Multi-dimensional classification of GABAergic interneurons with Bayesian network-modeled label uncertainty

Abstract Interneuron classification is an important and long-debated topic in neuroscience. A recent study provided a data set of digitally reconstructed interneurons classified by 42 leading neuroscientists according to a pragmatic classification scheme composed of five categorical variables, namely, of the interneuron type and four features of axonal morphology. From this data set we now learned a model which can classify interneurons, on the basis of their axonal morphometric parameters, into these five descriptive variables simultaneously. Because of differences in opinion among the neuroscientists, especially regarding neuronal type, for many interneurons we lacked a unique, agreed-upon classification, which we could use to guide model learning. Instead, we guided model learning with a probability distribution over the neuronal type and the axonal features, obtained, for each interneuron, from the neuroscientists’ classification choices. We conveniently encoded such probability distributions with Bayesian networks, calling them label Bayesian networks (LBNs), and developed a method to predict them. This method predicts an LBN by forming a probabilistic consensus among the LBNs of the interneurons most similar to the one being classified. We used 18 axonal morphometric parameters as predictor variables, 13 of which we introduce in this paper as quantitative counterparts to the categorical axonal features. We were able to accurately predict interneuronal LBNs. Furthermore, when extracting crisp (i.e., non-probabilistic) predictions from the predicted LBNs, our method outperformed related work on interneuron classification. Our results indicate that our method is adequate for multi-dimensional classification of interneurons with probabilistic labels. Moreover, the introduced morphometric parameters are good predictors of interneuron type and the four features of axonal morphology and thus may serve as objective counterparts to the subjective, categorical axonal features.

Multi-dimensional classification of GABAergic interneurons with Bayesian network-modeled label uncertainty

Interneuron classification is an important and long-debated topic in neuroscience. A recent study provided a data set of digitally reconstructed interneurons classified by 42 leading neuroscientists according to a pragmatic classification scheme composed of five categorical variables, namely, of the interneuron type and four features of axonal morphology. From this data set we now learned a model which can classify interneurons, on the basis of their axonal morphometric parameters, into these five descriptive variables simultaneously. Because of differences in opinion among the neuroscientists, especially regarding neuronal type, for many interneurons we lacked a unique, agreed-upon classification, which we could use to guide model learning. Instead, we guided model learning with a probability distribution over the neuronal type and the axonal features, obtained, for each interneuron, from the neuroscientists’ classification choices. We conveniently encoded such probability distributions with Bayesian networks, calling them label Bayesian networks (LBNs), and developed a method to predict them. This method predicts an LBN by forming a probabilistic consensus among the LBNs of the interneurons most similar to the one being classified. We used 18 axonal morphometric parameters as predictor variables, 13 of which we introduce in this paper as quantitative counterparts to the categorical axonal features. We were able to accurately predict interneuronal LBNs. Furthermore, when extracting crisp (i.e., non-probabilistic) predictions from the predicted LBNs, our method outperformed related work on interneuron classification. Our results indicate that our method is adequate for multi-dimensional classification of interneurons with probabilistic labels. Moreover, the introduced morphometric parameters are good predictors of interneuron type and the four features of axonal morphology and thus may serve as objective counterparts to the subjective, categorical axonal features.

Optimal laser intensity profiles for a uniform target illumination in direct-drive inertial confinement fusion

A numerical method providing the optimal laser intensity profiles for a direct-drive inertial confinement fusion scheme has been developed. The method provides an alternative approach to phase-space optimization studies, which can prove computationally expensive. The method applies to a generic irradiation configuration characterized by an arbitrary number NB of laser beams provided that they irradiate the whole target surface, and thus goes beyond previous analyses limited to symmetric configurations. The calculated laser intensity profiles optimize the illumination of a spherical target. This paper focuses on description of the method, which uses two steps: first, the target irradiation is calculated for initial trial laser intensities, and then in a second step the optimal laser intensities are obtained by correcting the trial intensities using the calculated illumination. A limited number of example applications to direct drive on the Laser MegaJoule (LMJ) are described.

Simulating the remote handling of the blanket segments in DEMO fusion reactor with thermo-mechanical meshfree multibody dynamics

The present study shows a first approach to the simulation of the remote handling oper- ation which takes into account the thermal and flexible behavior of the blanket segments and its implications on the remote handling equipment, in order to validate and improve its design.

Multisensor data fusion for accurate modelling of mobile objects

In the last decade, multi-sensor data fusion has become a broadly demanded discipline to achieve advanced solutions that can be applied in many real world situations, either civil or military. In Defence,accurate detection of all target objects is fundamental to maintaining situational awareness, to locating threats in the battlefield and to identifying and protecting strategically own forces. Civil applications, such as traffic monitoring, have similar requirements in terms of object detection and reliable identification of incidents in order to ensure safety of road users. Thanks to the appropriate data fusion technique, we can give these systems the power to exploit automatically all relevant information from multiple sources to face for instance mission needs or assess daily supervision operations. This paper focuses on its application to active vehicle monitoring in a particular area of high density traffic, and how it is redirecting the research activities being carried out in the computer vision, signal processing and machine learning fields for improving the effectiveness of detection and tracking in ground surveillance scenarios in general. Specifically, our system proposes fusion of data at a feature level which is extracted from a video camera and a laser scanner. In addition, a stochastic-based tracking which introduces some particle filters into the model to deal with uncertainty due to occlusions and improve the previous detection output is presented in this paper. It has been shown that this computer vision tracker contributes to detect objects even under poor visual information. Finally, in the same way that humans are able to analyze both temporal and spatial relations among items in the scene to associate them a meaning, once the targets objects have been correctly detected and tracked, it is desired that machines can provide a trustworthy description of what is happening in the scene under surveillance. Accomplishing so ambitious task requires a machine learning-based hierarchic architecture able to extract and analyse behaviours at different abstraction levels. A real experimental testbed has been implemented for the evaluation of the proposed modular system. Such scenario is a closed circuit where real traffic situations can be simulated. First results have shown the strength of the proposed system.

Microstructural and mechanical characterization of tungsten based materials for fusion reactors

El wolframio (W) y sus aleaciones se consideran los mejores candidatos para la construcción del divertor en la nueva generación de reactores de fusión nuclear. Este componente va a recibir las cargas térmicas más elevadas durante el funcionamiento del reactor ya que estará en contacto directo con el plasma. En los últimos años, después de un profundo análisis y siguiendo una estrategia de reducción de costes, la Organización de ITER tomó la decisión de construir el divertor integramente de wolframio desde el principio. Por ello, el wolframio no sólo actuará como material en contacto con el plasma (PFM), sino que también tendría aplicaciones estructurales. El wolframio, debido a sus excelentes propiedades termo-físicas, cumple todos los requerimientos para ser utilizado como PFM, sin embargo, su inherente fragilidad pone en peligro su uso estructural. Por tanto, uno de los principales objetivos de esta tesis es encontrar una aleación de wolframio con menor fragilidad. Durante éste trabajo, se realizó la caracterización microstructural y mecánica de diferentes materiales basados en wolframio. Sin embargo, ésta tarea es un reto debido a la pequeña cantidad de material suministrado, su reducido tamaño de grano y fragilidad. Por ello, para una correcta medida de todas las propiedades físicas y mecánicas se utilizaron diversas técnicas experimentales. Algunas de ellas se emplean habitualmente como la nanoindentación o los ensayos de flexión en tres puntos (TPB). Sin embargo, otras fueron especificamente desarrolladas e implementadas durante el desarrollo de esta tesis como es el caso de la medida real de la tenacidad de fractura en los materiales masivos, o de las medidas in situ de la tenacidad de fractura en las láminas delgadas de wolframio. Diversas composiciones de aleaciones de wolframio masivas (W-1% Y2O3, W-2% V-0.5% Y2O3, W-4% V-0.5% Y2O3, W-2% Ti-1% La2O3 y W-4% Ti-1% La2O3) se han estudiado y comparado con un wolframio puro producido en las mismas condiciones. Estas aleaciones, producidas por ruta pulvimetalúrgica de aleado mecánico (MA) y compactación isostática en caliente (HIP), fueron microstructural y mecánicamente caracterizadas desde 77 hasta 1473 K en aire y en alto vacío. Entre otras propiedades físicas y mecánicas se midieron la dureza, el módulo elástico, la resistencia a flexión y la tenacidad de fractura para todas las aleaciones. Finalmente se analizaron las superficies de fractura después de los ensayos de TPB para relacionar los micromecanismos de fallo con el comportamiento macroscópico a rotura. Los resultados obtenidos mostraron un comportamiento mecánico frágil en casi todo el intervalo de temperaturas y para casi todas las aleaciones sin mejoría de la temperatura de transición dúctil-frágil (DBTT). Con el fin de encontrar un material base wolframio con una DBTT más baja se realizó también un estudio, aún preliminar, de láminas delgadas de wolframio puro y wolframio dopado con 0.005wt.% potasio (K). Éstas láminas fueron fabricadas industrialmente mediante sinterizado y laminación en caliente y en frío y se sometieron posteriormente a un tratamiento térmico de recocido desde 1073 hasta 2673 K. Se ha analizado la evolución de su microestructura y las propiedades mecánicas al aumentar la temperatura de recocido. Los resultados mostraron la estabilización de los granos de wolframio con el incremento de la temperatura de recocido en las láminas delgadas de wolframio dopado con potasio. Sin embargo, es necesario realizar estudios adicionales para entender mejor la microstructura y algunas propiedades mecánicas de estos materiales, como la tenacidad de fractura. Tungsten (W) and tungsten-based alloys are considered to be the best candidate materials for fabricating the divertor in the next-generation nuclear fusion reactors. This component will experience the highest thermal loads during the operation of a reactor since it directly faces the plasma. In recent years, after thorough analysis that followed a strategy of cost reduction, the ITER Organization decided to built a full-tunsgten divertor before the first nuclear campaigns. Therefore, tungsten will be used not only as a plasma-facing material (PFM) but also in structural applications. Tungsten, due to its the excellent thermo-physical properties fulfils the requirements of a PFM, however, its use in structural applications is compromised due to its inherent brittleness. One of the objectives of this phD thesis is therefore, to find a material with improved brittleness behaviour. The microstructural and mechanical characterisation of different tunsgten-based materials was performed. However, this is a challenging task because of the reduced laboratory-scale size of the specimens provided, their _ne microstructure and their brittleness. Consequently, many techniques are required to ensure an accurate measurement of all the mechanical and physical properties. Some of the applied methods have been widely used such as nanoindentation or three-point bending (TPB) tests. However, other methods were specifically developed and implemented during this work such as the measurement of the real fracture toughness of bulk-tunsgten alloys or the in situ fracture toughness measurements of very thin tungsten foils. Bulk-tunsgten materials with different compositions (W-1% Y2O3, W-2% V- 0.5% Y2O3, W-4% V-0.5% Y2O3, W-2% Ti-1% La2O3 and W-4% Ti-1% La2O3) were studied and compared with pure tungsten processed under the same conditions. These alloys, produced by a powder metallurgical route of mechanical alloying (MA) and hot isostatic pressing (HIP), were microstructural and mechanically characterised from 77 to 1473 K in air and under high vacuum conditions. Hardness, elastic modulus, flexural strength and fracture toughness for all of the alloys were measured in addition to other physical and mechanical properties. Finally, the fracture surfaces after the TPB tests were analysed to correlate the micromechanisms of failure with the macroscopic behaviour. The results reveal brittle mechanical behaviour in almost the entire temperature range for the alloys and micromechanisms of failure with no improvement in the ductile-brittle transition temperature (DBTT). To continue the search of a tungsten material with lowered DBTT, a preliminary study of pure tunsgten and 0.005 wt.% potassium (K)-doped tungsten foils was also performed. These foils were industrially produced by sintering and hot and cold rolling. After that, they were annealed from 1073 to 2673 K to analyse the evolution of the microstructural and mechanical properties with increasing annealing temperature. The results revealed the stabilisation of the tungsten grains with increasing annealing temperature in the potassium-doped tungsten foil. However, additional studies need to be performed to gain a better understanding of the microstructure and mechanical properties of these materials such as fracture toughness.

Optimization of Dengue immunoassay by label-free interferometric optical detection method

In this communication we report a direct immunoassay for detecting dengue virus by means of a label-free interferometric optical detection method. We also demonstrate how we can optimize this sensing response by adding a blocking step able to significantly enhance the optical sensing response. The blocking reagent used for this optimization is a dry milk diluted in phosphate buffered saline. The recognition curve of dengue virus over the proposed surface sensor demonstrates the capacity of this method to be applied in Point of Care technology.

Fetal origins of the TEL-AML1 fusion gene in identical twins with leukemia

The TEL (ETV6)−AML1 (CBFA2) gene fusion is the most common reciprocal chromosomal rearrangement in childhood cancer occurring in ≈25% of the most predominant subtype of leukemia— common acute lymphoblastic leukemia. The TEL-AML1 genomic sequence has been characterized in a pair of monozygotic twins diagnosed at ages 3 years, 6 months and 4 years, 10 months with common acute lymphoblastic leukemia. The twin leukemic DNA shared the same unique (or clonotypic) but nonconstitutive TEL-AML1 fusion sequence. The most plausible explanation for this finding is a single cell origin of the TEL-AML fusion in one fetus in utero, probably as a leukemia-initiating mutation, followed by intraplacental metastasis of clonal progeny to the other twin. Clonal identity is further supported by the finding that the leukemic cells in the two twins shared an identical rearranged IGH allele. These data have implications for the etiology and natural history of childhood leukemia.

A synthetic all d-amino acid peptide corresponding to the N-terminal sequence of HIV-1 gp41 recognizes the wild-type fusion peptide in the membrane and inhibits HIV-1 envelope glycoprotein-mediated cell fusion

Recent studies demonstrated that a synthetic fusion peptide of HIV-1 self-associates in phospholipid membranes and inhibits HIV-1 envelope glycoprotein-mediated cell fusion, presumably by interacting with the N-terminal domain of gp41 and forming inactive heteroaggregates [Kliger, Y., Aharoni, A., Rapaport, D., Jones, P., Blumenthal, R. & Shai, Y. (1997) J. Biol. Chem. 272, 13496–13505]. Here, we show that a synthetic all d-amino acid peptide corresponding to the N-terminal sequence of HIV-1 gp41 (D-WT) of HIV-1 associates with its enantiomeric wild-type fusion (WT) peptide in the membrane and inhibits cell fusion mediated by the HIV-1 envelope glycoprotein. D-WT does not inhibit cell fusion mediated by the HIV-2 envelope glycoprotein. WT and D-WT are equally potent in inducing membrane fusion. D-WT peptide but not WT peptide is resistant to proteolytic digestion. Structural analysis showed that the CD spectra of D-WT in trifluoroethanol/water is a mirror image of that of WT, and attenuated total reflectance–fourier transform infrared spectroscopy revealed similar structures and orientation for the two enantiomers in the membrane. The results reveal that the chirality of the synthetic peptide corresponding to the HIV-1 gp41 N-terminal sequence does not play a role in liposome fusion and that the peptides’ chirality is not necessarily required for peptide–peptide interaction within the membrane environment. Furthermore, studies along these lines may provide criteria to design protease-resistant therapeutic agents against HIV and other viruses.

Collagen-binding growth factors: Production and characterization of functional fusion proteins having a collagen-binding domain

The autocrine/paracrine peptide signaling molecules such as growth factors have many promising biologic activities for clinical applications. However, one cannot expect specific therapeutic effects of the factors administered by ordinary drug delivery systems as they have limited target specificity and short half-lives in vivo. To overcome the difficulties in using growth factors as therapeutic agents, we have produced fusion proteins consisting of growth factor moieties and a collagen-binding domain (CBD) derived from Clostridium histolyticum collagenase. The fusion proteins carrying the epidermal growth factor (EGF) or basic fibroblast growth factor (bFGF) at the N terminal of CBD (CBEGF/CBFGF) tightly bound to insoluble collagen and stimulated the growth of BALB/c 3T3 fibroblasts as much as the unfused counterparts. CBEGF, when injected subcutaneously into nude mice, remained at the sites of injection for up to 10 days, whereas EGF was not detectable 24 h after injection. Although CBEGF did not exert a growth-promoting effect in vivo, CBFGF, but not bFGF, strongly stimulated the DNA synthesis in stromal cells at 5 days and 7 days after injection. These results indicate that CBD may be used as an anchoring unit to produce fusion proteins nondiffusible and long-lasting in vivo.

Cell-specific viral targeting mediated by a soluble retroviral receptor-ligand fusion protein

TVA, the cellular receptor for subgroup A avian leukosis viruses (ALV-A) can mediate viral entry when expressed as a transmembrane protein or as a glycosylphosphatidylinositol-linked protein on the surfaces of transfected mammalian cells. To determine whether mammalian cells can be rendered susceptible to ALV-A infection by attaching a soluble form of TVA to their plasma membranes, the TVA-epidermal growth factor (EGF) fusion protein was generated. TVA-EGF is comprised of the extracellular domain of TVA linked to the mature form of human EGF. Flow cytometric analysis confirmed that TVA-EGF is a bifunctional reagent capable of binding simultaneously to cell surface EGF receptors and to an ALV-A surface envelope-Ig fusion protein. TVA-EGF prebound to transfected mouse fibroblasts expressing either wild-type or kinase-deficient human EGF receptors, rendered these cells highly susceptible to infection by ALV-A vectors. Viral infection was blocked specifically in the presence of a recombinant human EGF protein, demonstrating that the binding of TVA-EGF to EGF receptors was essential for infectivity. These studies have demonstrated that a soluble TVA-ligand fusion protein can mediate viral infection when attached to specific cell surfaces, suggesting an approach for targeting retroviral infection to specific cell types.

Rapid and efficient fusion of phospholipid vesicles by the α-helical core of a SNARE complex in the absence of an N-terminal regulatory domain

A protease-resistant core domain of the neuronal SNARE complex consists of an α-helical bundle similar to the proposed fusogenic core of viral fusion proteins [Skehel, J. J. & Wiley, D. C. (1998) Cell 95, 871–874]. We find that the isolated core of a SNARE complex efficiently fuses artificial bilayers and does so faster than full length SNAREs. Unexpectedly, a dramatic increase in speed results from removal of the N-terminal domain of the t-SNARE syntaxin, which does not affect the rate of assembly of v-t SNARES. In the absence of this negative regulatory domain, the half-time for fusion of an entire population of lipid vesicles by isolated SNARE cores (≈10 min) is compatible with the kinetics of fusion in many cell types.

Content mixing and membrane integrity during membrane fusion driven by pairing of isolated v-SNAREs and t-SNAREs

Membrane bilayer fusion has been shown to be mediated by v- and t-SNAREs initially present in separate populations of liposomes and to occur with high efficiency at a physiologically meaningful rate. Lipid mixing was demonstrated to involve both the inner and the outer leaflets of the membrane bilayer. Here, we use a fusion assay that relies on duplex formation of oligonucleotides introduced in separate liposome populations and report that SNARE proteins suffice to mediate complete membrane fusion accompanied by mixing of luminal content. We also find that SNARE-mediated membrane fusion does not compromise the integrity of liposomes.

Comparison of fusion phage libraries displaying VH or single-chain Fv antibody fragments derived from the antibody repertoire of a vaccinated melanoma patient as a source of melanoma-specific targeting molecules

A single-chain Fv (scFv) fusion phage library derived from random combinations of VH and VL (variable heavy and light chains) domains in the antibody repertoire of a vaccinated melanoma patient was previously used to isolate clones that bind specifically to melanoma cells. An unexpected finding was that one of the clones encoded a truncated scFv molecule with most of the VL domain deleted, indicating that a VH domain alone can exhibit tumor-specific binding. In this report a VH fusion phage library containing VH domains unassociated with VL domains was compared with a scFv fusion phage library as a source of melanoma-specific clones; both libraries contained the same VH domains from the vaccinated melanoma patient. The results demonstrate that the clones can be isolated from both libraries, and that both libraries should be used to optimize the chance of isolating clones binding to different epitopes. Although this strategy has been tested only for melanoma, it is also applicable to other cancers. Because of their small size, human origin and specificity for cell surface tumor antigens, the VH and scFv molecules have significant advantages as tumor-targeting molecules for diagnostic and therapeutic procedures and can also serve as probes for identifying the cognate tumor antigens.

Antibodies to several conformation-dependent epitopes of gp120/gp41 inhibit CCR-5-dependent cell-to-cell fusion mediated by the native envelope glycoprotein of a primary macrophage-tropic HIV-1 isolate

The β-chemokine receptor CCR-5 is essential for the efficient entry of primary macrophage-tropic HIV-1 isolates into CD4+ target cells. To study CCR-5-dependent cell-to-cell fusion, we have developed an assay system based on the infection of CD4+ CCR-5+ HeLa cells with a Semliki Forest virus recombinant expressing the gp120/gp41 envelope (Env) from a primary clade B HIV-1 isolate (BX08), or from a laboratory T cell line-adapted strain (LAI). In this system, gp120/gp41 of the “nonsyncytium-inducing,” primary, macrophage-tropic HIV-1BX08 isolate, was at least as fusogenic as that of the “syncytium-inducing” HIV-1LAI strain. BX08 Env-mediated fusion was inhibited by the β-chemokines RANTES (regulated upon activation, normal T cell expressed and secreted) and macrophage inflammatory proteins 1β (MIP-1β) and by antibodies to CD4, whereas LAI Env-mediated fusion was insensitive to these β-chemokines. In contrast soluble CD4 significantly reduced LAI, but not BX08 Env-mediated fusion, suggesting that the primary isolate Env glycoprotein has a reduced affinity for CD4. The domains in gp120/gp41 involved in the interaction with the CD4 and CCR-5 molecules were probed using monoclonal antibodies. For the antibodies tested here, the greatest inhibition of fusion was observed with those directed to conformation-dependent, rather than linear epitopes. Efficient inhibition of fusion was not restricted to epitopes in any one domain of gp120/gp41. The assay was sufficiently sensitive to distinguish between antibody- and β-chemokine-mediated fusion inhibition using serum samples from patient BX08, suggesting that the system may be useful for screening human sera for the presence of biologically significant antibodies.