gebhart/patrepeval huggingface dataset:
Collagen-Induced Arthritis (2003)

Collagen-induced arthritis (CIA) is a polyarthritis induced by sensitization of susceptible strains of animals with collagen II (the major collagen of hyaline cartilage). Because the original description of the model in rats by Trentham et al. (1), it has become clear that species including rats, mice, and primates can develop CIA. In this respect, the disease is quite different to adjuvant-induced arthritis, which appears to be a disease restricted to rats.
Oligoclonality of V β 3 TCR chains in the CD8+ T cell population of rheumatoid arthritis patients (1996)

It has been established that oligoclonal expansion is a common feature of the CD8+ T cell population, particularly within the CD8+ CD57+ lymphocyte subset. In addition, clonal malignancies involving CD8+ CD57+ T cells (large granulocytic lymphocytic leukemias) are often accompanied by rheumatoid arthritis, Felty's syndrome, or both. Therefore, to identify disease-related alterations in the CD8+ T cell repertoire, we have compared the patterns of oligoclonality in the CD8+ T cells of rheumatoid arthritis patients (n = 32) with those of age-matched controls (n = 25). By using a multiplex PCR assay for the CDR3 length of TCR beta-chains, we have found a striking increase in the frequency of CD8+ oligoclonality involving V beta 3 TCR: 50% of the rheumatoid arthritis patients had evidence of oligoclonality in this TCR family compared with 4% of controls (p < 0.0002). In addition, two unrelated RA patients had clonally dominant CD8+ T cell beta receptors that were identical in amino acid sequence, suggesting selection by a common Ag. An analysis of a subset of RA patients with mAbs specific for V beta 3 TCR revealed the presence of clonal expansion in a minority of patients usually, but not exclusively, involving the CD57+ subset. These data define a phenotype of the T cell repertoire that is strongly associated with rheumatoid arthritis; the mechanisms and genetic and environmental factors that explain this phenomenon remain to be defined.
A Prospective Observational Study of Candidemia: Epidemiology, Therapy, and Influences on Mortality in Hospitalized Adult and Pediatric Patients (2003)

We conducted a prospective, multicenter observational study of adults (n=1447) and children (n=144) with candidemia at tertiary care centers in the United States in parallel with a candidemia treatment trial that included nonneutropenic adults. Candida albicans was the most common bloodstream isolate recovered from adults and children (45% vs. 49%) and was associated with high mortality (47% among adults vs. 29% among children). Three-month survival was better among children than among adults (76% vs. 54%; P<.001). Most children received amphotericin B as initial therapy, whereas most adults received fluconazole. In adults, Candida parapsilosis fungemia was associated with lower mortality than was non-parapsilosis candidemia (24% vs. 46%; P<.001). Mortality was similar among subjects with Candida glabrata or non-glabrata candidemia; mortality was also similar among subjects with C. glabrata candidemia who received fluconazole rather than other antifungal therapy. Subjects in the observational cohort had higher Acute Physiology and Chronic Health Evaluation II scores than did participants in the clinical trial (18.6 vs. 16.1), which suggests that the former subjects are more often excluded from therapeutic trials.
RNA polymerase II stalled at a thymine dimer: footprint and effect on excision repair (1997)

Bulky lesions in the template strand block the progression of RNA polymerase II (RNAP II) and are repaired more rapidly than lesions in the non-transcribed strand, which do not block transcription. In order to better understand the basis of this transcription-coupled repair we developed an in vitro system with purified transcription and nucleotide excision repair proteins and a plasmid containing the adenovirus major late promoter and a thymine dimer in the template strand downstream of the transcription start site. The footprint of RNAP II stalled at the thymine dimer, obtained using DNase I, lambda exonuclease and T4 polymerase 3'-->5'exonuclease, covers approximately 40 nt and is nearly symmetrical around the dimer. The ternary complex formed at the lesion site is rather stable, with a half-life of approximately 20 h. Surprisingly, addition of human repair proteins results in repair of transcription-blocking dimers in the ternary complex. The blocked polymerase neither inhibits nor stimulates repair and repair is observed in the absence of CSB protein, the putative human transcription-repair coupling factor.
AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals (2000)

Introduction of transgene DNA may lead to specific degradation of RNAs that are homologous to the transgene transcribed sequence through phenomena named post-transcriptional gene silencing (PTGS) in plants, quelling in fungi, and RNA interference (RNAi) in animals. It was shown previously that PTGS, quelling, and RNAi require a set of related proteins (SGS2, QDE-1, and EGO-1, respectively). Here we report the isolation of Arabidopsis mutants impaired in PTGS which are affected at the Argonaute1 (AGO1) locus. AGO1 is similar to QDE-2 required for quelling and RDE-1 required for RNAi. Sequencing of ago1 mutants revealed one amino acid essential for PTGS that is also present in QDE-2 and RDE-1 in a highly conserved motif. Taken together, these results confirm the hypothesis that these processes derive from a common ancestral mechanism that controls expression of invading nucleic acid molecules at the post-transcriptional level. As opposed to rde-1 and qde-2 mutants, which are viable, ago1 mutants display several developmental abnormalities, including sterility. These results raise the possibility that PTGS, or at least some of its elements, could participate in the regulation of gene expression during development in plants.
Histidine residues near the N terminus of staphylococcal alpha-toxin as reporters of regions that are critical for oligomerization and pore formation (1994)

Chemical modification of histidine residues in staphylococcal alpha-toxin leads to loss of functional activity. Site-directed mutants of the toxin in which each of the four histidine residues was replaced by several amino acids were therefore produced. The mutant proteins were purified and characterized. Exchange of H-259 or H-144 was sometimes tolerated without reduction in hemolytic activity. These histidine residues are thus not essential for toxin function. Exchange of H-35 and H-48, however, had marked effects. H-35 mutant toxins bound with high affinity to rabbit erythrocytes but displayed faulty oligomerization and were unable to form pores. H-48 mutant toxins also had severely impaired hemolytic activity due probably to faulty hexamerization. We interpret these results to indicate that the N-terminal domain of alpha-toxin in the region of H-35 and H-48 is involved in protomer-protomer interactions that underlie the hexamerization and pore-forming process.
APOBEC3G Inhibits DNA Strand Transfer during HIV-1 Reverse Transcription (2007)

Human APOBEC3G (hA3G) has been identified as an anti-HIV-1 host factor. The presence of hA3G in HIV-1 strongly inhibits the ability of the virus to produce new viral DNA upon infection. In this report, we demonstrate that the reduction of late viral DNA synthesis is due to the inhibition by hA3G of the strand transfer steps that occur during reverse transcription. Analysis of viral cDNA intermediates in vivo reveals that hA3G causes an inhibition of the minus and plus strand transfers, without having a significant impact on DNA elongation. Using an in vitro system to measure minus strand transfer similarly shows a dose-dependent reduction of strand transfer by hA3G. This inhibition of strand transfer occurs independently the editing activity of hA3G and is correlated with its ability to prevent RNaseH degradation of the template RNA.
Long-term effectiveness of asfotase alfa in adults with pediatric-onset hypophosphatasia in routine clinical practice (2020)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Genetic Analysis of Two Bile Salt Hydrolase Activities in Lactobacillus acidophilus NCFM (2005)

Two genes, bshA and bshB, encoding bile salt hydrolase enzymes (EC 3.5.1.24) were identified in the genome sequence of Lactobacillus acidophilus NCFM. Targeted inactivation of these genes via chromosomal insertion of an integration vector demonstrated different substrate specificities for these two enzymes.
A novel transgenic mouse model of CBS-deficient homocystinuria does not incur hepatic steatosis or fibrosis and exhibits a hypercoagulative phenotype that is ameliorated by betaine treatment (2010)

Cystathionine beta-synthase (CBS) catalyzes the condensation of homocysteine (Hcy) and serine to cystathionine, which is then hydrolyzed to cysteine by cystathionine gamma-lyase. Inactivation of CBS results in CBS-deficient homocystinuria more commonly referred to as classical homocystinuria, which, if untreated, results in mental retardation, thromboembolic complications, and a range of connective tissue disorders. The molecular mechanisms that underlie the pathology of this disease are poorly understood. We report here the generation of a new mouse model of classical homocystinuria in which the mouse cbs gene is inactivated and that exhibits low-level expression of the human CBS transgene under the control of the human CBS promoter. This mouse model, designated "human only" (HO), exhibits severe elevations in both plasma and tissue levels of Hcy, methionine, S-adenosylmethionine, and S-adenosylhomocysteine and a concomitant decrease in plasma and hepatic levels of cysteine. HO mice exhibit mild hepatopathy but, in contrast to previous models of classical homocystinuria, do not incur hepatic steatosis, fibrosis, or neonatal death with approximately 90% of HO mice living for at least 6months. Tail bleeding determinations indicate that HO mice are in a hypercoagulative state that is significantly ameliorated by betaine treatment in a manner that recapitulates the disease as it occurs in humans. Our findings indicate that this mouse model will be a valuable tool in the study of pathogenesis in classical homocystinuria and the rational design of novel treatments.
Human prostatic smooth muscle cells in culture: Estradiol enhances expression of smooth muscle cell‐specific markers (1997)

Smooth muscle cells (SMCs) constitute a major cellular component of prostatic stroma. SMC tension plays an important role in urethral obstruction secondary to benign prostatic hyperplasia (BPH). We have developed an in vitro procedure for the propagation of human prostatic SMCs. Tissue specimens from patients undergoing radical prostatectomy or cystectomy were enzymatically disaggregated and cultured in MCDB-131 medium supplemented with horse serum, insulin, conditioned medium from the tumor cell line CRL-5813, and steroid hormones. The medium was assembled on the basis of the effects these supplements have on the growth of SMC cultures and on the expression of the two markers desmin and smooth muscle myosin. Addition of 0.1 μM of estradiol to the growth medium dramatically increased expression of these SMC-specific markers. Dihydrotestosterone (DHT) and hydrocortisone had a similar, albeit less pronounced effect. At three to five passages, about two thirds of the cells were immunohistologically positive for smooth muscle myosin or desmin. Almost all cells were positive for the myofibroblast marker smooth muscle α-actin throughout 10 passages and more. In SMC cultures, cells staining for smooth muscle myosin and desmin were found to seek direct contact to myofibroblasts. They grew in aggregates on a layer of myofibroblasts which adhered to the surface of the culture vessel. As revealed by transmission electron microscopy the cultured cells exhibited morphological features of myofibroblasts. Characteristics of smooth muscle cells, such as prominent bundles of microfilaments associated with dense bodies, basal laminae investing the cells, and numerous caveolae at the cell surfaces were regularly observed in cultures of low passages. After several passages, these features were markedly decreased and organelles of the biosynthetic system became more prominent. In summary, we present an in vitro model of prostatic SMCs and demonstrate that steroid hormones have characteristic effects on these cells. SMC cultures are expected to facilitate investigation of the functions and properties of human prostatic SMCs. Prostate 30:117–129, 1997. © 1997 Wiley-Liss, Inc.
Adaptive texture maps (2002)

We introduce several new variants of hardware-based adaptive texture maps and present applications in two, three, and four dimensions. In particular, we discuss representations of images and volumes with locally adaptive resolution, lossless compression of light fields, and vector quantization of volume data. All corresponding texture decoders were successfully integrated into the programmable texturing pipeline of commercial off-the-shelf graphics hardware.
Emerging technologies on silicon (2005)

Moore's law and its mapping into the ITRS have been the most powerful drivers of the progress in microelectronics in the last decades. This paper discusses possible futures while approaching the "end-of-the-roadmap". We discuss long term evolutionary paths as well as some more disruptive approaches of the different building blocks of an information processing system - namely the processing unit, memory, interface and communication, and the interconnection of these elements -, taking into account some of the expected fundamental and practical limits. An enhanced progress is expected from a synergetic development of the building blocks and of the system architecture, with some exploratory paths departing from the present way of thinking, e.g. through bio-inspired architectures.
A Service-Oriented Data-Composition Architecture for Integrated Asset Management (2006)

Abstract The goal of an Integrated Asset Management (IAM) framework for the oil and gas industry is twofold. From the end users’ perspective, it should offer a single, easy-to-use user interface for specifying and executing a variety of workflows from reservoir simulations to economic evaluation. The framework should not require the user to be an expert in any of the underlying software applications; in fact, the details of selecting, configuring, and invoking the underlying software modules should be hidden from the end user. From the software development perspective, the IAM framework should facilitate seamless interaction of diverse and independently developed applications that accomplish various sub-tasks in the overall workflow. For instance, it should be possible to pipe the output of a reservoir simulator running on one machine to a forecasting and optimization toolkit running on another and in turn piping its output to a third piece of software that can convert the information into a set of reports in a specified format.
New antiinflammatory agents. 2. 5-Phenyl-3H-imidazo[4,5-c][1,8]naphthyridin-4(5H)-ones: a new class of nonsteroidal antiinflammatory agents with potent activity like glucocorticoids (1992)

We previously described new antiinflammatory agents, 4-hydroxy-2-oxo-1-phenyl-1H-1,8-naphthyridine-3-carboxamides 1. Further modification of the compounds bearing 1-phenyl-1,8-naphthyridin-2-one as a mother skeleton led to 5-phenylimidazo[4,5-c][1,8]naphthyridin-4(5H)-one derivatives 2 and 3. Regioselective synthesis of these compounds bearing a substituent at the 1- or 3-position was conducted according to the method shown in Schemes I and II. In this series of compounds, antiinflammatory activities were greatly influenced by the position and nature of substituents on imidazole. 3-Alkyl or 3-benzyl substitution result in the potent activity, but 1-substitution did not. Minor modification of the benzyl group reduced or eliminated the activity. Detailed examination of structure-activity relationships led to 3-benzyl-5-phenyl-3H-imidazo[4,5-c][1,8]naphthyridin-4(5H)-one (22), which exhibited potent oral antiinflammatory activities in carrageenan-, zymosan-, and reversed passive Arthus reaction-induced rat paw edemas (ED40 = 5.3, 0.37 mg/kg, ED50 = 0.47 mg/kg, respectively). This broad activity of 22 was like that of glucocorticoids. Compound 22 did not affect activities of CO and 5-LO enzymes and receptor binding of various ligands. As one of the mechanisms of action, induction of release of glucocorticoids was postulated. These results suggest that 22 represents a novel class of antiinflammatory agents.
Planarization Process for Fabricating Multi-Layer Nb Integrated Circuits Incorporating Top Active Layer (2009)

We have developed an advanced process for fabricating a next-generation multi-layer Nb integrated circuit structure incorporating a top active layer. In this structure, the passive-transmission-line (PTL) layer is placed between the top active layer and a DC-bias current layer at the bottom. This structure will make it possible to flexibly design active circuits and PTL wiring, and will also enable active circuits to be effectively shielded from magnetic fields generated by a large DC-bias current. Both the DC-bias current layer and the PTL layer are planarized; however, the top active layer is fabricated without planarization. To fabricate this new structure, it was necessary to achieve a better planarization process for junctions formed over underlying Nb patterns. The combined process we developed comprising additional SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> deposition and additional mechanical polishing after the standard Caldera planarization process results in superior planarization for junction formation. We obtained excellent characteristics of junctions formed over underlying pattern edges when they were fabricated on surfaces planarized using this new process. Using the process, we fabricated new 10-Nb-layer integrated circuit structures and estimated the characteristics of their circuit elements.
Unicompartmental and bicompartmental arthroplasty of the knee with a finned metal tibial-plateau implant. (1985)

We followed a series of ten patients (ten knees) who had a unicompartmental and twenty patients (twenty-two knees) who had a bicompartmental arthroplasty of the knee, in which a finned metal tibial-plateau implant had been used, for two to fourteen years (average, five years) postoperatively. According to the modified criteria of MacIntosh and Hunter, thirty knees (94 per cent) had a good result and two (6 per cent), a fair result. There were two complications: one intraoperative and one postoperative fracture of the tibial plateau. One patient with rheumatoid arthritis required a revision to a total knee arthroplasty at six months because of rapid progression of disease in the contralateral, untreated compartment. Our results suggest that with the proper indications this arthroplasty has a place in reconstructive surgery of the arthritic knee joint.
Effect of light intensity upon lipid composition ofNitzschia closterium (Cylindrotheca fusiformis) (1974)

Total fatty acid, total sterol, fatty acids of specific lipid classes, and unsaturated fatty acids produced inNitzschia closterium were compared qualitatively and quantitatively as a function of changes in light intensity. Increased levels of total fatty acids were observed in cells grown at high light intensity when compared to cells grown at low light intensity. However, the percentage of unsaturated fatty acid decreased under high light conditions. Fatty acid analysis of triglyceride and 1,3 diglyceride fractions indicated an increase in levels of fatty acid at high light intensity when compared to low light intensity, while levels of polar lipid fatty acids increased at low light intensity. These analyses can be taken to indicate an increase in triglyceride and diglyceride at high light and a decrease in polar lipid at high light. Levels of free fatty acids did not differ significantly with light intensity. The levels of total sterol also were unaffected by changes in light intensity. However, levels of sterol isolated as free sterol and sterol associated in a yet unknown manner in the polar lipid fraction varied with changes in light intensity. Levels of polar lipid sterol increased at high light intensity compared to low light intensity, while the opposite was true for free sterol. The greatest percentage of total sterol was found in the polar lipid class regardless of light intensity.
Macroparasite Group Report (1995)

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Understanding optical emissions from electrically stressed insulating polymers: electroluminescence in poly(ethylene terephthalate) and poly(ethylene 2,6-naphthalate) films (1997)

Wear-out and breakdown of polymers used as insulating materials are closely related to the dissipation of electrostatic energy in space charge regions. A fraction of this energy is radiated off by electroluminescence which can be considered as a pre-breakdown warning and provides a probe to investigate the mechanisms leading to structural degradation. Electroluminescence emission from two aromatic polyesters is studied - poly(ethylene terephthalate) and poly(ethylene 2,6-naphthalate). We investigate the excitation processes of the luminescent centres, the nature of the centres, and the relationship of the emission features to electrical ageing. Sample electroluminescence is excited by dc and ac voltages under a uniform field configuration. The discussion relies on the analysis of the charge transport process in the luminescent regime, the acquisition of electroluminescence and photoluminescence spectra, and the investigation of the field effect on photoluminescence.
Diamond as an electronic material (2008)

The combination of extreme electronic and thermal properties found in synthetic diamond produced by chemical vapor deposition (CVD) is raising considerable excitement over its potential use as a semiconductor material. Experimental studies have demonstrated charge-carrier mobilities1 of >3000 cm2V−1s−1 and thermal conductivities2 >2000 Wm−1K−1. The material has been predicted to have a breakdown field strength in excess of 10 MVcm−1. These figures suggest that, providing a range of technical challenges can be overcome, diamond would be particularly well suited to operation as a semiconductor material wherever high frequencies, high powers, high temperatures or high voltages are required.