gebhart/patrepeval huggingface dataset:
Fibroblast Growth Factor-2 Potentiates Vascular Smooth Muscle Cell Migration to Platelet-Derived Growth Factor (1997)

Fibroblast growth factor-2 (FGF-2) has been implicated in vascular smooth muscle cell (SMC) migration, a key process in vascular disease. We demonstrate here that FGF-2 promotes SMC motility by altering beta1 integrin-mediated interactions with the extracellular matrix (ECM). FGF-2 significantly increased surface expression of alpha2beta1, alpha3beta1, and alpha5beta1 integrins on human SMCs, as assessed by flow cytometry. The greatest increase was for the collagen-binding alpha2beta1 integrin. Despite this, FGF-2 did not increase SMC adhesion to type I collagen but instead promoted SMC elongation and SMC motility. The latter was evaluated by using a microchemotaxis chamber and by digital time-lapse video microscopy. Although FGF-2 was not chemotactic for human SMCs, cells preincubated with FGF-2 displayed a 3.1-fold increase in migration to the undersurface of porous type I collagen-coated membranes and a 2.1-fold increase in migration speed on collagen. Furthermore, chemotaxis to platelet-derived growth factor-BB on collagen was significantly greater in SMCs exposed to FGF-2. FGF-2-induced elongation and migration on collagen were inhibited by a blocking anti-alpha2beta1 antibody; however, SMC adhesion to collagen was unaffected. SMC migration on fibronectin was also enhanced by FGF-2, although less prominently: migration through porous membranes increased 1.8-fold, and migration speed increased 1.3-fold. Also, FGF-2 completely disassembled the smooth muscle alpha-actin-containing stress fiber network contemporaneously with the change in integrin expression and cell shape. We conclude that (1) exogenous FGF-2 promotes SMC migration and potentiates chemotaxis to PDGF-BB; (2) the promigratory effect of FGF-2 is especially prominent on type I collagen and is mediated by upregulation of alpha2beta1 integrin; and (3) FGF-2 disassembles actin stress fibers, which may promote differential utilization of alpha2beta1 integrin for motility but not adhesion. This dynamic SMC-ECM interplay may be an important mechanism by which FGF-2 facilitates SMC motility in vivo.
Zeolitisation of Diatoms (2005)

The development of low cost hierarchical porous materials based upon the zeolitisation of diatomaceous earth for fluid waste benification is described. Two preparative approaches invole: first, using the diatom as a support for zeolite nanocrystals; second, direct pseudomorphic transformation of the diatom into a zeolite. These hierarchical porous materials are potentially useful for important industrial processes in ion-exchange, catalysis and waste benefication.
Telomerase RNA function in recombinant Tetrahymena telomerase (1999)

Telomerase is a ribonucleoprotein reverse transcriptase specialized for use of a sequence within its integral RNA component as the template for DNA synthesis. Telomerase adds telomeric simple sequence repeats to single-stranded primers in vitro or chromosome ends in vivo. We have investigated the sequences and structures of recombinant Tetrahymena thermophila telomerase RNA necessary for physical association and activity with the catalytic protein subunit expressed in rabbit reticulocyte lysate. In contrast with previous results using another reconstitution method, we find that phylogenetically conserved primary sequences and a phylogenetically nonconserved secondary structure are essential for telomerase RNA function. Telomerase RNA binding to the catalytic protein subunit requires sequences 5' of the template and is highly sequence specific. Other telomerase RNA sequences are required for enzyme activity and proper template use but not for protein interaction affinity. In addition, we demonstrate that the production of active recombinant telomerase requires a factor in rabbit reticulocyte lysate that promotes ribonucleoprotein assembly. These studies demonstrate multiple functions for the telomerase RNA and indicate that recombinant telomerase activity requires more than the catalytic protein and RNA components of the enzyme that have been identified to date.
Fourier Transform Infrared Spectroscopic Studies of Clay and Shales (2010)

Fourier transform infrared spectroscopy (FTIR) technique is a powerful non-destructive technique that is used to study molecular interactions in a variety of materials. This technique is used to investigate the molecular interactions in geomaterials such as swelling clays and oil shales. This technique was used to study molecular interactions during swelling of expansive clay, interaction of swelling clay and fluids with various dielectric constants and mineral-kerogen interactions in oil shales. This research provides an insight into molecular interactions and their role on meso and macroscale properties of these geomaterials. This understanding is essential for geomaterials where molecular interactions play important role in influencing macroscale properties. An overview of our research on geomaterials using FTIR is presented in this paper.
Ophthalmic Drug Dosage Forms: Characterisation and Research Methods (2014)

This paper describes hitherto developed drug forms for topical ocular administration, that is, eye drops, ointments, in situ gels, inserts, multicompartment drug delivery systems, and ophthalmic drug forms with bioadhesive properties. Heretofore, many studies have demonstrated that new and more complex ophthalmic drug forms exhibit advantage over traditional ones and are able to increase the bioavailability of the active substance by, among others, reducing the susceptibility of drug forms to defense mechanisms of the human eye, extending contact time of drug with the cornea, increasing the penetration through the complex anatomical structure of the eye, and providing controlled release of drugs into the eye tissues, which allows reducing the drug application frequency. The rest of the paper describes recommended in vitro and in vivo studies to be performed for various ophthalmic drugs forms in order to assess whether the form is acceptable from the perspective of desired properties and patient's compliance.
Effect of 2,3-diphosphoglycerate on oxygen affinity of blood in sickle cell anemia (1970)

Blood of patients with sickle cell anemia (SS) exhibits decreased affinity for oxygen, although the oxygen affinity of hemoglobin S is the same as that of hemoglobin A. SS red cells contain more 2,3-diphosphoglycerate (DPG) than normal erythrocytes. The oxygen affinity of hemolyzed red cells is decreased by added DPG, and hemolysates prepared from SS red cells do not differ from normal hemolysates in this regard. Reduction of oxygen affinity to the levels found in intact SS red cells required DPG concentrations in excess of those found in most SS patients. The same was true of oxygen affinity of patients with pyruvate kinase deficiency. Other organic phosphates, as well as inorganic ions, are known to alter the oxygen affinity of dilute solutions of hemoglobin. These substances, the state of aggregation of hemoglobin molecules, and cytoarchitectural factors probably play roles in determining oxygen affinity of both normal and SS red cells.
Site-Specific Integration ofAgrobacterium tumefaciensT-DNA via Double-Stranded Intermediates (2003)

Agrobacterium tumefaciens-mediated genetic transformation involves transfer of a single-stranded T-DNA molecule (T strand) into the host cell, followed by its integration into the plant genome. The molecular mechanism of T-DNA integration, the culmination point of the entire transformation process, remains largely obscure. Here, we studied the roles of double-stranded breaks (DSBs) and double-stranded T-DNA intermediates in the integration process. We produced transgenic tobacco (Nicotiana tabacum) plants carrying an I-SceI endonuclease recognition site that, upon cleavage with I-SceI, generates DSB. Then, we retransformed these plants with two A. tumefaciens strains: one that allows transient expression of I-SceI to induce DSB and the other that carries a T-DNA with the I-SceI site and an integration selection marker. Integration of this latter T-DNA as full-length and I-SceI-digested molecules into the DSB site was analyzed in the resulting plants. Of 620 transgenic plants, 16 plants integrated T-DNA into DSB at their I-SceI sites; because DSB induces DNA repair, these results suggest that the invading T-DNA molecules target to the DNA repair sites for integration. Furthermore, of these 16 plants, seven plants incorporated T-DNA digested with I-SceI, which cleaves only double-stranded DNA. Thus, T-strand molecules can be converted into double-stranded intermediates before their integration into the DSB sites within the host cell genome.
RNA sequence analysis defines Dicer's role in mouse embryonic stem cells (2007)

Short RNA expression was analyzed from Dicer-positive and Dicer-knockout mouse embryonic [corrected] stem (ES) cells, using high-throughput pyrosequencing. A correlation of miRNA quantification with sequencing frequency estimates that there are 110,000 miRNAs per ES cell, the majority of which can be accounted for by six distinct miRNA loci. Four of these miRNA loci or their human homologues have demonstrated roles in cell cycle regulation or oncogenesis, suggesting that a major function of the miRNA pathway in ES cells may be to shape their distinct cell cycle. Forty-six previously uncharacterized miRNAs were identified, most of which are expressed at low levels and are less conserved than the set of known miRNAs. Low-abundance short RNAs matching all classes of repetitive elements were present in cells lacking Dicer, although the production of some SINE- and simple repeat-associated short RNAs appeared to be Dicer-dependent. These and other Dicer-dependent sequences resembled miRNAs. At a depth of sequencing that approaches the total number of 5' phosphorylated short RNAs per cell, miRNAs appeared to be Dicer's only substrate. The results presented suggest a model in which repeat-associated miRNAs serve as host defenses against repetitive elements, a function canonically ascribed to other classes of short RNA.
Podoplanin (d2-40): a new immunohistochemical marker for reactive follicular dendritic cells and follicular dendritic cell sarcomas. (2008)

The diagnosis of follicular dendritic cell (FDC) sarcoma can be challenging because of its morphologic overlaps with many other spindle cell neoplasms and, therefore, new phenotypic markers will be helpful in its differential diagnosis. Podoplanin is a mucin-type transmembrane glycoprotein that has recently been detected in reactive FDCs. In this study, we investigated the expression patterns of podoplanin using a new mouse monoclonal antibody D2-40, and compared them with CD21, a well-established FDC marker, in a comprehensive panel of cases. The panel included 4 FDC sarcomas, 38 spindle cell neoplasms of other types, 25 reactive lymphoid hyperplasia, and 117 lymphoid and 5 myeloid malignant hematopoietic neoplasms. Our study revealed that D2-40 strongly stained 3 of 4 FDC sarcomas. In contrast, D2-40 stained only 2/38 other spindle cell neoplasms tested. Furthermore, we observed that D2-40 highlighted more FDC meshworks than CD21 in Castleman's disease, follicular lymphoma, nodular lymphocyte predominance Hodgkin lymphoma, and residual reactive germinal centers in a variety of lymphoma types. D2-40 and CD21 stained an equal number of cases of reactive lymphoid hyperplasia, progressively transformed germinal centers and angioimmunoblastic T-cell lymphoma. No expression of podoplanin was detected in normal or neoplastic lymphoid and myeloid cells. We conclude that podoplanin (D2-40) is a sensitive and specific FDC marker, which is superior or equal to CD21 in evaluating both reactive and neoplastic FDCs. In addition, our results suggest that podoplanin (D2-40) can be used to support the diagnosis of FDC sarcoma.
of EIN3 Transcription Factor (2003)

Summary 1990; Kieber et al., 1993). Genetic and molecular characterization of these mu- Plants use ethylene gas as a signal to regulate myriad tantshasunraveledalargelylinearethylenesignaltrans-developmental processes and stress responses. The duction pathway (Stepanova and Ecker, 2000). Briefly, Arabidopsis EIN3 protein is a key transcription factor ethylene is perceived by a family of ER-associated re- mediating ethylene-regulated gene expression and ceptors with sequence similarity to two-component his- morphological responses. Here, we report that EIN3 tidine kinases (Chang et al., 1993; Chen et al., 2002). protein levels rapidly increase in response to ethylene The ethylene receptors play a negative role, whereby and this response requires several ethylene-signaling ethylene binding acts to repress their activity (Hua and pathwaycomponentsincludingtheethylenereceptors Meyerowitz, 1998). Accordingly, gain-of-function muta- (ETR1 and EIN4), CTR1, EIN2, EIN5, and EIN6. In the tions in the receptors, which disrupt ethylene binding,
Ligand bridging mediates integrin alpha IIb beta 3 (platelet GPIIB-IIIA) dependent homotypic and heterotypic cell-cell interactions. (1991)

The aggregation of cells bearing recombinant integrin alpha IIb beta 3 (platelet GPIIb-IIIa) has been analyzed by two-color flow cytometry. As in normal platelets, aggregation requires functional alpha IIb beta 3, "activation" of alpha IIb beta 3, and fibrinogen (fg) binding to alpha IIb beta 3. Cellular aggregation required that both interacting cells express functional alpha IIb beta 3, because a binding defective mutant, alpha IIb beta 3 (D119----Y), failed to support interaction with wild type alpha IIb beta 3-bearing cells. In addition, cells bearing resting alpha IIb beta 3 were incorporated into aggregates formed by cells bearing a constitutively active mutant, alpha IIb beta 3 (beta 1-2), indicating that only one of the cells in an interacting pair must be activated. Finally, heterotypic interactions occurred between cells bearing activated alpha IIb beta 3 and cells bearing alpha V beta 3, a fg-binding integrin present on endothelial and tumor cells. Thus, ligand bridging between fg-binding integrins represents a mechanism of cell-cell interaction, cells bearing resting alpha IIb beta 3 (e.g., resting platelets) may be incorporated into aggregates formed by cells bearing activated alpha IIb beta 3, and alpha IIb beta 3 mediates heterotypic interactions with cells bearing other fg receptors.
Measurement of Placental Alpha-Microglobulin-1 in Cervicovaginal Discharge to Diagnose Rupture of Membranes (2007)

II.
Caspase-2 Mediates Neuronal Cell Death Induced by β-Amyloid (2000)

beta-amyloid (Abeta) has been proposed to play a role in the pathogenesis of Alzheimer's disease (AD). Deposits of insoluble Abeta are found in the brains of patients with AD and are one of the pathological hallmarks of the disease. It has been proposed that Abeta induces death by oxidative stress, possibly through the generation of peroxynitrite from superoxide and nitric oxide. In our current study, treatment with nitric oxide generators protected against Abeta-induced death, whereas inhibition of nitric oxide synthase afforded no protection, suggesting that formation of peroxynitrite is not critical for Abeta-mediated death. Previous studies have shown that aggregated Abeta can induce caspase-dependent apoptosis in cultured neurons. In all of the neuronal populations studied here (hippocampal neurons, sympathetic neurons, and PC12 cells), cell death was blocked by the broad spectrum caspase inhibitor N-benzyloxycarbonyl-val-ala-asp-fluoromethyl ketone and more specifically by the downregulation of caspase-2 with antisense oligonucleotides. In contrast, downregulation of caspase-1 or caspase-3 did not block Abeta(1-42)-induced death. Neurons from caspase-2 null mice were totally resistant to Abeta(1-42) toxicity, confirming the importance of this caspase in Abeta-induced death. The results indicate that caspase-2 is necessary for Abeta(1-42)-induced apoptosis in vitro.
Following the Inner Light (1996)

A few years ago, Christopher H. Contag attended a meeting at which investigators presented data obtained with the latest techniques for detecting viruses. As he listened to each speaker, the Stanford University virologist realized how frustrated he had become with the tools available to his profession. Consider the way researchers usually establish the normal course of a bacterial or viral infection, remarks Contag. They infect dozens, if not hundreds, of animals, usually mice. As the infection proceeds, the investigators kill groups of the mice and, using a variety of means, painstakingly examine the animals' tissues to determine how far the microorganisms have spread. Such experiments are costly and laborious; they also raise the ire of animal rights activists. Contag felt there had to be a better way. If we can track the trajectory of a bullet in space, we must be able to track a pathogen in a living animal, he says. Contag began to take a look at bioluminescence, the natural emission of light by organisms such as fireflies and certain bacteria. These creatures all owe their glow to an enzyme called luciferase. For more than a decade, scientists have made use of luciferase or the genes that encode it. For example, with the aid of this light-producing enzyme, they've discovered and studied the genes that establish circadian rhythms (SN: 8/12/95, p. 108). Pamela Contag, also at Stanford, has popped luciferase genes into salmonella bacteria to better study how the microbes interact with animal cells. After reading an article about detecting light that passes through tissue, Christopher Contag wondered if bioluminescent microorganisms inside living animals might be observable from the outside. Fortunately, David Benaron, a medical imaging researcher at Stanford, was nearby. virologist strolled over to Benaron's office and outlined his proposition. thought it was an unusual mixture of ideas. But I have to tell you my first reaction was, that's impossible, says Benaron. Benaron's main concern was that the greenish yellow glow emitted by the standard luciferase-induced chemical reaction would be mostly absorbed and scattered by the animal tissues. That reservation didn't stop him from agreeing to give the idea a try, however. Benaron and the two Contags decided to test first whether bioluminescent microbes could shine through dead tissue. The easiest source of tissue was the grocery store, so we picked up chicken breast, beef liver, and lamb kidney, laughs Christopher Contag. In their initial experiment, the investigators placed a vial of Pamela Contag's glowing salmonella inside a thawed chicken breast. bacterial light had to penetrate about half a centimeter of meat to reach a highly sensitive photon detector. Sure enough, light came out, says Benaron. That glimmer has since led to what hntirrininaict (.nrr1nn qtiwnrt of the I Tniversity of Nottingham in England calls some of the most important work in microbiology in a decade.
Functional Interactions in the Brain: Use of Correlations between Regional Metabolic Rates (1991)

Correlation coefficients between pairs of regional metabolic rates have been used to study patterns of functional associations among brain regions in humans and animals. An overview is provided concerning the additional information about brain functioning this type of analysis yields. A computer simulation model is presented for the purpose of giving a partial validation for correlational analysis. The model generates a set of simulated metabolic data upon which correlational analysis is performed. Because the underlying pattern of functional couplings in the model is known, these simulations demonstrate that the correlation coefficient between normalized metabolic rates is proportional to the strength of the functional coupling constant and that correlational analysis yields information on regional involvement in neural systems not evident in the pattern of absolute metabolic values.
Wearable cuff-less PTT-based system for overnight blood pressure monitoring (2013)

A wearable cuff-less pulse transit time (PTT) based monitoring device is developed for ambulatory blood pressure (BP) monitoring. Ten healthy subjects (aged 27 ± 4 years old) underwent 24-hour ambulatory BP monitoring using 1) a standard brachial cuff-based oscillometric device as reference and 2) the proposed cuff-less PTT measuring system. Raw PTT and BP measurements were linearly interpolated and then smoothed by a low-pass filter to remove aliasing effect caused by the low sampling rate and synchronized. Resampled PTT and BP were assessed for correlation using correlation coefficients and Bland-Altman plots. Our study showed that PTT estimated systolic BP most accurately within 4.8 ± 4.3 mmHg on healthy young subjects during sleep time. We conclude from this study that the proposed cuff-less PTT-based BP monitoring system has potential to be a less intrusive alternative to standard oscillometric method for long-term overnight BP monitoring.
Enhancement of the antiproliferative action of 1- -D-arabinofuranosylcytosine by methotrexate in murine leukemic cells (L5178Y). (1973)

Summary Enhancement of the rate of acute cell death was demonstrated in murine leukemic cells (L5178Y) sequentially treated with methotrexate (MTX) and 1-β-d-arabinofuranosylcytosine (ara-C). Cells in exponential phase of growth were incubated with ara-C- 3 H alone and after limited and continuous exposure to MTX, in the presence of hypoxanthine and serine. A time course study was undertaken to determine the duration of the synergistic effect of MTX and ara-C on cell death. L5178Y cells, after 2 hr of exposure to MTX, were washed and resuspended in MTX-free medium; then ara-C was added to different incubations at different time intervals. MTX exerted its enhancing effect for only 60 min in the MTX-free medium. The effect of MTX does not appear to be accumulation of cells in the ara-C-sensitive S phase. Column chromatography with epichlorohydrin triethanolamine cellulose was used to determine the cold acid-soluble phosphorylated derivatives of ara-C. Increase in cytosine arabinoside triphosphate above control level was noted in cells pretreated with MTX. The increased phosphorylation of ara-C and cytosine arabinoside triphosphate and its incorporation into an RNA fraction may be responsible for enhanced cell death.
Action-Affect-Gender Classification Using Multi-task Representation Learning (2017)

Recent work in affective computing focused on affect from facial expressions, and not as much on body. This work focuses on body affect. Affect does not occur in isolation. Humans usually couple affect with an action; for example, a person could be running and happy. Recognizing body affect in sequences requires efficient algorithms to capture both the micro movements that differentiate between happy and sad and the macro variations between different actions. We depart from traditional approaches for time-series data analytics by proposing a multi-task learning model that learns a shared representation that is well-suited for action-affect-gender classification. For this paper we choose a probabilistic model, specifically Conditional Restricted Boltzmann Machines, to be our building block. We propose a new model that enhances the CRBM model with a factored multi-task component that enables scaling over larger number of classes without increasing the number of parameters. We evaluate our approach on two publicly available datasets, the Body Affect dataset and the Tower Game dataset, and show superior classification performance improvement over the state-of-the-art.