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Portraying the Expression Landscapes of B-CellLymphoma-Intuitive Detection of Outlier Samples and of Molecular Subtypes
Lydia Hopp,Kathrin Lembcke,Hans Binder,Henry Wirth
Biology , 2013, DOI: 10.3390/biology2041411
Abstract: We present an analytic framework based on Self-Organizing Map (SOM) machine learning to study large scale patient data sets. The potency of the approach is demonstrated in a case study using gene expression data of more than 200 mature aggressive B-cell lymphoma patients. The method portrays each sample with individual resolution, characterizes the subtypes, disentangles the expression patterns into distinct modules, extracts their functional context using enrichment techniques and enables investigation of the similarity relations between the samples. The method also allows to detect and to correct outliers caused by contaminations. Based on our analysis, we propose a refined classification of B-cell Lymphoma into four molecular subtypes which are characterized by differential functional and clinical characteristics.
A Global Genome Segmentation Method for Exploration of Epigenetic Patterns
Lydia Steiner,Lydia Hopp,Henry Wirth,J?rg Galle,Hans Binder,Sonja J. Prohaska,Thimo Rohlf
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0046811
Abstract: Current genome-wide ChIP-seq experiments on different epigenetic marks aim at unraveling the interplay between their regulation mechanisms. Published evaluation tools, however, allow testing for predefined hypotheses only. Here, we present a novel method for annotation-independent exploration of epigenetic data and their inter-correlation with other genome-wide features. Our method is based on a combinatorial genome segmentation solely using information on combinations of epigenetic marks. It does not require prior knowledge about the data (e.g. gene positions), but allows integrating the data in a straightforward manner. Thereby, it combines compression, clustering and visualization of the data in a single tool. Our method provides intuitive maps of epigenetic patterns across multiple levels of organization, e.g. of the co-occurrence of different epigenetic marks in different cell types. Thus, it facilitates the formulation of new hypotheses on the principles of epigenetic regulation. We apply our method to histone modification data on trimethylation of histone H3 at lysine 4, 9 and 27 in multi-potent and lineage-primed mouse cells, analyzing their combinatorial modification pattern as well as differentiation-related changes of single modifications. We demonstrate that our method is capable of reproducing recent findings of gene centered approaches, e.g. correlations between CpG-density and the analyzed histone modifications. Moreover, combining the clustered epigenetic data with information on the expression status of associated genes we classify differences in epigenetic status of e.g. house-keeping genes versus differentiation-related genes. Visualizing the distribution of modification states on the chromosomes, we discover strong patterns for chromosome X. For example, exclusively H3K9me3 marked segments are enriched, while poised and active states are rare. Hence, our method also provides new insights into chromosome-specific epigenetic patterns, opening up new questions how “epigenetic computation” is distributed over the genome in space and time.
Properties of Galaxies in and around Voids
Ulrich Hopp
Physics , 1997,
Abstract: Two surveys for intrinsically faint galaxies towards nearby voids have been conducted at the MPI f\"ur Astronomie, Heidelberg. One selected targets from a new diameter limited ($\Phi \ge 5''$) catalog with morphological criteria while the other used digitized objective prism Schmidt plates to select mainly HII dwarf galaxies. For some 450 galaxies, redshifts and other optical data were obtained. We studied the spatial distribution of the sample objects, their luminosity function, and their intrinsic properties. Most of the galaxies belong to already well known sheets and filaments. But we found about a dozen highly isolated galaxies in each sample (nearest neighborhood distance $\ge 3 h_{75}^{-1} Mpc$). These tend to populate additional structures and are not distributed homogeneously throughout the voids. As our results on 'void galaxies' still suffer from small sample statistics, I also tried to combine similar existing surveys of nearby voids to get further hints on the larger structure and on the luminosity function of the isolated galaxies. No differences in the luminosity function of sheet and void galaxies could be found. The optical and infrared properties of both samples are in the normal range for samples dominated by late-type dwarfs. Follow-up HI studies show that the isolated dwarfs in both samples have unusual high amount of neutral gas for a given luminosity.
Distance, structure and bright stellar content of the dwarf irregular galaxy UGC 685
Ulrich Hopp
Physics , 1998, DOI: 10.1051/aas:1999134
Abstract: B,R, and J frames taken with the Calar Alto 3.5m telescope of the dwarf irregular galaxy UGC 685 are presented. The brightest part of the stellar population is resolved in B and R, very few also in J. The stellar color-magnitude diagram is discussed. An estimate of the distance to UGC 685 of 5.5 Mpc is derived based on the brightest blue supergiant stars. Most of the resolved bright stars show colors in the range $-0.1 \le B-R \le +0.7$. The continuum light of the unresolved stars is distributed rather regular in B, R, and J, showing only minor irregularities. This surface brightness distribution follows an exponential law in all three colors with a scale length $r_c = 0.33$ kpc. The central surface brightnesses are $21.57 \pm 0.09 mag/\Box''$, $20.65 \pm 0.06mag/\Box''$, and $20.11 \pm 0.11 mag/\Box''$, in B, R, and J, respectively. The surface brightness can be traced out to 5 $r_c$ in B and R. Thus, UGC 685 belongs to the class of dwarfs where the HI distribution is much more extended (here 2.6 times) than the optical (stellar) light distribution, but contrary to many objects of this type, it does not belong to the class of low-surface brightness objects. The overall colors are $B-R = + 0.97$, $B-J = +1.55$ and the magnitude is B = 14.55 ($M_B^o$ = -14.5). The classification as an irregular dwarf results from the few HII regions of UGC 685. On an H${\alpha}$ Calar Alto 2.2m telescope CCD image, I identified only 5 HII regions. The total H${\alpha}$ flux corresponds to a mildly on-going star formation with a rate of 0.003 \Msolar yr$^{-1}$, a low rate even in comparison to other dwarfs. The available data do not indicate any major deviation from this rather low star formation rate within the last $10^9$ yr.
Relative importance of different physical processes on upper crustal specific heat flow in the Eifel-Maas region, Central Europe and ramifications for the production of geothermal energy  [PDF]
Lydia Dijkshoorn, Christoph Clauser
Natural Science (NS) , 2013, DOI: 10.4236/ns.2013.52A039

We study the recent upper crustal heat flow variations caused by long-term physical processes such as paleoclimate, erosion, sedimentation and mantle plume upwelling. As specific heat flow is a common lower boundary condition in many models of heat en fluid flow in the Earth’s crust we quantify its long-term transient variation caused by paleoclimate, erosion or sedimentation, mantle plume upwelling and deep groundwater flow. The studied area extends between the Eifel mountains and the Maas river inCentral Europe. The total variation due to these processes in our study area amounts to tectonic events manifested in the studied area 20 mW/m2, about 30% of the present day specific heat flow in the region.

External Innovation Implementation Determinants and Performance Measurement: A Case Study from the Pharmaceutical Industry  [PDF]
Matthew Coates, Lydia Bals
Technology and Investment (TI) , 2013, DOI: 10.4236/ti.2013.42016

With an increasing amount of externally sourced innovations, a major success factor for innovation-dependent indus- tries such as the pharmaceutical industry is to successfully implement innovations from outside. Existing frameworks emphasize creating a strong climate for implementation by developing the learning capabilities of the organization, but there is still much to be learned about the process of implementing innovations that have been in-sourced by companies. As a research setting that is particularly innovation-driven and not well-studied yet, this study examines the key deter- minants for innovation implementation based on a case study in the pharmaceutical industry. The results of 25 expert interviews and a survey with 67 respondents led to the resulting framework and a corresponding performance meas- urement system. The results reveal the importance of supporting systems and show differences in perception of early and late Research & Development functions.

The Profile of Secondary Metabolites of Sponge Clathria reinwardtii Extract as a Result of Fe Accumulation in Spermonde Archipelago  [PDF]
Lydia Melawaty, Kristiana Pasau
Advances in Biological Chemistry (ABC) , 2015, DOI: 10.4236/abc.2015.57023
Abstract: Study on the effect of Fe metal concentrations in Spermonde Archipelago on secondary metabolites production from sponge was conducted. The percent of peak area and m/z from GC-MS at tR = 13.555 were affected by accumulated Fe in Chlathria reinwardtii, where at high Fe concentration a lower percent peak area was produced compared to Clathria rein-wardtii extract at low Fe concentration. Chromatogram CR-LL-DCM produced 2 peaks at tR = 21.401 and 25.174 which were not observed in CR-BC-DCM chromatogram. This indicated that Clathria reinwardtii in Lae-Lae island produced metabolite secondary compounds that were not produced by Clahtria reinwardtii in Barrang Caddi island. FT-IR analysis indicated that Clathria reinwardtii accumulating Fe with highest and lowest concentration produced strong peaks at wavenumber of about 3400 cm-1 for O-H and N-H stretches. O-H pliable and C-O stretch peaks at wavenumber of about 1200 cm-1 had changes from medium intensity at low Fe concentration (CR-BC-DCM) to weak at high Fe concentration (CR-LL-DCM).
The relationship of mineral and geochemical composition to artificial radionuclide partitioning inYenisei river sediments downstream frommining-and-chemical combine rosatom  [PDF]
Bondareva Lydia, Artamonova Svetlana
Natural Science (NS) , 2011, DOI: 10.4236/ns.2011.37073
Abstract: Discharges from the Mining-and-Chemical Com- bine (MCC) of Rosatom, downstream from Krasnoyarsk-26, near of the Krasnoyarsk resulted in radioactive contamination of sedi-ments of the River Yenisei. The concentration of artificial gammaemitting radionuclides (137Cs, 60Co, 152Eu, and 241Am) was determined to analyze the migration processes leading to the transport of these radionuclides. The concentration of artificial radionuclides in the surface layers of the studied area varied in wide ranges: 137Cs – 318 - 1800 Bq/kg, 60Co – 87 - 720 Bq/kg, 152Eu – 12 - 287 Bq/kg and 241Am – 6 - 76 Bq/kg. There was a sequence of migration of radionuclides investigated in the surface layer of sedi-ments that were collected in the near zone of influence of the MCC: 241Am ≈ 152Eu >60Co >137Cs. Radionuclide species have been found to be directly related to sediment structure and composition.
The Utilization of the National Qualifications Framework Level Descriptors as Criteria for Assessing Prior Experiential Learning to Access to Higher Learning Institutions of Namibia  [PDF]
Lydia Shaketange, Alex Kanyimba
Open Journal of Social Sciences (JSS) , 2017, DOI: 10.4236/jss.2017.510025
The assessment of experiential learning is the process of identification, articulation and legitimization of learning gained from years of work experience. The aim of this paper is to explore the utilization of level descriptors as criteria for assessing the prior experiential learning of candidates who aspire to access higher education. The recognition of the prior learning (RPL) concept has been embraced in education policies around the world as a process that assesses and recognises non-formal and informal learning attained by an individual, to determine the level of competency achieved. However, the implementation of the concept by higher education institutions remains insignificant. Some reasons cited relate to the method used to assess learning in admission tests, such as the recall of subject knowledge. It is argued in this paper that the alignment of individuals’ learning evidence with the National Qualifications Framework’s level descriptors is critical as an alternative route of assessment. The assessment method based on alignment of level descriptors allows for self-exploration and deeper reflection of own learning, giving insight not only into the self but also for the benefit of the host institution. Host institutions benefit from RPL, not only by choosing qualified candidates to enter their programmes, but also by having candidates who lived the experience and have understanding of the field of study. The alignment method is perceived to be a reflective strategy of assessing experiential learning and is born out of the transformative process which encourages deep learning and portrays the quality of potential candidates. Studies have shown no significant differences between the performances of students who accessed higher learning through Grade twelve certificates and those who accessed through RPL. Therefore, when an appropriate and robust method is adopted, RPL is feasible and beneficial to all involved.
Challenges and Opportunities for Implementing Recognition of Prior Learning at the University of Namibia  [PDF]
Lydia L. Shaketange
Creative Education (CE) , 2018, DOI: 10.4236/ce.2018.913150
Abstract: The University of Namibia (UNAM) has developed and approved a policy on the recognition of prior learning (RPL), but the implementation thereof is dormant. The purpose of this paper is to present potential challenges and opportunities that can influence the implementation of RPL at UNAM. The paper used a qualitative approach and the phenomenological design to solicit participants’ views, perceptions and experiences concerning RPL at UNAM. Semi-structured interview schedules were employed to collect data from 12 staff members of UNAM who were purposively chosen based on their positions that are key to providing information to answer the research questions. The findings reveal opportunities such as the availability of political will to implement RPL at the institution, the availability of expertise, capability in terms of technology and infrastructure, the availability of RPL policy, quality assurance and the assessment policy of the institution. Challenges identified are lack of ontological knowledge of what counts as RPL, how it is assessed and its validity and integrity. The data reveal high demands regarding training on issues of assessment and raising awareness of RPL at the institution. The paper recommends that the Ministry of Education, the Namibia Qualifications Authority and the National Council of Higher Learning spearhead a
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