gebhart/patrepeval huggingface dataset:
An amino acid has two sides: A new 2D measure provides a different view of solvent exposure (2005)

The concept of amino acid solvent exposure is crucial for understanding and predicting various aspects of protein structure and function. The traditional measures of solvent exposure however suffer from various shortcomings, like for example the inability to distinguish exposed, partly exposed, buried, and deeply buried residues. This article introduces a new measure of solvent exposure called Half-Sphere Exposure that addresses many of the shortcomings of other methods. The new measure outperforms other measures with respect to correlation with protein stability, conservation among fold homologs, amino acid-type dependency and interpretation. The measure consists of the number of Calpha atoms in two half spheres around a residue's Calpha atom. Conceptually, one of the half spheres corresponds to the side chain's neighborhood, the other half sphere being in the opposite direction. We show here that the two half spheres correspond to two regions around an amino acid that are surprisingly distinct in terms of geometry and energy. This aspect of protein structure introduced here forms the basis of the Half-Sphere Exposure measure. The results strongly suggest that in many respects, a 2D measure is inherently much better suited to describe solvent exposure than the traditional 1D measures. Importantly, Half-Sphere Exposure can be calculated from the Calpha atom coordinates only, which abolishes the need for a full-atom model to calculate solvent exposure. Hence, the measure can be used in protein structure prediction methods that are based on various simplified models. Half-Sphere Exposure has great potential for use in protein structure prediction and analysis.
Screening programmes for the early detection and prevention of oral cancer (2010)

Although there is evidence that a visual examination as part of a population based screening programme reduced the mortality rate of oral cancer in high-risk individuals, whilst producing a stage shift and improvement in survival rates across the population as a whole, the evidence is limited to one study and is associated with a high risk of bias. This was compounded by the fact that the effect of cluster randomisation was not accounted for in the analysis. Furthermore, no robust evidence was identified to support the use of other adjunctive technologies like toluidine blue, brush biopsy or fluorescence imaging within a primary care environment. Further randomised controlled trials are recommended to assess the efficacy, effectiveness and cost-effectiveness of a visual examination as part of a population based screening programme.
Cold Fusion: The Scientific Fiasco of the Century (1993)

A summary of the cold fusion fiasco, its history, claims, experimental questions, are presented in this book. The author gives in some detail good reasons why cold fusion has been disregarded by mainstream science. Disturbing questions about the behavior of scientific investigators and reactions to such events are raised.
Optimization of Pt-based spin-Hall-effect spintronic devices (2013)

We study experimentally the routes to improve the characteristics of the spin-Hall-effect devices based on permalloy/Pt bilayers by optimization of the Pt layer thickness and by the addition of an antiferromagnetic spin-sinking layer. We experimentally determine the spin-diffusion length in Pt and show that Pt thickness can be reduced down to 2 nm without degradation of the device characteristics caused by the spin accumulation effects, which provides possibilities for significant reduction of the required driving currents. We also show that the addition of a spin-sinking layer results in a non-monotonic dependence of device efficiency on the Pt thickness.
Photoinduced luminescence from the noble metals and its enhancement on roughened surfaces (1986)

Single-photon- and multiphoton-induced luminescence spectra were obtained from clean samples of silver, copper, and gold with both smooth and rough surfaces. The spectra reveal new features which are correlated with interband transitions at selected symmetry points in the Brillouin zone. Calculating luminescence spectra based on simplified models of the band structures of the noble metals and taking into account the Fresnel local-field corrections, we find qualitative agreement with the observed spectra from smooth samples. The agreement between theory and experiment is less satisfactory for rough samples. The influence of surface roughness on the luminescence is largely attributable to local-field enhancement in the rough surface protrusions.
Flavopiridol administered using a pharmacologically derived schedule is associated with marked clinical efficacy in refractory, genetically high-risk chronic lymphocytic leukemia (2006)

Despite promising preclinical studies with the cyclin-dependent kinase inhibitor flavopiridol in chronic lymphocytic leukemia (CLL) and other diseases, previous clinical trials with this agent have been disappointing. The discovery of differential protein binding of flavopiridol in human and bovine serum contributed to an effective pharmacokinetic-derived schedule of administration of this agent. On the basis of pharmacokinetic modeling using our in vitro results and data from a previous trial, we initiated a phase 1 study using a 30-minute loading dose followed by 4 hours of infusion administered weekly for 4 of 6 weeks in patients with refractory CLL. A group of 42 patients were enrolled on 3 cohorts (cohort 1, 30 mg/m2 loading dose followed by 30 mg/m2 4-hour infusion; cohort 2, 40 mg/m2 loading dose followed by 40 mg/m2 4-hour infusion; and cohort 3, cohort 1 dose for treatments 1 to 4, then a 30 mg/m2 loading dose followed by a 50 mg/m2 4-hour infusion). The dose-limiting toxicity using this novel schedule was hyperacute tumor lysis syndrome. Aggressive prophylaxis and exclusion of patients with leukocyte counts greater than 200x10(9)/L have made this drug safe to administer at the cohort 3 dose. Of the 42 patients treated, 19 (45%) achieved a partial response with a median response duration that exceeds 12 months. Responses were noted in patients with genetically high-risk disease, including 5 (42%) of 12 patients with del(17p13.1) and 13 (72%) of 18 patients with del(11q22.3). Flavopiridol administered using this novel schedule has significant clinical activity in refractory CLL. Patients with bulky disease and high-risk genetic features have achieved durable responses, thereby justifying further study of flavopiridol in CLL and other diseases.
Toxicity of platinum compounds (2003)

Since the introduction of platinum-based combination chemotherapy, particularly cisplatin, the outcome of the treatment of many solid tumours has changed. The leading platinum compounds in cancer chemotherapy are cisplatin, carboplatin and oxaliplatin. They share some structural similarities; however, there are marked differences between them in therapeutic use, pharmacokinetics and adverse effects profiles [1-4]. Compared to cisplatin, carboplatin has inferior efficacy in germ-cell tumour, head and neck cancer and bladder and oesophageal carcinoma, whereas both drugs seem to have comparable efficacy in advanced non-small cell and small cell lung cancer as well as ovarian cancer [5-7]. Oxaliplatin belongs to the group of diaminocyclohexane platinum compounds. It is the first platinum-based drug that has marked efficacy in colorectal cancer when given in combination with 5-fluorouracil and folinic acid [8,9]. Other platinum compounds such as oral JM216, ZD0473, BBR3464 and SPI-77, which is a pegylated liposomal formulation of cisplatin, are still under investigation [10-13], whereas nedaplatin has been approved in Japan for the treatment of non-small cell lung cancer and other solid tumours. This review focuses on cisplatin, carboplatin and oxaliplatin.
Fast, Radiation‐Hard Scintillating Detector: A Potential Application for Sol‐Gel Glass (1988)

To meet the present‐day rate and radiation dose requirements, one would like to have a scintillator with the high radiation resistance of pure silica glass and the short fluorescence decay time of organic fluors. The new technology of sol‐gel glass production permits the preparation of organic/inorganic composite materials by doping the silica gels with organic fluors. The procedure of production of monolithic organic/inorganic composite materials, such as 2‐(4‐ tert butylphenyl)‐5‐(4‐biphenylyl)‐1,3,4‐oxadiazole/SiO 2 , p ‐terphenyl/SiO 2 , p ‐quaterphenyl/SiO 2 , and 3‐hydroxyflavone/SiO 2 , and the associated characterization techniques are described. The efficiency of light production, the light attenuation, the time width of light pulse, and the radiation resistance of the scintillating sol‐gel glass are discussed. Preliminary results indicate that this technical advance will permit the creation of new materials with potential application such as particle detectors which are both radiation hard and fast.
Development and application of a multiplexable flow cytometry‐based assay to quantify cell‐mediated cytolysis (2010)

Although target cell cytolysis has been widely employed to describe effector function of cells, cytolysis assays as commonly employed do not generate quantitative data. In this report we describe the development and application of a statistically supported flow cytometry-based assay to quantify cell-mediated cytolysis. The assay depends on the use of the fluorescent dye CFSE to distinguish target from effector cells, the DNA intercalating dye 7AAD to distinguish dead from live cell events, and on the establishment of a cytolysis curve that allows for the derivation of statistically robust data. We demonstrate that the cytolysis curve is well described by a four parameter logistic regression model provided that (i) the range of effector to target (E:T) ratios studied allows for full description of the logistic curve, and (ii) an adequate number of data points are collected to estimate the model parameters. We show that the assay is highly reproducible and accurate, and comparable in sensitivity with the standard (51)Cr assay. We report on the potential for this assay to generate quantitative data on the cytolytic activity of both CD8 T and NK cells; describe a relationship between the efficiency of effector cell degranulation and target cell cytolysis throughout a range of E:T ratios, and demonstrate the potential to multiplex with other platforms to obtain broader datasets for the effector phenotype of cells. Appropriate use of this assay will enhance the ability to derive quantitative and integrated correlative datasets from basic, translational, and clinical studies.
Toll-like Receptor 2 Is Required for LPS-induced Toll-like Receptor 4 Signaling and Inhibition of Ion Transport in Renal Thick Ascending Limb (2012)

Previously we demonstrated that basolateral LPS inhibits HCO(3)(-) absorption in the renal medullary thick ascending limb (MTAL) through TLR4-dependent ERK activation. Here we report that the response of the MTAL to basolateral LPS requires TLR2 in addition to TLR4. The basolateral addition of LPS (ultrapure Escherichia coli K12) decreased HCO(3)(-) absorption in isolated, perfused MTALs from wild-type mice but had no effect in MTALs from TLR2(-/-) mice. In contrast, inhibition of HCO(3)(-) absorption by lumen LPS was preserved in TLR2(-/-) MTALs, indicating that TLR2 is involved specifically in mediating the basolateral LPS response. LPS also did not increase ERK phosphorylation in MTALs from TLR2(-/-) mice. TLR2 deficiency had no effect on expression of TLR4, MD-2, or MyD88. However, LPS-induced recruitment of MyD88 to the basolateral membrane was impaired in TLR2(-/-) MTALs. Inhibition of HCO(3)(-) absorption by LPS did not require CD14. Co-immunoprecipitation studies demonstrated an association between TLR4 and TLR2. Inhibition of HCO(3)(-) absorption by TLR2-specific ligands was preserved in MTALs from TLR4(-/-) mice. These results indicate that the effect of basolateral LPS to inhibit HCO(3)(-) absorption in the MTAL through MyD88-dependent ERK activation depends on a novel interaction between TLR4 and TLR2. TLR2 plays a dual role in the induction of intracellular signals that impair MTAL function, both through cooperation with TLR4 to mediate ERK signaling by LPS and through a TLR4-independent signaling pathway activated by Gram-positive bacterial ligands. Regulation of TLR2 expression and its interaction with TLR4 may provide new mechanisms for controlling and therapeutic targeting of TLR4-mediated LPS responses.
A.G.P.S. (A Good Place for Seismic) (1992)

Abstract The operational problems associated with acquiring seismic data in offshore frontier areas of S.E. Asia can usually be evaluated in terms of logistics, practicality and security. Navigation, the most important aspect of marine seismic acquisition, presents a unique challenge in terms of these three variables. The geographical and geometrical restrictions of shore-based navigation systems limit their use especially in frontier areas of S.E. Asia. such as Myanmar, Vietnam and Cambodia. The logistical difficulties of supporting a navigation chain especially in areas where security is a problem can not only cause operational delays, but prolonged interference can also escalate acquisition costs. As an alternative to standard shore-based navigation systems, satellite navigation systems, in particular the Global Positioning System (GPS), are discussed. Developed by the U.S. Department of Defense for military use, GPS has developed into a reliable navigation system. A brief introduction to satellite navigation including GPS is followed by two examples of seismic surveys recently acquired using only GPS as a navigation system. The reasons for selecting GPS as the primary and secondary navigation system in the first example, offshore Myanmar, were related to security and logistics. In the second example, offshore Cambodia, the geographic and geometric problems prompted the use of GPS. Both surveys were successfully acquired even though GPS was not fully operational.
Expression of BAFF (BLyS) in T cells infiltrating labial salivary glands from patients with Sjögren's syndrome (2004)

Primary Sjögren's syndrome (pSS) is an autoimmune disorder characterized by lymphocytic infiltration of the salivary glands. Most of the infiltrating cells are T cells, but other features of the disease include polyclonal B-cell activation, systemic production of autoantibodies, and increased risk of developing B-cell non-Hodgkin's lymphoma. Recently, a new tumour necrosis factor, the B-cell activating factor (BAFF; also known as BLyS), has been implicated in the polyclonal activation of B cells. Using immunohistochemistry, this study evaluated BAFF expression in labial salivary gland biopsies from 14 patients with pSS, 14 normal controls, and two patients with sarcoidosis. Labial salivary gland samples from seven patients with pSS, seven controls, and one patient with sarcoidosis were double-stained using indirect immunofluorescence. RT-PCR analysis was also performed on lip biopsy samples from two patients and two controls. In all 14 pSS specimens, infiltrating inflammatory cells strongly expressed BAFF protein, as did some ductal epithelial cells, but acinar cells were negative. Some B cells were present in the vicinity of the BAFF-positive cells. In the 14 normal labial salivary glands, some ductal cells were moderately positive, but acinar cells were negative. In the labial salivary glands from the two patients with sarcoidosis, infiltrating lymphocytes were not stained. BAFF mRNA expression was confirmed by RT-PCR in salivary glands from pSS patients. Double immunofluorescence revealed T cells and macrophages to be the main cell types expressing BAFF in salivary glands from pSS patients. In conclusion, BAFF may be expressed by T cells at the site of autoimmune damage and could play a role in the pathogenesis of pSS, particularly by triggering the activation of self-antigen-driven autoimmune B cells.
Effect of Recombinant Fibroblast Interferon and Recombinant Immune Interferon on Growth and the Antigenic Phenotype of Multidrug-Resistant Human Glioblastoma Multiforme Cells (1991)

To study the effect of drug resistance on the response of stage IV astrocytomas to interferon, a human glioblastoma multiforme cell line, GBM-18, was transfected with an expression-vector plasmid containing a human multidrug resistance (MDR) gene (pHaMDR1/A), and clones surviving in colchicine were isolated. GBM-18 multidrug-resistant subclones displayed cross-resistance to other chemotherapeutic agents, including vincristine, doxorubicin, and dactinomycin. The multidrug-resistant phenotype was reversible when GBM-18 multidrug-resistant cells were cultured in colchicine and the calcium-channel blocker verapamil. The level of the MDR1 gene (also known as PGY1) message was increased in GBM-18 multidrug-resistant cells selected for increased resistance to colchicine, and this effect was not correlated with an amplification of the MDR1 gene. In both parental GBM-18 and GBM-18 multidrug-resistant cells, growth was suppressed to a greater degree when cultures were treated with the combination of fibroblast interferon (IFN-beta) and immune interferon (IFN-gamma). Parental cells and multidrug-resistant subclones varied in their de novo and/or interferon-modulated expression of HLA class I and class II antigens, a high-molecular-weight melanoma-associated antigen, and intercellular adhesion molecule 1 (ICAM-1). Of the antigens tested, ICAM-1 and HLA class I antigens were the most sensitive to enhanced expression induced by IFN-beta and IFN-gamma when used alone or in combination. The results of the present study indicate that multidrug-resistant human glioblastoma multiforme cells retain their increased sensitivity to the antiproliferative activity of the combination of IFN-beta plus IFN-gamma, and differences in antigenic phenotype are apparent in independent multidrug-resistant glioblastoma multiforme clones.
Evaluating the use of recombinant human activated protein C in adult severe sepsis (2012)

Recombinant human activated protein C use was associated with a significant improvement in hospital mortality in patients who participated in the Surviving Sepsis Campaign.
Novel plasma biomarkers associated with liver disease severity in adults with nonalcoholic fatty liver disease (2016)

Specific plasma biomarkers are significantly associated with disease activity and severity of fibrosis in NAFLD and are potentially valuable tools for noninvasive stratification of patients with NAFLD and identification of targets for therapeutic intervention. (Hepatology 2017;65:65-77).
Heparin-induced thrombocytopenia: studies with a new low molecular weight heparinoid, Org 10172 (1989)

Studies were performed to determine the cross-reaction rate of the heparin-dependent antibody with Org 10172, a new low molecular weight heparinoid, and to investigate the effect of Org 10172 on platelet activation induced by the antibody. The plasmas of 17 patients with thrombocytopenia induced by standard heparin were shown, by platelet aggregation studies, to contain the heparin-dependent antibody. Of these 17 patient plasmas, only three cross-reacted with the heparinoid, producing a cross-reaction rate of 18%. When Org 10172 was added to a reaction mixture containing normal platelet-rich plasma, patient plasma, and standard heparin with non-cross-reacting plasmas, it inhibited platelet aggregation and thromboxane B2 production induced by the antibody, provided that the ratio of Org 10172 concentration (anti-Xa U/mL) to standard heparin concentration (IU/mL) exceeded 2.5 to 5.0. This inhibitory effect was observed only with platelet activation mediated by the antibody, but not by collagen (2 micrograms/mL) or ADP (5.0 mumol/L). Additionally, three of 17 patients with serious thrombosis, whose plasma showed no cross-reaction with the heparinoid, received Org 10172 treatment with a good response in each case. These findings suggest that Org 10172 may be a useful drug for the treatment of heparin-induced thrombocytopenia.
Kinetics of Formation of Ca2+ Complexes of Acyclic and Macrocyclic Poly(amino carboxylate) Ligands:  Bimolecular Rate Constants for the Fully-Deprotonated Ligands Reveal the Effect of Macrocyclic Ligand Constraints on the Rate-Determining Conversions of Rapidly-Formed Intermediates to the Final Complexes (1997)

The apparent bimolecular rate constants, k(1) (M(-)(1) s(-)(1)), for the formation of Ca(2+) complexes of a series of acyclic (edta, egta, cdta) and macrocyclic (dota, teta, do3a) poly(amino carboxylate) ligands were determined in the pH range 7-13 using the fluorescent ligand quin2 in a stopped-flow apparatus to monitor the ligand competition reaction. The k(1) values are observed to reach maximum constant values at high pH, characteristic of reactions involving the fully-deprotonated ligand species. Bimolecular formation constants k(Ca)(L), k(Ca)(HL), and k(Ca)(H)()2(L), characteristic of the reaction of the fully-deprotonated and mono- and diprotonated ligands, respectively, were derived from the pH dependence of the k(1) values. The k(Ca)(L) values of the acyclic ligands are edta, 4.1 x 10(9) M(-)(1) s(-)(1); egta, 2.1 x 10(9) M(-)(1) s(-)(1); and cdta, 2.3 x 10(9) M(-)(1) s(-)(1), while the corresponding values for the macrocyclic ligands are dota, 4.7 x 10(7) M(-)(1) s(-)(1); teta, 1.1 x 10(7) M(-)(1) s(-)(1); and do3a, 1.0 x 10(8) M(-)(1) s(-)(1). The smaller values for the macrocyclic ligands are consistent with ligand-dictated constraints imposed on the conversion of a stable intermediate to the final complex, a process which involves the simultaneous stripping of several water molecules from the first-coordination sphere of the Ca(2+) ion.
Tris(3-mercaptopropyl)-N-glycylaminomethane as a New Linker to Bridge Antibody with Metal Particles for Biological Cell Separations (2000)

Conjugates of nickel beads with CD8 and anti-red blood cell KC16 antibody were prepared by using the aminotrithiolate "spider" ligand, tris(3-mercaptopropyl)-N-glycylaminomethane, in its new function as a linker between the surface of nickel beads and antibody via activation of spider ligand attached to nickel beads with the common, heterobifunctional cross-linker, sulfosuccinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (sulfo-SMCC). Raw nickel beads were cleaned by either mild sonication in a bath or by stronger probe sonication to remove surface nickel oxide layers, before attachment of the spider ligand. Scanning electron micrographs of the nickel beads before and after probe sonication showed a marked change from a corrugated to a smooth bead surface. Analyses of the supernatants of conjugation mixtures for antibody gave surface densities of 2.5-5.2 mg/m(2) for CD8 and 0.6-12 mg/m(2) for KC16 antibody runs. The antibody-spider-nickel bead conjugates were used in magnetic bead depletions of targeted CD8+ lymphocytes or red blood cells (rbcs) in whole blood of normal donors. For CD8 cell depletions, the undepleted controls and supernatants of depleted samples were analyzed for CD8/CD4 cell populations by flow cytometry with appropriate fluorescent antibody markers. Enumeration of red blood cells, white blood cells (wbcs), and platelets (plts) in undepleted controls and supernatants of depleted samples were carried out on appropriate hematology counters. Whole blood titer results with various lots of either CD8-spider-nickel or KC16-spider-nickel bead conjugates showed varying degrees of depletion ability as indicated by bead-to-cell ratios of 2-32 for CD8 beads and by rbc-to-bead ratios of 1.2-10 for KC16 beads. Moreover, varying degrees of specificity of CD8 beads for CD8+ cells over CD4+ cells and of KC16 beads for rbcs over white blood cells and platelets were observed from the normalized nontargeted cell population figures in undepleted controls versus supernatants of depleted samples.