gebhart/patrepeval huggingface dataset:
How to fool radiologists with generative adversarial networks? A visual turing test for lung cancer diagnosis (2018)

Discriminating lung nodules as malignant or benign is still an underlying challenge. To address this challenge, radiologists need computer aided diagnosis (CAD) systems which can assist in learning discriminative imaging features corresponding to malignant and benign nodules. However, learning highly discriminative imaging features is an open problem. In this paper, our aim is to learn the most discriminative features pertaining to lung nodules by using an adversarial learning methodology. Specifically, we propose to use un-supervised learning with Deep Convolutional-Generative Adversarial Networks (DC-GANs) to generate lung nodule samples realistically. We hypothesize that imaging features of lung nodules will be discriminative if it is hard to differentiate them (fake) from real (true) nodules. To test this hypothesis, we present Visual Turing tests to two radiologists in order to evaluate the quality of the generated (fake) nodules. Extensive comparisons are performed in discerning real, generated, benign, and malignant nodules. This experimental set up allows us to validate the overall quality of the generated nodules, which can then be used to (1) improve diagnostic decisions by mining highly discriminative imaging features, (2) train radiologists for educational purposes, and (3) generate realistic samples to train deep networks with big data.
Production of Ginkgolides and Bilobalide by Ginkgo biloba Plants and Tissue Cultures (1999)

The accumulation of the terpenes ginkgolides and bilobalide in Ginkgo biloba was reported in plants as well as in plant cell cultures. Several hundred plants cultivated under controlled conditions in the field have been analyzed for their terpene production over many years. Cross-pollination experiments were performed with mature trees and the terpene content of the progeny was analyzed. The age of the tree is the main factor influencing the terpene content of the leaves as the level always decreases dramatically between young and old trees. 80 cell culture strains have been established and ginkgolides analyzed by GC/MS. These cell cultures reveal very low amounts of terpenes (1 microgram g-1 D.W. or less). On the contrary, isolated in vitro root cultures accumulate terpenes at the same concentration as the young plant leaves (4 mg g-1 D.W.). Attempts to obtain rapid growing roots or even hairy-roots did not succeed but the possibility to transform Ginkgo cell strains has been demonstrated.
Induction of WT1 (Wilms' tumor gene)-specific cytotoxic T lymphocytes by WT1 peptide vaccine and the resultant cancer regression (2004)

The Wilms' tumor gene WT1 is overexpressed in leukemias and various types of solid tumors, and the WT1 protein was demonstrated to be an attractive target antigen for immunotherapy against these malignancies. Here, we report the outcome of a phase I clinical study of WT1 peptide-based immunotherapy for patients with breast or lung cancer, myelodysplastic syndrome, or acute myeloid leukemia. Patients were intradermally injected with an HLA-A*2402-restricted, natural, or modified 9-mer WT1 peptide emulsified with Montanide ISA51 adjuvant at 0.3, 1.0, or 3.0 mg per body at 2-week intervals, with toxicity and clinical and immunological responses as the principal endpoints. Twenty-six patients received one or more WT1 vaccinations, and 18 of the 26 patients completed WT1 vaccination protocol with three or more injections of WT1 peptides. Toxicity consisted only of local erythema at the WT1 vaccine injection sites in patients with breast or lung cancer or acute myeloid leukemia with adequate normal hematopoiesis, whereas severe leukocytopenia occurred in patients with myelodysplastic syndrome with abnormal hematopoiesis derived from WT1-expressing, transformed hematopoietic stem cells. Twelve of the 20 patients for whom the efficacy of WT1 vaccination could be assessed showed clinical responses such as reduction in leukemic blast cells or tumor sizes and/or tumor markers. A clear correlation was observed between an increase in the frequencies of WT1-specific cytotoxic T lymphocytes after WT1 vaccination and clinical responses. It was therefore demonstrated that WT1 vaccination could induce WT1-specific cytotoxic T lymphocytes and result in cancer regression without damage to normal tissues.
OpenFst: A General and Efficient Weighted Finite-State Transducer Library (Extended Abstract of an Invited Talk) (2007)

We describe OpenFst, an open-source library for weighted finite-state transducers (WFSTs). OpenFst consists of a C++ template library with efficient WFST representations and over twenty-five oper- ations for constructing, combining, optimizing, and searching them. At the shell-command level, there are corresponding transducer file repre- sentations and programs that operate on them. OpenFst is designed to be both very efficient in time and space and to scale to very large problems. This library has key applications speech, image, and natural language processing, pattern and string matching, and machine learning. We give an overview of the library, examples of its use, details of its design that allow customizing the labels, states, and weights and the lazy evaluation of many of its operations. Further information and a download of the OpenFst library can be obtained from http://www.openfst.org.
Transplantation of enriched and purged peripheral blood progenitor cells from a single apheresis product in patients with non-Hodgkin's lymphoma (1995)

High-dose chemotherapy with or without radiotherapy followed by autologous transplantation of hematopoietic progenitor cells is an effective treatment for patients with high-risk or relapsed non-Hodgkin's lymphoma. Chemotherapy and/or hematopoietic growth factors have been used to mobilize progenitor cells in the peripheral blood for transplantation. However, the mobilized blood cell products have been found to be frequently contaminated with tumor cells, and techniques have not been developed to purge tumor cells from these products. In addition, the minimum number of hematopoietic progenitor cells required for engraftment has not yet been fully elucidated. We treated 21 patients with a single infusion of cyclophosphamide (4 g/m2) followed by daily administration of granulocyte colony-stimulating factor (G-CSF). After recovery of the white blood cell count, a single 3-hour apheresis collection was performed. The apheresis product was then applied to a discontinuous Percoll gradient. The low-density fractions resulting from this separation procedure were enriched for CD34+ progenitor cells (total cell yield, 19.5%; CD34+ cell recovery, 81.2%). These enriched cellular products were treated with a panel of anti-B cell or anti-T cell monoclonal antibodies and complement in an effort to remove residual tumor cells. After treatment of the patient with myeloablative therapies, the enriched and purged cells were reinfused. Hematologic recovery was rapid, with median neutrophil engraftment in 10 days [absolute neutrophil count (ANC), greater than 0.5 x 10(9)/L] and 11 days (ANC, greater than 1.0 x 10(9)/L). Median platelet transfusion independence required 13 days. The rapidity of multilineage engraftment correlated with the number of CD34+ cells per kilogram that were infused. Patients who received more than 2 x 10(6) CD34+ cells per kilogram had rapid hematologic engraftment, whereas those patients transplanted with less than 2 x 10(6) CD34+ cells per kilogram had slower platelet recovery. Modeling studies using a lymphoma cell line with a t(14; 18) chromosomal translocation demonstrated the successful removal of tumor cells assayed using the polymerase chain reaction (PCR) after the processing and purging. Four of the 21 patients had PCR-detectable lymphoma cells in the bone marrow and peripheral blood; however, the enriched and purged blood products reinfused in all four did not contain detectable tumor cells.(ABSTRACT TRUNCATED AT 400 WORDS)
Stem Cells And Myocardial Regeneration (2007)

Stem cells and myocardial regeneration / , Stem cells and myocardial regeneration / , کتابخانه دیجیتال جندی شاپور اهواز
In Vitro Selection of Mutations in the Human Immunodeficiency Virus Type 1 Reverse Transcriptase That Decrease Susceptibility to (−)-β- d -Dioxolane-Guanosine and Suppress Resistance to 3′-Azido-3′-Deoxythymidine (2000)

Human immunodeficiency virus type 1 (HIV-1) isolates resistant to (-)-beta-D-dioxolane-guanosine (DXG), a potent and selective nucleoside analog HIV-1 reverse transcriptase (RT) inhibitor, were selected by serial passage of HIV-1(LAI) in increasing drug concentrations (maximum concentration, 30 microM). Two independent selection experiments were performed. Viral isolates for which the DXG median effective concentrations (EC(50)s) increased 7.3- and 12.2-fold were isolated after 13 and 14 passages, respectively. Cloning and DNA sequencing of the RT region from the first resistant isolate identified a K65R mutation (AAA to AGA) in 10 of 10 clones. The role of this mutation in DXG resistance was confirmed by site-specific mutagenesis of HIV-1(LAI). The K65R mutation also conferred greater than threefold cross-resistance to 2',3'-dideoxycytidine, 2', 3'-dideoxyinosine, 2',3'-dideoxy-3'-thiacytidine, 9-(2-phosphonylmethoxyethyl)adenine, 2-amino-6-chloropurine dioxolane, dioxolanyl-5-fluorocytosine, and diaminopurine dioxolane but had only marginal effects on 3'-azido-3'-deoxthymidine (AZT) susceptibility. However, when introduced into a genetic background for AZT resistance (D67N, K70R, T215Y, T219Q), the K65R mutation reversed the AZT resistance. DNA sequencing of RT clones derived from the second resistant isolate identified the L74V mutation, previously reported to cause ddI resistance. The L74V mutation also decreased the AZT resistance when the mutation was introduced into a genetic background for AZT resistance (D67N, K70R, T215Y, T219Q) but to a lesser degree than the K65R mutation did. These findings indicate that DXG and certain 2',3'-dideoxy compounds (e.g., ddI) can select for the same resistance mutations and thus may not be optimal for use in combination. However, the combination of AZT with DXG or its orally bioavailable prodrug (-)-beta-D-2, 6-diaminopurine-dioxolane should be explored because of the suppressive effects of the K65R and L74V mutations on AZT resistance.
Rab proteins in endocytosis and Glut4 trafficking (2007)

The intracellular trafficking of numerous proteins requires a tight control to fulfil their physiological functions. It is the case of the adipocyte and muscle glucose transporter Glut4 that is retained intracellularly until insulin induces its recruitment to the plasma membrane. Rabs are evolutionarily conserved small GTPases that control intracellular traffic events from yeast to mammalian cells. In the past few decades, considerable progresses have been made in identifying the route of Glut4, the Rabs involved in controlling it, and more recently the connection between insulin signalling and Glut4 trafficking through Rab activity control.
Pratt and Whitney thermal barrier coatings (1995)

Thermal barrier coatings (TBCs) will be used to achieve the objectives of the Advanced Turbine Systems (ATS) program. They are used in aircraft engines and have accumulated millions upon millions of reliable hours. Differences in the duty cycles of the aircraft and industrial gas turbines are recognized as is the marked differences in environmental operational envelope. At the completion of this program the TBCs best suited to meet the needs of the ATS program will have been identified, tested, and confirmed.
Methods for interpreting and understanding deep neural networks (2017)

This paper provides an entry point to the problem of interpreting a deep neural network model and explaining its predictions. It is based on a tutorial given at ICASSP 2017. As a tutorial paper, the set of methods covered here is not exhaustive, but sufficiently representative to discuss a number of questions in interpretability, technical challenges, and possible applications. The second part of the tutorial focuses on the recently proposed layer-wise relevance propagation (LRP) technique, for which we provide theory, recommendations, and tricks, to make most efficient use of it on real data.
Volumetric determinations with CAD/CAM in prosthetics and orthotics: errors of measurement. (1995)

During the next decade CAD/CAM technique will probably become routine in prosthetics and orthotics, not only as a complement to manual techniques, but also introducing new possibilities. However, even complex and sophisticated techniques have errors of measurement that must be considered. Such errors are of two principal kinds: systematic errors and random errors. In this study we have evaluated the Swedish CAPOD system with respect to volumetric determinations. We used two types of reference objects for volume determinations: cylinders and amputation residual limb models. Three different sizes were examined of each type of object. Volume measurements with CAPOD were compared with volumes obtained by water immersion or mathematical calculation (cylinders only). We found a constant, linear systematic error of +2.5%. Such an error can easily be corrected for. The random error, represented by the coefficient of variation, was 0.5%, which means that there is a theoretical possibility to detect volume changes exceeding 1%. We consider the precision sufficient for clinical practice in prosthetics and orthotics. Biological variations due to soft tissue deformation must be added on top of these errors. Such deformations were not evaluated in this study.
Cathepsin Substrates as Cleavable Peptide Linkers in Bioconjugates, Selected from a Fluorescence Quench Combinatorial Library (1998)

Several extended peptide substrates for the human liver enzymes cathepsin B and cathepsin D have been selected as cleavable linkers for lysosomal proteolysis of bioconjugates. A one-bead-one-peptide combinatorial library of 9(4) fluorogenic substrates was employed. We designed this library to explore a set of substrates containing nonionizable/nonoxidizable groups to meet the requirements of prelabeling [Li et al. (1994) Bioconjugate Chem. 5, 101-104] as well as to yield stable conjugates whose preparation is straightforward.
Betacellulin and activin A coordinately convert amylase-secreting pancreatic AR42J cells into insulin-secreting cells. (1996)

Rat pancreatic AR42J cells possess exocrine and neuroendocrine properties. Activin A induces morphological changes and converts them into neuron-like cells. In activin-treated cells, mRNA for pancreatic polypeptide (PP) but not that for either insulin or glucagon was detected by reverse transcription-PCR. About 25% of the cells were stained by anti-PP antibody. When AR42J cells were incubated with betacellulin, a small portion of the cells were stained positively with antiinsulin and anti-PP antibodies. The effect of betacellulin was dose dependent, being maximal at 2 nM. Approximately 4% of the cells became insulin positive at this concentration, and mRNAs for insulin and PP were detected. When AR42J cells were incubated with a combination of betacellulin and activin A, approximately 10% of the cells became insulin positive. Morphologically, the insulin-positive cells were composed of two types of cells: neuron-like and round-shaped cells. Immunoreactive PP was found in the latter type of cells. The mRNAs for insulin, PP, glucose transporter 2, and glucokinase, but not glucagon, were detected. Depolarizing concentration of potassium, tolbutamide, carbachol, and glucagon-like peptide-1 stimulated the release of immunoreactive insulin. These results indicate that betacellulin and activin A convert amylase-secreting AR42J cells into cells secreting insulin. AR42J cells provide a model system to study the formation of pancreatic endocrine cells.
Transformations of biomass-derived platform molecules: from high added-value chemicals to fuels via aqueous-phase processing (2011)

Global warming issues and the medium-term depletion of fossil fuel reserves are stimulating researchers around the world to find alternative sources of energy and organic carbon. Biomass is considered by experts the only sustainable source of energy and organic carbon for our industrial society, and it has the potential to displace petroleum in the production of chemicals and liquid transportation fuels. However, the transition from a petroleum-based economy to one based on biomass requires new strategies since the petrochemical technologies, well-developed over the last century, are not valid to process the biomass-derived compounds. Unlike petroleum feedstocks, biomass derived platform molecules possess a high oxygen content that gives them low volatility, high solubility in water, high reactivity and low thermal stability, properties that favour the processing of these resources by catalytic aqueous-phase technologies at moderate temperatures. This tutorial review is aimed at providing a general overview of processes, technologies and challenges that lie ahead for a range of different aqueous-phase transformations of some of the key biomass-derived platform molecules into liquid fuels for the transportation sector and related high added value chemicals.
Identification and partial characterization of multiple native and neoantigenic epitopes of human C-reactive protein by using monoclonal antibodies. (1989)

Multiple mAb to human C-reactive protein (CRP) were prepared which reacted preferentially with either native CRP, modified CRP (expressing "neo-CRP" determinants) or both forms of the molecule. These mAb were divided into four groups according to their binding characteristics to various CRP preparations and CRP peptides by using a combination of ELISA, dot blot, and Western blot assays; they were further characterized based upon their reactivity with CRP in the presence of calcium and inhibition by phosphorylcholine. The first group consisted of mAb that reacted only with native CRP, and served to define four distinct native CRP epitopes. The second group consisted of mAb that reacted with native CRP and also with CRP modified by direct immobilization on polystyrene plates, urea-chelation or SDS treatment in the absence of calcium, thus identifying a fifth native CRP epitope; these mAb displayed significantly greater reactivity with native than with modified CRP. The third group included mAb that reacted only with modified CRP and with the larger amino-terminal fragment (residues 1-146) of pronase-cleaved CRP. The fourth group included mAb that reacted only with modified CRP and with the smaller carboxyl-terminal fragment (residues 147-206) of pronase-cleaved CRP; most of these antibodies also reacted with the carboxyl-terminal octapeptide (residues 199-206) of CRP. These experiments have identified mAb that react preferentially with distinct conformational and sequence-determined epitopes of native and modified forms of the CRP molecule, respectively; provide partial identification of the epitopes with which they interact; point to the presence of at least five epitopes on native CRP and at least three epitopes on modified CRP; and provide antibodies suitable for identification and quantitation of native and modified forms of CRP. The mAb directed against neo-CRP epitopes may help identify the presence of this pentraxin and antigenically-related proteins at previously unappreciated sites.
Low‐conductance chloride channel activated by cAMP in the epithelial cell line T84 (1990)

We have studied the modulation and pharmacological properties of two anion channels in T84 cells by recording single channel and transepithelial currents. One channel had an outwardly rectifying current-voltage I/V curve, was rarely active in cell-attached patches, and was unaffected by cAMP. The other channel had lower conductance (8.7 pS at 37 degrees C) and a more ohmic I/V relationship. Exposure to cAMP increased the probability of observing low-conductance channel activity in cell-attached patches greater than 6-fold. Extracellular DIDS (4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid) or [IAA-94 (an indanyloxyacetic acid) inhibited the outward rectifier but did not affect the low-conductance channel or cAMP-stimulated transepithelial current. These results suggest the low-conductance Cl channel may contribute to apical membrane conductance during cAMP-stimulated secretion.
Induction in a murine tumor of immunogenic tumor variants by transfection with a foreign gene. (1988)

Transfection of the undifferentiated murine colon carcinoma line CT-26 with the gene coding for the hemagglutination antigen (HA) of influenza virus resulted in the generation of highly immunogenic tumor cells. CT-26 cells transfected with HA not only failed to grow in syngeneic mice but also protected normal animals against a challenge with otherwise lethal doses of parental nontransfected cells. The immunogenicity of HA-transfected cells appeared to correlate with surface HA expression in that tumorigenic clones of HA-transfected CT-26 cells expressed little HA, while immunogenic clones were high expressers of HA. Irradiation of immunogenic HA clones did not abrogate their immunogenicity. These observations demonstrate that immune recognition of a poorly immunogenic tumor can be produced by immunization with tumor cells expressing a defined, foreign cell surface antigen.
CFTR: Mechanism of Anion Conduction (1999)

CFTR: Mechanism of Anion Conduction. Physiol. Rev. 79, Suppl.: S47-S75, 1999. - The purpose of this review is to collect together the results of recent investigations of anion conductance by the cystic fibrosis transmembrane conductance regulator along with some of the basic background that is a prerequisite for developing some physical picture of the conduction process. The review begins with an introduction to the concepts of permeability and conductance and the Nernst-Planck and rate theory models that are used to interpret these parameters. Some of the physical forces that impinge on anion conductance are considered in the context of permeability selectivity and anion binding to proteins. Probes of the conduction process are considered, particularly permeant anions that bind tightly within the pore and block anion flow. Finally, structure-function studies are reviewed in the context of some predictions for the origin of pore properties.
Alterations of the Notch pathway in lung cancer (2009)

Notch signaling regulates cell specification and homeostasis of stem cell compartments, and it is counteracted by the cell fate determinant Numb. Both Numb and Notch have been implicated in human tumors. Here, we show that Notch signaling is altered in approximately one third of non-small-cell lung carcinomas (NSCLCs), which are the leading cause of cancer-related deaths: in approximately 30% of NSCLCs, loss of Numb expression leads to increased Notch activity, while in a smaller fraction of cases (around 10%), gain-of-function mutations of the NOTCH-1 gene are present. Activation of Notch correlates with poor clinical outcomes in NSCLC patients without TP53 mutations. Finally, primary epithelial cell cultures, derived from NSCLC harboring constitutive activation of the Notch pathway, are selectively killed by inhibitors of Notch (gamma-secretase inhibitors), showing that the proliferative advantage of these tumors is dependent upon Notch signaling. Our results show that the deregulation of the Notch pathway is a relatively frequent event in NSCLCs and suggest that it might represent a possible target for molecular therapies in these tumors.