gebhart/patrepeval huggingface dataset:
Interferon-&#945; / &#946;-Receptor Interactions: A Complex Story Unfolding (2002)

The Type I interferons (IFN-alpha/beta) exhibit pleiotropic biological activities. Notably, the different IFN subtypes activate the same cell surface receptor complex to mediate variable responses. Accumulating evidence suggests that distinct differences in critical amino acid residues among the different IFN-alphas and IFN-beta determine the nature of the ligand-receptor interaction and the subsequent responses. This review focuses on IFN-receptor interactions, the key residues involved in this interaction and the potential for targeted modifications of the ligand to enhance bioactivity.
Sustained induction of fetal hemoglobin by pulse butyrate therapy in sickle cell disease. (1999)

High levels of fetal hemoglobin (Hb F) protect from many of the complications of sickle cell disease and lead to improved survival. Butyrate and other short chain fatty acids were previously shown to increase Hb F production in erythroid cells in vitro and in animal models in vivo. However, butyrates are also known to inhibit the proliferation of many cell types, including erythroid cells. Experience with the use of butyrate in animal models and in early clinical trials demonstrated that the Hb F response may be lost after prolonged administration of high doses of butyrate. We hypothesized that this loss of response may be a result of the antiproliferative effects of butyrate. We designed a regimen consisting of intermittent or pulse therapy in which butyrate was administered for 4 days followed by 10 to 24 days with no drug exposure. This pulse regimen induced fetal globin gene expression in 9 of 11 patients. The mean Hb F in this group increased from 7.2% to 21.0% (P <.002) after intermittent butyrate therapy for a mean duration of 29.9 weeks. This was associated with a parallel increase in the number of F cells and F reticulocytes. The total hemoglobin levels also increased from a mean of 7.8 g/dL to a mean of 8.8 g/dL (P <.006). The increased levels of Hb F were sustained in all responders, including 1 patient who has been on pulse butyrate therapy for more than 28 months. This regimen, which resulted in a marked and sustained increase in Hb F levels in more than two thirds of the adult sickle cell patients enrolled in this study, was well tolerated without adverse side effects. These encouraging results require confirmation along with an appropriate evaluation of clinical outcomes in a larger number of patients with sickle cell disease.
Antibodies against sialophorin (CD43) enhance the capacity of dendritic cells to cluster and activate T lymphocytes (1997)

CD43 is a leukocyte membrane glycoprotein rich in negatively charged sialic acid residues that may act as an anti-adhesion molecule. In this study, we analyzed the expression and function of CD43 on epidermal Langerhans cells (LC) and dendritic cells derived from adherent peripheral blood monocytes treated with granulocyte-macrophage CSF and IL-4 (Mo-DC). Both freshly isolated LC (fLC) and Mo-DC expressed uniformly high amounts of membrane CD43, with levels unchanged in 48-h cultured LC or in TNF-alpha-treated Mo-DC. When fLC or Mo-DC were transiently preincubated with anti-CD43 mAb or neuraminidase, they formed much larger clusters with T cells as compared with cells incubated with control mAb. Moreover, a significantly increased proliferation of naive allogeneic T cells in a primary MLR assay was induced. Anti-CD43-treated Mo-DC also presented tetanus toxoid to primed T cells more efficiently. Immunofluorescence and immunogold electron microscopy showed that following Ab cross-linking and warming to 37 degrees C, CD43 is progressively removed from the cell surface and is internalized within endosomes and vacuoles. In addition, fLC and Mo-DC incubated with anti-CD43 mAb increased expression of HLA-DR, ICAM-1, B7-1, B7-2, CD40, and CD83 after 24 h, and this was partially prevented by culturing cells in the presence of cycloheximide. We thus postulate that membrane CD43, other than serving as anti-adhesion molecule, can mediate activation signals in immature DC, leading to augmented expression of adhesion/costimulatory molecules and Ag-presenting function.
Selection of cell lines resistant to anti-transferrin receptor antibody: evidence for a mutation in transferrin receptor. (1984)

Some anti-murine transferrin receptor monoclonal antibodies block iron uptake in mouse cell lines and inhibit cell growth. We report here the selection and characterization of mutant murine lymphoma cell lines which escape this growth inhibition by anti-transferrin receptor antibody. Growth assays and immunoprecipitation of transferrin receptor in hybrids between independently derived mutants or between mutants and antibody-susceptible parental cell lines indicate that all of the selected lines have a similar genetic alteration that is codominantly expressed in hybrids. Anti-transferrin receptor antibodies and transferrin itself still bind to the mutant lines with saturating levels and Kd values very similar to those of the parental lines. However, reciprocal clearing experiments by immunoprecipitation and reciprocal blocking of binding to the cell surface with two anti-transferrin receptor antibodies indicate that the mutant lines have altered a fraction of their transferrin receptors such that the growth-inhibiting antibody no longer binds, whereas another portion of their transferrin receptors is similar to those of the parental lines and binds both antibodies. These results argue that the antibody-selected mutant cell lines are heterozygous in transferrin receptor expression, probably with a mutation in one of the transferrin receptor structural genes.
Terahertz imaging of biological tissue using a chirped probe pulse (2001)

There is increasing interest among research groups around the world in the terahertz portion of the electromagnetic spectrum. T-ray systems, driven by ultrafast THz pulses, offer a number of unique advantages over other techniques and are under investigation for a wide range of applications. Biomedical diagnostics is an area of particular emphasis. The sub-millimetre spectroscopic measurements obtained from T-ray systems contain a wealth of information about the sample under test. A number of hurdles, however, hinder the application of T-ray technology. One of the major hurdles to be overcome is the slow acquisition speed of modern THz systems. The chirped probe pulse technique offers a significant improvement in this context. We present results demonstrating the terahertz responses of biological samples measured using a chirped probe pulse, and discuss the problem of data processing and extracting sample characteristics. We show that different types of tissue can be classified based on their terahertz response measured with the chirped probe pulse technique. We consider chicken and beef samples and differentiate between bone and normal tissue. We demonstrate the performance of linear filter models for feature extraction and show that these models are significantly more accurate than a number of intuitive features.
High-speed videography using a dense camera array (2004)

We demonstrate a system for capturing multi-thousand frame-per-second (fps) video using a dense array of cheap 30 fps CMOS image sensors. A benefit of using a camera array to capture high-speed video is that we can scale to higher speeds by simply adding more cameras. Even at extremely high frame rates, our array architecture supports continuous streaming to disk from all of the cameras. This allows us to record unpredictable events, in which nothing occurs before the event of interest that could be used to trigger the beginning of recording. Synthesizing one high-speed video sequence using images from an array of cameras requires methods to calibrate and correct those cameras' varying radiometric and geometric properties. We assume that our scene is either relatively planar or is very far away from the camera and that the images can therefore be aligned using projective transforms. We analyze the errors from this assumption and present methods to make them less visually objectionable. We also present a new method to automatically color match our sensors. Finally, we demonstrate how to compensate for spatial and temporal distortions caused by the electronic rolling shutter, a common feature of low-end CMOS sensors.
Experimental and Simulated EMG Responses in the Study of the Human Spinal Cord (2013)

Advances in the study of human spinal cord neurophysiology have been strongly based on the analysis of the electrical activity of muscles (electromyogram EMG). The EMG measured over the skin reflects the general behavior of motor units (MUs) and hence of spinal moto‐ neurons (MNs). It can be used, for instance, to infer changes in the behavior of neuronal circuits within the spinal cord during the performance of a motor task or in response to peripheral and/or descending inputs.
Airborne influenza virus detection with four aerosol samplers using molecular and infectivity assays: considerations for a new infectious virus aerosol sampler (2009)

As a first step in conducting studies of airborne influenza transmission, we compared the collection performance of an SKC Biosampler, a compact cascade impactor (CCI), Teflon filters, and gelatin filters by collecting aerosolized influenza virus in a one-pass aerosol chamber. Influenza virus infectivity was determined using a fluorescent focus assay and influenza virus nucleic acid (originating from viable and non-viable viruses) was measured using quantitative PCR. The results showed that the SKC Biosampler recovered and preserved influenza virus infectivity much better than the other samplers - the CCI, Teflon, and gelatin filters recovered only 7-22% of infectious viruses compared with the Biosampler. Total virus collection was not significantly different among the SKC Biosampler, the gelatin, and Teflon filters, but was significantly lower in the CCI. Results from this study show that a new sampler is needed for virus aerosol sampling, as commercially available samplers do not efficiently collect and conserve virus infectivity. Applications for a new sampler include studies of airborne disease transmission and bioterrorism monitoring. Design parameters for a new sampler include high collection efficiency for fine particles and liquid sampling media to preserve infectivity. Practical Implications New air samplers are needed to study infectious airborne viruses and learn about airborne disease transmission. As a first step in designing a new air sampler to collect influenza virus we evaluated four commercial samplers and determined necessary design parameters for a new collector.
Anisotropic gels and plasticized networks formed by liquid crystal molecules (1991)

Abstract Two component mixtures containing liquid crystalline diacrylates and liquid crystal molecules with no reactive groups have been made. Upon photopolymeriz-ation of the mixtures anisotropic networks containing liquid crystal molecules which were not chemically attached to the networks were created. In these systems the behaviour of the liquid crystal molecules was found to be dominated by the network molecules. Even when the liquid crystal molecules in these networks were heated above their isotropic transition temperature they remained partly oriented, thus contributing to the anisotropy of the system.
300-mm Monolithic Silicon Photonics Foundry Technology (2019)

A competitive 300-mm silicon photonics foundry technology has been developed by GLOBALFOUNDRIES for general availability, which takes advantage of advanced CMOS process technology and provides a manufacturing scale. A state-of-the-art process design kit offers a codesign environment with access to a comprehensive photonics device library along with a monolithically integrated SOI CMOS device library. Advances in automated wafer-level optical test enable statistical photonic device characterization for development, photonic modeling, and manufacturing controls. The key challenges and solutions in developing a manufacturable photonic technology with state-of-the-art performance are described, as well as a roadmap for next generation high-performance monolithic silicon photonics are outlined.
Parallel manipulators: state of the art and perspectives. (1992)

[in Japanese]
27.12 MHz large voltage gain resonant converter with low voltage stress (2013)

This paper presents the design and implementation of a high frequency switching power converter with a large voltage gain and air core inductors. Specifically, we demonstrate a 40 W, 30 V to 300 V dc-dc converter switching at 27.12 MHz. Operating at this frequency reduces bulk energy storage over conventional low frequency designs and allows for fast transient response. We implement a resonant converter based on the Φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> inverter of [1]. In this paper, we evaluate and compare two rectifier topologies with lower voltage stress than the class E rectifiers described in [2], to get large voltage ratios. Unique to this design is the ability to provide short bursts of high voltage while promising excellent performance and high power density.
A derivative of staurosporine (CGP 41 251) shows selectivity for protein kinase C inhibition and In vitro anti‐proliferative as well as In vivo anti‐tumor activity (1989)

Analogues of staurosporine were synthesized and their ability to inhibit protein kinases was examined. Staurosporine is a potent but non-selective inhibitor of in vitro protein kinase C(PKC) activity (IC50 6.0 nM). The derivative CGP 41 251 had reduced PKC activity with an IC50 of 50 nM but showed a high degree of selectivity when assayed for inhibition of cyclic AMP-dependent protein kinase (IC50 2.4 microM), S6 kinase (IC50 5.0 microM) and tyrosine-kinase-specific activity of epidermal growth factor receptor (IC50 3.0 microM). Staurosporine and CGP 41 251 exerted growth inhibition in the human bladder carcinoma line T-24, human promyelocytic leukemia line HL-60 and bovine corneal endothelial cells at concentrations which correlated well with in vitro PKC inhibition. In addition, both compounds inhibited the release of H2O2 from human monocytes pre-treated with 12-O-tetradecanoyl-phorbol-13-acetate at non-toxic concentrations. In vivo anti-tumor activity was examined in T-24 human bladder carcinoma xenografts in athymic nude mice. Tumor growth inhibition tests revealed significant anti-tumor activity (2p less than 0.001) at 1/10 of the maximum tolerated doses for both compounds. By contrast, a closely related derivative of staurosporine (CGP 42 700) was inactive at concentrations of over 100 microM in all in vitro enzyme and anti-proliferative assays as well as in animal tumor models. Our data suggest an association between PKC inhibition and anti-proliferative and anti-tumor activity.
Nerve growth factor and its receptors in tumors of nervous system (2008)

Nerve growth factor (NGF) and its high affinity receptor tyrosine kinase (TrkA)are indis-pensable for the development of nervous system. Latest researches reveal that over-expression of NGF and TrkA is related to better outcome in neuroblastoma and medulloblastoma. While in glioma, the over-expression and nuclear translocation of NGF and TrkA are indicators of malignant degree. Study of the expression and sub-cel-lular cocalization of NGF and TrkA can provide new way for the diagnosis and therapy of nervous system tumors.

Key words: 
Nerve growth factor;  Receptors,nerve growth factor;  Neoplasms,neuroepithelial
The kill rule for multicore (2007)

Multicore has shown significant performance and power advantages over single cores in commercial systems with a 2--4 cores. Applying a corollary of Moore's Law for multicore, we expect to see 1K multicore chips within a decade. 1K multicore systems introduce significant architectural challenges. One of these is the power efficiency challenge. Today's cores consume 10's of watts. Even at about one watt per core, a 1K-core chip would need to dissipate 1K watts! This paper discusses the "Kill rule for multicore" for power-efficient multicore design, an approach inspired by the "Kiss rule for RISC processor design". Kill stands for <u>K</u>ill if <u>l</u>ess than <u>l</u>inear, and represents a design approach in which any additional area allocated to a resource within a core, such as a cache, is carefully traded off against using the area for additional cores. The Kill Rule states that we must increase resource size (for example, cache size) only if for every 1% increase in core area there is at least a 1% increase in core performance.
Deciphering Pactamycin Biosynthesis and Engineered Production of New Pactamycin Analogues (2009)

Pactamycin is an aminocyclopentitol-derived natural product that has potent antibacterial and antitumor activities. Sequence analysis of an 86 kb continuous region of the chromosome from Streptomyces pactum ATCC 27456 revealed a gene cluster involved in the biosynthesis of pactamycin. Gene inactivation of the Fe-S radical SAM oxidoreductase (ptmC) and the glycosyltransferase (ptmJ), individually abrogated pactamycin biosynthesis; this confirmed the involvement of the ptm gene cluster in pactamycin biosynthesis. The polyketide synthase gene (ptmQ) was found to support 6-methylsalicylic acid (6-MSA) synthesis in a heterologous host, S. lividans T7. In vivo inactivation of ptmQ in S. pactum impaired pactamycin and pactamycate production but led to production of two new pactamycin analogues, de-6-MSA-pactamycin and de-6-MSA-pactamycate. The new compounds showed equivalent cytotoxic and antibacterial activities with the corresponding parent molecules and shed more light on the structure-activity relationship of pactamycin.
Tumor Microenvironment of Metastasis in Human Breast Carcinoma: A Potential Prognostic Marker Linked to Hematogenous Dissemination (2009)

TMEM density predicted the development of systemic, hematogenous metastases. The ability of TMEM to predict distant metastasis was independent of lymph node status and other currently used prognosticators. Quantitation of TMEM may be a useful new prognostic marker for breast cancer patients.
Epigenetic Effects on Transgene Expression (2003)

Gene expression in eukaryotes is regulated primarily at the level of transcription. The genomes of higher eukaryotes contain many more genes than are used in any single differentiated cell type, and cell differentiation can be viewed as the result of decisions regarding which genes will be expressed. The mechanisms of transcriptional control have been intensively studied for more than a decade, resulting in considerable understanding of the organization of DNA elements that control the transcription of individual genes (promoters and enhancers), the factors that bind these elements, and the basal transcription apparatus. These studies have been primarily concerned with mechanisms regulating the rate of transcription of an active gene, rather than mechanisms that determine whether a gene will be transcriptionally active at all. However, it is arguable that the decision to transcribe a gene is the critical determinant; work done over several decades points to complex systems regulating the on/off switch in transcription, but the workings of these systems are still relatively obscure. In general, these systems involve what are termed epigenetic processes, i.e., processes whereby genes are rendered inactive that do not involve changes in the actual DNA sequence. At present there are two known forms of epigenetic modification: DNA methylation and chromatin packaging. Changes in either one or both of these are frequently associated with the silencing of genes.
Adversarial Examples for Semantic Segmentation and Object Detection (2017)

It has been well demonstrated that adversarial examples, i.e., natural images with visually imperceptible perturbations added, cause deep networks to fail on image classification. In this paper, we extend adversarial examples to semantic segmentation and object detection which are much more difficult. Our observation is that both segmentation and detection are based on classifying multiple targets on an image (e.g., the target is a pixel or a receptive field in segmentation, and an object proposal in detection). This inspires us to optimize a loss function over a set of targets for generating adversarial perturbations. Based on this, we propose a novel algorithm named Dense Adversary Generation (DAG), which applies to the state-of-the-art networks for segmentation and detection. We find that the adversarial perturbations can be transferred across networks with different training data, based on different architectures, and even for different recognition tasks. In particular, the transfer ability across networks with the same architecture is more significant than in other cases. Besides, we show that summing up heterogeneous perturbations often leads to better transfer performance, which provides an effective method of black-box adversarial attack.
Multiple Hybrid Formation in Natural Populations: Concerted Evolution of the Internal Transcribed Spacer of Nuclear Ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae) (2003)

DNA sequence variation of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA from Arabis holboellii, A. drummondii, and its putative hybrid A. divaricarpa was analyzed to study hybrid speciation in a species system geographically covering nearly the entire North American continent. Based on molecular systematics the investigated species are better combined under the genus Boechera. Multiple intraindividual ITS copies were detected in numerous accessions of A. divaricarpa, and, to a minor extent, in the parental taxa. Comparative phylogenetic analysis demonstrates that reticulate evolution is common. Consequently, concerted evolution of ITS regions resulted in different types of ITS fragments not only in hybrid populations but also in one of the parental taxa, A. holboellii. Hybrid formation often occurred independently at different sites and at different times, which is reflected by ITS copies resampling the original parental sequence variation in different ways. Some biogeographic structuring of genetic diversity is apparent and mirrors postglacial migration routes. Hybridization, reticulation, and apomixis are assumed to be the major forces driving speciation processes in this species complex. Analysis of conserved regions and secondary structures of the ITS region provided no evidence that, in this system, hybrid ITS evolution is predominantly driven in a particular direction. However, two regions in the ITS1 and ITS2, respectively, show higher mutation rates than expected from outgroup comparisons. Strong evidence for the occurrence of apomixis in A. holboellii and A. divaricarpa has come from pollen size measurements and estimations of pollen quality, which favor the hypothesis that A. drummondii served as paternal hybridization partner more frequently than A. holboellii.