950 resultados para Similarity analysis


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Background Parasitic wasps constitute one of the largest group of venomous animals. Although some physiological effects of their venoms are well documented, relatively little is known at the molecular level on the protein composition of these secretions. To identify the majority of the venom proteins of the endoparasitoid wasp Chelonus inanitus (Hymenoptera: Braconidae), we have randomly sequenced 2111 expressed sequence tags (ESTs) from a cDNA library of venom gland. In parallel, proteins from pure venom were separated by gel electrophoresis and individually submitted to a nano-LC-MS/MS analysis allowing comparison of peptides and ESTs sequences. Results About 60% of sequenced ESTs encoded proteins whose presence in venom was attested by mass spectrometry. Most of the remaining ESTs corresponded to gene products likely involved in the transcriptional and translational machinery of venom gland cells. In addition, a small number of transcripts were found to encode proteins that share sequence similarity with well-known venom constituents of social hymenopteran species, such as hyaluronidase-like proteins and an Allergen-5 protein. An overall number of 29 venom proteins could be identified through the combination of ESTs sequencing and proteomic analyses. The most highly redundant set of ESTs encoded a protein that shared sequence similarity with a venom protein of unknown function potentially specific of the Chelonus lineage. Venom components specific to C. inanitus included a C-type lectin domain containing protein, a chemosensory protein-like protein, a protein related to yellow-e3 and ten new proteins which shared no significant sequence similarity with known sequences. In addition, several venom proteins potentially able to interact with chitin were also identified including a chitinase, an imaginal disc growth factor-like protein and two putative mucin-like peritrophins. Conclusions The use of the combined approaches has allowed to discriminate between cellular and truly venom proteins. The venom of C. inanitus appears as a mixture of conserved venom components and of potentially lineage-specific proteins. These new molecular data enrich our knowledge on parasitoid venoms and more generally, might contribute to a better understanding of the evolution and functional diversity of venom proteins within Hymenoptera.

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Digital signal processing (DSP) techniques for biological sequence analysis continue to grow in popularity due to the inherent digital nature of these sequences. DSP methods have demonstrated early success for detection of coding regions in a gene. Recently, these methods are being used to establish DNA gene similarity. We present the inter-coefficient difference (ICD) transformation, a novel extension of the discrete Fourier transformation, which can be applied to any DNA sequence. The ICD method is a mathematical, alignment-free DNA comparison method that generates a genetic signature for any DNA sequence that is used to generate relative measures of similarity among DNA sequences. We demonstrate our method on a set of insulin genes obtained from an evolutionarily wide range of species, and on a set of avian influenza viral sequences, which represents a set of highly similar sequences. We compare phylogenetic trees generated using our technique against trees generated using traditional alignment techniques for similarity and demonstrate that the ICD method produces a highly accurate tree without requiring an alignment prior to establishing sequence similarity.

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In this study, 231 strains of Yersinia enterocolitica, 25 strains of Y. intermedia, and 10 strains of Y. bercovieri from human and porcine sources (including reference strains) were analyzed using amplified fragment length polymorphism (AFLP), a whole-genome fingerprinting method for subtyping bacterial isolates. AFLP typing distinguished the different Yersinia species examined. Representatives of Y. enterocolitica biotypes 1A, 1B, 2, 3, and 4 belonged to biotype-related AFLP clusters and were clearly distinguished from each other. Y. enterocolitica biotypes 2, 3, and 4 appeared to be more closely related to each other (83% similarity) than to biotypes 1A (11%) and 1B (47%). Biotype 1A strains exhibited the greatest genetic heterogeneity of the biotypes studied. The biotype 1A genotypes were distributed among four major clusters, each containing strains from both human and porcine sources, confirming the zoonotic potential of this organism. The AFLP technique is a valuable genotypic method for identification and typing of Y. enterocolitica and other Yersinia spp.

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In the context of a synchronic lexical study of the Ede varieties of West Africa, this paper investigates whether the use of different criteria sets to judge the similarity of lexical features in different language varieties yields matching conclusions regarding the relative relationships and clustering of the investigated varieties and thus leads to similar recommendations for further sociolinguistic research. Word lists elicited in 28 Ede varieties were analyzed with the inspection method. To explore the effects of different similarity judgment criteria, two different similarity judgment criteria sets were applied to the elicited data to identify similar lexical items. The quantification of these similarity decisions led to the computation of two similarity matrices which were subsequently analyzed by means of correlation analysis and multidimensional scaling. The findings of this analysis suggest compatible conclusions regarding the relative relationships and clustering of the investigated Ede varieties. However, the matching clustering results do not necessarily lead to the same recommendations for more in-depth sociolinguistic research, when interpreted in terms of an absolute lexical similarity threshold. The indicated ambiguities suggest the usefulness of focusing on the relative, rather than absolute in establishing recommendations for further sociolinguistic research.

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Cluster randomized trials (CRTs) use as the unit of randomization clusters, which are usually defined as a collection of individuals sharing some common characteristics. Common examples of clusters include entire dental practices, hospitals, schools, school classes, villages, and towns. Additionally, several measurements (repeated measurements) taken on the same individual at different time points are also considered to be clusters. In dentistry, CRTs are applicable as patients may be treated as clusters containing several individual teeth. CRTs require certain methodological procedures during sample calculation, randomization, data analysis, and reporting, which are often ignored in dental research publications. In general, due to similarity of the observations within clusters, each individual within a cluster provides less information compared with an individual in a non-clustered trial. Therefore, clustered designs require larger sample sizes compared with non-clustered randomized designs, and special statistical analyses that account for the fact that observations within clusters are correlated. It is the purpose of this article to highlight with relevant examples the important methodological characteristics of cluster randomized designs as they may be applied in orthodontics and to explain the problems that may arise if clustered observations are erroneously treated and analysed as independent (non-clustered).

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Attention has recently been drawn to Enterococcus faecium because of an increasing number of nosocomial infections caused by this species and its resistance to multiple antibacterial agents. However, relatively little is known about the pathogenic determinants of this organism. We have previously identified a cell-wall-anchored collagen adhesin, Acm, produced by some isolates of E. faecium, and a secreted antigen, SagA, exhibiting broad-spectrum binding to extracellular matrix proteins. Here, we analysed the draft genome of strain TX0016 for potential microbial surface components recognizing adhesive matrix molecules (MSCRAMMs). Genome-based bioinformatics identified 22 predicted cell-wall-anchored E. faecium surface proteins (Fms), of which 15 (including Acm) had characteristics typical of MSCRAMMs, including predicted folding into a modular architecture with multiple immunoglobulin-like domains. Functional characterization of one [Fms10; redesignated second collagen adhesin of E. faecium (Scm)] revealed that recombinant Scm(65) (A- and B-domains) and Scm(36) (A-domain) bound to collagen type V efficiently in a concentration-dependent manner, bound considerably less to collagen type I and fibrinogen, and differed from Acm in their binding specificities to collagen types IV and V. Results from far-UV circular dichroism measurements of recombinant Scm(36) and of Acm(37) indicated that these proteins were rich in beta-sheets, supporting our folding predictions. Whole-cell ELISA and FACS analyses unambiguously demonstrated surface expression of Scm in most E. faecium isolates. Strikingly, 11 of the 15 predicted MSCRAMMs clustered in four loci, each with a class C sortase gene; nine of these showed similarity to Enterococcus faecalis Ebp pilus subunits and also contained motifs essential for pilus assembly. Antibodies against one of the predicted major pilus proteins, Fms9 (redesignated EbpC(fm)), detected a 'ladder' pattern of high-molecular-mass protein bands in a Western blot analysis of cell surface extracts from E. faecium, suggesting that EbpC(fm) is polymerized into a pilus structure. Further analysis of the transcripts of the corresponding gene cluster indicated that fms1 (ebpA(fm)), fms5 (ebpB(fm)) and ebpC(fm) are co-transcribed, a result consistent with those for pilus-encoding gene clusters of other Gram-positive bacteria. All 15 genes occurred frequently in 30 clinically derived diverse E. faecium isolates tested. The common occurrence of MSCRAMM- and pilus-encoding genes and the presence of a second collagen-binding protein may have important implications for our understanding of this emerging pathogen.

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The Soehner-Dmochowski strain of murine sarcoma virus (MuSV-SD) was derived from a bone tumor of a New Zealand Black (NZB) rat infected with the Moloney strain of MuSV, which carries the gene encoding the v-mos protein. Serial passage of cell-free tumor extracts both decreased the latent period and resulted in osteosarcomas. Cells from a late passage tumor were established in culture, cell-free extracts frozen, and later inoculated into newborn NZB rats. One of the resulting bone tumors was established in culture and clonal cell lines derived, of which S4 was selected for the present study. The objectives of the study were two-fold: an examination of the genetic organization of MuSV-SD, and an examination of the biochemical characteristics of the viral proteins, since this is an acutely transforming virus which may yield insights into the mechanism of transformation caused by the v-mos protein. Blot hybridization of digested S4 genomic DNA reveals three candidate MuSV-SD integrated viral DNAs. The largest of these, MuSV-SD-6.5, was cloned from an S4 cosmid library, and the complete MuSV-SD-mos sequence was determined. The predicted amino acid sequence of the v-mos protein was compared to that of MuSV-124 and Ht-1, which show a 96.5% and 97.1% similarity, respectively. To characterize the MuSV-SD-mos protein further, immunochemical assays were performed using anti-mos antisera. The immunoblot analysis and immunoprecipitation assays demonstrated that similar levels of the v-mos protein were present in cells chronically infected with either MuSV-SD or MuSV-124; however, the immune complex kinase assay revealed greatly reduced in vitro serine kinase activity of the MuSV-SD-mos protein compared to that of MuSV-124. Sequence analysis demonstrated that the serine at amino acid residue 358 of the MuSV-SD-mos protein, like that of MuSV-Ht-1, had been mutated to a glycine. Mutations of this serine residue have been shown to affect the detectable in vitro kinase activity, however, v-mos proteins containing this mutation still retain transforming properties. Therefore, although the characteristic in vitro kinase activity of the MuSV-SD-mos protein has not been demonstrated, it is clear that this virus is a potent transforming agent. ^

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We consider one-dimensional Schrödinger-type operators in a bounded interval with non-self-adjoint Robin-type boundary conditions. It is well known that such operators are generically conjugate to normal operators via a similarity transformation. Motivated by recent interests in quasi-Hermitian Hamiltonians in quantum mechanics, we study properties of the transformations and similar operators in detail. In the case of parity and time reversal boundary conditions, we establish closed integral-type formulae for the similarity transformations, derive a non-local self-adjoint operator similar to the Schrödinger operator and also find the associated “charge conjugation” operator, which plays the role of fundamental symmetry in a Krein-space reformulation of the problem.

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Structure-function analysis of human Integrator subunit 4 Anupama Sataluri Advisor: Eric. J. Wagner, Ph.D. Uridine-rich small nuclear RNAs (U snRNA) are RNA Polymerase-II (RNAPII) transcripts that are ubiquitously expressed and are known to be essential for gene expression. snRNAs play a key role in mRNA splicing and in histone mRNA expression. Inaccurate snRNA biosynthesis can lead to diseases related to defective splicing and histone mRNA expression. Although the 3′ end formation mechanism and processing machinery of other RNAPII transcripts such as mRNA has been well studied, the mechanism of snRNA 3′ end processing has remained a mystery until the recent discovery of the machinery that mediates this process. In 2005, a complex of 14 subunits (the Integrator complex) associated with RNA Polymerase-II was discovered. The 14subunits were annotated Integrator 1-14 based on their size. The subunits of this complex together were found to facilitate 3′ end processing of snRNA. Identification of the Integrator complex propelled research in the direction of understanding the events of snRNA 3’end processing. Recent studies from our lab confirmed that Integrator subunit (IntS) 9 and 11 together perform the endonucleolytic cleavage of the nascent snRNA 3′ end to generate mature snRNA. However, the role of other members of the Integrator complex remains elusive. Current research in our lab is focused on deciphering the role of each subunit within the Integrator complex This work specifically focuses on elucidating the role of human Integrator subunit 4 (IntS4) and understanding how it facilitates the overall function of the complex. IntS4 has structural similarity with a protein called “Symplekin”, which is part of the mRNA 3’end processing machinery. Symplekin has been thoroughly researched in recent years and structure-function correlation studies in the context of mRNA 3’end processing have reported a scaffold function for Symplekin due to the presence of HEAT repeat motifs in its N-terminus. Based upon the structural similarity between IntS4 and Symplekin, we hypothesized that Integrator subunit 4 may be behaving as a Symplekin-like scaffold molecule that facilitates the interaction between other members of the Integrator Complex. To answer this question, the two important goals of this study were to: 1) identify the region of IntS4, which is important for snRNA 3′ end processing and 2) determine binding partners of IntS4 which promote its function as a scaffold. IntS4 structurally consists of a highly conserved N-terminus with 8 HEAT repeats, followed by a nonconserved C- terminus. A series of siRNA resistant N and C-terminus deletion constructs as well as specific point mutants within its N-terminal HEAT repeats were generated for human IntS4 and, utilizing a snRNA transcriptional readthrough GFP-reporter assay, we tested their ability to rescue misprocessing. This assay revealed a possible scaffold like property of IntS4. To probe IntS4 for interaction partners, we performed co-immunoprecipitation on nuclear extracts of IntS4 expressing stable cell lines and identified IntS3 and IntS5 among other Integrator subunits to be binding partners which facilitate the scaffold like function of hIntS4. These findings have established a critical role for IntS4 in snRNA 3′ end processing, identified that both its N and C termini are essential for its function, and mapped putative interaction domains with other Integrator subunits.

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A multiproxy analysis based on planktic foraminiferal abundances, derived SSTs, and stable planktic isotopes measurements together with alkenone abundances and Uk'37 SSTs was performed on late MIS 6 to early MIS 5d sediment recovered from Site 975 (ODP Leg 161) in the South Balearic Islands basin (Western Mediterranean) with emphasis on reconstructing the climate progression of the last interglacial period. A number of abrupt climate changes related to alternative influence of nutrient rich northern and oligotrophic southern water masses were revealed. Heinrich event 11 and cooling events C27, C26, C25, C24, C23, which have been previously described in the North Atlantic, were recognized. However, in comparison to the eastern North Atlantic mid-latitude region, events C27 and C26 at Site 975 seem to be significantly more pronounced. Together with evidence of a two-phase climate optimum with maximum SSTs reached during its later phase, this implies a close similarity in climate dynamics between the Western Mediterranean and the Nordic seas. We propose that postglacial effects in the Nordic seas had an influence on the western Mediterranean climate via atmospheric circulation and that these effects competed with the insolation force.

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A total of 106 potential duplicate cases involved 277 accessions were detected on the basis of passport data in the durum wheat collection maintained in the CRF-INIA. Similarity between accessions was measured by agro-morphological traits. The 90% of the agro-morphological duplication were verified with gliadin proteins, allowing identification of similar material with greater refinement than agro-morphological data. However, the results indicated not to decide for rationalisation only on the basis of molecular data.

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A total of 106 potential duplicate cases involved 277 accessions were detected on the basis of passport data in the durum wheat collection maintained in the CRF-INIA. Similarity between accessions was measured by agro-morphological traits. The 90% of the agro-morphological duplication were verified with gliadin proteins, allowing identification of similar material with greater refinement than agro-morphological data. However, the results indicated not to decide for rationalisation only on the basis of molecular data

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Linked data offers a promising setting to encode, publish and share metadata of resources. As the matter of fact, it is already adopted by data producers such as European Environment Agency, US and some EU Governs, whose first ambition is to share (meta)data making their processes more effective and transparent. Such as an increasing interest and involvement of data providers surely represents a genuine witness of the web of data success, but in a longer perspective, frameworks supporting linked data consumers in their decision making processes will be a compelling need. In this respect, the talk is introducing SSONDE, a framework enabling in detailed comparison, ranking and selection of linked data resources through the analysis of their RDF ontology driven metadata. SSONDE implements an instance similarity especially designed to support in resource selection, namely the process stakeholders engage to choose a set of resources suitable for a given analysis purpose: (i) it deploys an asymmetric similarity assessment to emphasize information about gains and losses the stakeholders get adopting a resource in place of another; (ii) it relies on an explicit formalization of contexts to tailor the similarity assessment with respect to specific user-defined selection goals. The talk aims at providing an insight on SSONDE instance similarity and it will briefly describe some examples of SSONDE deployment in the context of linked data consumption.

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Idea Management Systems are an implementation of open innovation notion in the Web environment with the use of crowdsourcing techniques. In this area, one of the popular methods for coping with large amounts of data is duplicate de- tection. With our research, we answer a question if there is room to introduce more relationship types and in what degree would this change affect the amount of idea metadata and its diversity. Furthermore, based on hierarchical dependencies between idea relationships and relationship transitivity we propose a number of methods for dataset summarization. To evaluate our hypotheses we annotate idea datasets with new relationships using the contemporary methods of Idea Management Systems to detect idea similarity. Having datasets with relationship annotations at our disposal, we determine if idea features not related to idea topic (e.g. innovation size) have any relation to how annotators perceive types of idea similarity or dissimilarity.

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Esta tesis presenta un análisis teórico del funcionamiento de toberas magnéticas para la propulsión espacial por plasmas. El estudio está basado en un modelo tridimensional y bi-fluido de la expansión supersónica de un plasma caliente en un campo magnético divergente. El modelo básico es ampliado progresivamente con la inclusión de términos convectivos dominantes de electrones, el campo magnético inducido por el plasma, poblaciones electrónicas múltiples a distintas temperaturas, y la capacidad de integrar el flujo en la región de expansión lejana. La respuesta hiperbólica del plasma es integrada con alta precisión y eficiencia haciendo uso del método de las líneas características. Se realiza una caracterización paramétrica de la expansión 2D del plasma en términos del grado de magnetización de iones, la geometría del campo magnético, y el perfil inicial del plasma. Se investigan los mecanismos de aceleración, mostrando que el campo ambipolar convierte la energía interna de electrones en energía dirigida de iones. Las corrientes diamagnéticas de Hall, que pueden hallarse distribuidas en el volumen del plasma o localizadas en una delgada capa de corriente en el borde del chorro, son esenciales para la operación de la tobera, ya que la fuerza magnética repulsiva sobre ellas es la encargada de confinar radialmente y acelerar axialmente el plasma. El empuje magnético es la reacción a esta fuerza sobre el motor. La respuesta del plasma muestra la separación gradual hacia adentro de los tubos de iones respecto de los magnéticos, lo cual produce la formación de corrientes eléctricas longitudinales y pone el plasma en rotación. La ganancia de empuje obtenida y las pérdidas radiales de la pluma de plasma se evalúan en función de los parámetros de diseño. Se analiza en detalle la separación magnética del plasma aguas abajo respecto a las líneas magnéticas (cerradas sobre sí mismas), necesaria para la aplicación de la tobera magnética a fines propulsivos. Se demuestra que tres teorías existentes sobre separación, que se fundamentan en la resistividad del plasma, la inercia de electrones, y el campo magnético que induce el plasma, son inadecuadas para la tobera magnética propulsiva, ya que producen separación hacia afuera en lugar de hacia adentro, aumentando la divergencia de la pluma. En su lugar, se muestra que la separación del plasma tiene lugar gracias a la inercia de iones y la desmagnetización gradual del plasma que tiene lugar aguas abajo, que permiten la separación ilimitada del flujo de iones respecto a las líneas de campo en condiciones muy generales. Se evalúa la cantidad de plasma que permanece unida al campo magnético y retorna hacia el motor a lo largo de las líneas cerradas de campo, mostrando que es marginal. Se muestra cómo el campo magnético inducido por el plasma incrementa la divergencia de la tobera magnética y por ende de la pluma de plasma en el caso propulsivo, contrariamente a las predicciones existentes. Se muestra también cómo el inducido favorece la desmagnetización del núcleo del chorro, acelerando la separación magnética. La hipótesis de ambipolaridad de corriente local, común a varios modelos de tobera magnética existentes, es discutida críticamente, mostrando que es inadecuada para el estudio de la separación de plasma. Una inconsistencia grave en la derivación matemática de uno de los modelos más aceptados es señalada y comentada. Incluyendo una especie adicional de electrones supratérmicos en el modelo, se estudia la formación y geometría de dobles capas eléctricas en el interior del plasma. Cuando dicha capa se forma, su curvatura aumenta cuanto más periféricamente se inyecten los electrones supratérmicos, cuanto menor sea el campo magnético, y cuanto más divergente sea la tobera magnética. El plasma con dos temperaturas electrónicas posee un mayor ratio de empuje magnético frente a total. A pesar de ello, no se encuentra ninguna ventaja propulsiva de las dobles capas, reforzando las críticas existentes frente a las propuestas de estas formaciones como un mecanismo de empuje. Por último, se presenta una formulación general de modelos autosemejantes de la expansión 2D de una pluma no magnetizada en el vacío. El error asociado a la hipótesis de autosemejanza es calculado, mostrando que es pequeño para plumas hipersónicas. Tres modelos de la literatura son particularizados a partir de la formulación general y comparados. Abstract This Thesis presents a theoretical analysis of the operation of magnetic nozzles for plasma space propulsion. The study is based on a two-dimensional, two-fluid model of the supersonic expansion of a hot plasma in a divergent magnetic field. The basic model is extended progressively to include the dominant electron convective terms, the plasma-induced magnetic field, multi-temperature electron populations, and the capability to integrate the plasma flow in the far expansion region. The hyperbolic plasma response is integrated accurately and efficiently with the method of the characteristic lines. The 2D plasma expansion is characterized parametrically in terms of the ion magnetization strength, the magnetic field geometry, and the initial plasma profile. Acceleration mechanisms are investigated, showing that the ambipolar electric field converts the internal electron energy into directed ion energy. The diamagnetic electron Hall current, which can be distributed in the plasma volume or localized in a thin current sheet at the jet edge, is shown to be central for the operation of the magnetic nozzle. The repelling magnetic force on this current is responsible for the radial confinement and axial acceleration of the plasma, and magnetic thrust is the reaction to this force on the magnetic coils of the thruster. The plasma response exhibits a gradual inward separation of the ion streamtubes from the magnetic streamtubes, which focuses the jet about the nozzle axis, gives rise to the formation of longitudinal currents and sets the plasma into rotation. The obtained thrust gain in the magnetic nozzle and radial plasma losses are evaluated as a function of the design parameters. The downstream plasma detachment from the closed magnetic field lines, required for the propulsive application of the magnetic nozzle, is investigated in detail. Three prevailing detachment theories for magnetic nozzles, relying on plasma resistivity, electron inertia, and the plasma-induced magnetic field, are shown to be inadequate for the propulsive magnetic nozzle, as these mechanisms detach the plume outward, increasing its divergence, rather than focusing it as desired. Instead, plasma detachment is shown to occur essentially due to ion inertia and the gradual demagnetization that takes place downstream, which enable the unbounded inward ion separation from the magnetic lines beyond the turning point of the outermost plasma streamline under rather general conditions. The plasma fraction that remains attached to the field and turns around along the magnetic field back to the thruster is evaluated and shown to be marginal. The plasmainduced magnetic field is shown to increase the divergence of the nozzle and the resulting plasma plume in the propulsive case, and to enhance the demagnetization of the central part of the plasma jet, contrary to existing predictions. The increased demagnetization favors the earlier ion inward separation from the magnetic field. The local current ambipolarity assumption, common to many existing magnetic nozzle models, is critically discussed, showing that it is unsuitable for the study of plasma detachment. A grave mathematical inconsistency in a well-accepted model, related to the acceptance of this assumption, is found out and commented on. The formation and 2D shape of electric double layers in the plasma expansion is studied with the inclusion of an additional suprathermal electron population in the model. When a double layer forms, its curvature is shown to increase the more peripherally suprathermal electrons are injected, the lower the magnetic field strength, and the more divergent the magnetic nozzle is. The twoelectron- temperature plasma is seen to have a greater magnetic-to-total thrust ratio. Notwithstanding, no propulsive advantage of the double layer is found, supporting and reinforcing previous critiques to their proposal as a thrust mechanism. Finally, a general framework of self-similar models of a 2D unmagnetized plasma plume expansion into vacuum is presented and discussed. The error associated with the self-similarity assumption is calculated and shown to be small for hypersonic plasma plumes. Three models of the literature are recovered as particularizations from the general framework and compared.