gebhart/patrepeval huggingface dataset:
Poroelastic solution of an inclined borehole in a transversely isotropic medium (2026)

An analytical solution of an infinitely long borehole drilled perpendicular to the material isotropic symmetry plane of a transversely isotropic poroelastic medium is provided. The far-Field principal stresses have an arbitrary inclination with the borehole axis. Numerical examples are given to demonstrate the effects of anisotropy
Inhibition of HIV-1 gp160-dependent membrane fusion by a furin-directed alpha 1-antitrypsin variant. (1993)

Furin is a membrane-associated calcium-dependent serine endoprotease that cleaves proproteins on the carboxyl side of the consensus sequence -Arg-X-Lys/Arg-Arg-. Using site-directed mutagenesis, a variant alpha 1-antitrypsin (alpha 1-AT) was constructed which contains in its reactive site -Arg-X-X-Arg-, the minimal sequence required for efficient processing by furin (Molloy, S. S., Bresnahan, P. A., Leppla, S. H., Klimpel, K. R., and Thomas, G. (1992) J. Biol. Chem. 267, 16396-16402). This alpha 1-AT variant, [Arg355 Arg358]alpha 1-AT (alpha 1-PDX), is greater than 3,000-fold more effective than [Arg358]alpha 1-AT (alpha 1-AT Pittsburgh, alpha 1-PIT) at inhibiting furin in vitro (K0.5 = 0.03 microgram/ml). Furthermore, the P4 Arg in alpha 1-PDX greatly attenuates the thrombin inhibitory properties of this serpin (> 300-fold) compared with alpha 1-PIT (which contains a P4 Ala), thus increasing the selectivity of alpha 1-PDX for furin. Expression studies show that alpha 1-PDX, and not alpha 1-PIT, blocks the processing of two furin substrates, pro-beta-nerve growth factor and human immunodeficiency virus (HIV)-1 gp160 in transfected cells. In addition, a syncytium assay shows that alpha 1-PDX blocks the membrane fusogenic properties of HIV-1 gp160. The potential use of alpha 1-PDX in manipulating the activation of proproteins in a tissue- and time-specific manner is discussed.
Site-Specific Amide Hydrogen/Deuterium Exchange in E. coli Thioredoxins Measured by Electrospray Ionization Mass Spectrometry (2001)

Mass spectrometry as an analytical tool to study protein folding and structure by hydrogen/deuterium exchange is a relatively new approach. In this study, site-specific amide deuterium content was measured in oxidized and reduced E. coli thioredoxins by using the b(n) ions in electrospray ionization CID MS/MS experiments after 20-s incubation in D(2)O phosphate-buffered solution (pH 5.7). The deuterium levels correlated well with reported NMR-determined H/D exchange rate constants. The deuterium measured by y(n) ions, however, showed much less reliable correlation with rate exchange data. In general, residues in alpha helices and beta sheets, when measured by b(n) ions, showed low incorporation of deuterium while loops and turns had high deuterium levels. Most amide sites in the two protein forms showed similar deuterium levels consistent with the expected similarity of their structures, but there were some differences. The turn consisting of residues 18-22 in particular showed more variability in deuterium content consistent with reported structural differences in the two forms. The deuterium uptake by thioredoxins alkylated at Cys-32 by S-(2-chloroethyl)glutathione and S-(2-chloroethyl)cysteine, in peptides 1-24 and 45-58, was similar to that observed for oxidized and reduced thioredoxins, but several residues, particularly Leu-53 and Thr-54, showed slightly elevated deuterium levels, suggesting that structural changes had occurred from alkylation of the protein at Cys-32. It is concluded that b(n) ions are reliable for determining the extent of site-specific amide hydrogen isotope exchange and that mass spectrometry is useful as a complementary technique to NMR and other analytical methods for probing regional structural characteristics of proteins.
Self-consistent coupled carrier transport full-wave EM analysis of semiconductor traveling-wave devices (2006)

We propose a rigorous finite-element-method (FEM) model for traveling-wave structures on doped semiconductor substrates based on a full-wave electromagnetic model coupled to a drift-diffusion description of carrier transport. The coupled model allows to describe field-carrier interactions in distributed structures, where strong low-frequency dispersion due to metal and semiconductor losses and multimodal behavior are observed. Slow-wave propagation, which is significant for photonic devices wherein synchronous optical-RF coupling is required, is also self-consistently accounted for. Numerical examples for some practical microwave structures exploited in RF and optoelectronic applications are included to illustrate the capabilities and effectiveness of the proposed numerical technique.
Detection of thrombopoietic activity in plasma by stimulation of suppressed thrombopoiesis (1970)

Rabbits in which thrombocytosis had been produced by five daily transfusions of platelet concentrates had suppressed endogenous thrombopoiesis, as reflected by decreased incorporation of selenomethionine-(75)Se ((75)SeM) into the circulating platelet mass. Rabbits in which endogenous thrombopoiesis had been suppressed by transfusion-induced thrombocytosis were used to detect thrombopoietic activity in rabbit plasma. Thrombopoietic activity was demonstrated in the plasma of both normal and thrombocytopenic donor rabbits. A dose response relationship was observed between the incorporation of (75)SeM into platelets and the dose of plasma administered. Infusion of 20-150 ml of plasma from thrombocytopenic donors increased the incorporation of (75)SeM into platelets from 52 to 107% above control values. A dose response effect also was seen after infusion of normal plasma, but normal plasma produced less effect than comparable doses of plasma from thrombocytopenic donors. Rabbits with transfusion-induced thrombocytosis appear to be more sensitive assay animals for the detection of thrombopoietic activity than animals with normal platelet counts. Changes in the rate of appearance and levels of (75)SeM may primarily indicate changes in platelet protein or platelet size and are apparently more sensitive indicators of the state of thrombopoiesis than are alterations in the numbers of circulating platelets. The results strongly support the concept of a humoral agent, i.e. thrombopoietin, that acts on megakaryocytes to regulate platelet production.
Meromorphic products determining near-fields (1989)

Abstract In this paper we continue our investigations of a construction method for subnear-rings of M(G) proposed by H. Wielandt. For a meromorphic product H, H ⊂ G k , G finite, we obtain necessary and sufficient conditions for M(G, k, H) to be a near-field.
Resistive switching in aluminum/anodized aluminum film structure without forming process (2009)

Metal-insulator-metal (MIM) structure was fabricated by partially anodizing aluminum film followed by deposition of another aluminum film. Unipolar resistive switching between a high-resistance state and a low-resistance state with a high resistance ratio (&amp;gt;∼104) was observed from the structure. The switching occurred without the requirement of a forming process, which was attributed to the pre-existing conductive filaments in the Al-rich AlxOy layer formed by the anodization. Each resistance state exhibited Ohmic behavior which could be explained by the metallic conduction and electron hopping from one isolated state to the next in the Al-rich AlxOy layer. The MIM structure showed good memory characteristics.
Using Peptide Loop Insertion Mutagenesis for the Evolution of Proteins (2010)

The insertion of peptide loops into the polypeptide chain of proteins at surface-exposed regions is an attractive avenue to modify the protein's properties or to evolve new functionalities. The strategy of peptide loop insertion has, for example, been used to create new binding sites in protein scaffolds and has led to the isolation of proteins with excellent binding affinities for various biological structures. Peptide loops have also been inserted into enzymes to modulate their catalytic properties. We recently used loop insertion mutagenesis to evolve a mutant of O(6)-alkylguanine-DNA-alkyltransferase (AGT) that reacts with the nonnatural substrate O(6)-propargylguanine for applications in molecular imaging. In this chapter, we describe in detail the protocols that we have applied (1) to identify sites in AGT that are permissive to loop insertion, (2) to manipulate DNA to create large loop insertion libraries, and (3) to identify mutants with desired properties. The experimental procedures are general and can easily be adapted for the insertion of peptide loops into other classes of enzymes or into any protein of interest.
MicroRNA in platinum-resistance of ovarian cancer (2011)

MircoRNAs (miRNAs) are widely existing inorganisms, non-coding small RNA. MircoR-NAs play important role in cell proliferation, apoptosis, stress resistance and fat metabolism. In vitro studies indicate that miRNAs are important factors in platinum resistance of ovarian cancer cell lines. However, the pathway of platinum resistance of ovarian cancers is complex. Studies find miRNA expression play important roles in the sensitivity of platinum resistance of ovarian cancer cell lines , and can be used as an early alert for platinum resistance. Changing the expression of miRNA even can reverse the platinum resistance . But the regular role of miRNAs in target genes network is still unconfirmed. Thus, more studies about miRNA in vivo and animal tumor models are needed to identify the function of miRNAs in platinum resistance of ovarian cancer.

Key words: 
MicroRNAs; Ovarian neoplasmas; Drug resistance, neoplasm
Breath Analysis Using Laser Spectroscopic Techniques: Breath Biomarkers, Spectral Fingerprints, and Detection Limits (2009)

Breath analysis, a promising new field of medicine and medical instrumentation, potentially offers noninvasive, real-time, and point-of-care (POC) disease diagnostics and metabolic status monitoring. Numerous breath biomarkers have been detected and quantified so far by using the GC-MS technique. Recent advances in laser spectroscopic techniques and laser sources have driven breath analysis to new heights, moving from laboratory research to commercial reality. Laser spectroscopic detection techniques not only have high-sensitivity and high-selectivity, as equivalently offered by the MS-based techniques, but also have the advantageous features of near real-time response, low instrument costs, and POC function. Of the approximately 35 established breath biomarkers, such as acetone, ammonia, carbon dioxide, ethane, methane, and nitric oxide, 14 species in exhaled human breath have been analyzed by high-sensitivity laser spectroscopic techniques, namely, tunable diode laser absorption spectroscopy (TDLAS), cavity ringdown spectroscopy (CRDS), integrated cavity output spectroscopy (ICOS), cavity enhanced absorption spectroscopy (CEAS), cavity leak-out spectroscopy (CALOS), photoacoustic spectroscopy (PAS), quartz-enhanced photoacoustic spectroscopy (QEPAS), and optical frequency comb cavity-enhanced absorption spectroscopy (OFC-CEAS). Spectral fingerprints of the measured biomarkers span from the UV to the mid-IR spectral regions and the detection limits achieved by the laser techniques range from parts per million to parts per billion levels. Sensors using the laser spectroscopic techniques for a few breath biomarkers, e.g., carbon dioxide, nitric oxide, etc. are commercially available. This review presents an update on the latest developments in laser-based breath analysis.
Facilitated neurogenic inflammation in complex regional pain syndrome (2001)

Complex regional pain syndrome (CRPS) is characterized by a variety of clinical features including spontaneous pain and hyperalgesia. Increased neuropeptide release from peripheral nociceptors has been suggested as a possible pathophysiologic mechanism triggering the combination of trophic changes, edema, vasodilatation and pain. In order to verify the increased neuropeptide release in CRPS, electrically induced neurogenic vasodilatation and protein extravasation were evaluated in patients and controls. We performed a prospective study on 10 patients with acute and untreated CRPS and 10 matched healthy controls. Neurogenic inflammation was elicited by strong transcutaneous electrical stimulation via intradermal microdialysis capillaries which simultaneously enabled measurement of protein extravasation. Laser-Doppler scanning was used to assess axon reflex vasodilatation. Axon reflex vasodilatation was significantly increased in CRPS patients (438 +/- 68% of baseline vs. 306 +/- 52%; P < 0.05) and transcutaneous electrical stimulation provoked protein extravasation only in the patients (before, 0.28 +/- 0.03 mg/ml; during stimulation, 0.34 +/- 0.04 mg/ml), whereas protein concentration steadily declined during stimulation in the healthy controls (before, 0.23 +/- 0.04 mg/ml; during stimulation, 0.18 +/- 0.04; P < 0.001). The time course of electrically induced protein extravasation in the patients resembled the one observed following application of exogenous substance P (SP). We conclude that neurogenic inflammation is facilitated in CRPS. Our results suggest an increased releasability of neuropeptides in CRPS.
Single rolled-up InGaAs/GaAs quantum dot microtubes integrated with silicon-on-insulator waveguides (2011)

We report on single rolled-up microtubes integrated with silicon-on-insulator waveguides. Microtubes with diameters of ~7 μm, wall thicknesses of ~250 nm, and lengths greater than 100 μm are fabricated by selectively releasing a coherently strained InGaAs/GaAs quantum dot layer from the handling GaAs substrate. The microtubes are then transferred from their host substrate to silicon-on-insulator waveguides by an optical fiber abrupt taper. The Q-factor of the waveguide coupled microtube is measured to be 1.5×10(5), the highest recorded for a semiconductor microtube cavity to date. The insertion loss and extinction ratio of the microtube are 1 dB and 34 dB respectively. By pumping the microtube with a 635 nm laser, the resonance wavelength is shifted by 0.7 nm. The integration of InGaAs/GaAs microtubes with silicon-on-insulator waveguides provides a simple, low loss, high extinction passive filter solution in the C+L band communication regime.
C-terminal Src kinase (CSK) and CSK-homologous kinase (CHK)—endogenous negative regulators of Src-family protein kinases (2005)

C-terminal Src kinase (CSK) and CSK-homologous kinase (CHK) are endogenous inhibitors of the Src-family protein tyrosine kinases (SFKs). Since constitutive activation of SFKs contributes to cancer formation and progression, to prevent excessive activation of SFKs, their activity in normal cells is kept at the basal level by CSK and CHK. CSK and CHK inactivate SFKs by specifically phosphorylating a consensus tyrosine (called Y(T)) near their C-termini. Upon phosphorylation, the phospho-Y(T) engages in intramolecular interactions that lock the SFK molecule in an inactive conformation. SFKs are anchored to the plasma membrane, while CSK and CHK are localized predominantly in the cytosol. To inhibit SFKs, CSK and CHK need to translocate to the plasma membrane. Recruitment of CSK and CHK to the plasma membrane is mediated by the binding of their SH2, SH3 and/or kinase domains to specific transmembrane proteins, G-proteins and adaptor proteins located near the plasma membrane. For CSK, membrane recruitment often accompanies activation. CSK and CHK employ two types of direct interactions with SFKs to achieve efficient Y(T) phosphorylation: (i) short-range interactions involving binding of the active sites of CSK and CHK to specific residues near Y(T), (ii) long-range non-catalytic interactions involving binding of SFKs to motifs located distally from the active sites of CSK and CHK. The interactions between CSK and SFKs are transient in nature. Unlike CSK, CHK binds tightly to SFKs to form stable protein complexes. The binding is non-catalytic as it is independent of Y(T). More importantly, the tight binding alone is sufficient to completely inhibit SFKs. This non-catalytic inhibitory binding represents a novel mechanism employed by CHK to inhibit SFKs. Given that SFKs are implicated in cancer development, compounds mimicking the non-catalytic inhibitory mechanism of CHK are potential anti-cancer therapeutics.
Fluoride is not an activator of the smaller (20-25 kDa) GTP-binding proteins (1991)

Effects of aluminum, magnesium, and fluoride (AMF) on members of both the trimeric G protein and smaller (20-25 kDa) monomeric GTP-binding protein families were examined. The dissociation of GDP from G proteins was blocked by AMF but was unchanged with the addition of AMF to any of six of the monomeric GTP-binding proteins. Biochemical activities and properties of one of the smaller GTP-binding proteins, ADP-ribosylation factor, were also found to be unaffected by AMF. It is concluded that the ability of AMF to activate the trimeric G proteins is not shared by the smaller GTP-binding proteins and thus should prove to be a useful discriminator between cellular activities regulated by these two families of regulatory proteins.
A Primary Xenograft Model of Small-Cell Lung Cancer Reveals Irreversible Changes in Gene Expression Imposed by Culture In vitro (2009)

Traditional approaches to the preclinical investigation of cancer therapies rely on the use of established cell lines maintained in serum-based growth media. This is particularly true of small-cell lung cancer (SCLC), where surgically resected tissue is rarely available. Recent attention has focused on the need for better models that preserve the integrity of cancer stem cell populations, as well as three-dimensional tumor-stromal interactions. Here we describe a primary xenograft model of SCLC in which endobronchial tumor specimens obtained from chemo-naive patients are serially propagated in vivo in immunodeficient mice. In parallel, cell lines grown in conventional tissue culture conditions were derived from each xenograft line, passaged for 6 months, and then reimplanted to generate secondary xenografts. Using the Affymetrix platform, we analyzed gene expression in primary xenograft, xenograft-derived cell line, and secondary xenograft, and compared these data to similar analyses of unrelated primary SCLC samples and laboratory models. When compared with normal lung, primary tumors, xenografts, and cell lines displayed a gene expression signature specific for SCLC. Comparison of gene expression within the xenograft model identified a group of tumor-specific genes expressed in primary SCLC and xenografts that was lost during the transition to tissue culture and that was not regained when the tumors were reestablished as secondary xenografts. Such changes in gene expression may be a common feature of many cancer cell culture systems, with functional implications for the use of such models for preclinical drug development.
MIL-100(Al, Fe) as water adsorbents for heat transformation purposes—a promising application (2011)

The adsorption/desorption of up to 0.75 g of water vapour per g of the porous MOFs 3D-{M3O(X)(H2O)2[btc]2·nH2O}, MIL-100 (M = Al, Fe; X = OH, F, btc = benzene-1,3,5-tricarboxylate, trimesate), occurs at small relative pressures of p/p0 < 0.4 and a comparatively small hysteresis. Together with very good cycle stability, these properties render both MIL-100(Al and Fe) very suitable candidates for thermally driven heat pumps or adsorption chillers.
Renal Transplantation (1994)

Renal transplantation is the treatment of choice for patients with end-stage renal disease. Better comprehension of the rejection response, improved preservation of organs, judicious use of cyclosporine, the application of antilymphocyte agents for the prevention and treatment of rejection, and specific protocols for the prevention and treatment of infection have all contributed to the recent improvement in outcome after renal transplantation.Immunobiology of Renal TransplantationThe Anti-Allograft (Rejection) ResponseRenal-allograft rejection depends on the coordinated activation of alloreactive T cells and antigen-presenting cells (e.g., monocyte-macrophages, dendritic cells, and B cells). Whereas acute rejection is a T-cell-dependent process, a broad array . . .
Substrate-induced inactivation of aromatase by allenic and acetylenic steroids (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSubstrate-induced inactivation of aromatase by allenic and acetylenic steroidsB. W. Metcalf, C. L. Wright, J. P. Burkhart, and J. O. JohnstonCite this: J. Am. Chem. Soc. 1981, 103, 11, 3221–3222Publication Date (Print):June 1, 1981Publication History Published online1 May 2002Published inissue 1 June 1981https://pubs.acs.org/doi/10.1021/ja00401a054https://doi.org/10.1021/ja00401a054research-articleACS PublicationsRequest reuse permissionsArticle Views175Altmetric-Citations123LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Leukotriene B4 Receptor-1 Is Essential for Allergen-Mediated Recruitment of CD8+ T Cells and Airway Hyperresponsiveness (2005)

Recent studies in both human and rodents have indicated that in addition to CD4+ T cells, CD8+ T cells play an important role in allergic inflammation. We previously demonstrated that allergen-sensitized and -challenged CD8-deficient (CD8-/-) mice develop significantly lower airway hyperresponsiveness (AHR), eosinophilic inflammation, and IL-13 levels in bronchoalveolar lavage fluid compared with wild-type mice, and that all these responses were restored by adoptive transfer of in vivo-primed CD8+ T cells or in vitro-generated effector CD8+ T cells (T(EFF)). Recently, leukotriene B4 and its high affinity receptor, BLT1, have been shown to mediate in vitro-generated T(EFF) recruitment into inflamed tissues. In this study we investigated whether BLT1 is essential for the development of CD8+ T cell-mediated allergic AHR and inflammation. Adoptive transfer of in vivo-primed BLT1+/+, but not BLT1-/-, CD8+ T cells into sensitized and challenged CD8-/- mice restored AHR, eosinophilic inflammation, and IL-13 levels. Moreover, when adoptively transferred into sensitized CD8-/- mice, in vitro-generated BLT1+/+, but not BLT1-/-, T(EFF) accumulated in the lung and mediated these altered airway responses to allergen challenge. These data are the first to show both a functional and an essential role for BLT1 in allergen-mediated CD8+ T(EFF) recruitment into the lung and development of AHR and airway inflammation.