gebhart/patrepeval huggingface dataset:
Nitric Oxide Synthase in Atherosclerosis and Vascular Injury (2000)

Gene therapy aims to intervene in a disease process by transfer and expression of specific genes in a target tissue or organ. Cardiovascular gene therapy in humans remains in its infancy, but in the last decade, experimental gene transfer has emerged as a powerful biological tool to investigate the function of specific genes in vascular disease pathobiology. Nitric oxide synthases, the enzymes that produce nitric oxide, have received considerable attention as potential candidates for vascular gene therapy because nitric oxide has pleiotropic antiatherogenic actions in the vessel wall, and abnormalities in nitric oxide biology are apparent very early in the atherogenic process. In this article, we review the use of nitric oxide synthases in experimental vascular gene therapy and assess the utility of these approaches for investigating the role of nitric oxide in atherosclerosis and their potential for human gene therapy.
Significant and Worthwhile Change in Teaching Practice (1990)

This paper addresses two questions: What is involved in bringing about significant and worthwhile change in teaching practices? How can or should research aid in this process? In order to do so, two related literatures will be explored—teacher change and learning to teach. These literatures will be used to develop a third perspective, which will be grounded in examples from a teacher change research project which is funded by the Office of Educational Research and Improvement (OERI), U.S. Department of Education. This perspective suggests that empirical premises derived from research ( Fenstermacher, 1986 ) be considered as warranted practice, which, in combination with teachers's practical knowledge, become the content of reflective teacher change. It also suggests that practice should be viewed as activity embedded in theory. The paper concludes with suggestions for ways of approaching the introduction of research into teachers' ways of thinking.
Increased expression of the NG2 chondroitin-sulfate proteoglycan after brain injury (1994)

Injury to the adult mammalian CNS results in reactive changes among the glial cells surrounding the site of damage. Recently, an unusual class of glial cells has been identified within the intact adult rat cerebellum on the basis of the expression of the NG2 chondroitin-sulfate proteoglycan (Levine and Card, 1987). To determine whether the cells that express the NG2 proteoglycan show reactive changes after injury, small puncture lesions were made into the cerebelli of adult rats, and changes among astrocytes, microglia and NG2-positive cells were examined using immunohistochemical staining with cell type-specific marker antibodies. Beginning at 24 hr after lesion, NG2-positive cells immediately adjacent to the lesion site bound the anti-NG2 antibodies more heavily than cells within the undamaged areas of the cerebellum. This increase in anti-NG2 immunoreactivity was transient, reaching a maximum at 7 d postlesion and declining slowly thereafter. The increase in anti-NG2 immunoreactivity was accompanied by an increase in the levels of mRNA encoding the NG2 core protein as demonstrated by in situ hybridization. NG2-positive cells adjacent to the lesion site incorporated 3H-thymidine into their nuclei beginning at 24 hr postlesion and increased in number. Concurrent with these changes, microglia became activated and increased in number, monocytes invaded the damaged tissue, and an astrocytic scar formed. These observations demonstrate that the cells that express the NG2 proteoglycan are a reactive cell type that responds to brain injury. The increased expression of the NG2 chondroitin-sulfate proteoglycan may contribute to the failure of damaged CNS axons to regenerate successfully.
Identifying and managing adverse environmental health effects: 4. Pesticides. (2002)

Pesticide exposure can cause many different health effects, from acute problems such as dermatitis and asthma exacerbation to chronic problems such as chronic obstructive pulmonary disease and cancer. The resulting clinical presentations are undifferentiated, and specific knowledge of the links to environmental exposures is often required for effective diagnosis. In this article we illustrate the use of the CH2OPD2 mnemonic (Community, Home, Hobbies, Occupation, Personal habits, Drugs and Diet), a history-taking tool that assists physicians in quickly identifying possible environmental exposures. We also provide clinical information on the epidemiology, clinical presentations, treatment and prevention of pesticide exposures.
DAD1 Is Required for the Function and the Structural Integrity of the Oligosaccharyltransferase Complex (1998)

Asparagine-linked glycosylation is a highly conserved protein modification reaction that occurs in all eukaryotic organisms. The oligosaccharyltransferase (OST), which has its active site exposed on the luminal face of the endoplasmic reticulum (ER), catalyzes the transfer of preassembled high mannose oligosaccharides onto certain asparagine residues of nascent polypeptides. The mammalian OST complex was initially thought to be composed of three transmembrane proteins, ribophorin I (RI), ribophorin II (RII), and OST48. Most recently, a small integral membrane protein of 12 kDa called DAD1 has been identified as an additional member of the mammalian OST complex. A point mutation in the DAD1 gene is responsible for the temperature-sensitive phenotype of a baby hamster kidney-derived cell line (tsBN7) that undergoes apoptosis at the non-permissive temperature. Furthermore, the mutant protein DAD1 is not detectable in tsBN7 cells 6 h after shifting the cells to the non-permissive temperature. This temperature-sensitive cell line offered unique opportunities to study the effects caused by the loss of one OST subunit on the other three subunits and also on N-linked glycosylation. Western blot analysis of cell lysates showed that after 6 h at the non-permissive temperature, steady-state levels of the ribophorins were reduced by about 50%, and OST48 was barely detectable. On the other hand, steady-state levels of other components of the rough ER, such as the alpha-subunits of the TRAP (translocon-associated membrane protein) and the Sec61 complex, which are components of the translocation apparatus, are not affected by the instability of the OST subunits. Furthermore, N-glycosylation of the ribophorins was seriously affected 6 h after shifting the cells to the non-permissive temperature, and after 12 h they were synthesized only in the non-glycosylated form. As may be expected, this defect in the OST complex at the non-permissive temperature caused also the underglycosylation of a secretory glycoprotein. We concluded that degradation of DAD1 at the non-permissive temperature not only affects the stability of OST48 and the ribophorins but also results in the functional inactivation of the OST complex.
Characterization of directed differentiation by high-throughput single-cell RNA-Seq (2014)

Directed differentiation of cells in vitro is a powerful approach for dissection of developmental pathways, disease modeling and regenerative medicine, but analysis of such systems is complicated by heterogeneous and asynchronous cellular responses to differentiation-inducing stimuli. To enable deep characterization of heterogeneous cell populations, we developed an efficient digital gene expression profiling protocol that enables surveying of mRNA in thousands of single cells at a time. We then applied this protocol to profile 12,832 cells collected at multiple time points during directed adipogenic differentiation of human adipose-derived stem/stromal cells in vitro. The resulting data reveal the major axes of cell-to-cell variation within and between time points, and an inverse relationship between inflammatory gene expression and lipid accumulation across cells from a single donor.
Loss Analysis of Single-Mode Fiber Splices (1977)

This paper analyses losses caused by the misalignment of two fibers joined in a splice. We consider the possibility that the two fibers of different dimensions are separated in longitudinal direction and are tilted or offset with respect to each other. Central to our discussion is the observation that the modes of single-mode fibers are very nearly gaussian in shape regardless of the fiber type step-index or graded-index. The splice losses are thus related to the corresponding losses of gaussian beams. We specify the relation between the actual mode field and the gaussian beam that matches this field optimally. The trade-off between slice tolerances with respect to tilt and offset is expressed as an “uncertainty principle. “ Because of the near-gaussian nature of single-mode fiber fields, our results are immediately applicable to the excitation of single-mode fibers by gaussian-shaped laser beams.
The Clair Discovery, west of the Shetland Isles (1995)

Introduction 

Recent exploration has heightened awareness of the hydrocarbon potential west of the Shetland Isles. Several discoveries have been announced in the past couple of years which suggest that the area may become a highly significant oil province. These finds have renewed interest in the Clair Discovery, which was originally found almost twenty years ago and contains reserves estimated to be in excess of three billion barrels of oil.

Geological evolution of the Clair region 

At the end of the Caledonian Orogeny, following collision of the Laurentian-Greenland and Fennoscandian–Russian continental plates ([Ziegler 1988][1]), a series of 'Old Red' fault-bounded, inter-montane molasse basins developed in late Silurian to early Devonian times. A model of extensional collapse of the over-thickened crust along old Caledonian lineaments or thrusts, has been proposed by several workers ([McClay et al. 1986][2]; [Norton et al. 1987][3]; [Coward et al. 1989][4], [Seranne, 1992][5]) for these actively subsiding basins.

The Clair discovery (Fig. 1) lies within the West Shetland Basin (WSB) which developed in such a tectonic setting, linked to the Shetland Spine Fault on its easterly margin (Fig. 2). Reconstruction of Devonian basins ([Duindam and van Hoorn 1987][6]) shows the WSB and the Clair area to be associated with a system of dominantly NE–SW-trending linked extensional faults. These faults separate the WSB from the main Orcadian Basin to the east by an area of uplifted basement known as the Shetland Platform. The area has been affected by several episodes of deformation including two main phases of extension . . .

 [1]: #ref-8
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 [4]: #ref-3
 [5]: #ref-7
 [6]: #ref-4
beta 2-Microglobulin modified with advanced glycation end products is a major component of hemodialysis-associated amyloidosis. (1993)

beta 2-Microglobulin (beta 2M) is a major constituent of amyloid fibrils in hemodialysis-associated amyloidosis, a complication of long-term hemodialysis patients. Amyloid fibril proteins were isolated from connective tissues forming carpal tunnels in hemodialysis patients with carpal tunnel syndrome. Two-dimensional polyacrylamide gel electrophoresis and Western blotting demonstrated that most of the beta 2M forming amyloid fibrils exhibited a more acidic pI value than normal beta 2M. This acidic beta 2M was also found in a small fraction of beta 2M in sera and urine from these patients, whereas heterogeneity was not observed in healthy individuals. We purified acidic and normal beta 2M from the urine of long-term hemodialysis patients and compared their physicochemical and immunochemical properties. Acidic beta 2M, but not normal beta 2M, was brown in color and fluoresced, both of which are characteristics of advanced glycation end products (AGEs) of the Maillard reaction. Immunochemical studies showed that acidic beta 2M reacted with anti-AGE antibody and also with an antibody against an Amadori product, an early product of the Maillard reaction, but normal beta 2M did not react with either antibody. Incubating normal beta 2M with glucose in vitro resulted in a shift to a more acidic pI, generation of fluorescence, and immunoreactivity to the anti-AGE antibody. The beta 2M forming amyloid fibrils also reacted with anti-AGE antibody. These data provided evidence that AGE-modified beta 2M is a dominant constituent of the amyloid deposits in hemodialysis-associated amyloidosis.
BioBERT: a pre-trained biomedical language representation model for biomedical text mining (2019)

We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.
Progress towards the integration of optical proximity correction and directed self-assembly of block copolymers with graphoepitaxy (2012)

A photomask design flow for generating guiding patterns used in graphoepitaxial DSA processes is proposed and tested. In this flow, a new fast DSA model is employed for DSA structure verification. The execution speed and accuracy of the fast model were benchmarked with our previously reported Monte Carlo method. We demonstrated the process window verification using the OPC/DSA flow with the fast DSA model and compared this with experimental results in the guiding patterns simulated by e-beam lithography.
Identification and purification of natural killer cell stimulatory factor (NKSF), a cytokine with multiple biologic effects on human lymphocytes. (1989)

We have identified and purified a novel cytokine, NK cell stimulatory factor (NKSF), from the cell-free supernatant fluid of the phorbol diester-induced EBV-transformed human B lymphoblastoid cell line RPMI 8866. NKSF activity is mostly associated to a 70-kD anionic glycoprotein. The purified 70-kD protein, isolated from an SDS-PAGE gel, yields upon reduction two small species of molecular masses of 40 and 35 kD, suggesting that this cytokine is a heterodimer. When added to human PBL, purified NKSF preparations induce IFN-gamma production and synergize with rIL-2 in this activity, augment the NK cell-mediated cytotoxicity of PBL preparations against both NK-sensitive and NK-resistant target cell lines, and enhance the mitogenic response of T cells to mitogenic lectins and phorbol diesters. The three activities remain associated through different purification steps resulting in a 9,200-fold purification, and purified NKSF mediates the three biological activities at concentrations in the range of 0.1-10 pM. These data strongly suggest that the same molecule mediates these three activities, although the presence of traces of contaminant peptides even in the most purified NKSF preparations does not allow us to exclude the possibility that distinct biologically active molecules have been co-purified. The absence of other known cytokines in the purified NKSF preparations, the unusual molecular conformation of NKSF, the high specific activity of the purified protein, and the spectrum of biological activities distinguish NKSF from other previously described cytokines.
Crystallographic and NMR Studies of the Serine Proteases (1982)

Since the serine proteases form the most thoroughly understood family of enzymes, it is of some interest to consider what the two principal physical techniques of studying enzymes, crystallography and nuclear magnetic resonance (NMR), have told us about the details of their enzymatic mechanism. Due to limitations of space, this review cannot be compre­ hensive nor can it describe the history of the current ideas concerning the action of these enzymes. Two major issues have attracted the attention of both diffraction and NMR studies in the past ten years: the first concerns the nature and the role of the catalytic triad of serine 195, histidine 57, and aspartic acid 102; the second is the possibility of induced distortions upon complexa­ tion of either the substrate or the enzyme. We first consider these issues in terms of the crystallographic studies and then of the NMR experi­ ments. Finally, we interpret these results in terms of a detailed structural and electronic mechanism. Our conclusions, subject to further test, are that the triad does not exist in the resting state of the enzyme because the serine-histidine bond is not formed. However, we suggest that this bond does form upon complexation with substrates allowing the triad to play an important role in catalysis.
Induction of cellular resistance against Kupffer cell-derived oxidant stress: A novel concept of hepatoprotection by ischemic preconditioning (2003)

Ischemic preconditioning (IP) triggers protection of the liver from prolonged subsequent ischemia. However, the underlying protective mechanisms are largely unknown. We investigated whether and how IP protects the liver against reperfusion injury caused by Kupffer cell (KC)-derived oxidants. IP before 90 minutes of warm ischemia of rat livers in vivo significantly reduced serum alanine aminotransferase (AST) levels and leukocyte adherence to sinusoids and postsinusoidal venules during reperfusion. This protective effect was mimicked by postischemic intravenous infusion of glutathione (GSH), an antioxidative strategy against KC-derived H(2)O(2). Interestingly, no additional protection was achieved by infusion of GSH to preconditioned animals. These findings and several additional experiments strongly suggest IP mediated antioxidative effects: IP prevented oxidant cell injury in isolated perfused rat livers after selective KC activation by zymosan. Moreover, IP prevented cell injury and pertubations of the intracellular GSH/GSSG redox system caused by direct infusion of H(2)O(2) (0.5 mmol/L). IP-mediated resistance against H(2)O(2) could neither be blocked by the adenosine A2a antagonist DMPX nor mimicked by A2a agonist CGS21680. In contrast, H(2)O(2) resistance was abolished by the p38 mitogen-activated protein kinase (p38 MAPK) inhibitor SB203580, but induced when p38 MAPK was directly activated by anisomycin. In conclusion, we propose a novel concept of hepatoprotection by IP: protection of liver cells by enhancing their resistance against KC-derived H(2)O(2). Activation of p38 MAPK and preservation of the intracellular GSH/oxidized glutathione (GSSG) redox system, but not adenosine A2a receptor stimulation, seems to be pivotal for the development of H(2)O(2) resistance in preconditioned livers.
Effects of Cyproterone Acetate on Experimentally Induced Canine Prostatic Hyperplasia (1980)

The effect of 3 alpha-androstanediol (3 alpha-diol), 17 beta-estradiol (E2) and cyproterone acetate (CA) on prostates in castrated beagle dogs were investigated by histological and histochemical examinations. A significant increase of prostatic weight occurred after 6 months' treatment with 3 alpha-diol alone and in combination with E2. Histologically and histochemically, two different types of prostatic enlargement were observed: first, administration of 3 alpha-diol resulted in diffuse glandular hyperplasia with replacement of functional activity monitored by strongly positive reactions for acid phosphatase, aminopeptidase and zinc. Second, 3 alpha-diol plus E2 produced stratified squamous metaplasia with cystic lumina and loss of the typical morphological structure. These glands showed negative reactions for acid phosphatase, aminopeptidase and zinc. In both types of prostatic hyperplasia CA abolished epithelial or metaplastic proliferation and induced atrophy of glandular epithelium. In estrogenized dogs activation of the fibromuscular stroma was obvious. CA prevented prostatic hyperplasia by atrophying epithelial effects.
Nonthreshold-Based Event Detection for 3D Environment Monitoring in Sensor Networks (2008)

Event detection is a crucial task for wireless sensor network applications, especially environment monitoring. Existing approaches for event detection are mainly based on some predefined threshold values, and thus are often inaccurate and incapable of capturing complex events. For example, in coal mine monitoring scenarios, gas leakage or water osmosis can hardly be described by the overrun of specified attribute thresholds, but some complex pattern in the full-scale view of the environmental data. To address this issue, we propose a non-threshold based approach for the real 3D sensor monitoring environment. We employ energy-efficient methods to collect a time series of data maps from the sensor network and detect complex events through matching the gathered data to spatio-temporal data patterns. Finally, we conduct trace driven simulations to prove the efficacy and efficiency of this approach on detecting events of complex phenomena from real-life records.
ReviewIsoprostanes: Novel Bioactive Products of Lipid Peroxidation (2003)

Isoprostanes, are a novel group of prostaglandin-like compounds that are biosynthesised from esterified polyunsaturated fatty acid (PUFA) through a non-enzymatic free radical-catalysed reaction. Several of these compounds possess potent biological activity, as evidenced mainly through their pulmonary and renal vasoconstrictive effects, and have short half-lives. It has been shown that isoprostanes act as full or partial agonists through thromboxane receptors. Both human and experimental studies have indicated associations of isoprostanes and severe inflammatory conditions, ischemia-reperfusion, diabetes and atherosclerosis. Reports have shown that F2-isoprostanes are authentic biomarkers of lipid peroxidation and can be used as potential in vivo indicators of oxidant stress in various clinical conditions, as well as in evaluations of antioxidants or drugs for their free radical-scavenging properties. Higher levels of F2-isoprostanes have been found in the normal human pregnancy compared to non-pregnancy, but their physiological role has not been well studied so far. Since bioactive F2-isoprostanes are continuously formed in various tissues and large amounts of these potent compounds are found unmetabolised in their free acid form in the urine in normal basal conditions with a wide inter-individual variation, their role in the regulation of normal physiological functions could be of further biological interest, but has yet to be disclosed. Their potent biological activity has attracted great attention among scientists, since these compounds are found in humans and animals in both physiological and pathological conditions and can be used as reliable biomarkers of lipid peroxidation.
Effect of Extracts from Rabbit Leukocytes on Levels of Acute Phase Globulins in Rat Serum (1971)

SummaryExtracts were prepared from rabbit polymorphonuclear leukocytes by procedures previously shown to yield activity for pyrogenicity and lowering of plasma iron and zinc levels. Rats were injected ip with these extracts, and 10 to 48 hr later their serum was assayed for acute phase globulins by immunological techniques. Positive responses were observed for α1- and α2-AP globulins; whereas responses to injections of control extracts were uniformly negative. The data were interpreted to indicate that one or more proteins synthesized and excreted by leukocytes can act as humoral intermediates in the stimulation of serum acute phase globulins during a variety of acute and chronic disorders.
Heat shock protein-peptide complexes for use in vaccines (1996)

The heat shock proteins gp96, HSP70, and HSP90 are complexed to a diverse array of cellular proteins and peptides as a consequence of their chaperone functions. There is good experimental evidence that vaccination with these heat shock protein-peptide complexes elicit immune responses against chaperoned peptide antigens. As shown with gp96, this requires internalization of the heat shock protein-peptide complexes by macrophages and processing of the chaperoned peptides for class I restricted presentation. Via this process, primarily CD8+ antigen-specific T cells are primed by gp96 vaccination. This might represent a general mechanism for priming of MHC-class I restricted T cells by professional antigen-presenting cells. At least gp96 has been shown to be associated with peptides that are not selected by the MHC haplotype of the harboring cell. This allows for immunization with gp96-peptide complexes across MHC barriers, for example against shared tumor antigens or viral antigens.