Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival.

in PLoS ONE (2015), 10(5), 0126522

Breast cancer stem cells (CSCs) are thought to drive recurrence and metastasis. Their identity has been linked to the epithelial to mesenchymal transition (EMT) but remains highly controversial since ... [more ▼]

Breast cancer stem cells (CSCs) are thought to drive recurrence and metastasis. Their identity has been linked to the epithelial to mesenchymal transition (EMT) but remains highly controversial since-depending on the cell-line studied-either epithelial (E) or mesenchymal (M) markers, alone or together have been associated with stemness. Using distinct transcript expression signatures characterizing the three different E, M and hybrid E/M cell-types, our data support a novel model that links a mixed EM signature with stemness in 1) individual cells, 2) luminal and basal cell lines, 3) in vivo xenograft mouse models, and 4) in all breast cancer subtypes. In particular, we found that co-expression of E and M signatures was associated with poorest outcome in luminal and basal breast cancer patients as well as with enrichment for stem-like cells in both E and M breast cell-lines. This link between a mixed EM expression signature and stemness was explained by two findings: first, mixed cultures of E and M cells showed increased cooperation in mammosphere formation (indicative of stemness) compared to the more differentiated E and M cell-types. Second, single-cell qPCR analysis revealed that E and M genes could be co-expressed in the same cell. These hybrid E/M cells were generated by both E or M cells and had a combination of several stem-like traits since they displayed increased plasticity, self-renewal, mammosphere formation, and produced ALDH1+ progenies, while more differentiated M cells showed less plasticity and E cells showed less self-renewal. Thus, the hybrid E/M state reflecting stemness and its promotion by E-M cooperation offers a dual biological rationale for the robust association of the mixed EM signature with poor prognosis, independent of cellular origin. Together, our model explains previous paradoxical findings that breast CSCs appear to be M in luminal cell-lines but E in basal breast cancer cell-lines. Our results suggest that targeting E/M heterogeneity by eliminating hybrid E/M cells and cooperation between E and M cell-types could improve breast cancer patient survival independent of breast cancer-subtype. [less ▲]

Step-edge sputtering through grazing incidence ions investigated by scanning tunneling microscopy and molecular dynamics simulations

in Physical Review. B (2008), 77(19),

Scanning tunneling microscopy is used to quantify step-edge sputtering of Pt(111) at 550 K by grazing incidence ion bombardment with 5 keV Ar(+) ions. For bombardment conditions causing negligible erosion ... [more ▼]

Scanning tunneling microscopy is used to quantify step-edge sputtering of Pt(111) at 550 K by grazing incidence ion bombardment with 5 keV Ar(+) ions. For bombardment conditions causing negligible erosion on terraces, damage features associated with step bombardment allow us to visualize step retraction and thus to quantify the step-edge sputtering yield. An alternative method for step-edge yield determination, which is applicable under more general conditions, is the analysis of the concentration of ascending steps together with the removed amount as a function of ion fluence. Interestingly, the azimuthal direction of the impinging ions with respect to the surface significantly changes the sputtering yield at step edges. This change is attributed to the orientation dependence of subsurface channeling. Atomistic insight into step-edge sputtering and its azimuthal dependence is given by molecular dynamics simulations of ion impacts at 0 and 550 K. The simulations also demonstrate a strong dependence of the step-edge sputtering yield on temperature. [less ▲]

Steps Towards Semantic Code Search

Doctoral thesis (2021)

Code search can be a core activity in software development for enhancing productivity. Developers commonly reuse existing source code fragments by searching for codebases available in local or global ... [more ▼]

Code search can be a core activity in software development for enhancing productivity. Developers commonly reuse existing source code fragments by searching for codebases available in local or global repositories. Code search helps developers ease the implementation by supplying code snippets to reuse or understand specific concepts deeper during software development by providing various code snippets for the same tasks. In addition, reading real-world examples (the results of code search) is helpful for developers to make programs more reliable, faster, or secure as the examples have been tested and reused by many other developers. However, it is getting more challenging as the codebases are becoming larger since the large codebase can derive too many code candidates. Thus, the research community has invested substantial efforts in developing new techniques, combining methods, and applying more extensive data to improve the performance and efficiency of code search. Despite the significant efforts made by researchers in the field, code search still has many open problems that the community needs to address, such as lack of benchmarks, vocabulary mismatch (between natural language and source code), and low extensibility on programming languages. Our work focuses on the open issues and the momentum of the domain on semantic code search, which considers the meaning of the user query rather than concerning the syntactic similarity that most other studies have approached. The thesis begins with exploring general issues on code search by conducting a systematic literature review. The survey organizes and classifies the code search approaches with various directions such as learning-based, feedback-driven, dynamic techniques. It reveals insights and new research directions. Given the research directions by the survey, we concentrate on alleviating the vocabulary mismatch problem between free-form text query and source code to improve the overall performance of code search first. To understand the free-form text query, we leverage crowd knowledge. The survey also discovered that there are only a few code-to-code approaches and investigation on crowd-knowledge indicated there exists demand, especially on finding semantically similar source code, i.e., source code that is syntactically different but performs the same functionality. Therefore, we go further, reformulating the user code query with real-world code snippets. This allows catching the semantics from the source code. Given the semantic information, a user can search for desired source code by using their code fragments. In this context, the present dissertation aims to explore semantic code search by contributing to the following three building blocks: Review of state-of-the-art: Despite the growing interest in code search, a comprehensive survey or systematic literature review on the field of code search remains limited. We conducted a large-scale systematic literature review on the internet-scale code search. Our objective in this study was to devise a grounded approach to understand the procedure for the code search approach. We built an operational taxonomy on top of each procedure to categorize the approaches and provide insights on the selection of various approaches. Our investigation on the open issues from the literature guide researchers and practitioners to future research directions. CoCaBu: Source code terms such as method names and variable types are often different from conceptual words mentioned in a search query. This vocabulary mismatch problem can make code search inefficient. We presented COde voCABUlary (CoCaBu), an approach to resolving the vocabulary mismatch problem when dealing with free-form code search queries. Our approach leverages common developer questions and the associated expert answers to augment user queries with the relevant but missing structural code entities to improve matching relevant code examples within large code repositories. To instantiate this approach, we built GitSearch, a code search engine, on top of GitHub and Stack Overflow Q&A data. Experimental results, collected via several comparisons against the state-of-the-art code search and existing online search engines such as Google, show that CoCaBu provides qualitatively better results. Furthermore, our live study on the developer community indicates that it can retrieve acceptable or attractive answers for their questions. FaCoY: Most existing approaches focus on serving user queries provided as natural language free-form input. However, there exists a wide range of use-case scenarios where a code-to-code approach would be most beneficial. For example, research directions in code transplantation, code diversity, patch recommendation can leverage a code-to-code search engine to find essential ingredients for their techniques. Given the wide range of use-case for code-to-code search, we propose FaCoY, a novel approach for statically finding code snippets that may be semantically similar to user input code. FaCoY implements a query alternation strategy: instead of directly matching code query tokens with code in the search space, FaCoY first attempts to identify other tokens, which may also be relevant in implementing the functional behavior of the input code. The experimental results show that FaCoY is more effective than all the existing online code-to-code search engines, and it can also be used to find semantic code clones (i.e., Type-4). Moreover, the results proved that FaCoY could be helpful in code/patch recommendation. [less ▲]

Stereo estimation of depth along virtual cut planes

in International Conference on Computer Vision (ICCV) Workshop on Computer Vision in Vehicle Technology: From Earth to Mars (2011, November)

Stereo Reconstruction using Induced Symmetry and 3D scene priors

Doctoral thesis (2014)

Stereospecific modulation of the calcium channel in human erythrocytes by cholesterol and its oxidized derivatives.

in The Biochemical journal (1985), 227(1), 105-12

To study the effect of cholesterol and its pathophysiologically important oxidized derivatives (OSC) on the calcium entry channel, the human red blood cell was used as a model system. The calcium ejecting ... [more ▼]

To study the effect of cholesterol and its pathophysiologically important oxidized derivatives (OSC) on the calcium entry channel, the human red blood cell was used as a model system. The calcium ejecting adenosinetriphosphatase (ATPase) was inhibited by vanadate. The cells were loaded with OSC at concentrations between 1.25 X 10(-5) and 25 X 10(-5) mol/l. 22-Hydroxycholesterol, cholestan-3 beta,5 alpha,6 beta-triol, 5 alpha-cholestan-3 beta-ol,3 beta,5 alpha-dihydroxycholestan-6-one and 3 beta-hydroxy-5 alpha-cholestan-7-one stimulated 45Ca2+ influx by up to almost 90%, whereas 25-hydroxycholesterol, 7 beta-hydroxycholesterol, 20 alpha-hydroxycholesterol and 7-oxocholesterol inhibited influx by up to 75%. Both stimulation and inhibition were dependent on the amount of OSC incorporated into the membrane. More than 90% of the total modification of calcium influx by OSC was accounted for by an influence on the nitrendipine-inhibitable part of influx. Enrichment of cholesterol in the membrane greatly stimulated, and cholesterol depletion inhibited, Ca2+ influx. These results demonstrate that cholesterol and its oxidized derivatives are able to modulate the calcium channel in human red blood cells in a highly stereospecific manner. [less ▲]

Stereotype activation versus application: How teachers process and judge information about students from ethnic minorities and with low socioeconomic background

in Social Psychology of Education (2014), 17

Stereotype in der Kindheit

Speeches/Talks (2020)

Dr Sylvie Kerger est docteure en psychologie et enseignante-chercheuse à l’Université du Luxembourg. Elle enseigne au Bachelor en sciences de l’éducation et dans ses travaux de recherche, elle s’intéresse ... [more ▼]

Dr Sylvie Kerger est docteure en psychologie et enseignante-chercheuse à l’Université du Luxembourg. Elle enseigne au Bachelor en sciences de l’éducation et dans ses travaux de recherche, elle s’intéresse aux stéréotypes de genre dans l’enfance. Depuis leur plus jeune âge, les enfants sont confrontés à de nombreux stéréotypes de genre, notamment dans leur environnement familial, sociétal (par exemple, à travers le marketing genré) et éducatif. C’est notamment dans ce dernier contexte que la Dr Sylvie Kerger mène, ensemble avec la Dr Laurence Brasseur, un projet de recherche qui a été rendu possible grâce au financement du Ministère de l’égalité entre les femmes et les hommes. L’objectif de cette étude est de révéler les représentations du genre dans les manuels scolaires utilisés à l’école fondamentale au Luxembourg. Transmetteurs de valeurs et de connaissances, les manuels scolaires jouent un rôle prépondérant dans la socialisation. Grâce à un état des lieux du contexte luxembourgeois, ce projet permettra d’élaborer un ensemble de recommandations pour les acteurs concernés et fournira des outils qui faciliteront l’application d’un regard critique sur le matériel didactique. [less ▲]

Stereotypen gegenüber SchülerInnen mit Förderbedarf: Überzeugungen von erfahrenen Lehrkräften, Lehramtsstudierenden und SchülerInnen

Scientific Conference (2017, September)

„Stereotypen“ werden als sozial geteilte Meinungen über Verhaltensweisen und Persönlichkeitsmerkmale von Mitgliedern einer bestimmten Gruppe verstanden. Stereotypen beeinflussen nicht nur unser Denken und ... [more ▼]

„Stereotypen“ werden als sozial geteilte Meinungen über Verhaltensweisen und Persönlichkeitsmerkmale von Mitgliedern einer bestimmten Gruppe verstanden. Stereotypen beeinflussen nicht nur unser Denken und Verhalten, sondern haben auch Auswirkungen darauf, wie unsere Mitmenschen über sich selber denken und sich dementsprechend verhalten (z.B. Pygmalion Effekt). Aus den stereotyp-basierten Erwartungen gegenüber SchülerInnen mit Förderbedarf können Bildungsungleichheiten und eine reduzierte soziale Partizipation resultieren. Lehrerurteile können beispielsweise von Stereotypen geprägt sein und dementsprechend Bildungswege unangemessen beeinflussen. Ebenso können Schüler, geleitet von ihren stereotyp-basierten Überzeugungen, weniger bereit sein Freundschaften mit MitschülerInnen mit Förderbedarf einzugehen. Gemäss dem „Stereotyp Content Model“ (Fiske u.a., 2002) finden Einschätzungen von Aussengruppen entlang der Dimensionen „Wärme“ und „Kompetenz“ statt. Die „Wärme“ bestimmt dabei ob eine Person als negativ oder positiv wahrgenommen wird, wobei die „Kompetenz“ die Extremität dieses Eindrucks festlegt. Stereotypen sind verbunden mit differenziellen Emotionen. So werden z.B. warme Menschen mit niedriger Kompetenz als angenehm wahrgenommen. Ziel dieser Studie war die Ermittlung ob Überzeugungen über SchülerInnen mit Förderbedarf durch Stereotypen geprägt sind und diese je nach Förderbedarf variieren. Zusätzlich wurde untersucht ob Stereotypen zwischen den verschiedenen Akteuren in der Schule variieren (z.B. abhängig von professioneller Kompetenz). Lehrkräfte, Lehramtsstudierende und Schüler (N=103) bewerteten Schüler mit Verhaltensproblemen und Lernschwierigkeiten anhand von Vignetten in den beiden Dimensionen „Wärme und „Kompetenz“. SchülerInnen sowie Lehramtsstudierende kategorisierten Schüler mit Lernschwierigkeiten und Verhaltensproblemen beide als inkompetent. Schüler mit Verhaltensproblemen wurden zusätzlich auch als relativ kalt eingeschätzt, während Schüler mit Lernschwierigkeiten eher als warm wahrgenommen wurden. Erfahrene Lehrkräfte dagegen, bewerteten die Schüler mit Lernschwierigkeiten als warm aber inkompetent und die Schüler mit Verhaltensproblemen in beiden Dimensionen neutral. Unsere Befunde sind im Einklang mit vorherigen Forschungsergebnissen die belegen, dass Stereotypen je nach Förderbedarf varieren. Da Stereotypen Urteile und Verhalten beeinflussen, deuten unsere Befunde darauf hin, dass sich die Interaktionen mit SchülerInnen mit Lernschwierigkeiten und Verhaltensproblemen voneinander unterscheiden. [less ▲]

Stereotypen und Einstellungen in Bezug auf Schüler mit sonderpädagogischem Förderbedarf

Scientific Conference (2016, November 12)