gebhart/patrepeval huggingface dataset:
Ultrasound examination in ovarian cancer patients. A comparison with second look laparotomy. (1989)

A series of 129 patients with International Federation of Gynecology and Obstetrics (FIGO) stage III-IV ovarian cancer, were evaluated with ultrasound examination and second look surgery. Results of both modalities were correlated in order to assess the reliability of ultrasound in detecting residual disease. After six cycles of chemotherapy, ultrasound was negative in 94 patients and positive in 35 patients. At second look, 57 patients were in complete pathologic remission, 16 had microscopic residual disease, 23 had macroscopic disease less than 2 cm, and 33 had macroscopic disease greater than 2 cm. Correlating ultrasonography and laparotomy, high correlations were seen in patients with no residual disease (92.2%); on the other hand, ultrasound examinations exhibited poor sensitivity and specificity in patients with microscopic disease (6.2%) and residual disease less than 2 cm (8.6%). Using ultrasound discrimination among patients with no residual disease, microscopic disease, or macroscopic disease less than 2 cm does not appear possible. Our suggestion is that ultrasound is not able to replace second look laparotomy in the detection of minimal residual disease in ovarian cancer patients.
Mycotin: A lectin involved in the adherence of Mycobacteria to macrophages (1994)

Pathogenic Mycobacteria colonize host macrophages. Attachment of these organisms to macrophages is the preliminary step prior to invasion of the macrophages by the bacteria. Western blot confirmed that walls of Mycobacterium avium and Mycobacterium tuberculosis contain molecules which are immunologically related to mycotin, a lectin found in Mycobacterium smegmatis. We have demonstrated that the adherence of Mycobacteria to macrophages is significantly inhibited by anti-mycotin antibody or the mycotin-specific sugar, mannan. These observations suggest that prevention of the interaction of mycotin-related molecules on the surfaces of Mycobacteria with mannose-specific receptors on macrophages, offers an important approach for blocking attachment of pathogenic Mycobacteria to macrophages, thereby preventing infection.
Inference of haplotypes from PCR-amplified samples of diploid populations. (1990)

Direct sequencing of genomic DNA from diploid individuals leads to ambiguities on sequencing gels whenever there is more than one mismatching site in the sequences of the two orthologous copies of a gene. While these ambiguities cannot be resolved from a single sample without resorting to other experimental methods (such as cloning in the traditional way), population samples may be useful for inferring haplotypes. For each individual in the sample that is homozygous for the amplified sequence, there are no ambiguities in the identification of the allele's sequence. The sequences of other alleles can be inferred by taking the remaining sequence after "subtracting off" the sequencing ladder of each known site. Details of the algorithm for extracting allelic sequences from such data are presented here, along with some population-genetic considerations that influence the likelihood for success of the method. The algorithm also applies to the problem of inferring haplotype frequencies of closely linked restriction-site polymorphisms.
Preparation of sharp polycrystalline tungsten tips for scanning tunneling microscopy imaging (1996)

The fabrication of scanning tunneling microscopy (STM) tips by dc downward electrochemical polishing and ion milling has been investigated. The influence of parameters, such as voltage, immersion depth, cutoff time, and solution concentration, on the shape and sharpness of electropolished W tips are presented. Both electropolished and ion milled tips, which were characterized by transmission electron microscopy (TEM), were tested on Au films deposited on 〈100〉 oriented Si. The effects of tip radius on STM images are discussed thoroughly, and the results are also compared to atomic force microscopy (AFM) and TEM images.
On the characterization of optical fiber network components with optical frequency domain reflectometry (1997)

The basic features of coherent optical frequency domain reflectometry are presented. The ultimate limits of range and sensitivity were discussed, as well as polarization effects. It is shown that this technique is very suitable for optical network components characterization, and accurate measurements of a number of such components are presented.
Isolation and restriction site maps of the genes encoding five Mycobacterium tuberculosis proteins (1987)

A series of recombinant phage expressing five Mycobacterium tuberculosis antigens were isolated. Restriction maps for these antigens were deduced, and the size of the expressed proteins was determined.
Optical pumping of Rb vapor using high-powerGa1−xAlxAs diode laser arrays (1995)

The use of high-power ${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Al}}_{\mathit{x}}$As diode laser arrays for optical pumping of Rb vapor has been examined both theoretically and experimentally. Our studies show that large atomic polarizations can be obtained using the broad spectral output of a diode laser array if the Rb resonance line is collisionally broadened by several atmospheres of a buffer gas. The objective was to study the effectiveness of diode laser arrays as light sources for optically pumped spin-exchange polarized $^{3}\mathrm{He}$ targets. The average Rb polarization was deduced at three different Rb vapor pressures using the polarization induced in the $^{3}\mathrm{He}$ buffer gas. The largest $^{3}\mathrm{He}$ polarization observed was 53% using a 20-W diode array with 1.9-nm full width at half maximum spectral width in 10.5 amagat of $^{3}\mathrm{He}$. This result compares favorably with other light sources for this target. The measured average Rb polarizations are compared to theoretical calculations.
The role of bacteria in airway inflammation in exacerbations of chronic obstructive pulmonary disease (2006)

Research on the role of bacteria in causing inflammation in chronic obstructive pulmonary disease has been neglected for decades. Research should be directed at further evaluating the role of bacterial antigens in airway inflammation. Reducing or modulating bacterial infection of the airways in chronic obstructive pulmonary disease has the potential to reduce airway inflammation by eliminating an important inciting cause.
Primary Cells as Feeder Cells for Coculture Expansion of Human Hematopoietic Stem Cells from Umbilical Cord Blood—A Comparative Study (2008)

Although umbilical cord blood (UCB) has been widely accepted as an alternative source of hematopoietic stem cells (HSC) for transplantation, its use in adults is restricted because of low absolute HSC numbers. To overcome this obstacle, expansion of HSC in coculture with feeder cells is a promising possibility. In this study, we compared the potential of three human primary cell types, namely, mesenchymal stem cells (MSC), human umbilical cord vein endothelial cells (HUVEC), and Wharton's jelly cells (WJC), for use as feeder cells in a potentially clinically applicable coculture system. In first experiments, we evaluated procedures needed to obtain feeder cells, the possibility to separate them from cells derived from CD34(+) cells after coculture, their ability to activate allogeneic T cells, and their survival in CD34(+)-adapted medium. Finally, we compared their support for UCB-derived CD34(+) expansion. MSC and WJC were superior to HUVEC in terms of ease and reliability of isolation procedures needed. None of the potential feeder cells expressed CD34 or CD45, thus providing markers for cell sorting after coculture. Other markers (CD31, CD90, CD105, CD166) were expressed differently on feeder cell types. While MSC in higher concentrations did not activate allogeneic T cells, those were stimulated by lower concentrations of MSC as shown by CD25, CD69, and CD71 expression. In contrast, HUVEC and WJC were proven to activate T cells at all ratios tested. Feeder cells survived a 7-day culture in CD34(+)-adapted medium. In cocultures of UCB CD34(+)cells with primary feeder cells, mononuclear cell expansion was 30- to 60-fold, colony-forming cell expansion 20- to 40-fold, and cobblestone area-forming cell expansion 10- to 50-fold. We conclude that after a careful further evaluation especially of their immunological properties, all three primary cell types might possibly be suitable for use in a potentially clinically applicable system for expansion from UCB CD34(+)cells, with WJC being best choice and MSC still superior to HUVEC.
Studies of immunomodulating actions of carotenoids. I. Effects ofβ‐carotene and astaxanthin on murine lymphocyte functions and cell surface marker expression inin vitroculture system (1991)

The immunomodulating effects of carotenoids (beta-carotene and astaxanthin) on mouse lymphocytes were studied in in vitro culture system by use of assay for mitogen responses of spleen cells, thymocyte proliferation, interleukin 2 production, and antibody (Ab) production in vitro in response to sheep red blood cells. Changes of cell surface markers on spleen lymphocytes including Ia antigen (Ag), surface immunoglobulin, B220, and Thy-1 Ag were also examined. At a concentration of 10(-8) M, carotenoids did not show any significant effect on mitogen responses (phytohemagglutinin P and concanavalin A) on murine spleen cells, irrespective of the concentrations of mitogens used. Interleukin 2 production by murine spleen cells was not significantly altered by carotenoids in the culture media (10(-7) to 10(-9) M). [3H]thymidine incorporation by B6 thymocytes was somewhat enhanced in the presence of astaxanthin or beta-carotene when cultured in the concentration of 10(6)/ml. At higher concentrations of cells (5 x 10(6)/ml), such an effect was not observed. In assays of in vitro Ab production in response to sheep red blood cells, B6 spleen cells produced significantly more Ab-forming cells (plaque-forming cells, immunoglobulins M and G) in the presence of astaxanthin (greater than 10(-8) M) but not beta-carotene. Expression of Ia Ag seemed to be moderately enhanced on both Thy-1+ and Thy-1- spleen cells in the presence of astaxanthin (greater than 10(-9) M) but not beta-carotene. The expression of Thy-1 and surface immunoglobulin seemed unchanged with the treatment of these carotenoids. These results indicate that immunomodulating actions of carotenoids are not necessarily related to provitamin A activity, because astaxanthin, which does not have provitamin A activity, showed more significant effects in these bioassays and also indicate that such actions of carotenoid demonstrated in this study may be difficult to explain only by its oxygen-quenching capacity.
Meta-Analysis of Microarray Data IdentifiesGAS6Expression as an Independent Predictor of Poor Survival in Ovarian Cancer (2013)

Seeking new biomarkers for epithelial ovarian cancer, the fifth most common cause of death from all cancers in women and the leading cause of death from gynaecological malignancies, we performed a meta-analysis of three independent studies and compared the results in regard to clinicopathological parameters. This analysis revealed that GAS6 was highly expressed in ovarian cancer and therefore was selected as our candidate of choice. GAS6 encodes a secreted protein involved in physiological processes including cell proliferation, chemotaxis, and cell survival. We performed immunohistochemistry on various ovarian cancer tissues and found that GAS6 expression was elevated in tumour tissue samples compared to healthy control samples (). In addition, GAS6 expression was also higher in tumours from patients with residual disease compared to those without. Our data propose GAS6 as an independent predictor of poor survival, suggesting GAS6, both on the mRNA and on the protein level, as a potential biomarker for ovarian cancer. In clinical practice, the staining of a tumour biopsy for GAS6 may be useful to assess cancer prognosis and/or to monitor disease progression.
Increased Levels of LPS-Binding Protein in Bovine Blood and Milk Following Bacterial Lipopolysaccharide Challenge (2003)

Several species of gram-negative bacteria, including Escherichia coli, Klebsiella pneumoniae, and various species of Enterobacter, are common mastitis pathogens. All of these bacteria are characterized by the presence of endotoxin or lipopolysaccharide (LPS) in their outer membrane. The bovine mammary gland is highly sensitive to LPS, and LPS has been implicated, in part, in the pathogenesis of gram-negative mastitis. Recognition of LPS is a key event in the innate immune response to gram-negative infection and is mediated by the accessory molecules CD14 and LPS-binding protein (LBP). The objective of the current study was to determine whether LBP levels increased in the blood and mammary gland following LPS challenge. The left and right quarters of five midlactating Holstein cows were challenged with either saline or LPS (100 microg), respectively, and milk and blood samples collected. Basal levels of plasma and milk LBP were 38 and 6 microg/ml, respectively. Plasma LBP levels increased as early as 8 h post-LPS challenge and reached maximal levels of 138 microg/ ml by 24 h. Analysis of whey samples derived from LPS-treated quarters revealed an increase in milk LBP by 12 h. Similar to plasma, maximal levels of milk LBP (34 microg/ml) were detected 24 h following the initial LPS challenge. Increments in milk LBP levels paralleled a rise in soluble CD14 (sCD14) levels and initial rises in the levels of these proteins were temporally coincident with maximal neutrophil recruitment to the inflamed gland. Because LBP and sCD14 are known to enhance LPS-induced host cell activation and to facilitate detoxification of LPS, these data are consistent with a role for these molecules in mediating mammary gland responses to LPS.
A “slow” homotetrameric kinesin-related motor protein purified from Drosophila embryos. (1994)

Pan-kinesin peptide antibodies (Cole, D. G., Cande, W. Z., Baskin, R. J., Skoufias, D. A., Hogan, C. J., and Scholey, J. M. (1992) J. Cell Sci. 101, 291-301; Sawin, K. E., Mitchinson, T. J., and Wordeman, L. G. (1992) J. Cell Sci. 101, 303-313) were used to identify and isolate kinesin-related proteins (KRPs) from Drosophila melanogaster embryonic cytosol. These KRPs cosedimented with microtubules (MTs) polymerized from cytosol treated with AMP-PNP (adenyl-5'-yl imidodiphosphate), and one of them, KRP130, was further purified from ATP eluates of the embryonic MTs. Purified KRP130 behaves as a homotetrameric complex composed of four 130-kDa polypeptide subunits which displays a "slow" plus-end directed motor activity capable of moving single MTs at 0.04 +/- 0.01 microns/s. The 130-kDa subunit of KRP130 was tested for reactivity with monoclonal and polyclonal antibodies that are specific for various members of the kinesin superfamily. Results indicate that the KRP130 subunit is related to Xenopus Eg5 (Sawin, K. E., Le Guellec, K. L., Philippe, M., Mitchinson, T. J. (1992) Nature 359, 540-543), a member of the BimC subfamily of kinesins. Therefore, KRP130 appears to be the first Drosophila KRP, and the first member of the BimC subfamily in any organism, to be purified from native tissue as a multimeric motor complex.
The Addition of Aryl Azides to Norbornene. A Kinetic Investigation (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Addition of Aryl Azides to Norbornene. A Kinetic InvestigationPeter Scheiner, John H. Schomaker, Stan Deming, William J. Libbey, and Gerhard P. NowackCite this: J. Am. Chem. Soc. 1965, 87, 2, 306–311Publication Date (Print):January 1, 1965Publication History Published online1 May 2002Published inissue 1 January 1965https://pubs.acs.org/doi/10.1021/ja01080a030https://doi.org/10.1021/ja01080a030research-articleACS PublicationsRequest reuse permissionsArticle Views864Altmetric-Citations64LEARN 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
Regularization methods for neural networks and related models (2015)

Neural networks have become very popular in the last few years.They have demonstrated the best results in areas of image classification, image segmentation, speech recognition, and text processing.The major breakthrough happened in early 2010s, when it became feasible to train deep neural networks (DNN) on a GPU, which made the training process several hundred times faster.At the same time, large labeled datasets with millions of objects, such as Im-ageNet [16], became available.The GPU implementation of a convolutional DNN with over 10 layers and millions of parameters could handle the Ima-geNet dataset in just a few days.As a result, such networks could decrease classification error in the image classification competition LSVRC-2010 [54] by 40% compared with the hand-made feature algorithms.Deep neural networks are able to demonstrate excellent results on tasks with a complex classification function and sufficient amount of training data.However, since DNN models have a huge number of parameters, they can also be easily overfitted, when the amount of training data is not large enough.Thus, regularization techniques for neural networks are crucially important to make them applicable to a wide range of problems.In this thesis we provide a comprehensive overview of existing regularization techniques for neural networks and provide their theoretical explanation.Training of neural networks is performed using the Backpropagation algorithm (BP).Standard BP has two passes: forward and backward.It computes the predictions for the current input and the loss function in the forward pass, and the derivatives of the loss function with respect to the input and weights on the backward pass.The nature of the data usually assumes that two very close data points have the same label.This means that the predictions of a classifier I would especially like to thank all my colleagues from the Machine Learning group, which became my good friends: Simone Romano, Goce Ristanoski, Jiazhen He, Florin Schimbinschi, Andrey Kan.You were one of the reasons that called me to come to the office every day.I can fairly say that it would impossible to be enthusiastic for all time without you.We have had a lot of great moments at the university and outside it, and I value it.I would also like to thank all my other colleagues from the Machine Learning group, the Cloud Computing group, and other groups
Recent Developments and New Perspectives in the Heck Reaction (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRecent Developments and New Perspectives in the Heck ReactionWalter Cabri and Ilaria CandianiCite this: Acc. Chem. Res. 1995, 28, 1, 2–7Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/ar00049a001https://doi.org/10.1021/ar00049a001research-articleACS PublicationsRequest reuse permissionsArticle Views9408Altmetric-Citations897LEARN 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
Augmented antitumor effects of radiation therapy by 4-1BB antibody (BMS-469492) treatment. (2006)

These results suggest that monoclonal antibodies against 4-1BB may not only be efficacious in cancer immunotherapy, but may also have utility when applied in combination with conventional anticancer treatments, such as radiation therapy.
Clinical‐grade purification of natural killer cells in haploidentical hematopoietic stem cell transplantation (2008)

Donors with a high NK-cell count in peripheral blood are likely to provide NK-cell products with the highest cell number. However, maximal NK-cell dose is limited and high NK-cell doses may only be obtained for patients with a low body weight, making children and young adults the best candidates for NK-cell therapy.
Gene name errors are widespread in the scientific literature (2016)

The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions.
Coding theorems for turbo code ensembles (2002)

This paper is devoted to a Shannon-theoretic study of turbo codes. We prove that ensembles of parallel and serial turbo codes are "good" in the following sense. For a turbo code ensemble defined by a fixed set of component codes (subject only to mild necessary restrictions), there exists a positive number /spl gamma//sub 0/ such that for any binary-input memoryless channel whose Bhattacharyya noise parameter is less than /spl gamma//sub 0/, the average maximum-likelihood (ML) decoder block error probability approaches zero, at least as fast as n/sup -/spl beta//, where /spl beta/ is the "interleaver gain" exponent defined by Benedetto et al. in 1996.
Addition of sialidase or p38 MAPK inhibitors does not ameliorate decrements in platelet in vitro storage properties caused by 4 °C storage (2014)

Addition of either sialidase or p38 MAPK inhibitors do not improve any in vitro parameters of PLTs stored at 4 °C in 100% plasma.
ETCH CHARACTERISTICS OF COFESIB MAGNETIC FILMS USING INDUCTIVELY COUPLED PLASMA REACTIVE ION ETCHING FOR MAGNETIC RANDOM ACCESS MEMORY (2006)

ABSTRACT Inductively coupled plasma reactive ion etching of CoFeSiB magnetic thin films was studied in a Cl2/O2/Ar gas mix. The etch rate, etch selectivity and etch profile of this magnetic film were examined on varying gas concentration, coil rf power, gas pressure and dc-bias voltage. As the Cl2 gas increased, the etch rate monotonously decreased and etch residues decreased but etch slope was slanted. The use of the TiN hard mask gave rise to high selectivity of CoFeSiB to the TiN mask due to large decrease in etch rate of TiN in Cl2/O2/Ar gas mix. The addition of O2 into the gas mix led to the anisotropic etching of CoFeSiB films without the etch residues.