Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes

Many types of tumors exhibit chromosomal losses or gains, as well as local amplifications and deletions. Within any given tumor type, sample specific amplifications and deletionsare also observed. Typically, a region that is aberrant in more tumors,or whose copy number change is stronger, would be considered as a more promising candidate to be biologically relevant to cancer. We sought for an intuitive method to define such aberrations and prioritize them. We define V, the volume associated with an aberration, as the product of three factors: a. fraction of patients with the aberration, b. the aberrations length and c. its amplitude. Our algorithm compares the values of V derived from real data to a null distribution obtained by permutations, and yields the statistical significance, p value, of the measured value of V. We detected genetic locations that were significantly aberrant and combined them with chromosomal arm status to create a succint fingerprint of the tumor genome. This genomic fingerprint is used to visualize the tumors, highlighting events that are co ocurring or mutually exclusive. We allpy the method on three different public array CGH datasets of Medulloblastoma and Neuroblastoma, and demonstrate its ability to detect chromosomal regions that were known to be altered in the tested cancer types, as well as to suggest new genomic locations to be tested. We identified a potential new subtype of Medulloblastoma, which is analogous to Neuroblastoma type 1.Comment: 34 pages, 3 figures; to appear in Cancer Informatic

Detection and imaging of the oxygen deficiency in single crystalline YBa2_{\text{2}}Cu3_{\text{3}}O7−δ_{\text{7}-\delta} thin films using a positron beam

Single crystalline YBa$_{\text{2}}$Cu$_{\text{3}}$O$_{\text{7}-\delta}$ (YBCO) thin films were grown by pulsed laser deposition (PLD) in order to probe the oxygen deficiency $\delta$ using a mono-energetic positron beam. The sample set covered a large range of $\delta$ (0.191<$\delta$<0.791) yielding a variation of the critical temperature $T_{\text{c}}$ between 25 and 90\,K. We found a linear correlation between the Doppler broadening of the positron electron annihilation line and $\delta$ determined by X-ray diffraction (XRD). Both, the origin of the found correlation and the influence of metallic vacancies, were examined with the aid of ab-initio calculations that allowed us (i) to exclude the presence of Y vacancies and (ii) to ensure that positrons still probe $\delta$ despite the potential presence of Ba or Cu vacancies. In addition, by scanning with the positron beam the spatial variation of $\delta$ could be analyzed. It was found to fluctuate with a standard deviation of up to $0.079(5)$ within a single YBCO film

Mehanizam toksičnosti i detoksikacije organofosfornih spojeva s naglaskom na istraživanja u Hrvatskoj

This review comprises studies on the mechanisms of toxicity and detoxication of organophosphorus (OP) compounds done in Croatia in different research areas. One area is the synthesis of antidotes against OP poisoning and their in vivo testing in experimental animals. In vitro studies included in this review focus on the mechanisms of reversible inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), protection of cholinesterases from inhibition by OPs, and reactivation of phosphylated cholinesterases. The third area comprises distribution profiles of BChE and paraoxonase (PON) phenotypes in selected population groups and the detection of OPs and metabolites in humans. Finally, methods are described for the detection of OP compounds in human blood and other media by means of cholinesterase inhibitionPrikazana su istraživanja vođena u Hrvatskoj na različitim područjima mehanizma toksičnosti i detoksikacije organofosfornih (OP) spojeva. Jedno je područje sinteza antidota protiv otrovanja OP spojevima i testiranje in vivo antidota na eksperimentalnim životinjama. Istraživanja in vitro odnose se na mehanizam reverzibilne inhibicije acetilkolinesteraze (AChE) i buturilkolinesteraze (BChE), zaštitu kolinesteraza od inhibicije OP spojevima te reaktivaciju fosfiliranih kolinesteraza. Treće je područje distribucija fenotipova BChE i paraoksonaze (PON) u odabranim populacijama te detekcija OP spojeva i njihovih metabolita u ljudima. Na kraju su opisane metode detekcije OP spojeva u ljudskoj krvi i drugim medijima koje se osnivaju na inhibiciji kolinesteraza

Capture and release of a conditional state of a cavity QED system by quantum feedback

Detection of a single photon escaping an optical cavity QED system prepares a nonclassical state of the electromagnetic field. The evolution of the state can be modified by changing the drive of the cavity. For the appropriate feedback, the conditional state can be captured (stabilized) and then released. This is observed by a conditional intensity measurement that shows suppression of vacuum Rabi oscillations for the length of the feedback pulse and their subsequent return

Engaging Complexities: Working Against Simplification as an Agenda for Qualitative Research Today. Adele Clarke in Conversation With Reiner Keller

En 2005, Adele CLARKE publicó su libro sobre "Análisis situacional", bien recibida elaboración de la metodología de teoría fundamentada. El análisis situacional (AS) combina las tradiciones más viejas así como las más recientes de la sociología pragmática, especialmente las de la Escuela de Chicago y la teoría de mundos/arenas sociales de Anselm STRAUSS, con la perspectiva de FOUCAULT sobre el discurso, el pensamiento feminista y la epistemología post-positivista. En esta entrevista con Reiner KELLER, ella explica los fundamentos teóricos y las motivaciones académicas de este enfoque y describe las estrategias analíticas concretas propuestas por el AS. En el momento oportuno, ella narra sus experiencias pasadas, desde sus primeros encuentros con la investigación cualitativa hasta las influencias más recientes desde los estudios feministas y de ciencias y tecnología. CLARKE también aclara donde se coloca el AS dentro del campo más amplio de las metodologías cualitativas y aborda cuestiones relativas a la contribución del AS para el análisis de cambios sociales complejos. El AS está diseñado para ofrecer una heurística analítica capaz de confrontar estas complejidades con un conjunto amplio de estrategias para hacer investigación cualitativa.URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs140212Im Jahr 2005 veröffentlichte Adele CLARKE unter dem Titel "Situational Analysis" (dt. "Situationsanalyse") eine viel beachtete Weiterführung der Grounded-Theory-Methodologie. Darin verbindet sie ältere und jüngere Traditionen der pragmatistischen Soziologie, insbesondere der Chicago School und des Social World/Arena-Ansatzes von Anselm STRAUSS mit diskursorientierten Perspektiven FOUCAULTs, feministischen Positionen und postpositivistischer Epistemologie. Im Interview mit Reiner KELLER erläutert sie die theoretischen Grundlagen und wissenschaftlichen Motivationen, die diesem Ansatz zu Grunde liegen, sowie die darin vorgeschlagenen konkreten Analysestrategien. Dabei spannt sie einen weiten Bogen von ihren ersten Kontakten mit qualitativer Forschung bis hin zu jüngeren Einflüssen aus der feministischen Forschung sowie der Wissenschafts- und Technologieforschung. Zugleich thematisiert sie die Verortung der Situationsanalyse im Feld der qualitativen Methodologien und diskutiert die Frage nach deren Bedeutung in der Analyse komplexer aktueller gesellschaftlicher Entwicklungen. Ziel der Situationsanalyse ist die Bereitstellung einer Analyseheuristik, die dieser Komplexität mit entschieden erweiterten qualitativen Forschungsstrategien begegnet.URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs140212In 2005, Adele CLARKE first published her book on "Situational Analysis," a well-received elaboration of grounded theory methodology. Situational analysis (SA) combines older as well as more recent traditions of pragmatist sociology, especially those of the Chicago School and social worlds/arenas theory by Anselm STRAUSS, with FOUCAULT's perspective on discourse, feminist thinking, and post-positivist epistemology. In this interview with Reiner KELLER, she explains the theoretical foundations and academic motivations of this approach, and describes the concrete analytical strategies proposed by SA. In due course, she recounts her past experiences, from her very first encounters with qualitative research up to more recent influences from feminist studies and science &amp; technology studies. CLARKE also clarifies where SA is positioned within the broader field of qualitative methodologies, and discusses questions regarding the contribution of SA to the analysis of complex social change. SA is designed to offer an analytical heuristic able to confront these complexities with a considerably expanded set of strategies for doing qualitative research.URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs14021

Engaging Complexities: Working Against Simplification as an Agenda for Qualitative Research Today. Adele Clarke in Conversation With Reiner Keller

En 2005, Adele CLARKE publicó su libro sobre "Análisis situacional", bien recibida elaboración de la metodología de teoría fundamentada. El análisis situacional (AS) combina las tradiciones más viejas así como las más recientes de la sociología pragmática, especialmente las de la Escuela de Chicago y la teoría de mundos/arenas sociales de Anselm STRAUSS, con la perspectiva de FOUCAULT sobre el discurso, el pensamiento feminista y la epistemología post-positivista. En esta entrevista con Reiner KELLER, ella explica los fundamentos teóricos y las motivaciones académicas de este enfoque y describe las estrategias analíticas concretas propuestas por el AS. En el momento oportuno, ella narra sus experiencias pasadas, desde sus primeros encuentros con la investigación cualitativa hasta las influencias más recientes desde los estudios feministas y de ciencias y tecnología. CLARKE también aclara donde se coloca el AS dentro del campo más amplio de las metodologías cualitativas y aborda cuestiones relativas a la contribución del AS para el análisis de cambios sociales complejos. El AS está diseñado para ofrecer una heurística analítica capaz de confrontar estas complejidades con un conjunto amplio de estrategias para hacer investigación cualitativa.URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs140212Im Jahr 2005 veröffentlichte Adele CLARKE unter dem Titel "Situational Analysis" (dt. "Situationsanalyse") eine viel beachtete Weiterführung der Grounded-Theory-Methodologie. Darin verbindet sie ältere und jüngere Traditionen der pragmatistischen Soziologie, insbesondere der Chicago School und des Social World/Arena-Ansatzes von Anselm STRAUSS mit diskursorientierten Perspektiven FOUCAULTs, feministischen Positionen und postpositivistischer Epistemologie. Im Interview mit Reiner KELLER erläutert sie die theoretischen Grundlagen und wissenschaftlichen Motivationen, die diesem Ansatz zu Grunde liegen, sowie die darin vorgeschlagenen konkreten Analysestrategien. Dabei spannt sie einen weiten Bogen von ihren ersten Kontakten mit qualitativer Forschung bis hin zu jüngeren Einflüssen aus der feministischen Forschung sowie der Wissenschafts- und Technologieforschung. Zugleich thematisiert sie die Verortung der Situationsanalyse im Feld der qualitativen Methodologien und diskutiert die Frage nach deren Bedeutung in der Analyse komplexer aktueller gesellschaftlicher Entwicklungen. Ziel der Situationsanalyse ist die Bereitstellung einer Analyseheuristik, die dieser Komplexität mit entschieden erweiterten qualitativen Forschungsstrategien begegnet.URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs140212In 2005, Adele CLARKE first published her book on "Situational Analysis," a well-received elaboration of grounded theory methodology. Situational analysis (SA) combines older as well as more recent traditions of pragmatist sociology, especially those of the Chicago School and social worlds/arenas theory by Anselm STRAUSS, with FOUCAULT's perspective on discourse, feminist thinking, and post-positivist epistemology. In this interview with Reiner KELLER, she explains the theoretical foundations and academic motivations of this approach, and describes the concrete analytical strategies proposed by SA. In due course, she recounts her past experiences, from her very first encounters with qualitative research up to more recent influences from feminist studies and science &amp; technology studies. CLARKE also clarifies where SA is positioned within the broader field of qualitative methodologies, and discusses questions regarding the contribution of SA to the analysis of complex social change. SA is designed to offer an analytical heuristic able to confront these complexities with a considerably expanded set of strategies for doing qualitative research.URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs14021

Plasma Cortisol in Men – Relationship With Atherosclerosis of Retinal Arteries

The production of cortisol increases in acute stress but the effects of chronic stress on plasma cortisol are still controversial. Stress on the other hand plays a role in coronary artery disease (CAD) and carotid atherosclerosis. Since there is no data about plasma cortisol and atherosclerosis of the retinal arteries, the purpose of this study was to explore the relationship between plasma cortisol in 101 adult males with the degree of their retinal vessels atherosclerosis. The results were compared with those in 47 matched apparently healthy men with no retinal vessels changes. The atherosclerotic changes of retinal vessels were determined by direct ophthalmoscopy and graded (1–4) according to Scheie. Morning plasma cortisol levels were determined by radioimmunoassay using commercial kits. The results were compared by using chi-square test. No association between morning plasma cortisol concentrations and retinal vessels atherosclerosis could be found. The results of this study do not support a role for physiological levels of plasma cortisol in the development of atherosclerosis, at least of the retinal arteries, in men

Possible indicators for low dimensional superconductivity in the quasi-1D carbide Sc3CoC4

The transition metal carbide Sc3CoC4 consists of a quasi-one-dimensional (1D) structure with [CoC4]_{\inft} polyanionic chains embedded in a scandium matrix. At ambient temperatures Sc3CoC4 displays metallic behavior. At lower temperatures, however, charge density wave formation has been observed around 143K which is followed by a structural phase transition at 72K. Below T^onset_c = 4.5K the polycrystalline sample becomes superconductive. From Hc1(0) and Hc2(0) values we could estimate the London penetration depth ({\lambda}_L ~= 9750 Angstroem) and the Ginsburg-Landau (GL) coherence length ({\xi}_GL ~= 187 Angstroem). The resulting GL-parameter ({\kappa} ~= 52) classifies Sc3CoC4 as a type II superconductor. Here we compare the puzzling superconducting features of Sc3CoC4, such as the unusual temperature dependence i) of the specific heat anomaly and ii) of the upper critical field H_c2(T) at T_c, and iii) the magnetic hysteresis curve, with various related low dimensional superconductors: e.g., the quasi-1D superconductor (SN)_x or the 2D transition-metal dichalcogenides. Our results identify Sc3CoC4 as a new candidate for a quasi-1D superconductor.Comment: 4 pages, 5 figure