gebhart/patrepeval huggingface dataset:
Probabilistic graphical models and computational metabolic models applied to the analysis of metabolomics data in breast cancer (2018)

Metabolomics has great potential in the development of new biomarkers in cancer. In this study, metabolomics and gene expression data from breast cancer tumor samples were analyzed, using (1) probabilistic graphical models to define associations using quantitative data without other a priori information; and (2) Flux Balance Analysis and flux activities to characterize differences in metabolic pathways. A metabolite network was built through the use of probabilistic graphical models. Interestingly, the metabolites were organized into metabolic pathways in this network, thus it was possible to establish differences between breast cancer subtypes at the metabolic pathway level. Additionally, the lipid metabolism node had prognostic value. A second network associating gene expression with metabolites was built. Associations were established between the biological functions of genes and the metabolites included in each node. A third network combined flux activities from Flux Balance Analysis and metabolomics data, showing coherence between the metabolic pathways of the flux activities and the metabolites in each branch. In this study, probabilistic graphical models were valuable for the functional analysis of metabolomics data from a functional point of view, allowing new hypotheses in metabolomics and associating metabolomics data with the patient9s clinical outcome.
Ultrasonic Testing to Determine Water-Cement Ratio for Freshly Mixed Concrete (1998)

Abstract The objective of the research presented here was to find promising directions for the development of ultrasonic test method(s) for the direct, instantaneous determination of the water-cement ratio (W/C) in fresh mortar or concrete. The importance of W/C is related to potential strength development and, to a certain extent, the durability potential of the hardened concrete. Since previous efforts during the past 50 years have been unsuccessful in testing fresh concrete due to the complexity of the problem, innovative, high-risk/high-gain methods were selected in the present work. The methods are considered innovative since a literature search detected no sign that they have been used for testing fresh concrete before. The following test methods were tried out for testing fresh concrete: • ultrasonic methods used regularly for testing hardened concrete; • solidification of the fresh mixtures by freezing or heat treatment or accelerating admixture + heat treatment before testing; • use of high-intensity stress waves by lithotripter; • the direct contact method. None of these methods produced a satisfactory solution for the instantaneous determination of the water-cement ratio, although interesting side results were obtained. It is hoped that both the positive and negative results presented will help researchers in their work on ultrasonic testing of concrete.
Protein Phosphorylation in Intact Superior Cervical Ganglion During Regeneration (1990)

The incorporation of radioactive phosphate into proteins of both normal and regenerating superior cervical ganglion nerve of the rat is reported. Incorporation studies carried out by in vitro and in vivo methods are compared. In the in vitro method, excised intact ganglia or their homogenates were incubated in the presence of inorganic phosphate or ATP, respectively, under various conditions. Proteins were analyzed by gel electrophoresis followed by autoradiography, in which quantitative but not qualitative differences between regenerating and control cases were apparent. In the in vivo procedure, inorganic phosphate was injected into the living animal 4 h before removal of ganglia. At least fivefold more proteins became labeled in vivo than in vitro, whereas no similarity in the pattern of labeling between the two methods was observed. For example, the most heavily labeled protein in the in vivo method, tentatively identified as microtubule-associated protein-2, was not detected on autoradiograms of proteins labeled by the in vitro method. In this latter method, an 85-kDa species and growth-associated protein-43 were always labeled, and the extent of their phosphorylation was enhanced by the additional presence of phosphatidylserine and Ca2+, a result indicating that these labeled species are substrates of protein kinase C. The in vitro conditions also led to the labeling of proteins identified as alpha- and beta-tubulin. Comparison of the methods suggests that removal of the ganglion interferes with the function of protein phosphorylation systems and that this effect involves elements of the cytoskeleton.
The CDT mStar environment (1997)

This paper presents the mStar environment, which creates an environment for truly a mChat, which allows for text based group chat; mVote, which allows for distributed voting and mWeb for shared WWW objects. These are all desktop and IP-multicast based and symmetric. The mStar environment also includes mh4OD, which is a VCR-like tool for recording and playback of teamwork sessions, and mTunne1, which is an application for handling IP-multicast traffic on narrow links in the network (such as ISDN/modem) and network segments that does hot support IP:multicast.. It allows for scaling and tranrforming of the network based data in various ways. KepOrdS: IP-multicast, desktop conferencing, distributed presentations, digital recoding, teamwork, distance education, better-than-being-there.
Traditional TCP congestion control algorithms evaluation in wired-cum-wireless networks (2015)

Congestion control algorithms exist for decades to prevent package loss in intense traffic networks. Several solutions developed over the years tried to solve this problem, including the creation of new algorithms. However, hybrid wired and wireless networks, or wired-cum-wireless, common in modern days, bring new challenges to programmers and engineers who try to overcome the numerous new problems that this kind of network presents. This work carries out a performance comparison, in a wired-cum-wireless network, using TCP congestion control algorithms variants: New Reno and CUBIC. The comparison is to determine which of those algorithms performs better in several situations, like multiple disconnections caused by mobility, interference and congested links. The results showed that the CUBIC is a more stable and fair algorithm, but it has a significantly less data flow than New Reno.
High energy, diode-pumped Yb-doped solid-state lasers for inertial fusion drivers (2008)

An 1-kJ laser system ldquoGENBUrdquo has been conceptually designed by using a large-aperture active-mirror amplifier with a cryogenic Yb:YAG ceramic, as a milestone for a new IFE reactor driver. A 1-J system ldquoGENBU-Kidrdquo is under construction for power-scaling up to 1 kJ.
Power-efficient I/O design considerations for high-bandwidth applications (2011)

Power-efficiency results from several generations of I/O interfaces with specific goals are presented as well as the tradeoffs made within and across those designs. Foundational work in active-power reduction at a single rate for a symmetric system, the subsequent application of that work to a burst-mode asymmetric interface, and recent research on low-overhead bursting are discussed. Dynamic voltage frequency scaling and efficiency increases enabled by system level interconnect improvements are also considered as important techniques.
Preparation and Structure of Dibromobis(N,N-diethyldithiocarbamato)-thionitrosyltechnetium(III) (1991)

The title compound, [Tc (NS)(S2CNEt2)2Br2], has been prepared by the reaction of [ TcN (S2CNEt2)2] with SOBr2, and its crystal structure has been determined by single-crystal X-ray diffraction methods at 23±1°C. Crystals are orthorhombic, space group Pnma , with a 14.864(7), b 15.857(7), c 8.938(4)?, and Z 4. Full-matrix least-squares refinement gave a final R value of 0.047 for 1685 independent reflections. The technetium atom is seven-coordinate with a distorted pentagonal- bipyramidal coordination geometry. The thionitrosyl ligand and a bromo ligand occupy the axial positions, with the thionitrosyl group exerting a small trans influence with Tc-Brtrans 2.595(1) and Tc-Brcis 2.564(1)?. The coordination of the thionitrosyl group is essentially linear with Tc -N=S 177.2(7)°, Tc -N 1.754(9), and N=S 1.504(9)?.
Cellular and axonal migrations are misguided along both body axes in the maternal-effect <i>mau-2</i> mutants of <i>Caenorhabditis elegans</i> (1997)

We have characterized the mau-2 mutants of Caenorhabditis elegans and found that migrating cells and axons are mispositioned along both the antero-posterior and dorsoventral body axes. This is in contrast to previously characterized guidance mutations in Caenorhabditis and in Drosophila, which have been found to be axis-specific. Two observations suggest that mau-2 acts very early during development: most behavioral phenotypes of mau-2 can be rescued by a maternal effect, and variations in expressivity involve an entire body side at a time. The possibility that mau-2 is involved in the spatial organization of guidance cues encoded by other genes is discussed.
Data mining with sparse grids using simplicial basis functions (2001)

Recently we presented a new approach [18] to the classification problem arising in data mining. It is based on the regularization network approach but, in contrast to other methods which employ ansatz functions associated to data points, we use a grid in the usually high-dimensional feature space for the minimization process. To cope with the curse of dimensionality, we employ sparse grids [49]. Thus, only O(hn-1nd-1) instead of O(hn-d) grid points and unknowns are involved. Here d denotes the dimension of the feature space and hn = 2-n gives the mesh size. We use the sparse grid combination technique [28] where the classification problem is discretized and solved on a sequence of conventional grids with uniform mesh sizes in each dimension. The sparse grid solution is then obtained by linear combination. In contrast to our former work, where d-linear functions were used, we now apply linear basis functions based on a simplicial discretization. This allows to handle more dimensions and the algorithm needs less operations per data point.We describe the sparse grid combination technique for the classification problem, give implementational details and discuss the complexity of the algorithm. It turns out that the method scales linearly with the number of given data points. Finally we report on the quality of the classifier built by our new method on data sets with up to 10 dimensions. It turns out that our new method achieves correctness rates which are competitive to that of the best existing methods.
Concepts for Domain Wall Motion in Nanoscale Ferromagnetic Elements due to Spin Torque and in Particular Oersted Fields (2009)

Herein, different concepts for domain wall propagation based on currents and fields that could potentially be used in magnetic data storage devices based on domains and domain walls are reviewed. By direct imaging, we show that vortex and transverse walls can be displaced using currents due to the spin transfer torque effect. For the case of field-induced wall motion, particular attention is paid to the influence of localized fields and local heating on the depinning and propagation of domain walls. Using an Au nanowire adjacent to a permalloy structure with a domain wall, the depinning field of the wall, when current pulses are injected into the Au nanowire, was studied. The current pulse drastically modified the depinning field, which depended on the interplay between the externally applied field direction and polarity of the current, leading subsequently to an Oersted field and heating of the permalloy at the interface with the Au wire. Placing the domain wall at various distances from the Au wire and studying different wall propagation directions, the range of Joule heating and Oersted field was determined; both effects could be separated. Approaches beyond conventional field- and current-induced wall displacement are briefly discussed.
Hyper‐spectral Raman imaging using a diffractive optical element (2003)

Abstract A modification to a conventional imaging Raman microscope to allow the acquisition of quasi‐confocal spectra from multiple discrete Raman sampling volumes is reported. Preliminary performance was demonstrated by generating an extended area hyper‐spectral chemical map of a number of ground sulfur crystals deposited on an aluminium mirror. Images generated using this multiplexed sampling arrangement were found to contain a number of weak ghost images (cross‐talk), corresponding to inadequate separation of the focused laser spots at the sample. Copyright © 2003 John Wiley & Sons, Ltd.
Therapeutic use of regulatory T cells for graft‐versus‐host disease (2019)

Regulatory T cells (Treg cells) represent a CD4<sup>+</sup> T-cell lineage that plays a critical role in restraining immune responses to self and foreign antigens and associated inflammation. Due to the suppressive function of Treg cells, inhibition or ablation of these cells can be used to boost the immunity against malignant cells. On the other hand, augmenting the activity of Treg cells can be employed for the treatment of inflammatory or autoimmune diseases and allogeneic conflicts associated with transplantation. Graft-versus-host disease (GvHD) is a leading cause of morbidity and mortality after haematopoietic stem cell transplantation (HSCT). In this review, we describe basic biological properties of Treg cells and their role in GvHD. We focus on the application of adoptive transfer of Treg cells and the therapeutic modulation of their activity for the prevention and treatment of GvHD in pre-clinical models and in clinical settings. We also discuss the main obstacles to applying Treg cell-based therapies for GvHD in clinical practice.
Quantitative method for estimating characteristics of conductive filament in ReRAM (2014)

A quantitative 3D conductive filament model for ReRAM is developed based on a hopping percolation theory without any fitting parameter. According to the theory, the dimensions and oxygen vacancy concentration of the conductive filament are functions of the resistance distribution. We perform Monte Carlo simulations for calculating the resistance distribution and derive the physical parameters for quantitative simulation based on the relation between resistivity and the oxygen concentration of TaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> . The dimensions and oxygen vacancy concentration are estimated by simulating the resistance distribution. The estimated conductive filament diameters are corroborated by EBAC and TEM observations.
Tau load is associated with apolipoprotein E genotype and the amount of amyloid β protein, Aβ<sub>40</sub>, in sporadic and familial Alzheimer's disease (2003)

The total amount of hyperphosphorylated tau protein (p-tau load), present as neurofibrillary tangles (NFTs), neuropil threads or plaque neurites, was quantified in the frontal cortex of 109 cases of sporadic Alzheimer's disease (AD) and 35 cases of familial AD due to missense mutations in the presenilin-1, presenilin-2 and amyloid precursor protein genes. p-tau load was inversely correlated with age at onset of illness in both sporadic and familial AD but not with duration of disease. There was no difference in p-tau load between cases of familial AD and others with sporadic AD, matching the familial cases for apolipoprotein E (APO E) genotype. However, p-tau was greater in cases of familial and sporadic AD in the presence of APO E epsilon4 allele and increased with gene dose. Conversely, p-tau load tended to be lower when epsilon2 allele was present. In sporadic AD, tau load was highly significantly correlated with amyloid beta40 (Abeta40), but not Abeta42(43), load. These data indicate that the burden of pathological tau deposited in the brain in both familial and sporadic AD is favoured in the presence of APO E epsilon4 allele and also related to the amount of Abeta40, this also being higher when epsilon4 allele is present. Abeta40 plaques are rich in microglial cells and it is possible that p-tau pathology in AD is triggered by reaction of microglial cells to the presence of Abeta40 and not this peptide directly.
Involvement of the subthalamic nucleus in engagement with behaviourally relevant stimuli (2009)

In this study we investigate how the basal ganglia (BG) may process the behavioural relevance of environmental cues by recording local field potentials (LFPs) in the subthalamic nucleus of patients with Parkinson's disease who had undergone implantation of electrodes for deep brain stimulation. Fourteen patients were recorded as they performed a paradigm dissociating warning cue presentation from programming related to execution of specific tasks. Target and non-target warning cues of differing behavioural relevance were contrasted, and we evaluated if warning cue-evoked activities varied according to whether the eventual task to be performed was motor or cognitive and whether patients were receiving or withdrawn from dopaminergic therapy. Warning cues evoked a complex temporal sequence of activities with three epochs over the 760 ms following the onset of the warning cue. In contrast to the initial evoked LFP, evoked activities over two later periods were significantly influenced by behavioural relevance and by treatment state. The early activity was likely related to the initial orientating of attention induced by a novel target, while the delayed responses in our paradigm may reflect processing related to the non-motor resource implications of cues. The results suggest that the BG are intimately involved in the evaluation of changes in the environment and of their behavioural significance. The latter process is partly modulated by dopamine. Weakness in this function might contribute to the behavioural impairment that can follow BG lesions and surgery.
Low-Temperature Etching of 0.2 µm Al Patterns Using a SiO<sub>2</sub> Mask (1992)

The effects of etching temperature and gases on the microloading and critical dimension (CD) shifts are investigated for Al etching using a SiO 2 mask. Al etching with a SiO 2 mask using Cl 2 gas at low temperature achieved etching resistance against the mask, selective Al etching of underlying SiO 2 , suppression of microloading, CD shift, and after-corrosion. Al etching of 0.2 µm was successfully achieved by using the SiO 2 mask and Cl 2 gas chemistry at low temperature.
Einsatz und Eignung von PROLOG zur Entwicklung eines Expertensystems für labormedizinische Fragestellungen (1985)

Article Einsatz und Eignung von PROLOG zur Entwicklung eines Expertensystems für labormedizinische Fragestellungen was published on January 1, 1985 in the journal Biomedical Engineering / Biomedizinische Technik (volume 30, issue s1).
Identification of human candidate genes for male infertility by digital differential display (2001)

Evidence for the importance of genetic factors in male fertility is accumulating. In the literature and the Mendelian Cytogenetics Network database, 265 cases of infertile males with balanced reciprocal translocations have been described. The candidacy for infertility of 14 testis-expressed transcripts (TETs) were examined by comparing their chromosomal mapping position to the position of balanced reciprocal translocation breakpoints found in the 265 infertile males. The 14 TETs were selected by using digital differential display (electronic subtraction) to search for apparently testis-specific transcripts in the TIGR database. The testis specificity of the 14 TETs was further examined by reverse transcription-polymerase chain reaction (RT-PCR) on adult and fetal tissues showing that four TETs (TET1 to TET4) were testis-expressed only, six TETs (TET5 to TET10) appeared to be differentially expressed and the remaining four TETs (TET11 to TET14) were ubiquitously expressed. Interestingly, the two tesis expressed-only transcripts, TET1 and TET2, mapped to chromosomal regions where seven and six translocation breakpoints have been reported in infertile males respectively. Furthermore, one ubiquitously, but predominantly testis-expressed, transcript, TET11, mapped to 1p32-33, where 13 translocation breakpoints have been found in infertile males. Interestingly, the mouse mutation, skeletal fusions with sterility, sks, maps to the syntenic region in the mouse genome. Another transcript, TET7, was the human homologue of rat Tpx-1, which functions in the specific interaction of spermatogenic cells with Sertoli cells. TPX-1 maps to 6p21 where three cases of chromosomal breakpoints in infertile males have been reported. Finally, TET8 was a novel transcript which in the fetal stage is testis-specific, but in the adult is expressed in multiple tissues, including testis. We named this novel transcript fetal and adult testis-expressed transcript (FATE).
THYMUS-DERIVED CELL (T CELL) ACTIVATION BY HETEROLOGOUS ANTIGENS AS A REPLACEMENT OF SPECIFIC IMMUNE T CELLS IN THE TRANSFER OF THE SECONDARY RESPONSE TO SHEEP ERYTHROCYTES (1972)

Spleen cells from LAF(1) mice hyperimmune to sheep erythrocytes (SE) lost their ability to transfer a secondary response to irradiated recipients after incubation with anti-theta and rabbit complement in vitro. Small numbers of specific immune cells even when taken 3 days after a primary SE injection reconstituted the direct and indirect plaque-forming cell responses. Larger numbers of cells sensitized to B. abortus (or keyhole limpet hemocyanin), and given together with the corresponding antigen, also partially reconstituted the ability to respond to SE. This property was mediated by theta-bearing cells and was interpreted as due to a nonspecific humoral factor liberated by specifically activated T cells and acting on B cell proliferation or maturation.
ZBED6 Modulates the Transcription of Myogenic Genes in Mouse Myoblast Cells (2014)

ZBED6 is a recently discovered transcription factor, unique to placental mammals, that has evolved from a domesticated DNA transposon. It acts as a repressor at the IGF2 locus. Here we show that ZBED6 acts as a transcriptional modulator in mouse myoblast cells, where more than 700 genes were differentially expressed after Zbed6-silencing. The most significantly enriched GO term was muscle protein and contractile fiber, which was consistent with increased myotube formation. Twenty small nucleolar RNAs all showed increased expression after Zbed6-silencing. The co-localization of histone marks and ZBED6 binding sites and the effect of Zbed6-silencing on distribution of histone marks was evaluated by ChIP-seq analysis. There was a strong association between ZBED6 binding sites and the H3K4me3, H3K4me2 and H3K27ac modifications, which are usually found at active promoters, but no association with the repressive mark H3K27me3. Zbed6-silencing led to increased enrichment of active marks at myogenic genes, in agreement with the RNA-seq findings. We propose that ZBED6 preferentially binds to active promoters and modulates transcriptional activity without recruiting repressive histone modifications.