gebhart/patrepeval huggingface dataset:
Characterization of the expression of MHC proteins in human embryonic stem cells (2002)

Human embryonic stem (ES) cells are pluripotent cells that may be used in transplantation medicine. These cells can be induced to differentiate into cells from the three embryonic germ layers both in vivo and in vitro. To determine whether human ES cells might be rejected after transplantation, we examined cell surface expression of the MHC proteins in these cells. Our results show very low expression levels of MHC class I (MHC-I) proteins on the surface of human ES cells that moderately increase on in vitro or in vivo differentiation. A dramatic induction of MHC-I proteins was observed when the cells were treated with IFN-gamma but not with IFN-alpha or -beta. However, all three IFNs induced expression of MHC-I proteins in differentiated human ES cells. MHC-II proteins and HLA-G were not expressed on the surface of undifferentiated or differentiated cells. Ligands for natural killer cell receptors were either absent or expressed in very low levels in human ES cells and in their differentiated derivatives. In accordance, natural killer cytotoxic assays demonstrated only limited lysis of both undifferentiated and differentiated cells. To initiate a histocompatibility databank of human ES cells, we have isotyped several of the published ES cell lines for their human leukocyte antigens. In conclusion, our results demonstrate that human ES cells can express high levels of MHC-I proteins and thus may be rejected on transplantation.
Tau Nitration Occurs at Tyrosine 29 in the Fibrillar Lesions of Alzheimer's Disease and Other Tauopathies (2006)

The neurodegenerative tauopathies are a clinically diverse group of diseases typified by the pathological self-assembly of the microtubule-associated tau protein. Although tau nitration is believed to influence the pathogenesis of these diseases, the precise residues modified, and the resulting effects on tau function, remain enigmatic. Previously, we demonstrated that nitration at residue Tyr29 markedly inhibits the ability of tau to self-associate and stabilize the microtubule lattice (Reynolds et al., 2005b, 2006). Here, we report the first monoclonal antibody to detect nitration in a protein-specific and site-selective manner. This reagent, termed Tau-nY29, recognizes tau only when nitrated at residue Tyr29. It does not cross-react with wild-type tau, tau mutants singly nitrated at Tyr18, Tyr197, and Tyr394, or other proteins known to be nitrated in neurodegenerative diseases. By Western blot analysis, Tau-nY29 detects soluble tau and paired helical filament tau from severely affected Alzheimer's brain but fails to recognize tau from normal aged brain. This observation suggests that nitration at Tyr29 is a disease-related event that may alter the intrinsic ability of tau to self-polymerize. In Alzheimer's brain, Tau-nY29 labels the fibrillar triad of tau lesions, including neurofibrillary tangles, neuritic plaques, and, to a lesser extent, neuropil threads. Intriguingly, although Tau-nY29 stains both the neuronal and glial tau pathology of Pick disease, it detects only the neuronal pathology in corticobasal degeneration and progressive supranuclear palsy without labeling the predominant glial pathology. Collectively, our findings provide the first direct evidence that site-specific tau nitration is linked to the progression of the neurodegenerative tauopathies.
Balancing the hidden and exposed node problems with power control in CSMA/CA-based wireless networks (2005)

Media access control (MAC) mechanism design is a key problem in wireless networking. One problem is hidden nodes, which are allowed to transmit, but which interfere with a receiver causing a collision. Another problem is exposed nodes, which are not allowed to transmit although they would not interfere, thus limiting spatial reuse. MAC designs, like IEEE 802.11, try to solve both of these problems, but are not wholly successful. Other MAC designs attempt to control the transmit power, both to lower power use and to minimize exposed nodes. This results in a worsened hidden node problem. We present a power control MAC that balances the hidden and exposed node problem. The idea is to use no more power than is needed to eliminate the hidden nodes, thus limiting the exposed nodes. We present simulation results that show our design outperforms both 802.11 and previous power control MACs.
Evolutionary distinct mechanisms regulate apolipoprotein A-I gene expression: differences between avian and mammalian apoA-I gene transcription control regions. (1992)

In mammals, the apolipoprotein (apo) A-I gene is expressed predominantly in liver and intestine, while in avian species it is expressed in all tissues. Although liver and intestine are the major sites of chicken apoA-I mRNA synthesis, there are appreciable amounts of apoA-I mRNA in kidney, ovary/testes, brain, lung, skeletal, and heart muscle. In this study, the nucleotide sequences of the chicken apoA-I gene and its 5' flanking region, as well as the sequences involved in the expression of this gene, have been determined. The gene spans 1.5 kilobases and contains 4 exons and 3 introns, closely resembling the mammalian apoA-I gene. To determine the sequences involved in the expression of the chicken apoA-I gene, plasmid constructs containing serial deletions of the 5' flanking region of the chicken apoA-I gene fused to the bacterial chloramphenicol acetyltransferase (CAT) gene were transfected in human hepatoma (HepG2), colon carcinoma (Caco2), epithelial (Hela), mouse embryonal fibroblast (NIH3T3) cells, and quail myoblasts (QMLA29). The shortest deletion construct, containing 60 bp of the 5' upstream region, was sufficient for maximal transcriptional activity in all cell lines tested. This region contains a short sequence (nucleotides -60 to -54) that is highly conserved in birds and mammals, and an Sp1 binding site. Although the sequence between nucleotides -232 and -101 of the 5' region of the chicken apoA-I gene is partially homologous to the hepatic cell-specific enhancer of the mammalian apoA-I gene (located between nucleotides -222 and -110 upstream of the human apoA-I gene transcription start site), this chicken sequence is transcriptionally inactive in HepG2 cells. These results suggest that differences in the cis-acting regulatory elements of the apoA-I gene play a fundamental role in determining the differences in the tissue-specific expression of this gene in avian and mammalian species.
Volume‐selective 3D turbo spin echo imaging for vascular wall imaging and distensibility measurement (2003)

A volume-selective TSE method has been used for carotid artery wall imaging and measurement of distensibility in normal subjects. Larger coverage of the vessel, and therefore more information for clinical diagnostics, was achieved with the same overall scan time with an SNR comparable to that of 2D full FOV images.
The Phosphodiesterase-5 Inhibitor Vardenafil Is a Potent Inhibitor of ABCB1/P-Glycoprotein Transporter (2011)

One of the major causes of chemotherapy failure in cancer treatment is multidrug resistance (MDR) which is mediated by the ABCB1/P-glycoprotein. Previously, through the use of an extensive screening process, we found that vardenafil, a phosphodiesterase 5 (PDE-5) inhibitor significantly reverses MDR in ABCB1 overexpressing cancer cells, and its efficacy was greater than that of tadalafil, another PDE-5 inhibitor. The present study was designed to determine the reversal mechanisms of vardenafil and tadalafil on ABC transporters-mediated MDR. Vardenafil or tadalafil alone, at concentrations up to 20 µM, had no significant toxic effects on any of the cell lines used in this study, regardless of their membrane transporter status. However, vardenafil when used in combination with anticancer substrates of ABCB1, significantly potentiated their cytotoxicity in ABCB1 overexpressing cells in a concentration-dependent manner, and this effect was greater than that of tadalafil. The sensitivity of the parenteral cell lines to cytotoxic anticancer drugs was not significantly altered by vardenafil. The differential effects of vardenafil and tadalafil appear to be specific for the ABCB1 transporter as both vardenafil and tadalafil had no significant effect on the reversal of drug resistance conferred by ABCC1 (MRP1) and ABCG2 (BCRP) transporters. Vardenafil significantly increased the intracellular accumulation of [(3)H]-paclitaxel in the ABCB1 overexpressing KB-C2 cells. In addition, vardenafil significantly stimulated the ATPase activity of ABCB1 and inhibited the photolabeling of ABCB1 with [(125)I]-IAAP. Furthermore, Western blot analysis indicated the incubation of cells with either vardenafil or tadalafil for 72 h did not alter ABCB1 protein expression. Overall, our results suggest that vardenafil reverses ABCB1-mediated MDR by directly blocking the drug efflux function of ABCB1.
Type III Protein Secretion Systems in Bacterial Pathogens of Animals and Plants (1998)

Various gram-negative animal and plant pathogens use a novel, sec-independent protein secretion system as a basic virulence mechanism. It is becoming increasingly clear that these so-called type III secretion systems inject (translocate) proteins into the cytosol of eukaryotic cells, where the translocated proteins facilitate bacterial pathogenesis by specifically interfering with host cell signal transduction and other cellular processes. Accordingly, some type III secretion systems are activated by bacterial contact with host cell surfaces. Individual type III secretion systems direct the secretion and translocation of a variety of unrelated proteins, which account for species-specific pathogenesis phenotypes. In contrast to the secreted virulence factors, most of the 15 to 20 membrane-associated proteins which constitute the type III secretion apparatus are conserved among different pathogens. Most of the inner membrane components of the type III secretion apparatus show additional homologies to flagellar biosynthetic proteins, while a conserved outer membrane factor is similar to secretins from type II and other secretion pathways. Structurally conserved chaperones which specifically bind to individual secreted proteins play an important role in type III protein secretion, apparently by preventing premature interactions of the secreted factors with other proteins. The genes encoding type III secretion systems are clustered, and various pieces of evidence suggest that these systems have been acquired by horizontal genetic transfer during evolution. Expression of type III secretion systems is coordinately regulated in response to host environmental stimuli by networks of transcription factors. This review comprises a comparison of the structure, function, regulation, and impact on host cells of the type III secretion systems in the animal pathogens Yersinia spp., Pseudomonas aeruginosa, Shigella flexneri, Salmonella typhimurium, enteropathogenic Escherichia coli, and Chlamydia spp. and the plant pathogens Pseudomonas syringae, Erwinia spp., Ralstonia solanacearum, Xanthomonas campestris, and Rhizobium spp.
Study of the Hyperthermal Proton Bombardment Effects on Self-Assembled Monolayers of Dodecanethiol on Au(111) (2008)

Proton bombardment on self-assembled monolayers (SAMs) of dodecanethiol formed on a gold surface is performed and its effect is studied by scanning tunneling microscope (STM) and time-of-flight secondary ion mass spectrometry (TOF−SIMS). STM gives clear evidence that a relatively uniform layer of organic nanoclusters with different sizes and densities can be created on the surface. Analysis of the mass spectra collected from the SAM samples reveals that large hydrocarbon fragments from the bombarded sample area show higher intensity than those from the virgin area, which is a strong indication that selective C−H bond cleavage and cross-linking are induced by the proton beam bombardment. We demonstrate that the size and density of the clusters can be harnessed by controlling the proton beam energy and fluence. The clusters grow bigger, at the expense of a decreasing number density, with increasing proton energy or fluence.
Beneficial Effect of Brewers′ Yeast Extract on Daily Activity in a Murine Model of Chronic Fatigue Syndrome (2006)

The aim of this study was to assess the effect of Brewers' yeast extract (BYE) on daily activity in a mouse model of chronic fatigue syndrome (CFS). CFS was induced by repeated injection of Brucella abortus (BA) antigen every 2 weeks. BYE was orally administered to mice in a dose of 2 g per kg per day for 2 weeks before injecting BA and for 4 weeks thereafter. We evaluated daily running activity in mice receiving BYE as compared with that in untreated mice. Weekly variation of body weight (BW) and survival in both groups was monitored during the observation period. Spleen weight (SW), SW/BW ratio, percent splenic follicular area and expression levels of interferon-gamma (IFN-gamma) and interleukin-10 (IL-10) mRNA in spleen were determined in both groups at the time of sacrifice. The daily activity during 2 weeks after the second BA injection was significantly higher in the treated group than in the control. There was no difference in BW between both groups through the experimental course. Two mice in the control died 2 and 7 days after the second injection, whereas no mice in the treated group died. Significantly decreased SW and SW/BW ratio were observed in the treated mice together with elevation of splenic follicular area. There were suppressed IFN-gamma and IL-10 mRNA levels in spleens from the treated mice. Our results suggest that BYE might have a protective effect on the marked reduction in activity following repeated BA injection via normalization of host immune responses.
Self‐maintenance capacity of CFU‐S (1980)

The numbers of CFU-S which developed in spleen colonies were measured 11 days after injection of irradiated mice with marrow from normal mice or mice which had been treated in one of a variety of ways. The broad spread of CFU-S numbers, seen by other authors, in colonies derived from normal marrow was confirmed. However, the range and distribution of CFU-S per colony was generally different in colonies derived from the marrow of mice which were recovering or had recovered from some form of depopulation. From the data obtained, the mean CFU-S/colony, M1, and the probability of self-renewal, p, of the CFU-S were calculated. These values are used to calculate the number of cell cycles undergone during development of the colony and, by making certain assumptions, the cell cycle time of the CFU-S. The plot of p against log M for the various samples measured should be linear if all CFU-S proliferate at the same rate in a growing colony. It is not linear, however, so that CFU-S obtained under different experimental conditions do not all undergo the same number of cycles. In general, treatments given to the mice result in a lowering of the capacity for self-renewal of their CFU-S and also to a shortening of their cell cycle time. Some of the possible implications of these findings are discussed.
Escherichia coli Shiga toxin. (2000)

The Stx family contains two types called Stx1 (verotoxin 1: VT1 or Shiga-like toxin: SLT1) and Stx2 (VT2, SLT2); both toxins are encoded by bacteriophages. Stx1 is identical to Shiga toxin produced by Shigella dysenteriae type I. Stx2 is heterogeneous and immunologically different from Stx1. Although many variations are found in Stx family, all Stx has an A-B structure: the A subunit has N-glycosidase activity and the B subunit binds to a membrane glycolipid, globotriaosylceramide (Gb3). The A subunit cleaves a single adenine residue from the 28S rRNA component of eukaryotic ribosomes, resulting in inhibition of protein synthesis. Stx-producing Escherichia coli (STEC) is known to cause hemorrhagic enterocolitis and hemolytic-uremic syndrome (HUS). Stx plays a role in the occurrence of blood in the feces and in the HUS by their action on the endothelial cells of blood vessels in the intestinal submucosa and in the renal glomeruli. Epidemiologically, Stx2 seems to be more important than Stx1 in development of HUS. The action of Stx is not limited to inhibition of protein synthesis. Stx induces macrophages to express tumor necrosis factor alpha (TNF-alpha), interleukin-1 beta (IL-1 beta), and interleukin-6 (IL-6) in vitro. These cytokines and lipopolysaccharide (LPS) are reported to increase the susceptibility of cells to Stx. A variety of cells such as tubular epithelial cells, may be targets for Stx-mediated apoptosis. Apoptosis is considered to contribute to the pathogenesis of HUS caused by STEC. In this review, recent progress in Stx-related research is summarized.
Changes in immunologic variables (TNF-a, sCD8 and sCD4) during danazol treatment in patients with endometriosis. (1997)

This study indicates that danazol significantly reduces endometriosis-associated autoimmune abnormalities.
Oxidative folding of cystine‐rich peptides vs regioselective cysteine pairing strategies (1996)

The methodology of regioselective cysteine pairings in synthetic multiple-cystine peptides has progressed in the past years to an efficiency that allows for at least three specific inter- and intrachain disulfide bridgings. Conformational studies on various multiple-cystine peptides like hormones, protease inhibitors, and toxins revealed that these bioactive peptides, generated by posttranslational processing of precursor proteins, are folded into miniprotein-like compact globular structures of remarkable stability. This strongly suggests protein domain or subdomain properties of these families of peptides, and thus sufficient sequence-encoded information for correct oxidative refolding under appropriate experimental conditions. From intensive research on the mechanisms and pathways of oxidative refolding of proteins in vivo and in vitro, the efficient methods have emerged for simulating nature in the regeneration of native folds not only for intact proteins, but also for protein domains and subdomains. In fact, the results obtained in the oxidative folding of excised protein fragments and of relatively low mass products of posttranslational processings show that this procedure is indeed a simple way of preparing peptides with several disulfide bonds, if optimization of reaction conditions is performed in terms of redox buffer, temperature, and additives capable of disrupting aggregates and of stabilizing nascent secondary structures. Moreover, with increased knowledge about stable, small natural cystine frameworks, their use instead of artificial templates should facilitate engineering of synthetic miniproteins with specific conformation and tailored functions.
Comparison of Visual-Manual and Voice Interaction With Contemporary Navigation System HMIs (2005)

&lt;div class="htmlview paragraph"&gt;Typically, driver interactions with in-vehicle devices such as navigation systems have been accomplished using a visual-manual interface. As a result of recent advances in technology, voice activated interfaces are being introduced, which reduce or eliminate the need for manual inputs and related visual scanning. This paper compares driver use of contemporary examples of the 2 different types of interface for several types of navigation destination entry tasks based on over-the-road evaluations. These data include glance behavior, HMI interactions (manual inputs, etc.), driver/vehicle response and performance including lane deviations, and subjective ratings. In general, the results show that, for a given task, the example contemporary voice activated systems result in fewer glances, shorter glance durations, fewer entry steps, improved driver/vehicle performance, and improved subjective ratings for ease of task accomplishment and mental workload.&lt;/div&gt;
Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid (1994)

The sequence of a 2,437-bp DNA segment from the naphthalene upper catabolic pathway operon of plasmid NAH7 was determined. This segment contains three large open reading frames designated nahQ', nahE, and nahD. The first of these is the 3' end of an open reading frame that has no known function, the second (993 bp) encodes trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (deduced molecular weight, 36,640), and the third (609 bp) encodes 2-hydroxychromene-2-carboxylate isomerase (deduced molecular weight, 23,031). This DNA has a high degree of sequence homology (greater than 91% for the first 2161 bp) with a DNA segment from the dox (dibenzothiophene oxidation) operon of Pseudomonas sp. strain C18, which encodes a pathway analogous to that encoded by NAH7. However, 84 bp downstream from nahD, the last gene in the nah operon, this homology ends. This 84-bp sequence at the downstream end of nah and dox homology has 76% homology to a sequence that occurs just upstream of the nah promoter in NAH7. These directly repeated 84-bp sequences thus encompass the upper-pathway nah operon and constitute the ends of a highly conserved region.
Ultra-shallow in-situ-doped raised source/drain structure for sub-tenth micron CMOS (2002)

A new raised source/drain (RSD) structure is proposed, which combines facet controlled in-situ-doped selective Si epitaxial growth (SEG) and solid-phase diffusion (SPD). This can provide ultra-shallow junctions without sacrificing the parasitic resistance or capacitance. 0.1 /spl mu/m pMOSFETs with 20 nm deep junctions exhibiting excellent electrical characteristics and reliability were demonstrated. CMOS process compatibility was also confirmed.
Comparison of Fasciotomy Wound Closures Using Traditional Dressing Changes and the Vacuum-Assisted Closure Device (2009)

Fasciotomy wounds can be a major contributor to length of stay for patients as well as a difficult reconstructive challenge. Once the compartment pressure has been relieved and stabilized, the wound should be closed as quickly and early as possible to avoid later complications. Skin grafting can lead to morbidity and scarring at both the donor and fasciotomy site. Primary closure results in a more functional and esthetic outcome with less morbidity for the patient, but can often be difficult to achieve secondary to edema, skin retraction, and skin edge necrosis. Our objective was to examine fasciotomy wound outcomes, including time to definitive closure, comparing traditional wet-to-dry dressings, and the vacuum-assisted closure (VAC) device. This retrospective chart review included a consecutive series of patients over a 10-year period. This series included 458 patients who underwent 804 fasciotomies. Of these fasciotomy wounds, 438 received exclusively VAC. dressings, 270 received only normal saline wet-to-dry dressings, and 96 were treated with a combination of both. Of the sample, 408 patients were treated with exclusively VAC therapy or wet-to-dry dressings and 50 patients were treated with a combination of both. In comparing all wounds, there was a statistically significant higher rate of primary closure using the VAC versus traditional wet-to-dry dressings (P < 0.05 for lower extremities and P < 0.03 for upper extremities). The time to primary closure of wounds was shorter in the VAC. group in comparison with the non-VAC group. This study has shown that the use of the VAC for fasciotomy wound closure results in a higher rate of primary closure versus traditional wet-to-dry dressings. In addition, the time to primary closure of wounds or time to skin grafting is shorter when the VAC was employed. The VAC used in the described settings decreases hospitalization time, allows for earlier rehabilitation, and ultimately leads to increased patient satisfaction.