gebhart/patrepeval huggingface dataset:
Development of a Radiolabeled Nucleic Acid Probe for the Detection of Encephalomyocarditis Virus of Swine (1993)

Encephalomyocarditis virus (EMCV) is a member of the genus Cardiovirus of the family Picomaviridae and infects a number of species including mice, elephants, squirrels, swine, and humans. EMCV infections in swine are usually sporadic in nature throughout the world. EMCV causes encephalitis and myocarditis with high mortality in young piglets and has also been associated with maternal reproductive disease in swine. 4,15,16,19 Transplacental infection in pregnant sows has been demonstrated, but the role of EMCV in clinical reproductive disease in the US swine herds is unclear. Serologic evidence of EMCV infection in swine without clinical problem has been reported. 22 Serologic data suggest that EMCV infections are widespread in the US swine herds, but EMCV has been isolated from only a limited number of cases. 10-14,26 Whether the poor success in EMCV isolation from aborted fetuses is due to the lability of EMCV or to the lack of any role of EMCV in swine reproductive disease has not been resolved. The presence of blocking antibodies may also interfere with the isolation of EMCV from clinical specimens. The recent isolation of porcine reproductive and respiratory syndrome (PRRS) virus from herds with reproductive failure has further confused what role EMCV has in swine reproductive failure in the US swine herds. EMCV isolates are closely related antigenically and there is probably only 1 serotype of EMCV. Variants of EMCV have been isolated that differ in organ tropism and pathogenicity. 1 Antigenic and genomic variability among various EMCV strains has also been reported and may be associated with the diversity in pathogenicity. 1,7,11,24,24 VP1 is the major polypeptide of EMCV against which virus neutralizing antibodies are directed. The VP1 gene is also the least conserved capsid gene among different members of Picornavirus. In contrast, the VP3 and VP4 genes and the 5' nontranslated region of EMCV are more conserved. 13,14,20,26 The major objective of the present study was to determine whether a nucleic acid probe specific for EMCV infection in swine could be developed. Such a probe would be useful in determining the prevalence and role of EMCV, if any, in swine reproductive failure. The EMCV strains used for this study were NVSL-FL, MN-25, ATCC VR-129B, Georgia, OVL-5/90, and Mengo. The NVSL-FL strain was isolated initially from pigs in Florida. The MN-25 strain was isolated from an aborted swine fetus obtained from a Minnesota farm that had a history of acute reproductive failure and neonatal losses. The ATCC VR-129B was originally isolated from a chimpanzee
Generation of hybrid genes and proteins by vaccinia virus-mediated recombination: application to human immunodeficiency virus type 1 env (1990)

The ability of poxviruses to undergo intramolecular recombination within tandemly arranged homologous sequences can be used to generate chimeric genes and proteins. Genes containing regions of nucleotide homology will recombine to yield a single sequence composed of portions of both original genes. A recombinant virus containing two genes with a number of conserved regions will yield a population of recombinant viruses containing a spectrum of hybrid sequences derived by recombination between the original genes. This scheme has been used to generate hybrid human immunodeficiency virus type 1 env genes. Recombinant vaccinia viruses that contain two divergent env genes in tandem array have been constructed. In the absence of selective pressure to maintain both genes, recombination between conserved homologous regions in these genes generated a wide range of progeny, each of which expressed a novel variant polypeptide encoded by the newly created hybrid env gene. Poxvirus-mediated recombination may be applied to map type-specific epitopes, to create novel pharmaceuticals such as hybrid interferons, to study receptor-binding or enzyme substrate specificities, or to mimic the antigenic diversity found in numerous pathogens.
Differential Expression of Vascular Endothelial Growth Factor (Vascular Permeabilty Factor) Forms in Rat Tissues (1995)

Vascular endothelial growth factor (VEGF)/vascular permeability factor (VPF), exists as multiple forms due to alternative splicing of mRNA. VEGF165/164 (human/rodent homologue) is often assumed to be the predominant form, although truly quantitative assessments are lacking. We have used the RNase protection assay to directly quantitate the relative abundance of VEGF mRNA forms in five rat tissues (brain, kidney, lung, spleen, and heart) and two rat glioma cell lines (C6 and 9L). The three major forms, which code for proteins of 188, 164, and 120 amino acids, were observed in all of the tissues and cells examined. However, the relative abundance differed among the samples. VEGF188 was the predominant form (> 50% of total VEGF mRNA) in heart and lung, but was the least abundant form (6-15%) in all other samples. VEGF164 was lower (approximately 25%) in heart and lung, but was predominant (> 50%) in brain and kidney. VEGF164 and VEGF120 were present in equimolar amounts (each form approximately 46% of total) in the spleen, C6, and 9L. VEGF120 was also present in kidney (38%) and lung (27%) and was least abundant (approximately 15%) in brain and heart. A rat homologue of VEGF206 was not observed. VEGF mRNA splicing occurs in a tissue-specific manner. The assumption that the predominant physiologic form of VEGF is a VEGF165/164 homodimer should be viewed with caution.
Finding Deceptive Opinion Spam by Any Stretch of the Imagination (2011)

Consumers increasingly rate, review and research products online. Consequently, websites containing consumer reviews are becoming targets of opinion spam. While recent work has focused primarily on manually identifiable instances of opinion spam, in this work we study deceptive opinion spam---fictitious opinions that have been deliberately written to sound authentic. Integrating work from psychology and computational linguistics, we develop and compare three approaches to detecting deceptive opinion spam, and ultimately develop a classifier that is nearly 90% accurate on our gold-standard opinion spam dataset. Based on feature analysis of our learned models, we additionally make several theoretical contributions, including revealing a relationship between deceptive opinions and imaginative writing.
Manual Chest Compression vs Use of an Automated Chest Compression Device During Resuscitation Following Out-of-Hospital Cardiac Arrest (2006)

clinicaltrials.gov Identifier: NCT00120965.
Complex formation of human thrombospondin with osteonectin (1988)

Human thrombospondin, a 450-kDa glycoprotein isolated from platelets and endothelial cells, specifically interacts with osteonectin, a protein of 30 kDa isolated from bovine bones and human platelets. Using ELISA, purified osteonectin binds to solid-phase-adsorbed thrombospondin with a dissociation constant (Kd) of 0.7 nM. Binding of thrombospondin to solid-phase-adsorbed osteonectin was also observed (Kd = 0.86 nM). The interaction of thrombospondin with solid-phase-adsorbed osteonectin was significantly decreased (81% inhibition) when using an excess of fluid-phase osteonectin. Thrombospondin-osteonectin complex formation was calcium-dependent as shown by a 50-80% inhibition in the presence of EDTA. None of the proteins known to interact with thrombospondin (fibrinogen, fibronectin, collagen, plasminogen) had a significant inhibitory effect on thrombospondin-osteonectin complex formation. This selective interaction was confirmed by affinity chromatography. Iodinated osteonectin, previously incubated with purified thrombospondin, specifically bound to an anti-thrombospondin monoclonal antibody (P10) linked to protein-A--Sepharose 4B. Elution of the anti-thrombospondin antibody from protein A allowed the recovery of the thrombospondin-osteonectin complex in the eluate, as judged by SDS/polyacrylamide gel electrophoresis and autoradiography. Blotting of purified thrombospondin to osteonectin adsorbed onto nitrocellulose further confirmed complex formation. In addition, when released from thrombin-stimulated platelets, thrombospondin and osteonectin bound to anti-thrombospondin IgG-coated plates indicating that osteonectin was complexed to thrombospondin once the platelet-release reaction has occurred.
Activating Mutations in the Epidermal Growth Factor Receptor Underlying Responsiveness of Non–Small-Cell Lung Cancer to Gefitinib (2004)

A subgroup of patients with non-small-cell lung cancer have specific mutations in the EGFR gene, which correlate with clinical responsiveness to the tyrosine kinase inhibitor gefitinib. These mutations lead to increased growth factor signaling and confer susceptibility to the inhibitor. Screening for such mutations in lung cancers may identify patients who will have a response to gefitinib.
On Control of a Pitching and Surging Wave Energy Converter (2011)

The paper presents a model of a pitching and surging wave-energy converter, investigates the tuning problem in regular seas, and presents a practical tuning technique for time-domain studies in irregular seas. The proposed tuning technique is evaluated on a specific device with defined features in irregular seas where the capabilities of the proposed control approach are assessed. Realistic performance analysis of the proposed technique is performed in time-domain studies where the proposed adaptive technique and some other passive and adaptive tuning methods are used. The passive tuning methods are based on tuning the device's natural frequency to peak and energy frequencies and use fixed power takeoff settings. The proposed adaptive tuning approach employs sliding Discrete Fourier Transform for wave properties estimation. The approach then utilizes the estimated wave properties in optimizing the power capture of a pitching and surging device by adjusting the power takeoff system parameters. The paper also presents details of a comparative study on power capture performances of a pitching-and-surging device with that of a heaving device in the same sea states. The practical implications of the results and recommendations are also presented.
The relationship between molecular structure and mesomorphic properties of 2,2′- and 3,2′-difluoroterphenyls synthesized by palladium-catalysed cross-couplings (1995)

Abstract Several homologues of two structurally different types of mesogenic difluoroterphenyls have been prepared. One set of compounds contains two inner-core fluoro-substituents and the other set possesses both an inner-core and an outer-core fluoro-substituent. The use of various types of palladium-catalysed cross-coupling reactions was invaluable in the synthesis (for example, selective couplings, and couplings to trifluoromethanesulphonate derivatives). Additionally, a novel selective lithiation is reported. The mesogenic materials are all low melting and the types of mesophase generated are considerably structure dependent. However, most of the materials support the tilted Sc phase which is required of ferroelectric host materials. The mesomorphic behaviour of these novel materials is discussed in terms of the molecular structure and the structure/property relationships are compared with those for difluoroterphenyls with different arrangements of lateral fluoro-substitution.
Therapy of glioblastoma multiforme improved by the antimutagenic chloroquine (2003)

Chronic administration of chloroquine greatly enhanced the response of GBM to antineoplastic treatment. Because the cytotoxicity of chloroquine on malignant cells is negligible, these favorable results appear mediated by its strong antimutagenic effect that precludes the appearance of resistant clones during radiotherapy and chemotherapy.
Microtubule dynamics at the G2/M transition: abrupt breakdown of cytoplasmic microtubules at nuclear envelope breakdown and implications for spindle morphogenesis. (1996)

We recently developed a direct fluorescence ratio assay (Zhai, Y., and G.G. Borisy. 1994. J. Cell Sci. 107:881-890) to quantify microtubule (MT) polymer in order to determine if net MT depolymerization occurred upon anaphase onset as the spindle was disassembled. Our results showed no net decrease in polymer, indicating that the disassembly of kinetochore MTs was balanced by assembly of midbody and astral MTs. Thus, the mitosis-interphase transition occurs by a redistribution of tubulin among different classes of MTs at essentially constant polymer level. We now examine the reverse process, the interphase-mitosis transition. Specifically, we quantitated both the level of MT polymer and the dynamics of MTs during the G2/M transition using the fluorescence ratio assay and a fluorescence photoactivation approach, respectively. Prophase cells before nuclear envelope breakdown (NEB) had high levels of MT polymer (62%) similar to that previously reported for random interphase populations (68%). However, prophase cells just after NEB had significantly reduced levels (23%) which recovered as MT attachments to chromosomes were made (prometaphase, 47%; metaphase, 56%). The abrupt reorganization of MTs at NEB was corroborated by anti-tubulin immunofluorescence staining using a variety of fixation protocols. Sensitivity to nocodazole also increased at NEB. Photoactivation analyses of MT dynamics showed a similar abrupt change at NEB, basal rates of MT turnover (pre-NEB) increased post-NEB and then became slower later in mitosis. Our results indicate that the interphase-mitosis (G2/M) transition of the MT array does not occur by a simple redistribution of tubulin at constant polymer level as the mitosis-interphase (M/G1) transition. Rather, an abrupt decrease in MT polymer level and increase in MT dynamics occurs tightly correlated with NEB. A subsequent increase in MT polymer level and decrease in MT dynamics occurs correlated with chromosome attachment. These results carry implications for understanding spindle morphogenesis. They indicate that changes in MT dynamics may cause the steady-state MT polymer level in mitotic cells to be lower than in interphase. We propose that tension exerted on the kMTs may lead to their lengthening and thereby lead to an increase in the MT polymer level as chromosomes attach to the spindle.
Pseudo-random-bit-sequence phase modulation for reduced errors in a fiber optic gyroscope (2016)

Low noise and drift in a laser-driven fiber optic gyroscope (FOG) are demonstrated by interrogating the sensor with a low-coherence laser. The laser coherence was reduced by broadening its optical spectrum using an external electro-optic phase modulator driven by either a sinusoidal or a pseudo-random bit sequence (PRBS) waveform. The noise reduction measured in a FOG driven by a modulated laser agrees with the calculations based on the broadened laser spectrum. Using PRBS modulation, the linewidth of a laser was broadened from 10 MHz to more than 10 GHz, leading to a measured FOG noise of only 0.00073 deg/√h and a drift of 0.023 deg/h. To the best of our knowledge, these are the lowest noise and drift reported in a laser-driven FOG, and this noise is below the requirement for the inertial navigation of aircraft.
A Test for Normality Based on Sample Entropy (1976)

Summary A test of the composite hypothesis of normality is introduced. The test is based on the property of the normal distribution that its entropy exceeds that of any other distribution with a density that has the same variance. The test statistic is based on a class of estimators of entropy constructed here. The test is shown to be a consistent test of the null hypothesis for all alternatives without a singular continuous part. The power of the test is estimated against several alternatives. It is observed that the test compares favourably with other tests for normality.
Anticancer Effects of Adriamycin-Loaded Hydroxyapatite Implants Determined in a Swarm Rat Chondrosarcoma Model (1994)

We investigated the antitumor effects of adriamycin (ADR)-loaded hydroxyapatite (HAP) beads in a Swarm rat chondrosarcoma model. When one ADR-loaded HAP bead (ADR: 0.8 mg/bead) was implanted into the central portion of a rat bearing tumor, the ADR-loaded HAP beads showed good therapeutic effects, increasing the life span (ILS) by 90%. Signifìcantly, leukopenia and diarrhea were not observed. These results suggest that HAP delivery offers an interesting and a potentially effective method.
T lineage differentiation from human embryonic stem cells (2006)

Harnessing the ability of genetically manipulated human embryonic stem cells (hESC) to differentiate into appropriate lineages could revolutionize medical practice. These cells have the theoretical potential to develop into all mature cell types; however, the actual ability to develop into all hematopoietic lineages has not been demonstrated. Using sequential in vitro coculture on murine bone marrow stromal cells, and engraftment into human thymic tissues in immunodeficient mice, we demonstrate that hESC can differentiate through the T lymphoid lineage. Stable transgene expression was maintained at high levels throughout differentiation, suggesting that genetically manipulated hESC hold potential to treat several T cell disorders.
Unique Nuclear Matrix Protein Alterations in Head and Neck Squamous Cell Carcinomas: Intermediate Biomarker Candidates (1996)

The progression of normal squamous epithelium to a malignant metastatic phenotype may depend on cellular genetic events and the failure of host mechanisms. Intermediate biomarkers are needed to more effectively identify and quantify malignant progression and develop the potential for specific treatments and prevention strategies. The nuclear matrix is the RNA-protein scaffold of the nucleus, which controls in part nuclear shape, DNA organization, and DNA function. Nuclear matrix proteins in all previously studied cell types show a common set of nuclear matrix proteins and a subset of tissue- and cell type-specific proteins. In every system studied to date, the nuclear matrix has been demonstrated to undergo quantifiable alterations in its protein composition with transformation to the malignant phenotype. The loss and gain of nuclear matrix proteins are being investigated as biomarkers for malignant transformation in breast, colon, and prostate carcinoma. We have investigated nuclear matrix protein composition in laryngeal and oral cavity primary squamous cell tumors and metastatic cervical lymph nodes. Laryngeal carcinoma demonstrated the gain of two specific nuclear matrix proteins in comparison with noncancerous squamous epithelium. Squamous cell carcinoma matrixes demonstrate greater heterogeneity than do previously studied adenocarcinoma matrixes, and yet they display specific matrix proteins that may represent important potential biomarkers.
Blocking of HIV-1 Infection by Targeting CD4 to Nonraft Membrane Domains (2002)

Human immunodeficiency virus (HIV)-1 infection depends on multiple lateral interactions between the viral envelope and host cell receptors. Previous studies have suggested that these interactions are possible because HIV-1 receptors CD4, CXCR4, and CCR5 partition in cholesterol-enriched membrane raft domains. We generated CD4 partitioning mutants by substituting or deleting CD4 transmembrane and cytoplasmic domains and the CD4 ectodomain was unaltered. We report that all CD4 mutants that retain raft partitioning mediate HIV-1 entry and CD4-induced Lck activation independently of their transmembrane and cytoplasmic domains. Conversely, CD4 ectodomain targeting to a nonraft membrane fraction results in a CD4 receptor with severely diminished capacity to mediate Lck activation or HIV-1 entry, although this mutant binds gp120 as well as CD4wt. In addition, the nonraft CD4 mutant inhibits HIV-1 X4 and R5 entry in a CD4+ cell line. These results not only indicate that HIV-1 exploits host membrane raft domains as cell entry sites, but also suggest new strategies for preventing HIV-1 infection.
A new heat transfer model to predict cooling rates for rapid freezing fixation (1988)

SUMMARY A simple heat transfer model is presented to show that convection from the cryogen to the specimen is the limiting step in rapid freezing of small samples for electron microscopy when the Biot modulus, which measures the ratio of convective to conductive heat transfer, ( hd / k ) &lt; 1. In comparison to the commonly accepted conduction‐limited model, the convection‐limited model predicts that cooling rates are proportional to the surface area/volume ratio, independent of the sample thermal conductivity, and inversely proportional to the product of sample density and heat capacity. Literature values of experimentally measured cooling rates fit the convection limited model. Simple analogies to predict the heat transfer coefficient as a function of cryogen properties, specimen geometry and cryogen velocity are presented.
Biologic Significance of Quantitative Estrogen Receptor Immunohistochemical Assay by Image Analysis in Breast Cancer (1994)

The authors assayed 209 stage I and II mammary carcinomas for the estrogen receptor (ER) with an immunocytochemical assay (ICA) and quantitated the nuclear stain with the SAMBA 4000 Cell Image Analysis System (Imaging Products International, Inc., Chantilly, VA). The cases had been followed for 54-214 months (average, 64 months). The results were correlated with the patients' overall and disease-free survival times. Three of the parameters obtained from the quantitative analysis were evaluated: labeling index, mean optical density, and quick score. Statistical analysis was performed with the Kaplan-Meier product limit estimator for quantitated values and Cox regression for risk of mortality and disease progression. Mean optical density of the nuclei at a cut-off value of 10 produced the strongest association between quantitative ERICA and overall and disease-free survival times in discriminating high- and low-risk groups (P = .016 and P = .018, respectively). When the mean optical density results were categorized into ranges of values of potential biologic significance according to overall survival times, patients with mean optical density greater than 15 were found to be at lowest risk; patients with values between 5 and 15 had a statistically significant intermediate risk; and the group with values less than 5 had the worst outcome (P = .018). The probability of disease-free survival also was statistically significant (P = .038) among the three groups with cut-off points of less than 10, 10-35, and greater than 35. These results showed that quantified optical density has better discriminating power for risk prediction than that obtained by the biochemical assay for ER at a cut-off value of 10 or 20 fmol/mg. Estrogen receptor ICA has been adequately shown to be as or more accurate than ligand-binding assays. Our results corroborate those studies and support the utility of ICA assays for ER by showing that quantitation performed by image analysis is an objective and reproducible method yielding clinical prognostic information of higher reliability than that given by the dextran-coated charcoal ER assay.