gebhart/patrepeval huggingface dataset:
CT-SPECT fusion plus conjugate views for determining dosimetry in iodine-131-monoclonal antibody therapy of lymphoma patients. (1994)

The quantitative SPECT plus conjugate views method may be of general utility for macro-dosimetry of 131I therapies.
Targeting Tyrosine Kinases in Cancer: The Second Wave (2006)

One of the most exciting developments in cancer research in recent years has been the clinical validation of molecularly targeted drugs that inhibit the action of pathogenic tyrosine kinases. Treatment of appropriately selected patients with these drugs can alter the natural history of their disease and improve survival. The clinical validation of these "first-generation" tyrosine kinase inhibitors has been the prelude to a second wave of advances in molecular targeting that is expected to further change the way we classify and treat cancer. Efforts are now being directed at identifying the tumor subtypes and patients who will benefit the most from these drugs. In addition, new compounds that circumvent acquired resistance to the first-generation tyrosine kinase inhibitors are being tested in patients with refractory disease. Agents directed against new molecular targets are also being explored.
Class II MHC quantitative binding motifs derived from a large molecular database with a versatile iterative stepwise discriminant analysis meta-algorithm. (1999)

Software is available commercially; data are free over the Internet.
The automatic generation of extended queries (1989)

In the extended vector space model, each document vector consists of a set of subvectors representing the multiple concepts or concept classes present in the document. Typical information concepts, in addition to the usual content terms or descriptors, include author names, bibliographic links, etc. The extended vector space model is known to improve retrieval effectiveness. However, a major impediment to the use of the extended model is the construction of an extended query. In this paper, we describe a method for automatically extending a query containing only content terms (a single concept class) to a representation containing multiple concept classes. No relevance feedback is involved. Experiments using the CACM collection resulted in an average precision 34% better than that obtained using the standard single-concept term vector model.
NK Cell Anti-Tumor Immune Responses Are Impaired by Sorafenib but Not by Sunitinib (2008)

Abstract Natural killer (NK) cells play an important role in the surveillance of tumors by exerting cellular cytotoxicity and also due to their ability to secrete immunoregulatory cytokines. A variety of intracellular kinases like PI3K, MAPKs or STAT molecules are involved in the regulation of NK cell functions. Therefore, treatment of tumor patients with small molecule inhibitors targeting various protein kinases may also largely affect NK cell anti-tumor reactivity. The multikinase inhibitors Sunitinib (SUTENT®) and Sorafenib (NEXAVAR®) have been approved for the treatment of patients with metastatic Renal Cell Carcinoma (RCC), and are now also being evaluated in various other tumor entities including AML. Both compounds target, among others, PDGF receptors, VEGF receptors, Flt3 and c-kit. Sorafenib additionally inhibits the MAPK pathway members B-RAF and c-RAF. Here we report that Sorafenib but not Sunitinib substantially reduces NK cell cytotoxicity as revealed by analysis of cell surface CD107a expression as a surrogate marker for mobilization of cytolytic granules on NK cells from ten healthy donors. In line, pharmacological levels of Sorafenib but not Sunitinib largely reduced lysis of several solid tumor and leukemia cell lines by primary NK cells, and this inhibitory effect of Sorafenib occurred concentration dependently. Furthermore, Sorafenib but not Sunitinib concentration dependently impaired NK cell IFN-γ production in coculture experiments with different tumor cell lines. Since Sorafenib, in contrast to Sunitinib, also potently inhibits RAF which is involved in MAPK activation we determined the influence of the two compounds on ERK phosphorylation which is important for the activation of NK cell anti-tumor reactivity. While Sunitinib had no effect, Sorafenib, alike the specific MEK inhibitor PD98059, markedly reduced ERK phosphorylation in NK cells. Taken together, out results indicate that NK cell-mediated anti-tumor immune responses are impaired by Sorafenib but not by Sunitinib via inhibition of signaling pathways crucial for NK cell effector functions. Thus, Sunitinib is exquisitely suitable in diseases and for therapeutic approaches which rely on a sufficient anti-tumor immune response like e.g. allogenic stem cell transplantation in AML or immunotherapeutic approaches in RCC patients.
Chromatin Immunoprecipitation (ChIP) on Chip Experiments Uncover a Widespread Distribution of NF-Y Binding CCAAT Sites Outside of Core Promoters (2005)

The CCAAT box is a prototypical promoter element, almost invariably found between -60 and -100 upstream of the major transcription start site. It is bound and activated by the histone fold trimer NF-Y. We performed chromatin immunoprecipitation (ChIP) on chip experiments on two different CpG islands arrays using chromatin from hepatic HepG2 and pre-B cell leukemia NALM-6 cell lines, with different protocols of probe preparation and labeling. We analyzed and classified 239 known or predicted targets; we validated several by conventional ChIPs with anti-YB and anti-YC antibodies, in vitro EMSAs, and ChIP scanning. The importance of NF-Y binding for gene expression was verified by the use of a dominant negative NF-YA mutant. All but four genes are new NF-Y targets, falling into different functional categories. This analysis reinforces the notion that NF-Y is an important regulator of cell growth, and novel unexpected findings emerged from this unbiased approach. (i) A remarkable proportion of NF-Y targets, 40%, are complex transcriptional units composed of divergent, convergent, and tandem promoters. (ii) 40-50% of NF-Y sites are not in core promoters but are in introns or at distant 3' or 5' locations. The abundance of "unorthodox" CCAAT positions highlights an unexpected complexity of the NF-Y-mediated transcriptional network.
Blur filtration fails to preserve privacy for home-based video conferencing (2006)

Always-on video provides rich awareness for distance-separated coworkers. Yet video can threaten privacy, especially when it captures telecommuters working at home. We evaluated video blurring, an image masking method long touted to balance privacy and awareness. Results show that video blurring is unable to balance privacy with awareness for risky situations. Reactions by participants suggest that other popular image masking techniques will be problematic as well. The design implication is that image masking techniques will not suffice for privacy protection in video-based telecommuting situations. Other context-aware privacy-protecting strategies are required, as illustrated in our prototype context-aware home media space.
Direct single-cell biomass estimates for marine bacteria via Archimedes’ principle (2016)

Microbes are an essential component of marine food webs and biogeochemical cycles, and therefore precise estimates of their biomass are of significant value. Here, we measured single-cell biomass distributions of isolates from several numerically abundant marine bacterial groups, including Pelagibacter (SAR11), Prochlorococcus and Vibrio using a microfluidic mass sensor known as a suspended microchannel resonator (SMR). We show that the SMR can provide biomass (dry mass) measurements for cells spanning more than two orders of magnitude and that these estimates are consistent with other independent measures. We find that Pelagibacterales strain HTCC1062 has a median biomass of 11.9±0.7 fg per cell, which is five- to twelve-fold smaller than the median Prochlorococcus cell's biomass (depending upon strain) and nearly 100-fold lower than that of rapidly growing V. splendidus strain 13B01. Knowing the biomass contributions from various taxonomic groups will provide more precise estimates of total marine biomass, aiding models of nutrient flux in the ocean.
Intravenous immunoglobulins in immunodeficiencies: more than mere replacement therapy (2011)

Intravenous immunoglobulin (IVIG) is a therapeutic compound prepared from pools of plasma obtained from several thousand healthy blood donors. For more than 20 years, IVIG has been used in the treatment of a wide range of primary and secondary immunodeficiencies. IVIG now represents a standard therapeutic option for most antibody deficiencies. Routinely, IVIG is used in patients with X-linked agammaglobulinaemia (XLA), common variable immunodeficiency (CVID), X-linked hyper-IgM, severe combined immunodeficiency, Wiskott-Aldrich syndrome, and selective IgG class deficiency. In addition, IVIG is used extensively in the treatment of a wide variety of autoimmune disorders. IVIG is administered at distinct doses in the two clinical settings: whereas immunodeficient patients are treated with replacement levels of IVIG, patients with autoimmune and inflammatory diseases are administered with very high doses of IVIG. Several lines of experimental evidence gathered in the recent years suggest that the therapeutic beneficial effect of IVIG in immunodeficiencies reflects an active role for IVIG, rather than a mere passive transfer of antibodies.
Induction of antibodies against GM2 ganglioside by immunizing melanoma patients using GM2-keyhole limpet hemocyanin + QS21 vaccine: a dose-response study. (2000)

In a previous randomized Phase III trial (P. O. Livingston et al, J. Clin. Oncol., 12: 1036-1044, 1994), we demonstrated that immunization with GM2 and bacille Calmette-Guerin reduced the risk of relapse in stage III melanoma patients who were free of disease after surgical resection and who had no preexisting anti-GM2 antibodies. That vaccine formulation induced IgM anti-GM2 antibodies in 74% but induced IgG anti-GM2 antibodies in only 10% of the patients. To optimize the immune response against GM2, a reformulated vaccine was produced conjugating GM2 to keyhole limpet hemocyanin (KLH) and using the adjuvant QS21 (GM2-KLH/QS21). In pilot studies, 70 microg of vaccine induced IgG anti-GM2 antibodies in 76% of the patients. We wished to define the lowest vaccine dose that induced consistent, high-titer IgM and IgG antibodies against GM2. Fifty-two melanoma patients who were free of disease after resection but at high risk for relapse were immunized with GM2-KLH/QS21 vaccine at GM2 doses of 1, 3, 10, 30, or 70 ILg on weeks 1, 2, 3, 4, 12, 24, and 36. Serum collected at frequent and defined intervals was tested for anti-GM2 antibodies. Overall, 88% of the patients developed IgM anti-GM2 antibodies; 71% also developed IgG anti-GM2 antibodies. GM2-KLH doses of 3-70 microg seemed to be equivalent in terms of peak titers and induction of anti-GM2 antibodies. At the 30-microg dose level, 50% of the patients developed complement fixing anti-GM2 antibodies detectable at a serum dilution of 1:10. We conclude that the GM2-KLH/QS21 formulation is more immunogenic than our previous formulation and that 3 microg is the lowest dose that induces consistent, high-titer IgM and IgG antibodies against GM2.
A New Viscoelastic Surfactant for High Temperature Carbonate Acidizing (2012)

Abstract Diverting agents have been widely used during matrix acidizing treatments to accomplish the uniform distribution of acid solutions across the target zones. One of the most popular formulas is based on viscoelastic surfactants (VES) which showed good results in the lab and field tests. A major limitation with the conventional VES is temperature. Most of these surfactants do not hold viscosity at temperatures greater than 250°F. A new VES that can be used at higher temperatures was developed. The apparent viscosity of the spent VES-based acids was measured as a function of temperature and shear rate at 300 psi. Various corrosion inhibitors were mixed together with the new VES to find out the most compatible formula. A coreflood test was conducted on a 20 in. long carbonate core to examine the performance of the new surfactant. The core was CAT scanned before and after the experiment to observe the wormholes created by the new system. The acid contained 20 wt% HCl and 4 vol% VES. Spent acids of the new VES had a high viscosity up to 325°F. Several corrosion inhibitors were identified that can be mixed with the new system without affecting the apparent viscosity of the spent acid. Similar to current VES, mutual solvent is recommended in the post flush to reduce the fluid viscosity and remove any gel from the core. CAT scan of the core show wider and tortuous wormholes, indicative of good retardation of the new VES-based acid system.
Role of Substrate Metal in Gold Nanoparticle Enhanced Surface Plasmon Resonance Imaging (2000)

Using Au nanoparticles, it is possible under certain experimental conditions to considerably enhance the sensitivity of a conventional surface plasmon resonance (SPR) device. In this report, we examine the mechanism of this enhancement and discuss the experimental factors that are crucial to the performance of such a nanoparticle based SPR device. Among these factors, the surface plasmon-supporting metal substrate plays a major role. We demonstrate this by comparing experimental SPR data for Au and Ag substrates. In both cases, ∼25−30 nm diameter Au particles are attached to the substrate metal via a sandwiched monolayer of 1,6-hexanedithiol. The width and the efficiency of SPR for both substrates are affected by the Au particles. However, the particle-induced shift in the SPR angle is observed only for the Au substrate. This observation is explained in terms of competitive effects of propagating surface plasmons in the substrate metal and localized surface plasmons in the Au nanoparticles.
Coherent Control of Femtosecond Energy Localization in Nanosystems (2002)

We predict and quantitatively evaluate the unique possibility of concentrating the energy of an ultrafast excitation of a nanosystem in a small part of the whole system by means of coherent control (phase modulation of the exciting ultrashort pulse). Such concentration is due to dynamic properties of surface plasmons and leads to local fields enhanced by orders of magnitude. This effect exists for both "engineered" and random nanosystems. We also discuss possible applications.
Quantitative study of single molecule location estimation techniques (2009)

Estimating the location of single molecules from microscopy images is a key step in many quantitative single molecule data analysis techniques. Different algorithms have been advocated for the fitting of single molecule data, particularly the nonlinear least squares and maximum likelihood estimators. Comparisons were carried out to assess the performance of these two algorithms in different scenarios. Our results show that both estimators, on average, are able to recover the true location of the single molecule in all scenarios we examined. However, in the absence of modeling inaccuracies and low noise levels, the maximum likelihood estimator is more accurate than the nonlinear least squares estimator, as measured by the standard deviations of its estimates, and attains the best possible accuracy achievable for the sets of imaging and experimental conditions that were tested. Although neither algorithm is consistently superior to the other in the presence of modeling inaccuracies or misspecifications, the maximum likelihood algorithm emerges as a robust estimator producing results with consistent accuracy across various model mismatches and misspecifications. At high noise levels, relative to the signal from the point source, neither algorithm has a clear accuracy advantage over the other. Comparisons were also carried out for two localization accuracy measures derived previously. Software packages with user-friendly graphical interfaces developed for single molecule location estimation (EstimationTool) and limit of the localization accuracy calculations (FandPLimitTool) are also discussed.
Specificity of the S1 nuclease from Aspergillus oryzae. (1975)

Conditions are described for digesting single-stranded DNA by S1 nuclease without introducing breaks in double-stranded DNA. The enzyme is inhibited by low concentrations of various compounds of phosphate. Under certain conditions S1 nuclease cleaves the strand opposite a nick in bacteriophage T5 DNA; under other conditions, the enzyme cleaves a loop in one strand of heteroduplex lambdaDNA while leaving the opposite strand intact. S1 nuclease makes many single strand breaks in ultraviolet-irradiated duplex lambdaDNA. Superhelical DNA of phiX174 (Form I) is converted first to a relaxed circular molecule (Form II), and then to a linear molecule (Form III) by cleavage at one site per molecule. Since the cleavage occurs at many sites in the population of molecules, the partially single-stranded regions in phiX174 superhelical DNA are not determined by specific nucleotide sequences.
Bioartificial Dermal Substitute: A Preliminary Report on Its Use for the Management of Complex Combat-Related Soft Tissue Wounds (2007)

Bioartificial dermal substitute grafting, when coupled with subatmospheric dressing management and delayed split-thickness skin grafting, is an effective technique for managing complex combat-related soft tissue wounds with exposed tendon. This can potentially lessen the need for local rotational or free flap coverage.
Matrix metalloproteinase 2 releases active soluble ectodomain of fibroblast growth factor receptor 1. (1996)

Recent studies have demonstrated the existence of a soluble fibroblast growth factor (FGF) receptor type 1 (FGFR1) extracellular domain in the circulation and in vascular basement membranes. However, the process of FGFR1 ectodomain release from the plasma membrane is not known. Here we report that the 72-kDa gelatinase A (matrix metalloproteinase type 2, MMP2) can hydrolyze the Val368-Met369 peptide bond of the FGFR1 ectodomain, eight amino acids upstream of the transmembrane domain, thus releasing the entire extracellular domain. Similar results were obtained regardless of whether FGF was first bound to the receptor or not. The action of MMP2 abolished binding of FGF to an immobilized recombinant FGFR1 ectodomain fusion protein and to Chinese hamster ovary cells overexpressing FGFR1 The released recombinant FGFR1 ectodomain was able to bind FGF after MMP2 cleavage, suggesting that the cleaved soluble receptor maintained its FGF binding capacity. The activity of MMP2 could not be reproduced by the 92-kDa gelatinase B (MMP9) and was inhibited by tissue inhibitor of metalloproteinase type 2. These studies demonstrate that FGFR1 may be a specific target for MMP2 on the cell surface, yielding a soluble FGF receptor that may modulate the mitogenic and angiogenic activities of FGF.
Formation of worm-like micelles from a polystyrene–polybutadiene–polystyrene block copolymer in ethyl acetate (1980)

An investigation has been made of micelle formation by a polystyrene–polybutadiene–polystyrene block copolymer in ethyl acetate, which is a selectively bad solvent for polybutadiene; the number-average molecular weights of the three blocks were 12900, 66000 and 13700, respectively. As the temperature was raised dilute solutions of the copolymer in ethyl acetate showed a distinct cloud-point, which moved to higher temperatures with increases in concentration. On raising the temperature further the solutions gradually became clear again.Light scattering and electron microscopy studies showed that the onset of cloudiness was due to the formation of long worm-like micelles from spherical micelles. The clearing of solutions at higher temperatures occurred because the micelles dissociated to form copolymer molecules in the free-chain form. The cores of both types of micelle were composed of swollen polybutadiene blocks and the outer fringes of the micelles of polystyrene blocks. The spherical micelles had a fairly narrow size distribution. The worm-like micelles had a wide distribution of contour lengths but possessed a narrow size distribution in the radial direction.A second polystyrene–polybutadiene–polystyrene copolymer having shorter blocks than the first copolymer showed a similar type of solution behaviour at lower temperaturs.
Convenient Strategies for the Preparation of Modified 2(3H)-Benzothiazolethiones (1996)

Abstract 4-Alkyl-2-bromoanilines and 4-alkoxy-2-chloroanilines were synthesized conveniently and submitted to cyclization reaction with potassium O-ethyl dithiocarbonate to afford 6-substituted 2(3H)-benzothiazolethiones in good yields.
Beneficial Effects of Soy Phytoestrogen Intake in Postmenopausal Women With Type 2 Diabetes (2002)

These results show that dietary supplementation with soy phytoestrogens favorably alters insulin resistance, glycemic control, and serum lipoproteins in postmenopausal women with type 2 diabetes, thereby improving their cardiovascular risk profile.
Blockade of the interleukin-2 receptor by anti-Tac antibody: inhibition of human lymphocyte activation. (1983)

We have previously shown that monoclonal anti-Tac antibody inhibits the proliferation of interleukin-2 (IL-2) dependent human continuous T cell lines. Further, we have shown that anti-Tac specifically blocks greater than 95% of the binding of radiolabeled II-2 to a continuous T cell line. In view of these data, we suggested that anti-Tac antibody may bind to and block the human T cell receptor for IL-2. We now report the effects of anti-Tac on the activation of human peripheral blood T lymphocytes. We find that anti-Tac: 1) blocks T cell proliferation induced by soluble antigens (80-90%), autologous antigens (90%) and alloantigens (75-90%); 2) partially inhibits T cell proliferation induced by mitogenic lectins, including Concanavalin A (50-88%), pokeweed mitogen (40-87%), and phytohemagglutinin (20-80%); 3) abrogates (greater than 95%) the generation of cytolytic T lymphocytes in allogeneic cell cocultures, but does not inhibit killing by cytolytic T lymphocytes once formed; 4) and inhibits T cell dependent pokeweed mitogen activated B cell immunoglobulin production (78-95%). We further demonstrate that anti-Tac inhibition of proliferation is not secondary to diminished production of IL-2. Finally, in antigen induced T cell proliferative assays, we demonstrate that the addition of highly purified IL-2 reverses the inhibitory effects of anti-Tac. These data are consistent with the hypothesis that anti-Tac recognizes the human IL-2 receptor and illustrate ways in which this antibody can be used to modulate the human immune response.