865 resultados para domain-specific visual languages


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The lateral amygdala (LA) receives information from auditory and visual sensory modalities, and uses this information to encode lasting memories that predict threat. One unresolved question about the amygdala is how multiple memories, derived from different sensory modalities, are organized at the level of neuronal ensembles. We previously showed that fear conditioning using an auditory conditioned stimulus (CS) was spatially allocated to a stable topography of neurons within the dorsolateral amygdala (LAd) (Bergstrom et al, 2011). Here, we asked how fear conditioning using a visual CS is topographically organized within the amygdala. To induce a lasting fear memory trace we paired either an auditory (2 khz, 55 dB, 20 s) or visual (1 Hz, 0.5 s on/0.5 s off, 35 lux, 20 s) CS with a mild foot shock unconditioned stimulus (0.6 mA, 0.5 s). To detect learning-induced plasticity in amygdala neurons, we used immunohistochemistry with an antibody for phosphorylated mitogen-activated protein kinase (pMAPK). Using a principal components analysis-based approach to extract and visualize spatial patterns, we uncovered two unique spatial patterns of activated neurons in the LA that were associated with auditory and visual fear conditioning. The first spatial pattern was specific to auditory cued fear conditioning and consisted of activated neurons topographically organized throughout the LAd and ventrolateral nuclei (LAvl) of the LA. The second spatial pattern overlapped for auditory and visual fear conditioning and was comprised of activated neurons located mainly within the LAvl. Overall, the density of pMAPK labeled cells throughout the LA was greatest in the auditory CS group, even though freezing in response to the visual and auditory CS was equivalent. There were no differences detected in the number of pMAPK activated neurons within the basal amygdala nuclei. Together, these results provide the first basic knowledge about the organizational structure of two different fear engrams within the amygdala and suggest they are dissociable at the level of neuronal ensembles within the LA

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Background Strand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC genome browser that introduced the custom track concept that enabled researchers to simultaneously visualize gene expression at a particular locus from multiple experiments. Our objective of the software tool is to provide friendly interface for visualization of RNAseq datasets. Results This paper introduces a visualization tool (RNASeqBrowser) that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks -- all being dynamically built from the BAM file. Paired reads are also connected in the browser to enable easier identification of novel exon/intron borders and chimaeric transcripts. Strand specific RNAseq data is also supported by RNASeqBrowser that displays reads above (positive strand transcript) or below (negative strand transcripts) a central line. Finally, RNASeqBrowser was designed for ease of use for users with few bioinformatic skills, and incorporates the features of many genome browsers into one platform. Conclusions The features of RNASeqBrowser: (1) RNASeqBrowser integrates UCSC genome browser and NGS visualization tools such as IGV. It extends the functionality of the UCSC genome browser by adding several new types of tracks to show NGS data such as individual raw reads, SNPs and InDels. (2) RNASeqBrowser can dynamically generate RNA secondary structure. It is useful for identifying non-coding RNA such as miRNA. (3) Overlaying NGS wiggle data is helpful in displaying differential expression and is simple to implement in RNASeqBrowser. (4) NGS data accumulates a lot of raw reads. Thus, RNASeqBrowser collapses exact duplicate reads to reduce visualization space. Normal PC’s can show many windows of NGS individual raw reads without much delay. (5) Multiple popup windows of individual raw reads provide users with more viewing space. This avoids existing approaches (such as IGV) which squeeze all raw reads into one window. This will be helpful for visualizing multiple datasets simultaneously. RNASeqBrowser and its manual are freely available at http://www.australianprostatecentre.org/research/software/rnaseqbrowser webcite or http://sourceforge.net/projects/rnaseqbrowser/ webcite

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Background The various cell types and their relative numbers in multicellular organisms are controlled by growth factors and related extracellular molecules which affect genetic expression pathways. However, these substances may have both/either inhibitory and/or stimulatory effects on cell division and cell differentiation depending on the cellular environment. It is not known how cells respond to these substances in such an ambiguous way. Many cellular effects have been investigated and reported using cell culture from cancer cell lines in an effort to define normal cellular behaviour using these abnormal cells. A model is offered to explain the harmony of cellular life in multicellular organisms involving interacting extracellular substances. Methods A basic model was proposed based on asymmetric cell division and evidence to support the hypothetical model was accumulated from the literature. In particular, relevant evidence was selected for the Insulin-Like Growth Factor system from the published data, especially from certain cell lines, to support the model. The evidence has been selective in an attempt to provide a picture of normal cellular responses, derived from the cell lines. Results The formation of a pair of coupled cells by asymmetric cell division is an integral part of the model as is the interaction of couplet molecules derived from these cells. Each couplet cell will have a receptor to measure the amount of the couplet molecule produced by the other cell; each cell will be receptor-positive or receptor-negative for the respective receptors. The couplet molecules will form a binary complex whose level is also measured by the cell. The hypothesis is heavily supported by selective collection of circumstantial evidence and by some direct evidence. The basic model can be expanded to other cellular interactions. Conclusions These couplet cells and interacting couplet molecules can be viewed as a mechanism that provides a controlled and balanced division-of-labour between the two progeny cells, and, in turn, their progeny. The presence or absence of a particular receptor for a couplet molecule will define a cell type and the presence or absence of many such receptors will define the cell types of the progeny within cell lineages.

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Background: Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human. Result: The shared core biology between chimpanzee and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain. Remarkably, out of 587 chimpanzee kinases no human orthologue with greater than 95% sequence identity could be identified for 160 kinases. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin/Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. Conclusion: Though the chimpanzee and human are evolutionary very close, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This analysis provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles.

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The dissertation analyzes and elaborates upon the changing map of U.S. ethno-racial formation from the vantage point of North American Studies, multi-disciplinary cultural studies, and the criticism of visual culture. The focus is on four contemporary Mexican American (Chicana) women photographers, whose art production is discussed, on the one hand, in the context of the Euro-American history of photographic genres and, on the other hand, in the context of so-called decolonizing cultural and academic discourses produced by Mexican Americans themselves. The manuscript consists of two parts. Part I outlines the theoretical and methodological domain of the study, positioning it in the interstices of American studies, European postmodern criticism, postcolonial feminist theory, and the theories of visual culture, particularly of art photography. In addition, the main issues and paradigms of Chicano Studies (Mexican American ethnic studies) are introduced. Part II consists of seven essays, each of which discusses rather independently a particular photographic work or a series of photographs, formulating and defending arguments about their meaning, position in the history of photographic genres, and their cultural and socio-political significance. The study closes with a discussion about ethno-racial identity formation and the role of Chicana photography therein - in embodying and reproducing new subjectivities, alternative categories of knowledge, and open ended historical narratives. It is argued that, symbolically, the "Wild Zone" of gendered and race-specific knowledge becomes associated with the body of the mother, a recurrent image in Chicana art works under discussion. Embedded in this image, the construction of an alternative notion of a family thus articulates the parameters of a matrifocal ethno-racial community unified by the proliferation of differences rather than by conformities typical of nationalistic ideologies. While focusing on art photography, the study as a whole simultaneously constructs, from a European vantage point, a "thick" description of Mexican American history, identities, communities, cultural practices, and self-representations about which very little is known in Finland.

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In this study I look at what people want to express when they talk about time in Russian and Finnish, and why they use the means they use. The material consists of expressions of time: 1087 from Russian and 1141 from Finnish. They have been collected from dictionaries, usage guides, corpora, and the Internet. An expression means here an idiomatic set of words in a preset form, a collocation or construction. They are studied as lexical entities, without a context, and analysed and categorized according to various features. The theoretical background for the study includes two completely different approaches. Functional Syntax is used in order to find out what general meanings the speaker wishes to convey when talking about time and how these meanings are expressed in specific languages. Conceptual metaphor theory is used for explaining why the expressions are as they are, i.e. what kind of conceptual metaphors (transfers from one conceptual domain to another) they include. The study has resulted in a grammatically glossed list of time expressions in Russian and Finnish, a list of 56 general meanings involved in these time expressions and an account of the means (constructions) that these languages have for expressing the general meanings defined. It also includes an analysis of conceptual metaphors behind the expressions. The general meanings involved turned out to revolve around expressing duration, point in time, period of time, frequency, sequence, passing of time, suitable time and the right time, life as time, limitedness of time, and some other notions having less obvious semantic relations to the others. Conceptual metaphor analysis of the material has shown that time is conceptualized in Russian and Finnish according to the metaphors Time Is Space (Time Is Container, Time Has Direction, Time Is Cycle, and the Time Line Metaphor), Time Is Resource (and its submapping Time Is Substance), Time Is Actor; and some characteristics are added to these conceptualizations with the help of the secondary metaphors Time Is Nature and Time Is Life. The limits between different conceptual metaphors and the connections these metaphors have with one another are looked at with the help of the theory of conceptual integration (the blending theory) and its schemas. The results of the study show that although Russian and Finnish are typologically different, they are very similar both in the needs of expression their speakers have concerning time, and in the conceptualizations behind expressing time. This study introduces both theoretical and methodological novelties in the nature of material used, in developing empirical methodology for conceptual metaphor studies, in the exactness of defining the limits of different conceptual metaphors, and in seeking unity among the different facets of time. Keywords: time, metaphor, time expression, idiom, conceptual metaphor theory, functional syntax, blending theory

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Guanylyl cyclases (GCs) are enzymes that generate cyclic GMP and regulate different physiologic and developmental processes in a number of organisms. GCs possess sequence similarity to class III adenylyl cyclases (ACs) and are present as either membrane-bound receptor GCs or cytosolic soluble GCs. We sought to determine the evolution of GCs using a large-scale bioinformatic analysis and found multiple lineage-specific expansions of GC genes in the genomes of many eukaryotes. Moreover, a few GC-like proteins were identified in prokaryotes, which come fused to a number of different domains, suggesting allosteric regulation of nucleotide cyclase activity Eukaryotic receptor GCs are associated with a kinase homology domain (KHD), and phylogenetic analysis of these proteins suggest coevolution of the KHD and the associated cyclase domain as well as a conservation of the sequence and the size of the linker region between the KHD and the associated cyclase domain. Finally, we also report the existence of mimiviral proteins that contain putative active kinase domains associated with a cyclase domain, which could suggest early evolution of the fusion of these two important domains involved in signa transduction.

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The visual systems of humans and animals represent physical reality in a modified way, depending on the specific demands that the species in question has for survival. The ability to perceive visual illusions is found in independently evolved visual systems, from honeybees to humans. In humans, the ability emerges early, at the age of four months. Thus the perception of illusion is likely to reflect visual processes of fundamental importance for object perception in natural vision. The experiments reported in this thesis employed various modifications of the Kanizsa triangle, a drawn configuration composed of three black disks with missing sectors on a white background. The sectors appear to form the tips of a triangle. The visual system completes the physically empty area between the disks, generally called inducers, with giving the perception of an illusory triangle. The illusory triangle consists of an illusory surface bounded by illusory contours; the triangle appears brighter than and to lie above the background. If the sectors are coloured, the colour fills the illusory area, a phenomenon known as neon colour spreading . We investigated spatial limitations on the perception of Kanizsa-type illusions and how other stimuli and viewing parameters affected these limitations. We also studied complex configurations thick, bent, mobile and chromatic inducers - to determine whether illusions combining several attributes can be perceived. The results suggest that the visual system is highly effective in completing a percept. The perception of an illusory figure is spatially scale invariant when perceived at threshold. The processing time and the number of fixations modify the percept, making the perception of the illusion more probable in various viewing conditions. Furthermore, the fact that the illusion can be perceived when only one inducer is physically present at any given moment indicates the potential of single inducers. Apparently, modelling illusory figure perception will require a combination of low-level, local processes and higher-level integrative processes. Our studies with stimuli combining several attributes relevant to object perception demonstrate that the perception of an illusory figure is flexible and is maintained also when it contains colour and volume and when shown in movement. All in all, the results confirm the assumed importance of the visual processes related with the perception of illusory figures in everyday viewing. This is indicated by the variety of inducer modifications that can be made without destroying the percept. Furthermore, the illusion can acquire additional attributes from such modifications. Due to individual differences in the perception of illusory figures, universal values for absolute performance are not always meaningful, but stable trends and general relations do exist.

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The present thesis discusses relevant issues in education: 1) learning disabilities including the role of comorbidity in LDs, and 2) the use of research-based interventions. This thesis consists of a series of four studies (three articles), which deepens the knowledge of the field of special education. Intervention studies (N=242) aimed to examine whether training using a nonverbal auditory-visual matching computer program had a remedial effect in different learning disabilities, such as developmental dyslexia, Attention Deficit Disorder (ADD) and Specific Language Impairment (SLI). These studies were conducted in both Finland and Sweden. The intervention’s non-verbal character made an international perspective possible. The results of the intervention studies confirmed, that the auditory-visual matching computer program, called Audilex had positive intervention effects. In Study I of children with developmental dyslexia there were also improvements in reading skills, specifically in reading nonsense words and reading speed. These improvements in tasks, which are thought to rely on phonological processing, suggest that such reading difficulties in dyslexia may stem in part from more basic perceptual difficulties, including those required to manage the visual and auditory components of the decoding task. In Study II the intervention had a positive effect on children with dyslexia; older students with dyslexia and surprisingly, students with ADD also benefited from this intervention. In conclusion, the role of comorbidity was apparent. An intervention effect was evident also in students’ school behavior. Study III showed that children with SLI experience difficulties very similar to those of children with dyslexia in auditory-visual matching. Children with language-based learning disabilities, such as dyslexia and SLI benefited from the auditory-visual matching intervention. Also comorbidity was evident among these children; in addition to formal diagnoses, comorbidity was explored with an assessment inventory, which was developed for this thesis. Interestingly, an overview of the data of this thesis shows positive intervention effects in all studies despite learning disability, language, gender or age. These findings have been described by a concept inter-modal transpose. Self-evidently these issues need further studies. In learning disabilities the aim in the future will also be to identify individuals at risk rather than by deficit; this aim can be achieved by using research-based interventions, intensified support in general education and inclusive special education. Keywords: learning disabilities, developmental dyslexia, attention deficit disorder, specific language impairment, language-based learning disabilities, comorbidity, auditory-visual matching, research-based interventions, inter-modal transpose

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Sexing wild marine mammals that show little to no sexual dimorphism is challenging. For sirenians that are difficult to catch or approach closely, molecular sexing from tissue biopsies offers an alternative method to visual discrimination. This paper reports the results of a field study to validate the use of two sexing methods: (1) visual discrimination of sex vs (2) molecular sexing based on a multiplex PCR assay which amplifies the male-specific SRY gene and differentiates ZFX and ZFY gametologues. Skin samples from 628 dugongs (Dugong dugon) and 100 Florida manatees (Trichechus manatus latirostris) were analysed and assigned as male or female based on molecular sex. These individuals were also assigned a sex based on either direct observation of the genitalia and/or the association of the individual with a calf. Individuals of both species showed 93 to 96% congruence between visual and molecular sexing. For the remaining 4 to 7%, the discrepancies could be explained by human error. To mitigate this error rate, we recommend using both of these robust techniques, with routine inclusion of sex primers into microsatellite panels employed for identity, along with trained field observers and stringent sample handling.

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Purpose To explore the effect of small-aperture optics, designed to aid presbyopes by increasing ocular depth-of-focus, on measurements of the visual field. Methods Simple theoretical and ray-tracing models were used to predict the impact of different designs of small-aperture contact lenses or corneal inlays on the proportion of light passing through natural pupils of various diameters as a function of the direction in the visual field. The left eyes of five healthy volunteers were tested using three afocal, hand-painted opaque soft contact lenses (www.davidthomas.com). Two were opaque over a 10 mm diameter but had central clear circular apertures of 1.5 and 3.0 mm in diameter. The third had an annular opaque zone with inner and outer diameters of 1.5 and 4.0 mm, approximately simulating the geometry of the KAMRA inlay (www.acufocus.com). A fourth, clear lens was used for comparison purposes. Visual fields along the horizontal meridian were evaluated up to 50° eccentricity with static automated perimetry (Medmont M700, stimulus Goldmann-size III; www.medmont.com). Results According to ray-tracing, the two lenses with the circular apertures were expected to reduce the relative transmittance of the pupil to zero at specific field angles (around 60° for the conditions of the experimental measurements). In contrast, the annular stop had no effect on the absolute field but relative transmittance was reduced over the central area of the field, the exact effects depending upon the natural pupil diameter. Experimental results broadly agreed with these theoretical expectations. With the 1.5 and 3.0 mm pupils, only minor losses in sensitivity (around 2 dB) in comparison with the clear-lens case occurred across the central 10° radius of field. Beyond this angle, sensitivity losses increased, to reach about 7 dB at the edge of the measured field (50°). The field results with the annular stop showed at most only a slight loss in sensitivity (≤3 dB) across the measured field. Conclusion The present theoretical and experimental results support earlier clinical findings that KAMRA-type annular stops, unlike circular artificial pupils, have only minor effects on measurements of the visual field.

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A frequency-domain positivity condition is derived for linear time-varying operators in2and is used to develop2stability criteria for linear and nonlinear feedback systems. These criteria permit the use of a very general class of operators in2with nonstationary kernels, as multipliers. More specific results are obtained by using a first-order differential operator with a time-varying coefficient as multiplier. Finally, by employing periodic multipliers, improved stability criteria are derived for the nonlinear damped Mathieu equation with a forcing function.

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The paradigm of computational vision hypothesizes that any visual function -- such as the recognition of your grandparent -- can be replicated by computational processing of the visual input. What are these computations that the brain performs? What should or could they be? Working on the latter question, this dissertation takes the statistical approach, where the suitable computations are attempted to be learned from the natural visual data itself. In particular, we empirically study the computational processing that emerges from the statistical properties of the visual world and the constraints and objectives specified for the learning process. This thesis consists of an introduction and 7 peer-reviewed publications, where the purpose of the introduction is to illustrate the area of study to a reader who is not familiar with computational vision research. In the scope of the introduction, we will briefly overview the primary challenges to visual processing, as well as recall some of the current opinions on visual processing in the early visual systems of animals. Next, we describe the methodology we have used in our research, and discuss the presented results. We have included some additional remarks, speculations and conclusions to this discussion that were not featured in the original publications. We present the following results in the publications of this thesis. First, we empirically demonstrate that luminance and contrast are strongly dependent in natural images, contradicting previous theories suggesting that luminance and contrast were processed separately in natural systems due to their independence in the visual data. Second, we show that simple cell -like receptive fields of the primary visual cortex can be learned in the nonlinear contrast domain by maximization of independence. Further, we provide first-time reports of the emergence of conjunctive (corner-detecting) and subtractive (opponent orientation) processing due to nonlinear projection pursuit with simple objective functions related to sparseness and response energy optimization. Then, we show that attempting to extract independent components of nonlinear histogram statistics of a biologically plausible representation leads to projection directions that appear to differentiate between visual contexts. Such processing might be applicable for priming, \ie the selection and tuning of later visual processing. We continue by showing that a different kind of thresholded low-frequency priming can be learned and used to make object detection faster with little loss in accuracy. Finally, we show that in a computational object detection setting, nonlinearly gain-controlled visual features of medium complexity can be acquired sequentially as images are encountered and discarded. We present two online algorithms to perform this feature selection, and propose the idea that for artificial systems, some processing mechanisms could be selectable from the environment without optimizing the mechanisms themselves. In summary, this thesis explores learning visual processing on several levels. The learning can be understood as interplay of input data, model structures, learning objectives, and estimation algorithms. The presented work adds to the growing body of evidence showing that statistical methods can be used to acquire intuitively meaningful visual processing mechanisms. The work also presents some predictions and ideas regarding biological visual processing.

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The PRP17 gene product is required for the second step of pre-mRNA splicing reactions. The C-terminal half of this protein bears four repeat units with homology to the beta transducin repeat. Missense mutations in three temperature-sensitive prp17 mutants map to a region in the N-terminal half of the protein. We have generated, in vitro, 11 missense alleles at the beta transducin repeat units and find that only one affects function in vivo. A phenotypically silent missense allele at the fourth repeat unit enhances the slow-growing phenotype conferred by an allele at the third repeat, suggesting an interaction between these domains. Although many missense mutations in highly conserved amino acids lack phenotypic effects, deletion analysis suggests an essential role for these units. Only mutations in the N-terminal nonconserved domain of PRP17 are synthetically lethal in combination with mutations in PRP16 and PRP18, two other gene products required for the second splicing reaction. A mutually allele-specific interaction between Prp17 and snr7, with mutations in U5 snRNA, was observed. We therefore suggest that the functional region of Prp17p that interacts with Prp18p, Prp16p, and U5 snRNA is the N terminal region of the protein.

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The purpose of this thesis project is to study changes in the physical state of cell membranes during cell entry, including how these changes are connected to the presence of ceramide. The role of enzymatical manipulation of lipids in bacterial internalization is also studied. A novel technique, where a single giant vesicle is chosen under the microscope and an enzyme coupled-particle attached to the micromanipulator pipette towards the vesicle, is used. Thus, the enzymatic reaction on the membrane of the giant vesicle can be followed in real-time. The first aim of this study is to develop a system where the localized sphingomyelinase membrane interaction could be observed on the surface of the giant vesicle and the effects could be monitored with microscopy. Domain formation, which resembles acid sphingomyelinase (ASMase), causes CD95 clustering in the cell membrane due to ceramide production (Grassmé et al., 2001a; Grassmé et al., 2001b) and the formation of small vesicles inside the manipulated giant vesicle is observed. Sphingomyelinase activation has also been found to be an important factor in the bacterial and viral invasion process in nonphagocytic cells (Grassmé et al., 1997; Jan et al., 2000). Accordingly, sphingomyelinase reactions in the cell membrane might also give insight into bacterial or viral cellular entry events. We found sphingomyelinase activity in Chlamydia pneumonia elementarybodies (EBs). Interestingly, the bacterium enters host cells by endocytosis but the internalization mechanism of Chlamydia is unknown. The hypothesis is that sphingomyelin is needed for host cell entry in the infection of C. pneumonia. The second project focuses on this subject. The goal of the third project is to study a role of phosphatidylserine as a target for a membrane binding protein. Phosphatidylserine is chosen because of its importance in fusion processes. This will be another example for the importance of lipids in cell targeting, internalization, and externalization.