Melanoma patients respond to a cytotoxic T lymphocyte-defined self-peptide with diverse and nonoverlapping T-cell receptor repertoires.

HLA-A2+ melanoma patients develop naturally a strong CD8+ T cell response to a self-peptide derived from Melan-A. Here, we have used HLA-A2/peptide tetramers to isolate Melan-A-specific T cells from tumor-infiltrated lymph nodes of two HLA-A2+ melanoma patients and analyzed their TCR beta chain V segment and complementarity determining region 3 length and sequence. We found a broad diversity in Melan-A-specific immune T-cell receptor (TCR) repertoires in terms of both TCR beta chain variable gene segment usage and clonal composition. In addition, immune TCR repertoires selected in the patients were not overlapping. In contrast to previously characterized CD8+ T-cell responses to viral infections, this study provides evidence against usage of highly restricted TCR repertoire in the natural response to a self-differentiation tumor antigen.

An efficient and effective localization method for networked disjoint top-view cameras

Disjoint top-view networked cameras are among the most commonly utilized networks in many applications. One of the open questions for these cameras' study is the computation of extrinsic parameters (positions and orientations), named extrinsic calibration or localization of cameras. Current approaches either rely on strict assumptions of the object motion for accurate results or fail to provide results of high accuracy without the requirement of the object motion. To address these shortcomings, we present a location-constrained maximum a posteriori (LMAP) approach by applying known locations in the surveillance area, some of which would be passed by the object opportunistically. The LMAP approach formulates the problem as a joint inference of the extrinsic parameters and object trajectory based on the cameras' observations and the known locations. In addition, a new task-oriented evaluation metric, named MABR (the Maximum value of All image points' Back-projected localization errors' L2 norms Relative to the area of field of view), is presented to assess the quality of the calibration results in an indoor object tracking context. Finally, results herein demonstrate the superior performance of the proposed method over the state-of-the-art algorithm based on the presented MABR and classical evaluation metric in simulations and real experiments.

Overview of the INEX 2008 Ad Hoc Track

This paper gives an overview of the INEX 2008 Ad Hoc Track. The main goals of the Ad Hoc Track were two-fold. The first goal was to investigate the value of the internal document structure (as provided by the XML mark-up) for retrieving relevant information. This is a continuation of INEX 2007 and, for this reason, the retrieval results are liberalized to arbitrary passages and measures were chosen to fairly compare systems retrieving elements, ranges of elements, and arbitrary passages. The second goal was to compare focused retrieval to article retrieval more directly than in earlier years. For this reason, standard document retrieval rankings have been derived from all runs, and evaluated with standard measures. In addition, a set of queries targeting Wikipedia have been derived from a proxy log, and the runs are also evaluated against the clicked Wikipedia pages. The INEX 2008 Ad Hoc Track featured three tasks: For the Focused Task a ranked-list of nonoverlapping results (elements or passages) was needed. For the Relevant in Context Task non-overlapping results (elements or passages) were returned grouped by the article from which they came. For the Best in Context Task a single starting point (element start tag or passage start) for each article was needed. We discuss the results for the three tasks, and examine the relative effectiveness of element and passage retrieval. This is examined in the context of content only (CO, or Keyword) search as well as content and structure (CAS, or structured) search. Finally, we look at the ability of focused retrieval techniques to rank articles, using standard document retrieval techniques, both against the judged topics as well as against queries and clicks from a proxy log.

Direct estimate of transport length scales in semiconducting polymers

A method for determining the electron/hole transport length scale of model semiconducting polymer systems by scanning a narrow-light probe beam over the nonoverlapping anode/cathode region in asymmetric sandwich device structures is presented (see figure). Electron versus hole collection efficacy, and disorder and spatial anisotropy in the electrical transport parameters can be estimated.

Multiple imaging and multichannel optical processing with split lenses

The use of split lenses for multiple imaging and multichannel optical processing is demonstrated. Conditions are obtained for nonoverlapping of multipled images and avoiding crosstalk in the multichannel processing. Almost uniform intensity across the multipled images is an advantage here, while the low ƒ/No. of the split lens segments puts a limit in the resolution in image processing. Experimental results of multiple imaging and of a few multichannel processing are presented.

Independent Transport and Sorting of Functionally Distinct Protein Families in Tetrahymena thermophila Dense Core Secretory Granules

Dense core granules (DCGs) in Tetrahymena thermophila contain two protein classes. Proteins in the first class, called granule lattice (Grl), coassemble to form a crystalline lattice within the granule lumen. Lattice expansion acts as a propulsive mechanism during DCG release, and Grl proteins are essential for efficient exocytosis. The second protein class, defined by a C-terminal beta/gamma-crystallin domain, is poorly understood. Here, we have analyzed the function and sorting of Grt1p (granule tip), which was previously identified as an abundant protein in this family. Cells lacking all copies of GRT1, together with the closely related GRT2, accumulate wild-type levels of docked DCGs. Unlike cells disrupted in any of the major GRL genes, Delta GRT1 Delta GRT2 cells show no defect in secretion, indicating that neither exocytic fusion nor core expansion depends on GRT1. These results suggest that Grl protein sorting to DCGs is independent of Grt proteins. Consistent with this, the granule core lattice in Delta GRT1 Delta GRT2 cells appears identical to that in wild-type cells by electron microscopy, and the only biochemical component visibly absent is Grt1p itself. Moreover, gel filtration showed that Grl and Grt proteins in cell homogenates exist in nonoverlapping complexes, and affinity-isolated Grt1p complexes do not contain Grl proteins. These data demonstrate that two major classes of proteins in Tetrahymena DCGs are likely to be independently transported during DCG biosynthesis and play distinct roles in granule function. The role of Grt1p may primarily be postexocytic; consistent with this idea, DCG contents from Delta GRT1 Delta GRT2 cells appear less adhesive than those from the wild type.

Complete genome sequence of lymphocystis disease virus isolated from China

Lymphocystis diseases in fish throughout the world have been extensively described. Here we report the complete genome sequence of lymphocystis disease virus isolated in China (LCDV-C), an LCDV isolated from cultured flounder (Paralichthys olivaceus) with lymphocystis disease in China. The LCDV-C genome is 186,250 bp, with a base composition of 27.25% G+C. Computer-assisted analysis revealed 240 potential open reading frames (ORFs) and 176 nonoverlapping putative viral genes, which encode polypeptides ranging from 40 to 1,193 amino acids. The percent coding density is 67%, and the average length of each ORF is 702 bp. A search of the GenBank database using the 176 individual putative genes revealed 103 homologues to the corresponding ORFs of LCDV-1 and 73 potential genes that were not found in LCDV-1 and other iridoviruses. Among the 73 genes, there are 8 genes that contain conserved domains of cellular genes and 65 novel genes that do not show any significant homology with the sequences in public databases. Although a certain extent of similarity between putative gene products of LCDV-C and corresponding proteins of LCDV-1 was revealed, no colinearity was detected when their ORF arrangements and coding strategies were compared to each other, suggesting that a high degree of genetic rearrangements between them has occurred. And a large number of tandem and overlapping repeated sequences were observed in the LCDV-C genome. The deduced amino acid sequence of the major capsid protein (MCP) presents the highest identity to those of LCDV-1 and other iridoviruses among the LCDV-C gene products. Furthermore, a phylogenetic tree was constructed based on the multiple alignments of nine MCP amino acid sequences. Interestingly, LCDV-C and LCDV-1 were clustered together, but their amino acid identity is much less than that in other clusters. The unexpected levels of divergence between their genomes in size, gene organization, and gene product identity suggest that LCDV-C and LCDV-1 shouldn't belong to a same species and that LCDV-C should be considered a species different from LCDV-1.

Similar T-cell immune responses induced by group M consensus env immunogens with wild-type or minimum consensus variable regions.

Consensus HIV-1 genes can decrease the genetic distances between candidate immunogens and field virus strains. To ensure the functionality and optimal presentation of immunologic epitopes, we generated two group-M consensus env genes that contain variable regions either from a wild-type B/C recombinant virus isolate (CON6) or minimal consensus elements (CON-S) in the V1, V2, V4, and V5 regions. C57BL/6 and BALB/c mice were primed twice with CON6, CON-S, and subtype control (92UG37_A and HXB2/Bal_B) DNA and boosted with recombinant vaccinia virus (rVV). Mean antibody titers against 92UG37_A, 89.6_B, 96ZM651_C, CON6, and CON-S Env protein were determined. Both CON6 and CON-S induced higher mean antibody titers against several of the proteins, as compared with the subtype controls. However, no significant differences were found in mean antibody titers in animals immunized with CON6 or CON-S. Cellular immune responses were measured by using five complete Env overlapping peptide sets: subtype A (92UG37_A), subtype B (MN_B, 89.6_B and SF162_B), and subtype C (Chn19_C). The intensity of the induced cellular responses was measured by using pooled Env peptides; T-cell epitopes were identified by using matrix peptide pools and individual peptides. No significant differences in T-cell immune-response intensities were noted between CON6 and CON-S immunized BALB/c and C57BL/6 mice. In BALB/c mice, 10 and eight nonoverlapping T-cell epitopes were identified in CON6 and CON-S, whereas eight epitopes were identified in 92UG37_A and HXB2/BAL_B. In C57BL/6 mice, nine and six nonoverlapping T-cell epitopes were identified after immunization with CON6 and CON-S, respectively, whereas only four and three were identified in 92UG37_A and HXB2/BAL_B, respectively. When combined together from both mouse strains, 18 epitopes were identified. The group M artificial consensus env genes, CON6 and CON-S, were equally immunogenic in breadth and intensity for inducing humoral and cellular immune responses.

Nichtüberlappende Gebietszerlegungsmethoden für lineare und quasilineare (monotone und nichtmonotone) Probleme

In dieser Arbeit werden nichtüberlappende Gebietszerlegungsmethoden einerseits hinsichtlich der zu lösenden Problemklassen verallgemeinert und andererseits in bisher nicht untersuchten Kontexten betrachtet. Dabei stehen funktionalanalytische Untersuchungen zur Wohldefiniertheit, eindeutigen Lösbarkeit und Konvergenz im Vordergrund. Im ersten Teil werden lineare elliptische Dirichlet-Randwertprobleme behandelt, wobei neben Problemen mit dominantem Hauptteil auch solche mit singulärer Störung desselben, wie konvektions- oder reaktionsdominante Probleme zugelassen sind. Der zweite Teil befasst sich mit (gleichmäßig) monotonen koerziven quasilinearen elliptischen Dirichlet-Randwertproblemen. In beiden Fällen wird das Lipschitz-Gebiet in endlich viele Lipschitz-Teilgebiete zerlegt, wobei insbesondere Kreuzungspunkte und Teilgebiete ohne Außenrand zugelassen sind. Anschließend werden Transmissionsprobleme mit frei wählbaren $L^{\infty}$-Parameterfunktionen hergeleitet, wobei die Konormalenableitungen als Funktionale auf geeigneten Funktionenräumen über den Teilrändern ($H_{00}^{1/2}(\Gamma)$) interpretiert werden. Die iterative Lösung dieser Transmissionsprobleme mit einem Ansatz von Deng führt auf eine Substrukturierungsmethode mit Robin-artigen Transmissionsbedingungen, bei der eine Auswertung der Konormalenableitungen aufgrund einer geschickten Aufdatierung der Robin-Daten nicht notwendig ist (insbesondere ist die bekannte Robin-Robin-Methode von Lions als Spezialfall enthalten). Die Konvergenz bezüglich einer partitionierten $H^1$-Norm wird für beide Problemklassen gezeigt. Dabei werden keine über $H^1$ hinausgehende Regularitätsforderungen an die Lösungen gestellt und die Gebiete müssen keine zusätzlichen Glattheitsvoraussetzungen erfüllen. Im letzten Kapitel werden nichtmonotone koerzive quasilineare Probleme untersucht, wobei das Zugrunde liegende Gebiet nur in zwei Lipschitz-Teilgebiete zerlegt sein soll. Das zugehörige nichtlineare Transmissionsproblem wird durch Kirchhoff-Transformation in lineare Teilprobleme mit nichtlinearen Kopplungsbedingungen überführt. Ein optimierungsbasierter Lösungsansatz, welcher einen geeigneten Abstand der rücktransformierten Dirichlet-Daten der linearen Teilprobleme auf den Teilrändern minimiert, führt auf ein optimales Kontrollproblem. Die dabei entstehenden regularisierten freien Minimierungsprobleme werden mit Hilfe eines Gradientenverfahrens unter minimalen Glattheitsforderungen an die Nichtlinearitäten gelöst. Unter zusätzlichen Glattheitsvoraussetzungen an die Nichtlinearitäten und weiteren technischen Voraussetzungen an die Lösung des quasilinearen Ausgangsproblems, kann zudem die quadratische Konvergenz des Newton-Verfahrens gesichert werden.

The Role of Epistemic Monitoring in Language Comprehension

In der psycholinguistischen Forschung ist die Annahme weitverbreitet, dass die Bewertung von Informationen hinsichtlich ihres Wahrheitsgehaltes oder ihrer Plausibilität (epistemische Validierung; Richter, Schroeder & Wöhrmann, 2009) ein strategischer, optionaler und dem Verstehen nachgeschalteter Prozess ist (z.B. Gilbert, 1991; Gilbert, Krull & Malone, 1990; Gilbert, Tafarodi & Malone, 1993; Herbert & Kübler, 2011). Eine zunehmende Anzahl an Studien stellt dieses Zwei-Stufen-Modell von Verstehen und Validieren jedoch direkt oder indirekt in Frage. Insbesondere Befunde zu Stroop-artigen Stimulus-Antwort-Kompatibilitätseffekten, die auftreten, wenn positive und negative Antworten orthogonal zum aufgaben-irrelevanten Wahrheitsgehalt von Sätzen abgegeben werden müssen (z.B. eine positive Antwort nach dem Lesen eines falschen Satzes oder eine negative Antwort nach dem Lesen eines wahren Satzes; epistemischer Stroop-Effekt, Richter et al., 2009), sprechen dafür, dass Leser/innen schon beim Verstehen eine nicht-strategische Überprüfung der Validität von Informationen vornehmen. Ausgehend von diesen Befunden war das Ziel dieser Dissertation eine weiterführende Überprüfung der Annahme, dass Verstehen einen nicht-strategischen, routinisierten, wissensbasierten Validierungsprozesses (epistemisches Monitoring; Richter et al., 2009) beinhaltet. Zu diesem Zweck wurden drei empirische Studien mit unterschiedlichen Schwerpunkten durchgeführt. Studie 1 diente der Untersuchung der Fragestellung, ob sich Belege für epistemisches Monitoring auch bei Informationen finden lassen, die nicht eindeutig wahr oder falsch, sondern lediglich mehr oder weniger plausibel sind. Mithilfe des epistemischen Stroop-Paradigmas von Richter et al. (2009) konnte ein Kompatibilitätseffekt von aufgaben-irrelevanter Plausibilität auf die Latenzen positiver und negativer Antworten in zwei unterschiedlichen experimentellen Aufgaben nachgewiesen werden, welcher dafür spricht, dass epistemisches Monitoring auch graduelle Unterschiede in der Übereinstimmung von Informationen mit dem Weltwissen berücksichtigt. Darüber hinaus belegen die Ergebnisse, dass der epistemische Stroop-Effekt tatsächlich auf Plausibilität und nicht etwa auf der unterschiedlichen Vorhersagbarkeit von plausiblen und unplausiblen Informationen beruht. Das Ziel von Studie 2 war die Prüfung der Hypothese, dass epistemisches Monitoring keinen evaluativen Mindset erfordert. Im Gegensatz zu den Befunden anderer Autoren (Wiswede, Koranyi, Müller, Langner, & Rothermund, 2013) zeigte sich in dieser Studie ein Kompatibilitätseffekt des aufgaben-irrelevanten Wahrheitsgehaltes auf die Antwortlatenzen in einer vollständig nicht-evaluativen Aufgabe. Die Ergebnisse legen nahe, dass epistemisches Monitoring nicht von einem evaluativen Mindset, möglicherweise aber von der Tiefe der Verarbeitung abhängig ist. Studie 3 beleuchtete das Verhältnis von Verstehen und Validieren anhand einer Untersuchung der Online-Effekte von Plausibilität und Vorhersagbarkeit auf Augenbewegungen beim Lesen kurzer Texte. Zusätzlich wurde die potentielle Modulierung dieser Effeke durch epistemische Marker, die die Sicherheit von Informationen anzeigen (z.B. sicherlich oder vielleicht), untersucht. Entsprechend der Annahme eines schnellen und nicht-strategischen epistemischen Monitoring-Prozesses zeigten sich interaktive Effekte von Plausibilität und dem Vorhandensein epistemischer Marker auf Indikatoren früher Verstehensprozesse. Dies spricht dafür, dass die kommunizierte Sicherheit von Informationen durch den Monitoring-Prozess berücksichtigt wird. Insgesamt sprechen die Befunde gegen eine Konzeptualisierung von Verstehen und Validieren als nicht-überlappenden Stufen der Informationsverarbeitung. Vielmehr scheint eine Bewertung des Wahrheitsgehalts oder der Plausibilität basierend auf dem Weltwissen – zumindest in gewissem Ausmaß – eine obligatorische und nicht-strategische Komponente des Sprachverstehens zu sein. Die Bedeutung der Befunde für aktuelle Modelle des Sprachverstehens und Empfehlungen für die weiterführende Forschung zum Vehältnis von Verstehen und Validieren werden aufgezeigt.

Mapping of domains on HIV envelope protein mediating association with calnexin and protein-disulfide isomerase.

The cell catalysts calnexin (CNX) and protein-disulfide isomerase (PDI) cooperate in establishing the disulfide bonding of the HIV envelope (Env) glycoprotein. Following HIV binding to lymphocytes, cell-surface PDI also reduces Env to induce the fusogenic conformation. We sought to define the contact points between Env and these catalysts to illustrate their potential as therapeutic targets. In lysates of Env-expressing cells, 15% of the gp160 precursor, but not gp120, coprecipitated with CNX, whereas only 0.25% of gp160 and gp120 coprecipitated with PDI. Under in vitro conditions, which mimic the Env/PDI interaction during virus/cell contact, PDI readily associated with Env. The domains of Env interacting in cellulo with CNX or in vitro with PDI were then determined using anti-Env antibodies whose binding site was occluded by CNX or PDI. Antibodies against domains V1/V2, C2, and the C terminus of V3 did not bind CNX-associated Env, whereas those against C1, V1/V2, and the CD4-binding domain did not react with PDI-associated Env. In addition, a mixture of the latter antibodies interfered with PDI-mediated Env reduction. Thus, Env interacts with intracellular CNX and extracellular PDI via discrete, largely nonoverlapping, regions. The sites of interaction explain the mode of action of compounds that target these two catalysts and may enable the design of further new competitive agents.

High functional coherence in k-partite protein cliques of protein interaction networks

We introduce a new topological concept called k-partite protein cliques to study protein interaction (PPI) networks. In particular, we examine functional coherence of proteins in k-partite protein cliques. A k-partite protein clique is a k-partite maximal clique comprising two or more nonoverlapping protein subsets between any two of which full interactions are exhibited. In the detection of PPI’s k-partite maximal cliques, we propose to transform PPI networks into induced K-partite graphs with proteins as vertices where edges only exist among the graph’s partites. Then, we present a k-partite maximal clique mining (MaCMik) algorithm to enumerate k-partite maximal cliques from K-partite graphs. Our MaCMik algorithm is applied to a yeast PPI network. We observe that there does exist interesting and unusually high functional coherence in k-partite protein cliques—most proteins in k-partite protein cliques, especially those in the same partites, share the same functions. Therefore, the idea of k-partite protein cliques suggests a novel approach to characterizing PPI networks, and may help function prediction for unknown proteins.

Using gene-history and expression analyses to assess the involvement of LGI genes in human disorders

Mutations in the leucine-rich, glioma-inactivated 1 gene, LGI1, cause autosomal-dominant lateral temporal lobe epilepsy via unknown mechanisms. LGI1 belongs to a subfamily of leucine-rich repeat genes comprising four members (LGI1–LGI4) in mammals. In this study, both comparative developmental as well as molecular evolutionary methods were applied to investigate the evolution of the LGI gene family and, subsequently, of the functional importance of its different gene members. Our phylogenetic studies suggest that LGI genes evolved early in the vertebrate lineage. Genetic and expression analyses of all five zebrafish lgi genes revealed duplications of lgi1 and lgi2, each resulting in two paralogous gene copies with mostly nonoverlapping expression patterns. Furthermore, all vertebrate LGI1 orthologs experience high levels of purifying selection that argue for an essential role of this gene in neural development or function. The approach of combining expression and selection data used here exemplarily demonstrates that in poorly characterized gene families a framework of evolutionary and expression analyses can identify those genes that are functionally most important and are therefore prime candidates for human disorders.

Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)

By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards (Chlamydosaurus kingii) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark-recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.

A comprehensive analytical subdomain model and its field solutions for surface-mounted permanent magnet machines

This paper presents a comprehensive analytical subdomain model together with its field solutions for predicting the magnetic field distributions in surface-mounted permanent magnet (PM) machines. The tooth tips and slotting effects during open-circuit, armature reaction, and on-load conditions are considered when deriving the model and developing its solutions. The model derivations and field solutions are extended from a previous model, and can be applied to PM machines with any combinations of slot and pole numbers and any magnetization patterns in the magnets. This model is initially formulated according to Laplace's and Poisson's equations in 2-D polar coordinates by the separation of variables technique in four subdomains, such as magnet, airgap, winding slots, and slot-openings. The field solution of each subdomain is obtained applying the appropriate boundary conditions and interface conditions between every two subdomains, respectively, which can precisely account for the mutual influence between slots. Finite element analysis (FEA) is later deployed to validate the analytical results in a surface-mounted PM machine that has nonoverlapping winding arrangement. For validation purposes, PM machines having 3-slot/2-pole with parallel magnetization and 12-slot/10-pole with either parallel or radial magnetizations are used for comparisons. Computation of global quantities for the motor which include the phase back-EMF and cogging torque is also included. The results indicate that the proposed analytical model can accurately predict the magnetic field distributions in each subdomain and the motor's global quantities, which are in good agreement with those obtained from the FEA.