gebhart/patrepeval huggingface dataset:
Glucose-inducible hypertrophy and suppression of anion efflux in rat beta cells (2002)

Hypertrophy of beta cells from obese fa/fa rats is associated with increased sensitivity to basal glucose. Exposure to glucose in culture distorts insulin secretion more in beta cells from large than small islets from fa/fa rats. The aim of the present study is to investigate whether increased beta cell volume is associated with both glucose hypersensitivity and altered activity of the glucose-sensitive anion conductance. Beta cells from fa/fa rats had increased volume compared with those from lean rats after 24 h culture. Three-day exposure to 25 mM glucose in culture induced 10-15% hypertrophy in beta cells from lean rats and basal secretion from intact islets was increased tenfold. Estimates of ion channel activity were made from measurement of radiolabeled ion efflux. Taurine efflux, a marker of glucose-regulated anion channel activity, was reduced after high glucose exposure but no alterations in glucose-dependent K+ efflux were detected. The reverse hemolytic plaque assay was used to determine the contributions of the number of secreting cells (recruitment) versus secretion per cell in beta cells from enlarged (>250 microm diameter), intermediate (125-250 microm) and small (<125 microm) islets from lean and obese rats exposed to conditions mimicking hyperglycemia. After overnight culture, basal secretion was twofold greater from beta cells of large fa/fa islets compared with all other groups. Recruitment at low glucose was increased in all lean or fa/fa beta cells derived from >125 microm islets. When beta cells from small islets were exposed to supra-physiological glucose for 3 days, recruitment was increased at basal glucose and blunted at high glucose. Glucose exposure converts the recruitment profile of beta cells from small islets to resemble that of beta cells from large islets while inducing cellular hypertrophy and reduced anion conductance. However, hypertrophy alone did not predict functional characteristics of overnight-cultured beta cells from fa/fa rats.
Modeling User Search Behavior (2006)

Web usage mining is a main research area in Web mining focused on learning about Web users and their interactions with Web sites. Main challenges in Web usage mining are the application of data mining techniques to Web data in an efficient way and the discovery of non trivial user behaviour patterns. In this paper we focus the attention on search engines analyzing query log data and showing several models about how users search and how users use search engine results.
Host specificity of the colonization of murine gastric epithelium by lactobacilli (1984)

Strains of Lactobacillus isolated from animals of several species were examined for their capacity to colonize the lumens and form layers on the keratinized nonsecreting epithelium in the stomachs of monoassociated ex-germfree mice. All strains tested could be cultured at comparable population levels from the stomachs of the mono-associated mice. With one exception, however, only strains previously isolated from rodents were able to form thick continuous layers on the gastric epithelial surface. The exception was a strain isolated from calf feces. This strain formed a layer on the epithelial surface, comparable to layers seen in animals associated with strains from rodents.
B MESON RECONSTRUCTION AND LIFETIME STUDIES WITH THE MARK-II AT PEP. (1988)

We have measured the lifetime of an ensemble of particles containing b quarks, tagged with a high p/sub T/ lepton from their semileptonic decay. Using a method which estimates the production point of each particle in the beam ellipse, we measured a lifetime of 0.98 +- 0.12 +- 0.13 psec. We have also studied methods of partially reconstructing B mesons decaying into D/sup/star//minus// mesons plus charged leptons or mesons. We have searched the Mark II PEP data samples and find five candidates for B/sup 0/ decay. Four of these B/sup 0/ candidates form good vertices, and their measured proper lifetimes are presented. 18 refs.
Solute diffusion in hydrated polymer networks. Part 1.—Cellulose gels (1975)

Translational diffusion measurements on different homologous series (n-alcohols, polyhydric alcohols, oligosaccharides and alkali metal chlorides) and polyethylene oxide polymers in a densely crosslinked water-swollen cellulose gel (83 % water) are described. Solute diffusion coefficients in the gel phase are considerably lower than for free diffusion. The range of diffusion coefficients was 3.6 × 10–6 to 0.12 × 10–6 with corresponding ratios to free diffusion values 0.235 to 0.09. It is shown that the effect of the polymer matrix is a constant factor for the smaller molecules and that the reduction is due to a network-induced increase in the local viscosity of the medium. Only at high molecular weight does an increased collision frequency of the solute with polymer segments result in additional reduction of diffusion coefficients.
Efficiently supporting ad hoc queries in large datasets of time sequences (1997)

Ad hoc querying is difficult on very large datasets, since it is usually not possible to have the entire dataset on disk. While compression can be used to decrease the size of the dataset, compressed data is notoriously difficult to index or access. In this paper we consider a very large dataset comprising multiple distinct time sequences. Each point in the sequence is a numerical value. We show how to compress such a dataset into a format that supports ad hoc querying, provided that a small error can be tolerated when the data is uncompressed. Experiments on large, real world datasets ( AT&amp;T customer calling patterns) show that the proposed method achieves an average of less than 5% error in any data value after compressing to a mere 2.5% of the original space ( i.e. , a 40:1 compression ratio), with these numbers not very sensitive to dataset size. Experiments on aggregate queries achieved a 0.5% reconstruction error with a space requirement under 2%.
In vivo tracking of T cell development, ablation, and engraftment in transgenic zebrafish (2004)

Transgenic zebrafish that express GFP under control of the T cell-specific tyrosine kinase (lck) promoter were used to analyze critical aspects of the immune system, including patterns of T cell development and T cell homing after transplant. GFP-labeled T cells could be ablated in larvae by either irradiation or dexamethasone added to the water, illustrating that T cells have evolutionarily conserved responses to chemical and radiation ablation. In transplant experiments, thymocytes from lck-GFP fish repopulated the thymus of irradiated wild-type fish only transiently, suggesting that the thymus contains only short-term thymic repopulating cells. By contrast, whole kidney marrow permanently reconstituted the T lymphoid compartment of irradiated wild-type fish, suggesting that long-term thymic repopulating cells reside in the kidney.
Chloroplast Targeting of Bacterial β-Glucuronidase with a Pea Transit Peptide in Transgenic Tobacco Plants (1991)

Transit peptides located at the amino termini of the chloroplast precursor proteins are necessary and sufficient components to accomplish import of chloroplast proteins into chloroplasts. We introduced a chimeric gene consisting of a coding sequence of Pisum sativum small subunit of ribulose 1.5-bisphosphate carboxylase/oxygenase (rbcS) transit peptide and the gene coding for bacterial β-glucuronidase (GUS) into tobacco (Nicotiana tabacum L.) cells by Agrobacterium tumefaciens/binary vector system. Transformed tobacco cells with the chimeric gene were in vitro regenerated and the transgenic plants developed were assayed for the expression of GUS and targeting of GUS into chloroplasts by northern blot analysis and measurement of GUS activity. Northern blot analysis confirmed that the fused gene of Gus and the coding sequence for the transit peptide was properly integrated into tobacco chromosome and transcribed. Fractionated chloroplasts from the transgenic tobacco plants showed significant levels of GUS activities. These results indicate that the pea transit peptide is sufficient to transport GUS across the chloroplast envelope into chloroplast in transgenic tobacco plants.
Position Location: Triangulation Versus Circulation (1978)

Position location algorithms, using data from electronic surveillance systems have, for the most part, been based upon statistical analysis of the points of intersection of the lines of bearing. These triangulation ion algorithms may well minimize the effect of random measurement errors on the location estimate, but few existing algorithms account for systematic (bias) errors. An algorithm based upon intersecting circles which eliminates certain types of systematic error is presented with simulation data utilized to compare the position location estimates obtained from both triangulation and circulation algorithms.
Abstract 3622: Complete workflow for detection of low frequency somatic mutations from cell-free DNA using Ion Torrent™ platforms (2016)

Abstract Research detecting of somatic mutations in circulating cell-free DNA (cfDNA) using research blood samples from subjects previously diagnosed with cancer provides a potential non-invasive approach to monitor cancer status and evaluate cancer evolution in the future. However, most of the existing mutation detection methods show insufficient sensitivity to detect cfDNA mutations since only small amount of mutant gene fragments, derived from tumor cells, is present in a large amount of normal circulating DNA background. We demonstrated a complete workflow that includes blood collection, cfDNA isolation, library preparation, sequencing, and data analysis to enable detection of rare DNA variants in blood plasma samples. Blood samples were collected using Streck™ DNA tubes followed by plasma preparation and cfDNA isolation using MagMAX™ Cell-Free DNA Isolation Kit. Library preparation was performed using Oncomine™ lung cfDNA kit. Barcoded libraries were pooled and sequenced on Ion Torrent™ Next Generation Sequencing Platforms. Sequencing data was analyzed in Torrent Suite™ using variantCaller-cfDNA plugin. ∼150 biomarkers relevant to non-small cell lung cancer were interrogated in one sequencing run. We demonstrated detection sensitivity at 0.1% frequency using engineered mutants that were spiked into control DNA samples. The workflow was tested on a set of research samples from matched tumor FFPE and blood plasma collected from research subjects with non-small cell lung cancer (NSCLC). About 1 mL of plasma was processed using the workflow described above. RecoverAll™ Multi-Sample RNA/DNA Isolation Workflow was used to isolate DNA from FFPE samples, followed by library preparation, sequencing and data analysis using the same workflow described above. Summary of variant calls from matched cfDNA and FFPE tumor samples are presented here. Results indicate high sensitivity of the workflow and expected levels of concordance between variants detected in the two types of research samples. In this study, we developed a highly sensitive and reliable research workflow to detect rare somatic mutations in circulating cfDNA samples. Significant overlapping of mutations discovered in FFPE tumor and cfDNA samples suggests that this workflow may be used to monitor tumor dynamics in NSCLC and potentially other tumors in the future. Disclaimer: For research use only. Not for use in diagnostic procedures. Citation Format: Jian Gu, Dumitru Brinza, Ann Mongan, Richard Chien, Dalia Dhingra, Fiona Hyland, Kelli Bramlett. Complete workflow for detection of low frequency somatic mutations from cell-free DNA using Ion Torrent™ platforms. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3622.
Relationship Between Virulence and Immunity as Revealed in Recent Studies of the Fl Capsule of Yersinia pestis (1995)

Yersinia pestis, the causative agent of plague, possesses multiple virulence determinants encoded on its three plasmids and on its chromosome. We evaluated the role of the protein capsule F1 in virulence an immunity against plague. Strains lacking F1, either those that are naturally occurring or those with genetically defined nonpolar mutations in the structural gene, retained their virulence for mice and nonhuman primates. However, both active immunization with F1, from either a recombinant vector or Y. pestis, and passive immunization with F1 monoclonal antibody protected mice from experimental infection with wild-type F1-positive organisms. These results suggest that protective immunogens like F1 need not be essential for virulence. The rare isolation of virulent F1-negative organisms from F1-immunized animals infected with F1-positive strains supports this conclusion and also suggests that, in addition to F1, an optimal vaccine against plague should include essential virulence factors as immunogens.
The roles of surfactant proteins A and D in innate immunity (2000)

Research over the last decade on the surfactant proteins SP-A and SP-D suggests roles beyond surfactant lipid homeostasis, involving their participation in innate immune defence. SP-A and SP-D bind and agglutinate an impressive array of non-self structures, ranging from bacteria and fungi to allergens and environmental inorganic substrates. Complementing binding. SP-A and SP-D initiate and enhance immune cell ingestion and killing of targets. Recently, some exciting developments have extended and clarified their contributions to innate immunity. Knockout mice for SP-A and SP-D have been developed. The SP-A knockout confirms that SP-A plays a key role in defence against lung pathogens and reveals the underlying defense mechanisms that require SP-A. These surfactant proteins have also been shown to have important roles in modulating the immune response, instructing, yet quenching, the immune reactions in the lung. The crystal structure of SP-D plus functional studies with recombinantly altered forms of SP-A and SP-D has begun to characterise the structural motifs responsible for mediating their immune functions. Linkage and polymorphism analysis is explaining the role these genes may play in lung diseases and infection.
Chimeric Azalides with Functionalized Western Portions (1996)

A series of chimeric azalides which are homologous to the potent azalide antibiotic 9-deoxo-8a-aza-8a-homoerythromycin A (2) in their eastern halves, but which have functionally complex western halves derived from a variety of sources, including carbohydrates, is reported.The erythromycin derived azalide antibiotics, the prototypes of which are 9-deoxo-9a-am-9a-methyl-8ahomoerythromycin A (1) and 9-deoxo-&-aza-8a-methyl-8a-homoerythromycin A (2), combine the safety of erythromycin with an expanded gram negative spectrum and wider tolerance to oral administrati~n.~In a previous report, we described the conversion of the erythromycin-derived acyclic fragment (3) to a class of "chimeric" azalides2 which have eastern portions corresponding to those found in 1 or 2, but which have western portions (represented by " A in the figure) simplified to a chain of methylene groups.3We now report the extension of our "cut and paste" method to the synthesis of chimeric 8a-azalides with more highly functionalized western portions (4) H ~N 3 ' HOh.&"chimeT annelati
Separation of rabbit marrow precursor cells by combined isopycnic sedimentation and electronic cell sorting (1978)

Separation of developing cells into fractions of differing stages of maturity is critical to effective biochemical study of the process of cellular differentiation. Density gradient techniques utilizing rate- zonal or isopycnic separations have permitted partial separations based on cell mass or cell density. In this study the separation of various rabbit marrow cells was improved by high-speed flow analysis and sorting in a Coulter Two-Parameter Cell Sorter. After preliminary isopycnic separation of marrow cells in Ficoll-Hypaque, cells were sorted into lymphoid and myeloid elements, utilizing light-scatter (LS) profiles to determine sorting. Characteristic LS patterns were present for erythrocytes, lymphocytes, devitalized cells, and granulocytes. When erythrocytes and their precursors were removed by hypotonic lysis, the remaining granulocytes could be sorted to give samples with much greater purity with respect to developmental stage than was possible with density gradients alone. Thus the combination of techniques represents a significant improvement in the ability to study the mechanisms of normal or altered cellular maturation.
Genetically Modified T Cells to Target Glioblastoma (2013)

Despite advances in surgical procedures, radiation, and chemotherapy the outcome for patients with glioblastoma (GBM) remains poor. While GBM cells express antigens that are potentially recognized by T cells, GBMs prevent the induction of GBM-specific immune responses by creating an immunosuppressive microenvironment. The advent of gene transfer has allowed the rapid generation of antigen-specific T cells as well as T cells with enhanced effector function. Here we review recent advances in the field of cell therapy with genetically modified T cells and how these advances might improve outcomes for patients with GBM in the future.
Lysophosphatidate Acyltransferase in the Microsomes from Maturing Seeds of Meadowfoam (Limnanthes alba) (1990)

Lysophosphatidate (LPA) acyltransferase (EC 2.3. 1.51) in the microsomes from the maturing seeds of meadowfoam (Limnanthes alba), nasturtium (Tropaeolum majus), palm (Syagrus cocoides), castor bean (Ricinus communis), soybean (Glycine max), maize (Zea mays), and rapeseed (Brassica napus) were tested for their specificities toward 1-oleoyl-LPA or 1-erucoyl-LPA, and oleoyl coenzyme A (CoA) or erucoyl CoA. All the enzymes could use either of the two acyl acceptors and oleoyl CoA, but only the meadowfoam enzyme could use erucoyl CoA as the acyl donor to produce dierucoyl phosphatidic acid (PA). The meadowfoam enzyme was studied further. It had an optimal activity at pH 7 to 8, and its activity was inhibited by 1 millimolar MnCl(2), ZnCl(2), or p-chloromercuribenzoate. In a test of substrate specificity using increasing concentrations of either 1-oleoyl-LPA or 1-erucoyl-LPA, and either oleoyl CoA or erucoyl CoA, the enzyme activity in producing PA was highest for dioleoyl-PA, followed successively by 1-oleoyl-2-erucoyl-PA, dierucoyl-PA, and 1-erucoyl-2-oleoyl-PA. In a test of substrate selectivity using a fixed combined concentration, but varying proportions, of 1-oleoyl-LPA and 1-erucoyl-LPA, and of oleoyl CoA and erucoyl CoA, the enzyme showed a pattern of acyl preference similar to that observed in the test of substrate specificity, but the preference toward oleoyl moiety in the substrates was slightly stronger. The meadowfoam microsomes could convert [(14)C]glycerol-3-phosphate to diacylglycerols and triacylglycerols in the presence of erucoyl CoA. The meadowfoam LPA acyltransferase is unique in its ability to produce dierucoyl-PA, and should be a prime candidate for use in the production of trierucin oils in rapeseed via genetic engineering.
Axial filament involvement in the motility of Leptospira interrogans (1979)

Motility mutants of Leptospira interrogans serovar illini were isolated and analyzed by dark-field and electron microscopy. Mutants were obtained by screening for small colonies after nitrosoguanidine treatment. One class of mutants did not have hook- or spiral-shaped ends. In addition, the axial filaments from these mutants were not coiled. An analysis of revertants of two of the mutants in this class indicated that the mutations were pleiotropic with respect to motility, hook- and spiral-shaped ends, and axial filament coiling. We conclude that the axial filaments and the hook- and spiral-shaped ends are involved in L. interrogans motility.
Reporting physisorption data for gas/solid systems with special reference to the determination of surface area and porosity (Recommendations 1984) (1985)

Abstract
Cytokine-induced killer (CIK) cells: from basic research to clinical translation (2015)

The accumulation of basic researches and clinical studies related to cytokine-induced killer (CIK) cells has confirmed their safety and feasibility in treating malignant diseases. This review summarizes the available published literature related to the biological characteristics and clinical applications of CIK cells in recent years. A number of clinical trials with CIK cells have been implemented during the progressive phases of cancer, presenting potential widespread applications of CIK cells for the future. Furthermore, this review briefly compares clinical applications of CIK cells with those of other adoptive immunotherapeutic cells. However, at present, there are no uniform criteria or large-scale preparations of CIK cells. The overall clinical response is difficult to evaluate because of the use of autologous CIK cells. Based on these observations, several suggestions regarding uniform criteria and universal sources for CIK cell preparations and the use of CIK cells either combined with chemotherapy or alone as a primary strategy are briefly proposed in this review. Large-scale, controlled, grouped, and multi-center clinical trials on CIK cell-based immunotherapy should be conducted under strict supervision. These interventions might help to improve future clinical applications and increase the clinical curative effects of CIK cells for a broad range of malignancies in the future.
Dengue 4 Virus Monoclonal Antibodies Identify Epitopes that Mediate Immune Infection Enhancement of Dengue 2 Viruses (1987)

Nineteen monoclonal antibodies produced to dengue type 4 virus (DEN-4) strain 4328-S were tested for their ability to mediate antibody-dependent infection enhancement (ADE) with seven DEN-2 strains in P-388D1 mouse macrophage-like cells. In this first study of the distribution of enhancing epitopes on multiple DEN-2 strains reacted with monoclonal antibodies to a different serotype (DEN-4), DEN-4 monospecific antibodies produced ADE with DEN-2 viruses, indicating the presence of DEN-4-like determinants on DEN-2 viruses. Analysis differentiated at least one and possibly more DEN-2 strain subgroups, one of which (isolates AHF-110 and AHF-191) was previously identified by DEN-2 monoclonal antibody analysis. The study demonstrates the heterogeneous distribution of dengue complex and DEN-4 epitopes on DEN-2 strains. Monoclonal antibodies are valuable tools for study of the biology of ADE and its relation to dengue shock syndrome.
A Mid-Level Representation for Melody-Based Retrieval in Audio Collections (2008)

Searching audio collections using high-level musical descriptors is a difficult problem, due to the lack of reliable methods for extracting melody, harmony, rhythm, and other such descriptors from unstructured audio signals. In this paper, we present a novel approach to melody-based retrieval in audio collections. Our approach supports audio, as well as symbolic queries and ranks results according to melodic similarity to the query. We introduce a beat-synchronous melodic representation consisting of salient melodic lines, which are extracted from the analyzed audio signal. We propose the use of a 2D shift-invariant transform to extract shift-invariant melodic fragments from the melodic representation and demonstrate how such fragments can be indexed and stored in a song database. An efficient search algorithm based on locality-sensitive hashing is used to perform retrieval according to similarity of melodic fragments. On the cover song detection task, good results are achieved for audio, as well as for symbolic queries, while fast retrieval performance makes the proposed system suitable for retrieval in large databases.