gebhart/patrepeval huggingface dataset:
Molecular cloning and sequence analysis of the cDNA for a human serine protease reponsible for activation of hepatocyte growth factor. Structural similarity of the protease precursor to blood coagulation factor XII (1993)

Hepatocyte growth factor (HGF) is a potent mitogen for parenchymal liver cells, epithelial cells, and endothelial cells and may play an important role in liver regeneration following hepatic injury. HGF is homologous to plasminogen and is first synthesized and secreted as an inactive single-chain precursor and then activated to a heterodimeric form by endoproteolytic processing. Recently, a novel serine protease responsible for this processing (HGF activator) has been purified from fetal bovine serum (Shimomura, T., Ochiai, M., Kondo, J., and Morimoto, Y. (1992) Cytotechnology 8, 219-229). In this study, we purified HGF activator from human serum and determined its partial amino acid sequence. Based on the amino acid sequence, we have molecularly cloned the cDNA for human HGF activator. The nucleotide sequence of the cDNA revealed that HGF activator is derived from the COOH-terminal half region of a precursor protein of 655 amino acids and that the precursor consists of multiple putative domains homologous to those observed in blood coagulation factor XII. These domains may be involved in the conversion of the precursor to the active form of HGF activator.
c-Jun Expression and Activation are Restricted to CD30+ Lymphoproliferative Disorders (2007)

Cellular Jun (c-Jun), a member of the JUN family, is an activator protein-1 transcription factor involved in cell differentiation, proliferation, and apoptosis that can be activated by phosphorylation at serine-73 and -63 residues. Using tissue microarrays and immunohistochemistry, we investigated c-Jun expression and serine-73 phosphorylation in 112 CD30 lymphomas and 232 CD30 lymphomas of B- or T-cell lineage, and 24 cases of lymphomatoid papulosis. c-Jun was expressed exclusively by CD30 lymphoproliferative disorders including 41/41 (100%) classical Hodgkin lymphoma (cHL), 20/23 (87%) anaplastic lymphoma kinase (ALK)+ anaplastic large cell lymphoma (ALCL), 18/26 (69%) ALK- ALCL, 5/9 (56%) primary cutaneous ALCL, 4/11 (36%) CD30 diffuse large B-cell lymphoma (DLBCL), and 11/24 (46%) cases of lymphomatoid papulosis. The percentage of c-Jun-positive tumor cells was highest in cHL and ALCL (P=0.002). In contrast, all CD30 lymphomas, including nodular lymphocyte predominant HL and CD30 non-Hodgkin lymphomas of B- or T-cell lineage were negative for c-Jun. Serine-73 phosphorylated c-Jun (p-c-Jun), the activated form of c-Jun, was expressed more frequently and at a higher level in cHL and ALK+ ALCL than other CD30 tumors. The percentage of p-c-Jun-positive tumor cells correlated significantly with the percentage of total c-Jun-positive cells (P<0.0001), suggesting that activated c-Jun positively regulates total c-Jun levels in CD30 lymphomas through a well-established positive feedback loop. We conclude that CD30 lymphomas are characterized by common patterns of c-Jun expression and activation suggesting a potential role of c-Jun in the pathogenesis of these tumors.
Human breast adenocarcinoma cell lines promote angiogenesis by providing cells with uPA‐PAI‐1 and by enhancing their expression (2002)

During angiogenesis, endothelial cells use uPA and PAI-1 to migrate and degrade the basement membrane surrounding capillary blood vessels. Invasive tumor cells produce a large amount of uPA that could bind uPAR present at the endothelial cell surface to facilitate their invasion. To verify this hypothesis, endothelial cells were incubated with conditioned medium (CM) from two breast cancer cell lines (MCF7 and MDA MB 231 cells). Within a short incubation period (30 min) with both CM, an increase of uPA, PAI-1 and uPA-PAI-1 complex was detected in endothelial cell layer as assessed by casein zymography, ELISA and uPA immunostaining. The extent of this enhancement was related to the levels of uPA secreted by tumor cells (high in MDA MB 231 cells and low in MCF7 cells). After 2 hr of incubation, the CM from both tumor cells upregulated uPA and PAI-1 mRNA levels in endothelial cells in a time-dependent manner. The uPA increase in the cell layer could not be attributable to an increase of uPAR level. Only the CM from highly invasive MDA MB 231 cells increased the angiogenic morphotype of endothelial cells assessed in a collagen gel. A single addition of amino-terminal fragment of uPA (ATF) was able to abolish the angiogenic effect induced by MDA MB 231 cell CM. Our data demonstrate that the interactions occurring between breast tumor cells and endothelial cells can modulate tumor angiogenesis at least by two mechanisms: an increase of uPA and PAI-1 cell surface-binding and of their expression by endothelial cells.
Chlamydia and myocarditis: An old bug bugging seriously* (2007)

Experimental Critical Care, Department of Research, Department of Internal Medicine, University Hospital, Basle, Switzerland Urs Eriksson holds a Swiss National Foundation professorship in Critical Care Medicine and Internal Medicine.
Enabling energy efficient continuous sensing on mobile phones with LittleRock (2010)

Although mobile phones are ideal platforms for continuous human centric sensing, the state of the art phone architectures today have not been designed to support continuous sensing applications. Currently, sampling and processing sensor data on the phone requires the main processor and associated components to be continuously on, creating a large energy overhead that can severely impact the battery lifetime of the phone. We will demonstrate Little Rock, a novel sensing architecture for mobile phones, where sampling and, when possible, processing of sensor data is offloaded to a dedicated low-power processor. This approach enables the phone to perform continuous sensing three orders of magnitude more energy efficiently compared to the normal approaches.
Vaccines for Gonorrhea: Can We Rise to the Challenge? (2011)

Immune responses to the gonococcus after natural infection ordinarily result in little immunity to reinfection, due to antigenic variation of the gonococcus, and redirection or suppression of immune responses. Brinton and colleagues demonstrated that parenteral immunization of male human volunteers with a purified pilus vaccine gave partial protection against infection by the homologous strain. However, the vaccine failed in a clinical trial. Recent vaccine development efforts have focused on the female mouse model of genital gonococcal infection. Here we discuss the state of the field, including our unpublished data regarding efficacy in the mouse model of either viral replicon particle (VRP) vaccines, or outer membrane vesicle (OMV) vaccines. The OMV vaccines failed, despite excellent serum and mucosal antibody responses. Protection after a regimen consisting of a PorB-VRP prime plus recombinant PorB boost was correlated with apparent Th1, but not with antibody, responses. Protection probably was due to powerful adjuvant effects of the VRP vector. New tools including novel transgenic mice expressing human genes required for gonococcal infection should enable future research. Surrogates for immunity are needed. Increasing antimicrobial resistance trends among gonococci makes development of a vaccine more urgent.
Comparison of electrical and magnetic stimulations to assess quadriceps muscle function (2008)

This study aimed to 1) compare electrical and magnetic stimulations for quadriceps muscle function assessment, and 2) ascertain whether the ratios of the second twitch elicited by supramaximal electrical and magnetic femoral nerve stimulation at 10 and 100 Hz (T2(10:100)) and the total twitch force elicited by the same types of stimulations (Fpaired(10:100)) are equivalent to the standard low- to high-frequency force ratio associated with submaximal electrical tetanic stimulations (Ftet(10:100)). Quadriceps force and vastus lateralis EMG were recorded at rest (n = 21 subjects), immediately after, and 30 min after a 30-min downhill run (n = 10) when 1) supramaximal electrical nerve stimulation (ENS), 2) magnetic nerve stimulation (MNS) and 3) submaximal electrical muscle stimulation (EMS) were delivered in random order at 1 (single stimulation), 10, and 100 Hz (paired stimulations). Ten- and 100-Hz 500-ms tetani were also evoked with EMS to determine Ftet(10:100). Before exercise, contractile properties with single and paired stimulations were similar for ENS and MNS (all intraclass correlation coefficients k > 0.90), but smaller for EMS (P < 0.001). M-wave characteristics were also similar for ENS and MNS (all k > 0.90). After exercise, changes in all parameters did not differ between methods. With fatigue, the changes in Ftet(10:100) were inconsistently correlated with the changes in T2(10:100) (r(2) = 0.24-0.73, P = 0.002-0.15) but better correlated with the changes in Fpaired(10:100) (immediately after exercise: r(2) = 0.80-0.83, P < 0.001; 30 min after exercise: r(2) = 0.46-0.82, P = 0.001-0.03). We conclude that ENS and MNS provide similar quadriceps muscle function assessment, while Fpaired(10:100) is a better index than T2(10:100) of low- to high-frequency fatigue of the quadriceps in vivo.
Genetic Relationship between Thirteen Genome Types of Adenovirus 11, 34, and 35 with Different Tropisms (1991)

Eleven genome types of adenovirus serotype 11 (Ad11) were identified among 20 strains isolated from healthy pregnant women and patients with urinary tract infections, respiratory tract infections, or pharyngoconjunctival fever by use of 13 restriction endonucleases: BamHI, BclI, BglI, BglII, BstEII, EcoRI, HindIII, HpaI, PstI, SalI, SmaI, XbaI, and XhoI. All genome types could be grouped into three genomic clusters according to their genetic homology expressed as pairwise comigrating restriction fragments. The genome types within a genomic cluster were very closely related. They shared on an average pairwise comigrating restriction fragments of 91.6-97.7%. The Ad11 strains of genomic clusters 1 and 3 were isolated from urine, whereas all the Ad11 strains isolated from the respiratory tract were identified as members of the genomic cluster 2. One genome type of Ad34 and one genome type of Ad35 were identified from a hemorrhagic cystitis patient and an organ transplant recipient, respectively. Both were closely related to Ad11. The genome type of Ad35 could be located in the Ad11 genomic cluster 1.
The Intercostal NMJ Assay — A New Alternative to the Conventional LD50 Assay for the Determination of the Therapeutic Potency of Botulinum Toxin Preparations (2008)

Therapeutic botulinum neurotoxin type A preparations have found an increasing number of clinical uses for a large variety of neuromuscular disorders and dermatological conditions. The accurate determination of potency in the clinical application of botulinum toxins is critical to ensuring clinical efficacy and safety, and is currently achieved by using a lethal dose (LD50) assay in mice. Ethical concerns and operational constraints associated with this assay have prompted the development of alternative assay systems that could potentially lead to its replacement. As one such alternative, we describe the development and evaluation of a novel ex vivo assay (the Intercostal Neuromuscular Junction [NMJ] Assay), which uses substantially fewer animals and addresses ethical concerns associated with the LD50 assay. The assay records the decay of force from electrically-stimulated muscle tissue sections in response to the toxin, and thus combines the important mechanisms of receptor binding, translocation, and the enzymatic action of the toxin molecule. Toxin application leads to a time-related and dose-related reduction in contractile force. A regression model describing the relationship between the applied dose and force decay was determined statistically, and was successfully tested as able to correctly predict the potency of an unknown sample. The tissue sections used were found to be highly reproducible, as determined through the innervation pattern and the localisation of NMJs in situ. Furthermore, the efficacy of the assay protocol to successfully deliver the test sample to the cellular target sites, was critically assessed by using molecular tracer molecules.
Thermal Activation of Superheated Lipid-Coated Perfluorocarbon Drops (2015)

This study explored the thermal conditions necessary for the vaporization of superheated perfluorocarbon nanodrops. Droplets C3F8 and C4F10 coated with a homologous series of saturated diacylphosphatidylcholines were formed by condensation of 4 μm diameter microbubbles. These drops were stable at room temperature and atmospheric pressure, but they vaporized back into microbubbles at higher temperatures. The vaporization transition was measured as a function of temperature by laser light extinction. We found that C3F8 and C4F10 drops experienced 90% vaporization at 40 and 75 °C, respectively, near the theoretical superheat limits (80–90% of the critical temperature). We therefore conclude that the metastabilty of these phase-change agents arises not from the droplet Laplace pressure altering the boiling point, as previously reported, but from the metastability of the pure superheated fluid to homogeneous nucleation. The rate of C4F10 drop vaporization was quantified at temperatures ranging from 55 to 75 °C, and an apparent activation energy barrier was calculated from an Arrhenius plot. Interestingly, the activation energy increased linearly with acyl chain length from C14 to C20, indicating that lipid interchain cohesion plays an important role in suppressing the vaporization rate. The vaporized drops (microbubbles) were found to be unstable to dissolution at high temperatures, particularly for C14 and C16. However, proper choice of the fluorocarbon and lipid species provided a nanoemulsion that could undergo at least ten reversible condensation/vaporization cycles. The vaporization properties presented in this study may facilitate the engineering of tunable phase-shift particles for diagnostic imaging, targeted drug delivery, tissue ablation, and other applications.
Optical microscope system for standardized cell measurements and analyses (1987)

A fully integrated optical microscope and computer workstation for the pathology laboratory is described along with a system module for that workstation, the Cell Measurement Program (CMP). This module allows for the acquisition and storage of digitized microscope images; measurement of a standard set of cell features, or descriptors, calibrated for accurate densitometry; and a comprehensive set of statistical analyses and display procedures. This system is useful in research in cell biology and in cancer research, allowing the investigator to use the microscope as a measuring instrument.
III-V concentrator solar cells simulation: a 2D/3D approach for the design and optimization (2005)

Simulation capacities of III-V compound solar cells were studied with a special emphasis on work conditions imposed by the use of an optical concentrator. The latest advances in computer technology and simulation software now allow to completely model such a large device as a solar cell. 2D and 3D physical simulations resulted to be fast and accurate, allowing the authors to develop a useful tool for future development of concentrator solar cells.
A closed-loop human simulator for investigating the role of feedback control in brain-machine interfaces (2010)

Neural prosthetic systems seek to improve the lives of severely disabled people by decoding neural activity into useful behavioral commands. These systems and their decoding algorithms are typically developed "offline," using neural activity previously gathered from a healthy animal, and the decoded movement is then compared with the true movement that accompanied the recorded neural activity. However, this offline design and testing may neglect important features of a real prosthesis, most notably the critical role of feedback control, which enables the user to adjust neural activity while using the prosthesis. We hypothesize that understanding and optimally designing high-performance decoders require an experimental platform where humans are in closed-loop with the various candidate decode systems and algorithms. It remains unexplored the extent to which the subject can, for a particular decode system, algorithm, or parameter, engage feedback and other strategies to improve decode performance. Closed-loop testing may suggest different choices than offline analyses. Here we ask if a healthy human subject, using a closed-loop neural prosthesis driven by synthetic neural activity, can inform system design. We use this online prosthesis simulator (OPS) to optimize "online" decode performance based on a key parameter of a current state-of-the-art decode algorithm, the bin width of a Kalman filter. First, we show that offline and online analyses indeed suggest different parameter choices. Previous literature and our offline analyses agree that neural activity should be analyzed in bins of 100- to 300-ms width. OPS analysis, which incorporates feedback control, suggests that much shorter bin widths (25-50 ms) yield higher decode performance. Second, we confirm this surprising finding using a closed-loop rhesus monkey prosthetic system. These findings illustrate the type of discovery made possible by the OPS, and so we hypothesize that this novel testing approach will help in the design of prosthetic systems that will translate well to human patients.
Humanization of an antibody directed against IgE. (1993)

IgE antibodies bind to specific high-affinity receptors on mast cells, leading to mast cell degranulation and release of mediators, such as histamine, which produce symptoms associated with allergy. Hence, anti-IgE antibodies that block binding of IgE to its high-affinity receptor are of potential therapeutic value in the treatment of allergy. These antibodies must also not bind to IgE once it is bound to the receptor because this would trigger histamine release. This study describes the humanization of a murine antibody, MaE11, with these characteristics. Variants of the humanized antibody were evaluated to probe the importance of framework residues on antibody binding and to determine which charged residues in the CDR interacted with IgE. We found that only five changes in human framework residues were required to provide for binding comparable to that of the original murine antibody.
Useful Prognostic Panel Markers to Express the Biological Tumor Status in Resected Lung Adenocarcinomas (2000)

The immunohistochemical expression of p53 and bcl-2 oncogenes and the expression of AgNOR cell proliferation index are critical values in the progression of lung adenocarcinomas. They can express the biological tumor status and indicate a more accurate prognosis.
Endothelial precursor cells as a model of tumor endothelium: characterization and comparison with mature endothelial cells. (2003)

Human umbilical vein endothelial cells (HUVEC) and human microvascular endothelial cells (HMVEC) have been the standards for cell-based assays in the field of angiogenesis research and in antiangiogenic drug discovery. These normal mature endothelial cells may not be most representative of human tumor endothelial cells. Human AC133+/CD34+ bone marrow progenitor cells were established in cell culture media containing vascular endothelial growth factor, basic fibroblast growth factor (bFGF), and heparin to drive differentiation toward the endothelial phenotype. The resulting cells designated endothelial precursor cells (EPC) have many of the same functional properties as mature endothelial cells represented by HUVEC and HMVEC. By SAGE analysis, the genes expressed by EPC are more similar to the genes expressed by endothelial cells isolated from fresh surgical specimens of human tumors than are the genes expressed by HUVEC and HMVEC. Analysis of several cell surface markers by flow cytometry showed that EPC, HUVEC, and HMVEC have similar expression of P1H12, vascular endothelial growth factor 2, and endoglin but that EPC have much lower expression of ICAM1, ICAM2, VCAM1, and thrombomodulin than do HUVEC and HMVEC. The EPC generated can form tubes/networks on Matrigel, migrate through porous membranes, and invade through thin layers of Matrigel similarly to HUVEC and HMVEC. However, in a coculture assay using human SKOV3 ovarian cancer cell clusters in collagen as a stimulus for invasion through Matrigel, EPC were able to invade into the malignant cell cluster, whereas HMVEC were not able to invade the malignant cell cluster. In vivo, a Matrigel plug assay where human EPC were suspended in the Matrigel allowed tube/network formation by human EPC to be carried out in a murine host. EPC may be a better model of human tumor endothelial cells than HUVEC and HMVEC and, thus, may provide an improved cell-based model for second generation antineoplastic antiangiogenic drug discovery.
Membrane Type 1 Matrix Metalloproteinase-associated Degradation of Tissue Inhibitor of Metalloproteinase 2 in Human Tumor Cell Lines (2000)

Tissue inhibitor of metalloproteinase 2 (TIMP-2) is required for the membrane type 1 matrix metalloproteinase (MT1-MMP)-dependent activation of pro-MMP-2 on the cell surface. MT1-MMP-bound TIMP-2 has been shown to function as a receptor for secreted pro-MMP-2, resulting in the formation of a trimolecular complex. In the presence of uncomplexed active MT1-MMP, the prodomain of cell surface-associated MMP-2 is cleaved, and activated MMP-2 is released. However, the behavior of MT1-MMP-bound TIMP-2 during MMP-2 activation is currently unknown. In this study, (125)I-labeled recombinant TIMP-2 ((125)I-rTIMP-2) was used to investigate the fate of TIMP-2 during pro-MMP-2 activation by HT1080 and transfected A2058 cells. HT1080 and A2058 cells transfected with MT1-MMP cDNA (but not vector-transfected A2058 cells) were able to bind (125)I-rTIMP-2, to activate pro-MMP-2, and to process MT1-MMP into an inactive 43-kDa form. Under these conditions, (125)I-rTIMP-2 bound to the cell surface was rapidly internalized and degraded in intracellular organelles through a bafilomycin A(1)-sensitive mechanism, and (125)I-bearing low molecular mass fragment(s) were released in the culture medium. These different processes were inhibited by hydroxamic acid-based synthetic MMP inhibitors and rTIMP-2, but not by rTIMP-1 or cysteine, serine, or aspartic proteinase inhibitors. These results support the concept that the MT1-MMP-dependent internalization and degradation of TIMP-2 by some tumor cells might be involved in the regulation of pericellular proteolysis.
Comparison of single- and dual-pass multiply-add fused floating-point units (1998)

Low power, low cost, and high performance factors dictate the design of many microprocessors targeted to the low power computing market. The floating point unit occupies a significant percentage of the silicon area in a microprocessor due its wide data bandwidth (for double precision computations) and the area occupied by the multiply array. For microprocessors designed for portable products, the design site of the floating point unit plays an important role in the low cost factor driven by reduced chip area. Some microprocessors have multiply-add fused floating point units with a reduced multiply array, requiring two passes through the array for operations involving double precision multiplies. The paper discusses the design complexities around the dual pass multiply array and its effect on area and performance. Floating point unit areas and their associated multiply array areas are compared for a single and dual pass implementation in a given technology (PowerPC 604eTM and PowerPC 603eTM microprocessors, respectively).