Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of epigenetic modifiers in hematopoiesis

De eigenschap van stamcellen om dode cellen en beschadigd weefsel te vervangen is te danken aan hun vermogen om te balanceren tussen vernieuwing en uitrijping in een of meerdere celtypes. Hematopoietische stamcellen (HSC) zijn de best bestudeerde volwassen stamcellen, en hun inadequate deling of uitrijping, of een abnormale immuunrespons van uit HSC gevormde cellen, kan leiden tot diverse aandoeningen, zoals kanker, beenmergfalen, en auto-immuunreacties. In dit proefschrift is de rol van twee epigenetische mechanismes, Polycomb eiwitten en DNA methyltransferases (Dnmt’s), in de regulatie van stamcel zelfvernieuwing en uitrijping onderzocht. We tonen aan dat er een verband is tussen deze twee mechanismes. Ten eerste, verschillende zogenaamde Cbx eiwitten concurreren met elkaar voor een plaats in het grote Polycomb eiwit complex. Afhankelijk van welk Cbx eiwit integreert, gaan stamcellen ofwel zichzelf vernieuwen ofwel uitrijpen. Dit grote Polycomb complex functioneert dus als een soort ‘schakelmechanisme’. Ten tweede tonen we aan dat Cbx7, het eiwit dat uiteindelijk zorgt voor vernieuwing van stamcellen, de hoeveelheid en functie van een ander belangrijk eiwit, Dnmt3a, beinvloedt. Het is bekend dat een verandering hierin kan leiden tot verstoring in de bloedcelvorming en ontwikkeling van leukemie. Onze data impliceren dat subtiele regulatie van epigenetische factoren essentieel is voor een goede functie van stamcellen en de daaruit gevormde rijpe bloedcellen. Daarnaast kan dergelijk inzicht uiteindelijk leiden tot het genereren van betere protocollen voor stamcelexpansie ex vivo, waardoor het potentieel van stamcellen voor klinische toepassingen in het kader van cel- of gentherapie verder kan worden onderzocht.
Mesencephalic type 1 astrocytes rescue dopaminergic neurons from death induced by serum deprivation

We have established a primary neuronal culture of the embryonic day 14 rat, ventral mesencephalic region, centered on the A8, A9, and A10 dopaminergic nuclei (approximately 1.0 mm3 of tissue). At 16 hr after plating on a substrate of poly-D-lysine, in a serum-free or serum- supplemented growth medium, using a microisland culturing method, 95% of the cells stained positive for neuron-specific enolase, 20% for tyrosine hydroxylase, and < 5% for vimentin. When the growth medium was supplemented with 10% fetal calf serum, the percentage of tyrosine hydroxylase-positive neurons increased significantly (p < 0.05) at the 7th and 10th days in culture, compared with the percentage present at 16 hr after plating. When cultured in a serum-free growth medium, the percentage of tyrosine hydroxylase-positive neurons decreased to < 5% and to 0% by the 5th and 7th days, respectively, while the percentage of GABA-IR neurons increased. The addition of serum to the serum-free culture rescued dopaminergic neurons from death induced by serum deprivation. The effect of serum was dependent both on the time of addition after plating, and on the percentage added. When the cells were plated in a serum-free medium, on a confluent, type 1 astrocyte monolayer, prepared from the ventral mesencephalon of the embryonic day 16 rat, the survival of dopaminergic neurons increased significantly (p < 0.01) at DIV5, versus survival after plating on poly-D-lysine. Conditioned medium prepared from the same mesencephalic type 1 astrocyte monolayer also rescued dopaminergic neurons from death. The rescue mediated by the astrocyte monolayer or the conditioned medium was not inhibited by the mitotic inhibitor cytosine arabino furanoside (1.0 microM). Type 1 astrocyte monolayers and conditioned media prepared from the striatum and cerebral cortex of the embryonic day 16 rat had weaker trophic effects than those mediated by mesencephalic glia. We conclude that serum deprivation causes the selective death of dopaminergic neurons in a primary culture of the rat E14 ventral mesencephalon. Type 1 astrocytes or the conditioned medium from type 1 astrocytes can rescue dopaminergic neurons from death induced by serum deprivation. (ABSTRACT TRUNCATED AT 400 WORDS)
Distinct Patterns of Desynchronized Limb Regression in Malagasy Scincine Lizards (Squamata, Scincidae)

Scincine lizards in Madagascar form an endemic clade of about 60 species exhibiting a variety of ecomorphological adaptations. Several subclades have adapted to burrowing and convergently regressed their limbs and eyes, resulting in a variety of partial and completely limbless morphologies among extant taxa. However, patterns of limb regression in these taxa have not been studied in detail. Here we fill this gap in knowledge by providing a phylogenetic analysis of DNA sequences of three mitochondrial and four nuclear gene fragments in an extended sampling of Malagasy skinks, and microtomographic analyses of osteology of various burrowing taxa adapted to sand substrate. Based on our data we propose to (i) consider Sirenoscincus Sakata & Hikida, 2003, as junior synonym of Voeltzkowia Boettger, 1893; (ii) resurrect the genus name Grandidierina Mocquard, 1894, for four species previously included in Voeltzkowia; and (iii) consider Androngo Brygoo, 1982, as junior synonym of Pygomeles Grandidier, 1867. By supporting the clade consisting of the limbless Voeltzkowia mira and the forelimb-only taxa V. mobydick and V. yamagishii, our data indicate that full regression of limbs and eyes occurred in parallel twice in the genus Voeltzkowia (as hitherto defined) that we consider as a sand-swimming ecomorph: in the Voeltzkowia clade sensu stricto the regression first affected the hindlimbs and subsequently the forelimbs, whereas the Grandidierina clade first regressed the forelimbs and subsequently the hindlimbs following the pattern prevalent in squamates. Timetree reconstructions for the Malagasy Scincidae contain a substantial amount of uncertainty due to the absence of suitable primary fossil calibrations. However, our preliminary reconstructions suggest rapid limb regression in Malagasy scincids with an estimated maximal duration of 6 MYr for a complete regression in Paracontias, and 4 and 8 MYr respectively for complete regression of forelimbs in Grandidierina and hindlimbs in Voeltzkowia.
High-level Data-Layout Transformations for Energy Reduction in Direct Mapped Caches

In order to reduce power consumption in data dominated embedded applications, a multi-level memory hierarchy containing caches is often introduced in the implementation. The cache memory used in this hierarchy must have simple tag-comparison mechanisms and tag array overhead for reduced energy. However, such cache architecture, a direct mapped cache, potentially also causes energy overhead due to the extra misses because of the limited freedom of its mapping organisation. An effective way to reduce the miss overhead is to careful place the data in main memory. We use a memory data-layout scheme that interleaves signals in main memory such these are mapped in different lines without conflicting each other. This method is integrated with an array padding technique for finer-tunning of the resulting data layout. In order to know where to place the data, we have studied the nature of the conflict misses in detail and developed a model to predict these for every signal of interest of the application. We show that it is possible to significantly reduce the miss rate and come as close to the theoretical lowest rate using a real-life multimedia kernel. Our results indicate that by adapting the data layout it is possible to reach using a direct mapped cache the equivalent miss rate of a 4 way associative cache of the same capacity. Hereby avoiding the overhead in energy per access of the more costly 4-way associative cache.
Parsing Algorithms for Regulated Grammars

—Petri nets, introduced by Carl Adam Petri [12] in 1962, provide a powerful mathematical formalism for describing and analyzing the ﬂow of information and control in concurrent systems. Petri nets can successfully be used as control mechanisms for grammars, i.e., the generative devices of formal languages. In recent papers [4], [5], [9], [16] Petri net controlled grammars have been introduced and investigated. It was shown that various regulated grammars such as random context, matrix, vector, valence grammars, etc., resulted from enriching context-free grammars with additional mechanisms can be uniﬁed into the Petri net formalism, i.e., a grammar and its control can be represented by a Petri net. This uniﬁcation allows approaching the membership (parsing) problem in formal language theory in the new point of view: instead of a usual derivation tree, one can use a Petri net derivation tree in which the control mechanism is also considered as a part of the tree. In this paper, we show that the parsing problem for regulated grammars can be solved by means of Petri net derivation trees constructed using the net unfolding. Moreover, we present a parsing algorithm for the deterministic restriction of Petri net controlled grammars based on the well-known Earley parsing algorithm.
Piecewise constant nonnegative matrix factorization

In this paper we propose a non-negative matrix factorization (NMF) model with piecewise-constant activation coefficients. This structure is enforced using a total variation penalty on the rows of the activation matrix. The resulting optimization problem is solved with a majorization-minimization procedure. The proposed algorithm is well suited to analyze data explained by underlying piecewise-constant sequences of states. Its properties are first illustrated using synthetic data. We then use it to solve a video structuring problem that involves both segmentation and clustering tasks. An improvement over a state-of-the-art temporally smoothed NMF algorithm of both clustering and segmentation quality measures is observed.
Optical Domain Down-Conversion of Microwave Signals for High Dynamic Range Microwave Fiber Optic Links

Optical downconversion of microwave signals offers the potential for reduced noise and higher dynamic range over electronic downconversion. A novel downconversion scheme is introduced which allows for remote reception of microwave signals and downconversion to intermediate frequencies or baseband in the optical domain. Experiments show low noise and intermodulation effects. Further extensions of the optical downconverter and potential gains are also discussed
“Gewoon jezelf zijn”: Jongerencultuur veertig jaar na mei 1968

De jongeren van nu zijn de erfgenamen van het gedachtegoed van de jaren ’60 en ’70. Die dromen van weleer over individuele vrijheid, persoonlijke authenticiteit en rebels conformisme leven in nieuwe vorm voort. Alleen zijn ze geen uiting van protest meer tegen de massaconsumptie en de massacultuur maar vormen er een integraal onderdeel van.
A Dual Role for SOX10 in the Maintenance of the Postnatal Melanocyte Lineage and the Differentiation of Melanocyte Stem Cell Progenitors

During embryogenesis, the transcription factor, Sox10, drives the survival and differentiation of the melanocyte lineage. However, the role that Sox10 plays in postnatal melanocytes is not established. We show in vivo that melanocyte stem cells (McSCs) and more differentiated melanocytes express SOX10 but that McSCs remain undifferentiated. Sox10 knockout (Sox10fl; Tg(Tyr::CreER)) results in loss of both McSCs and differentiated melanocytes, while overexpression of Sox10 (Tg(DctSox10)) causes premature differentiation and loss of McSCs, leading to hair graying. This suggests that levels of SOX10 are key to normal McSC function and Sox10 must be downregulated for McSC establishment and maintenance. We examined whether the mechanism of Tg(DctSox10) hair graying is through increased expression of Mitf, a target of SOX10, by asking if haploinsufficiency for Mitf (Mitfvga9) can rescue hair graying in Tg(DctSox10) animals. Surprisingly, Mitfvga9 does not mitigate but exacerbates Tg(DctSox10) hair graying suggesting that MITF participates in the negative regulation of Sox10 in McSCs. These observations demonstrate that while SOX10 is necessary to maintain the postnatal melanocyte lineage it is simultaneously prevented from driving differentiation in the McSCs. This data illustrates how tissue-specific stem cells can arise from lineage-specified precursors through the regulation of the very transcription factors important in defining that lineage.
Improving the performance of an FPGA based Model design for sensor monitoring using PlanAhead tool

The study in this paper is focused on the improvement of a field programmable gate arrays (FPGA) based design using a hierarchical analysis tool offered by XILINX PlanAheadtrade. During this work, PlanAhead software is used to address any problems on the physical side of our FPGA design flow in order to add more visibility and control. The target system is reading analog information recorded by a biomedical sensor in a transmitting unit attached to the patient. The recorded data is converted digitally using analog to digital converter (ADC) and sent to FSK transmitter through FPGA. Verilog HDL has been used to develop and implement the required functions of the FPGA, such as bus interfacing, data buffering, compression and framing. The system performance has been optimized using a recent comprehensive tool in order to reach and maintain the goals of the design
Going beyond the surface: studying multi-layer interaction above the tabletop

Lightweight spatially aware displays (Tangible Magic Lenses) are an effective approach for exploring complex information spaces within a tabletop environment. One way of using the 3D space above a horizontal surface is to divide it into discrete parallel layers stacked upon each other. Horizontal and vertical lens movements are essential tasks for the style of multi-layer interaction associated with it. We conducted a comprehensive user study with 18 participants investigating fundamental issues such as optimal number of layers and their thickness, movement and holding accuracies, and physical boundaries of the interaction volume. Findings include a rather limited overall interaction height (44 cm), a different minimal layer thickness for vertical and horizontal search tasks (1 cm/4 cm), a reasonable maximum number of layers depending on the primary task, and a convenience zone in the middle for horizontal search. Derived from that, design guidelines are also presented.
Impulsive Control and Synchronization for Delayed Neural Networks With Reaction–Diffusion Terms

This paper discuss the global exponential stability and synchronization of the delayed reaction-diffusion neural networks with Dirichlet boundary conditions under the impulsive control in terms of p-norm and point out the fact that there is no constant equilibrium point other than the origin for the reaction-diffusion neural networks with Dirichlet boundary conditions. Some new and useful conditions dependent on the diffusion coefficients are obtained to guarantee the global exponential stability and synchronization of the addressed neural networks under the impulsive controllers we assumed. Finally, some numerical examples are given to demonstrate the effectiveness of the proposed control methods.
Multirate nonlinear predictive control

This paper introduces a new approach to reduce the computational load of nonlinear model based predictive controllers. The idea is based on dividing a long prediction horizon into only a few equidistant intervals with piecewise constant control signals. After solving a first dynamic optimization problem the prediction horizon is halved, keeping the second half of the solution fixed. and doubling the sampling rate in the first half of the control horizon. Using these settings a second optimization is performed to improve the first acquired solution. This procedure is repeated until the applied control step has a reasonable sampling time. In this paper the multirate method is merged with the Quasi-Infinite Horizon Nonlinear Predictive Control scheme, based on augmenting the optimization problem with a terminal region condition and the objective function with a quadratic terminal cost term. Some illustrative simulation results are presented to show the improved stability and computational cost properties of the resulting control strategy without deteriorated quality of control.
IMPLEMENTATION OF A BRUSHLESS DC MOTOR AS A VIRTUAL MOTOR

Due to their simple structure, high efficiency, fas t dynamic response, Permanent Magnet Brushless DC (PMBLDC) machines are extensively used in automatio n, consumer electronics, electric vehicles and medical and industrial applications. Availability o f these high energy density permanent magnet materi als enhances the performance of PMBLDC motor drive and also reduces the size and losses in these machines. Depending on the application the controllers need t o be tested, for which motors of various ratings ar e required. Utilizing real motors of different sizes and capacities for development and testing is diffi cult and mundane. If the functionality of the motor can be r endered by a system on a chip, it will reduce the development time. Hence, the development of a virtu al BLDC motor is considered in this paper. A model of the BLDC motor is simulated, and its characteris ics are implemented on a FPGA. It allows the realization of motors of various ratings to be test ed by changing the parameters. This system function s as time and energy efficient solution for the testing and validation with out any risk of damage to motor or controller under test.
Model-based synthesis of plucked string instruments by using a class of scattering recurrent networks

A physical modeling method for electronic music synthesis of plucked-string tones by using recurrent networks is proposed. A scattering recurrent network (SRN) which is used to analyze string dynamics is built based on the physics of acoustic strings. The measured vibration of a plucked string is employed as the training data for the supervised learning of the SRN. After the network is well trained, it can be regarded as the virtual model for the measured string and used to generate tones which can be very close to those generated by its acoustic counterpart. The "virtual string" corresponding to the SRN can respond to different "plucks" just like a real string, which is impossible using traditional synthesis techniques such as frequency modulation and wavetable. The simulation of modeling a cello "A"-string demonstrates some encouraging results of the new music synthesis technique. Some aspects of modeling and synthesis procedures are also discussed.
A Phase I Clinical Trial of CHT-25 a 131I-Labeled Chimeric Anti-CD25 Antibody Showing Efficacy in Patients with Refractory Lymphoma

Purpose: There is a need for new treatments for Hodgkin and T-cell lymphoma due to the development of drug resistance in a proportion of patients. This phase I study of radioimmunotherapy used CHT-25, a chimeric antibody to the α-chain of the interleukin-2 receptor, CD25, conjugated to iodine-131 (131I) in patients with refractory CD25-positive lymphomas. Experimental Design: Fifteen patients were treated (Hodgkin lymphoma, 12; angioimmunoblastic T-cell lymphoma, 1; adult T-cell leukemia/lymphoma, 2). Tumor was monitored by computed tomography and in all but two patients by 18F-fluorodeoxyglucose positron emission tomography. Results: There were no grade 3 or 4 infusion reactions. At the maximum tolerated dose of 1,200 MBq/m2, the major side effect was delayed myelotoxicity with the nadir for platelets at 38 days and for neutrophils at 53 days. One patient treated with 2,960 MBq/m2 developed prolonged grade 4 neutropenia and thrombocytopenia and died of Pneumocystis jiroveci pneumonia. Nonhematologic toxicity was mild. Single photon emission computer tomography imaging showed tumor-specific uptake and retention of 131I and no excessive retention in normal organs. Of nine patients receiving ≥1,200 MBq/m2, six responded (three complete response and three partial response); one of six patients with administered radioactivity of ≤740 MBq/m2 had a complete response. Conclusions: CHT-25 is well tolerated with 1,200 MBq/m2 administered radioactivity and shows clinical activity in patients who are refractory to conventional therapies. Phase II studies are justified to determine efficacy and toxicity in a broader range of clinical scenarios. (Clin Cancer Res 2009;15(24):7701–10)
Prostaglandin E 2 enhances T-cell proliferation by inducing the costimulatory molecules OX 40 L , CD 70 , and 4-1 BBLon dendritic cells

Dendritic cell (DC)–based immunotherapy of malignant diseases relies on 2 critical parameters: antigen transport from the periphery to draining lymph nodes and efficient priming of primary and stimulation of secondary immune responses. Prostaglandin E2 (PGE2) signaling has been shown to be pivotal for DC migration toward lymph node–derived chemokines in vitro and in vivo. Here, we demonstrate that PGE2 induced the expression of the costimulatory molecules OX40L, CD70, and 4-1BBL on human DCs. Short triggering by PGE2 early during DC maturation was sufficient to induce the costimulatory molecules. The expression of the costimulatory molecules was independent of the maturation stimulus but strictly dependent on PGE2 on both monocytederived (Mo) DCs and peripheral blood myeloid (PB) DCs. PGE2-matured MoDCs showed enhanced costimulatory capacities resulting in augmented antigenspecific CD4 and CD8 T-cell proliferation in primary and recall T-cell responses. Blocking OX40/OX40L signaling impaired the enhanced T-cell proliferation induced by PGE2-matured MoDCs. Moreover, MoDCs matured in the presence of PGE2 induced the expression of OX40, OX40L, and CD70 on T cells facilitating T-cell/Tcell interaction that warrant long-lasting costimulation. This newly identified parameter will help to further optimize DCbased immunotherapy. (Blood. 2009;113: 2451-2460)
Control of an alternate arm converter connected to a star transformer

This paper details a novel energy management technique that is applied to the Alternate Arm Converter (AAC), to ensure converter stability. The control strategy is modeled in Matlab/Simulink and tested on a HVDC active and reactive power operating envelope. To realize the commercial benefits of the AAC, stability in all normal operating conditions is verified. Simulations run over the PQ envelope are shown and the commercial benefits of the new energy management technique assessed.
Measure-Valued Images, Associated Fractal Transforms, and the Affine Self-Similarity of Images

We construct a complete metric space $(Y,d_Y)$ of measure-valued images, $\mu : X \to {\cal M}(\mathbb{R}_g)$, where $X$ is the base or pixel space and ${\cal M}(\mathbb{R}_g)$ is the set of probability measures supported on the greyscale range $\mathbb{R}_g$. Such a formalism is well suited to nonlocal (NL) image processing, i.e., the manipulation of the value of an image function $u(x)$ based upon values $u(y_k)$ elsewhere in the image. We then show how the space $(Y,d_Y)$ can be employed with a general model of affine self-similarity of images that includes both same-scale as well as cross-scale similarity. We focus on two particular applications: NL-means denoising (same-scale) and multiparent block fractal image coding (cross-scale). In order to accommodate the latter, a method of fractal transforms is formulated over the metric space $(Y,d_Y)$. Under suitable conditions, a transform $M : Y \to Y$ is contractive, implying the existence of a unique fixed point measure-valued function $\bar \mu = M \bar \mu$. We also show that the pointwise moments of this measure satisfy a set of recursion relations that are generalizations of those satisfied by moments of invariant measures of iterated function systems with probabilities.