gebhart/patrepeval huggingface dataset:
Extracellular Transport of VirG Protein in Shigella (1995)

The ability of Shigella to spread within and between epithelial cells is a prerequisite for causing bacillary dysentery and requires the function encoded by the virG gene on the large plasmid. The outer membrane VirG (IcsA) protein is essential for bacterial spreading by eliciting polar deposition of filamentous actin (F-actin) in the cytoplasm of epithelial cells. Recent studies have indicated that an N-terminal 80-kDa VirG portion is exposed on the bacterial cell surface and released into the external medium, while the following 37-kDa C-terminal portion is embedded in the outer membrane, although little is known about the extracellular transport of the VirG protein. In this study, we attempted to elucidate the export pathway of VirG protein across the outer membrane and found that the C-terminal 37-kDa portion, termed VirG beta-core, serves as the self-transporter for the secretion of the preceding 80-kDa portion from the periplasmic side of the outer membrane to the external side. Indeed, foreign polypeptides such as MalE or PhoA covalently linked to the N terminus of VirG beta-core were transported to the external side of the outer membrane, and it was further shown that the folding structure of the passenger polypeptide at the periplasmic side of the outer membrane interferes with its translocation. Analysis of the secondary structure of VirG beta-core predicted that the critical structural property was a beta-barrel channel consisting of amphipathic anti-parallel transmembrane beta-strands, interspersed by hairpin turns and loops. These results thus strongly suggest that the secretion of VirG protein from Shigella is similar to the export system utilized by the IgA protease of Neisseria.
[Prognostic significance of p53 autoantibodies in serum of patients with breast carcinoma]. (1996)

Mutations in the p53 tumor suppressor gene are the most common genetic alterations associated with malignant tumors including breast and gynecologic carcinomas. Overexpression of p53 protein is a result of increased protein stability caused through conformationally alteration. Accumulation of mutant p53 in tumor cells may lead to a humoral immune response with development of p53 autoantibodies. In the present study we investigated the sera of 72 patients undergoing surgery for primary breast cancer and the relation between p53 antibody production, prognostic parameters and clinical outcome. Circulating p53 antibodies were detected in 15 of the 72 examined patients (21%). A correlation to conventional prognostic factors was not observed. Yet the overall survival was worse in patients with p53 antibodies (p < 0.04), suggesting a more aggressive tumor type.
Power and Linearity Characteristics of Field-Plated Recessed-Gate AlGaN–GaN HEMTs (2004)

Record power density and high-efficiency operation with AlGaN-GaN high-electron mobility transistor (HEMT) devices have been achieved by adopting a field-plated gate-recessed structure. Devices grown on SiC substrate yielded very high power density (18.8 W/mm with 43% power-added efficiency (PAE) as well as high efficiency (74% with 6 W/mm) under single-tone continuous-wave testing at 4 GHz. Devices also showed excellent linearity characteristics when measured under two-tone continuous-wave signals at 4 GHz. When biased in deep-class AB (33 mA/mm, 3% I/sub max/) device maintained a carrier to third-order intermodulation ratio of 30 dBc up to a power level of 2.4 W/mm with 53% PAE; increasing bias current to 66 mA/mm (6% I/sub max/) allowed high linear operation (45 dBc) up to a power level of 1.4 W/mm with 38% PAE.
Fractals: endlessly repeated geometrical figures (1992)

Fractals are shapes in which an identical motif repeats itself on an ever diminishing scale. A coastline, for instance, is a fractal, with each bay or headland having its own smaller bays and headlands--as is a with a trunk that separates into two smaller side branches, which in their turn separate into side branches that are smaller still. No longer mathematical curiosities, fractals are now a vital subject of mathematical study, practical application, and popular interest. For readers interested in graphic design, computers, and science and mathematics in general, Hans Lauwerier provides an accessible introduction to fractals that makes only modest use of mathematical techniques. Lauwerier calls this volume a book to work with. Readers with access to microcomputers can design new figures, as well as re-create famous examples. They can start with the final chapter, try out one of the programs described there (preferably in a compiled version such as TURBO BASIC), and consult the earlier chapters for whatever is needed to understand the fractals produced in this way. The first chapter, which builds on the relationship of binary number systems to the tree fractal described above, is the best place to start if one has no computer. There will be much to enjoy on the way, including the beautiful color illustrations.
High performance GeSi quantum-well PMOS on SIMOX (1992)

A new quantum-well GeSi-SIMOX PMOSFET is presented. The device consists of a Si/Ge/sub 0.3/Si/sub 0.7//Si quantum well, which is grown pseudomorphically on a SIMOX substrate. The effective channel mobility of this device has been found to be 90% higher than that of an identically processed conventional SIMOX PMOSFET.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Loss of Interleukin Receptor-Associated Kinase 4 Signaling Suppresses Amyloid Pathology and Alters Microglial Phenotype in a Mouse Model of Alzheimer's Disease (2012)

Alzheimer's disease (AD) is typified by the deposition of amyloid in the brain, which elicits a robust microglial-mediated inflammatory response that is associated with disease exacerbation and accelerated progression. Microglia are the principal immune effector cells in the brain and interact with fibrillar forms of Aβ (fAβ) through a receptor complex that includes Toll-like receptors (TLR) 2/4/6 and their coreceptors. Interleukin receptor-associated kinases (IRAKs) are essential intracellular signaling molecules for transduction of TLR signals. Studies of mouse models of AD in which the individual TLRs are knocked out have produced conflicting results on roles of TLR signaling in amyloid homeostasis. Therefore, we disrupted a common downstream TLR signaling element, IRAK4. We report that microglial IRAK4 is necessary in vitro for fAβ to activate the canonical pro-inflammatory signaling pathways leading to activation of p38, JNK, and ERK MAP kinases and to generate reactive oxygen species. In vivo the loss of IRAK4 function results in decreased Aβ levels in a murine model of AD. This was associated with diminished microgliosis and astrogliosis in aged mice. Analysis of microglia isolated from the adult mouse brain revealed an altered pattern of gene expression associated with changes in microglial phenotype that were associated with expression of IRF transcription factors that govern microglial phenotype. Further, loss of IRAK4 function also promoted amyloid clearance mechanisms, including elevated expression of insulin-degrading enzyme. Finally, blocking IRAK function restored olfactory behavior. These data demonstrate that IRAK4 activation acts normally to regulate microglial activation status and influence amyloid homeostasis in the brain.
Experiments on peak spectral efficiency of 50 bps/Hz with 12-by-12 MIMO multiplexing for future broadband packet radio access (2010)

This paper presents field experimental results of peak frequency efficiency of approximately 50 bps/Hz, i.e., 4.9 Gbps packet transmission in a 100-MHz channel bandwidth, using 12-by-12 MIMO-OFDM focusing on the influence of fading correlation between the transmitter and receiver antennas using vertically polarized antennas. Maximum likelihood detection (MLD)-based signal detection was employed to achieve such high frequency efficiency with the required received signal-to-noise power ratio (SNR) of less than 30 dB. From the field experimental results under non-line-of- sight conditions, we show that the required average received SNR to achieve the throughput of 4.9 Gbps is degraded by less than 0.5 dB when the receiver antenna separation is reduced from 40 cm (6.2¿) to 10 cm (1.5¿), while it is degraded by approximately 1.5 dB when the transmitter antenna separation is decreased from 70 cm (10.9¿) to 20 cm (3.1¿). Furthermore, we clarify that the required minimum antenna separations of the base station transmitter and mobile station receiver are 20 cm and 10 cm, respectively, in order to achieve the peak throughput of 4.9 Gbps at the average received SNR of less than 30 dB in a field environment.
Recombinant Antithrombin: Production and Role in Cardiovascular Disorder (2001)

Plasma-derived antithrombin (AT) concentrates have been used for the management of hereditary and acquired deficiencies since the early 1980s. Recombinant versions of other blood factors and their derivatives are increasingly becoming available, providing a safe and abundant supply of these important therapeutics. However, the complexity of the AT molecule and the large doses often required for supplementation treatments preclude the use of traditional cell culture bioreactors for recombinant production. The development of a very efficient expression system has been necessary for the cost-efficient recombinant production of AT. Transgenic production, with its ability to yield high levels of heterologous protein and its scale-up flexibility, is an attractive alternative to plasma fractionation. Purification of recombinant AT from the milk of transgenic dairy goats has been developed to provide a homogeneous, well-defined, and abundant supply of this factor. This article describes the production of recombinant AT and aspects of clinical applications of this molecule to cardiovascular disorders.
Patterns and severity of neuromuscular transmission failure in seronegative myasthenia gravis (2005)

Seronegative MG is heterogeneous with respect to the presence of antibodies to MuSK. Impairment of neuromuscular synaptic transmission in EDC is less marked in seronegative than seropositive MG despite the similar clinical severity. This discrepancy may partly reflect the distribution of affected muscles in seronegative patients, but it is possible that other factors, such as impaired excitation-contraction coupling resulting from RyR antibodies, contribute to the clinical phenotype.
Design and Synthesis of Potent Antitumor 5,4‘-Diaminoflavone Derivatives Based on Metabolic Considerations (1997)

Recently, we reported that 5,4'-diaminoflavone (1) exhibits potent and specific growth-inhibitory activity against the estrogen receptor (ER)-positive human breast cancer cell line MCF-7. However, when compound 1 was incubated with S-9 mix, its metabolites were observed. Moreover, addition of S-9 mix to the medium caused the drastic decrease in activity of compound 1. Since the 6-, 8-, and 3'-positions were considered to be metabolized oxidatively in vivo from MO calculations, a series of 5,4'-diaminoflavone derivatives substituted at such putative metabolic positions with various functional groups were synthesized aiming at the metabolically stable derivatives. Among them, 5,4'-diamino-6,8,3'-trifluoroflavone (14d) exhibited strong growth-inhibitory activity against MCF-7 cells even in the presence of S-9 mix. Moreover, orally administered compound 14d completely suppressed the growth of MCF-7 inoculated into nude mice, and the effect was more potent than that of compound 1. In addition to ER-positive breast cancer cells, compound 14d exhibited growth-inhibitory activity against a panel of human cancer cell lines including a part of ER-negative breast, endometrial, ovarian, and liver cancers. From these results, fluorine introduction to the putative metabolic positions of compound 1 was elucidated to be effective in the enhancement of the in vivo antitumor activity, probably due to the block of the metabolic deactivation.
Real Time Control Protocol (RTCP) attribute in Session Description Protocol (SDP) (2003)

The Session Description Protocol (SDP) is used to describe the parameters of media streams used in multimedia sessions. When a session requires multiple ports, SDP assumes that these ports have consecutive numbers. However, when the session crosses a network address translation device that also uses port mapping, the ordering of ports can be destroyed by the translation. To handle this, we propose an extension attribute to SDP.
Inflammation 2: its role in the healing of chronic wounds (2002)

Why do some wounds fail to heal in the expected time? Part two of this article on inflammation discusses the possible causes, which include recurrence of trauma, bacterial and other contamination and perhaps, above all, the ageing process.
Nonlinear mixed-effects modeling: individualization and prediction. (2004)

The development of biomathematical models for the prediction of fatigue and performance relies on statistical techniques to analyze experimental data and model simulations. Statistical models of empirical data have adjustable parameters with a priori unknown values. Interindividual variability in estimates of those values requires a form of smoothing. This traditionally consists of averaging observations across subjects, or fitting a model to the data of individual subjects first and subsequently averaging the parameter estimates. However, the standard errors of the parameter estimates are assessed inaccurately by such averaging methods. The reason is that intra- and inter-individual variabilities are intertwined. They can be separated by mixed-effects modeling in which model predictions are not only determined by fixed effects (usually constant parameters or functions of time) but also by random effects, describing the sampling of subject-specific parameter values from probability distributions. By estimating the parameters of the distributions of the random effects, mixed-effects models can describe experimental observations involving multiple subjects properly (i.e., yielding correct estimates of the standard errors) and parsimoniously (i.e., estimating no more parameters than necessary). Using a Bayesian approach, mixed-effects models can be "individualized" as observations are acquired that capture the unique characteristics of the individual at hand. Mixed-effects models, therefore, have unique advantages in research on human neurobehavioral functions, which frequently show large inter-individual differences. To illustrate this we analyzed laboratory neurobehavioral performance data acquired during sleep deprivation, using a nonlinear mixed-effects model. The results serve to demonstrate the usefulness of mixed-effects modeling for data-driven development of individualized predictive models of fatigue and performance.
Elimination of the NLRP3-ASC Inflammasome Protects against Chronic Obesity-Induced Pancreatic Damage (2011)

Clinical evidence that the blockade of IL-1β in type-2 diabetic patients improves glycemia is indicative of an autoinflammatory mechanism that may trigger adiposity-driven pancreatic damage. IL-1β is a key contributor to the obesity-induced inflammation and subsequent insulin resistance, pancreatic β-cell dysfunction, and the onset of type 2 diabetes. Our previous studies demonstrated that the ceramides activate the Nod-like receptor family, pyrin domain containing 3 (Nlrp3) inflammasome to cause the generation of mature IL-1β and ablation of the Nlrp3 inflammasome in diet-induced obesity improves insulin signaling. However, it remains unclear whether the posttranslational processing of active IL-1β in pancreas is regulated by the NLRP3 inflammasome or whether the alternate mechanisms play a dominant role in chronic obesity-induced pancreatic β-cell exhaustion. Here we show that loss of ASC, a critical adaptor required for the assembly of the NLRP3 and absent in melanoma 2 inflammasome substantially improves the insulin action. Surprisingly, despite lower insulin resistance in the chronically obese NLRP3 and ASC knockout mice, the insulin levels were substantially higher when the inflammasome pathway was eliminated. The obesity-induced increase in maturation of pancreatic IL-1β and pancreatic islet fibrosis was dependent on the NLRP3 inflammasome activation. Furthermore, elimination of NLRP3 inflammasome protected the pancreatic β-cells from cell death caused by long-term high-fat feeding during obesity with significant increase in the size of the islets of Langerhans. Collectively, this study provides direct in vivo evidence that activation of the NLRP3 inflammasome in diet-induced obesity is a critical trigger in causing pancreatic damage and is an important mechanism of progression toward type 2 diabetes.
Large blood vessel cooling in heated tissues: a numerical study (1995)

Large blood vessels can produce steep temperature gradients in heated tissues leading to inadequate tissue temperatures during hyperthermia. This paper utilizes a finite difference scheme to solve the basic equations of heat transfer and fluid flow to model blood vessel cooling. Unlike previous formulations, heat transfer coefficients were not used to calculate heat transfer to large blood vessels. Instead, the conservation form of the finite difference equations implicitly modelled this process. Temperature profiles of heated tissues near thermally significant vessels were calculated. Microvascular heat transfer was modelled either as an effective conductivity or a heat sink. An increase in perfusion in both microvascular models results in a reduction of the cooling effects of large vessels. For equivalent perfusion values, the effective conductivity model predicted more effective heating of the blood and adjacent tissue. Furthermore, it was found that optimal vessel heating strategies depend on the microvascular heat transfer model adopted; localized deposition of heat near vessels could produce higher temperature profiles when microvascular heat transfer was modelled according to the bioheat transfer equation (BHTE) but not the effective thermal conductivity equation (ETCE). Reduction of the blood flow through thermally significant vessels was found to be the most effective way of reducing localized cooling.
Feedback flow to improve model-based OPC calibration test patterns (2007)

Process models are responsible for the prediction of the latent image in the resist in a lithographic process. In order for the process model to calculate the latent image, information about the aerial image at each layout fragment is evaluated first and then some aerial image characteristics are extracted. These parameters are passed to the process models to calculate wafer latent image. The process model will return a threshold value that indicates the position of the latent image inside the resist, the accuracy of this value will depend on the calibration data that were used to build the process model in the first place. The calibration structures used in building the models are usually gathered in a single layout file called the test pattern. Real raw data from the lithographic process are measured and attached to its corresponding structure in the test pattern, this data is then applied to the calibration flow of the models. In this paper we present an approach to automatically detect patterns that are found in real designs and have considerable aerial image parameters differences with the nearest test pattern structure, and repair the test patterns to include these structures. This detect-and-repair approach will guarantee accurate prediction of different layout fragments and therefore correct OPC behavior.
Preferential T-cell receptor beta-chain variable gene use in myelin basic protein-reactive T-cell clones from patients with multiple sclerosis. (1991)

Multiple sclerosis is an autoimmune disease in which T lymphocytes reactive to myelin basic protein (BP) could play a central role. T cells specific for BP were cloned from the blood of multiple sclerosis patients and normal individuals, and expression of T-cell receptor variable region genes was analyzed. A remarkable bias for use of beta-chain variable region (V beta) 5.2 and, to a lesser extent, V beta 6.1 was seen among BP-specific clones from patients but not from controls. The preferential use of V beta 5.2 for BP recognition did not reflect altered expression of this V beta in the peripheral repertoire. Interestingly, shared V beta 5.2 usage was apparent for clones specific for different BP determinants, even when derived from the same individual. The concurrent demonstration by others (J. R. Oksenberg, M. A. Panzara, A. B. Begovich, H. Erlich, R. Murray, M. Sherritt, S. Stuart, C. C. Bernard, and L. Steinman, personal communication) that T cells within demyelinating areas of multiple sclerosis brains preferentially express V beta 5.2 and V beta 6.1 suggests that the BP-specific clones derived from blood may be relevant to disease pathogenesis. These findings may have important implications for the treatment of multiple sclerosis.
Laser-to-fiber coupling module using a micromachined alignment mirror (1996)

We report the fabrication of a laser-to-fiber coupling module that incorporates a movable silicon-micromachined alignment micromirror. The micromirror can position a beam on a fiber within a 0.17 μm standard deviation and has a range of motion of more than 200 μm. Measurements on the module have shown a reproducible coupling efficiency of 40%. The coupling module provides a means to compensate for placement inaccuracies of passively assembled optical components.
Lactobacillus reuteriprevents colitis by reducing P-selectin-associated leukocyte- and platelet-endothelial cell interactions (2009)

Recent findings indicate that dextran sodium sulfate (DSS)-induced colitis is associated with a prothrombogenic phenotype, with P-selectin playing a major role in platelet recruitment. It has been suggested that probiotics may ameliorate colonic inflammation. We therefore investigated how treatment with Lactobacillus reuteri influenced P-selectin expression, leukocyte and platelet endothelial cell interactions, and colitis severity in DSS-treated rats. Rats were divided into the following four groups: nontreated, DSS treated (5% in drinking water for 9 days), L. reuteri, and L. reuteri and DSS treated. The rats were anesthetized with Inactin (120 mg/kg ip), and the dual radiolabeled monoclonal antibody technique was used to quantify P-selectin expression. Leukocyte-endothelial and platelet-endothelial cell interactions were studied in colonic venules with intravital microscopy. Colitis severity was assessed using a disease activity index. Disease activity index increased, as did the expression of P-selectin in the entire colon after DSS treatment, but both were reduced to control levels with L. reuteri pretreatment. The increased platelet- and leukocyte-endothelial cell interactions after DSS treatment were abolished by pretreatment with L. reuteri. L. reuteri protects against DSS-induced colitis in rats. The protection is associated with reduced P-selectin expression and a decrease in leukocyte- and platelet-endothelial cell interactions.
Carbon Nanotube Substrates Boost Neuronal Electrical Signaling (2005)

We demonstrate the possibility of using carbon nanotubes (CNTs) as potential devices able to improve neural signal transfer while supporting dendrite elongation and cell adhesion. The results strongly suggest that the growth of neuronal circuits on a CNT grid is accompanied by a significant increase in network activity. The increase in the efficacy of neural signal transmission may be related to the specific properties of CNT materials, such as the high electrical conductivity.