gebhart/patrepeval huggingface dataset:
Allotransplantation of Culture-Isolated Neonatal Rat Islet Tissue: Absence of MHC Class II Positive Antigen-Presenting Cells in Nonimmunogenic Islets (1989)

When highly purified neonatal rat islet tissue, derived after 10 days in vitro, was allografted, it was found to be nonimmunogenic or weakly immunogenic. In contrast, nonislet pancreatic components, derived from the same culture system, transplanted with highly purified islet tissue resulted in rejection in 88% of cases. Extension of the culture period did not result in reduced immunogenicity of the nonislet material. Immunostaining of islet or nonislet tissue from the culture system failed to demonstrate major histocompatibility complex (MHC) class II positive cells in the islet tissue, whereas the presence of MHC class II staining cells in the nonislet components was clearly demonstrable. These results demonstrate that the islet tissue obtained by culture isolation is free of cells capable of stimulating an allogeneic immune response and are consistent with the hypothesis that the absence of MHC class II positive antigen-presenting cells reduces the immunogenicity of the tissue and enhances the survival of allogeneic grafts.
Oxidation of a diphosphene and dechlorination of an arylphosphonic dichloride: isolation of the diphosphene oxide (1983)

M. Yoshifuji, K. Ando, K. Toyota, I. Shima and N. Inamoto, J. Chem. Soc., Chem. Commun., 1983, 419 DOI: 10.1039/C39830000419
Antigen receptor-mediated protein tyrosine kinase activity is regulated by a pertussis toxin-sensitive G protein (1992)

Ligation of the Ag receptor on B cells is associated with a rapid increase in phosphorylation on tyrosine residues of multiple substrates. One of the substrates is the phosphoinositide-specific phospholipase C-gamma 1. Because activation of phospholipase C-gamma 1 seems to be dependent on tyrosine phosphorylation, it is assumed that the two signaling pathways, phosphatidylinositol turnover and tyrosine phosphorylation, might be linked. However, since the Ag receptor does not possess a kinase domain, it remains unclear how these signaling pathways are regulated by the Ag receptor. Previous studies have proposed the existence of a receptor-coupled G protein that regulates inositol phosphate production in B cells. We confirm that phosphoinositide turnover is regulated by a pertussis toxin (PT)-sensitive G protein, most probably by controlling phosphorylation of phospholipase C-gamma 1. We show that treatment of permeabilized B cells with a nonhydrolyzable GTP analogue guanosine 5'-[3-thio]triphosphate induced an increase in tyrosine phosphorylation of multiple substrates that are identical to the proteins phosphorylated after anti-IgM stimulation. Furthermore, binding of the inactive form of G proteins with guanosine 5'-[2-thio]-triphosphate blocked anti-IgM induced tyrosine phosphorylation in permeabilized B cells. The results indicate that an Ag receptor-coupled G protein controls protein tyrosine kinase activity. We show that this G protein is sensitive to PT because tyrosine phosphorylation mediated by the Ag receptor was inhibited by this toxin in a concentration-dependent manner. Similar concentrations of PT also blocked tyrosine phosphorylation on phospholipase C-gamma 1 and generation of inositol phosphates. Preincubation of intact B cells with PT resulted in inhibition of c-fos mRNA expression and DNA synthesis in anti-IgM stimulated B cells, indicating that post-transcriptional events are also controlled by the Ag-receptor coupled G protein. We conclude that Ag receptor-associated protein tyrosine kinase activity is regulated by a G protein. This PT-sensitive G protein also regulates phosphorylation and activation of phospholipase C-gamma 1 as well as later events in B cell activation such as c-fos mRNA expression and proliferation.
Dynamic model investigation of water pressures and accelerations encountered during landings of the Apollo spacecraft (1967)

Apollo spacecraft landing simulation to determine impact water pressures, accelerations, and landing dynamics
Numerical simulations of the Macondo well blowout reveal strong control of oil flow by reservoir permeability and exsolution of gas (2011)

In response to the urgent need for estimates of the oil and gas flow rate from the Macondo well MC252-1 blowout, we assembled a small team and carried out oil and gas flow simulations using the TOUGH2 codes over two weeks in mid-2010. The conceptual model included the oil reservoir and the well with a top boundary condition located at the bottom of the blowout preventer. We developed a fluid properties module (Eoil) applicable to a simple two-phase and two-component oil-gas system. The flow of oil and gas was simulated using T2Well, a coupled reservoir-wellbore flow model, along with iTOUGH2 for sensitivity analysis and uncertainty quantification. The most likely oil flow rate estimated from simulations based on the data available in early June 2010 was about 100,000 bbl/d (barrels per day) with a corresponding gas flow rate of 300 MMscf/d (million standard cubic feet per day) assuming the well was open to the reservoir over 30 m of thickness. A Monte Carlo analysis of reservoir and fluid properties provided an uncertainty distribution with a long tail extending down to 60,000 bbl/d of oil (170 MMscf/d of gas). The flow rate was most strongly sensitive to reservoir permeability. Conceptual model uncertainty was also significant, particularly with regard to the length of the well that was open to the reservoir. For fluid-entry interval length of 1.5 m, the oil flow rate was about 56,000 bbl/d. Sensitivity analyses showed that flow rate was not very sensitive to pressure-drop across the blowout preventer due to the interplay between gas exsolution and oil flow rate.
Refractive keratoplasty with intrastromal hydrogel lenticular implants. (1981)

The feasibility of using hydrogel lenticular implants of high water content to alter the anterior corneal curvature for purposes of refractive keratoplasty has been investigated in rabbits. Lenticules (6 mm in diameter) of Permalens (Perfilcon-A) were trephined from contact lens and implanted within an intralamellar pocket in the cornea. The in vitro glucose flux across the hydrogel (0.23 mm thick) was measured at 131 +/- 7 micrograms/cm(2)/hr. For clinical comparison, non-water-permeable disks of Teflon were also implanted. The Teflon implant caused an aseptic ulcer to develop anterior and central to the implant by 9 +/- 4 days. The hydrogel lenticular implant did not cause central ulceration during the 7 month postoperative follow-up. There was a thinning and eventual erosion of the stroma anterior to the edge of the hydrogel implant, 16 +/- 7 weeks. The glycogen contents of the epithelium anterior to (1) the sham operation, i.e., lamellar pocket dissection, (2) the implanted hydrogel lenticule with or without the presence of an erosion, and (3) the control corneas were statistically from the same population. Yet there was a slight dehydration of the stroma anterior to the hydrogel implant when compared to control tissue. A thin-edged implant lenticule design should overcome the stromal thinning caused by the thick-edge implants. During the short-term follow-up, the hydrogel lenticular implant proved to be successful as a refractive keratoplasty implant material.
Compact diode-pumped passively Q-switched tunable Er–Yb double-clad fiber laser (2002)

Efficient repetitive passive Q switching of a cladding-pumped Er-Yb fiber laser has been demonstrated by use of an external-cavity configuration containing a Co(2+): ZnS crystal as a saturable absorber. Energies of as much as 60muJ in pulses of durations as short as 3.5 ns (FWHM), corresponding to a peak power of >10kW, have been generated, and the maximum slope efficiency with respect to the absorbed pump power was 13%. Using a bulk diffraction grating in the Littrow configuration to provide wavelength-selective feedback, we tuned the passively Q -switched fiber laser over 31 nm from 1532 to 1563 nm. The prospects for further improvement in performance are discussed.
Fine pattern fabrication property of binary mask and attenuated phase shift mask (2009)

For 45nm and 32nm node technology, the challenges for resolution and CD control of mask patterns become the steeper mountain path. Especially, Sub Resolution Assist Feature (SRAF) is the smallest pattern on mask and amplifies the difficulty of mask fabrication. In order to improve the resolution of fine patterns, the influence of wet processing cannot be neglected, because it causes the pattern collapsing. Wet processing of mask-making can be divided into resist development and cleaning. In this study, the root causes of pattern collapsing are investigated at each wet processing. It is confirmed that thin resist can enhance the resolution limit of resist pattern and hard-mask blank, such as OMOG: Opaque MoSi On Glass, is suitable for thinner resist under 1500A. The pattern collapsing of OMOG is compared with that of Att.PSM at the cleaning before and after Cr stripping. Mask inspection finds that pattern collapsing can be suppressed by OMOG at both cleanings. It is because OMOG has lower cleaning stress than Att.PSM due to lower aspect-ratio. This benefit is demonstrated by cleaning stress simulation. Additionally, it is found that the SRAF size of OMOG can be wider than Att.PSM by optical simulation. From these results, OMOG has much advantage of fine pattern fabrication and is the optimal blank for 32nm node and beyond.
Enzymatic fragments as possible regulatory oligopeptides (2007)

The enzyme, bromelain, is known to catalyze protein proteolysis and to activate many protective processes occurring with participation of the nervous, immune, and endocrine systems. In this connection, a computer analysis of all the possible 4–6-member fragments of bromelain was performed by means of a comparison of their primary structures with amino acid sequences of all the known natural oligopeptides. Information from the EROP-Moscow data base that contains data on the structures and functions of natural oligopeptides and specially written computer programs were used for this purpose. It was shown that tetra-, penta-, and hexapeptide fragments of the bromelain molecules are involved in amino acid sequences of many natural oligopeptides, including antimicrobial oligopeptides, toxins, neuropeptides, and hormones. These results confirmed deep relationship between the basic regulatory systems. In connection with the obtained data, the process of oligopeptide biogenesis, the possibility of natural formation of regulatory oligopeptides from the bromelain molecules, and correspondence of the obtained results with the conception of oligopeptide continuum are discussed. A possible practical importance of active fragments of protein enzymes in regulatory processes of a living organism is noted.
The Predictive Role of Blood Glucose for Mortality in Subjects with Cardiovascular Disease (2005)

Using the Framingham Heart Study data (United States, 1948-1978), the authors examined the association of blood glucose with 2-year all-cause, cardiovascular, and noncardiovascular mortality in subjects with documented cardiovascular disease. After adjustment for systolic blood pressure, cholesterol, body mass index, cigarette smoking, and use of antihypertensive agents, they found that glucose was a strong, independent predictor of mortality. However, the relations for men and women were qualitatively different. For men, adjusted mortality risk increased very rapidly through the normal range (from 4.12% at 3.89 mmol/liter (70 mg/dl) to 12.26% at 5.55 mmol/liter (100 mg/dl)) and was flat at 12.26% thereafter. For women, risk was flat at 3.65% through the normal range and then increased rapidly, reaching 8.34% at 6.99 mmol/liter (126 mg/d), but increased much more slowly thereafter. Exactly analogous relations held for cardiovascular mortality. For men and women combined, noncardiovascular mortality increased from 1.82% at 3.89 mmol/liter to 2.06% at 5.55 mmol/liter to 2.29% at 6.99 mmol/liter (p for trend = 0.009). These findings suggest that although 5.55 mmol/liter (normal) may be a useful mortality risk division (albeit with different implications for the two sexes), 6.99 mmol/liter (diabetic) is not, especially for men.
The Use of “Gallium Citrate Scanning to Stage Malignancies of the Head and Neck (1974)

Summary The inaccuracy of palpation to detect cervical metastatic lymph node disease is emphasised. Approximately one third of patients with head and neck carcinoma will be diagnosed incorrectly with respect to metastatic disease in the neck regardless of the presence or not of palpable nodes. Normal but palpable nodes or anatomical prominences may cause difficulty in interpretation. This report gives details of experience with 67 Gallium citrate scanning in 14 patients with cervical masses, which were initially assumed to be metastatic in origin. The primary lesion was well demonstrated in two cases, and in four other cases positive e7 Ga scans corresponding with metastatic cervical lymph nodes were obtained. In six cases however the scan was negative; moreover there were two instances where chronically‐inflamed submandibular salivary glands gave “false positive” scans. On the basis of this experience, the f, T Ga scan appears to be of no help in staging head and neck malignancy.
Early Localization of<sup>125</sup>I-Labeled Human Growth Hormone in Adrenals and Other Organs of Immature Hypophysectomized Rats (1971)

Human growth hormone (HGH) labeled with 125I was injected intravenously into hypophysectomized, immature rats. One rat was frozen 6 min and another 20 min after injection by immersion in hexane cooled with dry ice. Whole-body sections were made of the frozen rats and autoradiograms were prepared by placing these sections on x-ray film. The autoradiograms revealed that, at both time intervals after injection, there was a high concentration of radioactive material in the kidney, liver and adrenal cortex. The only other tissues found to have a higher radioactive density than that of blood were the submandibular glands, nasal mucosa, gastric mucosa, bone and follicles of vibrissae. The radioactivity in the adrenal cortex was slightly higher in the zona glomerulosa than in the zona fasciculata and it was lowest in the zona reticularis. The concentration in the epiphyseal plates was no higher than that in bone or soft tissues. The radioactivity in the submandibular gland had the electrophoretic mobility of growth hormone and not free iodide. The distribution in 8 organs of 131I-albumin was compared with that of 125I-HGH at 6 and 20 min by removal of the organs and direct isotope counting. The distributions substantiated the specific localizations of HGH seen in the autoradiograms. Pretreatment of the rats with ACTH or HGH 6 min before administering the 125I-HGH altered the concentration of 12BI-HGH in kidney, liver and adrenals. (Endocrinology88: 1309, 1971)
Natural Auxotrophic Heterozygosity in<i>Candida Albicans</i> (1987)

Candida albicans is imperfect and diploid. This unusual genetic state permits the occurrence of strains heterozygous for recessive deleterious alleles. These alleles can be brought to homozygosity and therefore expression by UV irradiation-induced mitotic crossing over. Heterozygosity for recessive auxotrophic alleles is found in 10 to 15% of the strains. A wide variety of auxotrophic alleles have been found in such natural heterozygotes but one type, termed Suf +/- was found at an unusually high frequency. Some 5 to 10% of strains are of the Suf +/- type. Suf- homozygous auxotrophs are defective in sulfite reductase. Such auxotrophs require a source of reduced sulfur such as methionine or cysteine, alternatively inorganic thiosulfate will serve as a supplement. Complementation analysis of a variety of Suf- auxotrophs established that 11 out of 12 strains were in a single complementation group.
Horizontal Load Transfer in Structural Concrete Bridge Deck Overlays (1990)

Full‐depth structural concrete overlays in bridge deck rehabilitation require special interface design and construction joint preparation between the old bridge deck and the overlay in order to ensure monolithic structural action of the overlaid bridge superstructure under all loading conditions. The effectiveness of interface dowels for horizontal shear transfer in connection with clean and speciallyroughened contact surfaces is investigated. Preliminary analytical studies of the horizontal shear‐transfer behavior of overlaid reinforced concrete bridge decks and experimental results on the effects of interface preparations and dowels from shearblock tests, full‐scale transverse bridge deck slab panel tests, and a full‐scale prototype bridge deck test are presented. The full‐scale prototype bridge deck test was performed on a section of a reinforced concrete T‐girder bridge that had been in service for 25 years. A detailed account of analytical and experimental investigations of the horizontal load‐transfer behavior is presented, and the basis for simple capacity design considerations for dowel reinforcement in full‐depth structural concrete overlays is provided.
The bZIP Transactivator of Epstein-Barr Virus, BZLF1, Functionally and Physically Interacts with the p65 Subunit of NF-kB (1994)

The Epstein-Barr virus (EBV) BZLF1 (Z) immediate-early transactivator initiates the switch between latent and productive infection in B cells. The Z protein, which has homology to the basic leucine zipper protein c-Fos, transactivates the promoters of several replicative cycle proteins. Transactivation efficiency of the EBV BMRF1 promoter by Z is cell type dependent. In B cells, in which EBV typically exists in a latent form, Z activates the BMRF1 promoter inefficiently. We have discovered that the p65 component of the cellular factor NF-kappa B inhibits transactivation of several EBV promoters by Z. Furthermore, the inhibitor of NF-kappa B, I kappa B alpha, can augment Z-induced transactivation in the B-cell line Raji. Using glutathione S-transferase fusion proteins and coimmunoprecipitation studies, we demonstrate a direct interaction between Z and p65. This physical interaction, which requires the dimerization domain of Z and the Rel homology domain of p65, can be demonstrated both in vitro and in vivo. Inhibition of Z transactivation function by NF-kappa B p65, or possibly by other Rel family proteins, may contribute to the inefficiency of Z transactivator function in B cells and may be a mechanism of maintaining B-cell-specific viral latency.
ChemInform Abstract: Electrochemical Investigations of SrTiO<sub>3</sub> Boundaries. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
P116 A computable, causal biological network model suite for mechanistic evaluation of ulcerative colitis (2018)

Inflammatory bowel disease (IBD) is a chronic intestinal inflammatory disorder characterised by intermittent period of acute inflammatory flares and remission. It consists of two distinct phenotypes, Crohn’s disease and ulcerative colitis (UC). The cellular and molecular mechanisms behind UC pathogenesis are complex and there is a need for precise methods for disease diagnostics, evaluation of remission, and identification of subjects who would benefit from a given drug. Omics profiling is commonly used to gain a global understanding of molecular mechanisms behind phenotypes; however, the thousands of data points generated by the technologies need to be carefully analysed and interpreted in the context of well-defined biology. To provide a layer of mechanistic understanding of omics data beyond lists of differentially expressed genes, we have constructed a suite of causal biological network models for UC. Molecular interactions taking place during UC pathogenesis were captured from scientific literature, converted into the Biological Expression Language (BEL), and assembled into causal networks. Biological processes, such as dysregulation of tight junctions, bacterial translocation epithelial cell apoptosis and proliferation, were captured as individual network models included in the model suite. Key signalling molecules in the model backbone link to information about genes that they are known to regulate. Differential expression of these genes in disease state can be used to infer activity of the molecule in the model backbone – a process termed network scoring. We have used public transcriptomic datasets derived from clinical biopsies to score the UC model suite. Here we show the potential of these network models to quantitatively compare UC subject cohorts and pin down the molecular mechanisms separating these cohorts based on transcriptomics data. Network scoring could then be exploited in virtue of several applications. It could represent a sensitive diagnostic tool, be instrumental for the discrimination between IBD patients and subjects with other gastrointestinal conditions, and support appropriate approaches for patients stratification (e.g. treatment responders vs. non-responders, etc).
A System of Procedures for Identification of Simple Models Using Transient Step Response (2001)

In this paper, a system of procedures for identification using the transient step response is presented. The identification aims at modeling dynamic processes with simple models that have general second-order dynamics. The procedures consist of three parts, including classification of the response, selection of the model structure, and the estimation of parameters. Technically, this proposed system provides a strategy based on quantitative measures to identify the model structure and extends the identification of models to include possible RHP/LHP zeros and dead time. One important aspect of this proposed system of procedures is the minimization of the need for human decisions to be made during the identification process. With this advantage, it is then possible to facilitate the development of software to perform the identification automatically.
Basin Delineation with a 40-Hour Passive Seismic Record (2012)

Several geophysical methods exist to delineate the lower interface of a sedimentary basin. Most popularly employed are gravity and magnetic surveys and surface-wave inversion. While all three methods are successful overall in estimating an average basin depth, they fail to find a more detailed depth variation. As an alter- native, we consider three passive seismic techniques, using especially body waves. We analyze 40 hours of data, recorded with 110 stations installed over the Abu Gharadig basin in Egypt. In an earlier study we found the frequency band of 0.09-1.0 Hz to be dominated by body waves. As a first method we apply body-wave seismic interfero- metry (SI). Using body-wave noise, we extract PP and SS reflections from the basin floor. We estimate the depth of the basin to be around 4.8 km. As a second technique we estimate the resonance spectra of the basin, using the horizontal-to-vertical (H/V) spectral ratio. Using surface-wave noise, we find an extremum that is probably related to the complete sedimentary package. Using this peak, we find a basin depth of 5.4 km. Using S-phase arrivals, we find two extrema in the H/V, which are probably related to the S-wave resonances of two distinct layers in the basin. As a third method we compute receiver functions (RFs). Based on the RFs, we can confirm the presence of a large interface in the upper crust, but we cannot well constrain its depth.