gebhart/patrepeval huggingface dataset:
DNA Mismatch Repair Proteins Are Required for Efficient Herpes Simplex Virus 1 Replication (2011)

Herpes simplex virus 1 (HSV-1) is a double-stranded DNA virus that replicates in the nucleus of its human host cell and is known to interact with many cellular DNA repair proteins. In this study, we examined the role of cellular mismatch repair (MMR) proteins in the virus life cycle. Both MSH2 and MLH1 are required for efficient replication of HSV-1 in normal human cells and are localized to viral replication compartments. In addition, a previously reported interaction between MSH6 and ICP8 was confirmed by coimmunoprecipitation and extended to show that UL12 is also present in this complex. We also report for the first time that MLH1 associates with ND10 nuclear bodies and that like other ND10 proteins, MLH1 is recruited to the incoming genome. Knockdown of MLH1 inhibits immediate-early viral gene expression. MSH2, on the other hand, which is generally thought to play a role in mismatch repair at a step prior to that of MLH1, is not recruited to incoming genomes and appears to act at a later step in the viral life cycle. Silencing of MSH2 appears to inhibit early gene expression. Thus, both MLH1 and MSH2 are required but appear to participate in distinct events in the virus life cycle. The observation that MLH1 plays an earlier role in HSV-1 infection than does MSH2 is surprising and may indicate a novel function for MLH1 distinct from its known MSH2-dependent role in mismatch repair.
Mangosteen cultivation / (1995)

Mangosteen grown in a mixed horticultural holding 2 2 Mature mangosteen trees showing growth habit of tree 9 3 Preparation of fresh fruits for consumption 1 4 Garcinia hombroniana Pierre., the forest mangosteen 5
Reactive oxygen intermediates target CC(A/T)6GG sequences to mediate activation of the early growth response 1 transcription factor gene by ionizing radiation. (1993)

The cellular response to ionizing radiation includes induction of the early growth response 1 gene (EGR1). The present work has examined the involvement of reactive oxygen intermediates (ROIs) in this response. Exposure of human HL-525 cells, an HL-60 subclone deficient in protein kinase C-mediated signaling, to both ionizing radiation and H2O2 was associated with increases in EGR-1 transcripts. These increases in EGR-1 expression were inhibited by the antioxidant N-acetyl-L-cysteine (NAC). Nuclear run-on assays demonstrate that NAC inhibits the activation of EGR1 transcription by these agents. Previous studies have shown that induction of EGR1 by x-rays is conferred by serum response or CC(A/T)6GG (CArG) elements. The present studies demonstrate similar findings with H2O2 and the finding that activation of the EGR1 promoter region containing CArG elements is abrogated by NAC. Moreover, we show that NAC inhibits the ability of a single CArG box to confer x-ray and H2O2 inducibility when linked to a heterologous promoter. Taken together, these findings indicate that ROIs induce EGR1 transcription by activation of CArG elements.
Probabilistic optimum filtering for robust speech recognition (2002)

We present a new mapping algorithm for speech recognition that relates the features of simultaneous recordings of clean and noisy speech. The model is a piecewise linear transformation applied to the noisy speech feature. The transformation is a set of multidimensional linear least-squares filters whose outputs are combined using a conditional Gaussian model. The algorithm was tested using SRI's DECIPHER speech recognition system. Experimental results show how the mapping is used to reduce recognition errors when the training and testing acoustic environments do not match.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Near Infra-Red Photoimmunotherapy with Anti-CEA-IR700 Results in Extensive Tumor Lysis and a Significant Decrease in Tumor Burden in Orthotopic Mouse Models of Pancreatic Cancer (2015)

Photoimmunotherapy (PIT) of cancer utilizes tumor-specific monoclonal antibodies conjugated to a photosensitizer phthalocyanine dye IR700 which becomes cytotoxic upon irradiation with near infrared light. In this study, we aimed to evaluate the efficacy of PIT on human pancreatic cancer cells in vitro and in vivo in an orthotopic nude mouse model. The binding capacity of anti-CEA antibody to BxPC-3 human pancreatic cancer cells was determined by FACS analysis. An in vitro cytotoxicity assay was used to determine cell death following treatment with PIT. For in vivo determination of PIT efficacy, nude mice were orthotopically implanted with BxPC-3 pancreatic tumors expressing green fluorescent protein (GFP). After tumor engraftment, the mice were divided into two groups: (1) treatment with anti-CEA-IR700 + 690 nm laser and (2) treatment with 690 nm laser only. Anti-CEA-IR700 (100 μg) was administered to group (1) via tail vein injection 24 hours prior to therapy. Tumors were then surgically exposed and treated with phototherapy at an intensity of 150 mW/cm2 for 30 minutes. Whole body imaging was done subsequently for 5 weeks using an OV-100 small animal imaging system. Anti-CEA-IR700 antibody bound to the BxPC3 cells to a high degree as shown by FACS analysis. Anti-CEA-IR700 caused extensive cancer cell killing after light activation compared to control cells in cytotoxicity assays. In the orthotopic models of pancreatic cancer, the anti-CEA-IR700 group had significantly smaller tumors than the control after 5 weeks (p<0.001). There was no significant difference in the body weights of mice in the anti-CEA-IR700 and control groups indicating that PIT was well tolerated by the mice.
Ubiquitous Services System Based on SIP (2007)

In this paper, we present the ubiquitous services system that provides multimedia services, surveillance services and remote control services. This ubiquitous services system keeps the service session based on session initiation protocol (SIP) and supports the uniform interface for connecting the selected service to a suitable device by the operation of a general touch event. The service session of the ubiquitous services system is preserved even though an end-user moves from one computing environment to others. For getting the connected ubiquitous services, all that he has to do is to carry a small mobile pad, such as PDA or Cellular phone, which shows a list of devices that he can use as I/O devices of the on-going service session. He does not have to re-setup the session. When he clicks and selects the proper device among the devices listed on the pad, the session is immediately migrated to the selected device. In this paper, we describe the design of ubiquitous services system based on SIP and X.10 that supports both the user mobility and service session preservation in the ubiquitous wired/wireless network environment.
Cloning structural gene sacB, which codes for exoenzyme levansucrase of Bacillus subtilis: expression of the gene in Escherichia coli (1983)

A clone bearing the structural gene sacB, coding for the exoenzyme levansucrase, was isolated from a library of Bacillus subtilis DNA that was cloned in phage lambda charon 4A on the basis of the transforming activity of the chimeric DNA. This lambda clone also was found to contain the sacR and smo loci. Subcloning the sacB-sacR region in plasmid pBR325 resulted in a clone which directed levansucrase synthesis in Escherichia coli. The nucleotide sequence coding for the secreted protein was localized on the physical map of the cloned DNA.
Glucocorticoid Resistance and the Immune Function in the Immunodeficiency Syndrome (1998)

Glucocorticoids, the final product of HPA axis, and their receptors (GRs) on mononuclear cells are crucial mediators in the endocrine-immune interaction. An alteration in GRs involving a lower receptor affinity (Kd) for glucocorticoids has been found in a group of advanced AIDS patients, who developed Addisonian symptoms (weakness, weight loss, hypotension, hyponatremia, and intense mucocutaneous melanosis) in spite of hypercortisolism and normal or slightly elevated values of ACTH (AIDS-GR). In these patients, data for the suppression test showed decreased cortisol and ACTH suppression in response to exogenous dexamethasone. The inhibitory effect of dexamethasone on radiolabeled-thymidine incorporation in mononuclear cells from these patients was also reduced. Monocytes of AIDS-GR patients had a receptor Kd of 10.5 +/- 4.2 nmol/l that was higher than that of other AIDS patients (AIDS-C) (2.9 +/- 0.8 nmol/l) and normal subjects (2.0 +/- 0.8 nmol/l: p < 0.01). Correlations were found between plasmatic IFN-alpha and receptor Kd on monocytes of AIDS-GR (r = 0.77). Poly (i)-poly (c)-induced IFN-alpha production by monocytes was inhibited by glucocorticoids in the AIDS-C group and controls (approx. 80% in both groups): The effect was reversed by the receptor antagonist RU-486. By contrast, glucocorticoid did not inhibit IFN-alpha production in AIDS-GR group. In conclusion, levels of plasmatic IFN-alpha, a cytokine with antiviral properties, may be increased several times, and dexamethasone fails to inhibit monocytes' IFN-alpha production only in AIDS with cortisol resistance, a disturbance that confirms an important immunoregulatory role of glucocorticoids in HIV disease.
Stability of semiconductor strained-layer superlattices (1986)

The criteria for strained-layer growth of semiconductor superlattices are discussed. It is shown that to avoid misfit dislocations, careful attention has to be paid to the composition, geometry, and dimensions of the quantum well structure. Two critical thicknesses are found to apply to strained-layer superlattice growth, one relating to the thickness of individual layers and one relating to the overall thickness of the superlattice. We derive the relationship between these two critical values. Experimental studies of the GexSi1−x/Si on Si and GexSi1−x/Ge on Ge systems using electron microscopy, Raman scattering, and ion channeling show that exceeding the critical superlattice thickness results in a network of dislocations between the substrate and first superlattice layer.
Non-monotonicity of the Contact Angle from NaCl and MgCl2 Concentrations in Two Petroleum Fluids on Atomistically Smooth Surfaces (2016)

Wetting and alteration of wetting are among the most important material properties of fluid–fluid–substrate systems in biological and industrial systems. An important industrial application of wetting and wetting alteration is related to displacement of crude oil by water injection in porous media. Water injection in oil reservoirs has been used since the early periods of oil production. Recently, it has been discovered that the salt concentration in the injected water may have a significant effect on the oil recovery. The process is under active research for the need of an improved understanding. In this work, we investigate the governing elements of surface wettability with two different crude oils on two atomistically smooth surfaces (mica and quartz) and one smooth surface (calcite) as a function of the salt concentration (0–3 M) and type (mono- versus divalent). We investigate the change of wettability from NaCl and MgCl2 salts over a wide concentration for the first time. The measurements are based on long enough aging times and droplet sizes that give equilibrium and size-independent contact angles. Our measurements show a non-monotonic behavior, in that, as NaCl concentration increases, there is a decrease (increase of water-wetting) and then an increase (decrease of water-wetting) of the contact angle in all of the systems that we have studied. MgCl2 salt shows two trends with an increasing concentration. For mica and quartz, there is first a decrease of the contact angle and then an increase followed by a second sharp decrease at high MgCl2 concentrations. For calcite substrate, we observe an increase of the contact angle reaching a maximum and then a decrease with an increasing salt concentration. These observations have profound implications on the effect of salts on wettability alteration. The measurements have set the stage for atomistic simulations for a molecular understanding of the salt effect in complex fluids.
Single-pass constant- and variable-bit-rate MPEG-2 video compression (1999)

Most real-time MPEG-2 encoders are designed to perform in a constant-bit-rate (CBR) mode, in which buffer constraints are imposed to circumvent large deviations from a desired rate at any instant in time. Although such streams are generally good-quality sequences, certain types of operations or environments call for a more efficient real-time CBR encoder. The first part of the paper describes how a better-quality CBR video stream can be produced by estimating the relative complexity of a picture in comparison with the average complexity of the partially encoded stream and using it to adjust the compression parameters in a single-pass mode of operation. Our CBR encoder is particularly attractive for digital broadcast and editing environments, in which representations of higher-fidelity video objects in both display and freeze modes are constantly pursued. The second part of the paper describes the real-time generation of video streams with a variable-bit-rate (VBR) encoder. This mode of operation is high ly desirable for home entertainment and recreational events. We propose a robust single-pass VBR video encoder algorithm which is capable of learning and adapting itself to the complexity of image segments and thereafter creating streams which have constant visual picture quality. The new VBR scheme displays a better performance than the CBR encoder, particularly when special effects such as scene transitions, fades, or luminance changes are to be compressed. Both CBR and VBR encoders are fully compliant with the MPEG-2 standard and are easily implementable with IBM encoder architecture. Compression results for the new single-pass encoding algorithms and comparisons with previous CBR schemes are provided. The result suggests the suitability of our VBR approach for record/playback in storage media such as digital video disc (DVD) players, disk-based camcorders, and digital videocassette recorders (DVCRs). It further reflects the importance of our single-pass CBR scheme for providers of broadcast services , for which it allows more video programs to be allocated to a selected communication link, and for in-studio applications, for which it greatly facilitates visual analysis of captured streams.
Defective signal transduction induced by thromboxane A2 in a patient with a mild bleeding disorder: impaired phospholipase C activation despite normal phospholipase A2 activation (1993)

A patient with a mild bleeding disorder whose platelets responded defectively to thromboxane A2 (TXA2) was identified, and the mechanism of this dysfunction was analyzed. The platelets were defective in shape change, aggregation, and release reaction in response to synthetic TXA2 mimetic (STA2). When the platelet TXA2 receptor was examined with both a 125I-labeled derivative of a TXA2 receptor antagonist ([125I]-PTAOH) and [3H]-labeled TXA2 agonist ([3H]U-46619), the equilibrium dissociation rate constants (kd) and the maximal concentrations of binding sites (Bmax) of the platelets to both ligands were within normal ranges, suggesting that the binding capacity of their TXA2 receptor was normal. STA2 could not induce IP3 formation and intracellular Ca2+ mobilization, whereas these responses to thrombin were within normal ranges. GTPase activity was also decreased when the patient's platelet membrane was challenged with STA2. On the other hand, lysophosphatidylinositol formation, which is a direct indicator of phospholipase A2 (PLA2) activation, was found to be normal when the [3H]-inositol-labeled platelets were challenged with STA2. Thromboxane B2 (TXB2) was also produced in response to STA2. These results suggested that the abnormality in these platelets was impaired coupling between TXA2 receptor and phospholipase C (PLC) activation. Furthermore, it is also suggested that the activation of PLA2 and PLC are separable events in thromboxane-induced platelet activation.
Autonomic cardiovascular and respiratory control during prolonged spaceflights aboard the International Space Station (2007)

Impaired autonomic control represents a cardiovascular risk factor during long-term spaceflight. Little has been reported on blood pressure (BP), heart rate (HR), and heart rate variability (HRV) during and after prolonged spaceflight. We tested the hypothesis that cardiovascular control remains stable during prolonged spaceflight. Electrocardiography, photoplethysmography, and respiratory frequency (RF) were assessed in eight male cosmonauts (age 41-50 yr, body-mass index of 22-28 kg/m2) during long-term missions (flight lengths of 162-196 days). Recordings were made 60 and 30 days before the flight, every 4 wk during flight, and on days 3 and 6 postflight during spontaneous and controlled respiration. Orthostatic testing was performed pre- and postflight. RF and BP decreased during spaceflight (P < 0.05). Mean HR and HRV in the low- and high-frequency bands did not change during spaceflight. However, the individual responses were different and correlated with preflight values. Pulse-wave transit time decreased during spaceflight (P < 0.05). HRV reached during controlled respiration (6 breaths/min) decreased in six and increased in one cosmonaut during flight. The most pronounced changes in HR, BP, and HRV occurred after landing. The decreases in BP and RF combined with stable HR and HRV during flight suggest functional adaptation rather than pathological changes. Pulse-wave transit time shortening in our study is surprising and may reflect cardiac output redistribution in space. The decrease in HRV during controlled respiration (6 breaths/min) indicates reduced parasympathetic reserve, which may contribute to postflight disturbances.
Attenuation and dispersion of sound in dilute suspensions of spherical particles (2000)

This paper considers sound propagation in dilute suspensions of constant-mass particles that can translate and pulsate under the effects of a small amplitude sound wave. A new theory for sound attenuation and dispersion is developed on the basis of the changes of the suspension's compressibility produced by the relative motions between host fluid and particles. The approach, used earlier to treat propagation in rigid-particle suspensions, decouples the propagation problem from the more difficult problem of obtaining accurate descriptions for the fluid-particle interactions. In this work the role of the pulsational motion is included in the theoretical framework. The resulting theory is thus applicable to aerosols, bubbly liquids, emulsions, and hydrosols composed of elastic particles, and includes, as a special limit, rigid-particle suspensions. The results are expressed in terms of three complex quantities that describe, respectively, the particles' translational velocity, temperature, and pressure, relative to their counterparts in the fluid. Theoretical results for these quantities, applicable in wide frequency ranges, are available from previous studies [Temkin and Leung, J. Sound Vib. 49, 75-92 (1976), Temkin, J. Fluid. Mech. 380, 1-38 (1999)]. Together with the compressibility theory presented here, they provide a more general description of propagation in dilute suspensions than presently available. In the case of aerosols and hydrosols, the theory produces known results for the attenuation and the sound speed. For bubbly liquids and emulsions the new results presented here differ from those available in the literature. The differences are traced to the neglect in the existing theories of the acoustic pressure disturbance produced by the pulsations of the particles.
Treatment of diabetic ulcers (2006)

Diabetic ulcers are chronic wounds that are the result of repetitive trauma in the insensate foot. The presence of infection and peripheral vascular disease makes the treatment of these wounds demanding and requires a multidisciplinary approach. The main principles of the management include adherence to the principles of good wound care, such as aggressive debridement of all non-viable tissue, adequate off-loading of pressure, prompt treatment of infection and moist wound dressings. Over the last decade, new therapeutic modalities, including growth factors and living skin equivalents, have been available to the practicing physicians. Judicious use of advanced wound care products may provide the best means of treating these challenging wounds in an efficient and cost-effective way.
The Effect of Gabapentin on Neuropathic Pain (1997)

Gabapentin may be a useful adjunct for treating neuropathic pain with a minimum of side effects. Particular advantage may be gained with the use of this drug for postherpetic neuralgia and direct peripheral nerve injuries.
Regulation of System A Amino Acid Transport in 3T3-L1 Adipocytes by Insulin (1998)

The insulin-stimulated uptake of 2-(methylamino)isobutyric acid (MeAIB), a nonmetabolizable substrate for system A, in 3T3-L1 adipocytes was investigated. As cells took on a more adipogenic phenotype, the insulin-stimulated versus the saturable basal MeAIB uptake increased by 5-fold. The induced transport activity showed properties characteristic of system A, with a Km value of 190 microM. The half-life of the induced system A activity was independent of de novo mRNA and protein synthesis and was not accelerated by ambient amino acids, therefore, it was mechanistically distinct from the previously described adaptive and hormonal regulation of system A. Inhibition of mitogen-activated protein kinase kinase by PD98059, Ras farnesylation by PD152440 and B581, p70(S6K) by rapamycin, and phosphatidylinositol 3-kinase (PI 3'-K) by wortmannin and LY294002 revealed that only wortmannin and LY294002 inhibited the insulin-induced MeAIB uptake with IC50 values close to that previously reported for inhibition of PI 3'-K. These results suggest that the Ras/mitogen-activated protein kinase and pp70(S6K) insulin signaling pathways are neither required nor sufficient for insulin stimulation of MeAIB uptake, and activation of PI 3'-K or a wortmannin/LY294002-sensitive pathway may play an important role in regulation of system A transport by insulin in 3T3-L1 cells.
Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product (1987)

The iap gene in Escherichia coli is responsible for the isozyme conversion of alkaline phosphatase. We analyzed the 1,664-nucleotide sequence of a chromosomal DNA segment that contained the iap gene and its flanking regions. The predicted iap product contained 345 amino acids with an estimated molecular weight of 37,919. The 24-amino-acid sequence at the amino terminus showed features characteristic of a signal peptide. Two proteins of different sizes were identified by the maxicell method, one corresponding to the Iap protein and the other corresponding to the processed product without the signal peptide. Neither the isozyme-converting activity nor labeled Iap proteins were detected in the osmotic-shock fluid of cells carrying a multicopy iap plasmid. The Iap protein seems to be associated with the membrane.