gebhart/patrepeval huggingface dataset:
The immunosuppressive fungal metabolite gliotoxin specifically inhibits transcription factor NF-kappaB. (1996)

Opportunistic infections, such as aspergillosis, are among the most serious complications suffered by immunocompromised patients. Aspergillus fumigatus and other pathogenic fungi synthesize a toxic epipolythiodioxopiperazine metabolite called gliotoxin. Gliotoxin exhibits profound immunosuppressive activity in vivo. It induces apoptosis in thymocytes, splenocytes, and mesenteric lymph node cells and can selectively deplete bone marrow of mature lymphocytes. The molecular mechanism by which gliotoxin exerts these effects remains unknown. Here, we report that nanomolar concentrations of gliotoxin inhibited the activation of transcription factor NF-kappaB in response to a variety of stimuli in T and B cells. The effect of gliotoxin was specific because, at the same concentrations, the toxin did not affect activation of the transcription factor NF-AT or of interferon-responsive signal transducers and activators of transcription. Likewise, the activity of the constitutively DNA-binding transcription factors Oct-1 and cyclic AMP response element binding protein (CREB), as well as the activation of protein tyrosine kinases p56lck and p59fyn, was not altered by gliotoxin. Very high concentrations of gliotoxin prevented NF-kappaB DNA binding in vitro. However, in intact cells, inhibition of NF-kappaB did not occur at the level of DNA binding; rather, the toxin appeared to prevent degradation of IkappaB-alpha, NF-kappaB's inhibitory subunit. Our data raise the possibility that the immunosuppression observed during aspergillosis results in part from gliotoxin-mediated NF-kappaB inhibition.
A novel biometrics method to secure wireless body area sensor networks for telemedicine and m-health (2006)

The development of the wireless body area sensor network (BASN) is imperative for modern telemedicine and m-health, but security remains a formidable challenge yet to be resolved. As nodes of BASN are expected to be interconnected on or in the human body, the body itself can form an inherently secure communication pathway that is unavailable to all other kinds of wireless networks. This article explores the use of this conduit in the security mechanism of BASN; that is, by a biometrics approach that uses an intrinsic characteristic of the human body as the authentication identity or the means of securing the distribution of a cipher key to secure inter-BASN communications. The method was tested on 99 subjects with 838 segments of simultaneous recordings of electrocardiogram and photoplethysmogram. By using the interpulse interval (IPI) as the biometric trait, the system achieved a minimum half total error rate of 2.58 percent when the IPIs measured from signals, which were sampled at 1000 Hz, were coded into 128-bit binary sequences. The study opens up a few key issues for future investigation, including compensation schemes for the asynchrony of different channels, coding schemes, and other suitable biometric traits.
Design, construction, characterization, and application of a hyperspectral microarray scanner (2004)

We describe the design, construction, and operation of a hyperspectral microarray scanner for functional genomic research. The hyperspectral instrument operates with spatial resolutions ranging from 3 to 30 microm and records the emission spectrum between 490 and 900 nm with a spectral resolution of 3 nm for each pixel of the microarray. This spectral information, when coupled with multivariate data analysis techniques, allows for identification and elimination of unwanted artifacts and greatly improves the accuracy of microarray experiments. Microarray results presented in this study clearly demonstrate the separation of fluorescent label emission from the spectrally overlapping emission due to the underlying glass substrate. We also demonstrate separation of the emission due to green fluorescent protein expressed by yeast cells from the spectrally overlapping autofluorescence of the yeast cells and the growth media.
Nudging and Informed Consent (2013)

Libertarian paternalism's notion of "nudging" refers to steering individual decision making so as to make choosers better off without breaching their free choice. If successful, this may offer an ideal synthesis between the duty to respect patient autonomy and that of beneficence, which at times favors paternalistic influence. A growing body of literature attempts to assess the merits of nudging in health care. However, this literature deals almost exclusively with health policy, while the question of the potential benefit of nudging for the practice of informed consent has escaped systematic analysis. This article focuses on this question. While it concedes that nudging could amount to improper exploitation of cognitive weaknesses, it defends the practice of nudging in a wide range of other conditions. The conclusion is that, when ethically legitimate, nudging offers an important new paradigm for informed consent, with a special potential to overcome the classical dilemma between paternalistic beneficence and respect for autonomy.
Combining Ab Initio Computation with Experiments for Designing New Electrode Materials for Advanced Lithium Batteries: LiNi[sub 1/3]Fe[sub 1/6]Co[sub 1/6]Mn[sub 1/3]O[sub 2] (2004)

10.1149/1.1765032
Semidefinite Programming Approaches for Sensor Network Localization With Noisy Distance Measurements (2006)

A sensor network localization problem is to determine the positions of the sensor nodes in a network given incomplete and inaccurate pairwise distance measurements. Such distance data may be acquired by a sensor node by communicating with its neighbors. We describe a general semidefinite programming (SDP)-based approach for solving the graph realization problem, of which the sensor network localization problems is a special case. We investigate the performance of this method on problems with noisy distance data. Error bounds are derived from the SDP formulation. The sources of estimation error in the SDP formulation are identified. The SDP solution usually has a rank higher than the underlying physical space which, when projected onto the lower dimensional space, generally results in high estimation error. We describe two improvements to ameliorate such a difficulty. First, we propose a regularization term in the objective function that can help to reduce the rank of the SDP solution. Second, we use the points estimated from the SDP solution as the initial iterate for a gradient-descent method to further refine the estimated points. A lower bound obtained from the optimal SDP objective value can be used to check the solution quality. Experimental results are presented to validate our methods and show that they outperform existing SDP methods. Note to Practitioners—Wireless sensor networks consist of a large number of inexpensive wireless sensors deployed in a geographical area with the ability to communicate with their neighbors within a limited radio range. Wireless sensor networks are finding increasing applicability to a range of monitoring applications in civil and military scenarios, such as biodiversity and geographical monitoring, smart homes, industrial control, surveillance, and traffic monitoring. It is often very useful in the applications of sensor networks to know the locations of the sensors. Global positioning systems suffer from many drawbacks in this scenario, such as high cost, line-of-sight issues, etc. Therefore, there is a need to develop robust and efficient algorithms that can estimate or “localize” sensor positions in a network by using only the mutual distance measures (received signal strength, time of arrival) that the wireless sensors receive from their neighbors. This paper describes an algorithm that solves the sensor network localization problem using advanced optimization techniques. We also study the effect of using very noisy measurements and propose robust methods to deal with high noise. Finally, simulation results for the algorithms are presented to demonstrate their performance in terms of computational effort and accuracy.
DNA-binding site of major regulatory protein alpha 4 specifically associated with promoter-regulatory domains of alpha genes of herpes simplex virus type 1. (1986)

Herpes simplex virus type 1 genes form at least five groups (alpha, beta 1, beta 2, gamma 1, and gamma 2) whose expression is coordinately regulated and sequentially ordered in a cascade fashion. Previous studies have shown that functional alpha 4 gene product is essential for the transition from alpha to beta protein synthesis and have suggested that alpha 4 gene expression is autoregulatory. We have previously reported that labeled DNA fragments containing promoter-regulatory domains of three alpha (alpha 0, alpha 4, and alpha 27) and a gamma 2 gene form stable complexes with proteins from lysates of infected cells as detected by a gel electrophoresis binding assay and that monoclonal antibody to alpha 4 protein reduced the electrophoretic mobility of the complex of labeled DNA and protein from infected cells. In this study we identified one monoclonal antibody, H950, from a panel of monoclonal antibodies to the alpha 4 protein that blocks the formation of specific infected cell complexes with labeled DNA fragments containing promoter and regulatory domains of alpha genes. We also report the nucleotide sequence of the alpha 0 promoter domain protected from exonuclease III digestion by alpha 4 protein in the absence of H950 monoclonal antibody but not in its presence. In addition, we identified a 59-base-pair sequence from the regulatory domain of the alpha 4 gene that binds alpha 4 protein. Deletion clones of this fragment localize sequence elements required for formation of the alpha 4 protein-DNA complex. Furthermore, deletion of the in vitro binding site of the SP1 transcription factor from the 59-base-pair fragment did not affect the formation of the alpha 4 protein-DNA complex.
BRAF mutation detection and identification by cycling temperature capillary electrophoresis (2005)

BRAF mutations are found in many human tumors, namely melanomas ( approximately 70%) and colon carcinomas ( approximately 15%). This paper presents a method for identification of exon 15 BRAF mutations by denaturant capillary electrophoresis (CE), an analysis method that is sensitive, cost-effective (involving only polymerase chain reaction (PCR) and electrophoresis) and capable of high-throughput screening. In total, we found 21 (70%) out of 30 melanoma cell lines with BRAF mutations in exon 15: two of which were the p.Val600Asp (c.1799-800TG>AT) mutation, one cell line contained the p.Val600Arg (c.1798-99GT>AG) mutation, and 18 cell lines contained the p.Val600Glu (c.1799T>A) mutation. Of the nine cell lines that did not contain a BRAF mutation, five contained an NRAS mutation at exon 2, and no mutations were detected in NRAS exon 1. There was no overlap of NRAS and BRAF mutations in the same cell line. In addition, we looked at 221 colon biopsy samples and identified one further BRAF mutation, the p.Asp594Gly (c.1781A>G) mutation, in seven samples. The p.Val600Glu mutation was identified in 11 of the colon biopsy samples. Using the four mutations of BRAF exon 15, we then constructed a denaturing CE standard capable of distinguishing between each of the mutations; therefore, sequencing does not need to be performed to confirm the mutation. In conclusion, this sensitive, cost-effective mutation assay for BRAF (and RAS) will provide the opportunity to detect and determine mutations without the need to purify samples for sequencing. Future large-scale studies will provide the clinical usefulness of such mutations.
Removal of surface charge-charge interactions from ubiquitin leaves the protein folded and very stable (2002)

The contribution of solvent-exposed charged residues to protein stability was evaluated using ubiquitin as a model protein.We combined site-directed mutagenesis and specific chemical modifications to first replace all Arg residues with Lys, followed by carbomylation of Lys-amino groups.Under the conditions in which all carboxylic groups are protonated (at pH 2), the chemically modified protein is folded and very stable (⌬G ‫ס‬ 18 kJ/mol).These results indicate that surface charge-charge interactions are not an essential fundamental force for protein folding and stability.
The Computational Brain (1992)

Before this book was published in 1992, conceptual frameworks for brain function were based on the behavior of single neurons, applied globally. This book developed a different conceptual framework, based on large populations of neurons. This was done by showing that patterns of activities among the units in trained artificial neural network models had properties that resembled those recorded from populations of neurons recorded one at a time. It is one of the first books to bring together computational concepts and behavioral data within a neurobiological framework. Aimed at a broad audience of neuroscientists, computer scientists, cognitive scientists, and philosophers, the book is written for both expert and novice. This anniversary edition offers a new preface by the authors that puts the book in the context of current research. This approach influenced a generation of researchers in the field of neuroscience. Even today, when neuroscientists can routinely record from hundreds of neurons using optics rather than electricity, and the 2013 White House BRAIN initiative heralded a new era in innovative neurotechnologies, the main message of this book is still relevant.
Dynamic blastomere behaviour reflects human embryo ploidy by the four-cell stage (2012)

Previous studies have demonstrated that aneuploidy in human embryos is surprisingly frequent with 50-80% of cleavage-stage human embryos carrying an abnormal chromosome number. Here we combine non-invasive time-lapse imaging with karyotypic reconstruction of all blastomeres in four-cell human embryos to address the hypothesis that blastomere behaviour may reflect ploidy during the first two cleavage divisions. We demonstrate that precise cell cycle parameter timing is observed in all euploid embryos to the four-cell stage, whereas only 30% of aneuploid embryos exhibit parameter values within normal timing windows. Further, we observe that the generation of human embryonic aneuploidy is complex with contribution from chromosome-containing fragments/micronuclei that frequently emerge and may persist or become reabsorbed during interphase. These findings suggest that cell cycle and fragmentation parameters of individual blastomeres are diagnostic of ploidy, amenable to automated tracking algorithms, and likely of clinical relevance in reducing transfer of embryos prone to miscarriage.
Spectral amplitude warping (SAW) for noise spectrum shaping in audio coding (2002)

In this paper, we present a new approach to shape the coding noise in speech and audio coders. The approach, called spectral amplitude warping (SAW), consists essentially of a pre- and post-processing which apply a nonlinear transformation to the signal short-term spectrum prior to, and after, encoding. Since it is possible to view SAW as a separate entity from the coder, the noise shaping capability of an existing coder can be improved without modifying the coder itself. Using SAW as a pre- and post-process to the G.722 wideband speech coding standard, it was found in an informal listening test that the quality of the 64 kb/s operating mode can be achieved at only 48 kb/s. The price to be paid is an additional delay.
Inositolphosphoglycan second messengers. (1994)

The mechanisms by which cellular receptors can elicit different biological responses in a maturation state-dependent manner is one of the central problems in cell differentiation which remains to be resolved. The signals generated are likely to be due to additional (as yet unknown) transmembrane signalling pathways. In addition, the recent observation that a single growth factor receptor can activate a whole family of different putative second messengers and that the combinatorial interactions and stoichiometric ratios between the different messengers determine the resulting biological activities has opened up a whole new area of cell biology. It has been proposed that membrane GPI-anchors may function in signal transduction. We have recently confirmed the presence of a family of inositolphosphoglycan second messengers. Partial structural data suggests that these second messengers are not derived from known GPI membrane anchors and may thus constitute a novel class of non-protein-conjugated GPI.
Espesura esmeralda: casa Laminata de Kruunenberg & Van der Erve en Leerdam (2002)

En la que se conoce como 'capital del vidrio', esta casa Laminata ensaya una via alternativa para utilizar dicho material, del que se valora su cualidad maciza y la calidad de luz obtenida.
On the Incorporation Mechanism of Hydrophobic Quantum Dots in Silica Spheres by a Reverse Microemulsion Method (2008)

In this work, we show strong experimental evidence in favor of a proposed incorporation mechanism of hydrophobic semiconductor nanocrystals (or quantum dots, QDs) in monodisperse silica spheres (diameter ∼35 nm) by a water-in-oil (W/O) reverse microemulsion synthesis. Fluorescence spectroscopy is used to investigate the rapid ligand exchange that takes place at the QD surface upon addition of the various synthesis reactants. It is found that hydrolyzed TEOS has a high affinity for the QD surface and replaces the hydrophobic amine ligands, which enables the transfer of the QDs to the hydrophilic interior of the micelles where silica growth takes place. By hindering the ligand exchange using stronger binding thiol ligands, the position of the incorporated QDs can be controlled from centered to off-center and eventually to the surface of the silica spheres. The proposed incorporation mechanism explains how we can have high control over the incorporation of single QDs exactly in the middle of silica spheres. It is likely that the proposed mechanism also applies to the incorporation of other hydrophobic nanocrystals in silica using the same method. In conjunction with our findings, we were able to make QD/silica particles with an unprecedented quantum efficiency of 35%.
Immunological Challenges and Therapies in Xenotransplantation (2014)

Xenotransplantation, or the transplantation of cells, tissues, or organs between different species, was proposed a long time ago as a possible solution to the worldwide shortage of human organs and tissues for transplantation. In this setting, the pig is currently seen as the most likely candidate species. In the last decade, progress in this field has been remarkable and includes a better insight into the immunological mechanisms underlying the rejection process. Several immunological hurdles nonetheless remain, such as the strong antibodymediated and innate or adaptive cellular immune responses linked to coagulation derangements, precluding indefinite xenograft survival. This article reviews our current understanding of the immunological mechanisms involved in xenograft rejection and the potential strategies that may enable xenotransplantation to become a clinical reality in the not-toodistant future.
Adenosine deaminase inhibitors: synthesis and structure activity relationships of imidazole analogs of erythro-9-(2-hydroxy-3-nonyl)adenine (1991)

A series of erythro-1-(2-hydroxy-3-nonyl)imidazole derivatives have been synthesized and evaluated for adenosine deaminase (ADA) inhibitory activity, in order to introduce simplifications in the ADA inhibitors erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA, 1a) and 3-deaza-EHNA (1c). Opening the pyrimidine or pyridine ring of EHNA or 3-deaza-EHNA respectively led to compounds which are still ADA inhibitors. The most potent compound was erythro-1-(2-hydroxy-3-nonyl)imidazole-4-carboxamide (5, Ki = 3.53 x 10(-8) M), which provided potential donor and acceptor sites for hydrogen bonding. Lack of one of this sites could account for the order of potency of all compounds examined in this series. Opening the same ring in adenosine and in 3-deazaadenosine led to fully inactive compounds. These results support the hypothesis of the existence, at or near the enzyme active site, of a hydrophobic region able to bind the erythro-nonyl moiety.
Adaptive model-based neural network control (2002)

A form of adaptive model-based control is proposed and experimentally evaluated. An adaptive model-based neural network controller (AMBNNC) uses multilayer perceptron artificial neural networks to estimate the payload during high-speed manipulator motion. The payload estimate adapts the feedforward compensator to unmodeled system dynamics and payload variation. The neural nets are trained through repetitive training on trajectory tracking error data. The AMBNNC was experimentally evaluated on the third link of a PUMA-560 manipulator. Tracking performance was evaluated for a wide range of payload and trajectory conditions and compared to a nonadaptive model-based controller. The superior tracking accuracy of the AMBNNC demonstrates the potential of the technique.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A copy network with shared buffers for large-scale multicast ATM switching (1993)

An architecture for the copy network that is an integral part of multicast ATM switches is described. The architecture makes use of the property that the broadcast banyan network (BBN) is nonblocking if the active inputs are cyclically concentrated and the outputs are monotone. In the architecture, by employing a token ring reservation scheme, the outputs of the copy network are reserved before a multicast cell is replicated. By the copy principle, the number of copies requested by a multicast call is not limited by the size of the copy network so that very large multicast switches can be configured in a modular fashion. The sequence of cells is preserved in the structure. Though physically separated, buffers within the copy network are completely shared, so that the throughput can reach 100%, and the cell delay and the cell loss probability can be made to be very small. The cell delay is estimated analytically and by computer simulation, and the results of both are found to agree with each other. The relationship between the cell loss probability under various traffic parameters and buffer sizes is studied by computer simulation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A thresholding multiresolution block matching algorithm (1997)

In this paper, we present a thresholding multiresolution block matching algorithm. Preventing blocks that satisfy a predefined accuracy criterion from further processing saves computation. In three experiments which have quite different motion complexities, the proposed algorithm outperforms the fastest existing multiresolution block matching algorithm. Specifically, it reduces the processing time ranging from 14% to 20%, while maintaining almost the same quality of the reconstructed image.