gebhart/patrepeval huggingface dataset:
The roles of BST‐2 in murine B cell development and on virus propagation (2023)

The bone marrow (BM) stromal cell antigen-2 (BST-2), also known as tetherin, CD317, PDCA-1, or HM1.24, is a membrane protein overexpressed in several types of tumors and may act as a promising target for cancer treatment via antibody-dependent cellular cytotoxicity. BST-2 is also expressed in human BM stromal cells (BMSC), which support B cell development. While the activity of BST-2 as an antiviral factor has been demonstrated, the expression patterns and the role of BST-2 on B-cell development and activation have not been investigated, especially in vivo. In this study, Bst2 knockout (Bst2<sup>-/-</sup> ) mice were generated to assess the role of BST-2 on B cell development and activation. It was observed that BST-2 was not expressed in BMSC or all B cell progenitors even in wild-type mice and does not play a significant role in B cell development. In addition, the loss of BST-2 had no effect on B cell activation. Furthermore and in contrast to the well-known antiviral role of BST-2, infection of vesicular stomatitis Indiana virus to the BM cells collected from the Bst2<sup>-/-</sup> mice produced less infectious virus compared with that from the WT mice. These results suggest that murine BST-2 is different from human BST-2 in the expression pattern, physiological function, in vivo, and might possess positive role on VSV replication.
3R optical regeneration: an all-optical solution with BER improvement (2006)

We demonstrate that an optical regenerator architecture providing re-amplification, re-shaping, and re-timing based on the principle of spectral shift followed by filtering can lead to bit error ratio improvement of the signal passing through it. This is in contrast with typical regenerators based on the usual principle of power conversion from a transfer function, which are unable to improve the bit error ratio. At first, we provide the theoretical basis that explains this improvement. Then we present the regenerator architecture based on spectral shift followed by filtering and provide experimental evidence of bit error ratio improvement of a noisy signal from 3x10(-6) without regenerator to 2x10(-10) with regenerator.
Protein S-Palmitoylation Is Responsive to External Signals and Plays a Regulatory Role in Microneme Secretion in Plasmodium falciparum Merozoites (2020)

Protein S-palmitoylation is an important post-translational modification (PTM) in blood stages of the malaria parasite, <i>Plasmodium falciparum</i>. S-palmitoylation refers to reversible covalent modification of cysteine residues of proteins by saturated fatty acids. In vivo, palmitoylation is regulated by concerted activities of DHHC palmitoyl acyl transferases (DHHC PATs) and acyl protein thioesterases (APTs), which are enzymes responsible for protein palmitoylation and depalmitoylation, respectively. Here, we investigate the role of protein palmitoylation in red blood cell (RBC) invasion by <i>P. falciparum</i> merozoites. We demonstrate for the first time that free merozoites require PAT activity for microneme secretion in response to exposure to the physiologically relevant low [K<sup>+</sup>] environment, characteristic of blood plasma. We have adapted copper catalyzed alkyne azide chemistry (CuAAC) to image palmitoylation in merozoites and found that exposure to low [K<sup>+</sup>] activates PAT activity in merozoites. Moreover, using acyl biotin exchange chemistry (ABE) and confocal imaging, we demonstrate that a calcium dependent protein kinase, PfCDPK1, an essential regulator of key invasion processes such as motility and microneme secretion, undergoes dynamic palmitoylation and localizes to the merozoite membrane. Treatment of merozoites with the PAT inhibitor, 2-bromopalmitate (2-BP), effectively inhibits microneme secretion and RBC invasion by the parasite, thus opening the possibility of targeting <i>P. falciparum</i> PATs for antimalarial drug discovery to inhibit blood stage growth of malaria parasites.
9F-2 Heat Conductive Array Transducer for Phase-Conversion Molecular Imaging (2007)

A heat conductive array transducer was designed for transmitting high power ultrasound as well as transmitting and receiving wideband pulse waves. In phase-conversion ultrasonic molecular imaging, tissue-selective nano-droplets are converted to contrast microbubbles by a long duration ultrasonic pulse with a relatively high amplitude. When a conventional imaging array transducer was used, sensitivity of transducer decreased caused by some breakdown processes. In this study, we firstly examined the breakdown process based on experiments and numerical simulations. The experimental result was consistent with the simulation result assuming peeling of the adhesive between two PZT layers. A new transducer structure using a heat conducting acoustic isolation layer (AIL) on a metal heat sink block was conceived to inhibit this type of breakdown while maintaining the wide bandwidth for imaging with a high resolution. Heat generated in the PZT and adjacent layers can diffuse into a metal heat conductor through the AIL. Since the AIL reflects pulses, a possible unwanted response due to reflection at the opposite side of the metal block will be suppressed. The temperature rise and the ultrasonic pulse response of the transducer were calculated using PZFlex. The temperature rise in the transducer immediately after driving at 40 V for 25 s with 1% duty ratio was 37 degrees for the proposed structure, much lower than that for the conventional structure of 56 degrees. No serious unwanted response was observed for the proposed structure. These results show that the proposed structure will be useful for a high-power wideband phased array transducer.
Time-Averaged Realistic Maximum Power Levels for the Assessment of Radio Frequency Exposure for 5G Radio Base Stations Using Massive MIMO (2017)

In this paper, a model for time-averaged realistic maximum power levels for the assessment of radio frequency (RF) electromagnetic field (EMF) exposure for the fifth generation (5G) radio base stations (RBS) employing massive MIMO is presented. The model is based on a statistical approach and developed to provide a realistic conservative RF exposure assessment for a significant proportion of all possible downlink exposure scenarios (95th percentile) in-line with requirements in a recently developed International Electrotechnical Commission standard for RF EMF exposure assessments of RBS. Factors, such as RBS utilization, time-division duplex, scheduling time, and spatial distribution of users within a cell are considered. The model is presented in terms of a closed-form equation. For an example scenario corresponding to an expected 5G RBS product, the largest realistic maximum power level was found to be less than 15% of the corresponding theoretical maximum. For far-field exposure scenarios, this corresponds to a reduction in RF EMF limit compliance distance with a factor of about 2.6. Results are given for antenna arrays of different sizes and for scenarios with beamforming in both azimuth and elevation.
The Role of Risk Aversion and Technical Trading in the Behaviour of Financial Markets (2011)

In this paper we show how agent based social simulation helps us to improve some of the traditional models and theories in financial economics. In particular, we explore the links between the micro-behaviour of investors and the aggregated behaviour of Stock Markets. First, we build an agent based model of an artificial financial market, populated only with rational investors. We observe that the statistical features of this market are in agreement with the theoretical markets suggested by mainstream financial economics, but far away from the features shown by real financial markets, like the Spanish Ibex-35, the Spanish Stock Market main Index. In order to fill the gap, we introduce heterogeneity in the model. We add psychological investors, as suggested by Kahnemen and Tversky (1979), and we are able to reproduce non-normality, excess kurtosis, excess volatility, and volatility clustering. Then, we introduce technical traders, and we also get from the model higher levels of excess volatility and unit roots. In other words, psychological dealers seem to be responsible for volatility clustering, whereas technical traders trend to introduce unit roots into the process. All these “financial patterns” are a common feature not only for Spanish Ibex-35, also the most important stock markets. We conclude that agent based social simulation helps us to fill the gap between economic theory and real markets, as we explain the statistical features of financial time series from the bottom-up.Request access from your librarian to read this chapter's full text.
Pre-processing methods for handwritten Arabic documents (2005)

In order to improve the readability and the automatic recognition of handwritten document images, preprocessing steps are imperative. These steps in addition to conventional steps of noise removal and filtering include text normalization such as baseline correction, slant normalization and skew correction. These steps make the feature extraction process more reliable and effective. Recently Arabic handwriting recognition has received some attention from the research community. Due to the unique nature of the script, the conventional methods do not prove to be effective. In our work, we describe an orientation independent technique for baseline detection of Arabic words. In addition to that we describe, in the rest of the paper, our techniques for slant normalization, slope correction, line and word separation in handwritten Arabic documents. We show how the baseline can be exploited for slope and skew correction before proceeding with the steps of line and word separation.
Accumulated helix-destabilizing mutations in the leucine zipper of c-Fos leads to attenuation and temperature sensitivity of function. (1993)

Fos protein heterodimerizes through one surface of an alpha-helical domain called the leucine zipper. We have investigated the effect of destabilizing this domain by multiply substituting small residues of its non-interacting surface with glycine. Ternary complex formation between mutated Fos, Jun and DNA was determined in vitro in the presence of denaturant. We also tested the ability of constitutively expressed, mutated Fos proteins to support anchorage independent growth of the cell line Rat1A. Combinations of two substitutions are tolerated in both assays of Fos function, while four substitutions resulted in attenuation in both functions. Rat1A expressing one of the quadruple mutants also showed temperature sensitivity in anchorage independent growth. In dense monolayers of these cells, stromelysin (a Fos-responsive gene product) decreased in abundance as a function of temperature and was less abundant even at 34 degrees C than in cells that overexpressed the wild-type c-fos mRNA. However the mutant transgene itself appeared to show temperature sensitive expression. We suggest that creating a range of glycine substitutions for small residues in the non-interacting face of a leucine zipper might be of general use as a strategy to produce attenuated mutants of other transcription factors.
Diversity‐Oriented Synthesis of Pochonins and Biological Evaluation against a Panel of Kinases (2006)

Pochonins A-F were recently characterized as six new members of the naturally occurring family of 14-membered resorcylic acid lactones. As there are a high number of ATPase and kinase inhibitors among natural resorcylic lactones, a library based on the pochonin scaffold, with five points of diversity, was prepared which includes diversity beyond that of the natural analogues. The library was synthesized by using solid-supported reagents amenable to automation. Testing the library for its inhibition against a panel of 24 kinases at 10 microM afforded a >14 % hit rate. These results demonstrate the potential of the resorcylides towards the inhibition of therapeutically relevant kinases.
Transforming growth factor-beta inhibition of cytokine-induced vascular cell adhesion molecule-1 expression in human astrocytes (1998)

Leukocyte transmigration across the blood-brain barrier (BBB) is a cardinal feature of central nervous system (CNS) inflammation. Astrocytes form an integral part, both structurally and functionally, of the BBB. Vascular cell adhesion molecule-1 (VCAM-1), a member of the immunoglobulin gene superfamily, is involved in extravasation into inflamed tissues and activation of T-lymphocytes. In this study, we investigated the role of TGF-beta, an immunosuppressive cytokine, in regulating cytokine-induced VCAM-1 expression in astrocytes. Human astroglioma cell lines and primary human fetal astrocytes were examined for VCAM-1 gene expression after treatment with proinflammatory cytokines (TNF-alpha, IL-1beta, IFN-gamma) in the absence or presence of TGF-beta. Astroglioma cell lines as well as primary human fetal astrocytes expressed low levels of VCAM-1 constitutively, and the proinflammatory cytokines induced marked increases in VCAM-1 expression, particularly TNF-alpha and IL-1beta. The inclusion of TGF-beta1 or TGF-beta2 with the proinflammatory cytokines inhibited VCAM-1 gene expression to varying degrees (33-93%) in all the astroglioma cell lines and primary fetal cells. These results indicate that TGF-beta is an important regulator of cytokine induced VCAM-1 expression on astrocytes and may prove useful clinically in controlling CNS inflammation.
MATCH: a new industry-focused approach to medical device development (2005)

Healthcare) is a new collaboration in the UK that aims to support the healthcare sector by creating methods to assess the value of medical devices from concept through to mature product. A major aim of MATCH is to encourage the inclusion of the user throughout the product lifecycle in order to achieve devices that truly meet the requirements of their users. A review of the published literature indicates that user requirements are mainly collected during the design and evaluation stage of the product lifecycle whilst other areas, including the concept stage, have less user involvement. Complementing the literature review is an in-depth consultation with the medical device industry, which has identified a number of barriers encountered by companies when attempting to capture user requirements. These will be addressed by a number of case study projects, performed in collaboration with our industrial partners, that will examine the application and utility of different approaches to collecting and analysing data on user requirements. MATCH is focused on providing advice to device developers on how to select and apply methods that have maximum theoretical strength, practical application, cost-effectiveness and likelihood of wide sector acceptance. Feedback will be sought in order to ensure that the needs of the diverse medical device sector are met.
Detection of Single- and Double-Strand DNA Breaks After Traumatic Brain Injury in Rats: Comparison of In Situ Labeling Techniques Using DNA Polymerase I, the Klenow Fragment of DNA Polymerase I, and Terminal Deoxynucleotidyl Transferase (2001)

DNA damage is a common sequela of traumatic brain injury (TBI). Available techniques for the in situ identification of DNA damage include DNA polymerase I-mediated biotin-dATP nick-translation (PANT), the Klenow fragment of DNA polymerase I-mediated biotin-dATP nick-end labeling (Klenow), and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL). While TUNEL has been widely utilized to detect primarily double-strand DNA breaks, the use of PANT to detect primarily single-strand DNA breaks and Klenow to detect both single- and double-strand DNA breaks has not been reported after TBI. Accordingly, coronal brain sections from naive rats and rats at 0, 0.5, 1, 2, 6, 24, and 72 h (n = 3-5/group) after controlled cortical impact with imposed secondary insult were processed using the PANT, Klenow, and TUNEL methods. Cells with DNA breaks were detected by PANT in the ipsilateral hemisphere as early as 0.5 h after injury and were maximal at 6 h (cortex = 66.3+/-15.8, dentate gyrus 58.6+/-12.8, CA1 = 15.8+/-5.9, CA3 = 12.8+/-4.2 cells/x 400 field, mean +/- SEM, all p < 0.05 versus naive). Cells with DNA breaks were detected by Klenow as early as 30 min and were maximal at 24 h (cortex = 56.3+/-14.3, dentate gyrus 78.0+/-16.7, CA1 = 25.8+/-4.7, CA3 = 29.3+/-15.1 cells/x 400 field, all p < 0.05 versus naive). Cells with DNA breaks were not detected by TUNEL until 2 h and were maximal at 24 h (cortex = 47.7+/-21.4, dentate gyrus 63.0+/-11.9, CA1 = 5.6+/-5.4, CA3 = 6.9+/-3.7 cells/x 400 field, cortex and dentate gyrus p < 0.05 versus naive). Dual-label immunofluorescence revealed that PANT-positive cells were predominately neurons. These data demonstrate that TBI results in extensive DNA damage, which includes both single- and double-strand breaks in injured cortex and hippocampus. The presence of multiple types of DNA breaks implicate several pathways in the evolution of DNA damage after TBI.
Persistence of clonal T‐cell expansions following high‐dose chemotherapy and autologous peripheral blood progenitor cell rescue (2000)

Analysing the regeneration of T lymphocytes after high-dose chemotherapy with autologous peripheral blood progenitor cell rescue (PBPCR) may help elucidate the mechanisms of immune recovery. The T-cell receptor variable beta chain (TCRBV) repertoire of adult patients undergoing high-dose chemotherapy was analysed by flow cytometry, before and after treatment. Four patients were found to have a stable expansion present (TCRBV3, 17, 21 and 22) ranging from 8% to 42% of the CD4(+) or CD8(+) repertoire. We demonstrated that, in these patients, following high-dose chemotherapy and autologous stem cell transplantation, the clonal expansions reappeared in peripheral blood and returned to pretransplant levels. Three expansions (CD3(+)CD8(+)TCRBV3(+), CD3(+)CD4(+)TCRBV21(+) and CD3(+)CD8(+)TCRBV22(+)) were further defined by sequence analysis of the complementarity-determining region (CDR)3 portion within the TCR rearrangements. These were shown to be predominantly clonal, with the same sequences being identified in peripheral blood before and after PBPCR, providing evidence that the overwhelming majority of T cells in these expansions arise from mature lymphocytes. This study demonstrated that patients undergoing autologous PBPCR for high-dose chemotherapy regenerate clonal expansions, consistent with pretreatment levels. They also regenerate T-cell repertoires with each TCRBV family represented to a similar level as that prior to high-dose chemotherapy.
786. Development of Zero-CpG Plasmids with Reduced Inflammatory Responses Following Delivery of Lipid/pDNA Complexes to the Mouse Lung (2006)

Nonviral gene therapy is being developed for the treatment of Cystic Fibrosis (CF) lung disease. To date, such approaches have been limited by the poor duration of expression observed and a have also resulted in inflammatory responses following delivery of lipid/ plasmid DNA (pDNA) complexes to the lungs of mice and human subjects. This inflammatory response appears to be due in part to the detection by toll-like receptor 9 of CpG motifs present in pDNA. The majority of first generation pDNA vectors used in pre-clinical and clinical studies contained a large number of immune-stimulatory CpG motifs and one approach to reducing inflammation is to reduce or completely remove CpGs from the pDNA. Therefore we have constructed two novel series of pDNA vectors. Second generation pDNA vectors were constructed from elements with a low CpG content (such as the Genzyme ΔCpG plasmid backbone), which reduced the overall number of CpGs by approximately 50%. Third generation plasmids were constructed from elements that contained no CpG motifs (ΔCpG R6K origin, ΔCpG ZeoR, Murine CMV enhancer, human EF1a promoter) to produce zero-CpG plasmids. Versions of these plasmids that expressed luciferase reporter gene were complexed with Genzyme lipid 67 and delivered to mouse lung by nasal instillation (BALB/c, n=10, 80μg pDNA/100μl). At 24-hours post-dosing, bronchoalveolar lavage fluid (BALF) was collected and the level of IL-12, IFN-γ, TNF-α and total cells was determined. Untreated controls mice had very low levels of all four markers (0%). Mice that received CpG-rich first generation plasmid complexes had elevated levels of all four inflammatory markers (100%). Delivery of second generation (CpG-reduced) plasmids to the mouse lung did not significantly reduce levels IL-12 (105%), TNF-α (60%), IFN-γ (86%) or total cells (80%) (Mann-Whitney U P>0.05). However, following delivery of third generation (zero- CpG) plasmid complexes, levels of IL-12 (10%), TNF-α (0%), IFN-γ (4%) and total cells (14%) were indistinguishable from untreated control mice (P<0.01). Furthermore, at 24-hours post- dosing, luciferase activity in the lung was 10-fold higher from third generation plasmids compared with all other treated groups (P<0.001). In addition, expression from the zero-CpG plasmids persisted for at least 60 days post-dosing while the CpG containing plasmids resulted in only transient expression in the mouse lung (<7 days). These studies suggest that partial reduction of CpG content is no sufficient to reduce the inlfammation observed in mouse lung airway gene transfer models. However the lack of an inflammatory response following delivery of zero-CpG plasmids suggests that these vectors represent a significant advance in terms of safety and efficacy of nonviral delivery to the lung. Further studies outlining the development and testing of clinically relevant zero-CpG will also be presented.
The perceptual importance of selected voice quality parameters (2002)

It is well known, that personal voice qualities differ in the speakers use of temporal structures, F0 contours, articulation precision, vocal effort and type of phonation. Whereas temporal structures and F0 contours can be measured directly in the acoustic signal and conclusions about articulation precision can be made from the formant structure, this paper focuses especially on the vocal effort and the type of phonation. These voice quality percepts are a combination of several acoustic voice quality parameters: the glottal pulse shape in the time domain or damping of the harmonics in the frequency domain, spectral distribution of turbulent signal components and voicing irregularities. In an investigation on emotionally loaded speech material it could be shown, that the named acoustic parameters are useful for differentiating between the emotions happiness, sadness, anger, fear and boredom. The perceptual importance of the above acoustic parameters is investigated in perception experiments with synthetic and resynthesized speech.
Multiple-step ahead prediction for non linear dynamic systems: A Gaussian Process treatment with propagation of the uncertainty (2003)

We consider the problem of multi-step ahead prediction in time series analysis using the non-parametric Gaussian process model. k-step ahead forecasting of a discrete-time non-linear dynamic system can be performed by doing repeated one-step ahead predictions. For a state-space model of the form y t = f(y t 1 ; : : : ; y t L ), the prediction of y at time t + k is based on the estimates ^ y t+k 1 ; : : : ; ^ y t+k L of the previous outputs.