gebhart/patrepeval huggingface dataset:
Prostate-specific antigen as a marker for prostatic cancer: a monoclonal and a polyclonal immunoassay compared. (1987)

We evaluated the clinical utility of prostate-specific antigen (PSA) in diagnosis and management of prostatic cancer, using a monoclonal immunoradiometric assay (M-PSA) and a polyclonal radioimmunoassay (P-PSA). Assay CVs ranged from 1.3% to 4.9% (M-PSA) and from 5.1% to 8.0% (P-PSA). Detection limits were 0.1 microgram/L (M-PSA) and 0.2 microgram/L (P-PSA). Reference intervals established for healthy men were: 0-2.8 micrograms/L (M-PSA) and 0-4.2 micrograms/L (P-PSA). The regression equation for the PSA concentrations (0-100 micrograms/L) measured in normal men, men with primary prostatic cancer, and men with benign prostatic hypertrophy (BPH) was: P-PSA = 1.603 M-PSA - 0.120 microgram/L (r = 0.9923, n = 201). The P-PSA calibrators yielded one-half their assigned values when analyzed by the M-PSA assay. With either assay there were proportional increases in PSA values with advancing cancer. The proportion of PSA values exceeding the reference interval was 50% for patients with stage A prostatic cancer, 80% (stage B), 100% (stages C and D), and 65% for men with BPH. After radical prostatectomy, the follow-up PSA values for most patients were within the reference intervals for women (0-0.2 microgram/L for M-PSA, 0-0.8 microgram/L for P-PSA). Most patients with above-normal PSA values have clinically detectable disease.
Vaccinia Virus Envelope H3L Protein Binds to Cell Surface Heparan Sulfate and Is Important for Intracellular Mature Virion Morphogenesis and Virus Infection In Vitro and In Vivo (2000)

An immunodominant antigen, p35, is expressed on the envelope of intracellular mature virions (IMV) of vaccinia virus. p35 is encoded by the viral late gene H3L, but its role in the virus life cycle is not known. This report demonstrates that soluble H3L protein binds to heparan sulfate on the cell surface and competes with the binding of vaccinia virus, indicating a role for H3L protein in IMV adsorption to mammalian cells. A mutant virus defective in expression of H3L (H3L(-)) was constructed; the mutant virus has a small plaque phenotype and 10-fold lower IMV and extracellular enveloped virion titers than the wild-type virus. Virion morphogenesis is severely blocked and intermediate viral structures such as viral factories and crescents accumulate in cells infected with the H3L(-) mutant virus. IMV from the H3L(-) mutant virus are somewhat altered and less infectious than wild-type virions. However, cells infected by the mutant virus form multinucleated syncytia after low pH treatment, suggesting that H3L protein is not required for cell fusion. Mice inoculated intranasally with wild-type virus show high mortality and severe weight loss, whereas mice infected with H3L(-) mutant virus survive and recover faster, indicating that inactivation of the H3L gene attenuates virus virulence in vivo. In summary, these data indicate that H3L protein mediates vaccinia virus adsorption to cell surface heparan sulfate and is important for vaccinia virus infection in vitro and in vivo. In addition, H3L protein plays a role in virion assembly.
Neuronal and glial cell type-specific promoters within adenovirus recombinants restrict the expression of the apoptosis-inducing molecule Fas ligand to predetermined brain cell types, and abolish peripheral liver toxicity. (1999)

Gene therapy using Fas ligand (FasL) for treatment of tumours and protection of transplant rejection is hampered because of the systemic toxicity of FasL. In the present study, recombinant replication-defective adenovirus vectors (RAds) encoding FasL under the control of either the neuronal-specific neuronal-specific enolase (NSE) promoter or the astrocyte-specific glial fibrillary acidic protein (GFAP) promoter have been constructed. The cell type-specific expression of FasL in both neurons and glial cells in primary cultures, and in neuronal and glial cell lines is demonstrated. Furthermore, transgene expression driven by the neuronal and glial promoter was not detected in fibroblastic or epithelial cell lines. Expression of FasL driven by a major immediate early human cytomegalovirus promoter (MIEhCMV) was, however, achieved in all cells tested. As a final test of the stringency of transgene-specific expression, the RAds were injected directly into the bloodstream of mice. The RAds encoding FasL under the control of the non-cell type-specific MIEhCMV promoter induced acute generalized liver haemorrhage with hepatocyte apoptosis, while the RAds containing the NSE or GFAP promoter sequences were completely non-toxic. This demonstrates the specificity of transgene expression, enhanced safety during systemic administration, and tightly regulated control of transgene expression of highly cytotoxic gene products, encoded within transcriptionally targeted RAds.
Disruption of the YeastN-Myristoyl Transferase Gene Causes Recessive Lethality (1989)

The structural gene for N-myristoyl transferase (NMT1) has been cloned from the budding yeast Saccharomyces cerevisiae. The gene encodes a polypeptide of 455 amino acids (Mr = 52,837) that has no identifiable significant primary sequence homology with any protein in currently available databases. Overexpression of NMT activity was achieved by means of the yeast episomal plasmid YEp24 without obvious effects on growth kinetics, cell morphology, or acylprotein metabolic labeling patterns. Insertional mutagenesis of the NMT1 locus on yeast chromosome XII caused recessive lethality, indicating that this protein acyltransferase activity is necessary for vegetative cell growth.
The Development of a Data Processing System with Personal Computer of MS@ Standard System for Flow Injection Analysis (1988)

Since one of the merits of flow injection analysis (FIA) is rapid measurement, the time taken for data processing reduces the usefulness of the method. In this study, a personal computer of MSX^ standard system, which has a Z80A- type chip as CPU and more than 8 Kbyte of RAM, with a data acquisition system of -our own making, was introduced to facilitate data processing for FIA; a program written in MSX- BASIC was also developed. This system was applied to determination of glucose in control sera, and the results were compared with those of an analog recorded system. It was found that our 8 bit system had enough resolution for the FIA data processing.
Determination of the Oxide Layer Thickness in Core−Shell Zerovalent Iron Nanoparticles (2008)

Zerovalent iron (nZVI) nanoparticles have long been used in the electronic and chemical industries due to their magnetic and catalytic properties. Increasingly, applications of nZVI have also been reported in environmental engineering because of their ability to degrade a wide variety of toxic pollutants in soil and water. It is generally assumed that nZVI has a core-shell morphology with zerovalent iron as the core and iron oxide/hydroxide in the shell. This study presents a detailed characterization of the nZVI shell thickness using three independent methods. High-resolution transmission electron microscopy analysis provides direct evidence of the core-shell structure and indicates that the shell thickness of fresh nZVI was predominantly in the range of 2-4 nm. The shell thickness was also determined from high-resolution X-ray photoelectron spectroscopy (HR-XPS) analysis through comparison of the relative integrated intensities of metallic and oxidized iron with a geometric correction applied to account for the curved overlayer. The XPS analysis yielded an average shell thickness in the range of 2.3-2.8 nm. Finally, complete oxidation reaction of the nZVI particles by Cu(II) was used as an indication of the zerovalent iron content of the particles, and these observations further correlate the chemical reactivity of the particles and their shell thicknesses. The three methods yielded remarkably similar results, providing a reliable determination of the shell thickness, which fills an essential gap in our knowledge about the nZVI structure. The methods presented in this work can also be applied to the study of the aging process of nZVI and may also prove useful for the measurement and characterization of other metallic nanoparticles.
Spoken language understanding using long short-term memory neural networks (2014)

Neural network based approaches have recently produced record-setting performances in natural language understanding tasks such as word labeling. In the word labeling task, a tagger is used to assign a label to each word in an input sequence. Specifically, simple recurrent neural networks (RNNs) and convolutional neural networks (CNNs) have shown to significantly outperform the previous state-of-the-art - conditional random fields (CRFs). This paper investigates using long short-term memory (LSTM) neural networks, which contain input, output and forgetting gates and are more advanced than simple RNN, for the word labeling task. To explicitly model output-label dependence, we propose a regression model on top of the LSTM un-normalized scores. We also propose to apply deep LSTM to the task. We investigated the relative importance of each gate in the LSTM by setting other gates to a constant and only learning particular gates. Experiments on the ATIS dataset validated the effectiveness of the proposed models.
Wnt7a is a novel inducer of β-catenin-independent tumor-suppressive cellular senescence in lung cancer (2015)

Cellular senescence is an initial barrier for carcinogenesis. However, the signaling mechanisms that trigger cellular senescence are incompletely understood, particularly in vivo. Here we identify Wnt7a as a novel upstream inducer of cellular senescence. In two different mouse strains (C57Bl/6J and FVB/NJ), we show that the loss of Wnt7a is a major contributing factor for increased lung tumorigenesis owing to reduced cellular senescence, and not reduced apoptosis, or autophagy. Wnt7a-null mice under de novo conditions and in both the strains display E-cadherin-to-N-cadherin switch, reduced expression of cellular senescence markers and reduced expression of senescence-associated secretory phenotype, indicating a genetic predisposition of these mice to increased carcinogen-induced lung tumorigenesis. Interestingly, Wnt7a induced an alternate senescence pathway, which was independent of β-catenin, and distinct from that of classical oncogene-induced senescence mediated by the well-known p16(INK4a) and p19(ARF) pathways. Mechanistically, Wnt7a induced cellular senescence via inactivation of S-phase kinase-associated protein 2, an important alternate regulator of cellular senescence. Additionally, we identified Iloprost, a prostacyclin analog, which initiates downstream signaling cascades similar to that of Wnt7a, as a novel inducer of cellular senescence, presenting potential future clinical translational strategies. Thus pro-senescence therapies using either Wnt7a or its mimic, Iloprost, might represent a new class of therapeutic treatments for lung cancer.
Phase-shifting lithography: Maskmaking and its application (1993)

The use of phase-shifting masks (PSMs) allows substantial improvement in resolution and depth-of-focus of optical systems. Before the advantages of PSMs can be realized in a production process, several problems of mask technology must be solved. In order to advance PSMs from a development tool to a production tool for very large scale integration (VLSI) devices, the technologies concerning mask fabrication, mask inspection, and mask repair have been investigated. A silicone-based resist has been developed for simplifying the mask fabrication processes. The printability and detectability of shifter defects have been investigated in order to specify the requirements of systems of PSM manufacture and inspection. The developed silicone-based resist has been applied for mask defect repair. These technologies can bring PSMs closer to being a practical production tool for VLSI. To verify the effectiveness of PSMs for device manufacturing, PSMs have been successfully applied to gate definition of a high-speed GaAs field effect transistor, contact hole fabrication, and storage node (cell capacitor) fabrication of a dynamic random access memory device.
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers (2018)

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy.
Proteome‐Wide Profiling of Targets of Cysteine reactive Small Molecules by Using Ethynyl Benziodoxolone Reagents (2015)

In this study, we present a highly efficient method for proteomic profiling of cysteine residues in complex proteomes and in living cells. Our method is based on alkynylation of cysteines in complex proteomes using a "clickable" alkynyl benziodoxolone bearing an azide group. This reaction proceeds fast, under mild physiological conditions, and with a very high degree of chemoselectivity. The formed azide-capped alkynyl-cysteine adducts are readily detectable by LC-MS/MS, and can be further functionalized with TAMRA or biotin alkyne via CuAAC. We demonstrate the utility of alkynyl benziodoxolones for chemical proteomics applications by identifying the proteomic targets of curcumin, a diarylheptanoid natural product that was and still is part of multiple human clinical trials as anticancer agent. Our results demonstrate that curcumin covalently modifies several key players of cellular signaling and metabolism, most notably the enzyme casein kinase I gamma. We anticipate that this new method for cysteine profiling will find broad application in chemical proteomics and drug discovery.
Thrombosis and anticoagulation. (1999)

Most of the major advances in thrombosis research have occurred in the last 50 years, reflecting progress in biomedical sciences and clinical trials methodology. Improved understanding of the mechanisms of thrombogenesis has led to the discovery of a plethora of new antithrombotic agents that target many of the key steps in blood coagulation and platelet activation. Although most of these compounds are still under development, low-molecular-weight heparins (LMWH), glycoprotein (GP) IIb/IIIa receptor antagonists, and inhibitors of the adenosine diphosphate (ADP) receptor on platelets have already established their niche in the clinic. The vessel wall has emerged as a major player, both in protecting against and in promoting thrombosis, and as we approach the new millennium, compounds are being developed that have the potential to prevent and treat thrombosis by modulating vessel wall function.
Blockade of Complement Inhibits Obliterative Bronchiolitis in Rat Tracheal Allografts (2000)

The role of complement activation in the development of obliterative bronchiolitis, a manifestation of chronic lung allograft rejection, was investigated in the heterotopic rat tracheal allograft model. An increase in intragraft complement components C3 and C5b-9 (membrane attack complex) as well as IgM and IgG deposits were demonstrated during the progressive loss of respiratory epithelium and airway occlusion in nontreated allografts compared with syngeneic grafts. A 7-d treatment with recombinant human soluble complement receptor type 1 (sCR1; 20 mg/kg/d, intraperitoneal), an inhibitor of both the classic and alternative complement pathways, significantly decreased epithelial necrosis and intragraft neutrophil infiltration, and reduced obliterative changes by 40%. Immunohistochemical analysis of the grafts showed that sCR1 treatment significantly decreased early C5b-9 and IgG deposits, neutrophil chemoattractant IL-8 immunoreactivity, and ICAM-1 expression. Treatment with sCR1 was associated with increased staining for Th2 cytokines, in particular IL-10, with concomitant downregulation of IL-2 and TNF-alpha immunoreactivity. In contrast, sCR1 treatment did not affect the number of graft-infiltrating CD4(+) and CD8(+) T cells, CD45(+) B cells, ED1(+) and ED3(+) macrophages, or immune activation with expression of IL-2Ralpha or MHC class II. In conclusion, this is the first study to demonstrate that blockade of complement activation attenuates the development of OB and suggests that in addition to T cell-driven responses, humoral and antigen-independent immune responses also operate in the disease process. A blockade of complement activation renders the chemokine milieu unattractive to neutrophils and also modulates the alloimmune response toward Th2 cytokines, which may have an antiproliferative role in fibroproliferative disorders.
Hidden Markov support vector machines (2003)

This paper presents a novel discriminative learning technique for label sequences based on a combination of the two most successful learning algorithms, Support Vector Machines and Hidden Markov Models which we call Hidden Markov Support Vector Machine.
Single nucleotide polymorphism genotyping using locked nucleic acid (LNA™) (2003)

Locked nucleic acid (LNA) is a new class of bicyclic high affinity DNA analogs. LNA-containing oligonucleotides confer significantly increased affinity against their complementary DNA targets, increased mismatch discrimination (delta Tm) and allow full control of the melting point of the hybridization reaction. LNA chemistry is completely compatible with the traditional DNA phosphoramidite chemistry and therefore LNA-DNA mixmer oligonucleotides can be designed with complete freedom for optimal performance. These properties render LNA oligonucleotides very well suited for SNP genotyping and have enabled several approaches for enzyme-independent SNP genotyping based on allele-specific hybridization. In addition, allele-specific PCR assays relying on enzymatically-enhanced discrimination can be improved using LNA-modified oligonucleotides. The use of LNA transforms enzyme-independent genotyping approaches into experimentally simple, robust and cost-effective assays, which are highly suited for genotyping in clinical and industrial settings.
Inhibition of tumor metastasis by heparanase inhibiting species of heparin. (1995)

Heparanase activity correlates with the metastatic potential of lymphoma, melanoma and mammary adenocarcinoma cell lines. We investigated the ability of various modified species of heparin and size-homogeneous oligosaccharides derived from depolymerized heparin to inhibit (1) heparanase-mediated degradation of heparan sulfate in a naturally produced subendothelial extracellular matrix (ECM), and (2) lung colonization of B16-BL6 melanoma cells in C57BL mice. Inhibition of heparanase was best achieved by heparin species containing 16 or more sugar units and having sulfate groups at both the N and O positions. Low-sulfate oligosaccharides were less effective heparanase inhibitors than medium- and high-sulfate fractions of the same-size saccharide. While O-desulfation abolished the heparanase-inhibiting effect of heparin, O-sulfated, N-substituted (e.g. N-acetyl or N-hexanoyl) species of heparin retained high inhibitory activity. Potent inhibitors of heparanase activity were also efficient inhibitors of tumor invasion and lung colonization. Heparin fractions with high and low anticoagulant activity expressed similar high antiheparanase and antimetastatic activities. Structural requirement for the inhibition of melanoma cell heparanase and lung colonization by species of heparin were different from those identified for (1) release of ECM-bound basic fibroblast growth factor (b-FGF) and (2) stimulation of b-FGF receptor binding and mitogenic activity. These results indicate that various nonanticoagulant species of heparin and other polyanionic molecules differing in size, sulfation and substituted groups can be designed to elicit specific effects resulting in the inhibition of cell invasion in tumor metastasis and autoimmunity, or stimulation of neovascularization and wound healing.
Novel Hydrogen Compounds from a Potassium Carbonate Electrolytic Cell (2000)

Novel compounds containing hydrogen in new hydride and polymeric states that demonstrate novel hydrogen chemistry have been isolated following the electrolysis of a K2CO3 electrolyte with the production of excess energy. Inorganic hydride clusters K[KH KHCO3]n+ and hydrogen polymer ions such as OH23+ and H16- were identified by time-of-flight secondary ion mass spectroscopy. The presence of compounds containing new states of hydrogen was confirmed by X-ray photoelectron spectroscopy, X-ray diffraction, Fourier transform infrared spectroscopy, Raman spectroscopy, and proton nuclear magnetic resonance spectroscopy.
Biphotonic process for recording holograms with continuous-wave lasers in the near infrared (1987)

A new process that permits the recording of holograms produced by laser sources emitting in the near infrared is presented. The recording process involves the sensitization of singlet oxygen and the oxidation of an adapted trap. Finally, a second photon initiates a photopolymerization, which induces changes in refractive index and creates the hologram.
Molecular characterization and dynamics of hepatitis C virus replication in human fetal hepatocytes infected in vitro (1997)

The molecular features of hepatitis C virus (HCV) replication in human fetal hepatocytes (HFHs) were addressed in this study. Using a competitive reverse-transcription polymerase chain reaction (RT-PCR) assay for the quantitation of HCV-RNA molecules, the highest level of viral replication was detected 30 days' postinfection. At this time point, viral particles of 41 to 45 nm in diameter accumulated in the cell cytoplasm. Their density in cell extracts and culture medium was distributed between heavy (1.180-1.360 g/cm3) and light fractions (1.105-1.050 g/cm3) of a sucrose gradient, while, in the serum inoculum, they had a positive fraction at 1.180 g/cm3. In infected HFHs, minus-strand HCV RNA was observed in fractions displaying a sedimentation coefficient of 28 S to 18 S, while plus-strand HCV RNA showed a peak restricted to the 21 S fraction; the HCV RNA of serum inoculum had a sedimentation coefficient of 38 to 40 S, which revealed the presence of HCV RNA of unique positive polarity. The 21 S RNA fraction of cell extracts was resistant to 20 minutes of RNase I digestion, while the same incubation time totally inactivated a comparable amount of HCV RNA purified from the serum inoculum, revealing the presence of completely and/or partially double-stranded HCV-RNA molecules in the infected cells. Detection in HFHs of replicative forms and replicative intermediates suggests that the dynamic profile of HCV replication in these cells is similar to that described in other flaviviruses.