gebhart/patrepeval huggingface dataset:
A new algorithm for automatic assessment of the degree of TB-infection using images of ZN-stained sputum smear (2010)

This paper describes a new algorithm for automatic assessment of the degree of TB-infection, by counting the number of Mycobacteria i.e., acid fast bacilli (AFB) in the color images of ZN-stained sputum smear. This algorithm consists of two stages. The first (“pre-processing”) stage involves exploiting color information to segment the candidate AFB in the image from the background, based on classification of pixels in the HSI color-space using Mahalanobis distance. In this context, we introduce a novel “divide and conquer” strategy to improve the robustness of color-classification. The pre-processing stage is followed by connected component labeling, size-thresholding to remove noisy objects, proximity-grouping by using a novel proximity-test algorithm, and area-based classification. Our algorithm identifies and counts the number of AFB irrespective of their shapes, can handle bacilli with beaded structure (which are important and are specific to TB) and has shown reasonable success in isolating clumps. A total of 205 images of ZN-stained sputum smears taken from more than 12 patients were considered in our experiments. Results on 169 images, based on HSI clusters built from 36 other images, are encouraging. Some of the images used in building the data-base and also in validation, include those sent by the RNTCP (Govt. of India) for training-purposes.
Enzymology, biochemistry and immunology (1992)

The proceedings of a conference which aims to provide an up-to-date overview of current research in the nitric oxide field. This volume covers the biochemical and immunological aspects of the subject. Topics covered include the biological implications of nitric oxide synthesis.
Oncolysis of malignant human melanoma tumors by Coxsackieviruses A13, A15 and A18 (2011)

Many RNA viruses are displaying great promise in the field of oncolytic virotherapy. Previously, we reported that the picornavirus Coxsackievirus A21 (CVA21) possessed potent oncolytic activity against cultured malignant melanoma cells and melanoma xenografts in mice. In the present study, we demonstrate that three additional Group A Coxsackieviruses; Coxsackievirus A13 (CVA13), Coxsackievirus A15 (CVA15) and Coxsackievirus A18 (CVA18), also have similar oncolytic activity against malignant melanoma. Each of the viruses grew quickly to high titers in cancer cells expressing ICAM-1 and intratumoral injection of preformed subcutaneous SK-Mel-28 xenografts in mice with CVA13, CVA15 and CVA18 resulted in significant tumor volume reduction.As preexisting immunity could potentially hinder oncolytic virotherapy, sera from stage IV melanoma patients and normal controls were tested for levels of protective antibody against the panel of oncolytic Coxsackieviruses. Serum neutralization assays revealed that 3 of 21 subjects possessed low levels of anti-CVA21 antibodies, while protective antibodies for CVA13, CVA15 and CVA18 were not detected in any sample. Serum from individuals who were seropositive for CVA21 failed to exhibit cross-neutralization of CVA13, CVA15 and CVA18. From these studies it can be concluded that the administration of CVA13, CVA15 or CVA18 could be employed as a potential multivalent oncolytic therapy against malignant melanoma.
Benzene-Free Synthesis of Catechol:  Interfacing Microbial and Chemical Catalysis (2005)

The toxicity of aromatics frequently limits the yields of their microbial synthesis. For example, the 5% yield of catechol synthesized from glucose by Escherichia coli WN1/pWL1.290A under fermentor-controlled conditions reflects catechol's microbial toxicity. Use of in situ resin-based extraction to reduce catechol's concentration in culture medium and thereby its microbial toxicity during its synthesis from glucose by E. coli WN1/pWL1.290A led to a 7% yield of catechol. Interfacing microbial with chemical synthesis was then explored where glucose was microbially converted into a nontoxic intermediate followed by chemical conversion of this intermediate into catechol. Intermediates examined include 3-dehydroquinate, 3-dehydroshikimate, and protocatechuate. 3-Dehydroquinate and 3-dehydroshikimate synthesized, respectively, by E. coli QP1.1/pJY1.216A and E. coli KL3/pJY1.216A from glucose were extracted and then reacted in water heated at 290 degrees C to afford catechol in overall yields from glucose of 10% and 26%, respectively. The problematic extraction of these catechol precursors from culture medium was subsequently circumvented by high-yielding chemical dehydration of 3-dehydroquinate and 3-dehydroshikimate in culture medium followed by extraction of the resulting protocatechuate. After reaction of protocatechuate in water heated at 290 degrees C, the overall yields of catechol synthesized from glucose via chemical dehydration of 3-dehydroquinate and chemical dehydration of 3-dehydroshikimate were, respectively, 25% and 30%. Direct synthesis of protocatechuate from glucose using E. coli KL3/pWL2.46B followed by its extraction and chemical decarboxylation in water gave a 24% overall yield of catechol from glucose. In situ resin-based extraction of protocatechaute synthesized by E. coli KL3/pWL2.46B followed by chemical decarboxylation of this catechol percursor was then examined. This employment of both strategies for dealing with the microbial toxicity of aromatic products led to the highest overall yield with catechol synthesized in 43% overall yield from glucose.
Nanometer-Sized Amino Acids for the Synthesis of Nanometer-Scale Water-Soluble Molecular Rods of Precise Length (2007)

This paper introduces the unnatural amino acid Abc2K as a nanometer-length building block for the creation of water-soluble molecular rods of exceptional size. Abc2K is a water-soluble variant of the unnatural amino acid 4‘-amino-[1,1‘-biphenyl]-4-carboxylic acid (Abc) with lysinelike propyloxyammonium side chains at the 2- and 5-positions. The protected building block Fmoc-Abc2K(Boc)-OH (1) can be used in standard Fmoc-based solid-phase peptide synthesis to create water-soluble rodlike peptides in nanometer unit lengths up to at least ten nanometers. Oligomers up to and including the decamer were easily prepared on a Rink amide resin. These peptides are easy to purify and characterize by standard reverse-phase HPLC, 1H NMR, and ESI-MS techniques. The Abc2K amino acid can be combined with various standard amino acids to provide well behaved hybrid and biologically relevant peptides. Building block 1 is efficiently prepared on a multigram scale from commercially available starting materials by way of the Suzuki cross-coupling reaction. Molecular modeling studies of Abc2K oligomers show only minor effects from torsional and bending motions and support a model in which the oligomers are relatively straight and rigid. Fluorescence resonance energy transfer (FRET) studies are consistent with a model in which the Abc2K oligomers behave as rigid rods with a length of 1.0 nm per monomer unit.
A New Class of Peroxisome Proliferator-activated Receptor Agonists with a Novel Binding Epitope Shows Antidiabetic Effects (2004)

The peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors belonging to the NR1 subfamily of nuclear receptors. The PPARs play key roles in the control of glucose and lipid homeostasis, and the synthetic isoform-specific PPAR agonists are used clinically to improve insulin sensitivity and to lower serum triglyceride levels. All of the previously reported PPAR agonists form the same characteristic interactions with the receptor, which have been postulated to be important for the induction of agonistic activity. Here we describe a new class of PPARalpha/gamma modulators, the 5-substituted 2-benzoylaminobenzoic acids (2-BABAs). As shown by x-ray crystallography, the representative compounds BVT.13, BVT.762, and BVT.763, utilize a novel binding epitope and lack the agonist-characteristic interactions. Despite this, some compounds within the 2-BABA family are potent agonists in a cell-based reporter gene assay. Furthermore, BVT.13 displays antidiabetic effects in ob/ob mice. We concluded that the 2-BABA binding mode can be used to design isoform-specific PPAR modulators with biological activity in vivo.
Automated design of pin-constrained digital microfluidic arrays for lab-on-a-chip applications* (2006)

Microfluidics-based biochips, also referred to as lab-on-a-chip (LoC), are devices that integrate fluid-handling functions such as sample preparation, analysis, separation, and detection. This emerging technology combines electronics with biology to open new application areas such as point-of-care diagnosis, on-chip DNA analysis, and automated drug discovery. We propose a design automation method for pin-constrained LoCs that manipulate nanoliter volumes of discrete droplets on a microfluidic array. In contrast to the direct-addressing scheme that has been studied thus far in the literature, we assign a small number of independent control pins to a large number of electrodes in the LoC, thereby reducing design complexity and product cost. We apply the proposed method to a microfluidic array for a set of multiplexed bioassays.
Hematopoietic Stem Cell Mobilization with Agents Other than G-CSF (2012)

Hematopoietic stem and progenitor mobilization has revolutionized the field of hematopoietic transplantation. Currently, hematopoietic grafts acquired from the peripheral blood of patients or donors treated with granulocyte-colony stimulating factor (G-CSF) are the preferred source for transplantation. G-CSF mobilization regimens, however, are associated with known morbidities and a significant number of normal donors and patient populations fail to mobilize sufficient numbers of hematopoietic stem and progenitor cells for transplantation, necessitating the need for non-G-CSF mobilization strategies. Mechanistic studies evaluating hematopoietic bone marrow niche interactions have uncovered novel agents with the capacity for hematopoietic mobilization. This chapter provides a comprehensive overview of mobilizing agents, other than G-CSF, and experimental procedures and technical aspects important to evaluate and define their hematopoietic mobilizing activities alone and in combination.
The atmospheric-pressure plasma jet: a review and comparison to other plasma sources (1998)

Atmospheric-pressure plasmas are used in a variety of materials processes. Traditional sources include transferred arcs, plasma torches, corona discharges, and dielectric barrier discharges. In arcs and torches, the electron and neutral temperatures exceed 3000/spl deg/C and the densities of charge species range from 10/sup 16/-10/sup 19/ cm/sup -3/. Due to the high gas temperature, these plasmas are used primarily in metallurgy. Corona and dielectric barrier discharges produce nonequilibrium plasmas with gas temperatures between 50-400/spl deg/C and densities of charged species typical of weakly ionized gases. However, since these discharges are nonuniform, their use in materials processing is limited. Recently, an atmospheric-pressure plasma jet has been developed, which exhibits many characteristics of a conventional, low-pressure glow discharge. In the jet, the gas temperature ranges from 25-200/spl deg/C, charged-particle densities are 10/sup 11/-10/sup 12/ cm/sup -3/, and reactive species are present in high concentrations, i.e., 10-100 ppm. Since this source may be scaled to treat large areas, it could be used in applications which have been restricted to vacuum. In this paper, the physics and chemistry of the plasma jet and other atmospheric-pressure sources are reviewed.
Volatility Characteristics of Blends of Gasoline with Ethyl Tertiary-Butyl Ether (ETBE) (1990)

&lt;div class="htmlview paragraph"&gt;Ethyl tertiary-butyl ether (ETBE), a reaction product of ethanol and isobutylene, has been proposed as a high-octane blending component for gasoline. Laboratory studies have been conducted to determine how the addition of ETBE to gasoline affects the volatility characteristics of the fuel, and how the effects of ETBE compare with those of the commonly used oxygenates, ethanol and MTBE. The amount of vapor generated in bench-scale simulated evaporative emissions tests with each of those three oxygenates was also determined.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The vapor pressures of gasoline-ETBE blends decreased linearly as the concentration of ETBE was increased. In contrast, ethanol addition raises the vapor pressure of gasoline, although in a nonlinear fashion. ETBE increased the mid-range volatility of the fuel, in the same way as a pure hydrocarbon of similar vapor pressure and boiling point.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;In the simulated evaporative emissions tests, a gasoline-ETBE blend generated much less diurnal and hot soak vapor than a gasoline-ethanol blend.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The results of this study lead to the conclusion that, based on evaporative emissions considerations, the use of ETBE in gasoline is preferable to the use of ethanol, from which ETBE is made.&lt;/div&gt;
Plane-wave decomposition of the sound field on a sphere by spherical convolution (2004)

Spherical microphone arrays have been recently studied for sound analysis and sound recordings, which have the advantage of spherical symmetry facilitating three-dimensional analysis. This paper complements the recent microphone array design studies by presenting a theoretical analysis of plane-wave decomposition given the sound pressure on a sphere. The analysis uses the spherical Fourier transform and the spherical convolution, where it is shown that the amplitudes of the incident plane waves can be calculated as a spherical convolution between the pressure on the sphere and another function which depends on frequency and the sphere radius. The spatial resolution of plane-wave decomposition given limited bandwidth in the spherical Fourier domain is formulated, and ways to improve the computation efficiency of plane-wave decomposition are introduced. The paper concludes with a simulation example of plane-wave decomposition.
Association of Csk-homologous Kinase (CHK) (formerly MATK) with HER-2/ErbB-2 in Breast Cancer Cells (1997)

Protein-tyrosine kinases, such as HER-2/ErbB-2, have been specifically linked to breast cancer. The Csk-homologous kinase (CHK), formerly MATK, is a tyrosine kinase that contains the Src homology 2 and 3 (SH2 and SH3) domains and demonstrates homology ( approximately 50%) to the Csk tyrosine kinase. Like Csk, CHK is able to phosphorylate and inactivate Src family kinases. In this report, we investigated whether CHK is expressed in breast cancer tissues and whether it participates in the ErbB-2 signaling pathway in T47D and MCF-7 breast cancer cell lines. Immunostaining of the CHK protein in breast tissues demonstrated that primary invasive ductal carcinomas, stage II (13 of 15 cases) and stage I (8 of 15 cases), expressed the CHK protein, while this protein was not detected in the adjacent normal tissues from the same patients. To study the role of CHK in the ErbB-2 signaling pathway, glutathione S-transferase fusion proteins containing the SH2 and SH3 domains of CHK were generated. CHK-SH2 and CHK-SH3-SH2, but not CHK-SH3 or CHK-NH2-SH3, precipitated the tyrosine-phosphorylated ErbB-2 upon stimulation with heregulin. EGF or interleukin-6 stimulation of T47D cells failed to induce CHK-SH2 association with ErbB-2, the EGF-receptor, or the interleukin-6 receptor. In vivo association of the tyrosine-phosphorylated ErbB-2 with CHK was observed in co-immunoprecipitation studies with anti-CHK antibodies. EGF-R, ErbB-3, and ErbB-4 were not detected in the CHK immunoprecipitates or in the precipitates of the GST-SH2 fusion proteins of CHK, suggesting that the association of CHK with ErbB-2 upon heregulin stimulation is receptor-specific (ErbB-2) and ligand-specific (heregulin). These results indicate that CHK might participate in signaling in breast cancer cells by associating, via its SH2 domain, with ErbB-2 following heregulin stimulation.
Combining Long Short Term Memory and Convolutional Neural Network for Cross-Sentence n-ary Relation Extraction (2018)

We propose in this paper a combined model of Long Short Term Memory and Convolutional Neural Networks (LSTM-CNN) that exploits word embeddings and positional embeddings for cross-sentence n-ary relation extraction. The proposed model brings together the properties of both LSTMs and CNNs, to simultaneously exploit long-range sequential information and capture most informative features, essential for cross-sentence n-ary relation extraction. The LSTM-CNN model is evaluated on standard dataset on cross-sentence n-ary relation extraction, where it significantly outperforms baselines such as CNNs, LSTMs and also a combined CNN-LSTM model. The paper also shows that the LSTM-CNN model outperforms the current state-of-the-art methods on cross-sentence n-ary relation extraction.
Immunodominant deters the response to other tumor antigens thereby favoring escape: prevention by vaccination with tumor variants selected with cloned cytolytic T cells <i>in vitro</i> (1996)

Variant cancer cells which arise from the parent tumor during tumor progression can escape immunity but retain antigens. We have mixed highly immunogenic (A+B+) murine parental cancer cells with less immunogenic (A-B+) variant cancer cells to construct a model of a cancer containing escape variants. When such mixtures of cancer cells were injected into normal mice, the variant cells grew out because immune responsiveness to the B antigen on the variant was hindered by dominance of the A antigen on the surrounding parental tumor cells. However, A-B+ variant cells inoculated alone at a separate site induced B specific cytolytic T cells and were rejected. Moreover, mice immunized with A-B+ cells rejected a challenge which contained a mixture of variant and parental cancer cells, while immunization with A+B+ cells was ineffective. Thus, variant tumor cells selected from parental tumor cells by cytolytic T cells in vitro can be used to induce protective immunity against variants expected to escape tumor immunity in vivo. The immunodominance of the A antigen may be related to its ability to induce a much more rapid CTL response than the B antigen, since we show in another model that the pre-existence of a CTL response to one antigen prevented the subsequent induction of CTL to another antigen injected at the same site, even if both antigens were equally efficient at inducing CTL. These results indicate that immunodominance can affect strong as well as weak antigens. Vaccination with individual antigens at separate sites rather than with multiple antigens at one site may, therefore, be needed to prevent tumor escape and tumor recurrence or to counteract infectious diseases.
Expression of matrix metalloproteinases in the muscle of patients with inflammatory myopathies (2000)

Because collagen IV is prominent on the muscle membrane, the overexpression of matrix metalloproteinases (MMPs) 2 and 9 on the non-necrotic muscle fibers in polymyositis (PM) and sporadic inclusion body myositis (s-IBM) may facilitate lymphocyte adhesion and enhance T-cell-mediated cytotoxicity by degrading extracellular matrix proteins. The findings may have practical implications in considering therapeutic trials with MMP inhibitors in patients with PM and s-IBM.
Successful chemotherapy of experimental neuroendocrine lung tumors in hamsters with an antagonist of Ca2+/calmodulin. (1990)

The chemotherapeutic effect of B859-35, the (-)-enantiomer of dihydropyrine 3-methyl-5-3-(4,4-diphenyl-1-piperidinyl)-propyl-1,4-dihydro-2,6-dimethy l-4- (3-nitrophenyl)-pyridine-3,5-dicarboxylate-hydrochloride (niguldipine), was tested on tumors induced in Syrian golden hamsters by N-nitrosodiethylamine (DEN). Peripheral pulmonary adenomas/adenocarcinomas were induced in hamsters maintained under ambient air conditions by multiple s.c. injections of DEN for 20 weeks. We have reproducibly shown that within this time interval lung adenomas develop in a significant number of the animals. The carcinogen treatment was discontinued at this point and one group of these hamsters was given B859-35 intragastrically 5 days/week for 20 weeks while the second group of such tumor-bearing hamsters were kept for an identical time interval without further treatment. Neuroendocrine lung tumors were induced in hamsters maintained in an atmosphere of 60% O2 by multiple s.c. injections of DEN for 8 weeks. We have reproducibly shown that within this short time interval neuroendocrine lung tumors develop in a significant number of the animals. The carcinogen treatment was discontinued at this point and the animals were returned to ambient air conditions. One group of these tumor-bearing hamsters was then given B859-35 intragastrically 5 days/week for 20 weeks while a second group of these hamsters was kept untreated for an identical time interval. A control group was given s.c. injections of saline for 20 weeks under ambient air conditions. A dramatic and selective anticarcinogenic effect of B859-35 was observed on the neuroendocrine lung tumors and nasal cavity tumors induced by DEN/hyperoxia while tumors of larynx/trachea were not affected. B859-35 had no effect on peripheral adenomas/adenocarcinomas, nasal cavity tumors, papillary polyps of larynx/trachea, or liver tumors induced by DEN under ambient air conditions.
Data Entry for Mobile Devices Using Soft Keyboards: Understanding the Effects of Keyboard Size and User Tasks (2003)

Abstract As mobile, handheld computing devices become more common and are used for an ever-increasing variety of tasks, new mechanisms for data entry must be investigated. Personal digital assistants often provide a small stylus-activated soft keyboard, as do some mobile phones that include touch screens. However, there is little data regarding the importance of keyboard size or the users' tasks, the effectiveness of these keyboards, or user reactions to these keyboards. In this article, an experiment designed to investigate these issues in the context of a palm-style QWERTY keyboard is described. In this study, 30 novices completed 6 realistic tasks using either a small, medium, or large soft keyboard. The results not only confirm that keyboard size does not affect data entry rates but that making the keyboard smaller does not increase error rates or negatively impact preference ratings. However, tasks that required users to switch between the alphabetic keyboard and the numeric keyboard do result in significantly slower data entry rates. A model that accurately predicts the time required to enter predefined text is presented, and directions for future research are discussed.
A gate-array-based 666 MHz VLSI test system (2002)

A 666 MHz VLSI test system with a dedicated memory test pattern generator was developed. A loose-timing data transfer scheme was employed for better integration of a shared-resource unit into the per-pin tester-architecture, Timing control resolution of 12.5 ps was achieved within a normal framework of a gate array LSI. A simple and low-cost timing calibration-technique was developed to offer accurate test timings. Parallel operation of the memory test pattern generators was used to realize a non-interrupted pattern generation at the maximum speed.
Heterogeneity of Functional Properties of Clone 66 Murine Breast Cancer Cells Expressing Various Stem Cell Phenotypes (2013)

These data demonstrate that Clone 66 murine breast cancer cells that express stem cell phenotypes are heterogeneous and exhibit different functional properties, and this may also be the case for human breast cancer stem cells.