gebhart/patrepeval huggingface dataset:
A Consensus Insulin Response Element Is Activated by an ETS-related Transcription Factor (1995)

Insulin increases expression of somatostatin-chloramphenicol acetyltransferase (CAT) constructs 10-fold and thymidine kinase-CAT constructs 5-fold in GH4 cells. These responses are similar to our previously reported data on insulin-increased prolactin-CAT expression. They are also observed in HeLa cells and are thus not cell type specific. The evidence suggests that the insulin responsiveness of these genes is mediated by an Ets-related transcription factor. First, linker-scanning mutations and/or deletions of the prolactin, somatostatin, and thymidine kinase promoters suggest that their insulin responsiveness is mediated by the sequence CGGA. This sequence is identical with the response element of the Ets-related transcription factors. Second, CGGA-containing sequences placed at -88 in the delta MTV-CAT reporter plasmid conferred insulin responsiveness to the mammary tumor virus promoter. Third, expression of the DNA-binding domain of c-Ets-2, which acts by blocking effects mediated by Ets-related transcription factors, inhibits the response of these promoters to insulin. Finally, the Ets-related proteins Sap and Elk-1 bind to the prolactin, somatostatin, and thymidine kinase insulin-response elements. An Ets-like element was found in all insulin-sensitive promoters examined and may serve a similar function in those promoters.
Application of focused ion beam technology to maskless ion implantation in a molecular beam epitaxy grown GaAs or AlGaAs epitaxial layer for three-dimensional pattern doping crystal growth (1986)

We report on a new microfabrication process in UHV, implemented with a focused ion beam implanter (FIBI)–molecular beam epitaxy (MBE) crystal growth system with a computer controlled ion beam writing system. By using this combination process technology, GaAs/AlGaAs multilayer pattern doping structures are fabricated by iteration of growing a molecular beam epitaxy (MBE) GaAs or AlGaAs layer followed by implanting focused ion beams, arbitrarily choosing such impurity ions as Be ( p-type) or Si (n-type). This process technology is considered as a basis for integrating optical or electrical devices three dimensionally. An application of this technology to a new structure for an AlGaAs/GaAs DH laser is also described.
<title>Reduction of coding artifacts at low bit rates</title> (1998)

Many video and image coding standards such as MPEG, H.261, H.263, and JPEG are based on the discrete cosine transform (DCT). They subdivide images or frames into blocks that are encoded independently. DCT coefficients that are considered to be less important are discarded. The achievable compression ratios are normally limited by visible discontinuities along block boundaries, the so-called blocking artifacts. In this paper, a postprocessing algorithm based on Markov random fields (MRF) is proposed that efficiently removes blocking effects, while retaining the sharpness of the image and without introducing new artifacts. To prevent blurring of dominant edges. The decoded image is segmented into regions which are then enhanced separately. The segmentation is preformed in two steps. A novel texture detector first identifies all texture regions, before the remaining monotone areas are partitioned by an MRF segmentation algorithm. A new edge component has been incorporated to improve the detection of dominant edges. The proposed enhancement stage calculates the MAP estimate of the unknown original image, which is modeled by an MRF. An efficient implementation is presented, and experiments demonstrate that our proposed postprocessor gives very good results both objectively and subjectively.
Epipolar Geometry of Opti-Acoustic Stereo Imaging (2007)

Optical and acoustic cameras are suitable imaging systems to inspect underwater structures, both in regular maintenance and security operations. Despite high resolution, optical systems have limited visibility range when deployed in turbid waters. In contrast, the new generation of high-frequency (MHz) acoustic cameras can provide images with enhanced target details in highly turbid waters, though their range is reduced by one to two orders of magnitude compared to traditional low-/midfrequency (10s-100s KHz) sonar systems. It is conceivable that an effective inspection strategy is the deployment of both optical and acoustic cameras on a submersible platform, to enable target imaging in a range of turbidity conditions. Under this scenario and where visibility allows, registration of the images from both cameras arranged in binocular stereo configuration provides valuable scene information that cannot be readily recovered from each sensor alone. We explore and derive the constraint equations for the epipolar geometry and stereo triangulation in utilizing these two sensing modalities with different projection models. Theoretical results supported by computer simulations show that an opti-acoustic stereo imaging system outperforms a traditional binocular vision with optical cameras, particularly for increasing target distance and (or) turbidity.
In vitro cleavage of hepatitis C virus polyprotein substrates by purified recombinant NS3 protease (1995)

The non-structural protein NS3 of hepatitis C virus has been expressed in bacteria as a polyhistidine fusion protein which can be produced in a soluble form and easily purified by affinity chromatography. Using an in vitro transcription and translation system we have been able to demonstrate that this protein can proteolytically process substrate molecules derived from the non-structural region of the polyprotein. Using this assay system we have been able to optimize basic biochemical characteristics of the purified enzyme. Parallel experiments show that the full-length NS3 protein also possesses ATPase activity, indicating the bifunctional nature of the protein. In contrast, purified NS3 in which the predicted catalytic serine has been mutated loses protease but retains ATPase activity.
Controlling Stem Cell Fate with Material Design (2009)

Advances in our understanding of stem cell interactions with their environment are leading to the development of new materials-based approaches to control stem cell behavior toward cellular culture and tissue regeneration applications. Materials can provide cues based on chemistry, mechanics, structure, and molecule delivery that control stem cell fate decisions and matrix formation. These approaches are helping to advance clinical translation of a range of stem cell types through better expansion techniques and scaffolding for use in tissue engineering approaches for the regeneration of many tissues. With this in mind, this progress report covers basic concepts and recent advances in the use of materials for manipulating stem cells.
Using Honeynets for Internet Situational Awareness (2005)

Abstract—Effective network security administration depends to a great extent on having accurate, concise, high-quality information about malicious activity in one’s network. Honeynets can potentially provide such detailed information, but the volume and diversity of this data can prove overwhelming. In this paper we explore ways to integrate honeypot data into daily network security monitoring with a goal of sufficiently classifying and summarizing the data to provide ongoing “situational awareness. ” We present such a system, built using the Bro NIDS, and discuss experiences drawn from six months operation. One key aspect of this environment is its ability to provide insight into large-scale events. We look at the problem of accurately classifying botnet sweeps and worm outbreaks, which turns out to be difficult to grapple with due to the high dimensionality of such incidents. Using datasets collected during a number of these events, we explore the utility of several analysis methods, finding that when used together they show promise for contributing towards effective situational awareness. I.
Detection of prostate-specific membrane antigen on HUVECs in response to breast tumor-conditioned medium (2011)

Prostate-specific membrane antigen (PSMA), a well-known biomarker of prostate cancer, has also been found to be highly expressed in the neovasculature of multiple non-prostatic solid tumors. As a consequence, it has the potential to become a biomarker for tumor-associated vasculature. Herein, we describe an in vitro model for assessing PSMA expression associated with tube formation by primary human umbilical vein endothelial cells (HUVECs) cultured in Matrigel and induced by tumor-conditioned medium (TCM) derived from human breast cancer cells (MDA-MB-231). In contrast to vascular endothelial growth factor (VEGF)-containing endothelial cell medium, TCM induced higher expression of PSMA in HUVECs. The vessel-like tubes were detected by imaging with fluorescent PSMA inhibitors. Consequently, this in vitro model is expected to enable subsequent studies aimed at determining the role of PSMA in angiogenesis and factors that induce it.
e-service robot in home healthcare (2002)

As the population-aging problem is increasingly pressing on society, and the associated healthcare costs are taking up an incremental percentage of the GNP, various inexpensive support systems for elderly people staying alone at home are becoming very demanding. Fortunately, as the Internet continues to expand exponentially and accesses to the Internet become more prevalent in our daily life, home healthcare systems based on teleoperated mobile robot platform via the Internet become feasible. In this paper, we describe a feasibility study and a basic platform design of a teleoperated home healthcare system via the Internet, which include a literature review of the state of the art in research on this topic, discussions on some open problems and challenges facing researchers in this area and a basic platform design of a home healthcare system via the Internet current under implementation in our research lab.
Fialuridine and its metabolites inhibit DNA polymerase gamma at sites of multiple adjacent analog incorporation, decrease mtDNA abundance, and cause mitochondrial structural defects in cultured hepatoblasts. (1996)

The thymidine analog fialuridine deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-iodouracil (FIAU) was toxic in trials for chronic hepatitis B infection. One mechanism postulated that defective mtDNA replication was mediated through inhibition of DNA polymerase-gamma (DNA pol-gamma), by FIAU triphosphate (FIALTP) or by triphosphates of FIAU metabolites. Inhibition kinetics and primer-extension analyses determined biochemical mechanisms of FIAU, 1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl) -5-methyluracil (FAU), 1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)uracil triphosphate (TP) inhibition of DNA pol-gamma. dTMP incorporation by DNA pol-gamma was inhibited competitively by FIAUTP, FMAUTP, and FAUTP (K1=0.015, 0.03, and 1.0 microM, respectively). By using oliginucleotide template-primers. DNA pol-gamma incorporated each analog into DNA opposite a single adenosine efficiently without effects on DNA chain elongation. Incorporation of multiple adjacent analogs at positions of consecutive adenosines dramatically impaired chain elongation by DNA pol-gamma. Effects of FIAU, FMAU, and FAU on HepG2 cell mmtDNA abundance and ultrastructure were determined. After 14 days, mtDNA decreased by 30% with 20 microM FIAU or 20 microM FMAU and decreased less than 10% with 100 microM FAU. FIAU and FMAU disrupted mitochondria and caused accumulation of intracytoplasmic lipid droplets. Biochemical and cell biological findings suggest that FIAU and its metabolites inhibit mtDNA replication, most likely at positions of adenosine tracts, leading to decreased mtDNA and mitochondrial ultrastructural defects.
Two distinct human cloned T cell lines that exhibit natural killer-like and anti-human effector activities. (1982)

Cloned T cell lines from mixed lymphocyte cultures stimulated with autologous Epstein Barr virus- (EBV) transformed lymphoblastoid cell line (LCL) cells were established using a limiting dilution technique in the presence of T cell growth factor (TCGF). The T cell lines included two distinct clones of cytotoxic T cells (Tc) in addition to EBV-specific Tc. A cytotoxic profile of one cloned line was similar to that of endogenous NK cells in peripheral blood. The other cloned Tc line showed an anti-human cytotoxicity. The susceptible targets for this latter Tc line were various human cells, including autologous LCL and peripheral blood lymphocytes (PBL), stimulated with pokeweed mitogen, along with NK-sensitive and NK-resistant cell lines. Weak cytotoxic activity was detected against various xenogeneic cell lines. Furthermore, autologous and allogeneic cloned T cell lines were resistant to killing by the anti-human effector clone. These t wo distinct cloned Tc lines expressed the Leu-1 and Leu-2a antigens, which are markers of suppressor/cytotoxic T cells.
Gd-Enhanced Dynamic Magnetic Resonance Imaging of Breast Masses (1999)

The combination of morphologic and hemodynamic analyses of contrast-enhanced dynamic magnetic resonance imaging is valuable for characterizing breast masses. Pharmacokinetic parameters such as k and f reflect histologic architecture of breast masses. We believe that MR imaging may be of value for diagnosis of breast masses.
Semantic clustering of images using patterns of relevance feedback (2008)

User-supplied data such as browsing logs, click-through data, and relevance feedback judgements are an important source of knowledge during semantic indexing of documents such as images and video. Low-level indexing and abstraction methods are limited in the manner with which semantic data can be dealt. In this paper and in the context of this semantic data, we apply latent semantic analysis on two forms of user-supplied data, real-world and artificially generated relevance feedback judgements in order to examine the validity of using artificially generated interaction data for the study of semantic image clustering.
Influence of Geometry of Transplanted Tooth and Bone on Transformation of Fibroblasts (1973)

Allogeneic transplants of demineralized powdered bone or whole teeth in different shapes transformed fibroblasts to cartilage and bone. Coarse powders of bone elicited significantly higher yields of transformation products than fine powder did; criteria of transformation included histologic findings, alkaline phosphatase activity, 35S and 32P incorporation. The temporal sequence of fibro-blast-chondroblast-osteoblast transformation was profoundly influenced by the geometry of the transformant. The incursion of capillaries among the transformed cells resulted in chondrolysis.
Confinement of Long‐Lived Triplet Excitons in Organic Semiconducting Host–Guest Systems (2017)

Abstract Long‐lived triplet excitons on organic molecules easily deactivate at room temperature because of the presence of thermally activated nonradiative pathways. This study demonstrates long‐lived phosphorescence at room temperature resulting from suppression of the nonradiative deactivation of triplet excitons in conventional organic semiconducting host–guest systems. The nonradiative deactivation pathway strongly depends on the triplet energy gap between the guest emitting molecules and the host matrices. The triplet energy gap required to confine the long‐lived triplet excitons (≈0.5 eV) is much larger than that of conventional host–guest systems for phosphorescent emitters. By effectively confining the triplet excitons, this study demonstrates long‐lived room‐temperature phosphorescence under optical and electrical excitation.
Safety and efficacy of rituximab in systemic lupus erythematosus: Results from 136 patients from the French autoimmunity and rituximab registry (2010)

Data from the AIR registry show a satisfactory tolerance profile and clinical efficacy of RTX in patients with SLE. The contrasting results with those from recent RCTs leave open the question of the therapeutic use of RTX in SLE. Additional controlled studies with new designs are needed to define the place of RTX in the therapeutic arsenal for SLE.
The pathogenesis of non-freezing cold nerve injury. Observations in the rat (1997)

Non-freezing cold nerve injury is uncommon in civilian practice, but may reach epidemic proportions in war zones. Studied since the time of Hippocrates, its aetiology has remained elusive. We sought to replicate experimentally, a peripheral nerve cold temperature gradient, since this has been emphasized in clinical descriptions. Our observations, in the rat, of the vasa nervorum show that cold-induced intravascular aggregation is followed by a 'no-reflow' phenomenon which culminates in endothelial damage and delayed thrombotic occlusion.
Membrane Microdomains and Vascular Biology (2003)

The classic model of cell plasma membrane organizationis that of a uniform, fluid environment in which protein and lipid constituents diffuse rapidly in an unrestricted fashion. Recent experimental evidence, however, reveals a far more complex membrane organization consisting of microdo-mains assembled from lipid constituents that have distinct biophysical characteristics. Such microdomains or “lipid rafts ” are typically detergent-resistant and highly enriched with cholesterol and sphingolipids compared with the overall membrane lipid bilayer environment.1 These defined regions of lipid domains sequester proteins that mediate signal transduction in a variety of cell types, including endothelial cells and myocytes. Lipid rafts move or “float ” as a coherent structural unit within the liquid-disordered lipid bilayer and can also cluster with other rafts to form larger platforms. The basis for differences in fluidity between rafts and the sur-
New Concepts in Administration of Drugs in Tablet Form : Formulation and Evaluation of a Sublingual Tablet for Rapid Absorption, and Presentation of an Individualised Dose Administration System (2003)

This thesis presents two new concepts in oral drug administration and the results of evaluation of some relevant formulation factors. Investigation into improving the homogeneity of mixtures for tableting indicated that it may be possible to obtain interactive dry mixtures of micronised drugs containing drug proportions as low as 0.015% w/w. By studying the relationship between disintegration time and tensile strength, it was found that the microstructure surrounding the disintegrant particles may influence the disintegration process. Therefore, avoidance of excipients which are highly deformable or very soluble in water will result in more rapid disintegration. Further, it is possible to increase the bioadhesive properties of a non-bioadhesive carrier material by forming interactive mixtures containing a fine particulate bioadhesive material. The new sublingual tablet concept presented is based on interactive mixtures consisting of a water-soluble carrier covered with fine drug particles and a bioadhesive component. With this approach, it is possible to obtain rapid dissolution in combination with bioadhesive retention of the drug in the oral cavity. Clinical data indicate that this allows rapid sublingual absorption while simultaneously avoiding intestinal absorption. An individualised dose administration system is also presented. This system is based on the use of standardised units (microtablets), each containing a sub-therapeutic amount of the active ingredient. The required dose is fine-tuned by electronically counting out a specific number of these units using an automatic dose dispenser. A patient handling study supported the suggestion that the dosage of some medications can be more easily and safely individualised for each patient with this method than by using traditional methods of mixing different standard tablet strengths or dividing tablets.
Inhibition of Oxygen-Induced Retinopathy in RTP801-Deficient Mice (2004)

In the absence of RTP801 expression, development of retinopathy in the mouse model of ROP was significantly attenuated, thus implying an important role of RTP801 in the pathogenesis of ROP.
T cell activation by anti‐T3 antibodies: Comparison of IgG1 and IgG2b switch variants and direct evidence for accessory function of macrophage Fc receptors (1986)

The human T3 antigen is closely associated with the T cell receptor. Some anti-T3 antibodies cause T cell proliferation in the presence of monocytes which have Fc receptors (FcR) that bind particular antibody subclasses. Such an interaction is thought to determine whether or not an anti-T3 antibody is mitogenic. We examined the mitogenicity of an IgG1 antibody, UCHT1, and an IgG2b switch variant of identical specificity, UCHT1B. With autologous monocytes, 76% of individuals responded to UCHT1 and 9% to UCHT1B, falling into three patterns of responsiveness. Both antibodies in the absence of monocytes induced responsiveness to recombinant interleukin 2, even for UCHT1B nonresponder T cells. The proliferation induced by UCHT1B, however, was always less than that induced by UCHT1. These findings demonstrate the critical role played by the Fc region for mitogenesis, and suggest a possible role for the hinge region. We then obtained direct evidence that mitogenicity can be mediated exclusively via FcR. Mouse macrophages have distinct FcR: FcRI binds IgG2a but FcRII binds IgG1 and IgG2b and its function can be inhibited by the specific antibody 2.4G2. Because UCHT1 and UCHT1B were of the correct subclass to interact with FcRII we examined the accessory function of mouse peritoneal macrophages. Without exception, human T cells now responded to both antibodies. Proliferation was drastically inhibited by 2.4G2 but not by an irrelevant anti-macrophage antibody, F4/80, nor by an anti-human neutrophil FcR antibody, 3G8. Furthermore, 2.4G2 did not inhibit the accessory function of mouse macrophages for OKT3, an IgG2a antibody that presumably interacts with FcRI, and did not inhibit the function of human monocytes for UCHT1 and UCHT1B. Mouse B cells, in contrast to macrophages, have an FcR which binds all three subclasses, but which can be inhibited by 2.4G2. B cells, however, were not accessory cells for mitogenesis with UCHT1, UCHT1B or OKT3. These findings are discussed in relation to other requirements for T cell activation by anti-T3 antibodies.
Process Authentication for High System Assurance (2013)

This paper points out the need in modern operating system kernels for a process authentication mechanism, where a process of a user-level application proves its identity to the kernel. Process authentication is different from process identification. Identification is a way to describe a principal; PIDs or process names are identifiers for processes in an OS environment. However, the information such as process names or executable paths that is conventionally used by OS to identify a process is not reliable. As a result, malware may impersonate other processes, thus violating system assurance. We propose a lightweight secure application authentication framework in which user-level applications are required to present proofs at runtime to be authenticated to the kernel. To demonstrate the application of process authentication, we develop a system call monitoring framework for preventing unauthorized use or access of system resources. It verifies the identity of processes before completing the requested system calls. We implement and evaluate a prototype of our monitoring architecture in Linux. The results from our extensive performance evaluation show that our prototype incurs reasonably low overhead, indicating the feasibility of our approach for cryptographically authenticating applications and their processes in the operating system.