gebhart/patrepeval huggingface dataset:
Methylation status of c-fms oncogene in HCC and its relationship with clinical pathology (2001)

The mechanism that DNA hypomethylation leads to activation of oncogene and occurrence of malignant neoplasm is being increasingly recognized by researchers. Normal DNA methylation plays important role in stabilizing the phenotype of cell. DNA methylation status reduction and/or pattern alteration are related to activation and abnormally high expression of some oncogenes and cellular malignancy[1-6]. c-fms oncogene encodes for colony stimulating factor 1 receptor (CSF-1R)[7], c-fms/CSF-1R was highlyexpressed in hepatocellular carcinoma (HCC) tissue, but the mechanism remained obscure[8,9]. In this study, restrictive endonucleases Hpa II/Msp I digestion and Southern blot were used to study methylation status alteration of c-fms oncogene in HCC tissue and matching circum-cancer liver tissue, meanwhile the relationship between the alteration and clinical pathology of HCC was investigated. The gist of this study was to clarify the mechanism leading to c-fms oncogene high expression in hepatocellular carcinogenesis.
Holographic interference lithography for integrated optics (1978)

In this paper, some of our recent work in the use of holographic interference lithography and various material removal techniques to corrugate thin-film optical waveguides are reviewed. The specific applications of these periodic thin-film devices in the distributed feedback and distributed Bragg reflector semiconductor laser, and as output grating couplers, are described. Recent results in the use and fabrication of chirped and curved-line gratings are also summarized.
Synthesis of thioester peptides for the incorporation of thioamides into proteins by native chemical ligation (2014)

Thioamides can be used as photoswitches, as reporters of local environment, as inhibitors of enzymes, and as fluorescence quenchers. We have recently demonstrated the incorporation of thioamides into polypeptides and proteins using native chemical ligation (NCL). In this protocol, we describe procedures for the synthesis of a thioamide precursor and an NCL-ready thioamide-containing peptide using Dawson's N-acyl-benzimidazolinone (Nbz) process. We include a description of the synthesis by NCL of a thioamide-labeled fragment of the neuronal protein α-synuclein.
Microstructural Control of Additively Manufactured Metallic Materials (2016)

In additively manufactured (AM) metallic materials, the fundamental interrelationships that exist between composition, processing, and microstructure govern these materials’ properties and potential improvements or reductions in performance. For example, by using AM, it is possible to achieve highly desirable microstructural features (e.g., highly refined precipitates) that could not otherwise be achieved by using conventional approaches. Simultaneously, opportunities exist to manage macro-level microstructural characteristics such as residual stress, porosity, and texture, the last of which might be desirable. To predictably realize optimal microstructures, it is necessary to establish a framework that integrates processing variables, alloy composition, and the resulting microstructure. Although such a framework is largely lacking for AM metallic materials, the basic scientific components of the framework exist in literature. This review considers these key components and presents them in a manner that highlights key interdependencies that would form an integrated framework to engineer microstructures using AM.
Non‐equilibrium Method for the Radioimmunoassay of Clozapine in the Presence of Metabolites (1977)

Cross-reactions with metabolites are an ever-recurring problem encountered in the use of radioimmunoassay techniques to determine active compounds in biological material. Metabolites may interfere with the assay of the parent drug to a variable extent. Taking 8-chloro-11-(4-methyl-1-piperazinyl)-5H-dibenzo[b,e][1,4]diazepine (clozapine as an example, it was shown that the extent to which the antiserum produced interacts with the parent drug and the metabolites can be estimated by determining the equilibrium constants and the kinetics. In the present case, therefore, it was advantageous to carry out the radioimmunoassay in disequilibrium, i.e. in order to differentiate the metabolites from the parent drug, the sample was incubated with the antiserum for 10 min, after which the labelled antigen was added and the reaction mixture again incubated for a brief, exactly timed interval. It was shown that cross-reactions did not occur in mixtures of clozapine and its N-demethyl and N-oxide metabolites in the propor tions 1:1:2 over a range of concentration of 1.5-48 ng clozapine per 100 microliter human plasma. The equilibrium constants measured with the clozapine goat antiserum were as follows: clozapine 1.2 X 10(8) M-1, the N-demethyl metabolite 4.6 X 10(7) M-1 and the N-oxide metabolite 3.7 X 10(7) M-1 (pH 7.5 and 20 degrees C).
Submission of lymph node tissue for ancillary studies decreases the accuracy of conventional breast cancer axillary node staging. (1999)

Pathologists are under increasing pressure to submit fresh tissue for ancillary studies and research protocols. In several tumor types (breast, lung, melanoma, colorectal, prostate), increased interest in detecting submicroscopic nodal metastases through reverse transcriptase polymerase chain reaction analysis of mRNA from portions of lymph nodes has precluded histologic analysis of the entire node for metastases. A retrospective review was undertaken of 227 breast cancer patients prospectively entered on a research protocol examining the usefulness of sentinel lymph node surgery. All of the patients ultimately underwent complete lymph node dissection. The research protocol required that all nodes greater than 8 mm in size be bisected and submitted separately. Positive lymph nodes were evaluated for unilateral or bilateral involvement in the node sections. Sixty node-positive patients were identified, yielding 230 positive nodes. One hundred seven of these nodes were confirmed to have been bisected. Carcinoma was identified in both lymph node sections in 64 (59.8%) nodes and in only one-half of the bisected lymph node in 43 (40.2%) nodes. Involvement of both sections was more likely when patients had multiple nodes positive. In 12 patients, involvement of one-half of the bisected nodes was the only evidence of metastatic disease (20.0% of node-positive patients). This evidence suggests that submission of less than the complete lymph node for histologic evaluation of metastatic disease decreases the accuracy of lymph node staging. Furthermore, a significant proportion of patients may be erroneously classified as histologically node negative.
Direct Conversion of Xylan to Ethanol by Recombinant Saccharomyces cerevisiae Strains Displaying an Engineered Minihemicellulosome (2012)

Arabinoxylan is a heteropolymeric chain of a β-1,4-linked xylose backbone substituted with arabinose residues, representing a principal component of plant cell walls. Here we developed recombinant Saccharomyces cerevisiae strains as whole-cell biocatalysts capable of combining hemicellulase production, xylan hydrolysis, and hydrolysate fermentation into a single step. These strains displayed a series of uni-, bi-, and trifunctional minihemicellulosomes that consisted of a miniscaffoldin (CipA3/CipA1) and up to three chimeric enzymes. The miniscaffoldin derived from Clostridium thermocellum contained one or three cohesin modules and was tethered to the cell surface through the S. cerevisiae a-agglutinin adhesion receptor. Up to three types of hemicellulases, an endoxylanase (XynII), an arabinofuranosidase (AbfB), and a β-xylosidase (XlnD), each bearing a C-terminal dockerin, were assembled onto the miniscaffoldin by high-affinity cohesin-dockerin interactions. Compared to uni- and bifunctional minihemicellulosomes, the resulting quaternary trifunctional complexes exhibited an enhanced rate of hydrolysis of arabinoxylan. Furthermore, with an integrated d-xylose-utilizing pathway, the recombinant yeast displaying the bifunctional minihemicellulosome CipA3-XynII-XlnD could simultaneously hydrolyze and ferment birchwood xylan to ethanol with a yield of 0.31 g per g of sugar consumed.
Isolation of three new isochroman-3-one metabolites from Oidiodendron rhodogenum Robak (1981)

The fungus Oidiodendron rhodogenum Robak produces curvulinic acid, fuscin, and three new isochroman-3-one metabolites for which the structures (3)–(5) are proposed. A second strain grown under the same conditions produces fuscin and dihydrofuscin.
Alterations in the Reproductive Patterns of Female Mice Exposed to Xenobiotics (1997)

Chemicals, by virtue of their varied interactions with biological molecules, are expected to differ in the way they may alter female reproduction. Reproductive toxicity may reflect effects either on the female germ cells or on various maternal processes such as ovulation, implantation, pregnancy, and parturition. In either case, the ultimate manifestation of chemical toxicity on female reproduction is a decrease in the number of normal young born. Very little information is available on the effects of chemicals that are nonhormonal in nature on the long-term ability of treated females to produce offspring. This report presents the results of long-term female total reproductive capacity (TRC) tests on 29 chemicals, including pharmaceuticals, pesticides, and alkylating and industrial agents. For each chemical, the minimum test involved an evaluation of the maximum tolerated dose administered as a single intraperitoneal injection. Females were single-pair mated with an untreated male for most of the female's reproductive life span (a minimum of 347 days posttreatment) and scored for the number of live births produced during this period. Confirmatory dominant lethal experiments or histological examinations for numbers of small follicles were carried out when mutagenic effects or cytotoxicity, respectively, were suspected as the basis for reduced fertility. Of the 29 chemicals studied, 17 had reproductive effects which may be grouped into one of three classes: (1) those that reduced the total number of young and litters per female, (2) those that reduced the total number of young but not of litters, and (3) those that had no significant effect on the total number of young produced but reduced the size of the first and/or second litters. The TRC provides a capacity for detecting a range of toxic insults upon female reproduction. Many of the chemicals were indeed shown to affect the reproductive performance of females through mutagenic and/or cytotoxic effects on follicles. In some cases, however, no causative mechanism could be identified for the observed reduction in reproductive performance. Nevertheless, with this report the number of chemicals tested by this TRC procedure has been quadrupled and the categories of chemicals tested have been substantially broadened.
Gesture reconition using depth image (2014)

In this paper, we propose and implement a novel method for recognizing gestures using depth image from Microsoft's Kinect sensor. Our approach consists of two parts: gesture segmentation and gesture classification. For gesture segmentation, we use a histogram based threshold method to segment gestures. We also used median filter for image filtering to remove noise. For gesture classification we used corrosion operation to find the palm center, and we devise a method based on Graham's Scan algorithm to find fingertips. The experimental results indicate that our method can effectively recognize gestures in different lighting conditions and could be used in real-time video processing.
Comparison of Ligand Density and Protein Adsorption on Dye-Affinity Membranes Using Different Spacer Arms (2000)

Abstract The use of 1,6-diaminohexane, 1,10-diaminodecane, 1,6-diaminohexane + ethylene glycol diglycidyl ether (EGDGE), and 1,10-diaminodecane + EGDGE as spacer arms for the immobilization of Cibacron Blue 3GA onto Immobilon AV membranes was investigated in this work. The dye ligand density was optimized by the employment of 1,6-diaminohexane, followed by 1,10-diaminodecane, 1,10-diaminodecane + EGDGE, and 1,6-diaminohexane + EGDGE. The adsorption properties of lysozyme onto the dye-affinity membranes were also studied. The results show that the use of 1,10-diaminodecane as a spacer molecule appears to offer the best adsorption capacity and hence results in the highest percentage of ligand utilization. Consequently, a 12-atom straight molecule such as 1,10-diaminodecane is a good choice for dye-affinity membrane separations. ACKNOWLEDGMENT This research was sponsored by the National Science Council of Republic of China (NSC 87-2214-E-005-005).
A new method to compensate for the sample-and-hold distortion (1985)

The aim of this correspondence is to develop a superior method to compensate for any kind of distortion caused by the interpolation of uniform samples. The spectra of interpolating functions, such as a zero-order hold, are analyzed. As a consequence, a novel method is proposed to equalize the distortion of an interpolating function. The realization is fairly simple and modular in concept.
α-Amanitin Tolerance in Mycophagous <i>Drosophila</i> (1983)

Six species of Drosophila were tested for tolerance to the mushroom toxin alpha-amanitin, a potent inhibitor of RNA polymerase II. Three nonmycophagous species-D. melanogaster, D. immigrans, and D. pseudoobscura-showed very low survival and long development times in the presence of amanitin. Three mycophagous species-D. putrida, D. recens, and D. tripunctata-showed little or no sensitivity. Analysis in vitro indicated that this tolerance is not based on alteration of the molecular structure of RNA polymerase II.
CONFIDENCE INTERVALS FOR THE LOG-NORMAL MEAN (1997)

In this paper we conduct a stimulation study to evaluate coverage error, interval width and relative bias of four main methods for the construction of confidence intervals of log-normal means: the naive method; Cox's method; a conservative method; and a parametric bootstrap method. The simulation study finds that the naive method is inappropriate, that Cox's method has the smallest coverage error for moderate and large sample sizes, and that the bootstrap method has the smallest coverage error for small sample sizes. In addition, Cox's method produces the smallest interval width among the three appropriate methods. We also apply the four methods to a real data set to contrast the differences.
Thin-Layer Immunoaffinity Chromatography with Bar Code Quantitation of C-Reactive Protein (1995)

A rapid thin-layer immunoaffinity chromatographic method for quantitation in serum of an acute phase reactant, C-reactive protein (CRP), which can differentiate between viral and bacteria] infections, is described, where material and reagent costs are minimal. The analysis is based on the "sandwich" assay format using monoclonal antibodies directed against two sites of CRP. One of the antibodies is covalently bound to defined zones on a thin-layer immunoaffinity chromatography membrane, while the other antibody is covalently bound to deeply dyed blue latex particles. After incubation (CRP sample and latex particles), the CRP-latex immunocomplex is allowed to migrate along the immunoaffinity chromatography membrane. In the presence of antigen, a sandwich is formed between the CRP-latex immunocomplex and membrane-bound antibodies, which results in the appearance of blue lines on the membrane. Antibody immobilization on the TLC membrane is made with a redesigned piezoelectric-driven ink-jet printer. The time required for the analysis is less than 10 min. Quantitation is achieved either by counting the lines visually, with scanning reflectometry, or with a modified bar code reader. The limit of detection was estimated in the low femtomolar range using the naked eye as detector.
Correction. Heterocyclic Basic Compounds. V. 2-Amino4-basically-substituted-pyrimidines. (1945)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCorrection. Heterocyclic Basic Compounds. V. 2-Amino4-basically-substituted-pyrimidines.Robert Adams and Frank WhitmoreCite this: J. Am. Chem. Soc. 1945, 67, 12, 2281Publication Date (Print):December 1, 1945Publication History Published online17 January 2003Published inissue 1 December 1945https://doi.org/10.1021/ja01228a619RIGHTS & PERMISSIONSArticle Views16Altmetric-Citations-LEARN 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 InReddit PDF (134 KB) Get e-Alerts Get e-Alerts
Linear diffraction grating interferometer with high alignment tolerance and high accuracy (2011)

We present an innovative structure of a linear diffraction grating interferometer as a long stroke and nanometer resolution displacement sensor for any linear stage. The principle of this diffractive interferometer is based on the phase information encoded by the ±1st order beams diffracted by a holographic grating. Properly interfering these two beams leads to modulation similar to a Doppler frequency shift that can be translated to displacement measurements via phase decoding. A self-compensation structure is developed to improve the alignment tolerance. LightTool analysis shows that this new structure is completely immune to alignment errors of offset, standoff, yaw, and roll. The tolerance of the pitch is also acceptable for most installation conditions. In order to compact the structure and improve the signal quality, a new optical bonding technology by mechanical fixture is presented so that the miniature optics can be permanently bonded together without an air gap in between. For the output waveform signals, a software module is developed for fast real-time pulse counting and phase subdivision. A laser interferometer HP5529A is employed to test the repeatability of the whole system. Experimental data show that within 15 mm travel length, the repeatability is within 15 nm.
Autonomous Vehicle Path Planning with Remote Sensing Data (2008)

Long range path planning for an autonomous ground vehicle with minimal a-priori data is still very much an open problem. Previous research has demonstrated that least cost paths generated from aerial LIDAR and GIS data could play a role in automatically determining suitable routes over otherwise unknown terrain. However, most of this research has been theoretical. Consequently, there is very little literature the effectiveness of these techniques in plotting paths of an actual autonomous vehicle. This research aims to develop an algorithm for using aerial LIDAR and imagery to plan paths for a full size autonomous car. Methods of identifying obstacles and potential roadways from the aerial LIDAR and imagery are reviewed. A scheme for integrating the path planning algorithms into the autonomous vehicle existing systems was developed and eight paths were generated and driven by an autonomous vehicle. The paths were then analyzed for their drivability and the model itself was validated against the vehicle measurements. The methods described were found to be suitable for generating paths both on and off road.
Sampling for Approximate Inference in Continuous Time Bayesian Networks. (2008)

We first present a sampling algorithm for continuous time Bayesian networks based on importance sampling. We then extend it to continuous-time particle filtering and smoothing algorithms. The three algorithms can estimate the expectation of any function of a trajectory, conditioned on any evidence set constraining the values of subsets of the variables over subsets of the timeline. We present experimental results on their accuracies and time efficiencies, and compare them to expectation propagation. 1
Rituximab in the treatment of refractory pulmonary sarcoidosis (2014)

To the Editor: 

Sarcoidosis is a chronic disease characterised by granulomatous depositions that can occur in virtually any organ system [1]. Currently, there is no US Food and Drug Administration (FDA)-approved therapy for sarcoidosis; however, corticosteroids have proven efficacious and are a commonly used treatment [2]. In patients with chronic or pulmonary disease who do not respond to corticosteroids, or in whom steroid use is contraindicated, agents such as methotrexate, azathioprine and tumour necrosis factor (TNF)-α antagonists may be effective [3, 4]. However, a need persists for patients who fail to respond to current options.

Sarcoidosis is a T-cell-mediated disease; however, humoral mechanisms may play a role in its pathogenesis [5]. Sarcoidosis is often associated with hypergammaglobulinaemia, autoantibody production and circulating immune complexes [6].

B-cell-targeted therapies have shown positive results in many T-cell-mediated autoimmune diseases. Rituximab is a chimeric monoclonal antibody that causes depletion of CD20+ B-cells [7]. Rituximab is FDA approved for the treatment of rheumatoid arthritis, granulomatosis with polyangiitis (Wegener’s) and microscopic polyangiitis, and is also being studied in Sjogren’s syndrome, systemic lupus erythematosus and vasculitis [8]. There have been case reports of the effectiveness of rituximab for sarcoidosis [9–11]. Given the evidence for humoral involvement in sarcoidosis pathogenesis, this study sought to evaluate the utility of B-cell depletion using rituximab in patients with refractory pulmonary sarcoidosis.

This was a prospective, open-label, phase I/II trial. The study was approved by the …
Photothermal therapy of tumors in lymph nodes using gold nanorods and near-infrared laser light with controlled surface cooling (2015)

Photothermal therapy (PTT) using near-infrared (NIR) laser light and gold nanorods (GNRs) shows promise as a novel cancer treatment modality. However, the laser intensity required to destroy tumor cells located beneath the skin is greater than the threshold intensity that causes skin damage; thus, irradiation with laser light damages the skin as well as the tumor. Here, we show that a temperature control system allows metastatic lymph nodes (LNs) to be treated by PTT using NIR laser light and GNRs, without skin damage. A mouse model of LN metastasis was developed by injection of tumor cells, and the tumor-bearing proper axillary LN was treated with NIR laser light after injection of GNRs. The skin temperature was maintained at 45 °C during irradiation by using a temperature control system. Bioluminescence imaging revealed that tumor progression was less in LNs exposed to NIR laser light and GNRs than in LNs exposed to NIR laser light alone or controls (no irradiation or GNRs). Furthermore, the skin and LN capsule were macroscopically intact on day 9 after irradiation with NIR laser light, whereas tumor cells within the LN showed apoptosis. A numerical analysis demonstrated that the high-temperature zone and the LN region showing damage were localized to an area up to 3 mm in depth. The proposed novel PTT technique, using NIR laser light and GNRs with controlled surface cooling, could be applied clinically to treat metastatic LNs located within or outside the area accessible for surgical dissection.