrate the importance of screening to determine the critical rules for highly cytotoxic antibodies.

Assessing total nitrogen in surface-water samples--precision and bias of analytical and computational methods

USGS Publications Warehouse

Rus, David L.; Patton, Charles J.; Mueller, David K.; Crawford, Charles G.

2013-01-01

The characterization of total-nitrogen (TN) concentrations is an important component of many surface-water-quality programs. However, three widely used methods for the determination of total nitrogen—(1) derived from the alkaline-persulfate digestion of whole-water samples (TN-A); (2) calculated as the sum of total Kjeldahl nitrogen and dissolved nitrate plus nitrite (TN-K); and (3) calculated as the sum of dissolved nitrogen and particulate nitrogen (TN-C)—all include inherent limitations. A digestion process is intended to convert multiple species of nitrogen that are present in the sample into one measureable species, but this process may introduce bias. TN-A results can be negatively biased in the presence of suspended sediment, and TN-K data can be positively biased in the presence of elevated nitrate because some nitrate is reduced to ammonia and is therefore counted twice in the computation of total nitrogen. Furthermore, TN-C may not be subject to bias but is comparatively imprecise. In this study, the effects of suspended-sediment and nitrate concentrations on the performance of these TN methods were assessed using synthetic samples developed in a laboratory as well as a series of stream samples. A 2007 laboratory experiment measured TN-A and TN-K in nutrient-fortified solutions that had been mixed with varying amounts of sediment-reference materials. This experiment identified a connection between suspended sediment and negative bias in TN-A and detected positive bias in TN-K in the presence of elevated nitrate. A 2009–10 synoptic-field study used samples from 77 stream-sampling sites to confirm that these biases were present in the field samples and evaluated the precision and bias of TN methods. The precision of TN-C and TN-K depended on the precision and relative amounts of the TN-component species used in their respective TN computations. Particulate nitrogen had an average variability (as determined by the relative standard deviation) of 13 percent. However, because particulate nitrogen constituted only 14 percent, on average, of TN-C, the precision of the TN-C method approached that of the method for dissolved nitrogen (2.3 percent). On the other hand, total Kjeldahl nitrogen (having a variability of 7.6 percent) constituted an average of 40 percent of TN-K, suggesting that the reduced precision of the Kjeldahl digestion may affect precision of the TN-K estimates. For most samples, the precision of TN computed as TN-C would be better (lower variability) than the precision of TN-K. In general, TN-A precision (having a variability of 2.1 percent) was superior to TN-C and TN-K methods. The laboratory experiment indicated that negative bias in TN-A was present across the entire range of sediment concentration and increased as sediment concentration increased. This suggested that reagent limitation was not the predominant cause of observed bias in TN-A. Furthermore, analyses of particulate nitrogen present in digest residues provided an almost complete accounting for the nitrogen that was underestimated by alkaline-persulfate digestion. This experiment established that, for the reference materials at least, negative bias in TN-A was caused primarily by the sequestration of some particulate nitrogen that was refractory to the digestion process. TN-K biases varied between positive and negative values in the laboratory experiment. Positive bias in TN-K is likely the result of the unintended reduction of a small and variable amount of nitrate to ammonia during the Kjeldahl digestion process. Negative TN-K bias may be the result of the sequestration of a portion of particulate nitrogen during the digestion process. Negative bias in TN-A was present across the entire range of suspended-sediment concentration (1 to 14,700 milligrams per liter [mg/L]) in the synoptic-field study, with relative bias being nearly as great at sediment concentrations below 10 mg/L (median of -3.5 percent) as that observed at sediment concentrations up to 750 mg/L (median of -4.4 percent). This lent support to the laboratory-experiment finding that some particulate nitrogen is sequestered during the digestion process, and demonstrated that negative TN-A bias was present in samples with very low suspended-sediment concentrations. At sediment concentrations above 750 mg/L, the negative TN-A bias became more likely and larger (median of -13.2 percent), suggesting a secondary mechanism of bias, such as reagent limitation. From a geospatial perspective, trends in TN-A bias were not explained by selected basin characteristics. Though variable, TN-K bias generally was positive in the synoptic-field study (median of 3.1 percent), probably as a result of the reduction of nitrate. Three alternative approaches for assessing TN in surface water were evaluated for their impacts on existing and future sampling programs. Replacing TN-A with TN-C would remove the bias from subsequent data, but this approach also would introduce discontinuity in historical records. Replacing TN-K with TN-C would lead to the removal of positive bias in TN-K in the presence of elevated nitrate. However, in addition to the issues that may arise from a discontinuity in the data record, this approach may not be applicable to regulatory programs that require the use of total Kjeldahl nitrogen for stream assessment. By adding TN-C to existing TN-A or TN-K analyses, historical-data continuity would be preserved and the transitional period could be used to minimize the impact of bias on data analyses. This approach, however, imposes the greatest burdens on field operations and in terms of analytical costs. The variation in these impacts on different sampling programs will challenge U.S. Geological Survey scientists attempting to establish uniform standards for TN sample collection and analytical determinations.

Differential effects of weight bias experiences and internalization on exercise among women with overweight and obesity.

PubMed

Pearl, Rebecca L; Puhl, Rebecca M; Dovidio, John F

2015-12-01

This study investigated the effects of experiences with weight stigma and weight bias internalization on exercise. An online sample of 177 women with overweight and obesity (M(age) = 35.48 years, M(BMI) = 32.81) completed questionnaires assessing exercise behavior, self-efficacy, and motivation; experiences of weight stigmatization; weight bias internalization; and weight-stigmatizing attitudes toward others. Weight stigma experiences positively correlated with exercise behavior, but weight bias internalization was negatively associated with all exercise variables. Weight bias internalization was a partial mediator between weight stigma experiences and exercise behavior. The distinct effects of experiencing versus internalizing weight bias carry implications for clinical practice and public health. © The Author(s) 2014.

Enhancement and Analysis of Human Antiaflatoxin B1 (AFB1) scFv Antibody-Ligand Interaction Using Chain Shuffling.

PubMed

Rangnoi, Kuntalee; Choowongkomon, Kiattawee; O'Kennedy, Richard; Rüker, Florian; Yamabhai, Montarop

2018-06-06

A human antiaflatoxin B1 (AFB1) scFv antibody (yAFB1-c3), selected from a naı̈ve human phage-displayed scFv library, was used as a template for improving and analysis of antibody-ligand interactions using the chain-shuffling technique. The variable-heavy and variable-light (VH/VL)-shuffled library was constructed from the VH of 25 preselected clones recombined with the VL of yAFB1-c3 and vice versa. Affinity selection from these libraries demonstrated that the VH domain played an important role in the binding of scFv to free AFB1. Therefore, in the next step, VH-shuffled scFv library was constructed from variable-heavy (VH) chain repertoires, amplified from the naı̈ve library, recombined with the variable-light (VL) chain of the clone yAFB1-c3. This library was then used to select a specific scFv antibody against soluble AFB1 by a standard biopanning method. Three clones that showed improved binding properties were isolated. Amino acid sequence analysis indicated that the improved clones have amino acid mutations in framework 1 (FR1) and the complementarity determining region (CDR1) of the VH chain. One clone, designated sAFH-3e3, showed 7.5-fold improvement in sensitivity over the original scFv clone and was selected for molecular binding studies with AFB1. Homology modeling and molecular docking were used to compare the binding of this and the original clones. The results confirmed that VH is more important than VL for AFB1 binding.

Construction of Rabbit Immune Antibody Libraries.

PubMed

Nguyen, Thi Thu Ha; Lee, Jong Seo; Shim, Hyunbo

2018-01-01

Rabbits have distinct advantages over mice as a source of target-specific antibodies. They produce higher affinity antibodies than mice, and may elicit strong immune response against antigens or epitopes that are poorly immunogenic or tolerated in mice. However, a great majority of currently available monoclonal antibodies are of murine origin because of the wider availability of murine fusion partner cell lines and well-established tools and protocols for fusion and cloning of mouse hybridoma. Phage-display selection of antibody libraries is an alternative method to hybridoma technology for the generation of target-specific monoclonal antibodies. High-affinity monoclonal antibodies from nonmurine species can readily be obtained by constructing immune antibody libraries from B cells of the immunized animal and screening the library by phage display. In this article, we describe the construction of a rabbit immune Fab library for the facile isolation of rabbit monoclonal antibodies. After immunization, B-cell cDNA is obtained from the spleen of the animal, from which antibody variable domain repertoires are amplified and assembled into a Fab repertoire by PCR. The Fab genes are then cloned into a phagemid vector and transformed to E. coli, from which a phage-displayed immune Fab library is rescued. Such a library can be biopanned against the immunization antigen for rapid identification of high-affinity, target-specific rabbit monoclonal antibodies.

Immune TB Antibody Phage Display Library as a Tool To Study B Cell Immunity in TB Infections.

PubMed

Hamidon, Nurul Hamizah; Suraiya, Siti; Sarmiento, Maria E; Acosta, Armando; Norazmi, Mohd Nor; Lim, Theam Soon

2018-03-01

B cells and in particular antibodies has always played second fiddle to cellular immunity in regard to tuberculosis (TB). However, recent studies has helped position humoral immunity especially antibodies back into the foray in relation to TB immunity. Therefore, the ability to correlate the natural antibody responses of infected individuals toward TB antigens would help strengthen this concept. Phage display is an intriguing approach that can be utilized to study antibody-mediated responses against a particular infection via harvesting the B cell repertoire from infected individuals. The development of disease-specific antibody libraries or immune libraries is useful to better understand antibody-mediated immune responses against specific disease antigens. This study describes the generation of an immune single-chain variable fragment (scFv) library derived from TB-infected individuals. The immune library with an estimated diversity of 10 9 independent clones was then applied for the identification of monoclonal antibodies against Mycobacterium tuberculosis α-crystalline as a model antigen. Biopanning of the library isolated three monoclonal antibodies with unique gene usage. This strengthens the role of antibodies in TB immunity in addition to the role played by cellular immunity. The developed library can be applied against other TB antigens and aid antibody-derived TB immunity studies in the future.

APPLICATION OF BIAS AND ADJUSTMENT TECHNIQUES TO THE ETA-CMAQ AIR QUALITY FORECAST

EPA Science Inventory

The current air quality forecast system, based on linking NOAA's Eta meteorological model with EPA's Community Multiscale Air Quality (CMAQ) model, consistently overpredicts surface ozone concentrations, but simulates its day-to-day variability quite well. The ability of bias cor...

Sex Bias in Research Design.

ERIC Educational Resources Information Center

Grady, Kathleen E.

1981-01-01

Presents feminist criticisms of selected aspects of research methods in psychology. Reviews data relevant to sex bias in topic selection, subject selection and single-sex designs, operationalization of variables, testing for sex differences, and interpretation of results. Suggestions for achieving more "sex fair" research methods are discussed.…

ENSO-driven energy budget perturbations in observations and CMIP models

DOE PAGES

Mayer, Michael; Fasullo, John T.; Trenberth, Kevin E.; ...

2016-03-19

Various observation-based datasets are employed to robustly quantify changes in ocean heat content (OHC), anomalous ocean–atmosphere energy exchanges and atmospheric energy transports during El Niño-Southern Oscillation (ENSO). These results are used as a benchmark to evaluate the energy pathways during ENSO as simulated by coupled climate model runs from the CMIP3 and CMIP5 archives. The models are able to qualitatively reproduce observed patterns of ENSO-related energy budget variability to some degree, but key aspects are seriously biased. Area-averaged tropical Pacific OHC variability associated with ENSO is greatly underestimated by all models because of strongly biased responses of net radiation atmore » top-of-the-atmosphere to ENSO. The latter are related to biases of mean convective activity in the models and project on surface energy fluxes in the eastern Pacific Intertropical Convergence Zone region. Moreover, models underestimate horizontal and vertical OHC redistribution in association with the generally too weak Bjerknes feedback, leading to a modeled ENSO affecting a too shallow layer of the Pacific. Vertical links between SST and OHC variability are too weak even in models driven with observed winds, indicating shortcomings of the ocean models. Furthermore, modeled teleconnections as measured by tropical Atlantic OHC variability are too weak and the tropical zonal mean ENSO signal is strongly underestimated or even completely missing in most of the considered models. In conclusion, results suggest that attempts to infer insight about climate sensitivity from ENSO-related variability are likely to be hampered by biases in ENSO in CMIP simulations that do not bear a clear link to future changes.« less

Active Learning to Overcome Sample Selection Bias: Application to Photometric Variable Star Classification

NASA Astrophysics Data System (ADS)

Richards, Joseph W.; Starr, Dan L.; Brink, Henrik; Miller, Adam A.; Bloom, Joshua S.; Butler, Nathaniel R.; James, J. Berian; Long, James P.; Rice, John

2012-01-01

Despite the great promise of machine-learning algorithms to classify and predict astrophysical parameters for the vast numbers of astrophysical sources and transients observed in large-scale surveys, the peculiarities of the training data often manifest as strongly biased predictions on the data of interest. Typically, training sets are derived from historical surveys of brighter, more nearby objects than those from more extensive, deeper surveys (testing data). This sample selection bias can cause catastrophic errors in predictions on the testing data because (1) standard assumptions for machine-learned model selection procedures break down and (2) dense regions of testing space might be completely devoid of training data. We explore possible remedies to sample selection bias, including importance weighting, co-training, and active learning (AL). We argue that AL—where the data whose inclusion in the training set would most improve predictions on the testing set are queried for manual follow-up—is an effective approach and is appropriate for many astronomical applications. For a variable star classification problem on a well-studied set of stars from Hipparcos and Optical Gravitational Lensing Experiment, AL is the optimal method in terms of error rate on the testing data, beating the off-the-shelf classifier by 3.4% and the other proposed methods by at least 3.0%. To aid with manual labeling of variable stars, we developed a Web interface which allows for easy light curve visualization and querying of external databases. Finally, we apply AL to classify variable stars in the All Sky Automated Survey, finding dramatic improvement in our agreement with the ASAS Catalog of Variable Stars, from 65.5% to 79.5%, and a significant increase in the classifier's average confidence for the testing set, from 14.6% to 42.9%, after a few AL iterations.

Quantitative spatiotemporal analysis of antibody fragment diffusion and endocytic consumption in tumor spheroids.

PubMed

Thurber, Greg M; Wittrup, K Dane

2008-05-01

Antibody-based cancer treatment depends upon distribution of the targeting macromolecule throughout tumor tissue, and spatial heterogeneity could significantly limit efficacy in many cases. Antibody distribution in tumor tissue is a function of drug dosage, antigen concentration, binding affinity, antigen internalization, drug extravasation from blood vessels, diffusion in the tumor extracellular matrix, and systemic clearance rates. We have isolated the effects of a subset of these variables by live-cell microscopic imaging of single-chain antibody fragments against carcinoembryonic antigen in LS174T tumor spheroids. The measured rates of scFv penetration and retention were compared with theoretical predictions based on simple scaling criteria. The theory predicts that antibody dose must be large enough to drive a sufficient diffusive flux of antibody to overcome cellular internalization, and exposure time must be long enough to allow penetration to the spheroid center. The experimental results in spheroids are quantitatively consistent with these predictions. Therefore, simple scaling criteria can be applied to accurately predict antibody and antibody fragment penetration distance in tumor tissue.

Quantitative Spatiotemporal Analysis of Antibody Fragment Diffusion and Endocytic Consumption in Tumor Spheroids

PubMed Central

Thurber, Greg M.; Wittrup, K. Dane

2010-01-01

Antibody-based cancer treatment depends upon distribution of the targeting macromolecule throughout tumor tissue, and spatial heterogeneity could significantly limit efficacy in many cases. Antibody distribution in tumor tissue is a function of drug dosage, antigen concentration, binding affinity, antigen internalization, drug extravasation from blood vessels, diffusion in the tumor extracellular matrix, and systemic clearance rates. We have isolated the effects of a subset of these variables by live-cell microscopic imaging of single-chain antibody fragments against carcinoembryonic antigen in LS174T tumor spheroids. The measured rates of scFv penetration and retention were compared with theoretical predictions based on simple scaling criteria. The theory predicts that antibody dose must be large enough to drive a sufficient diffusive flux of antibody to overcome cellular internalization, and exposure time must be long enough to allow penetration to the spheroid center. The experimental results in spheroids are quantitatively consistent with these predictions. Therefore, simple scaling criteria can be applied to accurately predict antibody and antibody fragment penetration distance in tumor tissue. PMID:18451160

Sampling bias in climate-conflict research

NASA Astrophysics Data System (ADS)

Adams, Courtland; Ide, Tobias; Barnett, Jon; Detges, Adrien

2018-03-01

Critics have argued that the evidence of an association between climate change and conflict is flawed because the research relies on a dependent variable sampling strategy1-4. Similarly, it has been hypothesized that convenience of access biases the sample of cases studied (the `streetlight effect'5). This also gives rise to claims that the climate-conflict literature stigmatizes some places as being more `naturally' violent6-8. Yet there has been no proof of such sampling patterns. Here we test whether climate-conflict research is based on such a biased sample through a systematic review of the literature. We demonstrate that research on climate change and violent conflict suffers from a streetlight effect. Further, studies which focus on a small number of cases in particular are strongly informed by cases where there has been conflict, do not sample on the independent variables (climate impact or risk), and hence tend to find some association between these two variables. These biases mean that research on climate change and conflict primarily focuses on a few accessible regions, overstates the links between both phenomena and cannot explain peaceful outcomes from climate change. This could result in maladaptive responses in those places that are stigmatized as being inherently more prone to climate-induced violence.

Overcoming ecologic bias using the two-phase study design.

PubMed

Wakefield, Jon; Haneuse, Sebastien J-P A

2008-04-15

Ecologic (aggregate) data are widely available and widely utilized in epidemiologic studies. However, ecologic bias, which arises because aggregate data cannot characterize within-group variability in exposure and confounder variables, can only be removed by supplementing ecologic data with individual-level data. Here the authors describe the two-phase study design as a framework for achieving this objective. In phase 1, outcomes are stratified by any combination of area, confounders, and error-prone (or discretized) versions of exposures of interest. Phase 2 data, sampled within each phase 1 stratum, provide accurate measures of exposure and possibly of additional confounders. The phase 1 aggregate-level data provide a high level of statistical power and a cross-classification by which individuals may be efficiently sampled in phase 2. The phase 2 individual-level data then provide a control for ecologic bias by characterizing the within-area variability in exposures and confounders. In this paper, the authors illustrate the two-phase study design by estimating the association between infant mortality and birth weight in several regions of North Carolina for 2000-2004, controlling for gender and race. This example shows that the two-phase design removes ecologic bias and produces gains in efficiency over the use of case-control data alone. The authors discuss the advantages and disadvantages of the approach.

Analysis of Observational Studies in the Presence of Treatment Selection Bias: Effects of Invasive Cardiac Management on AMI Survival Using Propensity Score and Instrumental Variable Methods

PubMed Central

Stukel, Thérèse A.; Fisher, Elliott S; Wennberg, David E.; Alter, David A.; Gottlieb, Daniel J.; Vermeulen, Marian J.

2007-01-01

Context Comparisons of outcomes between patients treated and untreated in observational studies may be biased due to differences in patient prognosis between groups, often because of unobserved treatment selection biases. Objective To compare 4 analytic methods for removing the effects of selection bias in observational studies: multivariable model risk adjustment, propensity score risk adjustment, propensity-based matching, and instrumental variable analysis. Design, Setting, and Patients A national cohort of 122 124 patients who were elderly (aged 65–84 years), receiving Medicare, and hospitalized with acute myocardial infarction (AMI) in 1994–1995, and who were eligible for cardiac catheterization. Baseline chart reviews were taken from the Cooperative Cardiovascular Project and linked to Medicare health administrative data to provide a rich set of prognostic variables. Patients were followed up for 7 years through December 31, 2001, to assess the association between long-term survival and cardiac catheterization within 30 days of hospital admission. Main Outcome Measure Risk-adjusted relative mortality rate using each of the analytic methods. Results Patients who received cardiac catheterization (n=73 238) were younger and had lower AMI severity than those who did not. After adjustment for prognostic factors by using standard statistical risk-adjustment methods, cardiac catheterization was associated with a 50% relative decrease in mortality (for multivariable model risk adjustment: adjusted relative risk [RR], 0.51; 95% confidence interval [CI], 0.50–0.52; for propensity score risk adjustment: adjusted RR, 0.54; 95% CI, 0.53–0.55; and for propensity-based matching: adjusted RR, 0.54; 95% CI, 0.52–0.56). Using regional catheterization rate as an instrument, instrumental variable analysis showed a 16% relative decrease in mortality (adjusted RR, 0.84; 95% CI, 0.79–0.90). The survival benefits of routine invasive care from randomized clinical trials are between 8% and 21 %. Conclusions Estimates of the observational association of cardiac catheterization with long-term AMI mortality are highly sensitive to analytic method. All standard risk-adjustment methods have the same limitations regarding removal of unmeasured treatment selection biases. Compared with standard modeling, instrumental variable analysis may produce less biased estimates of treatment effects, but is more suited to answering policy questions than specific clinical questions. PMID:17227979

Implicit racial bias as a moderator of the association between racial discrimination and hypertension: a study of Midlife African American men.

PubMed

Chae, David H; Nuru-Jeter, Amani M; Adler, Nancy E

2012-01-01

Empirical findings on racial discrimination and hypertension risk have been inconsistent. Some studies have found no association between self-reported experiences of discrimination and cardiovascular health outcomes, whereas others have found moderated or curvilinear relationships. The current cross-sectional study examined whether the association between racial discrimination and hypertension is moderated by implicit racial bias among African American midlife men. This study examined the data on 91 African American men between 30 and 50 years of age. Primary variables were self-reported experiences of racial discrimination and unconscious racial bias as measured by the Black-White Implicit Association Test. Modified Poisson regression models were specified, examining hypertension, defined as a mean resting systolic level of at least 140 mm Hg or diastolic level of at least 90 mm Hg, or self-reported history of cardiovascular medication use with a physician diagnosis of hypertension. No main effects for discrimination or implicit racial bias were found, but the interaction of the two variables was significantly related to hypertension (χ(2)(1) = 4.89, p < .05). Among participants with an implicit antiblack bias, more frequent reports of discrimination were associated with a higher probability of hypertension, whereas among those with an implicit problack bias, it was associated with lower risk. The combination of experiencing racial discrimination and holding an antiblack bias may have particularly detrimental consequences on hypertension among African American midlife men, whereas holding an implicit problack bias may buffer the effects of racial discrimination. Efforts to address both internalized racial bias and racial discrimination may lower cardiovascular risk in this population.

Characterization of the scope and magnitude of biotin interference in susceptible Roche Elecsys competitive and sandwich immunoassays.

PubMed

Trambas, Christina; Lu, Zhong; Yen, Tina; Sikaris, Ken

2018-03-01

Background Biotin interference is a significant problem to which at-risk laboratories must now be attuned. We sought to systematically characterize the nature of this interference in Roche immunoassays. Methods Known concentrations of biotin were titrated into serum samples and the effects on competitive and sandwich immunoassays were analysed. The maximum and minimum concentrations examined reflect those likely to be achieved in individuals on 5 to 10 mg supplements at the lower end, and 100 to 300 mg biotin at the high end. Results A high variability in biotin tolerance was observed. Some assays, such as troponin T, TSH and antithyroid antibodies, were extremely sensitive to the lower concentrations of biotin (15.6 and 31.3 ng/mL), whereas the majority of assays were relatively resistant. At concentrations ≥500 ng/mL, all assays showed significant interference from biotin but, again, the magnitude of the interference was variable. The more sensitive assays showed profound analytical bias at biotin concentrations that occur with high-dose therapy. Conclusion Our data demonstrate high variability in biotin tolerance across Roche immunoassays. The shape of the dose-response curves provides more detailed information than the single manufacturer-quoted figure for biotin tolerance. Accordingly, these data may be used by laboratories for more accurate risk assessment in predicting the effects of biotin. Our data may also be extrapolated to guide timing of blood tests in patients on high-dose biotin therapy: it demonstrates the number of half-lives required to withhold biotin in order to decrease its concentration to below a given assay tolerance.

SAbDab: the structural antibody database

PubMed Central

Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo; Baker, Terry; Fuchs, Angelika; Georges, Guy; Shi, Jiye; Deane, Charlotte M.

2014-01-01

Structural antibody database (SAbDab; http://opig.stats.ox.ac.uk/webapps/sabdab) is an online resource containing all the publicly available antibody structures annotated and presented in a consistent fashion. The data are annotated with several properties including experimental information, gene details, correct heavy and light chain pairings, antigen details and, where available, antibody–antigen binding affinity. The user can select structures, according to these attributes as well as structural properties such as complementarity determining region loop conformation and variable domain orientation. Individual structures, datasets and the complete database can be downloaded. PMID:24214988

Statistical treatment for the wet bias in tree-ring chronologies: A case study from the InteriorWest, USA

Treesearch

Yan Sun; Matthew F. Bekker; R. Justin DeRose; Roger Kjelgren; S. -Y. Simon Wang

2017-01-01

Dendroclimatic research has long assumed a linear relationship between tree-ring increment and climate variables. However, ring width frequently underestimates extremely wet years, a phenomenon we refer to as ‘wet bias’. In this paper, we present statistical evidence for wet bias that is obscured by the assumption of linearity. To improve tree-ring-climate modeling, we...

Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method

PubMed Central

2016-01-01

We report a theoretical description and numerical tests of the extended-system adaptive biasing force method (eABF), together with an unbiased estimator of the free energy surface from eABF dynamics. Whereas the original ABF approach uses its running estimate of the free energy gradient as the adaptive biasing force, eABF is built on the idea that the exact free energy gradient is not necessary for efficient exploration, and that it is still possible to recover the exact free energy separately with an appropriate estimator. eABF does not directly bias the collective coordinates of interest, but rather fictitious variables that are harmonically coupled to them; therefore is does not require second derivative estimates, making it easily applicable to a wider range of problems than ABF. Furthermore, the extended variables present a smoother, coarse-grain-like sampling problem on a mollified free energy surface, leading to faster exploration and convergence. We also introduce CZAR, a simple, unbiased free energy estimator from eABF trajectories. eABF/CZAR converges to the physical free energy surface faster than standard ABF for a wide range of parameters. PMID:27959559

Studying Gender Bias in Physics Grading: The role of teaching experience and country

NASA Astrophysics Data System (ADS)

Hofer, Sarah I.

2015-11-01

The existence of gender-STEM (science, technology, engineering, and mathematics) stereotypes has been repeatedly documented. This article examines physics teachers' gender bias in grading and the influence of teaching experience in Switzerland, Austria, and Germany. In a 2 × 2 between-subjects design, with years of teaching experience included as moderating variable, physics teachers (N = 780) from Switzerland, Austria, and Germany graded a fictive student's answer to a physics test question. While the answer was exactly the same for each teacher, only the student's gender and specialization in languages vs. science were manipulated. Specialization was included to gauge the relative strength of potential gender bias effects. Multiple group regression analyses, with the grade that was awarded as the dependent variable, revealed only partial cross-border generalizability of the effect pattern. While the overall results in fact indicated the existence of a consistent and clear gender bias against girls in the first part of physics teachers' careers that disappeared with increasing teaching experience for Swiss teachers, Austrian teachers, and German female teachers, German male teachers showed no gender bias effects at all. The results are discussed regarding their relevance for educational practice and research.

A rapid, automated approach for quantitation of rotavirus and reovirus infectivity.

PubMed

Iskarpatyoti, Jason A; Willis, Janet Z; Guan, John; Morse, E Ashley; Ikizler, Miné; Wetzel, J Denise; Dermody, Terence S; Contractor, Nikhat

2012-09-01

Current microscopy-based approaches for immunofluorescence detection of viral infectivity are time consuming and labor intensive and can yield variable results subject to observer bias. To circumvent these problems, we developed a rapid and automated infrared immunofluorescence imager-based infectivity assay for both rotavirus and reovirus that can be used to quantify viral infectivity and infectivity inhibition. For rotavirus, monolayers of MA104 cells were infected with simian strain SA-11 or SA-11 preincubated with rotavirus-specific human IgA. For reovirus, monolayers of either HeLa S3 cells or L929 cells were infected with strains type 1 Lang (T1L), type 3 Dearing (T3D), or either virus preincubated with a serotype-specific neutralizing monoclonal antibody (mAb). Infected cells were fixed and incubated with virus-specific polyclonal antiserum, followed by an infrared fluorescence-conjugated secondary antibody. Well-to-well variation in cell number was normalized using fluorescent reagents that stain fixed cells. Virus-infected cells were detected by scanning plates using an infrared imager, and results were obtained as a percent response of fluorescence intensity relative to a virus-specific standard. An expected dose-dependent inhibition of both SA-11 infectivity with rotavirus-specific human IgA and reovirus infectivity with T1L-specific mAb 5C6 and T3D-specific mAb 9BG5 was observed, confirming the utility of this assay for quantification of viral infectivity and infectivity blockade. The imager-based viral infectivity assay fully automates data collection and provides an important advance in technology for applications such as screening for novel modulators of viral infectivity. This basic platform can be adapted for use with multiple viruses and cell types. Copyright © 2012 Elsevier B.V. All rights reserved.

An unusual cysteine VL87 affects the antibody fragment conformations without interfering with the disulfide bond formation.

PubMed

Attallah, Carolina; Aguilar, María Fernanda; Garay, A Sergio; Herrera, Fernando E; Etcheverrigaray, Marina; Oggero, Marcos; Rodrigues, Daniel E

2017-10-01

The Cys residues are almost perfectly conserved in all antibodies. They contribute significantly to the antibody fragment stability. The relevance of two natural contiguous Cys residues of an anti-recombinant human-follicle stimulation hormone (rhFSH) in a format of single-chain variable fragment (scFv) was studied. This scFv contains 5 Cys residues: V H 22 and V H 92 in the variable heavy chain (V H ) and V L 23, V L 87 and V L 88 in the variable light chain (V L ). The influence of two unusual contiguous Cys at positions V L 87 and V L 88 was studied by considering the wild type fragment and mutant variants: V L -C88S, V L -C87S, V L -C87Y. The analysis was carried out using antigen-binding ability measurement by indirect specific ELISA and a detailed molecular modeling that comprises homology methods, long molecular dynamics simulations and docking. We found that V L -C87 affected the antibody fragment stability without interfering with the disulfide bond formation. The effect of mutating the V L -C87 by a usual residue at this position like Tyr caused distant structural changes at the V H region that confers a higher mobility to the V H -CDR2 and V H -CDR3 loops improving the scFv binding to the antigen. Copyright © 2017 Elsevier Ltd. All rights reserved.

AXM mutagenesis: an efficient means for the production of libraries for directed evolution of proteins.

PubMed

Holland, Erika G; Buhr, Diane L; Acca, Felicity E; Alderman, Dawn; Bovat, Kristin; Busygina, Valeria; Kay, Brian K; Weiner, Michael P; Kiss, Margaret M

2013-08-30

Affinity maturation is an important part of the recombinant antibody development process. There are several well-established approaches for generating libraries of mutated antibody genes for affinity maturation, but these approaches are generally too laborious or expensive to allow high-throughput, parallel processing of multiple antibodies. Here, we describe a scalable approach that enables the generation of libraries with greater than 10(8) clones from a single Escherichia coli transformation. In our method, a mutated DNA fragment is produced using PCR conditions that promote nucleotide misincorporation into newly synthesized DNA. In the PCR reaction, one of the primers contains at least three phosphorothioate linkages at its 5' end, and treatment of the PCR product with a 5' to 3' exonuclease is used to preferentially remove the strand synthesized with the non-modified primer, resulting in a single-stranded DNA fragment. This fragment then serves as a megaprimer to prime DNA synthesis on a uracilated, circular, single-stranded template in a Kunkel-like mutagenesis reaction that biases nucleotide base-changes between the megaprimer and uracilated DNA sequence in favor of the in vitro synthesized megaprimer. This method eliminates the inefficient subcloning steps that are normally required for the construction of affinity maturation libraries from randomly mutagenized antibody genes. Copyright © 2013. Published by Elsevier B.V.

[Biases in the study of prognostic factors].

PubMed

Delgado-Rodríguez, M

1999-01-01

The main objective is to detail the main biases in the study of prognostic factors. Confounding bias is illustrated with social class, a prognostic factor still discussed. Within selection bias several cases are commented: response bias, specially frequent when the patients of a clinical trial are used; the shortcomings in the formation of an inception cohort; the fallacy of Neyman (bias due to the duration of disease) when the study begins with a cross-sectional study; the selection bias in the treatment of survivors for the different treatment opportunity of those living longer; the bias due to the inclusion of heterogeneous diagnostic groups; and the selection bias due to differential information losses and the use of statistical multivariate procedures. Within the biases during follow-up, an empiric rule to value the impact of the number of losses is given. In information bias the Will Rogers' phenomenon and the usefulness of clinical databases are discussed. Lastly, a recommendation against the use of cutoff points yielded by bivariate analyses to select the variable to be included in multivariate analysis is given.

Defect in IgV gene somatic hypermutation in common variable immuno-deficiency syndrome.

PubMed

Levy, Y; Gupta, N; Le Deist, F; Garcia, C; Fischer, A; Weill, J C; Reynaud, C A

1998-10-27

Common Variable Immuno-Deficiency (CVID) is the most common symptomatic primary antibody-deficiency syndrome, but the basic immunologic defects underlying this syndrome are not well defined. We report here that among eight patients studied (six CVID and two hypogammaglobulinemic patients with recurrent infections), there is in two CVID patients a dramatic reduction in Ig V gene somatic hypermutation with 40-75% of IgG transcripts totally devoid of mutations in the circulating memory B cell compartment. Functional assays of the T cell compartment point to an intrinsic B cell defect in the process of antibody affinity maturation in these two cases.

Seroprevalence of Toxoplasma gondii antibodies in humans from rural Western Amazon, Brazil.

PubMed

Cavalcante, G T; Aguilar, D M; Camargo, L M A; Labruna, M B; de Andrade, H F; Meireles, L R; Dubey, J P; Thulliez, P; Dias, R A; Gennari, S M

2006-06-01

Antibodies to Toxoplasma gondii were assayed in sera of 266 humans from 71 farms located at Rondônia State, Western Amazon, Brazil, by the modified agglutination test (MAT) and the indirect immunofluorescent antibody test (IFAT). Antibodies were found in 195 humans (73.3%), with MAT titers of 1:25 in 11, 1:50 in 11, 1:100 in 16, 1:200 in 27, 1:400 in 38, 1:800 in 37, 1:1,600 in 22, and 1:3,200 or higher in 33. From the 71 farms visited, 69 had seropositive humans. Prevalence of anti-T. gondii antibodies increased with age of the people (P < 0.05), and no difference was observed in the occurrence by gender (P > 0.05). A sanitary questionnaire was applied in each farm, and statistical association between the serologic status and several variables were analyzed. Home-grown vegetable consumption and origin of drinking water (well or river) were the independent variables that displayed significant association (P = 0.002 and 0.02, respectively). Higher values of occurrence were found in people with consumption of home-grown vegetables (76.1%) and people that drink well water (75.4%) compared with people that did not consume this type of food (61.9%) and drink river water (55.2%). By IFAT (> or = 1:16), 194 of 266 (73%) humans were seropositive and there was a good correlation between MAT and IFAT.

Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

PubMed Central

Sheng, Zizhang; Schramm, Chaim A.; Connors, Mark; Morris, Lynn; Mascola, John R.; Kwong, Peter D.; Shapiro, Lawrence

2016-01-01

Accumulation of somatic mutations in antibody variable regions is critical for antibody affinity maturation, with HIV-1 broadly neutralizing antibodies (bnAbs) generally requiring years to develop. We recently found that the rate at which mutations accumulate decreases over time, but the mechanism governing this slowing is unclear. In this study, we investigated whether natural selection and/or mutability of the antibody variable region contributed significantly to observed decrease in rate. We used longitudinally sampled sequences of immunoglobulin transcripts of single lineages from each of 3 donors, as determined by next generation sequencing. We estimated the evolutionary rates of the complementarity determining regions (CDRs), which are most significant for functional selection, and found they evolved about 1.5- to 2- fold faster than the framework regions. We also analyzed the presence of AID hotspots and coldspots at different points in lineage development and observed an average decrease in mutability of less than 10 percent over time. Altogether, the correlation between Darwinian selection strength and evolutionary rate trended toward significance, especially for CDRs, but cannot fully explain the observed changes in evolutionary rate. The mutability modulated by AID hotspots and coldspots changes correlated only weakly with evolutionary rates. The combined effects of Darwinian selection and mutability contribute substantially to, but do not fully explain, evolutionary rate change for HIV-1-targeting bnAb lineages. PMID:27191167

Bayesian analysis and classification of two Enzyme-Linked Immunosorbent Assay (ELISA) tests without a gold standard

PubMed Central

Zhang, Jingyang; Chaloner, Kathryn; McLinden, James H.; Stapleton, Jack T.

2013-01-01

Reconciling two quantitative ELISA tests for an antibody to an RNA virus, in a situation without a gold standard and where false negatives may occur, is the motivation for this work. False negatives occur when access of the antibody to the binding site is blocked. Based on the mechanism of the assay, a mixture of four bivariate normal distributions is proposed with the mixture probabilities depending on a two-stage latent variable model including the prevalence of the antibody in the population and the probabilities of blocking on each test. There is prior information on the prevalence of the antibody, and also on the probability of false negatives, and so a Bayesian analysis is used. The dependence between the two tests is modeled to be consistent with the biological mechanism. Bayesian decision theory is utilized for classification. The proposed method is applied to the motivating data set to classify the data into two groups: those with and those without the antibody. Simulation studies describe the properties of the estimation and the classification. Sensitivity to the choice of the prior distribution is also addressed by simulation. The same model with two levels of latent variables is applicable in other testing procedures such as quantitative polymerase chain reaction tests where false negatives occur when there is a mutation in the primer sequence. PMID:23592433

The concurrent multiplicative-additive approach for gauge-radar/satellite multisensor precipitation estimates

NASA Astrophysics Data System (ADS)

Garcia-Pintado, J.; Barberá, G. G.; Erena Arrabal, M.; Castillo, V. M.

2010-12-01

Objective analysis schemes (OAS), also called ``succesive correction methods'' or ``observation nudging'', have been proposed for multisensor precipitation estimation combining remote sensing data (meteorological radar or satellite) with data from ground-based raingauge networks. However, opposite to the more complex geostatistical approaches, the OAS techniques for this use are not optimized. On the other hand, geostatistical techniques ideally require, at the least, modelling the covariance from the rain gauge data at every time step evaluated, which commonly cannot be soundly done. Here, we propose a new procedure (concurrent multiplicative-additive objective analysis scheme [CMA-OAS]) for operational rainfall estimation using rain gauges and meteorological radar, which does not require explicit modelling of spatial covariances. On the basis of a concurrent multiplicative-additive (CMA) decomposition of the spatially nonuniform radar bias, within-storm variability of rainfall and fractional coverage of rainfall are taken into account. Thus both spatially nonuniform radar bias, given that rainfall is detected, and bias in radar detection of rainfall are handled. The interpolation procedure of CMA-OAS is built on the OAS, whose purpose is to estimate a filtered spatial field of the variable of interest through a successive correction of residuals resulting from a Gaussian kernel smoother applied on spatial samples. The CMA-OAS, first, poses an optimization problem at each gauge-radar support point to obtain both a local multiplicative-additive radar bias decomposition and a regionalization parameter. Second, local biases and regionalization parameters are integrated into an OAS to estimate the multisensor rainfall at the ground level. The approach considers radar estimates as background a priori information (first guess), so that nudging to observations (gauges) may be relaxed smoothly to the first guess, and the relaxation shape is obtained from the sequential optimization. The procedure is suited to relatively sparse rain gauge networks. To show the procedure, six storms are analyzed at hourly steps over 10,663 km2. Results generally indicated an improved quality with respect to other methods evaluated: a standard mean-field bias adjustment, an OAS spatially variable adjustment with multiplicative factors, ordinary cokriging, and kriging with external drift. In theory, it could be equally applicable to gauge-satellite estimates and other hydrometeorological variables.

De novo sequencing and resurrection of a human astrovirus-neutralizing antibody

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

Bogdanoff, Walter A.; Morgenstern, David; Bern, Marshall

Monoclonal antibody (mAb) therapeutics targeting cancer, autoimmune diseases, inflammatory diseases, and infectious diseases are growing exponentially. Although numerous panels of mAbs targeting infectious disease agents have been developed, their progression into clinically useful mAbs is often hindered by the lack of sequence information and/or loss of hybridoma cells that produce them. Here we combine the power of crystallography and mass spectrometry to determine the amino acid sequence and glycosylation modification of the Fab fragment of a potent human astrovirus-neutralizing mAb. We used this information to engineer a recombinant antibody single-chain variable fragment that has the same specificity as the parentmore » monoclonal antibody to bind to the astrovirus capsid protein. Furthermore, this antibody can now potentially be developed as a therapeutic and diagnostic agent.« less

De novo sequencing and resurrection of a human astrovirus-neutralizing antibody

DOE PAGES

Bogdanoff, Walter A.; Morgenstern, David; Bern, Marshall; ...

2016-03-14

Monoclonal antibody (mAb) therapeutics targeting cancer, autoimmune diseases, inflammatory diseases, and infectious diseases are growing exponentially. Although numerous panels of mAbs targeting infectious disease agents have been developed, their progression into clinically useful mAbs is often hindered by the lack of sequence information and/or loss of hybridoma cells that produce them. Here we combine the power of crystallography and mass spectrometry to determine the amino acid sequence and glycosylation modification of the Fab fragment of a potent human astrovirus-neutralizing mAb. We used this information to engineer a recombinant antibody single-chain variable fragment that has the same specificity as the parentmore » monoclonal antibody to bind to the astrovirus capsid protein. Furthermore, this antibody can now potentially be developed as a therapeutic and diagnostic agent.« less

Bias and robustness of uncertainty components estimates in transient climate projections

NASA Astrophysics Data System (ADS)

Hingray, Benoit; Blanchet, Juliette; Jean-Philippe, Vidal

2016-04-01

A critical issue in climate change studies is the estimation of uncertainties in projections along with the contribution of the different uncertainty sources, including scenario uncertainty, the different components of model uncertainty and internal variability. Quantifying the different uncertainty sources faces actually different problems. For instance and for the sake of simplicity, an estimate of model uncertainty is classically obtained from the empirical variance of the climate responses obtained for the different modeling chains. These estimates are however biased. Another difficulty arises from the limited number of members that are classically available for most modeling chains. In this case, the climate response of one given chain and the effect of its internal variability may be actually difficult if not impossible to separate. The estimate of scenario uncertainty, model uncertainty and internal variability components are thus likely to be not really robust. We explore the importance of the bias and the robustness of the estimates for two classical Analysis of Variance (ANOVA) approaches: a Single Time approach (STANOVA), based on the only data available for the considered projection lead time and a time series based approach (QEANOVA), which assumes quasi-ergodicity of climate outputs over the whole available climate simulation period (Hingray and Saïd, 2014). We explore both issues for a simple but classical configuration where uncertainties in projections are composed of two single sources: model uncertainty and internal climate variability. The bias in model uncertainty estimates is explored from theoretical expressions of unbiased estimators developed for both ANOVA approaches. The robustness of uncertainty estimates is explored for multiple synthetic ensembles of time series projections generated with MonteCarlo simulations. For both ANOVA approaches, when the empirical variance of climate responses is used to estimate model uncertainty, the bias is always positive. It can be especially high with STANOVA. In the most critical configurations, when the number of members available for each modeling chain is small (< 3) and when internal variability explains most of total uncertainty variance (75% or more), the overestimation is higher than 100% of the true model uncertainty variance. The bias can be considerably reduced with a time series ANOVA approach, owing to the multiple time steps accounted for. The longer the transient time period used for the analysis, the larger the reduction. When a quasi-ergodic ANOVA approach is applied to decadal data for the whole 1980-2100 period, the bias is reduced by a factor 2.5 to 20 depending on the projection lead time. In all cases, the bias is likely to be not negligible for a large number of climate impact studies resulting in a likely large overestimation of the contribution of model uncertainty to total variance. For both approaches, the robustness of all uncertainty estimates is higher when more members are available, when internal variability is smaller and/or the response-to-uncertainty ratio is higher. QEANOVA estimates are much more robust than STANOVA ones: QEANOVA simulated confidence intervals are roughly 3 to 5 times smaller than STANOVA ones. Excepted for STANOVA when less than 3 members is available, the robustness is rather high for total uncertainty and moderate for internal variability estimates. For model uncertainty or response-to-uncertainty ratio estimates, the robustness is conversely low for QEANOVA to very low for STANOVA. In the most critical configurations (small number of member, large internal variability), large over- or underestimation of uncertainty components is very thus likely. To propose relevant uncertainty analyses and avoid misleading interpretations, estimates of uncertainty components should be therefore bias corrected and ideally come with estimates of their robustness. This work is part of the COMPLEX Project (European Collaborative Project FP7-ENV-2012 number: 308601; http://www.complex.ac.uk/). Hingray, B., Saïd, M., 2014. Partitioning internal variability and model uncertainty components in a multimodel multireplicate ensemble of climate projections. J.Climate. doi:10.1175/JCLI-D-13-00629.1 Hingray, B., Blanchet, J. (revision) Unbiased estimators for uncertainty components in transient climate projections. J. Climate Hingray, B., Blanchet, J., Vidal, J.P. (revision) Robustness of uncertainty components estimates in climate projections. J.Climate

A residue-specific shift in stability and amyloidogenicity of antibody variable domains.

PubMed

Nokwe, Cardine N; Zacharias, Martin; Yagi, Hisashi; Hora, Manuel; Reif, Bernd; Goto, Yuji; Buchner, Johannes

2014-09-26

Variable (V) domains of antibodies are essential for antigen recognition by our adaptive immune system. However, some variants of the light chain V domains (VL) form pathogenic amyloid fibrils in patients. It is so far unclear which residues play a key role in governing these processes. Here, we show that the conserved residue 2 of VL domains is crucial for controlling its thermodynamic stability and fibril formation. Hydrophobic side chains at position 2 stabilize the domain, whereas charged residues destabilize and lead to amyloid fibril formation. NMR experiments identified several segments within the core of the VL domain to be affected by changes in residue 2. Furthermore, molecular dynamic simulations showed that hydrophobic side chains at position 2 remain buried in a hydrophobic pocket, and charged side chains show a high flexibility. This results in a predicted difference in the dissociation free energy of ∼10 kJ mol(-1), which is in excellent agreement with our experimental values. Interestingly, this switch point is found only in VL domains of the κ family and not in VLλ or in VH domains, despite a highly similar domain architecture. Our results reveal novel insight into the architecture of variable domains and the prerequisites for formation of amyloid fibrils. This might also contribute to the rational design of stable variable antibody domains. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Inhibitors in haemophilia A: a perspective on clotting factor products as a potential contributing factor.

PubMed

Mathew, P; Dinter, H; Church, N; Humphries, T J; Kulkarni, R

2016-05-01

The occurrence of a neutralizing antibody in previously untreated patients (PUPs) with haemophilia A appears to be the result of an intricate interplay of both genetic and environmental factors. Recently, the type of factor VIII (FVIII) product used in the PUPs population has been implicated as a risk factor for inhibitor development. The aim of this review was to explore in a systematic manner potential hypotheses for the product-related findings in these studies (i.e. differences in the expression system of the cell lines used to produce recombinant FVIII [rFVIII], differences in the administered antigen load or changes in clinical practice over time). Review of the available clinical studies illustrates the high degree of variability for the risk of inhibitor development for the same products across different studies. Differences in cell lines or antigen load were not found to provide a reasonable explanation. The possibility of changes in clinical practice over time and patient selection bias (i.e. the preferential use of one product over another in patients at higher risk for inhibitors) offers a potential explanation and should be carefully considered when evaluating the studies. © 2016 The Authors. Haemophilia Published by John Wiley & Sons Ltd.

Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

PubMed

Akiba, Hiroki; Tsumoto, Kouhei

2015-07-01

Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody-antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, thermodynamics of the contribution from aromatic, charged and hydrogen bond-forming amino acids are discussed, and their different characteristics have been elucidated. The information gives fundamental understanding of the antibody-antigen interaction. Furthermore, the consequences of antibody engineering are analysed from thermodynamic viewpoints: humanization to reduce immunogenicity and rational design to improve affinity. Amino acid residues outside hot-spots in the interface play important roles in these cases, and thus thermodynamic and kinetic parameters give much information about the antigen recognition. Thermodynamic analysis of mutant antibodies thus should lead to advanced strategies to design and select antibodies with high affinity. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Investigation of a panel of monoclonal antibodies and polyclonal sera against anthrax toxins resulted in identification of an anti-lethal factor antibody with disease-enhancing characteristics.

PubMed

Kulshreshtha, Parul; Tiwari, Ashutosh; Priyanka; Joon, Shikha; Sinha, Subrata; Bhatnagar, Rakesh

2015-12-01

Hybridomas were created using spleen of mice that were actively immunized with rLFn (recombinant N-terminal domain of lethal factor). Later on, separate group of mice were immunized with rLFn to obtain a polyclonal control for passive immunization studies of monoclonal antibodies. This led to the identification of one cohort of rLFn-immnized mice that harboured disease-enhancing polyclonal antibodies. At the same time, the monoclonal antibodies secreted by all the hybridomas were being tested. Two hybridomas secreted monoclonal antibodies (H10 and H8) that were cross-reactive with EF (edema factor) and LF (lethal factor), while the other two hybridomas secreted LF-specific antibodies (H7 and H11). Single chain variable fragment (LETscFv) was derived from H10 hybridoma. H11 was found to have disease-enhancing property. Combination of H11 with protective monoclonal antibodies (H8 and H10) reduced its disease enhancing nature. This in vitro abrogation of disease-enhancement provides the proof of concept that in polyclonal sera the disease enhancing character of a fraction of antibodies is overshadowed by the protective nature of the rest of the antibodies generated on active immunization. Copyright © 2015. Published by Elsevier Ltd.

B cell gene signature with massive intrahepatic production of antibodies to hepatitis B core antigen in hepatitis B virus-associated acute liver failure.

PubMed

Farci, Patrizia; Diaz, Giacomo; Chen, Zhaochun; Govindarajan, Sugantha; Tice, Ashley; Agulto, Liane; Pittaluga, Stefania; Boon, Denali; Yu, Claro; Engle, Ronald E; Haas, Mark; Simon, Richard; Purcell, Robert H; Zamboni, Fausto

2010-05-11

Hepatitis B virus (HBV)-associated acute liver failure (ALF) is a dramatic clinical syndrome due to a sudden loss of hepatic cells leading to multiorgan failure. The mechanisms whereby HBV induces ALF are unknown. Here, we show that liver tissue collected at the time of liver transplantation in two patients with HBV-associated ALF is characterized by an overwhelming B cell response apparently centered in the liver with massive accumulation of plasma cells secreting IgG and IgM, accompanied by complement deposition. We demonstrate that the molecular target of these antibodies is the hepatitis B core antigen (HBcAg); that these anti-bodies display a restricted variable heavy chain (V(H)) repertoire and lack somatic mutations; and that these two unrelated individuals with ALF use an identical predominant V(H) gene with unmutated variable domain (IGHV1-3) for both IgG and IgM anti-HBc antibodies, indicating that HBcAg is the target of a germline human V(H) gene. These data suggest that humoral immunity may exert a primary role in the pathogenesis of HBV-associated ALF.

Single chain variable fragment antibodies block aggregation and toxicity induced by familial ALS-linked mutant forms of SOD1.

PubMed

Ghadge, Ghanashyam D; Pavlovic, John D; Koduvayur, Sujatha P; Kay, Brian K; Roos, Raymond P

2013-08-01

Approximately 10% of amyotrophic lateral sclerosis (ALS) cases are familial (known as FALS) with an autosomal dominant inheritance pattern, and ~25% of FALS cases are caused by mutations in Cu/Zn superoxide dismutase (SOD1). There is convincing evidence that mutant SOD1 (mtSOD1) kills motor neurons (MNs) because of a gain-of-function toxicity, most likely related to aggregation of mtSOD1. A number of recent reports have suggested that antibodies can be used to treat mtSOD1-induced FALS. To follow up on the use of antibodies as potential therapeutics, we generated single chain fragments of variable region antibodies (scFvs) against SOD1, and then expressed them as 'intrabodies' within a motor neuron cell line. In the present study, we describe isolation of human scFvs that interfere with mtSOD1 in vitro aggregation and toxicity. These scFvs may have therapeutic potential in sporadic ALS, as well as FALS, given that sporadic ALS may also involve abnormalities in the SOD1 protein or activity. Copyright © 2013 Elsevier Inc. All rights reserved.

Blocking monocyte transmigration in in vitro system by an anti-CD99 human antibody in single chain fragment variable (scFv) format. Efficient large scale purification of biological active scFv from inclusion bodies in E. coli expression system

PubMed Central

Moricoli, Diego; Muller, William A.; Carbonella, Damiano Cosimo; Balducci, Maria Cristina; Dominici, Sabrina; Fiori, Valentina; Watson, Richard; Weber, Evan; Cianfriglia, Maurizio; Scotlandi, Katia; Magnani, Mauro

2015-01-01

Migration of leukocytes into a site of inflammation involves several steps mediated by various families of adhesion molecules. CD99 play a significant role in transendothelial migration (TEM) of leukocytes. Inhibition of TEM by specific monoclonal antibody (mAb) can provide a potent therapeutic approach to treating inflammatory conditions. However, the therapeutic utilization of whole IgG can lead to an inappropriate activation of Fc receptor-expressing cells inducing serious adverse side effects due to cytokine release. In this regard, specific recombinant antibody in single chain variable fragments (scFvs) originated by phage library may offer a solution by affecting TEM function in a safe clinical context. However, this consideration requires large scale production of functional scFv antibodies under GMP conditions and hence, the absence of toxic reagents utilized for the solubilization and refolding steps of inclusion bodies that may discourage industrial application of these antibody fragments. In order to apply the scFv anti-CD99 named C7A in a clinical setting we herein describe an efficient and large scale production of the antibody fragments expressed in E.coli as insoluble protein avoiding gel filtration chromatography approach, and laborious refolding step pre- and post-purification. Using differential salt elution which is a simple, reproducible and effective procedure we are able to separate scFv in monomer format from aggregates. The purified scFv antibody C7A exhibits inhibitory activity comparable to an antagonistic conventional mAb, thus providing an excellent agent for blocking CD99 signalling. Thanks to the original purification protocol that can be extended to other scFvs that are expressed as inclusion bodies in bacterial systems, the scFv anti-CD99 C7A herein described represents the first step towards the construction of new antibody therapeutic. PMID:24798881

Screening for single-chain variable fragment antibodies against multiple Cry1 toxins from an immunized mouse phage display antibody library.

PubMed

Dong, Sa; Bo, Zongyi; Zhang, Cunzheng; Feng, Jianguo; Liu, Xianjin

2018-04-01

Single-chain variable fragment (scFv) is a kind of antibody that possess only one chain of the complete antibody while maintaining the antigen-specific binding abilities and can be expressed in prokaryotic system. In this study, scFvs against Cry1 toxins were screened out from an immunized mouse phage displayed antibody library, which was successfully constructed with capacity of 6.25 × 10 7  CFU/mL. Using the mixed and alternative antigen coating strategy and after four rounds of affinity screening, seven positive phage-scFvs against Cry1 toxins were selected and characterized. Among them, clone scFv-3H9 (MG214869) showing relative stable and high binding abilities to six Cry1 toxins was selected for expression and purification. SDS-PAGE indicated that the scFv-3H9 fragments approximately 27 kDa were successfully expressed in Escherichia coli HB2151 strain. The purified scFv-3H9 was used to establish the double antibody sandwich enzyme-linked immunosorbent assay method (DAS-ELISA) for detecting six Cry1 toxins, of which the lowest detectable limits (LOD) and the lowest quantitative limits (LOQ) were 3.14-11.07 and 8.22-39.44 ng mL -1 , respectively, with the correlation coefficient higher than 0.997. The average recoveries of Cry1 toxins from spiked rice leaf samples were ranged from 84 to 95%, with coefficient of variation (CV) less than 8.2%, showing good accuracy for the multi-residue determination of six Cry1 toxins in agricultural samples. This research suggested that the constructed phage display antibody library based on the animal which was immunized with the mixture of several antigens under the same category can be used for the quick and effective screening of generic antibodies.

Anti-H antibody of unusually high titer showing variable reactivities against group A red cells and broad thermal amplitude in a patient with lymphoma.

PubMed

Choi, Seung Jun; Kim, Hoon Seok; Lee, Jaewoong; Song, Young-Sun; Lim, Jihyang

2018-02-01

We report a case of a patient with high titer anti-H antibody showing broad thermal amplitude and variable reactivities against group A red cells. A 62-year-old Korean female was diagnosed with diffuse large B cell lymphoma involving multiple organs. Her ABO/RhD type was A+ and her genotype was ABO*A.01.01/ABO*O.01.02. Antibody screening test (AST) and antibody identification test (IDT) were strongly positive for all reagent cells. Anti-human globulin (AHG) test revealed an antibody titer of 1:256 for 37 °C phase and trace positivity for poly- and mono-specific C3d. Reactivity was stronger for O+ red cells than that for A+ red cells across all temperatures tested (4 °C, room temperature (RT) and 37 °C). This was also found for AHG phase. Anti-IH was ruled out based on agglutination of O+ cord cells (CCs). Antibody was determined as IgM anti-H after DTT treatment. Three batches of 10 A+ red cells from random donors were tested with three consecutive serums for crossmatching using tube method. Interestingly, out of thirty A+ red cells tested, 20 cells at RT, 11 cells at 37 °C and 11 cells in the AHG phase showed reactivity of greater than 2+. The patient was transfused with 6 units of packed RBCs subsequently. Chemotherapy (R-CHOP regimen) and Helicobacter pylori eradication were then started. Her antibody titer gradually decreased following such treatment. In conclusion, we identified a case of patient with high titer anti-H with broad thermal amplitude, suggesting that anti-H antibodies might need to be considered for cases with pan-agglutination in AST and IDT. Copyright © 2018 Elsevier Ltd. All rights reserved.

A large observational study to concurrently assess persistence of measles specific B-cell and T-cell immunity in individuals following two doses of MMR vaccine

PubMed Central

Haralambieva, Iana H.; Ovsyannikova, Inna G.; O’Byrne, Megan; Pankratz, V. Shane; Jacobson, Robert M.; Poland, Gregory A.

2011-01-01

The measurement of measles-specific neutralizing antibodies, directed against the surface measles virus hemagglutinin and fusion proteins, is considered the gold standard in measles serology. We assessed functional measles-specific neutralizing antibody levels in a racially diverse cohort of 763 young healthy adolescents after receipt of two doses of measles-mumps-rubella vaccine, by the use of an automated plaque reduction microneutralization (PRMN) assay, and evaluated their relevance to protective antibody levels, as well as their associations with demographic and clinical variables. We also concurrently assessed measles-specific IFNγ Elispot responses and their relation to the observed antibody concentrations. The geometric mean titer for our cohort was 832 mIU/mL (95% CIs: 776; 891). Sixty-eight subjects (8.9%) had antibody concentrations of less than the protective threshold of 210 mIU/mL (corresponding to PRMN titer of 120; suggesting protection against symptomatic disease), and 177 subjects (23.2%) demonstrated persisting antibody concentrations above 1,841 mIU/mL (corresponding to PRMN titer of 1,052; suggesting total protection against viral infection), 7.4 years after vaccination, in the absence of wild-type virus boosting. The mean measles-specific IFNγ Elispot response for our cohort was 46 (95% CIs: 43; 49) IFNγ-positive spots per 200,000 cells with no relation of cellular immunity measures to the observed antibody concentrations. No significant associations between antibody titers and demographic and clinical variables, including gender and race, were observed in our study. In conclusion, in a large observational study of measles immunity, we used an automated high-throughput measles virus-specific neutralization assay to measure humoral immunity, and concurrently determined measles-specific cellular immunity to aid the assessment of potential susceptibility to measles in vaccinated populations. PMID:21539880

Collaborative Research: Process-Resolving Decomposition of the Global Temperature Response to Modes of Low Frequency Variability in a Changing Climate

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

Deng, Yi

2014-11-24

DOE-GTRC-05596 11/24/2104 Collaborative Research: Process-Resolving Decomposition of the Global Temperature Response to Modes of Low Frequency Variability in a Changing Climate PI: Dr. Yi Deng (PI) School of Earth and Atmospheric Sciences Georgia Institute of Technology 404-385-1821, yi.deng@eas.gatech.edu El Niño-Southern Oscillation (ENSO) and Annular Modes (AMs) represent respectively the most important modes of low frequency variability in the tropical and extratropical circulations. The projection of future changes in the ENSO and AM variability, however, remains highly uncertain with the state-of-the-science climate models. This project conducted a process-resolving, quantitative evaluations of the ENSO and AM variability in the modern reanalysis observationsmore » and in climate model simulations. The goal is to identify and understand the sources of uncertainty and biases in models’ representation of ENSO and AM variability. Using a feedback analysis method originally formulated by one of the collaborative PIs, we partitioned the 3D atmospheric temperature anomalies and surface temperature anomalies associated with ENSO and AM variability into components linked to 1) radiation-related thermodynamic processes such as cloud and water vapor feedbacks, 2) local dynamical processes including convection and turbulent/diffusive energy transfer and 3) non-local dynamical processes such as the horizontal energy transport in the oceans and atmosphere. In the past 4 years, the research conducted at Georgia Tech under the support of this project has led to 15 peer-reviewed publications and 9 conference/workshop presentations. Two graduate students and one postdoctoral fellow also received research training through participating the project activities. This final technical report summarizes key scientific discoveries we made and provides also a list of all publications and conference presentations resulted from research activities at Georgia Tech. The main findings include: 1) the distinctly different roles played by atmospheric dynamical processes in establishing surface temperature response to ENSO at tropics and extratropics (i.e., atmospheric dynamics disperses energy out of tropics during ENSO warm events and modulate surface temperature at mid-, high-latitudes through controlling downward longwave radiation); 2) the representations of ENSO-related temperature response in climate models fail to converge at the process-level particularly over extratropics (i.e., models produce the right temperature responses to ENSO but with wrong reasons); 3) water vapor feedback contributes substantially to the temperature anomalies found over U.S. during different phases of the Northern Annular Mode (NAM), which adds new insight to the traditional picture that cold/warm advective processes are the main drivers of local temperature responses to the NAM; 4) the overall land surface temperature biases in the latest NCAR model (CESM1) are caused by biases in surface albedo while the surface temperature biases over ocean are related to multiple factors including biases in model albedo, cloud and oceanic dynamics, and the temperature biases over different ocean basins are also induced by different process biases. These results provide a detailed guidance for process-level model turning and improvement, and thus contribute directly to the overall goal of reducing model uncertainty in projecting future changes in the Earth’s climate system, especially in the ENSO and AM variability.« less

Schooling and Frailty among Seniors.

ERIC Educational Resources Information Center

Leigh, J. Paul; Dhir, Rachna

1997-01-01

Schooling has beneficial influences on health, even late in life. This paper's contributions to the schooling/health debate include removing unobserved variable bias and the bias from self-efficacy, time, and risk preferences; discovering no racial differences; finding strong correlations between schooling and measures of frailty for those aged 65…

Ebola virus-like particles produced in insect cells exhibit dendritic cell stimulating activity and induce neutralizing antibodies

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

Ye Ling; Lin Jianguo; Sun Yuliang

2006-08-01

Recombinant baculoviruses (rBV) expressing Ebola virus VP40 (rBV-VP40) or GP (rBV-GP) proteins were generated. Infection of Sf9 insect cells by rBV-VP40 led to assembly and budding of filamentous particles from the cell surface as shown by electron microscopy. Ebola virus-like particles (VLPs) were produced by coinfection of Sf9 cells with rBV-VP40 and rBV-GP, and incorporation of Ebola GP into VLPs was demonstrated by SDS-PAGE and Western blot analysis. Recombinant baculovirus infection of insect cells yielded high levels of VLPs, which were shown to stimulate cytokine secretion from human dendritic cells similar to VLPs produced in mammalian cells. The immunogenicity ofmore » Ebola VLPs produced in insect cells was evaluated by immunization of mice. Analysis of antibody responses showed that most of the GP-specific antibodies were of the IgG2a subtype, while no significant level of IgG1 subtype antibodies specific for GP was induced, indicating the induction of a Th1-biased immune response. Furthermore, sera from Ebola VLP immunized mice were able to block infection by Ebola GP pseudotyped HIV virus in a single round infection assay, indicating that a neutralizing antibody against the Ebola GP protein was induced. These results show that production of Ebola VLPs in insect cells using recombinant baculoviruses represents a promising approach for vaccine development against Ebola virus infection.« less

The INNs and outs of antibody nonproprietary names

PubMed Central

Jones, Tim D.; Carter, Paul J.; Plückthun, Andreas; Vásquez, Max; Holgate, Robert G.E.; Hötzel, Isidro; Popplewell, Andrew G.; Parren, Paul W.H.I.; Enzelberger, Markus; Rademaker, Hendrik J.; Clark, Michael R.; Lowe, David C.; Dahiyat, Bassil I.; Smith, Victoria; Lambert, John M.; Wu, Herren; Reilly, Mary; Haurum, John S.; Dübel, Stefan; Huston, James S.; Schirrmann, Thomas; Janssen, Richard A.J.; Steegmaier, Martin; Gross, Jane A.; Bradbury, Andrew R.M.; Burton, Dennis R.; Dimitrov, Dimiter S.; Chester, Kerry A.; Glennie, Martin J.; Davies, Julian; Walker, Adam; Martin, Steve; McCafferty, John; Baker, Matthew P.

2016-01-01

An important step in drug development is the assignment of an International Nonproprietary Name (INN) by the World Health Organization (WHO) that provides healthcare professionals with a unique and universally available designated name to identify each pharmaceutical substance. Monoclonal antibody INNs comprise a –mab suffix preceded by a substem indicating the antibody type, e.g., chimeric (-xi-), humanized (-zu-), or human (-u-). The WHO publishes INN definitions that specify how new monoclonal antibody therapeutics are categorized and adapts the definitions to new technologies. However, rapid progress in antibody technologies has blurred the boundaries between existing antibody categories and created a burgeoning array of new antibody formats. Thus, revising the INN system for antibodies is akin to aiming for a rapidly moving target. The WHO recently revised INN definitions for antibodies now to be based on amino acid sequence identity. These new definitions, however, are critically flawed as they are ambiguous and go against decades of scientific literature. A key concern is the imposition of an arbitrary threshold for identity against human germline antibody variable region sequences. This leads to inconsistent classification of somatically mutated human antibodies, humanized antibodies as well as antibodies derived from semi-synthetic/synthetic libraries and transgenic animals. Such sequence-based classification implies clear functional distinction between categories (e.g., immunogenicity). However, there is no scientific evidence to support this. Dialog between the WHO INN Expert Group and key stakeholders is needed to develop a new INN system for antibodies and to avoid confusion and miscommunication between researchers and clinicians prescribing antibodies. PMID:26716992

Estimating and Modelling Bias of the Hierarchical Partitioning Public-Domain Software: Implications in Environmental Management and Conservation

PubMed Central

Olea, Pedro P.; Mateo-Tomás, Patricia; de Frutos, Ángel

2010-01-01

Background Hierarchical partitioning (HP) is an analytical method of multiple regression that identifies the most likely causal factors while alleviating multicollinearity problems. Its use is increasing in ecology and conservation by its usefulness for complementing multiple regression analysis. A public-domain software “hier.part package” has been developed for running HP in R software. Its authors highlight a “minor rounding error” for hierarchies constructed from >9 variables, however potential bias by using this module has not yet been examined. Knowing this bias is pivotal because, for example, the ranking obtained in HP is being used as a criterion for establishing priorities of conservation. Methodology/Principal Findings Using numerical simulations and two real examples, we assessed the robustness of this HP module in relation to the order the variables have in the analysis. Results indicated a considerable effect of the variable order on the amount of independent variance explained by predictors for models with >9 explanatory variables. For these models the nominal ranking of importance of the predictors changed with variable order, i.e. predictors declared important by its contribution in explaining the response variable frequently changed to be either most or less important with other variable orders. The probability of changing position of a variable was best explained by the difference in independent explanatory power between that variable and the previous one in the nominal ranking of importance. The lesser is this difference, the more likely is the change of position. Conclusions/Significance HP should be applied with caution when more than 9 explanatory variables are used to know ranking of covariate importance. The explained variance is not a useful parameter to use in models with more than 9 independent variables. The inconsistency in the results obtained by HP should be considered in future studies as well as in those already published. Some recommendations to improve the analysis with this HP module are given. PMID:20657734

[Research of Human-mouse Chimeric Antibodies Against Ebola Virus Nucleoprotein].

PubMed

Zhou, Rongping; Sun, Lina; Liu, Yang; Wu, Wei; Li, Chuan; Liang, Mifang; Qiu, Peihong

2016-01-01

The Ebola virus is highly infectious and can result in death in ≤ 90% of infected subjects. Detection of the Ebola virus and diagnosis of infection are extremely important for epidemic control. Presently, Chinese laboratories detect the nucleic acids of the Ebola virus by real-time reverse transcription-polymerase chain reaction (RT-PCR). However, such detection takes a relatively long time and necessitates skilled personnel and expensive equipment. Enzyme-linked immunosorbent assay (ELISA) of serum is simple, easy to operate, and can be used to ascertain if a patient is infected with the Ebola virus as well as the degree of infection. Hence, ELISA can be used in epidemiological investigations and is a strong complement to detection of nucleic acids. Cases of Ebola hemorrhagic fever have not been documented in China, so quality-control material for positive serology is needed. Construction and expression of human-mouse chimeric antibodies against the nucleoprotein of the Ebola virus was carried out. Genes encoding variable heavy (VH) and variable light (VL) chains were extracted and amplified from murine hybridoma cells. Genes encoding the VH and VL chains of monoclonal antibodies were amplified by RT-PCR. According to sequence analyses, a primer was designed to amplify functional sequences relative to VH and VL chain. The eukaryotic expression vector HL51-14 carrying some human antibody heavy chain- and light chain-constant regions was used. IgG antibodies were obtained by transient transfection of 293T cells. Subsequently, immunological detection and immunological identification were identified by ELISA, immunofluorescence assay, and western blotting. These results showed that we constructed and purified two human- mouse chimeric antibodies.

Immunoadsorption of anti-HLA antibodies for highly sensitized patients awaiting renal transplantation.

PubMed

Hiesse, C; Kriaa, F; Rousseau, P; Farahmand, H; Bismuth, A; Fries, D; Charpentier, B

1992-01-01

Fifteen end-stage renal disease patients with high titres of panel reactive (PRA) antibodies were treated with immunoadsorption (IA) on sepharose-bound protein A columns in order to remove anti-HLA antibodies and facilitate transplantation. Infectious complications were not observed after IA and transplantation, and the procedure was well tolerated. In spite of the use of adjunctive immunosuppressive treatment with cyclophosphamide and prednisolone, this method produced only variable effects in lowering panel reaction antibodies, and was hampered by high de novo resynthesis of anti-HLA antibodies. Patients whose pre-IA antibody titre was greater than or equal to 1:64 clearly did not benefit from the procedure, but other immunological criteria were not predictive of efficacy. Twelve patients were transplanted on the basis of a negative cross-match with current serum, historical sera being retrospectively tested. Surprisingly, seven patients received a well-matched graft with both pre- and post-IA negative cross-matching. Graft survival was 86% in this group. Conversely, in the group of five transplants which were performed in recipients having a positive historical cross-match with the donor, graft survival was only 40%. One patient died with a functional graft, and two grafts failed due to hyperacute humoral rejection. Humoral rejection in a third patient was successfully treated by a second IA course and administration of polyclonal IgG. We conclude that IA is a safe procedure for managing hyperimmunized transplant candidates. However, its efficacy remains variable, and a better definition of patients who should benefit from IA needs to be found.

Stability-Diversity Tradeoffs Impose Fundamental Constraints on Selection of Synthetic Human VH/VL Single-Domain Antibodies from In Vitro Display Libraries

PubMed Central

Henry, Kevin A.; Kim, Dae Young; Kandalaft, Hiba; Lowden, Michael J.; Yang, Qingling; Schrag, Joseph D.; Hussack, Greg; MacKenzie, C. Roger; Tanha, Jamshid

2017-01-01

Human autonomous VH/VL single-domain antibodies (sdAbs) are attractive therapeutic molecules, but often suffer from suboptimal stability, solubility and affinity for cognate antigens. Most commonly, human sdAbs have been isolated from in vitro display libraries constructed via synthetic randomization of rearranged VH/VL domains. Here, we describe the design and characterization of three novel human VH/VL sdAb libraries through a process of: (i) exhaustive biophysical characterization of 20 potential VH/VL sdAb library scaffolds, including assessment of expression yield, aggregation resistance, thermostability and tolerance to complementarity-determining region (CDR) substitutions; (ii) in vitro randomization of the CDRs of three VH/VL sdAb scaffolds, with tailored amino acid representation designed to promote solubility and expressibility; and (iii) systematic benchmarking of the three VH/VL libraries by panning against five model antigens. We isolated ≥1 antigen-specific human sdAb against four of five targets (13 VHs and 7 VLs in total); these were predominantly monomeric, had antigen-binding affinities ranging from 5 nM to 12 µM (average: 2–3 µM), but had highly variable expression yields (range: 0.1–19 mg/L). Despite our efforts to identify the most stable VH/VL scaffolds, selection of antigen-specific binders from these libraries was unpredictable (overall success rate for all library-target screens: ~53%) with a high attrition rate of sdAbs exhibiting false positive binding by ELISA. By analyzing VH/VL sdAb library sequence composition following selection for monomeric antibody expression (binding to protein A/L followed by amplification in bacterial cells), we found that some VH/VL sdAbs had marked growth advantages over others, and that the amino acid composition of the CDRs of this set of sdAbs was dramatically restricted (bias toward Asp and His and away from aromatic and hydrophobic residues). Thus, CDR sequence clearly dramatically impacts the stability of human autonomous VH/VL immunoglobulin domain folds, and sequence-stability tradeoffs must be taken into account during the design of such libraries. PMID:29375542

Impact of antibody subclass and disulfide isoform differences on the biological activity of CD200R and βklotho agonist antibodies.

PubMed

Grujic, Ognjen; Stevens, Jennitte; Chou, Robert Y-T; Weiszmann, Jennifer V; Sekirov, Laura; Thomson, Christy; Badh, Anita; Grauer, Stephanie; Chan, Brian; Graham, Kevin; Manchulenko, Kathy; Dillon, Thomas M; Li, Yang; Foltz, Ian N

2017-05-13

Agonism of cell surface receptors by monoclonal antibodies is dependent not only on its ability to bind the target, but also to deliver a biological signal through receptors to the cell. Immunoglobulin G2 antibodies (IgG2s) are made up of a mixture of distinct isoforms (IgG2-A, -B and A/B), which differ by the disulfide connectivity at the hinge region. When evaluating panels of agonistic antibodies against CD200 receptor (CD200R) or βklotho receptor (βklotho), we noticed striking activity differences of IgG1 or IgG2 antibodies with the same variable domains. For the CD200R antibody, the IgG2 antibody demonstrated higher activity than the IgG1 or IgG4 antibody. More significantly, for βklotho, agonist antibodies with higher biological activity as either IgG2 or IgG1 were identified. In both cases, ion exchange chromatography was able to isolate the bioactivity to the IgG2-B isoform from the IgG2 parental mixture. The subclass-related increase in agonist activity was not correlated with antibody aggregation or binding affinity, but was driven by enhanced avidity for the CD200R antibody. These results add to the growing body of evidence that show that conformational differences in the antibody hinge region can have a dramatic impact on the antibody activity and must be considered when screening and engineering therapeutic antibody candidates. The results also demonstrate that the IgG1 (IgG2-A like) or the IgG2-B form may provide the most active form of agonist antibodies for different antibodies and targets. Copyright © 2017 Elsevier Inc. All rights reserved.

Fast State-Space Methods for Inferring Dendritic Synaptic Connectivity

DTIC Science & Technology

2013-08-08

the results of 100 simulations with the same parameters as in Figures 4 and 5. As expected, the LARS/LARS+ results are (downward) biased and have low...with a strength slightly biased toward lower values. To measure the variability of the results across the 20 simulations , we computed for each...are downward biased and have low variance, and the OLS results are unbiased but have high variance. Note that for LARS+ the values above the median are

Associations between mood instability and emotional processing in a large cohort of bipolar patients.

PubMed

Bilderbeck, A C; Reed, Z E; McMahon, H C; Atkinson, L Z; Price, J; Geddes, J R; Goodwin, G M; Harmer, C J

2016-11-01

Aberrant emotional biases have been reported in bipolar disorder (BD), but results are inconsistent. Despite the clinical relevance of chronic mood variability in BD, there is no previous research investigating how the extent of symptom fluctuations in bipolar disorder might relate to emotional biases. This exploratory study investigated, in a large cohort of bipolar patients, whether instability in weekly mood episode symptoms and other clinical and demographic factors were related to emotional bias as measured in a simple laboratory task. Participants (N = 271, BDI = 206, BDII = 121) completed an 'emotional categorization and memory' task. Weekly self-reported symptoms of depression and mania were collected prospectively. In linear regression analyses, associations between cognitive bias and mood variability were explored together with the influence of demographic and clinical factors, including current medication. Greater accuracy in the classification of negative words relative to positive words was associated with greater instability in depressive symptoms. Furthermore, greater negative bias in free recall was associated with higher instability in manic symptoms. Participants diagnosed with BDII, compared with BDI, showed overall better word recognition and recall. Current antipsychotic use was associated with reduced instability in manic symptoms but this did not impact on emotional processing performance. Emotional processing biases in bipolar disorder are related to instability in mood. These findings prompt further investigation into the underpinnings as well as clinical significance of mood instability.

Gravity dependence of the effect of optokinetic stimulation on the subjective visual vertical.

PubMed

Ward, Bryan K; Bockisch, Christopher J; Caramia, Nicoletta; Bertolini, Giovanni; Tarnutzer, Alexander Andrea

2017-05-01

Accurate and precise estimates of direction of gravity are essential for spatial orientation. According to Bayesian theory, multisensory vestibular, visual, and proprioceptive input is centrally integrated in a weighted fashion based on the reliability of the component sensory signals. For otolithic input, a decreasing signal-to-noise ratio was demonstrated with increasing roll angle. We hypothesized that the weights of vestibular (otolithic) and extravestibular (visual/proprioceptive) sensors are roll-angle dependent and predicted an increased weight of extravestibular cues with increasing roll angle, potentially following the Bayesian hypothesis. To probe this concept, the subjective visual vertical (SVV) was assessed in different roll positions (≤ ± 120°, steps = 30°, n = 10) with/without presenting an optokinetic stimulus (velocity = ± 60°/s). The optokinetic stimulus biased the SVV toward the direction of stimulus rotation for roll angles ≥ ± 30° ( P < 0.005). Offsets grew from 3.9 ± 1.8° (upright) to 22.1 ± 11.8° (±120° roll tilt, P < 0.001). Trial-to-trial variability increased with roll angle, demonstrating a nonsignificant increase when providing optokinetic stimulation. Variability and optokinetic bias were correlated ( R 2 = 0.71, slope = 0.71, 95% confidence interval = 0.57-0.86). An optimal-observer model combining an optokinetic bias with vestibular input reproduced measured errors closely. These findings support the hypothesis of a weighted multisensory integration when estimating direction of gravity with optokinetic stimulation. Visual input was weighted more when vestibular input became less reliable, i.e., at larger roll-tilt angles. However, according to Bayesian theory, the variability of combined cues is always lower than the variability of each source cue. If the observed increase in variability, although nonsignificant, is true, either it must depend on an additional source of variability, added after SVV computation, or it would conflict with the Bayesian hypothesis. NEW & NOTEWORTHY Applying a rotating optokinetic stimulus while recording the subjective visual vertical in different whole body roll angles, we noted the optokinetic-induced bias to correlate with the roll angle. These findings allow the hypothesis that the established optimal weighting of single-sensory cues depending on their reliability to estimate direction of gravity could be extended to a bias caused by visual self-motion stimuli. Copyright © 2017 the American Physiological Society.

Accounting for interannual variability: A comparison of options for water resources climate change impact assessments

NASA Astrophysics Data System (ADS)

Johnson, Fiona; Sharma, Ashish

2011-04-01

Empirical scaling approaches for constructing rainfall scenarios from general circulation model (GCM) simulations are commonly used in water resources climate change impact assessments. However, these approaches have a number of limitations, not the least of which is that they cannot account for changes in variability or persistence at annual and longer time scales. Bias correction of GCM rainfall projections offers an attractive alternative to scaling methods as it has similar advantages to scaling in that it is computationally simple, can consider multiple GCM outputs, and can be easily applied to different regions or climatic regimes. In addition, it also allows for interannual variability to evolve according to the GCM simulations, which provides additional scenarios for risk assessments. This paper compares two scaling and four bias correction approaches for estimating changes in future rainfall over Australia and for a case study for water supply from the Warragamba catchment, located near Sydney, Australia. A validation of the various rainfall estimation procedures is conducted on the basis of the latter half of the observational rainfall record. It was found that the method leading to the lowest prediction errors varies depending on the rainfall statistic of interest. The flexibility of bias correction approaches in matching rainfall parameters at different frequencies is demonstrated. The results also indicate that for Australia, the scaling approaches lead to smaller estimates of uncertainty associated with changes to interannual variability for the period 2070-2099 compared to the bias correction approaches. These changes are also highlighted using the case study for the Warragamba Dam catchment.

Moderator Variables as Bias in Testing Black Children

ERIC Educational Resources Information Center

Williams, Robert L.

1975-01-01

The claim that tests of intelligence and abilities are the best predictors of academic success fails to examine closely the important moderator variable as test and criterion characteristics rather than as person characteristics. (EH)

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.

PubMed

Gil-Ley, Alejandro; Bussi, Giovanni

2015-03-10

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.

Compliance-Effect Correlation Bias in Instrumental Variables Estimators

ERIC Educational Resources Information Center

Reardon, Sean F.

2010-01-01

Instrumental variable estimators hold the promise of enabling researchers to estimate the effects of educational treatments that are not (or cannot be) randomly assigned but that may be affected by randomly assigned interventions. Examples of the use of instrumental variables in such cases are increasingly common in educational and social science…

Measurement variability error for estimates of volume change

Treesearch

James A. Westfall; Paul L. Patterson

2007-01-01

Using quality assurance data, measurement variability distributions were developed for attributes that affect tree volume prediction. Random deviations from the measurement variability distributions were applied to 19381 remeasured sample trees in Maine. The additional error due to measurement variation and measurement bias was estimated via a simulation study for...

Correcting power and p-value calculations for bias in diffusion tensor imaging.

PubMed

Lauzon, Carolyn B; Landman, Bennett A

2013-07-01

Diffusion tensor imaging (DTI) provides quantitative parametric maps sensitive to tissue microarchitecture (e.g., fractional anisotropy, FA). These maps are estimated through computational processes and subject to random distortions including variance and bias. Traditional statistical procedures commonly used for study planning (including power analyses and p-value/alpha-rate thresholds) specifically model variability, but neglect potential impacts of bias. Herein, we quantitatively investigate the impacts of bias in DTI on hypothesis test properties (power and alpha-rate) using a two-sided hypothesis testing framework. We present theoretical evaluation of bias on hypothesis test properties, evaluate the bias estimation technique SIMEX for DTI hypothesis testing using simulated data, and evaluate the impacts of bias on spatially varying power and alpha rates in an empirical study of 21 subjects. Bias is shown to inflame alpha rates, distort the power curve, and cause significant power loss even in empirical settings where the expected difference in bias between groups is zero. These adverse effects can be attenuated by properly accounting for bias in the calculation of power and p-values. Copyright © 2013 Elsevier Inc. All rights reserved.

[Study on correction of data bias caused by different missing mechanisms in survey of medical expenditure among students enrolling in Urban Resident Basic Medical Insurance].

PubMed

Zhang, Haixia; Zhao, Junkang; Gu, Caijiao; Cui, Yan; Rong, Huiying; Meng, Fanlong; Wang, Tong

2015-05-01

The study of the medical expenditure and its influencing factors among the students enrolling in Urban Resident Basic Medical Insurance (URBMI) in Taiyuan indicated that non response bias and selection bias coexist in dependent variable of the survey data. Unlike previous studies only focused on one missing mechanism, a two-stage method to deal with two missing mechanisms simultaneously was suggested in this study, combining multiple imputation with sample selection model. A total of 1 190 questionnaires were returned by the students (or their parents) selected in child care settings, schools and universities in Taiyuan by stratified cluster random sampling in 2012. In the returned questionnaires, 2.52% existed not missing at random (NMAR) of dependent variable and 7.14% existed missing at random (MAR) of dependent variable. First, multiple imputation was conducted for MAR by using completed data, then sample selection model was used to correct NMAR in multiple imputation, and a multi influencing factor analysis model was established. Based on 1 000 times resampling, the best scheme of filling the random missing values is the predictive mean matching (PMM) method under the missing proportion. With this optimal scheme, a two stage survey was conducted. Finally, it was found that the influencing factors on annual medical expenditure among the students enrolling in URBMI in Taiyuan included population group, annual household gross income, affordability of medical insurance expenditure, chronic disease, seeking medical care in hospital, seeking medical care in community health center or private clinic, hospitalization, hospitalization canceled due to certain reason, self medication and acceptable proportion of self-paid medical expenditure. The two-stage method combining multiple imputation with sample selection model can deal with non response bias and selection bias effectively in dependent variable of the survey data.

Comprehensive Cross-Clade Characterization of Antibody-Mediated Recognition, Complement-Mediated Lysis, and Cell-Mediated Cytotoxicity of HIV-1 Envelope-Specific Antibodies toward Eradication of the HIV-1 Reservoir.

PubMed

Mujib, Shariq; Liu, Jun; Rahman, A K M Nur-Ur; Schwartz, Jordan A; Bonner, Phil; Yue, Feng Yun; Ostrowski, Mario A

2017-08-15

Immunotherapy with passive administration of broadly neutralizing HIV-1 envelope-specific antibodies (bnAbs) in the setting of established infection in vivo has yielded mixed results. The contribution of different antibodies toward the direct elimination of infected cells is poorly understood. In this study, we determined the ability of 12 well-characterized anti-HIV-1 neutralizing antibodies to recognize and eliminate primary CD4 T cells infected with HIV-1 belonging to clades A, B, C, and D, via antibody-dependent complement-mediated lysis (ADCML) and antibody-dependent cell-mediated cytotoxicity (ADCC), in vitro We further tested unique combinations of these antibodies to determine the optimal antibody cocktails to be tested in future clinical trials. We report that antibody binding to infected CD4 T cells is highly variable and correlates with ADCML and ADCC processes. Particularly, antibodies targeting the envelope glycan shield (2G12) and V1/V2 site (PG9, PG16, and PGT145) are best at recognizing HIV-1-infected CD4 T cells. However, only PG9 and PG16 and their combinations with other bnAbs sufficiently induced the elimination of HIV-1-infected CD4 T cells by ADCML, ADCC, or both. Notably, CD4 binding site antibodies VRC01, 3BNC117, and NIH45-46 G54W did not exhibit recognition of infected cells and were unable to induce their killing. Future trials geared toward the development of a cure for HIV/AIDS should incorporate V1/V2 antibodies for maximal clearance of infected cells. With the use of only primary immune cells, we conducted a comprehensive cross-clade physiological analysis to aid the direction of antibodies as therapeutics toward the development of a cure for HIV/AIDS. IMPORTANCE Several antibodies capable of neutralizing the majority of circulating HIV-1 strains have been identified to date and have been shown to prevent infection in animal models. However, the use of combinations of such broadly neutralizing antibodies (bnAbs) for the treatment and eradication of HIV-1 in infected humans remains uncertain. In this study, we tested the ability of bnAbs to directly recognize and eliminate primary human CD4 T cells infected with diverse HIV-1 strains representative of the global epidemic by antibody-dependent pathways. We also tested several combinations of bnAbs in our assays in order to maximize the clearance of infected cells. We show that the ability of bnAbs to identify and kill infected cells is highly variable and that only a few of them are able to exert this function. Our data will help guide the formulation of bnAbs to test in future human trials aimed at the development of a cure. Copyright © 2017 American Society for Microbiology.

Biomarkers in the evolution of multiple sclerosis.

PubMed

Berger, Thomas

2017-11-01

Nonimaging biomarkers can be applied in differential diagnosis, evaluation of disease progression and therapy monitoring of multiple sclerosis (MS). Presence of oligoclonal IgG bands in cerebrospinal fluid is a diagnostic element and a negative predictor of MS evolution. AQP4 antibodies are pathogenic and diagnostic for neuromyelitis optica spectrum disorder. Antibodies to myelin oligodendrocyte glycoprotein develop in about 50% of predominantly pediatric patients with acute disseminated encephalomyelitis, but their possible role in pathogenesis is unknown. Currently, there are no individualized biomarkers suitable to track disease progression. Neutralizing antibodies against IFN-β, natalizumab and daclizumab arise with variable frequency and reduce treatment efficacy. The anti-John Cunningham virus antibody index has potential as a biomarker for risk of progressive multifocal leukoencephalopathy.

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies

PubMed Central

Doria-Rose, Nicole A.; Schramm, Chaim A.; Gorman, Jason; Moore, Penny L.; Bhiman, Jinal N.; DeKosky, Brandon J.; Ernandes, Michael J.; Georgiev, Ivelin S.; Kim, Helen J.; Pancera, Marie; Staupe, Ryan P.; Altae-Tran, Han R.; Bailer, Robert T.; Crooks, Ema T.; Cupo, Albert; Druz, Aliaksandr; Garrett, Nigel J.; Hoi, Kam H.; Kong, Rui; Louder, Mark K.; Longo, Nancy S.; McKee, Krisha; Nonyane, Molati; O’Dell, Sijy; Roark, Ryan S.; Rudicell, Rebecca S.; Schmidt, Stephen D.; Sheward, Daniel J.; Soto, Cinque; Wibmer, Constantinos Kurt; Yang, Yongping; Zhang, Zhenhai; Mullikin, James C.; Binley, James M.; Sanders, Rogier W.; Wilson, Ian A.; Moore, John P.; Ward, Andrew B.; Georgiou, George; Williamson, Carolyn; Abdool Karim, Salim S.; Morris, Lynn; Kwong, Peter D.; Shapiro, Lawrence; Mascola, John R.

2015-01-01

Summary Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01-12) were isolated from CAPRISA-donor CAP256; each antibody contained the protruding tyrosine-sulfated, anionic antigen-binding loop (CDR H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30–38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation, an important vaccine insight. PMID:24590074

An integrated top-down and bottom-up proteomic approach to characterize the antigen-binding fragment of antibodies.

PubMed

Dekker, Lennard; Wu, Si; Vanduijn, Martijn; Tolić, Nikolai; Stingl, Christoph; Zhao, Rui; Luider, Theo; Paša-Tolić, Ljiljana

2014-05-01

We have previously shown that different individuals exposed to the same antigen produce antibodies with identical mutations in their complementarity determining regions (CDR), suggesting that CDR tryptic peptides can serve as biomarkers for disease diagnosis and prognosis. Complete Fabs derived from disease specific antibodies have even higher potential; they could potentially be used for disease treatment and are required to identify the antigens toward which the antibodies are directed. However, complete Fab sequence characterization via LC-MS analysis of tryptic peptides (i.e. bottom-up) has proven to be impractical for mixtures of antibodies. To tackle this challenge, we have developed an integrated bottom-up and top-down MS approach, employing 2D chromatography coupled with Fourier transform mass spectrometry (FTMS), and applied this approach for full characterization of the variable parts of two pharmaceutical monoclonal antibodies with sensitivity comparable to the bottom-up standard. These efforts represent an essential step toward the identification of disease specific antibodies in patient samples with potentially significant clinical impact. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recent Trends in Antibody-based Oncologic Imaging

PubMed Central

Kaur, Sukhwinder; Venktaraman, Ganesh; Jain, Maneesh; Senapati, Shantibhusan; Garg, Pradeep K.; Batra, Surinder K.

2011-01-01

Antibodies, with their unmatched ability for selective binding to any target, are considered as potentially the most specific probes for imaging. Their clinical utility, however, has been limited chiefly due to their slow clearance from the circulation, longer retention in non-targeted tissues and the extensive optimization required for each antibody-tracer. The development of newer contrast agents, combined with improved conjugation strategies and novel engineered forms of antibodies (diabodies, minibodies, single chain variable fragments, and nanobodies), have triggered a new wave of antibody-based imaging approaches. Apart from their conventional use with nuclear imaging probes, antibodies and their modified forms are increasingly being employed with non-radioisotopic contrast agents (MRI and ultrasound) as well as newer imaging modalities, such as quantum dots, near infra red (NIR) probes, nanoshells and surface enhanced Raman spectroscopy (SERS). The review article provides new developments in the usage of antibodies and their modified forms in conjunction with probes of various imaging modalities such as nuclear imaging, optical imaging, ultrasound, MRI, SERS and nanoshells in preclinical and clinical studies on the diagnosis, prognosis and therapeutic responses of cancer. PMID:22104729

Somatic Hypermutation-Induced Changes in the Structure and Dynamics of HIV-1 Broadly Neutralizing Antibodies.

PubMed

Davenport, Thaddeus M; Gorman, Jason; Joyce, M Gordon; Zhou, Tongqing; Soto, Cinque; Guttman, Miklos; Moquin, Stephanie; Yang, Yongping; Zhang, Baoshan; Doria-Rose, Nicole A; Hu, Shiu-Lok; Mascola, John R; Kwong, Peter D; Lee, Kelly K

2016-08-02

Antibody somatic hypermutation (SHM) and affinity maturation enhance antigen recognition by modifying antibody paratope structure to improve its complementarity with the target epitope. SHM-induced changes in paratope dynamics may also contribute to antibody maturation, but direct evidence of this is limited. Here, we examine two classes of HIV-1 broadly neutralizing antibodies (bNAbs) for SHM-induced changes in structure and dynamics, and delineate the effects of these changes on interactions with the HIV-1 envelope glycoprotein (Env). In combination with new and existing structures of unmutated and affinity matured antibody Fab fragments, we used hydrogen/deuterium exchange with mass spectrometry to directly measure Fab structural dynamics. Changes in antibody structure and dynamics were positioned to improve complementarity with Env, with changes in dynamics primarily observed at the paratope peripheries. We conclude that SHM optimizes paratope complementarity to conserved HIV-1 epitopes and restricts the mobility of paratope-peripheral residues to minimize clashes with variable features on HIV-1 Env. Copyright © 2016 Elsevier Ltd. All rights reserved.

Recent Developments in Antibody-Based Assays for the Detection of Bacterial Toxins

PubMed Central

Zhu, Kui; Dietrich, Richard; Didier, Andrea; Doyscher, Dominik; Märtlbauer, Erwin

2014-01-01

Considering the urgent demand for rapid and accurate determination of bacterial toxins and the recent promising developments in nanotechnology and microfluidics, this review summarizes new achievements of the past five years. Firstly, bacterial toxins will be categorized according to their antibody binding properties into low and high molecular weight compounds. Secondly, the types of antibodies and new techniques for producing antibodies are discussed, including poly- and mono-clonal antibodies, single-chain variable fragments (scFv), as well as heavy-chain and recombinant antibodies. Thirdly, the use of different nanomaterials, such as gold nanoparticles (AuNPs), magnetic nanoparticles (MNPs), quantum dots (QDs) and carbon nanomaterials (graphene and carbon nanotube), for labeling antibodies and toxins or for readout techniques will be summarized. Fourthly, microscale analysis or minimized devices, for example microfluidics or lab-on-a-chip (LOC), which have attracted increasing attention in combination with immunoassays for the robust detection or point-of-care testing (POCT), will be reviewed. Finally, some new materials and analytical strategies, which might be promising for analyzing toxins in the near future, will be shortly introduced. PMID:24732203

An integrated top-down and bottom-up proteomic approach to characterize the antigen binding fragment of antibodies

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

Dekker, Leendert J.; Wu, Si; vanDuijn, Martijn M.

2014-05-31

We have previously shown that different individuals exposed to the same antigen produce antibodies with identical mutations in their complementarity determining regions (CDR), suggesting that CDR tryptic peptides can serve as biomarkers for disease diagnosis and prognosis. Complete Fabs derived from disease specific antibodies have even higher potential; they could potentially be used for disease treatment and are required to identify the antigens towards which the antibodies are directed. However, complete Fab sequence characterization via LC-MS analysis of tryptic peptides (i.e. bottom-up) has proven to be impractical for mixtures of antibodies. To tackle this challenge, we have developed an integratedmore » bottom-up and top-down MS approach, employing 2D chromatography coupled with Fourier transform mass spectrometry (FTMS), and applied this approach for full characterization of the variable parts of two pharmaceutical monoclonal antibodies with sensitivity comparable to the bottom-up standard. These efforts represent an essential step towards the identification of disease specific antibodies in patient samples with potentially significant clinical impact.« less

Neuronal Surface Antibody-Mediated Autoimmune Encephalitis

PubMed Central

Linnoila, Jenny J.; Rosenfeld, Myrna R.; Dalmau, Josep

2016-01-01

In the past few years, many autoimmune encephalitides have been identified, with specific clinical syndromes and associated antibodies against neuronal surface antigens. There is compelling evidence that many of these antibodies are pathogenic and most of these encephalitides are highly responsive to immunotherapies. The clinical spectra of some of these antibody-mediated syndromes, especially those reported in only a few patients, are evolving. Others, such as anti-N-methyl-D-aspartate (NMDA) receptor encephalitis, are well characterized. Diagnosis involves recognizing the specific syndromes and identifying the antibody in a patient’s cerebrospinal fluid (CSF) and/or serum. These syndromes are associated with variable abnormalities in CSF, magnetic resonance imaging, and electroencephalography. Treatment is often multidisciplinary and should be focused upon neutralizing the effects of antibodies and eliminating their source. Overlapping disorders have been noted, with some patients having more than one neurologic autoimmune disease. In other patients, viral infections such as herpes simplex virus encephalitis trigger robust antineuronal autoimmune responses. PMID:25369441

Development and characterization of novel chimeric monoclonal antibodies for broad spectrum neutralization of rabies virus.

PubMed

Kim, Pan Kyeom; Keum, Sun Ju; Osinubi, Modupe O V; Franka, Richard; Shin, Ji Young; Park, Sang Tae; Kim, Man Su; Park, Mi Jung; Lee, Soo Young; Carson, William; Greenberg, Lauren; Yu, Pengcheng; Tao, Xiaoyan; Lihua, Wang; Tang, Qing; Liang, Guodong; Shampur, Madhusdana; Rupprecht, Charles E; Chang, Shin Jae

2017-01-01

Current post-exposure prophylaxis for rabies virus infection has several limitations in terms of supply, cost, safety, and efficacy. Attempts to replace human or equine rabies immune globulins (HRIG or ERIG) have been made by several companies and institutes. We developed potent monoclonal antibodies to neutralize a broad spectrum of rabies viruses by screening hybridomas received from the U.S. Centers for Disease Control and Prevention (CDC). Two kinds of chimeric human antibodies (chimeric #7 and #17) were constructed by cloning the variable regions from selected hybridomas and the constant region of a human antibody. Two antibodies were bound to antigenic site III and I/IV, respectively, and were able to neutralize 51 field isolates of rabies virus that were isolated at different times and places such as Asia, Africa, North America, South America, and Australia. These two antibodies neutralize rabies viruses with high efficacy in an in vivo test using Syrian hamster and mouse models and show low risk for adverse immunogenicity.

Antibody derivatization and conjugation strategies: application in preparation of stealth immunoliposome to target chemotherapeutics to tumor.

PubMed

Manjappa, Arehalli S; Chaudhari, Kiran R; Venkataraju, Makam P; Dantuluri, Prudhviraju; Nanda, Biswarup; Sidda, Chennakesavulu; Sawant, Krutika K; Murthy, Rayasa S Ramachandra

2011-02-28

A great deal of effort has been made over the years to develop liposomes that have targeting vectors (oligosaccharides, peptides, proteins and vitamins) attached to the bilayer surface. Most studies have focused on antibody conjugates since procedures for producing highly specific monoclonal antibodies are well established. Antibody conjugated liposomes have recently attracted a great deal of interest, principally because of their potential use as targeted drug delivery systems and in diagnostic applications. A number of methods have been reported for coupling antibodies to the surface of stealth liposomes. The objective of this review is to enumerate various strategies which are employed in the modification and conjugation of antibodies to the surface of stealth liposomes. This review also describes various derivatization techniques of lipids prior and after their use in the preparation of liposomes. The use of single chain variable fragments and affibodies as targeting ligands in the preparation of immunoliposomes is also discussed. Copyright © 2010 Elsevier B.V. All rights reserved.

Progress in overcoming the chain association issue in bispecific heterodimeric IgG antibodies

PubMed Central

Klein, Christian; Sustmann, Claudio; Thomas, Markus; Stubenrauch, Kay; Croasdale, Rebecca; Schanzer, Jürgen; Brinkmann, Ulrich; Kettenberger, Hubert; Regula, Jörg T.; Schaefer, Wolfgang

2012-01-01

The development of bispecific antibodies has attracted substantial interest, and many different formats have been described. Those specifically containing an Fc part are mostly tetravalent, such as stabilized IgG-scFv fusions or dual-variable domain (DVD) IgGs. However, although they exhibit IgG-like properties and technical developability, these formats differ in size and geometry from classical IgG antibodies. Thus, considerable efforts focus on bispecific heterodimeric IgG antibodies that more closely mimic natural IgG molecules. The inherent chain association problem encountered when producing bispecific heterodimeric IgG antibodies can be overcome by several methods. While technologies like knobs-into-holes (KiH) combined with a common light chain or the CrossMab technology enforce the correct chain association, other approaches, e.g., the dual-acting Fab (DAF) IgGs, do not rely on a heterodimeric Fc part. This review discusses the state of the art in bispecific heterodimeric IgG antibodies, with an emphasis on recent progress. PMID:22925968

Empirical Recommendations for Improving the Stability of the Dot-Probe Task in Clinical Research

PubMed Central

Price, Rebecca B.; Kuckertz, Jennie M.; Siegle, Greg J.; Ladouceur, Cecile D.; Silk, Jennifer S.; Ryan, Neal D.; Dahl, Ronald E.; Amir, Nader

2014-01-01

The dot-probe task has been widely used in research to produce an index of biased attention based on reaction times (RTs). Despite its popularity, very few published studies have examined psychometric properties of the task, including test-retest reliability, and no previous study has examined reliability in clinically anxious samples or systematically explored the effects of task design and analysis decisions on reliability. In the current analysis, we utilized dot-probe data from three studies where attention bias towards threat-related faces was assessed at multiple (≥5) timepoints. Two of the studies were similar (adults with Social Anxiety Disorder, similar design features) while one was much more disparate (pediatric healthy volunteers, distinct task design). We explored the effects of analysis choices (e.g., bias score calculation formula, methods for outlier handling) on reliability and searched for convergence of findings across the three studies. We found that, when considering the three studies concurrently, the most reliable RT bias index utilized data from dot-bottom trials, comparing congruent to incongruent trials, with rescaled outliers, particularly after averaging across more than one assessment point. Although reliability of RT bias indices was moderate to low under most circumstances, within-session variability in bias (attention bias variability; ABV), a recently proposed RT index, was more reliable across sessions. Several eyetracking-based indices of attention bias (available in the pediatric healthy sample only) showed reliability that matched the optimal RT index (ABV). On the basis of these findings, we make specific recommendations to researchers using the dot probe, particularly those wishing to investigate individual differences and/or single-patient applications. PMID:25419646

Alternative Regression Equations for Estimation of Annual Peak-Streamflow Frequency for Undeveloped Watersheds in Texas using PRESS Minimization

USGS Publications Warehouse

Asquith, William H.; Thompson, David B.

2008-01-01

The U.S. Geological Survey, in cooperation with the Texas Department of Transportation and in partnership with Texas Tech University, investigated a refinement of the regional regression method and developed alternative equations for estimation of peak-streamflow frequency for undeveloped watersheds in Texas. A common model for estimation of peak-streamflow frequency is based on the regional regression method. The current (2008) regional regression equations for 11 regions of Texas are based on log10 transformations of all regression variables (drainage area, main-channel slope, and watershed shape). Exclusive use of log10-transformation does not fully linearize the relations between the variables. As a result, some systematic bias remains in the current equations. The bias results in overestimation of peak streamflow for both the smallest and largest watersheds. The bias increases with increasing recurrence interval. The primary source of the bias is the discernible curvilinear relation in log10 space between peak streamflow and drainage area. Bias is demonstrated by selected residual plots with superimposed LOWESS trend lines. To address the bias, a statistical framework based on minimization of the PRESS statistic through power transformation of drainage area is described and implemented, and the resulting regression equations are reported. Compared to log10-exclusive equations, the equations derived from PRESS minimization have PRESS statistics and residual standard errors less than the log10 exclusive equations. Selected residual plots for the PRESS-minimized equations are presented to demonstrate that systematic bias in regional regression equations for peak-streamflow frequency estimation in Texas can be reduced. Because the overall error is similar to the error associated with previous equations and because the bias is reduced, the PRESS-minimized equations reported here provide alternative equations for peak-streamflow frequency estimation.

Structure-Guided Combinatorial Engineering Facilitates Affinity and Specificity Optimization of Anti-CD81 Antibodies.

PubMed

Nelson, Bryce; Adams, Jarrett; Kuglstatter, Andreas; Li, Zhijian; Harris, Seth F; Liu, Yang; Bohini, Sandya; Ma, Han; Klumpp, Klaus; Gao, Junjun; Sidhu, Sachdev S

2018-07-06

Hepatitis C viral infection is the major cause of chronic hepatitis that affects as many as 71 million people worldwide. Rather than target the rapidly shifting viruses and their numerous serotypes, four independent antibodies were made to target the host antigen CD81 and were shown to block hepatitis C viral entry. The single-chain variable fragment of each antibody was crystallized in complex with the CD81 large extracellular loop in order to guide affinity maturation of two distinct antibodies by phage display. Affinity maturation of antibodies using phage display has proven to be critical to therapeutic antibody development and typically involves modification of the paratope for increased affinity, improved specificity, enhanced stability or a combination of these traits. One antibody was engineered for increased affinity for human CD81 large extracellular loop that equated to increased efficacy, while the second antibody was engineered for cross-reactivity with cynomolgus CD81 to facilitate animal model testing. The use of structures to guide affinity maturation library design demonstrates the utility of combining structural analysis with phage display technologies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparison of humanized IgG and FvFc anti-CD3 monoclonal antibodies expressed in CHO cells.

PubMed

Serpieri, Flavia; Inocencio, Andre; de Oliveira, Jose Marcelino; Pimenta, Alécio A; Garbuio, Angélica; Kalil, Jorge; Brigido, Marcelo M; Moro, Ana Maria

2010-07-01

Two humanized monoclonal antibody constructs bearing the same variable regions of an anti-CD3 monoclonal antibody, whole IgG and FvFc, were expressed in CHO cells. Random and site-specific integration were used resulting in similar expression levels. The transfectants were selected with appropriate selection agent, and the surviving cells were plated in semi-solid medium for capture with FITC-conjugated anti-human IG antibody and picked with the robotic ClonePix FL. Conditioned media from selected clones were purified by affinity chromatography and characterized by SDS-PAGE, Western-blot, SEC-HPLC, and isoelectric focusing. Binding to the target present in healthy human mononuclear cells was assessed by flow cytometry, as well as by competition between the two constructs and the original murine monoclonal antibody. The humanized constructs were not able to dislodge the murine antibody while the murine anti-CD3 antibody could dislodge around 20% of the FvFc or IgG humanized versions. Further in vitro and in vivo pre-clinical analyses will be carried out to verify the ability of the humanized versions to demonstrate the immunoregulatory profile required for a humanized anti-CD3 monoclonal antibody.

A simple technique investigating baseline heterogeneity helped to eliminate potential bias in meta-analyses.

PubMed

Hicks, Amy; Fairhurst, Caroline; Torgerson, David J

2018-03-01

To perform a worked example of an approach that can be used to identify and remove potentially biased trials from meta-analyses via the analysis of baseline variables. True randomisation produces treatment groups that differ only by chance; therefore, a meta-analysis of a baseline measurement should produce no overall difference and zero heterogeneity. A meta-analysis from the British Medical Journal, known to contain significant heterogeneity and imbalance in baseline age, was chosen. Meta-analyses of baseline variables were performed and trials systematically removed, starting with those with the largest t-statistic, until the I 2 measure of heterogeneity became 0%, then the outcome meta-analysis repeated with only the remaining trials as a sensitivity check. We argue that heterogeneity in a meta-analysis of baseline variables should not exist, and therefore removing trials which contribute to heterogeneity from a meta-analysis will produce a more valid result. In our example none of the overall outcomes changed when studies contributing to heterogeneity were removed. We recommend routine use of this technique, using age and a second baseline variable predictive of outcome for the particular study chosen, to help eliminate potential bias in meta-analyses. Copyright © 2017 Elsevier Inc. All rights reserved.

A systematic review and meta-analysis of cognitive bias to food stimuli in people with disordered eating behaviour.

PubMed

Brooks, Samantha; Prince, Alexis; Stahl, Daniel; Campbell, Iain C; Treasure, Janet

2011-02-01

Maladaptive cognitions about food, weight and shape bias attention, memory and judgment and may be linked to disordered eating behaviour. This paper reviews information processing of food stimuli (words, pictures) in people with eating disorders (ED). PubMed, Ovid, ScienceDirect, PsychInfo, Web of Science, Cochrane Library and Google Scholar were searched to December 2009. 63 studies measured attention, memory and judgment bias towards food stimuli in women with ED. Stroop tasks had sufficient sample size for a meta-analyses and effects ranged from small to medium. Other studies of attention bias had variable effects (e.g. the Dot-Probe task, distracter tasks and Startle Eyeblink Modulation). A meta-analysis of memory bias studies in ED and RE yielded insignificant effect. Effect sizes for judgment bias ranged from negligible to large. People with ED have greater attentional bias to food stimuli than healthy controls (HC). Evidence for a memory and judgment bias in ED is limited. Copyright © 2010 Elsevier Ltd. All rights reserved.

Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment.

PubMed

Stewart, Alex; Harrison, Joseph S; Regula, Lauren K; Lai, Jonathan R

2013-04-08

Analysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464-5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the major functional paratope in D5 and several antibodies derived from the same progenitor. Here we explore side chain requirements for affinity and specificity in D5 using phage display. Two D5-based libraries were prepared that contained diversity in all three light chain complementarity determining regions (LCDRs 1-3), and in the third HCDR (HCDR3). The first library allowed residues to vary among a restricted set of six amino acids (Tyr/Ala/Asp/Ser/His/Pro; D5-Lib-I). The second library was designed based on a survey of existing VH1-69 antibody structures (D5-Lib-II). Both libraries were subjected to multiple rounds of selection against 5-Helix, and individual clones characterized. We found that selectants from D5-Lib-I generally had moderate affinity and specificity, while many clones from D5-Lib-II exhibited D5-like properties. Additional analysis of the D5-Lib-II functional population revealed position-specific biases for particular amino acids, many that differed from the identity of those side chains in D5. Together these results suggest that there is some permissiveness for alternative side chains in the LCDRs and HCDR3 of D5, but that replacement with a minimal set of residues is not tolerated in this scaffold for 5-Helix recognition. This work provides novel information about this high-affinity interaction involving an antibody from the VH1-69 germline segment.

Influenza A(H7N9) Virus Antibody Responses in Survivors 1 Year after Infection, China, 2017

PubMed Central

Ma, Mai-Juan; Liu, Cheng; Wu, Meng-Na; Zhao, Teng; Wang, Guo-Lin; Yang, Yang; Gu, Hong-Jing; Cui, Peng-Wei; Pang, Yuan-Yuan; Tan, Ya-Yun; Hang, Hui; Lin, Bao; Qin, Jiang-Chun; Cheng, Li-Ling

2018-01-01

Avian influenza A(H7N9) virus has caused 5 epidemic waves in China since its emergence in 2013. We investigated the dynamic changes of antibody response to this virus over 1 year postinfection in 25 patients in Suzhou City, Jiangsu Province, China, who had laboratory-confirmed infections during the fifth epidemic wave, October 1, 2016–February 14, 2017. Most survivors had relatively robust antibody responses that decreased but remained detectable at 1 year. Antibody response was variable; several survivors had low or undetectable antibody titers. Hemagglutination inhibition titer was >1:40 for <40% of the survivors. Measured in vitro in infected mice, hemagglutination inhibition titer predicted serum protective ability. Our findings provide a helpful serologic guideline for identifying subclinical infections and for developing effective vaccines and therapeutics to counter H7N9 virus infections. PMID:29432091

Influenza A(H7N9) Virus Antibody Responses in Survivors 1 Year after Infection, China, 2017.

PubMed

Ma, Mai-Juan; Liu, Cheng; Wu, Meng-Na; Zhao, Teng; Wang, Guo-Lin; Yang, Yang; Gu, Hong-Jing; Cui, Peng-Wei; Pang, Yuan-Yuan; Tan, Ya-Yun; Hang, Hui; Lin, Bao; Qin, Jiang-Chun; Fang, Li-Qun; Cao, Wu-Chun; Cheng, Li-Ling

2018-04-01

Avian influenza A(H7N9) virus has caused 5 epidemic waves in China since its emergence in 2013. We investigated the dynamic changes of antibody response to this virus over 1 year postinfection in 25 patients in Suzhou City, Jiangsu Province, China, who had laboratory-confirmed infections during the fifth epidemic wave, October 1, 2016-February 14, 2017. Most survivors had relatively robust antibody responses that decreased but remained detectable at 1 year. Antibody response was variable; several survivors had low or undetectable antibody titers. Hemagglutination inhibition titer was >1:40 for <40% of the survivors. Measured in vitro in infected mice, hemagglutination inhibition titer predicted serum protective ability. Our findings provide a helpful serologic guideline for identifying subclinical infections and for developing effective vaccines and therapeutics to counter H7N9 virus infections.

Just tell me what to do: bringing back experimenter control in active contingency tasks with the command-performance procedure and finding cue density effects along the way.

PubMed

Hannah, Samuel D; Beneteau, Jennifer L

2009-03-01

Active contingency tasks, such as those used to explore judgments of control, suffer from variability in the actual values of critical variables. The authors debut a new, easily implemented procedure that restores control over these variables to the experimenter simply by telling participants when to respond, and when to withhold responding. This command-performance procedure not only restores control over critical variables such as actual contingency, it also allows response frequency to be manipulated independently of contingency or outcome frequency. This yields the first demonstration, to our knowledge, of the equivalent of a cue density effect in an active contingency task. Judgments of control are biased by response frequency outcome frequency, just as they are also biased by outcome frequency. (c) 2009 APA, all rights reserved

Avoiding and Correcting Bias in Score-Based Latent Variable Regression with Discrete Manifest Items

ERIC Educational Resources Information Center

Lu, Irene R. R.; Thomas, D. Roland

2008-01-01

This article considers models involving a single structural equation with latent explanatory and/or latent dependent variables where discrete items are used to measure the latent variables. Our primary focus is the use of scores as proxies for the latent variables and carrying out ordinary least squares (OLS) regression on such scores to estimate…

`Been There Done That': Disentangling Option Value Effects from User Heterogeneity When Valuing Natural Resources with a Use Component

NASA Astrophysics Data System (ADS)

Lyssenko, Nikita; Martínez-Espiñeira, Roberto

2012-11-01

Endogeneity bias arises in contingent valuation studies when the error term in the willingness to pay (WTP) equation is correlated with explanatory variables because observable and unobservable characteristics of the respondents affect both their WTP and the value of those variables. We correct for the endogeneity of variables that capture previous experience with the resource valued, humpback whales, and with the geographic area of study. We consider several endogenous behavioral variables. Therefore, we apply a multivariate Probit approach to jointly model them with WTP. In this case, correcting for endogeneity increases econometric efficiency and substantially corrects the bias affecting the estimated coefficients of the experience variables, by isolating the decreasing effect on option value caused by having already experienced the resource. Stark differences are unveiled between the marginal effects on WTP of previous experience of the resource in an alternative location versus experience in the location studied, Newfoundland and Labrador (Canada).

'Been there done that': disentangling option value effects from user heterogeneity when valuing natural resources with a use component.

PubMed

Lyssenko, Nikita; Martínez-Espiñeira, Roberto

2012-11-01

Endogeneity bias arises in contingent valuation studies when the error term in the willingness to pay (WTP) equation is correlated with explanatory variables because observable and unobservable characteristics of the respondents affect both their WTP and the value of those variables. We correct for the endogeneity of variables that capture previous experience with the resource valued, humpback whales, and with the geographic area of study. We consider several endogenous behavioral variables. Therefore, we apply a multivariate Probit approach to jointly model them with WTP. In this case, correcting for endogeneity increases econometric efficiency and substantially corrects the bias affecting the estimated coefficients of the experience variables, by isolating the decreasing effect on option value caused by having already experienced the resource. Stark differences are unveiled between the marginal effects on WTP of previous experience of the resource in an alternative location versus experience in the location studied, Newfoundland and Labrador (Canada).

Automated quantification of myocardial infarction from MR images by accounting for partial volume effects: animal, phantom, and human study.

PubMed

Heiberg, Einar; Ugander, Martin; Engblom, Henrik; Götberg, Matthias; Olivecrona, Göran K; Erlinge, David; Arheden, Håkan

2008-02-01

Ethics committees approved human and animal study components; informed written consent was provided (prospective human study [20 men; mean age, 62 years]) or waived (retrospective human study [16 men, four women; mean age, 59 years]). The purpose of this study was to prospectively evaluate a clinically applicable method, accounting for the partial volume effect, to automatically quantify myocardial infarction from delayed contrast material-enhanced magnetic resonance images. Pixels were weighted according to signal intensity to calculate infarct fraction for each pixel. Mean bias +/- variability (or standard deviation), expressed as percentage left ventricular myocardium (%LVM), were -0.3 +/- 1.3 (animals), -1.2 +/- 1.7 (phantoms), and 0.3 +/- 2.7 (patients), respectively. Algorithm had lower variability than dichotomous approach (2.7 vs 7.7 %LVM, P < .01) and did not differ from interobserver variability for bias (P = .31) or variability (P = .38). The weighted approach provides automatic quantification of myocardial infarction with higher accuracy and lower variability than a dichotomous algorithm. (c) RSNA, 2007.

Obligate multivalent recognition of cell surface tomoregulin following selection from a multivalent phage antibody library.

PubMed

Heitner, Tara; Satozawa, Noboru; McLean, Kirk; Vogel, David; Cobb, Ronald R; Liu, Bing; Mahmoudi, Mithra; Finster, Silke; Larsen, Brent; Zhu, Ying; Zhou, Hongxing; Müller-Tiemann, Beate; Monteclaro, Felipe; Zhao, Xiao-Yan; Light, David R

2006-12-01

A therapeutic antibody candidate (AT-19) isolated using multivalent phage display binds native tomoregulin (TR) as a mul-timer not as a monomer. This report raises the importance of screening and selecting phage antibodies on native antigen and reemphasizes the possibility that potentially valuable antibodies are discarded when a monomeric phage display system is used for screening. A detailed live cell panning selection and screening method to isolate multivalently active antibodies is described. AT-19 is a fully human antibody recognizing the cell surface protein TR, a proposed prostate cancer target for therapeutic antibody internalization. AT-19 was isolated from a multivalent single-chain variable fragment (scFv) antibody library rescued with hyperphage. The required multivalency for isolation of AT-19 is supported by fluorescence activated cell sorting data demonstrating binding of the multivalent AT-19 phage particles at high phage concentrations and failure of monovalent particles to bind. Pure monomeric scFv AT-19 does not bind native receptor on cells, whereas dimeric scFv or immunoglobulin G binds with nanomolar affinity. The isolation of AT-19 antibody with obligate bivalent binding activity to native TR is attributed to the use of a multivalent display of scFv on phage and the method for selecting and screening by alternate use of 2 recombinant cell lines.

[Regression analysis to select native-like structures from decoys of antigen-antibody docking].

PubMed

Chen, Zhengshan; Chi, Xiangyang; Fan, Pengfei; Zhang, Guanying; Wang, Meirong; Yu, Changming; Chen, Wei

2018-06-25

Given the increasing exploitation of antibodies in different contexts such as molecular diagnostics and therapeutics, it would be beneficial to unravel properties of antigen-antibody interaction with modeling of computational protein-protein docking, especially, in the absence of a cocrystal structure. However, obtaining a native-like antigen-antibody structure remains challenging due in part to failing to reliably discriminate accurate from inaccurate structures among tens of thousands of decoys after computational docking with existing scoring function. We hypothesized that some important physicochemical and energetic features could be used to describe antigen-antibody interfaces and identify native-like antigen-antibody structure. We prepared a dataset, a subset of Protein-Protein Docking Benchmark Version 4.0, comprising 37 nonredundant 3D structures of antigen-antibody complexes, and used it to train and test multivariate logistic regression equation which took several important physicochemical and energetic features of decoys as dependent variables. Our results indicate that the ability to identify native-like structures of our method is superior to ZRANK and ZDOCK score for the subset of antigen-antibody complexes. And then, we use our method in workflow of predicting epitope of anti-Ebola glycoprotein monoclonal antibody-4G7 and identify three accurate residues in its epitope.

Cognitive biases to healthy and unhealthy food words predict change in BMI.

PubMed

Calitri, Raff; Pothos, Emmanuel M; Tapper, Katy; Brunstrom, Jeffrey M; Rogers, Peter J

2010-12-01

The current study explored the predictive value of cognitive biases to food cues (assessed by emotional Stroop and dot probe tasks) on weight change over a 1-year period. This was a longitudinal study with undergraduate students (N = 102) living in shared student accommodation. After controlling for the effects of variables associated with weight (e.g., physical activity, stress, restrained eating, external eating, and emotional eating), no effects of cognitive bias were found with the dot probe. However, for the emotional Stroop, cognitive bias to unhealthy foods predicted an increase in BMI whereas cognitive bias to healthy foods was associated with a decrease in BMI. Results parallel findings in substance abuse research; cognitive biases appear to predict behavior change. Accordingly, future research should consider strategies for attentional retraining, encouraging individuals to reorient attention away from unhealthy eating cues.

The Use of Propensity Scores and Observational Data to Estimate Randomized Controlled Trial Generalizability Bias

PubMed Central

Pressler, Taylor R.; Kaizar, Eloise E.

2014-01-01

While randomized controlled trials (RCT) are considered the “gold standard” for clinical studies, the use of exclusion criteria may impact the external validity of the results. It is unknown whether estimators of effect size are biased by excluding a portion of the target population from enrollment. We propose to use observational data to estimate the bias due to enrollment restrictions, which we term generalizability bias. In this paper we introduce a class of estimators for the generalizability bias and use simulation to study its properties in the presence of non-constant treatment effects. We find the surprising result that our estimators can be unbiased for the true generalizability bias even when all potentially confounding variables are not measured. In addition, our proposed doubly robust estimator performs well even for mis-specified models. PMID:23553373

Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.

PubMed

Galvelis, Raimondas; Sugita, Yuji

2017-06-13

The free energy calculations of complex chemical and biological systems with molecular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e., importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbor density estimator (NNDE) and the artificial neural network (ANN) for the bias potential approximation. The bias potential is constructed iteratively from short biased MD simulations accounting for correlation among CVs. Our method is capable of achieving ergodic sampling and calculating free energy of polypeptides with up to 8-dimensional bias potential.

Compatibility check of measured aircraft responses using kinematic equations and extended Kalman filter

NASA Technical Reports Server (NTRS)

Klein, V.; Schiess, J. R.

1977-01-01

An extended Kalman filter smoother and a fixed point smoother were used for estimation of the state variables in the six degree of freedom kinematic equations relating measured aircraft responses and for estimation of unknown constant bias and scale factor errors in measured data. The computing algorithm includes an analysis of residuals which can improve the filter performance and provide estimates of measurement noise characteristics for some aircraft output variables. The technique developed was demonstrated using simulated and real flight test data. Improved accuracy of measured data was obtained when the data were corrected for estimated bias errors.

On Rater Agreement and Rater Training

ERIC Educational Resources Information Center

Wang, Binhong

2010-01-01

This paper first analyzed two studies on rater factors and rating criteria to raise the problem of rater agreement. After that the author reveals the causes of discrepencies in rating administration by discussing rater variability and rater bias. The author argues that rater bias can not be eliminated completely, we can only reduce the error to a…

Heaping-Induced Bias in Regression-Discontinuity Designs. NBER Working Paper No. 17408

ERIC Educational Resources Information Center

Barreca, Alan I.; Lindo, Jason M.; Waddell, Glen R.

2011-01-01

This study uses Monte Carlo simulations to demonstrate that regression-discontinuity designs arrive at biased estimates when attributes related to outcomes predict heaping in the running variable. After showing that our usual diagnostics are poorly suited to identifying this type of problem, we provide alternatives. We also demonstrate how the…

Reducing Bias Due to Systematic Attrition in Longitudinal Studies: The Benefits of Multiple Imputation

ERIC Educational Resources Information Center

Asendorpf, Jens B.; van de Schoot, Rens; Denissen, Jaap J. A.; Hutteman, Roos

2014-01-01

Most longitudinal studies are plagued by drop-out related to variables at earlier assessments (systematic attrition). Although systematic attrition is often analysed in longitudinal studies, surprisingly few researchers attempt to reduce biases due to systematic attrition, even though this is possible and nowadays technically easy. This is…

Bias in Student Survey Findings from Active Parental Consent Procedures

ERIC Educational Resources Information Center

Shaw, Thérèse; Cross, Donna; Thomas, Laura T.; Zubrick, Stephen R.

2015-01-01

Increasingly, researchers are required to obtain active (explicit) parental consent prior to surveying children and adolescents in schools. This study assessed the potential bias present in a sample of actively consented students, and in the estimates of associations between variables obtained from this sample. Students (n = 3496) from 36…

Effects of Perceived School Well-Being and Negative Emotionality on Students' Attentional Bias for Academic Stressors

ERIC Educational Resources Information Center

Scrimin, Sara; Moscardino, Ughetta; Altoè, Gianmarco; Mason, Lucia

2016-01-01

Background: Previous research indicates that children can display different attention allocation patterns in response to threat. However, data are lacking on the possible existence of an attentional bias in response to academic stressors, and whether variables related to school well-being (SWB) and students' individual characteristics may…

Internalized weight bias mediates the relationship between depressive symptoms and disordered eating behavior among women who think they are overweight.

PubMed

Sienko, Rachel M; Saules, Karen K; Carr, Meagan M

2016-08-01

This study tested the potential mediating role of Internalized Weight Bias (IWB) in the relationship between depressive symptoms (DEP-SX) and disordered eating behavior. In particular, we hypothesized that IWB may be an intervening variable in the well documented association between depression and disordered eating. College women (N=172) who were taking undergraduate psychology courses and who endorsed thinking they were overweight completed the Patient Health Questionnaire depression screener (PHQ-9), the Weight Bias Internalization Scale (WBIS), and the Eating Disorder Examination Questionnaire (EDE-Q). Bootstrapping mediation analyses were conducted to explore the relationships between these variables. IWB was significantly correlated with eating disorder symptoms and DEP-SX, but not Body Mass Index. Mediation analyses supported a model in which IWB mediated the relationship between DEP-SX and disordered eating behavior. Results indicate that individuals with elevated DEP-SX may be likely to internalize weight bias, which may in turn lead to maladaptive approaches to eating and weight control, regardless of one's actual weight status. Copyright © 2016 Elsevier Ltd. All rights reserved.

Inference for binomial probability based on dependent Bernoulli random variables with applications to meta‐analysis and group level studies

PubMed Central

Bakbergenuly, Ilyas; Morgenthaler, Stephan

2016-01-01

We study bias arising as a result of nonlinear transformations of random variables in random or mixed effects models and its effect on inference in group‐level studies or in meta‐analysis. The findings are illustrated on the example of overdispersed binomial distributions, where we demonstrate considerable biases arising from standard log‐odds and arcsine transformations of the estimated probability p^, both for single‐group studies and in combining results from several groups or studies in meta‐analysis. Our simulations confirm that these biases are linear in ρ, for small values of ρ, the intracluster correlation coefficient. These biases do not depend on the sample sizes or the number of studies K in a meta‐analysis and result in abysmal coverage of the combined effect for large K. We also propose bias‐correction for the arcsine transformation. Our simulations demonstrate that this bias‐correction works well for small values of the intraclass correlation. The methods are applied to two examples of meta‐analyses of prevalence. PMID:27192062

A Projection of Changes in Landfilling Atmospheric River Frequency and Extreme Precipitation over Western North America from the Large Ensemble CESM Simulations

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

Hagos, Samson M.; Leung, Lai-Yung R.; Yoon, Jin-Ho

Simulations from the Community Earth System Model Large Ensemble project are analyzed to investigate the impact of global warming on atmospheric rivers (ARs). The model has notable biases in simulating the subtropical jet position and the relationship between extreme precipitation and moisture transport. After accounting for these biases, the model projects an ensemble mean increase of 35% in the number of landfalling AR days between the last twenty years of the 20th and 21st centuries. However, the number of AR associated extreme precipitation days increases only by 28% because the moisture transport required to produce extreme precipitation also increases withmore » warming. Internal variability introduces an uncertainty of ±8% and ±7% in the projected changes in AR days and associated extreme precipitation days. In contrast, accountings for model biases only change the projected changes by about 1%. The significantly larger mean changes compared to internal variability and to the effects of model biases highlight the robustness of AR responses to global warming.« less

Comment on “Models of stochastic, spatially varying stress in the crust compatible with focal‐mechanism data, and how stress inversions can be biased toward the stress rate” by Deborah Elaine Smith and Thomas H. Heaton

USGS Publications Warehouse

Hardebeck, Jeanne L.

2015-01-01

This model makes specific predictions about the orientations and heterogeneity of earthquake focal mechanisms. Smith and Heaton (2011) attempt to validate this heterogeneous stress model using observations of earthquake focal‐mechanism variability from Hardebeck (2006). They then demonstrate that the model predicts a bias in the orientations of earthquake focal mechanisms, which are biased away from the background stress and toward the stressing rate. They suggest the focal‐mechanism bias in this model invalidates the large body of work over the last several decades, that has inferred stress orientations from the inversion of earthquake focal mechanisms. The question of whether or not the Smith and Heaton (2011) model is applicable to the real Earth is therefore important not only for understanding spatial stress variability but also for evaluating the numerous studies that have inferred crustal stress orientations from earthquake focal mechanisms (e.g., as compiled by Heidbach et al., 2008).

The social transmission of metacontrol policies: Mechanisms underlying the interpersonal transfer of persistence and flexibility.

PubMed

Hommel, Bernhard; Colzato, Lorenza S

2017-10-01

Humans often face binary cognitive-control dilemmas, with the choice between persistence and flexibility being a crucial one. Tackling these dilemmas requires metacontrol, i.e., the control of the current cognitive-control policy. As predicted from functional, psychometric, neuroscientific, and modeling approaches, interindividual variability in metacontrol biases towards persistence or flexibility could be demonstrated in metacontrol-sensitive tasks. These biases covary systematically with genetic predispositions regarding mesofrontal and nigrostriatal dopaminergic functioning and the individualistic or collectivistic nature of the cultural background. However, there is also evidence for mood- and meditation-induced intraindividual variability (with negative mood and focused-attention meditation being associated with a bias towards persistence, and positive mood and open-monitoring meditation being associated with a bias towards flexibility), suggesting that genetic and cultural factors do not determine metacontrol settings entirely. We suggest a theoretical framework that explains how genetic predisposition and cultural learning can lead to the implementation of metacontrol defaults, which however can be shifted towards persistence or flexibility by situational factors. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hedonic price models with omitted variables and measurement errors: a constrained autoregression-structural equation modeling approach with application to urban Indonesia

NASA Astrophysics Data System (ADS)

Suparman, Yusep; Folmer, Henk; Oud, Johan H. L.

2014-01-01

Omitted variables and measurement errors in explanatory variables frequently occur in hedonic price models. Ignoring these problems leads to biased estimators. In this paper, we develop a constrained autoregression-structural equation model (ASEM) to handle both types of problems. Standard panel data models to handle omitted variables bias are based on the assumption that the omitted variables are time-invariant. ASEM allows handling of both time-varying and time-invariant omitted variables by constrained autoregression. In the case of measurement error, standard approaches require additional external information which is usually difficult to obtain. ASEM exploits the fact that panel data are repeatedly measured which allows decomposing the variance of a variable into the true variance and the variance due to measurement error. We apply ASEM to estimate a hedonic housing model for urban Indonesia. To get insight into the consequences of measurement error and omitted variables, we compare the ASEM estimates with the outcomes of (1) a standard SEM, which does not account for omitted variables, (2) a constrained autoregression model, which does not account for measurement error, and (3) a fixed effects hedonic model, which ignores measurement error and time-varying omitted variables. The differences between the ASEM estimates and the outcomes of the three alternative approaches are substantial.

Influenza Vaccination in Patients with Common Variable Immunodeficiency (CVID).

PubMed

Mieves, Jan F; Wittke, Kirsten; Freitag, Helma; Volk, Hans-Dieter; Scheibenbogen, Carmen; Hanitsch, Leif G

2017-10-05

Vaccination against influenza in patients with primary antibody deficiency is recommended. Common variable immunodeficiency (CVID) is the most frequent and clinically relevant antibody deficiency disease and is by definition characterized by an impaired vaccination response. The purpose of this review is to present the current knowledge of humoral and cellular vaccine response to influenza in CVID patients. Studies conducted in CVID patients demonstrated an impaired humoral response upon influenza vaccination. Data on cellular immune response are in part conflicting, with two out of three studies showing responses similar to healthy controls. Available data suggest a benefit from influenza vaccination in CVID patients. Therefore, annual influenza vaccination in patients and their close household contacts is recommended.

Varicella-zoster virus immunity among health care workers in Catalonia.

PubMed

Urbiztondo, L; Bayas, J M; Broner, S; Costa, J; Esteve, M; Campins, M; Borrás, E; Domínguez, A

2014-10-14

To determine varicella-zoster virus (VZV) immunity among healthcare workers (HCWs). Cross-sectional study. HCWs attending voluntary periodic health examinations between June 2008 and December 2010. Six public hospitals and five primary care areas in Catalonia, Spain. A self-administered questionnaire was given to eligible HCWs. Variables including age, sex, professional category, type of centre, history of varicella infection, and VZV vaccination were collected. The study was carried out using a convenience sample. The prevalence of antibodies and positive and negative predictive values (PPV and NPV) of the history of clinical VZV infection or vaccination were calculated. Crude and adjusted odds ratios (OR and ORa) and their 95% confidence intervals (CI) were calculated to determine the variables associated with antibody prevalence. Of 705 HCWs who agreed to participate, 644 were finally included. The overall prevalence of antibodies to varicella was 94.9% (95% CI: 92.9-96.4). Of the variables studied, only age was associated with serological susceptibility to VZV. HCWs aged 25-35 years had the highest serological susceptibility (8.1%, 95% CI: 4.6-13.0). The prevalence of antibodies was 96% in subjects reporting previous VZV infection or vaccination, compared with 93% in subjects who did not report these states or did not know. The high proportion of serologically-susceptible HCWs found in this study indicates the need to develop for screening and vaccination strategies in Catalonia. Due to the high capacity of propagation of the VZV in health settings and its consequences, VZV vaccination programmes in HCWs should be reinforced. Copyright © 2014 Elsevier Ltd. All rights reserved.

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Peter, Emanuel K.

2017-12-01

In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

Comparative risk assessment and cessation information seeking among smokeless tobacco users.

PubMed

Jun, Jungmi; Nan, Xiaoli

2018-05-01

This research examined (1) smokeless tobacco users' comparative optimism in assessing the health and addiction risks of their own product in comparison with cigarettes, and (2) the effects of comparative optimism on cessation information-seeking. A nationally-representative sample from the 2015 Health Information National Trends Survey (HINTS)-FDA was employed. The analyses revealed the presence of comparative optimism in assessing both health and addiction risks among smokeless tobacco users. Comparative optimism was negatively correlated with most cessation information-seeking variables. Health bias (the health risk rating gap between the subject's own tobacco product and cigarettes) was associated with decreased intent to use cessation support. However, the health bias and addiction bias (the addiction risk rating gap between the subject's own tobacco product and cigarettes) were not consistent predictors of all cessation information-seeking variables, when covariates of socio-demographics and tobacco use status were included. In addition, positive correlations between health bias and past/recent cessation-information searches were observed. Optimisic biases may negatively influence cessation behaviors not only directly but also indirectly by influencing an important moderator, cessation information-seeking. Future interventions should prioritize dispelling the comparative optimism in perceiving risks of smokeless tobacco use, as well as provide more reliable cessation information specific to smokeless tobacco users. Copyright © 2018 Elsevier Ltd. All rights reserved.

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation.

PubMed

Peter, Emanuel K

2017-12-07

In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

Implicit and Explicit Representations of Hand Position in Tool Use

PubMed Central

Rand, Miya K.; Heuer, Herbert

2013-01-01

Understanding the interactions of visual and proprioceptive information in tool use is important as it is the basis for learning of the tool's kinematic transformation and thus skilled performance. This study investigated how the CNS combines seen cursor positions and felt hand positions under a visuo-motor rotation paradigm. Young and older adult participants performed aiming movements on a digitizer while looking at rotated visual feedback on a monitor. After each movement, they judged either the proprioceptively sensed hand direction or the visually sensed cursor direction. We identified asymmetric mutual biases with a strong visual dominance. Furthermore, we found a number of differences between explicit and implicit judgments of hand directions. The explicit judgments had considerably larger variability than the implicit judgments. The bias toward the cursor direction for the explicit judgments was about twice as strong as for the implicit judgments. The individual biases of explicit and implicit judgments were uncorrelated. Biases of these judgments exhibited opposite sequential effects. Moreover, age-related changes were also different between these judgments. The judgment variability was decreased and the bias toward the cursor direction was increased with increasing age only for the explicit judgments. These results indicate distinct explicit and implicit neural representations of hand direction, similar to the notion of distinct visual systems. PMID:23894307

On the use of nudging techniques for regional climate modeling: application for tropical convection

NASA Astrophysics Data System (ADS)

Pohl, Benjamin; Crétat, Julien

2014-09-01

Using a large set of WRF ensemble simulations at 70-km horizontal resolution over a domain encompassing the Warm Pool region and its surroundings [45°N-45°S, 10°E-240°E], this study aims at quantifying how nudging techniques can modify the simulation of deep atmospheric convection. Both seasonal mean climate, transient variability at intraseasonal timescales, and the respective weight of internal (stochastic) and forced (reproducible) variability are considered. Sensitivity to a large variety of nudging settings (nudged variables and layers and nudging strength) and to the model physics (using 3 convective parameterizations) is addressed. Integrations are carried out during a 7-month season characterized by neutral background conditions and strong intraseasonal variability. Results show that (1) the model responds differently to the nudging from one parameterization to another. Biases are decreased by ~50 % for Betts-Miller-Janjic convection against 17 % only for Grell-Dévényi, the scheme producing yet the largest biases; (2) relaxing air temperature is the most efficient way to reduce biases, while nudging the wind increases most co-variability with daily observations; (3) the model's internal variability is drastically reduced and mostly depends on the nudging strength and nudged variables; (4) interrupting the relaxation before the end of the simulations leads to an abrupt convergence towards the model's natural solution, with no clear effects on the simulated climate after a few days. The usefulness and limitations of the approach are finally discussed through the example of the Madden-Julian Oscillation, that the model fails at simulating and that can be artificially and still imperfectly reproduced in relaxation experiments.

Anti-GM1 antibodies as a model of the immune response to self-glycans.

PubMed

Nores, Gustavo A; Lardone, Ricardo D; Comín, Romina; Alaniz, María E; Moyano, Ana L; Irazoqui, Fernando J

2008-03-01

Glycans are a class of molecules with high structural variability, frequently found in the plasma membrane facing the extracellular space. Because of these characteristics, glycans are often considered as recognition molecules involved in cell social functions, and as targets of pathogenic factors. Induction of anti-glycan antibodies is one of the early events in immunological defense against bacteria that colonize the body. Because of this natural infection, antibodies recognizing a variety of bacterial glycans are found in sera of adult humans and animals. The immune response to glycans is restricted by self-tolerance, and no antibodies to self-glycans should exist in normal subjects. However, antibodies recognizing structures closely related to self-glycans do exist, and can lead to production of harmful anti-self antibodies. Normal human sera contain low-affinity anti-GM1 IgM-antibodies. Similar antibodies with higher affinity or different isotype are found in some neuropathy patients. Two hypotheses have been developed to explain the origin of disease-associated anti-GM1 antibodies. According to the "molecular mimicry" hypothesis, similarity between GM1 and Campylobacter jejuni lipopolysaccharide carrying a GM1-like glycan is the cause of Guillain-Barré syndrome associated with anti-GM1 IgG-antibodies. According to the "binding site drift" hypothesis, IgM-antibodies associated with disease originate through changes in the binding site of normally occurring anti-GM1 antibodies. We now present an "integrated" hypothesis, combining the "mimicry" and "drift" concepts, which satisfactorily explains most of the published data on anti-GM1 antibodies.

Reconciling the Structural Attributes of Avian Antibodies*

PubMed Central

Conroy, Paul J.; Law, Ruby H. P.; Gilgunn, Sarah; Hearty, Stephen; Caradoc-Davies, Tom T.; Lloyd, Gordon; O'Kennedy, Richard J.; Whisstock, James C.

2014-01-01

Antibodies are high value therapeutic, diagnostic, biotechnological, and research tools. Combinatorial approaches to antibody discovery have facilitated access to unique antibodies by surpassing the diversity limitations of the natural repertoire, exploitation of immune repertoires from multiple species, and tailoring selections to isolate antibodies with desirable biophysical attributes. The V-gene repertoire of the chicken does not utilize highly diverse sequence and structures, which is in stark contrast to the mechanism employed by humans, mice, and primates. Recent exploitation of the avian immune system has generated high quality, high affinity antibodies to a wide range of antigens for a number of therapeutic, diagnostic and biotechnological applications. Furthermore, extensive examination of the amino acid characteristics of the chicken repertoire has provided significant insight into mechanisms employed by the avian immune system. A paucity of avian antibody crystal structures has limited our understanding of the structural consequences of these uniquely chicken features. This paper presents the crystal structure of two chicken single chain fragment variable (scFv) antibodies generated from large libraries by phage display against important human antigen targets, which capture two unique CDRL1 canonical classes in the presence and absence of a non-canonical disulfide constrained CDRH3. These structures cast light on the unique structural features of chicken antibodies and contribute further to our collective understanding of the unique mechanisms of diversity and biochemical attributes that render the chicken repertoire of particular value for antibody generation. PMID:24737329

Antibody engineering of a cytotoxic monoclonal antibody 84 against human embryonic stem cells: Investigating the effects of multivalency on cytotoxicity.

PubMed

Klement, Maximilian; Zheng, Jiyun; Liu, Chengcheng; Tan, Heng-Liang; Wong, Victor Vai Tak; Choo, Andre Boon-Hwa; Lee, Dong-Yup; Ow, Dave Siak-Wei

2017-02-10

Antibody fragments have shown targeted specificity to their antigens, but only modest tissue retention times in vivo and in vitro. Multimerization has been used as a protein engineering tool to increase the number of binding units and thereby enhance the efficacy and retention time of antibody fragments. In this work, we explored the effects of valency using a series of self-assembling polypeptides based on the GCN4 leucine zipper multimerization domain fused to a single-chain variable fragment via an antibody upper hinge sequence. Four engineered antibody fragments with a valency from one to four antigen-binding units of a cytotoxic monoclonal antibody 84 against human embryonic stem cells (hESC) were constructed. We hypothesized that higher cytotoxicity would be observed for fragments with increased valency. Flow cytometry analysis revealed that the trimeric and tetrameric engineered antibody fragments resulted in the highest degree of cytotoxicity to the undifferentiated hESC, while the engineered antibody fragments were observed to have improved tissue penetration into cell clusters. Thus, a trade off was made for the trimeric versus tetrameric fragment due to improved tissue penetration. These results have direct implications for antibody-mediated removal of undifferentiated hESC during regenerative medicine and cell therapy. Copyright © 2016 The Author(s). Published by Elsevier B.V. All rights reserved.

The constant region affects antigen binding of antibodies to DNA by altering secondary structure.

PubMed

Xia, Yumin; Janda, Alena; Eryilmaz, Ertan; Casadevall, Arturo; Putterman, Chaim

2013-11-01

We previously demonstrated an important role of the constant region in the pathogenicity of anti-DNA antibodies. To determine the mechanisms by which the constant region affects autoantibody binding, a panel of isotype-switch variants (IgG1, IgG2a, IgG2b) was generated from the murine PL9-11 IgG3 autoantibody. The affinity of the PL9-11 antibody panel for histone was measured by surface plasmon resonance (SPR). Tryptophan fluorescence was used to determine wavelength shifts of the antibody panel upon binding to DNA and histone. Finally, circular dichroism spectroscopy was used to measure changes in secondary structure. SPR analysis revealed significant differences in histone binding affinity between members of the PL9-11 panel. The wavelength shifts of tryptophan fluorescence emission were found to be dependent on the antibody isotype, while circular dichroism analysis determined that changes in antibody secondary structure content differed between isotypes upon antigen binding. Thus, the antigen binding affinity is dependent on the particular constant region expressed. Moreover, the effects of antibody binding to antigen were also constant region dependent. Alteration of secondary structures influenced by constant regions may explain differences in fine specificity of anti-DNA antibodies between antibodies with similar variable regions, as well as cross-reactivity of anti-DNA antibodies with non-DNA antigens. Copyright © 2013 Elsevier Ltd. All rights reserved.

Assessment of the reliability of data collected for the Department of Veterans Affairs national surgical quality improvement program.

PubMed

Davis, Chester L; Pierce, John R; Henderson, William; Spencer, C David; Tyler, Christine; Langberg, Robert; Swafford, Jennan; Felan, Gladys S; Kearns, Martha A; Booker, Brigitte

2007-04-01

The Office of the Medical Inspector of the Department of Veterans Affairs (VA) studied the reliability of data collected by the VA's National Surgical Quality Improvement Program (NSQIP). The study focused on case selection bias, accuracy of reports on patients who died, and interrater reliability measurements of patient risk variables and outcomes. Surgical data from a sample of 15 VA medical centers were analyzed. For case selection bias, reviewers applied NSQIP criteria to include or exclude 2,460 patients from the database, comparing their results with those of NSQIP staff. For accurate reporting of patients who died, reviewers compared Social Security numbers of 10,444 NSQIP records with those found in the VA Beneficiary Identification and Records Locator Subsystem, VA Patient Treatment Files, and Social Security Administration death files. For measurement of interrater reliability, reviewers reabstracted 59 variables in each of 550 patient medical records that also were recorded in the NSQIP database. On case selection bias, the reviewers agreed with NSQIP decisions on 2,418 (98%) of the 2,460 cases. Computer record matching identified 4 more deaths than the NSQIP total of 198, a difference of about 2%. For 52 of the categorical variables, agreement, uncorrected for chance, was 96%. For 48 of 52 categorical variables, kappas ranged from 0.61 to 1.0 (substantial to almost perfect agreement); none of the variables had kappas of less than 0.20 (slight to poor agreement). This sample of medical centers shows adherence to criteria in selecting cases for the NSQIP database, for reporting deaths, and for collecting patient risk variables.

Regression Methods for Categorical Dependent Variables: Effects on a Model of Student College Choice

ERIC Educational Resources Information Center

Rapp, Kelly E.

2012-01-01

The use of categorical dependent variables with the classical linear regression model (CLRM) violates many of the model's assumptions and may result in biased estimates (Long, 1997; O'Connell, Goldstein, Rogers, & Peng, 2008). Many dependent variables of interest to educational researchers (e.g., professorial rank, educational attainment) are…

A two-phase sampling survey for nonresponse and its paradata to correct nonresponse bias in a health surveillance survey.

PubMed

Santin, G; Bénézet, L; Geoffroy-Perez, B; Bouyer, J; Guéguen, A

2017-02-01

The decline in participation rates in surveys, including epidemiological surveillance surveys, has become a real concern since it may increase nonresponse bias. The aim of this study is to estimate the contribution of a complementary survey among a subsample of nonrespondents, and the additional contribution of paradata in correcting for nonresponse bias in an occupational health surveillance survey. In 2010, 10,000 workers were randomly selected and sent a postal questionnaire. Sociodemographic data were available for the whole sample. After data collection of the questionnaires, a complementary survey among a random subsample of 500 nonrespondents was performed using a questionnaire administered by an interviewer. Paradata were collected for the complete subsample of the complementary survey. Nonresponse bias in the initial sample and in the combined samples were assessed using variables from administrative databases available for the whole sample, not subject to differential measurement errors. Corrected prevalences by reweighting technique were estimated by first using the initial survey alone and then the initial and complementary surveys combined, under several assumptions regarding the missing data process. Results were compared by computing relative errors. The response rates of the initial and complementary surveys were 23.6% and 62.6%, respectively. For the initial and the combined surveys, the relative errors decreased after correction for nonresponse on sociodemographic variables. For the combined surveys without paradata, relative errors decreased compared with the initial survey. The contribution of the paradata was weak. When a complex descriptive survey has a low response rate, a short complementary survey among nonrespondents with a protocol which aims to maximize the response rates, is useful. The contribution of sociodemographic variables in correcting for nonresponse bias is important whereas the additional contribution of paradata in correcting for nonresponse bias is questionable. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

A two centre observational study of simultaneous pulse oximetry and arterial oxygen saturation recordings in intensive care unit patients.

PubMed

Ebmeier, S J; Barker, M; Bacon, M; Beasley, R C; Bellomo, R; Knee Chong, C; Eastwood, G M; Gilchrist, J; Kagaya, H; Pilcher, J; Reddy, S K; Ridgeon, E; Sarma, N; Sprogis, S; Tanaka, A; Tweedie, M; Weatherall, M; Young, P J

2018-05-01

The influence of variables that might affect the accuracy of pulse oximetry (SpO₂) recordings in critically ill patients is not well established. We sought to describe the relationship between paired SpO₂/SaO₂ (oxygen saturation via arterial blood gas analysis) in adult intensive care unit (ICU) patients and to describe the diagnostic performance of SpO₂ in detecting low SaO₂ and PaO₂. A paired SpO₂/SaO₂ measurement was obtained from 404 adults in ICU. Measurements were used to calculate bias, precision, and limits of agreement. Associations between bias and variables including vasopressor and inotrope use, capillary refill time, hand temperature, pulse pressure, body temperature, oximeter model, and skin colour were estimated. There was no overall statistically significant bias in paired SpO₂/SaO₂ measurements; observed limits of agreement were +/-4.4%. However, body temperature, oximeter model, and skin colour, were statistically significantly associated with the degree of bias. SpO₂ <89% had a sensitivity of 3/7 (42.9%; 95% confidence intervals, CI, 9.9% to 81.6%) and a specificity of 344/384 (89.6%; 95% CI 86.1% to 92.5%) for detecting SaO₂ <89%. The absence of statistically significant bias in paired SpO₂/SaO₂ in adult ICU patients provides support for the use of pulse oximetry to titrate oxygen therapy. However, SpO₂ recordings alone should be used cautiously when SaO₂ recordings of 4.4% higher or lower than the observed SpO₂ would be of concern. A range of variables relevant to the critically ill had little or no effect on bias.

SU-F-I-80: Correction for Bias in a Channelized Hotelling Model Observer Caused by Temporally Variable Non-Stationary Noise

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

Favazza, C; Fetterly, K

2016-06-15

Purpose: Application of a channelized Hotelling model observer (CHO) over a wide range of x-ray angiography detector target dose (DTD) levels demonstrated substantial bias for conditions yielding low detectability indices (d’), including low DTD and small test objects. The purpose of this work was to develop theory and methods to correct this bias. Methods: A hypothesis was developed wherein the measured detectability index (d’b) for a known test object is positively biased by temporally variable non-stationary noise in the images. Hotelling’s T2 test statistic provided the foundation for a mathematical theory which accounts for independent contributions to the measured d’bmore » value from both the test object (d’o) and non-stationary noise (d’ns). Experimental methods were developed to directly estimate d’o by determining d’ns and subtracting it from d’b, in accordance with the theory. Specifically, d’ns was determined from two sets of images from which the traditional test object was withheld. This method was applied to angiography images with DTD levels in the range 0 to 240 nGy and for disk-shaped iodine-based contrast targets with diameters 0.5 to 4.0 mm. Results: Bias in d’ was evidenced by d’b values which exceeded values expected from a quantum limited imaging system and decreasing object size and DTD. d’ns increased with decreasing DTD, reaching a maximum of 2.6 for DTD = 0. Bias-corrected d’o estimates demonstrated sub-quantum limited performance of the x-ray angiography for low DTD. Findings demonstrated that the source of non-stationary noise was detector electronic readout noise. Conclusion: Theory and methods to estimate and correct bias in CHO measurements from temporally variable non-stationary noise were presented. The temporal non-stationary noise was shown to be due to electronic readout noise. This method facilitates accurate estimates of d’ values over a large range of object size and detector target dose.« less

A high-throughput platform for population reformatting and mammalian expression of phage display libraries to enable functional screening as full-length IgG.

PubMed

Xiao, Xiaodong; Douthwaite, Julie A; Chen, Yan; Kemp, Ben; Kidd, Sara; Percival-Alwyn, Jennifer; Smith, Alison; Goode, Kate; Swerdlow, Bonnie; Lowe, David; Wu, Herren; Dall'Acqua, William F; Chowdhury, Partha S

Phage display antibody libraries are a rich resource for discovery of potential therapeutic antibodies. Single-chain variable fragment (scFv) libraries are the most common format due to the efficient display of scFv by phage particles and the ease by which soluble scFv antibodies can be expressed for high-throughput screening. Typically, a cascade of screening and triaging activities are performed, beginning with the assessment of large numbers of E. coli-expressed scFv, and progressing through additional assays with individual reformatting of the most promising scFv to full-length IgG. However, use of high-throughput screening of scFv for the discovery of full-length IgG is not ideal because of the differences between these molecules. Furthermore, the reformatting step represents a bottle neck in the process because each antibody has to be handled individually to preserve the unique VH and VL pairing. These problems could be resolved if populations of scFv could be reformatted to full-length IgG before screening without disrupting the variable region pairing. Here, we describe a novel strategy that allows the reformatting of diverse populations of scFv from phage selections to full-length IgG in a batch format. The reformatting process maintains the diversity and variable region pairing with high fidelity, and the resulted IgG pool enables high-throughput expression of IgG in mammalian cells and cell-based functional screening. The improved process led to the discovery of potent candidates that are comparable or better than those obtained by traditional methods. This strategy should also be readily applicable to Fab-based phage libraries. Our approach, Screening in Product Format (SiPF), represents a substantial improvement in the field of antibody discovery using phage display.

The causal effects of home care use on institutional long-term care utilization and expenditures.

PubMed

Guo, Jing; Konetzka, R Tamara; Manning, Willard G

2015-03-01

Limited evidence exists on whether expanding home care saves money overall or how much institutional long-term care can be reduced. This paper estimates the causal effect of Medicaid-financed home care services on the costs and utilization of institutional long-term care using Medicaid claims data. A unique instrumental variable was applied to address the potential bias caused by omitted variables or reverse effect of institutional care use. We find that the use of Medicaid-financed home care services significantly reduced but only partially offset utilization and Medicaid expenditures on nursing facility services. A $1000 increase in Medicaid home care expenditures avoided 2.75 days in nursing facilities and reduced annual Medicaid nursing facility costs by $351 among people over age 65 when selection bias is addressed. Failure to address selection biases would misestimate the substitution and offset effects. Copyright © 2015 John Wiley & Sons, Ltd.

Variable-bias coin tossing

NASA Astrophysics Data System (ADS)

Colbeck, Roger; Kent, Adrian

2006-03-01

Alice is a charismatic quantum cryptographer who believes her parties are unmissable; Bob is a (relatively) glamorous string theorist who believes he is an indispensable guest. To prevent possibly traumatic collisions of self-perception and reality, their social code requires that decisions about invitation or acceptance be made via a cryptographically secure variable-bias coin toss (VBCT). This generates a shared random bit by the toss of a coin whose bias is secretly chosen, within a stipulated range, by one of the parties; the other party learns only the random bit. Thus one party can secretly influence the outcome, while both can save face by blaming any negative decisions on bad luck. We describe here some cryptographic VBCT protocols whose security is guaranteed by quantum theory and the impossibility of superluminal signaling, setting our results in the context of a general discussion of secure two-party computation. We also briefly discuss other cryptographic applications of VBCT.

Next-Generation DNA Sequencing of VH/VL Repertoires: A Primer and Guide to Applications in Single-Domain Antibody Discovery.

PubMed

Henry, Kevin A

2018-01-01

Immunogenetic analyses of expressed antibody repertoires are becoming increasingly common experimental investigations and are critical to furthering our understanding of autoimmunity, infectious disease, and cancer. Next-generation DNA sequencing (NGS) technologies have now made it possible to interrogate antibody repertoires to unprecedented depths, typically by sequencing of cDNAs encoding immunoglobulin variable domains. In this chapter, we describe simple, fast, and reliable methods for producing and sequencing multiplex PCR amplicons derived from the variable regions (V H , V H H or V L ) of rearranged immunoglobulin heavy and light chain genes using the Illumina MiSeq platform. We include complete protocols and primer sets for amplicon sequencing of V H /V H H/V L repertoires directly from human, mouse, and llama lymphocytes as well as from phage-displayed V H /V H H/V L libraries; these can be easily be adapted to other types of amplicons with little modification. The resulting amplicons are diverse and representative, even using as few as 10 3 input B cells, and their generation is relatively inexpensive, requiring no special equipment and only a limited set of primers. In the absence of heavy-light chain pairing, single-domain antibodies are uniquely amenable to NGS analyses. We present a number of applications of NGS technology useful in discovery of single-domain antibodies from phage display libraries, including: (i) assessment of library functionality; (ii) confirmation of desired library randomization; (iii) estimation of library diversity; and (iv) monitoring the progress of panning experiments. While the case studies presented here are of phage-displayed single-domain antibody libraries, the principles extend to other types of in vitro display libraries.

Immunoglobulin Heavy Chain Variable Region and Major Histocompatibility Region Genes Are Linked to Induced Graves' Disease in Females From Two Very Large Families of Recombinant Inbred Mice

PubMed Central

Aliesky, Holly; Banuelos, Bianca; Magana, Jessica; Williams, Robert W.; Rapoport, Basil

2014-01-01

Graves' hyperthyroidism is caused by antibodies to the TSH receptor (TSHR) that mimic thyroid stimulation by TSH. Stimulating TSHR antibodies and hyperthyroidism can be induced by immunizing mice with adenovirus expressing the human TSHR A-subunit. Prior analysis of induced Graves' disease in small families of recombinant inbred (RI) female mice demonstrated strong genetic control but did not resolve trait loci for TSHR antibodies or elevated serum T4. We investigated the genetic basis for induced Graves' disease in female mice of two large RI families and combined data with earlier findings to provide phenotypes for 178 genotypes. TSHR antibodies measured by inhibition of TSH binding to its receptor were highly significantly linked in the BXD set to the major histocompatibility region (chromosome 17), consistent with observations in 3 other RI families. In the LXS family, we detected linkage between T4 levels after TSHR-adenovirus immunization and the Ig heavy chain variable region (Igvh, chromosome 12). This observation is a key finding because components of the antigen binding region of Igs determine antibody specificity and have been previously linked to induced thyroid-stimulating antibodies. Data from the LXS family provide the first evidence in mice of a direct link between induced hyperthyroidism and Igvh genes. A role for major histocompatibility genes has now been established for genetic susceptibility to Graves' disease in both humans and mice. Future studies using arrays incorporating variation in the complex human Ig gene locus will be necessary to determine whether Igvh genes are also linked to Graves' disease in humans. PMID:25051451

A potent human anti-eotaxin1 antibody, CAT-213: isolation by phage display and in vitro and in vivo efficacy.

PubMed

Main, Sarah; Handy, Rachel; Wilton, Jane; Smith, Stephen; Williams, Liz; Fou, Leila Du; Andrews, John; Conroy, Louise A; May, Richard; Anderson, Ian; Vaughan, Tristan J

2006-12-01

The CC chemokine, eotaxin1 (CCL11) is an important regulator of eosinophil function. A marked accumulation of eosinophils in tissues has been correlated with the up-regulation of eotaxin1 expression in several diseases. The potential therapeutic value of neutralizing the effects of eotaxin1 in inflammatory conditions (including asthma) is under investigation. A human single-chain fragment variable antibody that neutralizes human eotaxin1 (CAT-212) was produced using antibody phage display and converted to whole antibody IgG4 format (CAT-213). A novel approach to lead optimization in which the length of the variable heavy chain complementarity-determining region 3 was reduced by one amino acid resulted in an increase in potency of >1000-fold compared with the parent anti-eotaxin1 antibody. The optimized antibody binds eotaxin1 with high affinity (80.4 pM) and specificity. CAT-213 and CAT-212 do not bind or neutralize a range of other human proteins including human monocyte chemoattractant protein-1, a structurally similar chemokine. CAT-213 neutralizes the ability of eotaxin1 to cause an increase in intracellular calcium signaling (with an IC(50) value of 2.86 nM), migration of CCR3-expressing L1.2 cells (with an IC(50) value of 0.48 nM), and inhibition of the eotaxin1-evoked shape change of human eosinophils in vitro (with an IC(50) of 0.71 nM). Local administration of CAT-213 to mice (1-100 microg kg(-1)) attenuates dermal eosinophilia induced by human eotaxin1, achieving >90% inhibition of eosinophil influx. CAT-213 may therefore be of therapeutic value in inhibiting diseases in which eotaxin1 and eosinophils play a major role, for example, severe asthma.

Primary antibody deficiencies at Queen Rania Children Hospital in Jordan: single center experience.

PubMed

Habahbeh, Zeyad M; Abu-Shukair, Mohammad E; Almutereen, Mohammad A; Alzyoud, Raed M; Wahadneh, Adel M

2014-03-01

Primary antibody deficiency, the most common primary immunodeficiency disorder, represents a heterogeneous spectrum of conditions caused by a defect in any critical stage of B cell development and is characterized by impaired production of normal amounts of antigen-specific antibodies. This retrospective study aimed at description and analysis of demographic, clinical, immunological features and complications of subjects diagnosed with primary antibody deficiency at a referral center in Jordan. The medical records of pediatric patients who were diagnosed as primary antibody deficiency (PAD) during the period from January 2006 to June 2013 were reviewed. Patients were diagnosed as PADs based on the Pan-American Group for Immunodeficiency (PAGID) and the European Society for Immunodeficiency (ESID) diagnostic criteria. A total number of 53 patients with PAD were identified; 37(70%) males and 16(30%) females, 16(30%) patients with congenital agammaglobulinemia, 16(30%) patients with common variable immunodeficiency, 4(7.5%) patients with IgG subclass deficiency, 10(19%) cases with transient hypogammaglobulinemia of infancy and 7(13.5%) patients as undefined PAD. The most common infection among patients was pneumonia (62%); followed by suppurative otitis media in 49% of patients. Cytopenia was the most noted autoimmune association and was found at prevalence of 22 %, other autoimmune associations (17%) including inflammatory arthritis, discoid lupus, inflammatory bowel disease, vasculitis and celiac disease. The prevalence of long-term complications was 58%, the most frequent ones were; stunted growth in 13%, bronchiectasis and lymphoproliferation in 11% for each. Our results indicated that congenital agammaglobulinemia and common variable immunodeficiency are the most frequent primary antibody deficiency in our patients. The awareness of families, general population as well as primary health physicians is crucial in the establishment of early diagnosis and prompt commencement of appropriate therapy for PADs.

Highly sensitive and unbiased approach for elucidating antibody repertoires

PubMed Central

Lin, Sherry G.; Ba, Zhaoqing; Du, Zhou; Zhang, Yu; Hu, Jiazhi; Alt, Frederick W.

2016-01-01

Developing B lymphocytes undergo V(D)J recombination to assemble germ-line V, D, and J gene segments into exons that encode the antigen-binding variable region of Ig heavy (H) and light (L) chains. IgH and IgL chains associate to form the B-cell receptor (BCR), which, upon antigen binding, activates B cells to secrete BCR as an antibody. Each of the huge number of clonally independent B cells expresses a unique set of IgH and IgL variable regions. The ability of V(D)J recombination to generate vast primary B-cell repertoires results from a combinatorial assortment of large numbers of different V, D, and J segments, coupled with diversification of the junctions between them to generate the complementary determining region 3 (CDR3) for antigen contact. Approaches to evaluate in depth the content of primary antibody repertoires and, ultimately, to study how they are further molded by secondary mutation and affinity maturation processes are of great importance to the B-cell development, vaccine, and antibody fields. We now describe an unbiased, sensitive, and readily accessible assay, referred to as high-throughput genome-wide translocation sequencing-adapted repertoire sequencing (HTGTS-Rep-seq), to quantify antibody repertoires. HTGTS-Rep-seq quantitatively identifies the vast majority of IgH and IgL V(D)J exons, including their unique CDR3 sequences, from progenitor and mature mouse B lineage cells via the use of specific J primers. HTGTS-Rep-seq also accurately quantifies DJH intermediates and V(D)J exons in either productive or nonproductive configurations. HTGTS-Rep-seq should be useful for studies of human samples, including clonal B-cell expansions, and also for following antibody affinity maturation processes. PMID:27354528

Fermentanomics: Relating quality attributes of a monoclonal antibody to cell culture process variables and raw materials using multivariate data analysis.

PubMed

Rathore, Anurag S; Kumar Singh, Sumit; Pathak, Mili; Read, Erik K; Brorson, Kurt A; Agarabi, Cyrus D; Khan, Mansoor

2015-01-01

Fermentanomics is an emerging field of research and involves understanding the underlying controlled process variables and their effect on process yield and product quality. Although major advancements have occurred in process analytics over the past two decades, accurate real-time measurement of significant quality attributes for a biotech product during production culture is still not feasible. Researchers have used an amalgam of process models and analytical measurements for monitoring and process control during production. This article focuses on using multivariate data analysis as a tool for monitoring the internal bioreactor dynamics, the metabolic state of the cell, and interactions among them during culture. Quality attributes of the monoclonal antibody product that were monitored include glycosylation profile of the final product along with process attributes, such as viable cell density and level of antibody expression. These were related to process variables, raw materials components of the chemically defined hybridoma media, concentration of metabolites formed during the course of the culture, aeration-related parameters, and supplemented raw materials such as glucose, methionine, threonine, tryptophan, and tyrosine. This article demonstrates the utility of multivariate data analysis for correlating the product quality attributes (especially glycosylation) to process variables and raw materials (especially amino acid supplements in cell culture media). The proposed approach can be applied for process optimization to increase product expression, improve consistency of product quality, and target the desired quality attribute profile. © 2015 American Institute of Chemical Engineers.

Cross-talk between clinical and host-response parameters of periodontitis in smokers.

PubMed

Nagarajan, R; Miller, C S; Dawson, D; Al-Sabbagh, M; Ebersole, J L

2017-06-01

Periodontal diseases are a major public health concern leading to tooth loss and have also been shown to be associated with several chronic systemic diseases. Smoking is a major risk factor for the development of numerous systemic diseases, as well as periodontitis. While it is clear that smokers have a significantly enhanced risk for developing periodontitis leading to tooth loss, the population varies regarding susceptibility to disease associated with smoking. This investigation focused on identifying differences in four broad sets of variables, consisting of: (i) host-response molecules; (ii) periodontal clinical parameters; (iii) antibody responses to periodontal pathogens and oral commensal bacteria; and (iv) other variables of interest, in a population of smokers with (n = 171) and without (n = 117) periodontitis. Bayesian network structured learning (BNSL) techniques were used to investigate potential associations and cross-talk between the four broad sets of variables. BNSL revealed two broad communities with markedly different topology between the populations of smokers, with and without periodontitis. Confidence of the edges in the resulting network also showed marked variations within and between the periodontitis and nonperiodontitis groups. The results presented validated known associations and discovered new ones with minimal precedence that may warrant further investigation and novel hypothesis generation. Cross-talk between the clinical variables and antibody profiles of bacteria were especially pronounced in the case of periodontitis and were mediated by the antibody response profile to Porphyromonas gingivalis. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Cross-talk between Clinical and Host Response Parameters of Periodontitis in Smokers

PubMed Central

Nagarajan, R.; Miller, C.S.; Dawson, D.; Al-Sabbagh, M.; Ebersole, J.L.

2016-01-01

Periodontal diseases are a major public health concern leading to tooth loss and also shown to be associated with several chronic systemic diseases. Smoking is a major risk factor for developing numerous systemic diseases, as well as periodontitis. While it is clear that smokers have a significantly enhanced risk for developing periodontitis leading to tooth loss, the population varies with regards to susceptibility to disease associated with smoking. This investigation focuses on identifying differences in four broad sets of variables consisting of: (a) host response molecules, (b) periodontal clinical parameters, (c) antibody measures for periodontal pathogens and oral commensal bacteria challenge, and (d) other variables of interest in a smoking population with (n = 171) and without periodontitis (n = 117). Subsequently, Bayesian network structured learning techniques (BNSL) techniques were used to investigate potential associations and cross-talk between the four broad sets of variables. BNSL revealed two broad communities with markedly different topology between the non-periodontitis and periodontitis smoking population. Confidence of the edges in the resulting network also showed marked variations within and between the periodontitis and non-periodontitis groups. The results presented validated known associations, as well as discovered new ones with minimal precedence that may warrant further investigation and novel hypothesis generation. Cross-talk between the clinical variables and antibody profiles of bacteria were especially pronounced in the case of periodontitis and mediated by the antibody response profile to P. gingivalis. PMID:27431617

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

PubMed Central

2015-01-01

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide. PMID:25838811

Bioreactor process parameter screening utilizing a Plackett-Burman design for a model monoclonal antibody.

PubMed

Agarabi, Cyrus D; Schiel, John E; Lute, Scott C; Chavez, Brittany K; Boyne, Michael T; Brorson, Kurt A; Khan, Mansoora; Read, Erik K

2015-06-01

Consistent high-quality antibody yield is a key goal for cell culture bioprocessing. This endpoint is typically achieved in commercial settings through product and process engineering of bioreactor parameters during development. When the process is complex and not optimized, small changes in composition and control may yield a finished product of less desirable quality. Therefore, changes proposed to currently validated processes usually require justification and are reported to the US FDA for approval. Recently, design-of-experiments-based approaches have been explored to rapidly and efficiently achieve this goal of optimized yield with a better understanding of product and process variables that affect a product's critical quality attributes. Here, we present a laboratory-scale model culture where we apply a Plackett-Burman screening design to parallel cultures to study the main effects of 11 process variables. This exercise allowed us to determine the relative importance of these variables and identify the most important factors to be further optimized in order to control both desirable and undesirable glycan profiles. We found engineering changes relating to culture temperature and nonessential amino acid supplementation significantly impacted glycan profiles associated with fucosylation, β-galactosylation, and sialylation. All of these are important for monoclonal antibody product quality. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Positive bias is a defining characteristic of aging to the same extent as declining performance.

PubMed

Simón, Teresa; Suengas, Aurora G; Ruiz-Gallego-Largo, Trinidad; Bandrés, Javier

2013-01-01

The aim of this study was to analyze whether one of the supposed gains of aging--positive bias--discriminates between young and older participants to the same extent as some of the losses in cognitive performance--recall and source monitoring--that come with age. Two age groups (N = 120)--young (M = 22.08, SD = 3.30) and older (M = 72.78, SD = 6.57)--carried out three tasks with varying levels of difficulty that included recall, recognition, and source monitoring using pictures, faces, and personal descriptors exchanged in a conversation as stimuli. The results of the discriminant analysis performed on 20 dependent variables indicated that six of them were key in discriminating between young and older participants. Younger participants outperformed older participants in recalling pictures, and in recognizing the descriptors exchanged in a conversation, as well as in monitoring their source. Just as important in discriminating between the two groups were the ability to recognize previously seen pictures, the likability rating they produced, and the recognition of faces with positive expressions--all superior in older participants. Thus, variables related to a positive bias--likability ratings and recognition of positive expressions--characterize the differences as a function of age as well as variables related to cognitive performance, such as recall and source monitoring. In addition, the likability ratings evoked by both pictures and faces were also significantly higher in the older participants with better cognitive performance than in those who performed poorly. This effect was not present in younger participants. The results are interpreted within the framework of socioemotional selectivity theory as evidence for a positive bias in old age. The connection between a positive bias and the maintenance of cognitive performance is also discussed.

Quality requirements for veterinary hematology analyzers in small animals-a survey about veterinary experts' requirements and objective evaluation of analyzer performance based on a meta-analysis of method validation studies: bench top hematology analyzer.

PubMed

Cook, Andrea M; Moritz, Andreas; Freeman, Kathleen P; Bauer, Natali

2016-09-01

Scarce information exists about quality requirements and objective evaluation of performance of large veterinary bench top hematology analyzers. The study was aimed at comparing the observed total error (TEobs ) derived from meta-analysis of published method validation data to the total allowable error (TEa ) for veterinary hematology variables in small animals based on experts' opinions. Ideally, TEobs should be < TEa . An online survey was sent to veterinary experts in clinical pathology and small animal internal medicine for providing the maximal allowable deviation from a given result for each variable. Percent of TEa = (allowable median deviation/clinical threshold) * 100%. Second, TEobs for 3 laser-based bench top hematology analyzers (ADVIA 2120; Sysmex XT2000iV, and CellDyn 3500) was calculated based on method validation studies published between 2005 and 2013 (n = 4). The percent TEobs = 2 * CV (%) + bias (%). The CV was derived from published studies except for the ADVIA 2120 (internal data), and bias was estimated from the regression equation. A total of 41 veterinary experts (19 diplomates, 8 residents, 10 postgraduate students, 4 anonymous specialists) responded. The proposed range of TEa was wide, but generally ≤ 20%. The TEobs was < TEa for all variables and analyzers except for canine and feline HGB (high bias, low CV) and platelet counts (high bias, high CV). Overall, veterinary bench top analyzers fulfilled experts' requirements except for HGB due to method-related bias, and platelet counts due to known preanalytic/analytic issues. © 2016 American Society for Veterinary Clinical Pathology.

Global longitudinal strain software upgrade: Implications for intervendor consistency and longitudinal imaging studies.

PubMed

Castel, Anne-Laure; Menet, Aymeric; Ennezat, Pierre-Vladimir; Delelis, François; Le Goffic, Caroline; Binda, Camille; Guerbaai, Raphaëlle-Ashley; Levy, Franck; Graux, Pierre; Tribouilloy, Christophe; Maréchaux, Sylvestre

2016-01-01

Speckle tracking can be used to measure left ventricular global longitudinal strain (GLS). To study the effect of speckle tracking software product upgrades on GLS values and intervendor consistency. Subjects (patients or healthy volunteers) underwent systematic echocardiography with equipment from Philips and GE, without a change in their position. Off-line post-processing for GLS assessment was performed with the former and most recent upgrades from these two vendors (Philips QLAB 9.0 and 10.2; GE EchoPAC 12.1 and 13.1.1). GLS was obtained in three myocardial layers with EchoPAC 13.1.1. Intersoftware and intervendor consistency was assessed. Interobserver variability was tested in a subset of patients. Among 73 subjects (65 patients and 8 healthy volunteers), absolute values of GLS were higher with QLAB 10.2 compared with 9.0 (intraclass correlation coefficient [ICC]: 0.88; bias: 2.2%). Agreement between EchoPAC 13.1.1 and 12.1 varied by myocardial layer (13.1.1 only): midwall (ICC: 0.95; bias: -1.1%), endocardium (ICC: 0.93; bias: 1.6%) and epicardial (ICC: 0.80; bias: -3.3%). Although GLS was comparable for QLAB 9.0 versus EchoPAC 12.1 (ICC: 0.95; bias: 0.5%), the agreement was lower between QLAB 10.2 and EchoPAC 13.1.1 endocardial (ICC: 0.91; bias: 1.1%), midwall (ICC: 0.73; bias: 3.9%) and epicardial (ICC: 0.54; bias: 6.0%). Interobserver variability of all software products in a subset of 20 patients was excellent (ICC: 0.97-0.99; bias: -0.8 to 1.0%). Upgrades of speckle tracking software may be associated with significant changes in GLS values, which could affect intersoftware and intervendor consistency. This finding has important clinical implications for the longitudinal follow-up of patients with speckle tracking echocardiography. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires.

PubMed

DeKosky, Brandon J; Lungu, Oana I; Park, Daechan; Johnson, Erik L; Charab, Wissam; Chrysostomou, Constantine; Kuroda, Daisuke; Ellington, Andrew D; Ippolito, Gregory C; Gray, Jeffrey J; Georgiou, George

2016-05-10

Elucidating how antigen exposure and selection shape the human antibody repertoire is fundamental to our understanding of B-cell immunity. We sequenced the paired heavy- and light-chain variable regions (VH and VL, respectively) from large populations of single B cells combined with computational modeling of antibody structures to evaluate sequence and structural features of human antibody repertoires at unprecedented depth. Analysis of a dataset comprising 55,000 antibody clusters from CD19(+)CD20(+)CD27(-) IgM-naive B cells, >120,000 antibody clusters from CD19(+)CD20(+)CD27(+) antigen-experienced B cells, and >2,000 RosettaAntibody-predicted structural models across three healthy donors led to a number of key findings: (i) VH and VL gene sequences pair in a combinatorial fashion without detectable pairing restrictions at the population level; (ii) certain VH:VL gene pairs were significantly enriched or depleted in the antigen-experienced repertoire relative to the naive repertoire; (iii) antigen selection increased antibody paratope net charge and solvent-accessible surface area; and (iv) public heavy-chain third complementarity-determining region (CDR-H3) antibodies in the antigen-experienced repertoire showed signs of convergent paired light-chain genetic signatures, including shared light-chain third complementarity-determining region (CDR-L3) amino acid sequences and/or Vκ,λ-Jκ,λ genes. The data reported here address several longstanding questions regarding antibody repertoire selection and development and provide a benchmark for future repertoire-scale analyses of antibody responses to vaccination and disease.

Designed Ankyrin Repeat Proteins: A New Approach to Mimic Complex Antigens for Diagnostic Purposes?

PubMed Central

Hausammann, Stefanie; Vogel, Monique; Kremer Hovinga, Johanna A.; Lacroix-Desmazes, Sebastien; Stadler, Beda M.; Horn, Michael P.

2013-01-01

Inhibitory antibodies directed against coagulation factor VIII (FVIII) can be found in patients with acquired and congenital hemophilia A. Such FVIII-inhibiting antibodies are routinely detected by the functional Bethesda Assay. However, this assay has a low sensitivity and shows a high inter-laboratory variability. Another method to detect antibodies recognizing FVIII is ELISA, but this test does not allow the distinction between inhibitory and non-inhibitory antibodies. Therefore, we aimed at replacing the intricate antigen FVIII by Designed Ankyrin Repeat Proteins (DARPins) mimicking the epitopes of FVIII inhibitors. As a model we used the well-described inhibitory human monoclonal anti-FVIII antibody, Bo2C11, for the selection on DARPin libraries. Two DARPins were selected binding to the antigen-binding site of Bo2C11, which mimic thus a functional epitope on FVIII. These DARPins inhibited the binding of the antibody to its antigen and restored FVIII activity as determined in the Bethesda assay. Furthermore, the specific DARPins were able to recognize the target antibody in human plasma and could therefore be used to test for the presence of Bo2C11-like antibodies in a large set of hemophilia A patients. These data suggest, that our approach might be used to isolate epitopes from different sets of anti-FVIII antibodies in order to develop an ELISA-based screening assay allowing the distinction of inhibitory and non-inhibitory anti-FVIII antibodies according to their antibody signatures. PMID:23626669

North Tropical Atlantic Climate Variability and Model Biases

NASA Astrophysics Data System (ADS)

Yang, Y.

2017-12-01

Remote forcing from El Niño-Southern Oscillation (ENSO) and local ocean-atmosphere feedback are important for climate variability over the North Tropical Atlantic. These two factors are extracted by the ensemble mean and inter-member difference of a 10-member Pacific Ocean-Global Atmosphere (POGA) experiment, in which sea surface temperatures (SSTs) are restored to the observed anomalies over the tropical Pacific but fully coupled to the atmosphere elsewhere. POGA reasonably captures main features of observed North Tropical Atlantic variability. ENSO forced and local North Tropical Atlantic modes (NTAMs) develop with wind-evaporation-SST feedback, explaining one third and two thirds of total variance respectively. Notable biases, however, exist. The seasonality of the simulated NTAM is delayed by one month, due to the late development of the North Atlantic Oscillation (NAO) in the model. A spurious band of enhanced sea surface temperature (SST) variance (SBEV) is identified over the northern equatorial Atlantic in POGA and 14 out of 23 CMIP5 models. The SBEV is especially pronounced in boreal spring and due to the combined effect of both anomalous atmospheric thermal forcing and oceanic vertical upwelling. While the tropical North Atlantic variability is only weakly correlated with the Atlantic Zonal Mode (AZM) in observations, the SBEV in CMIP5 produces conditions that drive and intensify the AZM variability via triggering the Bjerknes feedback. This partially explains why AZM is strong in some CMIP5 models even though the equatorial cold tongue and easterly trades are biased low.

Real-time measurement system for evaluation of the carotid intima-media thickness with a robust edge operator.

PubMed

Faita, Francesco; Gemignani, Vincenzo; Bianchini, Elisabetta; Giannarelli, Chiara; Ghiadoni, Lorenzo; Demi, Marcello

2008-09-01

The purpose of this report is to describe an automatic real-time system for evaluation of the carotid intima-media thickness (CIMT) characterized by 3 main features: minimal interobserver and intraobserver variability, real-time capabilities, and great robustness against noise. One hundred fifty carotid B-mode ultrasound images were used to validate the system. Two skilled operators were involved in the analysis. Agreement with the gold standard, defined as the mean of 2 manual measurements of a skilled operator, and the interobserver and intraobserver variability were quantitatively evaluated by regression analysis and Bland-Altman statistics. The automatic measure of the CIMT showed a mean bias +/- SD of 0.001 +/- 0.035 mm toward the manual measurement. The intraobserver variability, evaluated with Bland-Altman plots, showed a bias that was not significantly different from 0, whereas the SD of the differences was greater in the manual analysis (0.038 mm) than in the automatic analysis (0.006 mm). For interobserver variability, the automatic measurement had a bias that was not significantly different from 0, with a satisfactory SD of the differences (0.01 mm), whereas in the manual measurement, a little bias was present (0.012 mm), and the SD of the differences was noticeably greater (0.044 mm). The CIMT has been accepted as a noninvasive marker of early vascular alteration. At present, the manual approach is largely used to estimate CIMT values. However, that method is highly operator dependent and time-consuming. For these reasons, we developed a new system for the CIMT measurement that conjugates precision with real-time analysis, thus providing considerable advantages in clinical practice.

Using Propensity Score Methods to Approximate Factorial Experimental Designs to Analyze the Relationship between Two Variables and an Outcome

ERIC Educational Resources Information Center

Dong, Nianbo

2015-01-01

Researchers have become increasingly interested in programs' main and interaction effects of two variables (A and B, e.g., two treatment variables or one treatment variable and one moderator) on outcomes. A challenge for estimating main and interaction effects is to eliminate selection bias across A-by-B groups. I introduce Rubin's causal model to…

A Framework for Integrating Implicit Bias Recognition Into Health Professions Education.

PubMed

Sukhera, Javeed; Watling, Chris

2018-01-01

Existing literature on implicit bias is fragmented and comes from a variety of fields like cognitive psychology, business ethics, and higher education, but implicit-bias-informed educational approaches have been underexplored in health professions education and are difficult to evaluate using existing tools. Despite increasing attention to implicit bias recognition and management in health professions education, many programs struggle to meaningfully integrate these topics into curricula. The authors propose a six-point actionable framework for integrating implicit bias recognition and management into health professions education that draws on the work of previous researchers and includes practical tools to guide curriculum developers. The six key features of this framework are creating a safe and nonthreatening learning context, increasing knowledge about the science of implicit bias, emphasizing how implicit bias influences behaviors and patient outcomes, increasing self-awareness of existing implicit biases, improving conscious efforts to overcome implicit bias, and enhancing awareness of how implicit bias influences others. Important considerations for designing implicit-bias-informed curricula-such as individual and contextual variables, as well as formal and informal cultural influences-are discussed. The authors also outline assessment and evaluation approaches that consider outcomes at individual, organizational, community, and societal levels. The proposed framework may facilitate future research and exploration regarding the use of implicit bias in health professions education.

Response of puppies to canine-origin parvovirus vaccines.

PubMed

Carmichael, L E; Pollock, R V; Joubert, J C

1984-02-01

Pups 9-18 1/2 weeks old were given a single dose of 1 of 4 commercial, live, canine-origin parvovirus vaccines. All 4 vaccines evoked high levels of antibody in seronegative pups, but variable response in those with low levels of maternally derived antibodies. Vaccinal virus spread to unvaccinated contact controls and elicited essentially equivalent titers. No clinical signs of parvovirus infection were observed in vaccinates or controls.

Related Mechanisms of Antibody Somatic Hypermutation and Class Switch Recombination

PubMed Central

HWANG, JOYCE K.; ALT, FREDERICK W.; YEAP, LENG-SIEW

2015-01-01

The primary antibody repertoire is generated by mechanisms involving the assembly of the exons that encode the antigen-binding variable regions of immunoglobulin heavy (IgH) and light (IgL) chains during the early development of B lymphocytes. After antigen-dependent activation, mature B lymphocytes can further alter their IgH and IgL variable region exons by the process of somatic hypermutation (SHM), which allows the selection of B cells in which SHMs resulted in the production of antibodies with increased antigen affinity. In addition, during antigen-dependent activation, B cells can also change the constant region of their IgH chain through a DNA double-strand-break (DSB) dependent process referred to as IgH class switch recombination (CSR), which generates B cell progeny that produce antibodies with different IgH constant region effector functions that are best suited for a elimination of a particular pathogen or in a particular setting. Both the mutations that underlie SHM and the DSBs that underlie CSR are initiated in target genes by activation-induced cytidine deaminase (AID). This review describes in depth the processes of SHM and CSR with a focus on mechanisms that direct AID cytidine deamination in activated B cells and mechanisms that promote the differential outcomes of such cytidine deamination. PMID:26104555

Using llama derived single domain antibodies to target botulinum neurotoxins

NASA Astrophysics Data System (ADS)

Swain, Marla D.; Anderson, George P.; Bernstein, Rachael D.; Liu, Jinny L.; Goldman, Ellen R.

2010-04-01

Llama serum contains both conventional IgG as well as unique forms of antibody that contain only heavy chains where antigen binding is mediated through a single variable domain. These variable domains can be expressed recombinantly and are referred to as single domain antibodies (sdAb). SdAb are among the smallest known naturally derived antigen binding fragments, possess good solubility, thermal stability, and can refold after heat and chemical denaturation. Llamas were immunized with either BoNT A or B toxoid and phage display libraries prepared. Single domain antibodies (sdAb) that were able to detect botulinum neurotoxin (BoNT) serotypes A and B were selected from their respective libraries. Here, the binders obtained by panning the BoNT B library on either BoNT B toxoid or BoNT B complex toxoid coated plates or BoNT B toxin coupled microspheres are described. Using these panning methods, we selected for binders that showed specificity for BoNT B. Phage displayed binders were screened, moved to a protein expression vector and soluble sdAb was produced. Using a Luminex flow cytometer binders were evaluated in direct binding assays. We have exploited the unique properties of sdAb and used them as biological recognition elements in immuno-based sensors that can detect BoNT B.

Rapid Detection of Bacillus anthracis Spores Using Immunomagnetic Separation and Amperometry

PubMed Central

Waller, David F.; Hew, Brian E.; Holdaway, Charlie; Jen, Michael; Peckham, Gabriel D.

2016-01-01

Portable detection and quantitation methods for Bacillus anthracis (anthrax) spores in pure culture or in environmental samples are lacking. Here, an amperometric immunoassay has been developed utilizing immunomagnetic separation to capture the spores and remove potential interferents from test samples followed by amperometric measurement on a field-portable instrument. Antibody-conjugated magnetic beads and antibody-conjugated glucose oxidase were used in a sandwich format for the capture and detection of target spores. Glucose oxidase activity of spore pellets was measured indirectly via amperometry by applying a bias voltage after incubation with glucose, horseradish peroxidase, and the electron mediator 2,2′-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid). Target capture was mediated by polyclonal antisera, whereas monoclonal antibodies were used for signal generation. This strategy maximized sensitivity (500 target spores, 5000 cfu/mL), while also providing a good specificity for Bacillus anthracis spores. Minimal signal deviation occurs in the presence of environmental interferents including soil and modified pH conditions, demonstrating the strengths of immunomagnetic separation. The simultaneous incubation of capture and detection antibodies and rapid substrate development (5 min) result in short sample-to-signal times (less than an hour). With attributes comparable or exceeding that of ELISA and LFDs, amperometry is a low-cost, low-weight, and practical method for detecting anthrax spores in the field. PMID:27999382

Implementation of Instrumental Variable Bounds for Data Missing Not at Random.

PubMed

Marden, Jessica R; Wang, Linbo; Tchetgen, Eric J Tchetgen; Walter, Stefan; Glymour, M Maria; Wirth, Kathleen E

2018-05-01

Instrumental variables are routinely used to recover a consistent estimator of an exposure causal effect in the presence of unmeasured confounding. Instrumental variable approaches to account for nonignorable missing data also exist but are less familiar to epidemiologists. Like instrumental variables for exposure causal effects, instrumental variables for missing data rely on exclusion restriction and instrumental variable relevance assumptions. Yet these two conditions alone are insufficient for point identification. For estimation, researchers have invoked a third assumption, typically involving fairly restrictive parametric constraints. Inferences can be sensitive to these parametric assumptions, which are typically not empirically testable. The purpose of our article is to discuss another approach for leveraging a valid instrumental variable. Although the approach is insufficient for nonparametric identification, it can nonetheless provide informative inferences about the presence, direction, and magnitude of selection bias, without invoking a third untestable parametric assumption. An important contribution of this article is an Excel spreadsheet tool that can be used to obtain empirical evidence of selection bias and calculate bounds and corresponding Bayesian 95% credible intervals for a nonidentifiable population proportion. For illustrative purposes, we used the spreadsheet tool to analyze HIV prevalence data collected by the 2007 Zambia Demographic and Health Survey (DHS).

Estimation and applications of size-biased distributions in forestry

Treesearch

Jeffrey H. Gove

2003-01-01

Size-biased distributions arise naturally in several contexts in forestry and ecology. Simple power relationships (e.g. basal area and diameter at breast height) between variables are one such area of interest arising from a modelling perspective. Another, probability proportional to size PPS) sampling, is found in the most widely used methods for sampling standing or...

Immunoglobulin gene usage in the human anti-pathogen response.

PubMed

Newkirk, M M; Rioux, J D

1995-09-01

The human antibody response to foreign pathogens is generated to a relatively small number of target surface proteins and carbohydrates that nonetheless have an extensive array of epitopes. The study of human monoclonal antibodies to different pathogens shows that there are a diversity of mechanisms used to generate a sufficient repertoire of antibodies to combat the invading pathogens. Although many different immunoglobulin gene elements are used to construct the anti-pathogen response, some elements are used more often than would be expected if all elements were used randomly. For example, the immune response to Haemophilus influenzae polysaccharide appears to be quite narrow, being restricted primarily to a specific heavy-chain gene, 3-15, and a lambda light-chain family II member, 4A. In contrast, for the immune response to cytomegalovirus proteins, a wider group of gene elements is needed. It is also surprising that despite an investigator bias for IgG- rather than IgM-secreting immortal B cells (because of their high affinity and neutralizing abilities), 26% of light chains and 13% of heavy chains showed a very low level of somatic mutation, equivalent to an IgM molecule that has not undergone affinity maturation. Although some highly mutated IgG molecules are present in the anti-pathogen response, most of the monoclonal antibodies specific for viruses or bacteria have a level of somatic hypermutation similar to that of the adult IgM repertoire. A number of studies have shown that there are similarities in the antibody responses to pathogens and to self (autoantibodies).(ABSTRACT TRUNCATED AT 250 WORDS)

Accounting for measurement error in log regression models with applications to accelerated testing.

PubMed

Richardson, Robert; Tolley, H Dennis; Evenson, William E; Lunt, Barry M

2018-01-01

In regression settings, parameter estimates will be biased when the explanatory variables are measured with error. This bias can significantly affect modeling goals. In particular, accelerated lifetime testing involves an extrapolation of the fitted model, and a small amount of bias in parameter estimates may result in a significant increase in the bias of the extrapolated predictions. Additionally, bias may arise when the stochastic component of a log regression model is assumed to be multiplicative when the actual underlying stochastic component is additive. To account for these possible sources of bias, a log regression model with measurement error and additive error is approximated by a weighted regression model which can be estimated using Iteratively Re-weighted Least Squares. Using the reduced Eyring equation in an accelerated testing setting, the model is compared to previously accepted approaches to modeling accelerated testing data with both simulations and real data.

A laboratory study of the electromagnetic bias of rough surface scattering by water waves

NASA Technical Reports Server (NTRS)

Parsons, Chester L.; Miller, Lee S.

1990-01-01

The design, development, and use of a focused-beam radar to measure the electromagnetic bias introduced by the scattering of radar waves by a roughened water surface are discussed. The bias measurements were made over wide ranges of environmental conditions in a wavetank laboratory. Wave-elevation data were provided by standard laboratory capacitance probes. Backscattered radar power measurements coincident in time and space with the elevation data were produced by the radar. The two data sets are histogrammed to produce probability density functions for elevation and radar reflectivity, from which the electromagnetic bias is computed. The experimental results demonstrate that the electromagnetic bias is quite variable over the wide range of environmental conditions that can be produced in the laboratory. The data suggest that the bias is dependent upon the local wind field and on the amplitude and frequency of any background wave field that is present.

Associations among selective attention, memory bias, cognitive errors and symptoms of anxiety in youth.

PubMed

Watts, Sarah E; Weems, Carl F

2006-12-01

The purpose of this study was to examine the linkages among selective attention, memory bias, cognitive errors, and anxiety problems by testing a model of the interrelations among these cognitive variables and childhood anxiety disorder symptoms. A community sample of 81 youth (38 females and 43 males) aged 9-17 years and their parents completed measures of the child's anxiety disorder symptoms. Youth completed assessments measuring selective attention, memory bias, and cognitive errors. Results indicated that selective attention, memory bias, and cognitive errors were each correlated with childhood anxiety problems and provide support for a cognitive model of anxiety which posits that these three biases are associated with childhood anxiety problems. Only limited support for significant interrelations among selective attention, memory bias, and cognitive errors was found. Finally, results point towards an effective strategy for moving the assessment of selective attention to younger and community samples of youth.

Nonlinear vs. linear biasing in Trp-cage folding simulations

NASA Astrophysics Data System (ADS)

Spiwok, Vojtěch; Oborský, Pavel; Pazúriková, Jana; Křenek, Aleš; Králová, Blanka

2015-03-01

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.

Nonlinear vs. linear biasing in Trp-cage folding simulations.

PubMed

Spiwok, Vojtěch; Oborský, Pavel; Pazúriková, Jana; Křenek, Aleš; Králová, Blanka

2015-03-21

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.

The impact of non-response bias due to sampling in public health studies: A comparison of voluntary versus mandatory recruitment in a Dutch national survey on adolescent health.

PubMed

Cheung, Kei Long; Ten Klooster, Peter M; Smit, Cees; de Vries, Hein; Pieterse, Marcel E

2017-03-23

In public health monitoring of young people it is critical to understand the effects of selective non-response, in particular when a controversial topic is involved like substance abuse or sexual behaviour. Research that is dependent upon voluntary subject participation is particularly vulnerable to sampling bias. As respondents whose participation is hardest to elicit on a voluntary basis are also more likely to report risk behaviour, this potentially leads to underestimation of risk factor prevalence. Inviting adolescents to participate in a home-sent postal survey is a typical voluntary recruitment strategy with high non-response, as opposed to mandatory participation during school time. This study examines the extent to which prevalence estimates of adolescent health-related characteristics are biased due to different sampling methods, and whether this also biases within-subject analyses. Cross-sectional datasets collected in 2011 in Twente and IJsselland, two similar and adjacent regions in the Netherlands, were used. In total, 9360 youngsters in a mandatory sample (Twente) and 1952 youngsters in a voluntary sample (IJsselland) participated in the study. To test whether the samples differed on health-related variables, we conducted both univariate and multivariable logistic regression analyses controlling for any demographic difference between the samples. Additional multivariable logistic regressions were conducted to examine moderating effects of sampling method on associations between health-related variables. As expected, females, older individuals, as well as individuals with higher education levels, were over-represented in the voluntary sample, compared to the mandatory sample. Respondents in the voluntary sample tended to smoke less, consume less alcohol (ever, lifetime, and past four weeks), have better mental health, have better subjective health status, have more positive school experiences and have less sexual intercourse than respondents in the mandatory sample. No moderating effects were found for sampling method on associations between variables. This is one of first studies to provide strong evidence that voluntary recruitment may lead to a strong non-response bias in health-related prevalence estimates in adolescents, as compared to mandatory recruitment. The resulting underestimation in prevalence of health behaviours and well-being measures appeared large, up to a four-fold lower proportion for self-reported alcohol consumption. Correlations between variables, though, appeared to be insensitive to sampling bias.

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.

PubMed

Liu, Xuejun; Shi, Xinxin; Chen, Chunlin; Zhang, Li

2015-10-16

The high-throughput sequencing technology, RNA-Seq, has been widely used to quantify gene and isoform expression in the study of transcriptome in recent years. Accurate expression measurement from the millions or billions of short generated reads is obstructed by difficulties. One is ambiguous mapping of reads to reference transcriptome caused by alternative splicing. This increases the uncertainty in estimating isoform expression. The other is non-uniformity of read distribution along the reference transcriptome due to positional, sequencing, mappability and other undiscovered sources of biases. This violates the uniform assumption of read distribution for many expression calculation approaches, such as the direct RPKM calculation and Poisson-based models. Many methods have been proposed to address these difficulties. Some approaches employ latent variable models to discover the underlying pattern of read sequencing. However, most of these methods make bias correction based on surrounding sequence contents and share the bias models by all genes. They therefore cannot estimate gene- and isoform-specific biases as revealed by recent studies. We propose a latent variable model, NLDMseq, to estimate gene and isoform expression. Our method adopts latent variables to model the unknown isoforms, from which reads originate, and the underlying percentage of multiple spliced variants. The isoform- and exon-specific read sequencing biases are modeled to account for the non-uniformity of read distribution, and are identified by utilizing the replicate information of multiple lanes of a single library run. We employ simulation and real data to verify the performance of our method in terms of accuracy in the calculation of gene and isoform expression. Results show that NLDMseq obtains competitive gene and isoform expression compared to popular alternatives. Finally, the proposed method is applied to the detection of differential expression (DE) to show its usefulness in the downstream analysis. The proposed NLDMseq method provides an approach to accurately estimate gene and isoform expression from RNA-Seq data by modeling the isoform- and exon-specific read sequencing biases. It makes use of a latent variable model to discover the hidden pattern of read sequencing. We have shown that it works well in both simulations and real datasets, and has competitive performance compared to popular methods. The method has been implemented as a freely available software which can be found at https://github.com/PUGEA/NLDMseq.

Cognitive determinants of affective forecasting errors

PubMed Central

Hoerger, Michael; Quirk, Stuart W.; Lucas, Richard E.; Carr, Thomas H.

2011-01-01

Often to the detriment of human decision making, people are prone to an impact bias when making affective forecasts, overestimating the emotional consequences of future events. The cognitive processes underlying the impact bias, and methods for correcting it, have been debated and warrant further exploration. In the present investigation, we examined both individual differences and contextual variables associated with cognitive processing in affective forecasting for an election. Results showed that the perceived importance of the event and working memory capacity were both associated with an increased impact bias for some participants, whereas retrieval interference had no relationship with bias. Additionally, an experimental manipulation effectively reduced biased forecasts, particularly among participants who were most distracted thinking about peripheral life events. These findings have direct theoretical implications for understanding the impact bias, highlight the importance of individual differences in affective forecasting, and have ramifications for future decision making research. The possible functional role of the impact bias is discussed within the context of evolutionary psychology. PMID:21912580

Protein-phosphotyrosine proteome profiling by superbinder-SH2 domain affinity purification mass spectrometry, sSH2-AP-MS.

PubMed

Tong, Jiefei; Cao, Biyin; Martyn, Gregory D; Krieger, Jonathan R; Taylor, Paul; Yates, Bradley; Sidhu, Sachdev S; Li, Shawn S C; Mao, Xinliang; Moran, Michael F

2017-03-01

Recently, "superbinder" SH2 domain variants with three amino acid substitutions (sSH2) were reported to have 100-fold or greater affinity for protein-phosphotyrosine (pY) than natural SH2 domains. Here we report a protocol in which His-tagged Src sSH2 efficiently captures pY-peptides from protease-digested HeLa cell total protein extracts. Affinity purification of pY-peptides by this method shows little bias for pY-proximal amino acid sequences, comparable to that achieved by using antibodies to pY, but with equal or higher yield. Superbinder-SH2 affinity purification mass spectrometry (sSH2-AP-MS) therefore provides an efficient and economical approach for unbiased pY-directed phospho-proteome profiling without the use of antibodies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Treatment of VGKC complex antibody-associated limbic encephalitis: a systematic review.

PubMed

Radja, Guirindhra Koumar; Cavanna, Andrea Eugenio

2013-01-01

Limbic encephalitis is an autoimmune neuropsychiatric condition characterized by subacute cognitive symptoms, seizures, and affective changes. Although limbic encephalitis is usually caused by an immune reaction secondary to neoplasms, different types of potentially treatable non-paraneoplastic limbic encephalitis (nPLE) have recently been described. In particular, published studies have reported variable responses to immunosuppressive therapy in Voltage-Gated Potassium Channel (VGKC) complex antibody-associated nPLE. This systematic literature review found that the most significant improvements were reported by patients presenting with affective symptoms and consistent neuroradiological changes. In these patients, improved clinical outcomes correlated with the largest decreases in antibody titers.

A mutagenesis study of a catalytic antibody

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

Jackson, D.Y.; Prudent, J.R.; Baldwin, E.P.

1991-01-01

The authors have generated seven site-specific mutations in the genes encoding the variable region of the heavy chain domain (V{sub H}) of the phosphocholine-binding antibody S107.S107 is a member of a family of well-characterized highly homologous antibodies that bind phosphorylcholine mono- and diesters. Two of these antibodies, MOPC-167 and T15, have previously been shown to catalyze the hydrolysis of 4-nitrophenyl N-trimethylammonioethyl carbonate. Two conserved heavy-chain residues, Tyr-33 and Arg-52, were postulated to be involved in binding and hydrolysis of 4-nitrophenylcholine carbonate esters. To more precisely define the catalytic roles of these residues, three Arg-52 mutants (R52K, R52Q, R52C) and fourmore » Tyr-33 mutants (Y33H, Y33F, Y33E, Y33D) of antibody S107 were generated. The genes encoding the V{sub H} binding domain of S107 were inserted into plasmid pUC-fl, and in vitro mutagenesis was performed. These results not only demonstrate the importance of electrostatic interactions in catalysis by antibody S107 but also show that catalytic side chains can be introduced into antibodies to enhance their catalytic efficiency.« less

Principles for computational design of binding antibodies

PubMed Central

Pszolla, M. Gabriele; Lapidoth, Gideon D.; Norn, Christoffer; Dym, Orly; Unger, Tamar; Albeck, Shira; Tyka, Michael D.; Fleishman, Sarel J.

2017-01-01

Natural proteins must both fold into a stable conformation and exert their molecular function. To date, computational design has successfully produced stable and atomically accurate proteins by using so-called “ideal” folds rich in regular secondary structures and almost devoid of loops and destabilizing elements, such as cavities. Molecular function, such as binding and catalysis, however, often demands nonideal features, including large and irregular loops and buried polar interaction networks, which have remained challenging for fold design. Through five design/experiment cycles, we learned principles for designing stable and functional antibody variable fragments (Fvs). Specifically, we (i) used sequence-design constraints derived from antibody multiple-sequence alignments, and (ii) during backbone design, maintained stabilizing interactions observed in natural antibodies between the framework and loops of complementarity-determining regions (CDRs) 1 and 2. Designed Fvs bound their ligands with midnanomolar affinities and were as stable as natural antibodies, despite having >30 mutations from mammalian antibody germlines. Furthermore, crystallographic analysis demonstrated atomic accuracy throughout the framework and in four of six CDRs in one design and atomic accuracy in the entire Fv in another. The principles we learned are general, and can be implemented to design other nonideal folds, generating stable, specific, and precise antibodies and enzymes. PMID:28973872

Lipid contribution to the affinity of antigen association with specific antibodies conjugated to liposomes.

PubMed

Klegerman, Melvin E; Huang, Shaoling; Parikh, Devang; Martinez, Janet; Demos, Sasha M; Onyuksel, Hayat A; McPherson, David D

2007-07-01

Immunoliposomes, directed to clinically relevant cell-surface molecules with antibodies, antibody fragments or peptides, are used for site-specific diagnostic evaluation or delivery of therapeutic agents. We have developed intrinsically echogenic liposomes (ELIP) covalently linked to fibrin(ogen)-specific antibodies and Fab fragments for ultrasonic imaging of atherosclerotic plaques. In order to determine the effect of liposomal conjugation on the molecular dynamics of fibrinogen binding, we studied the thermodynamic characteristics of unconjugated and ELIP-conjugated antibody molecules. Utilizing radioimmunoassay and enzyme-linked immunosorbent assay protocols, binding affinities were derived from data obtained at three temperatures. The thermodynamic functions DeltaH(o) , DeltaG(o) and DeltaS(o) were determined from van't Hoff plots and equations of state. The resultant functions indicated that both specific and nonspecific associations of antibody molecules with fibrinogen occurred through a variety of molecular interactions, including hydrophophic, ionic and hydrogen bonding mechanisms. ELIP conjugation of antibodies and Fab fragments introduced a characteristic change in both DeltaH(o) and DeltaS(o) of association, which corresponded to a variable contribution to binding by phospholipid gel-liquid crystal phase transitions. These observations suggest that a reciprocal energy transduction, affecting the strength of antibody-antigen binding, may be a singular characteristic of immunoliposomes, having utility for optimization and further development of the technology.

Prevalence of antibodies to canine parvovirus and reaction to vaccination in client-owned, healthy dogs.

PubMed

Riedl, M; Truyen, U; Reese, S; Hartmann, K

2015-12-12

The purpose of this population-based cohort study was to assess current prevalence of antibodies to canine parvovirus (CPV) in adult, healthy dogs, including risk factors associated with lack of antibodies, and reaction to revaccination with a modified live vaccine (MLV). One hundred dogs routinely presented for vaccination were included in the study and vaccinated with a single dose of a combined MLV. Information was collected on signalment, origin, environment, vaccination history and side effects. Prevaccination and postvaccination antibodies were detected by haemagglutination inhibition. Univariate analysis, followed by multivariate logistic regression, was used to investigate association between different variables and presence of antibodies as well as titre increase. Protective CPV antibodies were present in 86.0 per cent of dogs. Intervals of more than four years since the last vaccination and rare contacts with other dogs were determined as main risk factors for the absence of antibodies. An increase in titres only occurred in 17.0 per cent of dogs. Dogs without protective titres before vaccination or with bodyweight <10 kg were more likely to have an adequate titre increase. Based on these findings, antibody status should be determined instead of periodic vaccinations to ensure reliable protection without unnecessary vaccinations in adult dogs. British Veterinary Association.

Beyond CDR-grafting: Structure-guided humanization of framework and CDR regions of an anti-myostatin antibody.

PubMed

Apgar, James R; Mader, Michelle; Agostinelli, Rita; Benard, Susan; Bialek, Peter; Johnson, Mark; Gao, Yijie; Krebs, Mark; Owens, Jane; Parris, Kevin; St Andre, Michael; Svenson, Kris; Morris, Carl; Tchistiakova, Lioudmila

2016-10-01

Antibodies are an important class of biotherapeutics that offer specificity to their antigen, long half-life, effector function interaction and good manufacturability. The immunogenicity of non-human-derived antibodies, which can be a major limitation to development, has been partially overcome by humanization through complementarity-determining region (CDR) grafting onto human acceptor frameworks. The retention of foreign content in the CDR regions, however, is still a potential immunogenic liability. Here, we describe the humanization of an anti-myostatin antibody utilizing a 2-step process of traditional CDR-grafting onto a human acceptor framework, followed by a structure-guided approach to further reduce the murine content of CDR-grafted antibodies. To accomplish this, we solved the co-crystal structures of myostatin with the chimeric (Protein Databank (PDB) id 5F3B) and CDR-grafted anti-myostatin antibody (PDB id 5F3H), allowing us to computationally predict the structurally important CDR residues as well as those making significant contacts with the antigen. Structure-based rational design enabled further germlining of the CDR-grafted antibody, reducing the murine content of the antibody without affecting antigen binding. The overall "humanness" was increased for both the light and heavy chain variable regions.

Beyond CDR-grafting: Structure-guided humanization of framework and CDR regions of an anti-myostatin antibody

PubMed Central

Apgar, James R.; Mader, Michelle; Agostinelli, Rita; Benard, Susan; Bialek, Peter; Johnson, Mark; Gao, Yijie; Krebs, Mark; Owens, Jane; Parris, Kevin; St. Andre, Michael; Svenson, Kris; Morris, Carl; Tchistiakova, Lioudmila

2016-01-01

ABSTRACT Antibodies are an important class of biotherapeutics that offer specificity to their antigen, long half-life, effector function interaction and good manufacturability. The immunogenicity of non-human-derived antibodies, which can be a major limitation to development, has been partially overcome by humanization through complementarity-determining region (CDR) grafting onto human acceptor frameworks. The retention of foreign content in the CDR regions, however, is still a potential immunogenic liability. Here, we describe the humanization of an anti-myostatin antibody utilizing a 2-step process of traditional CDR-grafting onto a human acceptor framework, followed by a structure-guided approach to further reduce the murine content of CDR-grafted antibodies. To accomplish this, we solved the co-crystal structures of myostatin with the chimeric (Protein Databank (PDB) id 5F3B) and CDR-grafted anti-myostatin antibody (PDB id 5F3H), allowing us to computationally predict the structurally important CDR residues as well as those making significant contacts with the antigen. Structure-based rational design enabled further germlining of the CDR-grafted antibody, reducing the murine content of the antibody without affecting antigen binding. The overall “humanness” was increased for both the light and heavy chain variable regions. PMID:27625211

A fully automated primary screening system for the discovery of therapeutic antibodies directly from B cells.

PubMed

Tickle, Simon; Howells, Louise; O'Dowd, Victoria; Starkie, Dale; Whale, Kevin; Saunders, Mark; Lee, David; Lightwood, Daniel

2015-04-01

For a therapeutic antibody to succeed, it must meet a range of potency, stability, and specificity criteria. Many of these characteristics are conferred by the amino acid sequence of the heavy and light chain variable regions and, for this reason, can be screened for during antibody selection. However, it is important to consider that antibodies satisfying all these criteria may be of low frequency in an immunized animal; for this reason, it is essential to have a mechanism that allows for efficient sampling of the immune repertoire. UCB's core antibody discovery platform combines high-throughput B cell culture screening and the identification and isolation of single, antigen-specific IgG-secreting B cells through a proprietary technique called the "fluorescent foci" method. Using state-of-the-art automation to facilitate primary screening, extremely efficient interrogation of the natural antibody repertoire is made possible; more than 1 billion immune B cells can now be screened to provide a useful starting point from which to identify the rare therapeutic antibody. This article will describe the design, construction, and commissioning of a bespoke automated screening platform and two examples of how it was used to screen for antibodies against two targets. © 2014 Society for Laboratory Automation and Screening.

Application of cyclodextrins in antibody microparticles: potentials for antibody protection in spray drying.

PubMed

Ramezani, Vahid; Vatanara, Alireza; Seyedabadi, Mohammad; Nabi Meibodi, Mohsen; Fanaei, Hamed

2017-07-01

Dry powder formulations are extensively used to improve the stability of antibodies. Spray drying is one of important methods for protein drying. This study investigated the effects of trehalose, hydroxypropyl beta cyclodextrin (HPBCD) and beta cyclodextrin (BCD) on the stability and particle properties of spray-dried IgG. D-optimal design was employed for both experimental design and analysis and optimization of the variables. The size and aerodynamic behavior of particles were determined using laser light scattering and glass twin impinger, respectively. In addition, stability, ratio of beta sheets and morphology of antibody were analyzed using size exclusion chromatography, IR spectroscopy and electron microscopy, respectively. Particle properties and antibody stability were significantly improved in the presence of HPBCD. In addition, particle aerodynamic behavior, in terms of fine-particle fraction (FPF), enhanced up to 52.23%. Furthermore, antibody was better preserved not only during spray drying, but also during long-term storage. In contrast, application of BCD resulted in the formation of larger particles. Although trehalose caused inappropriate aerodynamic property, it efficiently decreased antibody aggregation. HPBCD is an efficient excipient for the development of inhalable protein formulations. In this regard, optimal particle property and antibody stability was obtained with proper combination of cyclodextrins and simple sugars, such as trehalose.

Monovalent IgG4 molecules

PubMed Central

Wilkinson, Ian C.; Fowler, Susan B.; Machiesky, LeeAnn; Miller, Kenneth; Hayes, David B.; Adib, Morshed; Her, Cheng; Borrok, M. Jack; Tsui, Ping; Burrell, Matthew; Corkill, Dominic J.; Witt, Susanne; Lowe, David C.; Webster, Carl I.

2013-01-01

Antibodies have become the fastest growing class of biological therapeutics, in part due to their exquisite specificity and ability to modulate protein-protein interactions with a high biological potency. The relatively large size and bivalency of antibodies, however, limits their use as therapeutics in certain circumstances. Antibody fragments, such as single-chain variable fragments and antigen binding-fragments, have emerged as viable alternatives, but without further modifications these monovalent formats have reduced terminal serum half-lives because of their small size and lack of an Fc domain, which is required for FcRn-mediated recycling. Using rational engineering of the IgG4 Fc domain to disrupt key interactions at the CH3-CH3 interface, we identified a number of point mutations that abolish Fc dimerization and created half-antibodies, a novel monovalent antibody format that retains a monomeric Fc domain. Introduction of these mutations into an IgG1 framework also led to the creation of half-antibodies. These half-antibodies were shown to be soluble, thermodynamically stable and monomeric, characteristics that are favorable for use as therapeutic proteins. Despite significantly reduced FcRn binding in vitro, which suggests that avidity gains in a dimeric Fc are critical to optimal FcRn binding, this format demonstrated an increased terminal serum half-life compared with that expected for most alternative antibody fragments. PMID:23567207

Prophylaxis of experimentally induced ovomucoid allergy in neonatal pigs using Lactococcus lactis.

PubMed

Rupa, P; Schmied, J; Wilkie, B N

2011-03-15

Probiotic Lactococcus lactis (LL) is immunomodulatory and may prevent allergy by biasing from type-2 to a type-1 immune response. We hypothesized that newborn pigs pre-treated orally with LL are protected against allergy to ovomucoid (Ovm). Pigs were assigned to two treatment groups. Piglets were pretreated orally on days of age 1-7, 10, 12, 14, 21, 28 and 35 with LL (n=30) or medium (control, n=32) and sensitized to Ovm by intraperitoneal injection together with cholera toxin on days 14, 21 and 35. Pigs were orally challenged with egg white (day 46) and assigned scores for allergic signs. Outcomes were measured as direct skin tests, serum antibody to Ovm [IgG (H+L); IgE; IgG(1) and IgG(2)] and cytokine production by mitogen-stimulated blood mononuclear cells (BMC). Clinical signs and skin test positivity were less frequent in the LL group (p ≤ 0.0001). Serum antibody associated with IgG (H and L), IgE, IgG(1) or IgG(2) was significantly increased on day 46 (post-sensitization) compared to day 14 (pre-sensitization) (p ≤ 0.0001). The LL-treated pigs had more IgE and IgG(2)-related antibody activity and lower IgG(1)/IgG(2) and IgE/IgG(2) ratios indicating a type-1 bias in immune response (p ≤ 0.05). Concentration of type-2 cytokines interleukin IL-4 and IL-10 were significantly lower in supernatants of stimulated BMC of LL-treated pigs (p ≤ 0.0001). Interferon-γ, TGF-β and IL-13 were not detected in control or treated animals. Thus, oral treatment of neonatal pigs with LL significantly reduced subsequent frequency of allergy to Ovm associated with reduced type-2 immune response correlates hence supporting the "hygiene hypothesis" and potential use of LL as a neonatal immunoregulator. Copyright © 2010 Elsevier B.V. All rights reserved.

Structure-Based Design of Hepatitis C Virus Vaccines That Elicit Neutralizing Antibody Responses to a Conserved Epitope

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

Pierce, Brian G.; Boucher, Elisabeth N.; Piepenbrink, Kurt H.

Despite recent advances in therapeutic options, hepatitis C virus (HCV) remains a severe global disease burden, and a vaccine can substantially reduce its incidence. Due to its extremely high sequence variability, HCV can readily escape the immune response; thus, an effective vaccine must target conserved, functionally important epitopes. Using the structure of a broadly neutralizing antibody in complex with a conserved linear epitope from the HCV E2 envelope glycoprotein (residues 412 to 423; epitope I), we performed structure-based design of immunogens to induce antibody responses to this epitope. This resulted in epitope-based immunogens based on a cyclic defensin protein, asmore » well as a bivalent immunogen with two copies of the epitope on the E2 surface. We solved the X-ray structure of a cyclic immunogen in complex with the HCV1 antibody and confirmed preservation of the epitope conformation and the HCV1 interface. Mice vaccinated with our designed immunogens produced robust antibody responses to epitope I, and their serum could neutralize HCV. Notably, the cyclic designs induced greater epitope-specific responses and neutralization than the native peptide epitope. Beyond successfully designing several novel HCV immunogens, this study demonstrates the principle that neutralizing anti-HCV antibodies can be induced by epitope-based, engineered vaccines and provides the basis for further efforts in structure-based design of HCV vaccines. IMPORTANCEHepatitis C virus is a leading cause of liver disease and liver cancer, with approximately 3% of the world's population infected. To combat this virus, an effective vaccine would have distinct advantages over current therapeutic options, yet experimental vaccines have not been successful to date, due in part to the virus's high sequence variability leading to immune escape. In this study, we rationally designed several vaccine immunogens based on the structure of a conserved epitope that is the target of broadly neutralizing antibodies.In vivoresults in mice indicated that these antigens elicited epitope-specific neutralizing antibodies, with various degrees of potency and breadth. These promising results suggest that a rational design approach can be used to generate an effective vaccine for this virus.« less

Effect of heat-killed Escherichia coli, lipopolysaccharide, and muramyl dipeptide treatments on the immune response phenotype and allergy in neonatal pigs sensitized to the egg white protein ovomucoid.

PubMed

Schmied, Julie; Rupa, Prithy; Garvie, Sarah; Wilkie, Bruce

2012-12-01

Predisposition to food allergies may reflect a type 2 immune response (IR) bias in neonates due to the intrauterine environment required to maintain pregnancy. The hygiene hypothesis states that lack of early environmental stimulus leading to inappropriate development and bias in IR may also contribute. Here, the ability of heat-killed Escherichia coli, lipopolysaccharide (LPS), or muramyl dipeptide (MDP) to alter IR bias and subsequent allergic response in neonatal pigs was investigated. Three groups of three litters of pigs (12 pigs/litter) were given intramuscular injections of E. coli, LPS, MDP, or phosphate-buffered saline (PBS) (control) and subsequently sensitized to the egg white allergen ovomucoid using an established protocol. To evaluate change in IR bias, immunoglobulin isotype-associated antibody activity (AbA), concentrations of type 1 and 2 and proinflammatory cytokines released from mitogen-stimulated blood mononuclear cells, and the percentage of T-regulatory cells (T-regs) in blood were measured. Clinical signs of allergy were assessed after oral challenge with egg white. The greatest effect on IR bias was observed in MDP-treated pigs, which had a type 2-biased phenotype by isotype-specific AbA, cytokine production, and a low proportion of T-regs. LPS-treated pigs had decreased type 1- and type 2-associated AbA. E. coli-treated pigs displayed increased response to Ovm as AbA and had more balanced cytokine profiles, as well as the highest proportion of T-regs. Accordingly, pigs treated with MDP were more susceptible to allergy than PBS controls, while pigs treated with LPS were less susceptible. Treatment with E. coli did not significantly alter the frequency of clinical signs.

Effect of Heat-Killed Escherichia coli, Lipopolysaccharide, and Muramyl Dipeptide Treatments on the Immune Response Phenotype and Allergy in Neonatal Pigs Sensitized to the Egg White Protein Ovomucoid

PubMed Central

Schmied, Julie; Rupa, Prithy; Garvie, Sarah

2012-01-01

Predisposition to food allergies may reflect a type 2 immune response (IR) bias in neonates due to the intrauterine environment required to maintain pregnancy. The hygiene hypothesis states that lack of early environmental stimulus leading to inappropriate development and bias in IR may also contribute. Here, the ability of heat-killed Escherichia coli, lipopolysaccharide (LPS), or muramyl dipeptide (MDP) to alter IR bias and subsequent allergic response in neonatal pigs was investigated. Three groups of three litters of pigs (12 pigs/litter) were given intramuscular injections of E. coli, LPS, MDP, or phosphate-buffered saline (PBS) (control) and subsequently sensitized to the egg white allergen ovomucoid using an established protocol. To evaluate change in IR bias, immunoglobulin isotype-associated antibody activity (AbA), concentrations of type 1 and 2 and proinflammatory cytokines released from mitogen-stimulated blood mononuclear cells, and the percentage of T-regulatory cells (T-regs) in blood were measured. Clinical signs of allergy were assessed after oral challenge with egg white. The greatest effect on IR bias was observed in MDP-treated pigs, which had a type 2-biased phenotype by isotype-specific AbA, cytokine production, and a low proportion of T-regs. LPS-treated pigs had decreased type 1- and type 2-associated AbA. E. coli-treated pigs displayed increased response to Ovm as AbA and had more balanced cytokine profiles, as well as the highest proportion of T-regs. Accordingly, pigs treated with MDP were more susceptible to allergy than PBS controls, while pigs treated with LPS were less susceptible. Treatment with E. coli did not significantly alter the frequency of clinical signs. PMID:23081818

Bias correction of surface downwelling longwave and shortwave radiation for the EWEMBI dataset

NASA Astrophysics Data System (ADS)

Lange, Stefan

2018-05-01

Many meteorological forcing datasets include bias-corrected surface downwelling longwave and shortwave radiation (rlds and rsds). Methods used for such bias corrections range from multi-year monthly mean value scaling to quantile mapping at the daily timescale. An additional downscaling is necessary if the data to be corrected have a higher spatial resolution than the observational data used to determine the biases. This was the case when EartH2Observe (E2OBS; Calton et al., 2016) rlds and rsds were bias-corrected using more coarsely resolved Surface Radiation Budget (SRB; Stackhouse Jr. et al., 2011) data for the production of the meteorological forcing dataset EWEMBI (Lange, 2016). This article systematically compares various parametric quantile mapping methods designed specifically for this purpose, including those used for the production of EWEMBI rlds and rsds. The methods vary in the timescale at which they operate, in their way of accounting for physical upper radiation limits, and in their approach to bridging the spatial resolution gap between E2OBS and SRB. It is shown how temporal and spatial variability deflation related to bilinear interpolation and other deterministic downscaling approaches can be overcome by downscaling the target statistics of quantile mapping from the SRB to the E2OBS grid such that the sub-SRB-grid-scale spatial variability present in the original E2OBS data is retained. Cross validations at the daily and monthly timescales reveal that it is worthwhile to take empirical estimates of physical upper limits into account when adjusting either radiation component and that, overall, bias correction at the daily timescale is more effective than bias correction at the monthly timescale if sampling errors are taken into account.

A bias-corrected CMIP5 dataset for Africa using the CDF-t method - a contribution to agricultural impact studies

NASA Astrophysics Data System (ADS)

Moise Famien, Adjoua; Janicot, Serge; Delfin Ochou, Abe; Vrac, Mathieu; Defrance, Dimitri; Sultan, Benjamin; Noël, Thomas

2018-03-01

The objective of this paper is to present a new dataset of bias-corrected CMIP5 global climate model (GCM) daily data over Africa. This dataset was obtained using the cumulative distribution function transform (CDF-t) method, a method that has been applied to several regions and contexts but never to Africa. Here CDF-t has been applied over the period 1950-2099 combining Historical runs and climate change scenarios for six variables: precipitation, mean near-surface air temperature, near-surface maximum air temperature, near-surface minimum air temperature, surface downwelling shortwave radiation, and wind speed, which are critical variables for agricultural purposes. WFDEI has been used as the reference dataset to correct the GCMs. Evaluation of the results over West Africa has been carried out on a list of priority user-based metrics that were discussed and selected with stakeholders. It includes simulated yield using a crop model simulating maize growth. These bias-corrected GCM data have been compared with another available dataset of bias-corrected GCMs using WATCH Forcing Data as the reference dataset. The impact of WFD, WFDEI, and also EWEMBI reference datasets has been also examined in detail. It is shown that CDF-t is very effective at removing the biases and reducing the high inter-GCM scattering. Differences with other bias-corrected GCM data are mainly due to the differences among the reference datasets. This is particularly true for surface downwelling shortwave radiation, which has a significant impact in terms of simulated maize yields. Projections of future yields over West Africa are quite different, depending on the bias-correction method used. However all these projections show a similar relative decreasing trend over the 21st century.

Improving Antibody-Based Cancer Therapeutics Through Glycan Engineering.

PubMed

Yu, Xiaojie; Marshall, Michael J E; Cragg, Mark S; Crispin, Max

2017-06-01

Antibody-based therapeutics has emerged as a major tool in cancer treatment. Guided by the superb specificity of the antibody variable domain, it allows the precise targeting of tumour markers. Recently, eliciting cellular effector functions, mediated by the Fc domain, has gained traction as a means by which to generate more potent antibody therapeutics. Extensive mutagenesis studies of the Fc protein backbone has enabled the generation of Fc variants that more optimally engage the Fcγ receptors known to mediate cellular effector functions such as antibody-dependent cellular cytotoxicity (ADCC) and cellular phagocytosis. In addition to the protein backbone, the homodimeric Fc domain contains two opposing N-linked glycans, which represent a further point of potential immunomodulation, independent of the Fc protein backbone. For example, a lack of core fucose usually attached to the IgG Fc glycan leads to enhanced ADCC activity, whereas a high level of terminal sialylation is associated with reduced inflammation. Significant growth in knowledge of Fc glycosylation over the last decade, combined with advancement in genetic engineering, has empowered glyco-engineering to fine-tune antibody therapeutics. This has culminated in the approval of two glyco-engineered antibodies for cancer therapy: the anti-CCR4 mogamulizumab approved in 2012 and the anti-CD20 obinutuzumab in 2013. We discuss here the technological platforms for antibody glyco-engineering and review the current clinical landscape of glyco-engineered antibodies.

Molecular characterization of the monoclonal antibodies composing ZMAb: a protective cocktail against Ebola virus.

PubMed

Audet, Jonathan; Wong, Gary; Wang, Han; Lu, Guangwen; Gao, George F; Kobinger, Gary; Qiu, Xiangguo

2014-11-06

Ebola virus (EBOV) causes severe viral hemorrhagic fever in humans and non-human primates, with a case fatality rate of up to 88% in human outbreaks. Over the past 3 years, monoclonal antibody (mAb) cocktails have demonstrated high efficacy as treatments against EBOV infection. One such cocktail is ZMAb, which consists of three mouse antibodies, 1H3, 2G4, and 4G7. Here, we present the epitope binding properties of mAbs 1H3, 2G4, and 4G7. We showed that these antibodies have different variable region sequences, suggesting that the individual mAbs are not clonally related. All three antibodies were found to neutralize EBOV variant Mayinga. Additionally, 2G4 and 4G7 were shown to cross-inhibit each other in vitro and select for an escape mutation at the same position on the EBOV glycoprotein (GP), at amino acid 508. 1H3 selects an escape mutant at amino acid 273 on EBOV GP. Surface plasmon resonance studies showed that all three antibodies have dissociation constants on the order of 10(-7). In combination with previous studies evaluating the binding sites of other protective antibodies, our results suggest that antibodies targeting the GP1-GP2 interface and the glycan cap are often selected as efficacious antibodies for post-exposure interventions against EBOV.

From VGKC to LGI1 and Caspr2 encephalitis: The evolution of a disease entity over time.

PubMed

van Sonderen, A; Schreurs, M W J; Wirtz, P W; Sillevis Smitt, P A E; Titulaer, M J

2016-10-01

A wide variety of clinical syndromes has been associated with antibodies to voltage-gated potassium channels (VGKCs). Six years ago, it was discovered that patients do not truly have antibodies to potassium channels, but to associated proteins. This enabled the distinction of three VGKC-positive subgroups: anti-LGI1 patients, anti-Caspr2 patients and VGKC-positive patients lacking both antibodies. Patients with LGI1-antibodies have a limbic encephalitis, often with hyponatremia, and about half of the patients have typical faciobrachial dystonic seizures. Caspr2-antibodies cause a more variable syndrome of peripheral or central nervous system symptoms, almost exclusively affecting older males. Immunotherapy seems to be beneficial in patients with antibodies to LGI1 or Caspr2, stressing the need for early diagnosis. Half of the VGKC-positive patients lack antibodies to both LGI1 and Caspr2. This is a heterogeneous group of patients with a wide variety of clinical syndromes, raising the question whether VGKC-positivity is truly a marker of disease in these patients. Data regarding this issue are limited, but a recent study did not show any clinical relevance of VGKC-positivity in the absence of antibodies to LGI1 and Caspr2. The three VGKC-positive subgroups are essentially different, therefore, the lumping term 'VGKC-complex antibodies' should be abolished. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

A Monoclonal Antibody to Cryptococcus neoformans Glucuronoxylomannan Manifests Hydrolytic Activity for Both Peptides and Polysaccharides.

PubMed

Bowen, Anthony; Wear, Maggie P; Cordero, Radames J B; Oscarson, Stefan; Casadevall, Arturo

2017-01-13

Studies in the 1980s first showed that some natural antibodies were "catalytic" and able to hydrolyze peptide or phosphodiester bonds in antigens. Many naturally occurring catalytic antibodies have since been isolated from human sera and associated with positive and negative outcomes in autoimmune disease and infection. The function and prevalence of these antibodies, however, remain unclear. A previous study suggested that the 18B7 monoclonal antibody against glucuronoxylomannan (GXM), the major component of the Cryptococcus neoformans polysaccharide capsule, hydrolyzed a peptide antigen mimetic. Using mass spectrometry and Förster resonance energy transfer techniques, we confirm and characterize the hydrolytic activity of 18B7 against peptide mimetics and show that 18B7 is able to hydrolyze an oligosaccharide substrate, providing the first example of a naturally occurring catalytic antibody for polysaccharides. Additionally, we show that the catalytic 18B7 antibody increases release of capsular polysaccharide from fungal cells. A serine protease inhibitor blocked peptide and oligosaccharide hydrolysis by 18B7, and a putative serine protease-like active site was identified in the light chain variable region of the antibody. An algorithm was developed to detect similar sites present in unique antibody structures in the Protein Data Bank. The putative site was found in 14 of 63 (22.2%) catalytic antibody structures and 119 of 1602 (7.4%) antibodies with no annotation of catalytic activity. The ability of many antibodies to cleave antigen, albeit slowly, supports the notion that this activity is an important immunoglobulin function in host defense. The discovery of GXM hydrolytic activity suggests new therapeutic possibilities for polysaccharide-binding antibodies. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

The influence of antibody fragment format on phage display based affinity maturation of IgG

PubMed Central

Steinwand, Miriam; Droste, Patrick; Frenzel, Andrè; Hust, Michael; Dübel, Stefan; Schirrmann, Thomas

2014-01-01

Today, most approved therapeutic antibodies are provided as immunoglobulin G (IgG), whereas small recombinant antibody formats are required for in vitro antibody generation and engineering during drug development. Particularly, single chain (sc) antibody fragments like scFv or scFab are well suited for phage display and bacterial expression, but some have been found to lose affinity during conversion into IgG.   In this study, we compared the influence of the antibody format on affinity maturation of the CD30-specific scFv antibody fragment SH313-F9, with the overall objective being improvement of the IgG. The variable genes of SH313-F9 were randomly mutated and then cloned into libraries encoding different recombinant antibody formats, including scFv, Fab, scFabΔC, and FabΔC. All tested antibody formats except Fab allowed functional phage display of the parental antibody SH313-F9, and the corresponding mutated antibody gene libraries allowed isolation of candidates with enhanced CD30 binding. Moreover, scFv and scFabΔC antibody variants retained improved antigen binding after subcloning into the single gene encoded IgG-like formats scFv-Fc or scIgG, but lost affinity after conversion into IgGs. Only affinity maturation using the Fab-like FabΔC format, which does not contain the carboxy terminal cysteines, allowed successful selection of molecules with improved binding that was retained after conversion to IgG. Thus, affinity maturation of IgGs is dependent on the antibody format employed for selection and screening. In this study, only FabΔC resulted in the efficient selection of IgG candidates with higher affinity by combination of Fab-like conformation and improved phage display compared with Fab. PMID:24262918

Antibody class capture assays for varicella-zoster virus.

PubMed Central

Forghani, B; Myoraku, C K; Dupuis, K W; Schmidt, N J

1984-01-01

Pooled monoclonal antibodies to varicella-zoster virus (VZV) were used as "detector" antibodies in a four-phase enzyme immunofluorescence assay for determination of immunoglobulin M (IgM), IgA, and IgG antibodies to VZV. Polyclonal antisera specific for heavy chains of human IgM, IgA, and IgG were employed as "capture" antibodies on the solid phase. The antibody class capture assay (ACCA) for VZV IgM antibody detected high titers of virus-specific IgM in all patients with varicella and in 5 of 10 zoster patients. VZV IgM antibody was not detected in patients with primary herpes simplex virus infections or in other individuals without active VZV infection, with one exception, a patient with encephalitis who had other serological findings compatible with a reactivated VZV infection. VZV-specific IgA and IgG antibody titers demonstrable by ACCA were compared with those measured by solid-phase indirect enzyme immunofluorescence assay (EIFA). VZV IgA antibody titers detected in patients with varicella and zoster were variable and could not be considered to be reliable markers of active VZV infection. IgA antibody titers detected by ACCA tended to be higher than those demonstrated by solid-phase indirect EIFA in varicella and zoster patients. VZV IgG antibody titers detected by ACCA in patients with varicella, and to a lesser extent in zoster patients, were as high as or higher than those demonstrated by solid-phase indirect EIFA. However, ACCA was totally insensitive in detecting VZV IgG antibody in individuals with past infections with VZV and would not be a suitable approach for determination of immunity status to VZV. PMID:6330163

A Monoclonal Antibody to Cryptococcus neoformans Glucuronoxylomannan Manifests Hydrolytic Activity for Both Peptides and Polysaccharides*

PubMed Central

Wear, Maggie P.; Cordero, Radames J. B.; Oscarson, Stefan

2017-01-01

Studies in the 1980s first showed that some natural antibodies were “catalytic” and able to hydrolyze peptide or phosphodiester bonds in antigens. Many naturally occurring catalytic antibodies have since been isolated from human sera and associated with positive and negative outcomes in autoimmune disease and infection. The function and prevalence of these antibodies, however, remain unclear. A previous study suggested that the 18B7 monoclonal antibody against glucuronoxylomannan (GXM), the major component of the Cryptococcus neoformans polysaccharide capsule, hydrolyzed a peptide antigen mimetic. Using mass spectrometry and Förster resonance energy transfer techniques, we confirm and characterize the hydrolytic activity of 18B7 against peptide mimetics and show that 18B7 is able to hydrolyze an oligosaccharide substrate, providing the first example of a naturally occurring catalytic antibody for polysaccharides. Additionally, we show that the catalytic 18B7 antibody increases release of capsular polysaccharide from fungal cells. A serine protease inhibitor blocked peptide and oligosaccharide hydrolysis by 18B7, and a putative serine protease-like active site was identified in the light chain variable region of the antibody. An algorithm was developed to detect similar sites present in unique antibody structures in the Protein Data Bank. The putative site was found in 14 of 63 (22.2%) catalytic antibody structures and 119 of 1602 (7.4%) antibodies with no annotation of catalytic activity. The ability of many antibodies to cleave antigen, albeit slowly, supports the notion that this activity is an important immunoglobulin function in host defense. The discovery of GXM hydrolytic activity suggests new therapeutic possibilities for polysaccharide-binding antibodies. PMID:27872188

Adjusted Analyses in Studies Addressing Therapy and Harm: Users' Guides to the Medical Literature.

PubMed

Agoritsas, Thomas; Merglen, Arnaud; Shah, Nilay D; O'Donnell, Martin; Guyatt, Gordon H

2017-02-21

Observational studies almost always have bias because prognostic factors are unequally distributed between patients exposed or not exposed to an intervention. The standard approach to dealing with this problem is adjusted or stratified analysis. Its principle is to use measurement of risk factors to create prognostically homogeneous groups and to combine effect estimates across groups.The purpose of this Users' Guide is to introduce readers to fundamental concepts underlying adjustment as a way of dealing with prognostic imbalance and to the basic principles and relative trustworthiness of various adjustment strategies.One alternative to the standard approach is propensity analysis, in which groups are matched according to the likelihood of membership in exposed or unexposed groups. Propensity methods can deal with multiple prognostic factors, even if there are relatively few patients having outcome events. However, propensity methods do not address other limitations of traditional adjustment: investigators may not have measured all relevant prognostic factors (or not accurately), and unknown factors may bias the results.A second approach, instrumental variable analysis, relies on identifying a variable associated with the likelihood of receiving the intervention but not associated with any prognostic factor or with the outcome (other than through the intervention); this could mimic randomization. However, as with assumptions of other adjustment approaches, it is never certain if an instrumental variable analysis eliminates bias.Although all these approaches can reduce the risk of bias in observational studies, none replace the balance of both known and unknown prognostic factors offered by randomization.

Instrumental variables as bias amplifiers with general outcome and confounding.

PubMed

Ding, P; VanderWeele, T J; Robins, J M

2017-06-01

Drawing causal inference with observational studies is the central pillar of many disciplines. One sufficient condition for identifying the causal effect is that the treatment-outcome relationship is unconfounded conditional on the observed covariates. It is often believed that the more covariates we condition on, the more plausible this unconfoundedness assumption is. This belief has had a huge impact on practical causal inference, suggesting that we should adjust for all pretreatment covariates. However, when there is unmeasured confounding between the treatment and outcome, estimators adjusting for some pretreatment covariate might have greater bias than estimators without adjusting for this covariate. This kind of covariate is called a bias amplifier, and includes instrumental variables that are independent of the confounder, and affect the outcome only through the treatment. Previously, theoretical results for this phenomenon have been established only for linear models. We fill in this gap in the literature by providing a general theory, showing that this phenomenon happens under a wide class of models satisfying certain monotonicity assumptions. We further show that when the treatment follows an additive or multiplicative model conditional on the instrumental variable and the confounder, these monotonicity assumptions can be interpreted as the signs of the arrows of the causal diagrams.

Heterogeneity of Polyneuropathy Associated with Anti-MAG Antibodies

PubMed Central

Magy, Laurent; Kaboré, Raphaël; Mathis, Stéphane; Lebeau, Prisca; Ghorab, Karima; Caudie, Christiane; Vallat, Jean-Michel

2015-01-01

Polyneuropathy associated with IgM monoclonal gammopathy and anti-myelin associated glycoprotein (MAG) antibodies is an immune-mediated demyelinating neuropathy. The pathophysiology of this condition is likely to involve anti-MAG antibody deposition on myelin sheaths of the peripheral nerves and it is supposed to be distinct from chronic inflammatory demyelinating neuropathy (CIDP), another immune-mediated demyelinating peripheral neuropathy. In this series, we have retrospectively reviewed clinical and laboratory findings from 60 patients with polyneuropathy, IgM gammopathy, and anti-MAG antibodies. We found that the clinical picture in these patients is highly variable suggesting a direct link between the monoclonal gammopathy and the neuropathy. Conversely, one-third of patients had a CIDP-like phenotype on electrodiagnostic testing and this was correlated with a low titer of anti-MAG antibodies and the absence of widening of myelin lamellae. Our data suggest that polyneuropathy associated with anti-MAG antibodies is less homogeneous than previously said and that the pathophysiology of the condition is likely to be heterogeneous as well with the self-antigen being MAG in most of the patients but possibly being another component of myelin in the others. PMID:26065001

Antibodies elicited by the first non-viral prophylactic cancer vaccine show tumor-specificity and immunotherapeutic potential

PubMed Central

Lohmueller, Jason J.; Sato, Shuji; Popova, Lana; Chu, Isabel M.; Tucker, Meghan A.; Barberena, Roberto; Innocenti, Gregory M.; Cudic, Mare; Ham, James D.; Cheung, Wan Cheung; Polakiewicz, Roberto D.; Finn, Olivera J.

2016-01-01

MUC1 is a shared tumor antigen expressed on >80% of human cancers. We completed the first prophylactic cancer vaccine clinical trial based on a non-viral antigen, MUC1, in healthy individuals at-risk for colon cancer. This trial provided a unique source of potentially effective and safe immunotherapeutic drugs, fully-human antibodies affinity-matured in a healthy host to a tumor antigen. We purified, cloned, and characterized 13 IgGs specific for several tumor-associated MUC1 epitopes with a wide range of binding affinities. These antibodies bind hypoglycosylated MUC1 on human cancer cell lines and tumor tissues but show no reactivity against fully-glycosylated MUC1 on normal cells and tissues. We found that several antibodies activate complement-mediated cytotoxicity and that T cells carrying chimeric antigen receptors with the antibody variable regions kill MUC1+ target cells, express activation markers, and produce interferon gamma. Fully-human and tumor-specific, these antibodies are candidates for further testing and development as immunotherapeutic drugs. PMID:27545199

PREVALENCE OF ANTIBODIES FOR SELECTED CANINE PATHOGENS AMONG WOLVES (CANIS LUPUS) FROM THE ALASKA PENINSULA, USA.

PubMed

Watts, Dominique E; Benson, Anna-Marie

2016-07-01

We collected blood samples from wolves ( Canis lupus ) on the Alaska Peninsula, southwest Alaska, US, 2006-11 and tested sera for antibodies to canine adenovirus (CAV), canine coronavirus (CCV), canine distemper virus (CDV), canine herpesvirus (CHV), canine parainfluenza (CPI), canine parvovirus (CPV), Neospora caninum , and Toxoplasma gondii . Detected antibody prevalence was 90% for CAV, 28% for CCV, 12% for CDV, 93% for CHV, 0% for CPI, 20% for CPV, 0% for N. caninum, and 86% for T. gondii . Prevalence of CCV antibodies suggested a seasonal pattern with higher prevalence during spring (43%) than in fall (11%). Prevalence of CCV antibodies also declined during the 6-yr study with high prevalence during spring 2006-08 (80%, n=24) and low prevalence during spring 2009-11 (4%, n=24). Prevalence of N. caninum and T. gondii antibodies were highly variable in the study area during 2006-11. Results suggested that some pathogens might be enzootic on the Alaska Peninsula (e.g., CAV and CHV) while others may be epizootic (e.g., CCV, N. caninum , T. gondii ).

[Histocompatibility tests in a transplantation program].

PubMed

de-Leo-Cervantes, Claudia

2005-01-01

The importance of the role of the histocompatibility laboratory in solid organ transplantation is to perform HLA typing and determine the degree of HLA matching between recipient/donor. It is a useful tool to increase graft survival and decrease chronic rejection. HLA matching has a positive effect on kidney transplants and it has variable impact on other organ transplants. The crossmatch procedure is the most important test in a solid organ transplantation to evaluate the presence of recipient antibodies to antigens expressed on donor white cells. This test decreases the risk of hyperacute humoral rejection or early graft loss. Positive crossmatch is a contraindication for transplantation because it represents the existence of IgG recipient antibodies that will reath againts donor antigens. Antibody evaluation is important in donor-recipient selection and the responsability of the histocompatibility laboratory is to identify clinically relevant anti-donor HLA antibodies. This detection is useful to determine the degree of humoral alloimmunization, expressed as a percent panel reactive antibody (%PRA). This test also provides information about the antibody specificity and can be used for evaluate a patient's immune status providing a significant correlation in selecting donors.

Two-range magnetoelectric sensor

NASA Astrophysics Data System (ADS)

Bichurin, M.; Petrov, V.; Leontyev, V.; Saplev, A.

2017-01-01

In this study, we present a two-range magnetoelectric ME sensor design comprising of permendur (alloy of Fe-Co-V), nickel, and lead zirconate titanate (PZT) laminate composite. A systematic study was conducted to clarify the contribution of magnetostrictive layers variables to the ME response over the applied range of magnetic bias field. The two-range behavior was characterized by opposite sign of the ME response when magnetic dc bias is in different sub-ranges. The ME coefficient as a function of magnetic bias field was found to be dependent on the laminate composite structure.

Bias correction for rainrate retrievals from satellite passive microwave sensors

NASA Technical Reports Server (NTRS)

Short, David A.

1990-01-01

Rainrates retrieved from past and present satellite-borne microwave sensors are affected by a fundamental remote sensing problem. Sensor fields-of-view are typically large enough to encompass substantial rainrate variability, whereas the retrieval algorithms, based on radiative transfer calculations, show a non-linear relationship between rainrate and microwave brightness temperature. Retrieved rainrates are systematically too low. A statistical model of the bias problem shows that bias correction factors depend on the probability distribution of instantaneous rainrate and on the average thickness of the rain layer.

Forms of attrition in a longitudinal study of religion and health in older adults and implications for sample bias

PubMed Central

Hayward, R. David; Krause, Neal

2014-01-01

The use of longitudinal designs in the field of religion and health makes it important to understand how attrition bias may affect findings in this area. This study examines attrition in a 4-wave, 8-year study of older adults. Attrition resulted in a sample biased towards more educated and more religiously-involved individuals. Conditional linear growth curve models found that trajectories of change for some variables differed among attrition categories. Ineligibles had worsening depression, declining control, and declining attendance. Mortality was associated with worsening religious coping styles. Refusers experienced worsening depression. Nevertheless, there was no evidence of bias in the key religion and health results. PMID:25257794

Forms of Attrition in a Longitudinal Study of Religion and Health in Older Adults and Implications for Sample Bias.

PubMed

Hayward, R David; Krause, Neal

2016-02-01

The use of longitudinal designs in the field of religion and health makes it important to understand how attrition bias may affect findings in this area. This study examines attrition in a 4-wave, 8-year study of older adults. Attrition resulted in a sample biased toward more educated and more religiously involved individuals. Conditional linear growth curve models found that trajectories of change for some variables differed among attrition categories. Ineligibles had worsening depression, declining control, and declining attendance. Mortality was associated with worsening religious coping styles. Refusers experienced worsening depression. Nevertheless, there was no evidence of bias in the key religion and health results.

Parametric mapping of [18F]fluoromisonidazole positron emission tomography using basis functions.

PubMed

Hong, Young T; Beech, John S; Smith, Rob; Baron, Jean-Claude; Fryer, Tim D

2011-02-01

In this study, we show a basis function method (BAFPIC) for voxelwise calculation of kinetic parameters (K(1), k(2), k(3), K(i)) and blood volume using an irreversible two-tissue compartment model. BAFPIC was applied to rat ischaemic stroke micro-positron emission tomography data acquired with the hypoxia tracer [(18)F]fluoromisonidazole because irreversible two-tissue compartmental modelling provided good fits to data from both hypoxic and normoxic tissues. Simulated data show that BAFPIC produces kinetic parameters with significantly lower variability and bias than nonlinear least squares (NLLS) modelling in hypoxic tissue. The advantage of BAFPIC over NLLS is less pronounced in normoxic tissue. K(i) determined from BAFPIC has lower variability than that from the Patlak-Gjedde graphical analysis (PGA) by up to 40% and lower bias, except for normoxic tissue at mid-high noise levels. Consistent with the simulation results, BAFPIC parametric maps of real data suffer less noise-induced variability than do NLLS and PGA. Delineation of hypoxia on BAFPIC k(3) maps is aided by low variability in normoxic tissue, which matches that in K(i) maps. BAFPIC produces K(i) values that correlate well with those from PGA (r(2)=0.93 to 0.97; slope 0.99 to 1.05, absolute intercept <0.00002 mL/g per min). BAFPIC is a computationally efficient method of determining parametric maps with low bias and variance.

Does industrial waste taxation contribute to reduction of landfilled waste? Dynamic panel analysis considering industrial waste category in Japan.

PubMed

Sasao, Toshiaki

2014-11-01

Waste taxes, such as landfill and incineration taxes, have emerged as a popular option in developed countries to promote the 3Rs (reduce, reuse, and recycle). However, few studies have examined the effectiveness of waste taxes. In addition, quite a few studies have considered both dynamic relationships among dependent variables and unobserved individual heterogeneity among the jurisdictions. If dependent variables are persistent, omitted variables cause a bias, or common characteristics exist across the jurisdictions that have introduced waste taxes, the standard fixed effects model may lead to biased estimation results and misunderstood causal relationships. In addition, most existing studies have examined waste in terms of total amounts rather than by categories. Even if significant reductions in total waste amounts are not observed, some reduction within each category may, nevertheless, become evident. Therefore, this study analyzes the effects of industrial waste taxation on quantities of waste in landfill in Japan by applying the bias-corrected least-squares dummy variable (LSDVC) estimators; the general method of moments (difference GMM); and the system GMM. In addition, the study investigates effect differences attributable to industrial waste categories and taxation types. This paper shows that industrial waste taxes in Japan have minimal, significant effects on the reduction of final disposal amounts thus far, considering dynamic relationships and waste categories. Copyright © 2014 Elsevier Ltd. All rights reserved.

Targeting nanodisks via a single chain variable antibody--apolipoprotein chimera.

PubMed

Iovannisci, David M; Beckstead, Jennifer A; Ryan, Robert O

2009-02-06

Nanodisks (ND) are nanometer scale complexes of phospholipid and apolipoprotein that have been shown to function as drug delivery vehicles. ND harboring significant quantities of the antifungal agent, amphotericin B, or the bioactive isoprenoid, all trans retinoic acid, have been generated and characterized. As currently formulated, ND possess limited targeting capability. In this study, we constructed a single chain variable antibody (scFv).apolipoprotein chimera and assessed the ability of this fusion protein to form ND and recognize the antigen to which the scFv is directed. Data obtained revealed that alpha-vimentin scFv.apolipoprotein A-I is functional in ND formation and antigen recognition, opening the door to the use of such chimeras in targeting drug-enriched ND to specific tissues.

Aggregate Auto Travel Forecasting : State of the Art and Suggestions for Future Research

DOT National Transportation Integrated Search

1976-12-01

The report reviews existing forecasting models of auto vehicle miles of travel (VMT), and presents evidence that such models incorrectly omit time cost and spatial form variables. The omission of these variables biases parameter estimates in existing...

LYMPHOCYTIC THYROIDITIS IS ASSOCIATED WITH INCREASED NUMBER OF BENIGN CERVICAL NODES AND FEWER CENTRAL NECK COMPARTMENT METASTATIC LYMPH NODES IN PATIENTS WITH DIFFERENTIATED THYROID CANCER.

PubMed

Donangelo, Ines; Walts, Ann E; Bresee, Catherine; Braunstein, Glenn D

2016-10-01

Whether or not autoimmune thyroid disease influences the progression of differentiated thyroid cancer (DTC) remains controversial. Findings of previous studies are influenced by lead time bias and/or procedure bias selection. These biases can be reduced by studying a single-institution patient population that underwent a similar extent of surgical resection. From a cohort of 660 patients with DTC who underwent thyroidectomy, we retrospectively studied 357 patients who underwent total thyroidectomy and central compartment node dissection (CCND) for DTC between 2003 and 2013. Forty-one percent (140/345) of study patients had lymphocytic thyroiditis (LT), and 30% (91/301) had serum positive for thyroglobulin antibody (TgAb). LT was reported in 78% of the TgAb-positive cases. Sixty percent (213/357) of cases had metastatic thyroid carcinoma in 1 or more neck lymph nodes (55% [198/357] central compartment, and 22% [77/356] lateral compartment). Patients with LT had fewer metastatic cervical lymph nodes than those with no LT (2.7 ± 4.7 vs 3.5 ± 4.8, respectively, P = .0285). Patients with positive TgAb and thyroiditis had a larger number of benign cervical lymph nodes removed than those with negative TgAb or no LT. No significant difference was observed in age, tumor size, multifocality, extrathyroidal extension, vascular invasion, or frequency of cervical lymph node metastasis between TgAb-negative and -positive cases or between cases with and without LT. Lymphocytic thyroiditis is associated with fewer central neck compartment metastatic lymph nodes and a larger number of excised reactive benign cervical lymph nodes. Whether this association indicates a protective role of thyroid autoimmunity in lymph node spreading remains unclear. CCND = central compartment node dissection DTC = differentiated thyroid cancer HT = Hashimoto thyroiditis LT = lymphocytic thyroiditis TgAb = thyroglobulin antibody TPO = thyroid peroxidase.

Complement dependent cytotoxicity (CDC) activity of a humanized anti Lewis-Y antibody: FACS-based assay versus the 'classical' radioactive method -- qualification, comparison and application of the FACS-based approach.

PubMed

Nechansky, A; Szolar, O H J; Siegl, P; Zinoecker, I; Halanek, N; Wiederkum, S; Kircheis, R

2009-05-01

The fully humanized Lewis-Y carbohydrate specific monoclonal antibody (mAb) IGN311 is currently tested in a passive immunotherapy approach in a clinical phase I trail and therefore regulatory requirements demand qualified assays for product analysis. To demonstrate the functionality of its Fc-region, the capacity of IGN311 to mediate complement dependent cytotoxicity (CDC) against human breast cancer cells was evaluated. The "classical" radioactive method using chromium-51 and a FACS-based assay were established and qualified according to ICH guidelines. Parameters evaluated were specificity, response function, bias, repeatability (intra-day precision), intermediate precision (operator-time different), and linearity (assay range). In the course of a fully nested design, a four-parameter logistic equation was identified as appropriate calibration model for both methods. For the radioactive assay, the bias ranged from -6.1% to -3.6%. The intermediate precision for future means of duplicate measurements revealed values from 12.5% to 15.9% and the total error (beta-expectation tolerance interval) of the method was found to be <40%. For the FACS-based assay, the bias ranged from -8.3% to 0.6% and the intermediate precision for future means of duplicate measurements revealed values from 4.2% to 8.0%. The total error of the method was found to be <25%. The presented data demonstrate that the FACS-based CDC is more accurate than the radioactive assay. Also, the elimination of radioactivity and the 'real-time' counting of apoptotic cells further justifies the implementation of this method which was subsequently applied for testing the influence of storage at 4 degrees C and 25 degrees C ('stability testing') on the potency of IGN311 drug product. The obtained results demonstrate that the qualified functional assay represents a stability indicating test method.

Antibodies Targeting EMT

DTIC Science & Technology

2017-10-01

impact substrate usage in AKRs . The blue residues are variable positions between AKR1C1-4. These residues are near the active site and may play a ...with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS...and diagnostic biomarkers. We have developed a new technique allowing for discovery of new antibodies that disrupt a key process in cancer progression

Errors and uncertainties in regional climate simulations of rainfall variability over Tunisia: a multi-model and multi-member approach

NASA Astrophysics Data System (ADS)

Fathalli, Bilel; Pohl, Benjamin; Castel, Thierry; Safi, Mohamed Jomâa

2018-02-01

Temporal and spatial variability of rainfall over Tunisia (at 12 km spatial resolution) is analyzed in a multi-year (1992-2011) ten-member ensemble simulation performed using the WRF model, and a sample of regional climate hindcast simulations from Euro-CORDEX. RCM errors and skills are evaluated against a dense network of local rain gauges. Uncertainties arising, on the one hand, from the different model configurations and, on the other hand, from internal variability are furthermore quantified and ranked at different timescales using simple spread metrics. Overall, the WRF simulation shows good skill for simulating spatial patterns of rainfall amounts over Tunisia, marked by strong altitudinal and latitudinal gradients, as well as the rainfall interannual variability, in spite of systematic errors. Mean rainfall biases are wet in both DJF and JJA seasons for the WRF ensemble, while they are dry in winter and wet in summer for most of the used Euro-CORDEX models. The sign of mean annual rainfall biases over Tunisia can also change from one member of the WRF ensemble to another. Skills in regionalizing precipitation over Tunisia are season dependent, with better correlations and weaker biases in winter. Larger inter-member spreads are observed in summer, likely because of (1) an attenuated large-scale control on Mediterranean and Tunisian climate, and (2) a larger contribution of local convective rainfall to the seasonal amounts. Inter-model uncertainties are globally stronger than those attributed to model's internal variability. However, inter-member spreads can be of the same magnitude in summer, emphasizing the important stochastic nature of the summertime rainfall variability over Tunisia.