gebhart/patrepeval huggingface dataset:
Monokines regulate glycosylation of acute-phase proteins. (1987)

The acute-phase response to inflammatory stimuli, characterized by increased synthesis of acute-phase proteins (APP), is often accompanied by changes in the glycosylation patterns of some of these proteins. While expression of APP genes in hepatocytes is regulated by monokines, mechanisms governing changes in glycosylation are not known. Exposure of human hepatoma cell line Hep 3B to conditioned medium from LPS-activated human monocytes and to medium from the keratocarcinoma cell line COLO-16 led to increased synthesis of alpha 1 proteinase-inhibitor and ceruloplasmin and to alterations of their glycosylation patterns similar to those seen in human serum in various inflammatory states. IL-1, tumor necrosis factor, and hepatocyte stimulating factor I increased synthesis of ceruloplasmin without alterations in the pattern of its glycosylation. These findings demonstrate that altered glycosylation seen in plasma in some inflammatory states can be explained by the effects of monokines on glycosylation in hepatocytes and that gene expression and glycosylation of some APP during the acute-phase response may be regulated by different mechanisms.
Hybrid III--V on Silicon Lasers for Photonic Integrated Circuits on Silicon (2014)

This paper summarizes recent advances of integrated hybrid InP/SOI lasers and transmitters based on wafer bonding. At first the integration process of III-V materials on silicon is described. Then the paper reports on the results of single wavelength distributed Bragg reflector lasers with Bragg gratings etched on silicon waveguides. We then demonstrate that, thanks to the high-quality silicon bend waveguides, hybrid III-V/Si lasers with two integrated intra-cavity ring resonators can achieve a wide thermal tuning range, exceeding the C band, with a side mode suppression ratio higher than 40 dB. Moreover, a compact array waveguide grating on silicon is integrated with a hybrid III-V/Si gain section, creating a wavelength-selectable laser source with 5 wavelength channels spaced by 400 GHz. We further demonstrate an integrated transmitter with combined silicon modulators and tunable hybrid III-V/Si lasers. The integrated transmitter exhibits 9 nm wavelength tunability by heating an intra-cavity ring resonator, high extinction ratio from 6 to 10 dB, and excellent bit-error-rate performance at 10 Gb/s.
Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID (2011)

Viruses can create complex genetic populations within a host, and deep sequencing technologies allow extensive sampling of these populations. Limitations of these technologies, however, potentially bias this sampling, particularly when a PCR step precedes the sequencing protocol. Typically, an unknown number of templates are used in initiating the PCR amplification, and this can lead to unrecognized sequence resampling creating apparent homogeneity; also, PCR-mediated recombination can disrupt linkage, and differential amplification can skew allele frequency. Finally, misincorporation of nucleotides during PCR and errors during the sequencing protocol can inflate diversity. We have solved these problems by including a random sequence tag in the initial primer such that each template receives a unique Primer ID. After sequencing, repeated identification of a Primer ID reveals sequence resampling. These resampled sequences are then used to create an accurate consensus sequence for each template, correcting for recombination, allelic skewing, and misincorporation/sequencing errors. The resulting population of consensus sequences directly represents the initial sampled templates. We applied this approach to the HIV-1 protease (pro) gene to view the distribution of sequence variation of a complex viral population within a host. We identified major and minor polymorphisms at coding and noncoding positions. In addition, we observed dynamic genetic changes within the population during intermittent drug exposure, including the emergence of multiple resistant alleles. These results provide an unprecedented view of a complex viral population in the absence of PCR resampling.
Four-Dimensional Electron Microscopy (2010)

The discovery of the electron over a century ago and the realization of its dual character have given birth to one of the two most powerful imaging instruments: the electron microscope. The electron microscope's ability to resolve three-dimensional (3D) structures on the atomic scale is continuing to affect different fields, including materials science and biology. In this Review, we highlight recent developments and inventions made by introducing the fourth dimension of time in electron microscopy. Today, ultrafast electron microscopy (4D UEM) enables a resolution that is 10 orders of magnitude better than that of conventional microscopes, which are limited by the video-camera rate of recording. After presenting the central concept involved, that of single-electron stroboscopic imaging, we discuss prototypical applications, which include the visualization of complex structures when unfolding on different length and time scales. The developed UEM variant techniques are several, and here we illucidate convergent-beam and near-field imaging, as well as tomography and scanning-pulse microscopy. We conclude with current explorations in imaging of nanomaterials and biostructures and an outlook on possible future directions in space-time, 4D electron microscopy.
Alpha-fetoprotein and human chorionic gonadotropin-producing lung cancer (1987)

A 73-year-old man had primary lung cancer that produced both alphafetoprotein (AFP) and human chorionic gonadotropin (HCG). The preoperative serum AFP level of 1039 ng/ml decreased to the normal range 8 weeks after surgery. The preoperative serum HCG level of 11 mIU/ml, which temporarily decreased to the normal range after operation, soon increased thereafter. The serum HCG level decreased, however, to the normal range after postoperative mediastinal radiation therapy. During relapse, only the serum HCG level increased gradually to 26,000 mIU/ml 7 weeks before his death. The lung cancer was classified histologically as poorly differentiated adenocarcinoma. Immunohistochemically, AFP was detected in the mononuclear tumor cells of the primary tumor in the lung, and HCG was found in the giant cells of the subcarinal metastatic lymph node. The concanavalin A non-reactive fraction rate for AFP was 81.3%, and appeared to differ from those of hepatocellular carcinoma and yolk sac tumor.
Differential immobilization and hierarchical involvement of chemokines in monocyte arrest and transmigration on inflamed endothelium in shear flow (1999)

Monocyte extravasation into areas of inflammation involves sequential interactions of multiple adhesion molecules. However, differential contribution of chemokines produced by cytokine-stimulated endothelium and their receptors to leukocyte attachment and transmigration under flow conditions remains to be elucidated. The activation of endothelial cells with TNF-alpha up-regulated mRNA and protein expression of the CXC chemokine GRO-alpha and the CC chemokine monocyte chemotactic protein (MCP)-1, which act through the receptors CXCR2 and CCR2 expressed on monocytes, respectively. Whereas GRO-alpha was immobilized to endothelial cells via heparan sulfate proteoglycans, MCP-1 was secreted in a soluble form. Consequently, inhibition experiments with blocking peptide analogues and monoclonal antibodies revealed that GRO-alpha and its receptor CXCR2 but not MCP-1 and its receptors substantially contributed to conversion of rolling into firm, shear-resistant arrest of monocytes to TNF-alpha-stimulated endothelium in physiological flow. In contrast, MCP-1 and CCR2 but not GRO-alpha and CXCR2 mediated spreading, shape change and subsequent transendothelial migration, which was evident in flow but rarely in stasis and may thus require the establishment of a diffusible MCP-1 gradient. Differential patterns of presentation may determine a functional specialization and hierarchy of chemokines and their receptors in sequential steps of monocyte emigration on inflamed endothelium and shear flow.
The V.42bis standard for data-compressing modems (1992)

The CCITT V.42bis standard for data-compressing modems, a conservative and economically implementable scheme, is discussed from algorithmic, experimental, practical, and marketing standpoints. It is shown that 4.2bis compresses text about as well as the Lempel-Ziv-Welch algorithm of the Berkeley Unix Compress utility. Other Ziv-Lempel variants are discussed briefly.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Modulation of Cadherin and Catenins Expression by Tumor Necrosis Factor- α and Dexamethasone in Human Bronchial Epithelial Cells (2002)

Asthma is an inflammatory disease, and the epithelial mesenchymal unit appears to be of importance in regulating the disease mechanisms. Cell-cell adhesion plays an important role in tissue morphogenesis and homeostasis and is commonly mediated by cadherins, a family of Ca(2+)-dependent transmembrane adhesion receptors. The cadherin family is involved in control of the cellular architecture. Proinflammatory cytokines such as tumor necrosis factor (TNF)-alpha are involved in asthma and may interfere with epithelial integrity. In the present study, we investigated the role of TNF-alpha and dexamethasone on the expression of E-cadherin, beta-catenin, and gamma-catenin. We used two bronchial epithelial cell models: primary small airway epithelial cell cultures and primary culture obtained from human bronchial tubes. After 48 h of TNF-alpha stimulation with or without dexamethasone expression of E-cadherin, beta-catenin and gamma-catenin were analyzed using Western blot analysis and immunofluorescence. This study showed a decrease in the expression of adhesion molecules in both epithelial cell cultures after stimulation. Dexamethasone and anti-TNF-alpha inhibited this effect. In unstimulated cells, E-cadherin and beta- and gamma-catenin expression was membranous, expressed only on the lateral cell wall with minimal cytoplasmic expression. Immunoreactivity was cytoplasmic in stimulated cells. We demonstrated, using Western blot analysis and immunofluorescence, that proinflammatory cytokines could be responsible for structural damage to the epithelium and that this process was potentially reversed by steroids.
A novel quadrupole, quistor, quadrupole tandem mass spectrometer (1991)

Abstract A quadrupole, quistor, quadrupole tandem mass spectrometer allowing selected ion/selected molecule reactions was built. The quistor will be used as a reaction chamber for the study of organic ion‐molecule reactions. Ions are generated in a differentially pumped ion source, quadrupole mass selected and injected into the quistor. The ions are trapped in the quistor by the combined action of a deceleration lens, the presence of helium buffer gas and the quistor RF field. As a first test of the performance of the instrument, the reaction rate constant of the reaction of O 2 + ˙ with methane was measured to be 5 × 10 −12 cm 3 s −1 . This is in good agreement with literature values, indicating that the ions are near thermal equilibrium after a few milliseconds of trapping time.
Feature article - dPVS: an occlusion culling system for massive dynamic environments (2004)

A platform-independent occlusion culling library for dynamic environments, dPVS, can benefit such applications as CAD and modeling tools, time-varying simulations, and computer games. Visibility optimization is currently the most effective technique for improving rendering performance in complex 3D environments. The primary reason for this is that during each frame the pixel processing subsystem needs to determine the visibility of each pixel individually. Currently, rendering performance in larger scenes is input sensitive, and most of the processing time is wasted on rendering geometry not visible in the final image. Here we concentrate on real-time visualization using mainstream graphics hardware that has a z-buffer as a de facto standard for hidden surface removal. In an ideal system only the complexity of the geometry actually visible on the screen would significantly impact rendering time - 3D application performance should be output sensitive.
Bench-to-bedside review: The MET syndrome – the challenges of researching and adopting medical emergency teams (2007)

Studies of hospital performance highlight the problem of 'failure to rescue' in acutely ill patients. This is a deficiency strongly associated with serious adverse events, cardiac arrest, or death. Rapid response systems (RRSs) and their efferent arm, the medical emergency team (MET), provide early specialist critical care to patients affected by the 'MET syndrome': unequivocal physiological instability or significant hospital staff concern for patients in a non-critical care environment. This intervention aims to prevent serious adverse events, cardiac arrests, and unexpected deaths. Though clinically logical and relatively simple, its adoption poses major challenges. Furthermore, research about the effectiveness of RRS is difficult to conduct. Skeptics argue that inadequate evidence exists to support its widespread application. Indeed, supportive evidence is based on before-and-after studies, observational investigations, and inductive reasoning. However, implementing a complex intervention like RRS poses enormous logistic, political, cultural, and financial challenges. In addition, double-blinded randomised controlled trials of RRS are simply not possible. Instead, as in the case of cardiac arrest and trauma teams, change in practice may be slow and progressive, even in the absence of level I evidence. It appears likely that the accumulation of evidence from different settings and situations, though methodologically imperfect, will increase the rationale and logic of RRS. A conclusive randomised controlled trial is unlikely to occur.
Site‐Selective Immobilization of Ligands with Control of Density on Electroactive Microelectrode Arrays (2007)

Surface-bound redox-active quinone groups control the density of immobilized ligands on microelectrode arrays coated with self-assembled monolayers (see picture). The resulting conjugates are characterized by cyclic voltammetry and fluorescence microscopy to determine the density of immobilized ligands on each element of the microelectrode.
HapMap scanning of novel human minor histocompatibility antigens (2008)

Minor histocompatibility antigens (mHags) are molecular targets of allo-immunity associated with hematopoietic stem cell transplantation (HSCT) and involved in graft-versus-host disease, but they also have beneficial antitumor activity. mHags are typically defined by host SNPs that are not shared by the donor and are immunologically recognized by cytotoxic T cells isolated from post-HSCT patients. However, the number of molecularly identified mHags is still too small to allow prospective studies of their clinical importance in transplantation medicine, mostly due to the lack of an efficient method for isolation. Here we show that when combined with conventional immunologic assays, the large data set from the International HapMap Project can be directly used for genetic mapping of novel mHags. Based on the immunologically determined mHag status in HapMap panels, a target mHag locus can be uniquely mapped through whole genome association scanning taking advantage of the unprecedented resolution and power obtained with more than 3 000 000 markers. The feasibility of our approach could be supported by extensive simulations and further confirmed by actually isolating 2 novel mHags as well as 1 previously identified example. The HapMap data set represents an invaluable resource for investigating human variation, with obvious applications in genetic mapping of clinically relevant human traits.
First-In-Human Phase I Study of Lurbinectedin (PM01183) in Patients with Advanced Solid Tumors (2014)

A flat dose of 7.0 mg is the recommended dose for PM01183 as a 1-hour infusion q3wk. This dose is tolerated and active. Severe neutropenia occurred at this dose, although it was transient and with no clinical consequences in this study.
Improved performance of multi-bit delta-sigma analog to digital converters via requantization (1991)

System performance of an oversampled analog to digital converter (ADC) with feedback noise shaping is limited by the precision of the digital to analog converter (DAC) in the feedback path as well as by the number of integrators in the loop(s). Standard designs avoid the DAC precision problem by restricting the ADC and DAC to a single bit, while stability and matching considerations limit systems to three loops. This limit in turn defines the oversample ratio for a given effective bandwidth and noise performance. A simple modification to the oversampled ADC which avoids these limitations via requantization in the feedback path of the original delta-sigma loop structure is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cyclotorsion: A possible cause of residual astigmatism in refractive surgery (2002)

Significant cyclotorsion may occur under monocular viewing conditions. If monocular photorefractive keratectomy procedures are based on binocular keratometry readings, an undercorrection of myopic astigmatism may result. Individuals at risk should be identified before refractive keratectomy is performed.
3-D seismic discontinuity for faults and stratigraphic features: The coherence cube (1995)

Seismic data are usually acquired and processed for imaging reflections. This paper describes a method of processing seismic data for imaging discontinuities (e.g., faults and stratigraphic features). One application of this nontraditional process is a 3-D volume, or cube, of coherence coefficients within which faults are revealed as numerically separated surfaces. Figure 1 compares a traditional 3-D reflection amplitude time slice with the results of the new method. To our knowledge, this is the first published method of revealing fault surfaces within a 3-D volume for which no fault reflections have been recorded.
Corneal endothelial function and structure following cryo-injury in the rabbit. (1984)

Wide-field specular microscopy, fluorophotometry, pachymetry, and scanning electron microscopy are used to characterize a reproducible, in vivo model of corneal endothelial injury and recovery in the rabbit. Following an 8-mm central cryo-injury, the cornea remains thickened for as long as 3 weeks. Mean endothelial permeability to fluorescein is above normal for 10 days following injury, but by 14 days postinjury the endothelial permeability to fluorescein is not statistically significantly different from preinjury control values, thus indicating that endothelial permeability probably returns to normal by approximately 2 weeks postinjury. Cell morphology, as determined by scanning electron microscopy, is also essentially normal by 2 weeks postinjury. Endothelial permeability appears to recover before stromal thickness normalizes, suggesting a lag in recovery of endothelial pump function.
Understanding data lifetime (2006)

This dissertation describes a comprehensive approach to dealing with protecting sensitive data in memory. It differs from previous work in the area in two ways. First, although removing sensitive data promptly after use is an important and widely accepted practice for ensuring secrecy on computers, prior work has largely ignored both the importance and pitfalls of removing sensitive data from memory. Second, no systematic approaches exist today to ensure the removal of sensitive data in memory, and even if there were, there are no methods today by which one could actually evaluate their efficacy. 
This dissertation describes a systematic approach to dealing with these issues by proposing techniques to directly measure the availability of retained data in computers and to fix the associated issues in systems software and applications. All together, the examination of software issues associated with protecting sensitive data in memory is a problem we call the data lifetime problem. 
Ultimately, this dissertation demonstrates that: (1) Removing sensitive data from memory is an important aspect of computer security. Data can be retained in memory for a long time, and removing it is a hard problem particularly for large, complex pieces of software. Protecting sensitive data in memory is largely ignored in the design of systems today, and this lack of awareness can lead to serious security consequences. (2) Modern computer systems do a bad job of removing sensitive data from memory, and this can be precisely measured for complex pieces of software. This dissertation demonstrates a technique based on whole system simulation and hardware level taint analysis that provides a practical solution to the problem of diagnosing, measuring, and understanding data lifetime in large software systems. It also presents the only quantitative analysis of modern, real-world applications with respect to protecting sensitive data in memory. (3) Data lifetime can be minimized by architecting systems to directly address the problem of protecting sensitive data in memory, and that proper handling of sensitive data cannot be done purely by the application; systems support is required. It also demonstrates how such architectures can be effective at minimizing lifetime without compromising performance.
Pharmacokinetic and pharmacodynamic profiles of sumatriptan in migraine patients with headache recurrence or no response* (1996)

Headache recurrence and lack of headache relief after sumatriptan do not appear to be explained by pharmacokinetic or pharmacodynamic differences between patients, which may be an important finding for the development of novel antimigraine drugs.
Micro-channel heat exchanger optimization (2002)

A complete two-dimensional flow/thermal model of the micro-channel cooler is developed. Optimization of the design parameters with this model is demonstrated for the case of a 1 kW/cm/sup 2/ heat flux with the top surface at 25 degrees C. For this case, pure water could be used as the coolant, or 92% water/8% methanol (-5 degrees C freezing point) if the heat is to be dumped to ice/water. The flow rate should be about 50 cc/s per cm/sup 2/ of surface area. The distribution manifold channel spacing (center-to-center) should be 333 mu m (30 channels/cm). The fin height should be about 167 mu m (H/sub F//L=1). The distribution manifold channel widths should be about 200 mu m (W/L=0.6). The micro-channels should be between 7 mu m and 14 mu m wide, while the ratio of fin thickness to micro-channel width should be from 0.5 to 1.0. With these design parameters, an effective heat transfer coefficient (surface heat flux divided by surface to coolant inlet temperature difference) on the order of 100 W/cm/sup 2/ K will be achieved with a total pressure drop of only about 2 bar.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>