gebhart/patrepeval huggingface dataset:
Behavior of nucleolar proteins during the course of apoptosis in camptothecin‐treated HL60 cells (2000)

By means of immunofluorescence and immunoelectron microscopy we have studied the fate of different nucleolar components during the apoptotic process in camptothecin-treated HL60 cells. We have found that RNA polymerase I disappeared while UBF was associated with previously described fibrogranular threaded bodies. In contrast, fibrillarin, C23/nucleolin, and B23/nucleophosmin remained detectable in granular material present amid micronuclei of late apoptotic cells. Double immunolabeling experiments showed colocalization of both C23 and B23 with fibrillarin. Immunoblotting analysis showed that UBF was proteolytically degraded, whereas fibrillarin, C23/nucleolin, and B23/nucleophosmin were not. These results may help explain the presence of anti-nucleolar antibodies seen in various pathological disorders. J. Cell. Biochem. 78:264–277, 2000. © 2000 Wiley-Liss, Inc.
Clinical significance of sleep‐related breathing disorder in narcolepsy (2002)

Both the influence of comorbid obstructive sleep apnea-hypopnea syndrome (OSAHS) on daytime sleepiness and its pathological mechanism in 10 narcoleptic patients was studied. Mild elevation of esophageal negative pressure and obstruction in the velopharyngeal area, as observed by upper airway magnetic resonance imaging, during apneic episodes was observed in the subjects. Severity of the disorder was correlated positively with body mass index, and the latencies of the multiple sleep latency tests were not improved with nasal continuous positive airway pressure treatment in subjects. Pathogenesis of OSAHS in narcolepsy was thought to be almost similar to typical OSAHS, and that the disorder seemed to lack a pathological influence on daytime sleepiness.
<title>Chromeless phase-shifted masks: a new approach to phase-shifting masks</title> (1991)

This paper introduces a novel concept, 'chromeless phase-shifting', that eliminates the need for the use of chrome to form patterns in optical lithography. Chromeless phase-shifting uses 180 degree(s) phase-shifters on transparent glass to define patterns. The method relies ont eh destructive interference between phase-shifters and clear areas at the edges of the phase-shifters to define dark or opaque areas on the mask. Gratings sufficiently small will produce sufficient interference to completely inhibit the transmission of light (these gratings are thus named dark-field gratings). The combination of these effects makes is possible to form a wide range of patterns, from line-space patterns to isolated bright or dark areas. In this study, the lithography simulators SPLAT and SAMPLE were used to understand the principles behind this new scheme, and to verify various pattern designs. Simulation and experimental results are presented to demonstrate the concept.
Identification of upstream and intragenic regulatory elements that confer cell-type-restricted and differentiation-specific expression on the muscle creatine kinase gene. (1988)

Terminal differentiation of skeletal myoblasts is accompanied by induction of a series of tissue-specific gene products, which includes the muscle isoenzyme of creatine kinase (MCK). To begin to define the sequences and signals involved in MCK regulation in developing muscle cells, the mouse MCK gene has been isolated. Sequence analysis of 4,147 bases of DNA surrounding the transcription initiation site revealed several interesting structural features, some of which are common to other muscle-specific genes and to cellular and viral enhancers. To test for sequences required for regulated expression, a region upstream of the MCK gene from -4800 to +1 base pairs, relative to the transcription initiation site, was linked to the coding sequences of the bacterial chloramphenicol acetyltransferase (CAT) gene. Introduction of this MCK-CAT fusion gene into C2 muscle cells resulted in high-level expression of CAT activity in differentiated myotubes and no detectable expression in proliferating undifferentiated myoblasts or in nonmyogenic cell lines. Deletion mutagenesis of sequences between -4800 and the transcription start site showed that the region between -1351 and -1050 was sufficient to confer cell type-specific and developmentally regulated expression on the MCK promoter. This upstream regulatory element functioned independently of position, orientation, or distance from the promoter and therefore exhibited the properties of a classical enhancer. This upstream enhancer also was able to confer muscle-specific regulation on the simian virus 40 promoter, although it exhibited a 3- to 5-fold preference for its own promoter. In contrast to the cell type- and differentiation-specific expression of the upstream enhancer, the MCK promoter was able to function in myoblasts and myotubes and in nonmyogenic cell lines when combined with the simian virus 40 enhancer. An additional positive regulatory element was identified within the first intron of the MCK gene. Like the upstream enhancer, this intragenic element functioned independently of position, orientation, and distance with respect to the MCK promoter and was active in differentiated myotubes but not in myoblasts. These results demonstrate that expression of the MCK gene in developing muscle cells is controlled by complex interactions among multiple upstream and intragenic regulatory elements that are functional only in the appropriate cellular context.
CELL TO CELL INTERACTION IN THE IMMUNE RESPONSE (1968)

The number of discrete hemolytic foci and of hemolysin-forming cells arising in the spleens of heavily irradiated mice given sheep erythrocytes and either syngeneic thymus or bone marrow was not significantly greater than that detected in controls given antigen alone. Thoracic duct cells injected with sheep erythrocytes significantly increased the number of hemolytic foci and 10 million cells gave rise to over 1000 hemolysin-forming cells per spleen. A synergistic effect was observed when syngeneic thoracic duct cells were mixed with syngeneic marrow cells: the number of hemolysin-forming cells produced in this case was far greater than could be accounted for by summating the activities of either cell population given alone. The number of hemolytic foci produced by the mixed population was not however greater than that produced by an equivalent number of thoracic duct cells given without bone marrow. Thymus cells given together with syngeneic bone marrow enabled irradiated mice to produce hemolysin-forming cells but were much less effective than the same number of thoracic duct cells. Likewise syngeneic thymus cells were not as effective as thoracic duct cells in enabling thymectomized irradiated bone marrow-protected hosts to produce hemolysin-forming cells in response to sheep erythrocytes. Irradiated recipients of semiallogeneic thoracic duct cells produced hemolysin-forming cells of donor-type as shown by the use of anti-H2 sera. The identity of the hemolysin-forming cells in the spleens of irradiated mice receiving a mixed inoculum of semiallogeneic thoracic duct cells and syngeneic marrow was not determined because no synergistic effect was obtained in these recipients in contrast to the results in the syngeneic situation. Thymectomized irradiated mice protected with bone marrow for a period of 2 wk and injected with semiallogeneic thoracic duct cells together with sheep erythrocytes did however produce a far greater number of hemolysin-forming cells than irradiated mice receiving the same number of thoracic duct cells without bone marrow. Anti-H2 sera revealed that the antibody-forming cells arising in the spleens of these thymectomized irradiated hosts were derived, not from the injected thoracic duct cells, but from bone marrow. It is concluded that thoracic duct lymph contains a mixture of cell types: some are hemolysin-forming cell precursors and others are antigen-reactive cells which can interact with antigen and initiate the differentiation of hemolysin-forming cell precursors to antibody-forming cells. Bone marrow contains only precursors of hemolysin-forming cells and thymus contains only antigen-reactive cells but in a proportion that is far less than in thoracic duct lymph.
Factor XIII A subunit-deficient mice developed severe uterine bleeding events and subsequent spontaneous miscarriages (2003)

To understand the molecular pathology of factor XIII (FXIII) deficiency in vivo, its A subunit (FXIIIA)-knockout (KO) mice were functionally analyzed. Although homozygous FXIIIA female KO mice were capable of becoming pregnant, most of them died due to excessive vaginal bleeding during gestation. Abdominal incisions revealed that the uteri of the dead mice were filled with blood and that some embryos were much smaller than others within a single uterus. A series of histologic examinations of the pregnant animals suggested that massive placental hemorrhage and subsequent necrosis developed in the uteri of the FXIIIA KO mice on day 10 of gestation. This was true regardless of the genotypes of fetuses. These results are reminiscent of spontaneous miscarriage in pregnant humans with FXIII deficiency and indicate that maternal FXIII plays a critical role in uterine hemostasis and maintenance of the placenta during gestation.
Protein‐resistant surfaces prepared by PEO‐containing block copolymer surfactants (1989)

Polyethylene oxide(PEO)-containing nonionic polymeric surfactants were studied as a possible means to produce PEO-rich surfaces by a simple coating treatment of a common hydrophobic medical material--polyethylene. Surface tension and adsorption properties of PEO/polypropylene oxide(PPO) and PEO/polybutylene oxide(PBO) block copolymer surfactants on a hydrophobic surface (low density polyethylene, LDPE) were investigated, using the Wilhelmy plate surface tension technique and x-ray photoelectron spectroscopy(XPS). The protein resistance of the surfactant-treated surfaces was evaluated by XPS and 125I-labeled proteins. The data presented indicate that adsorption of the surfactants on LDPE is dependent on the molecular geometry of the surfactants. Adsorption of human albumin was significantly decreased on the surfactant-treated LDPE surfaces, as compared with the untreated surface. Surfactants suitable for the preparation of PEO-rich surfaces and possible mechanisms for their protein resistance are discussed.
Comparative Inhibitory Effects of Various Nucleoside and Nonnucleoside Analogues on Replication of Influenza Virus Types A and B In Vitro and In Ovo (1993)

Six nucleoside analogues, two sulfated polysaccharides, and four protease inhibitors were evaluated in vitro as inhibitors of influenza virus replication. Four guanosine analogues (mizoribine, ribavirin, pyrazofurin, and 5-ethynyl-1-beta-D-ribofuranosylimidazole-4-carboxamide), the sulfated polysaccharide dextran sulfate (molecular weight 500,000), and two protease inhibitors (camostat mesilate and nafamostat mesilate) were inhibitory to the replication of strains of influenza virus types A and B at concentrations down to 0.3 micrograms/mL. Of these seven compounds, ribavirin, camostat mesilate, and nafamostat mesilate were efficacious in both reducing the virus titer and increasing the survival rate of influenza virus-infected chick embryos. For camostat mesilate, the ED50 (required to improve the survival rate of influenza virus-infected chick embryos by 50%) was 0.80 micrograms/g, and its selectivity index, based on the ratio of the 50% toxic dose (required to reduce the viability of chick embryos by 50%) to ED50, was 280. Camostat mesilate deserves further exploration for its potential in the treatment of influenza virus infection.
The Immune Response Elicited by Mammary Adenocarcinoma Cells Transduced with Interferon- γ and Cytosine Deaminase Genes Cures Lung Metastases by Parental Cells (1998)

The parental cells of the TSA murine mammary adenocarcinoma (TSA-pc) were transfected with both the interferon-gamma (IFN-y) gene and the cytosine deaminase (CD) suicide gene to obtain a therapeutic vaccine active against TSA-pc lung metastases. Even in the absence of treatment with the prodrug 5-fluorocytosine (5-FC), the local growth of double transfectants (CD-y clones) was inhibited by a marked recruitment of granulocytes and macrophages. In mice harboring TSA-pc micrometastases, therapeutic vaccination with either IFN-gamma or CD single transfectants reduced the number of lung nodules, whereas CD-gamma double transfectants abrogated metastasis growth in up to 80% of mice. Treatment of mice with 5-FC did not alter the curative efficacy of CD-gamma double-transfectant cells. By contrast, in mice vaccinated with CD single-transfectant cells, 5-FC treatment caused a significant loss of their curative activity. Host T cells played an active role in the cure of lung metastases, because vaccination of nude mice with CD-gamma cells was uneffective.
Spatiotemporal magnetic field monitoring for MR (2008)

MR experiments frequently rely on signal encoding by the application of magnetic fields that vary in both space and time. The accurate interpretation of the resulting signals often requires knowledge of the exact spatiotemporal field evolution during the experiment. To better fulfill this need, a new approach is presented that enables measuring the field evolution concurrently with any MR sequence. Miniature NMR probes are used to monitor the MR phase evolution around the object under investigation. Based on these data, a global phase model is calculated that can then be used as a basis for processing the actual image or spectroscopic data. The new method is demonstrated by MRI of a phantom, using spin-warp, spiral, and EPI trajectories. Throughout, the monitoring results enabled highly accurate image reconstruction, even in the presence of massive gradient imperfections.
Quantification of Macrophage Content in Atherosclerotic Plaques by Optical Coherence Tomography (2003)

The high contrast and resolution of OCT enables the quantification of macrophages within fibrous caps. The unique capabilities of OCT for fibrous cap characterization suggest that this technology may be well suited for identifying vulnerable plaques in patients.
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing (2009)

Defining the transcriptome, the repertoire of transcribed regions encoded in the genome, is a challenging experimental task. Current approaches, relying on sequencing of ESTs or cDNA libraries, are expensive and labor-intensive. Here, we present a general approach for ab initio discovery of the complete transcriptome of the budding yeast, based only on the unannotated genome sequence and millions of short reads from a single massively parallel sequencing run. Using novel algorithms, we automatically construct a highly accurate transcript catalog. Our approach automatically and fully defines 86% of the genes expressed under the given conditions, and discovers 160 previously undescribed transcription units of 250 bp or longer. It correctly demarcates the 5' and 3' UTR boundaries of 86 and 77% of expressed genes, respectively. The method further identifies 83% of known splice junctions in expressed genes, and discovers 25 previously uncharacterized introns, including 2 cases of condition-dependent intron retention. Our framework is applicable to poorly understood organisms, and can lead to greater understanding of the transcribed elements in an explored genome.
<title>Update on optical systems for military head-mounted displays</title> (1999)

Early military applications of head mounted displays (HMDs) used the miniature CRT as the image source. The optical configurations in these systems took on a wide variety of sizes and shapes. Over the past few years, newer miniature image source technologies have emerged as serious contenders to replace the miniature CRT. These include a number of different technologies that result in new and unique optical designs. With the availability of more optical design techniques &amp; tools such as diamond turning, diffractive elements, graded index materials, etc., the optics now being developed take on forms with clear advantages over CRT based HMDs. This paper presents an overview of the HMD optical systems that have evolved for miliary applications, the functionality of the systems, and their relative performance capabilities.
Cancer Management: A Multidisciplinary Approach (2007)

The fundamental principle behind this book, as stated by the publisher, The Oncology Group (also publisher of the journal ONCOLOGY and news magazine Oncology News International) was to provide a truly integrated, multidisciplinary approach to the management of cancer patients. For this updated 10th edition, the editors have enlisted 114 medical, surgical, and radiation oncologists, whose contributions provide an excellent overview of the important principles of cancer management.
Gram-positive bacteria are held at a distance in the colon mucus by the lectin-like protein ZG16 (2016)

The distal colon functions as a bioreactor and harbors an enormous amount of bacteria in a mutualistic relationship with the host. The microbiota have to be kept at a safe distance to prevent inflammation, something that is achieved by a dense inner mucus layer that lines the epithelial cells. The large polymeric nets made up by the heavily O-glycosylated MUC2 mucin forms this physical barrier. Proteomic analyses of mucus have identified the lectin-like protein ZG16 (zymogen granulae protein 16) as an abundant mucus component. To elucidate the function of ZG16, we generated recombinant ZG16 and studied Zg16<sup>-/-</sup> mice. ZG16 bound to and aggregated Gram-positive bacteria via binding to the bacterial cell wall peptidoglycan. Zg16<sup>-/-</sup> mice have a distal colon mucus layer with normal thickness, but with bacteria closer to the epithelium. Using distal colon explants mounted in a horizontal perfusion chamber we demonstrated that treatment of bacteria with recombinant ZG16 hindered bacterial penetration into the mucus. The inner colon mucus of Zg16<sup>-/-</sup> animals had a higher load of Gram-positive bacteria and showed bacteria with higher motility in the mucus close to the host epithelium compared with cohoused littermate Zg16<sup>+/+</sup> The more penetrable Zg16<sup>-/-</sup> mucus allowed Gram-positive bacteria to translocate to systemic tissues. Viable bacteria were found in spleen and were associated with increased abdominal fat pad mass in Zg16<sup>-/-</sup> animals. The function of ZG16 reveals a mechanism for keeping bacteria further away from the host colon epithelium.
The Effects of Intranasal Budesonide on Allergen-induced Production of Interleukin-5 and Eotaxin, Airways, Blood, and Bone Marrow Eosinophilia, and Eosinophil Progenitor Expansion in Sensitized Mice (2002)

We have previously demonstrated that allergen inhalation induces expansion of bone marrow eosinophil progenitors in sensitized mice and subjects with asthma and that the inhaled corticosteroid, budesonide, reduced baseline but not allergen-induced increase in bone marrow eosinophil/basophil progenitors (EoB-CFU) in subjects with asthma. Here, we evaluated the effects of intranasal budesonide on allergen-induced increases in interleukin (IL)-5 and eotaxin in the airway and peripheral blood, expansion of bone marrow Eo-CFU and eosinophilia in bone marrow, peripheral blood and airway, as well as airway hyperresponsiveness, in ovalbumin (OVA)-sensitized mice. Budesonide treatment attenuated allergen-induced eosinophilia in bone marrow, peripheral blood, and airways as well as allergen-induced increases in bone marrow eosinophil progenitors but not allergen-induced increases in IL-5 or eotaxin 12 h following the second of two daily exposures to allergen; at later time points treatment was associated with attenuation of IL-5, eosinophilia, Eo-CFU, and airway hyperresponsiveness. These results suggest that a component of the mechanism by which corticosteroid treatment attenuates allergen-induced airway inflammation is through suppression of bone marrow eosinophilopoiesis, and that this is likely not mediated simply through the blocking of IL-5 production at the airway.
Permeation of Insulin, Calcitonin and Exenatide across Caco-2 Monolayers: Measurement Using a Rapid, 3-Day System (2013)

Short-term 3-day Caco-2 monolayers provide new opportunities for developing reproducible and high-throughput models for screening of therapeutic macromolecules for oral absorption.
A therapeutic aptamer inhibits angiogenesis by specifically targeting the heparin binding domain of VEGF 165 (2005)

Aptamers recognize their targets with extraordinary affinity and specificity. The aptamer-based therapeutic, Macugen, is derived from a modified 2'fluoro pyrimidine RNA inhibitor to vascular endothelial growth factor (VEGF) and is now being used to treat the wet form of age-related macular degeneration. This VEGF(165) aptamer binds specifically to the VEGF(165) isoform, a dimeric protein with a receptor-binding domain and a heparin-binding domain (HBD). To understand the molecular recognition between VEGF and this aptamer, binding experiments were used to show that the HBD contributes the majority of binding energy in the VEGF(165)-aptamer complex. A tissue culture-based competition assay demonstrated that the HBD effectively competes with VEGF(165) for aptamer binding in vivo. Comparison of NMR spectra revealed that structural features of the smaller HBD-aptamer complex are present in the full-length VEGF(164)-aptamer complex. These data show that the HBD provides the binding site for the aptamer and is the primary determinant for the affinity and specificity in the VEGF(165)-aptamer complex.
Techniques for Multi-User MIMO with Two-Way Training (2008)

We consider forward-link multiuser MIMO transmission, whereby K users are served by a base station with a large number of (potentially distributed) transmit antennas. We address the problem of channel state information (CSI) mismatch between the transmitter and the receivers with a two-way training scheme. In a quasi-static setting, the proposed scheme requires only K pilot symbols for uplink training and as little as one symbol for downlink training. In particular, we show that the performance of the system where the receiver has perfect channel knowledge can be approached with a small value of downlink training symbols. We consider two variants of linear MMSE precoders that take into account the quality of the channel state information at the transmitter and demonstrate that robust high sum-rate systems can be designed that rely on single-antenna receivers, provided that a large enough number of antennas is used for transmission. Finally, we sketch an example of implementations for the equal rate case.
Cardiovascular and Respiratory Considerations With Pharmacotherapy of Glaucoma and Ocular Hypertension (2008)

Glaucoma and ocular hypertension are highly prevalent conditions in individuals over the age of 40 and are commonly seen together in patients with cardiovascular disease. Many of the antiglaucoma medications, when systemically absorbed, affect the sympathetic and parasympathetic nervous systems of patients and can cause cardiovascular toxicity. Such adverse effects are frequently associated with the long-term use of potentially toxic agents in elderly people, who are most prone to chronic eye disease. Moreover, patients may not associate their symptoms with the topical eye medications, and consequently may not report adverse drug effects. Drug-drug interactions can also occur when patients are taking medications for both cardiovascular disease and glaucoma. In this review, the systemic toxicity of these agents is reviewed, along with possible drug-drug interactions. Mention is made of other antiglaucoma medications used alone and in combination with topical beta-blockers. Identification of genetic loci-a bold new step toward glaucoma treatment-is mentioned briefly at the end of the article.