gebhart/patrepeval huggingface dataset:
Quantitative Analysis of Apoptotic Cell Death Using Proton Nuclear Magnetic Resonance Spectroscopy (1997)

Quantification of apoptotic cell death in vivo has become an important area of investigation in patients with acute lymphoblastic leukemia (ALL). We have devised a noninvasive analytical method to estimate the percentage of apoptotic lymphoblasts in doxorubicin-treated Jurkat T-cell ALL cultures, using proton nuclear magnetic resonance spectroscopy (1H NMR). We have found that the ratio of the methylene (CH2) resonance (at 1.3 ppm) to the methyl (CH3) resonance (at 0.9 ppm) signal intensity, as observed by 1H NMR, is directly proportional to the percentage of apoptotic lymphoblasts in vitro. The correlation between the CH2/CH3 signal intensity ratio and the percentage of apoptotic lymphoblasts was optimal 24 to 28 hours after doxorubicin treatment (r2 = .947, N = 27 samples). There was also a direct temporal relationship between an increase in the CH2/CH3 signal intensity ratio and the onset of apoptosis as detected by nuclear morphologic analysis, fluorescein-annexin V flow cytometry, and DNA gel electrophoresis. Thin-layer chromatography confirmed that a dynamic and/or compositional change of the plasma membrane, rather than increases in lipase activity or fatty acid production, appears to account for the increase in the CH2/CH3 signal intensity ratio during apoptosis. 1H NMR may have clinical utility for the early noninvasive assessment of chemotherapeutic efficacy in patients with ALL.
Pharmacokinetics and Absorption of the Anticancer Agents Dasatinib and GDC-0941 under Various Gastric Conditions in Dogs – Reversing the Effect of Elevated Gastric pH with Betaine HCl (2013)

Changes in gastric pH can impact the dissolution and absorption of compounds presenting pH-dependent solubility. We assessed, in dogs, the effects of gastric pH-modifying agents on the oral absorption of two weakly basic anticancer drugs, dasatinib and GDC-0941. We also tested whether drug-induced hypochlorhydria could be temporarily mitigated using betaine HCl. Pretreatments with pentagastrin, famotidine, betaine HCl, or combinations of famotidine and betaine HCl were administered orally to dogs prior to drug dosing. The gastric pH was measured under each condition for up to 7 h, and the exposure of the compounds tested was calculated. The average gastric pH in fasted dogs ranged from 1.45 to 3.03. Pentagastrin or betaine HCl treatments lowered the pH and reduced its variability between dogs compared to control animals. In contrast, famotidine treatment maintained gastric pH at values close to 7 for up to 5 h, while betaine HCl transiently reduced the pH to approximately 2 in the famotidine-treated dogs. Famotidine pretreatment lowered GDC-0941 exposure by 5-fold, and decreased dasatinib measurable concentrations 30-fold, compared to the pentagastrin-treated dogs. Betaine HCl restored GDC-0941 AUC in famotidine-treated dogs to levels achieved in control animals, and increased dasatinib AUC to 1.5-fold that measured in control dogs. The results confirmed the negative impact of acid-reducing agents on the absorption of weakly basic drugs. They also suggested that betaine HCl coadministration may be a viable strategy in humans treated with acid-reducing agents in order to temporarily reduce gastric pH and restore drug exposure.
A potent opiate agonist protects against myocardial stunning during myocardial ischemia and reperfusion in rats (2005)

2',6'-Dimethyltyrosine-D-Arg-Phe-Lys-NH2 provides a cardioprotective effect against myocardial ischemia and reperfusion in vivo.
THE CLINICAL APPLICATION OF CRRT—CURRENT STATUS: Continuous Renal Replacement Therapy in Sepsis and Multisystem Organ Failure (2009)

This study reviews the role of continuous renal replacement therapy (CRRT) in sepsis with acute kidney injury (AKI) and septic shock with multiple organ failure. In addition to the conventional aim of replacing renal function in AKI, CRRT is often used with the concept of modulating immune response in sepsis. With the intention of influencing circulating levels of inflammatory mediators like cytokines and chemokines, the complement system, as well as factors of the coagulation system, several modifications of CRRT have been developed over the last years. These include high volume hemofiltration, high adsorption hemofiltration, use of high cut-off membranes, and hybrid systems like coupled plasma filtration absorbance. One of the most promising concepts may be the development of renal assist devices using renal tubular cells for implementing renal tubular function into CRRT.
Fibroblast Growth Factor 1 Regulates Signaling via the Glycogen Synthase Kinase-3β Pathway (2002)

We hypothesize that in neurodegenerative disorders such as Alzheimer's disease and human immunodeficiency virus encephalitis the neuroprotective activity of fibroblast growth factor 1 (FGF1) against several neurotoxic agents might involve regulation of glycogen synthase kinase-3beta (GSK3beta), a pathway important in determining cell fate. In primary rat neuronal and HT22 cells, FGF1 promoted a time-dependent inactivation of GSK3beta by phosphorylation at serine 9. Blocking FGF1 receptors with heparinase reduced this effect. The effects of FGF1 on GSK3beta were dependent on phosphatidylinositol 3-kinase (PI3K)-protein kinase B (Akt) because inhibitors of this pathway or infection with dominant negative Akt adenovirus blocked inactivation. Furthermore, treatment of neuronal cells with FGF1 resulted in ERK-independent Akt phosphorylation and beta-catenin translocation into the nucleus. On the other hand, infection with wild-type GSK3beta recombinant adenovirus-associated virus increased activity of GSK3beta and cell death, both of which were reduced by FGF1 treatment. Moreover, FGF1 protection against glutamate toxicity was dependent on GSK3beta inactivation by the PI3K-Akt but was independent of ERK. Taken together these results suggest that neuroprotective effects of FGF1 might involve inactivation of GSK3beta by a pathway involving activation of the PI3K-Akt cascades.
Noninvasive Prenatal Diagnosis: Past, Present, and Future (2009)

The presence of fetal cells in the maternal circulation was first noted by Georg Schmorl when he documented the presence of multinucleated syncytial giant cells of placental origin in the lung tissue of women who had died from complications of eclampsia. In the intervening century, advances in cellular and molecular biology further elucidated both the physiology and pathophysiology of communication within the fetomaternal unit. This concept is at the foundation of the rapidly expanding field of noninvasive prenatal diagnosis. However, the clinical utility of this phenomenon had been limited until the presence of cell-free fetal DNA circulating in the maternal plasma was reported in 1997 and fetal messenger RNA was demonstrated to circulate in the maternal plasma in 2000. These circulating nucleic acids are found free-floating in the maternal plasma, unencumbered by a surrounding fetal cell. The analysis of these 3 fetal markers (fetal cells, cell-free fetal DNA, and fetal messenger RNA) for diagnostic and screening purposes is now being developed. The scope of noninvasive prenatal diagnosis is not limited to only the diagnosis of fetal genetic traits and aneuploidies. Recently, researchers have focused their investigations on the role of cell-free fetal DNA and fetal messenger RNA in preeclampsia, intrauterine growth restriction, and preterm labor. These biomarkers, the result of inherent placental dysfunction or the byproducts of placental trophoblastic apoptosis, may allow for improvements in the diagnosis and management of high-risk pregnancies.
Dynamic topic models (2006)

A family of probabilistic time series models is developed to analyze the time evolution of topics in large document collections. The approach is to use state space models on the natural parameters of the multinomial distributions that represent the topics. Variational approximations based on Kalman filters and nonparametric wavelet regression are developed to carry out approximate posterior inference over the latent topics. In addition to giving quantitative, predictive models of a sequential corpus, dynamic topic models provide a qualitative window into the contents of a large document collection. The models are demonstrated by analyzing the OCR'ed archives of the journal Science from 1880 through 2000.
Growth of Carbon Nanotubes by Pyrolysis of Thiophene (2007)

The synthesis of carbon nanotubes (CNTs) by cobalt-catalyzed pyrolysis of thiophene has been investigated and optimized. The yield and the morphology of the synthesized product are highly sensitive to the experimental conditions. A synthesis temperature of 1000 °C is required for the decomposition of thiophene. The morphology and microstructure of the product are controlled by the thiophene vapor concentration and flow rate. High concentration of thiophene vapor deactivates the catalyst and results in the formation of carbon nanofibers or short CNTs with bad graphitization; the optimum thiophene concentration for CNTs growth is around 0.76−1%. Thiophene vapor at high flow rate produces Y-junction and multibranched CNTs. Three formation routes are proposed to illuminate the growth mechanism of the branched CNTs.
A Binding Site for Thrombin in the Apple 1 Domain of Factor XI (1996)

Previously we defined a binding site for high molecular weight kininogen (HK) in the A1 domain of factor XI (FXI). Since thrombin can activate FXI and HK inhibits the activation of FXI by thrombin, we have identified a thrombin binding site in FXI. Both the recombinant A1 domain (Glu1-Ser90) and a synthetic peptide (Phe56-Ser86) containing the HK binding site inhibited FXI activation by thrombin. Both a monoclonal antibody, 5F7, recognizing the A1 domain, and the rA1 domain were shown to be competitive inhibitors of thrombin-catalyzed FXI activation. The peptides Ala45-Arg54 and Val59-Arg70 acted synergistically to inhibit FXI activation by thrombin. Mutant rA1 domain constructs (Val64 --> Ala and Ile77 --> Ala), which do not inhibit FXI binding to HK, retain full capacity to inhibit FXI activation by thrombin. The peptide Ala45-Arg54 inhibited thrombin-catalyzed FXI activation, whereas it had no effect on FXI binding to HK. In contrast, the peptide Asn72-Leu83 (which inhibited FXI binding to HK) did not inhibit FXI activation by thrombin. Thus, a thrombin binding site exists in the A1 domain of FXI spanning residues Ala45-Arg70 that is contiguous with but separate and distinct from the HK binding site. These sites may regulate which ligand is bound to FXI and through which pathway FXI is activated.
Sn/Pd Catalyzation and Electroless Cu Deposition on TaN Diffusion Barrier Layers (2002)

The catalyzation of substrates was carried out by immersion in and solutions for electroless Cu deposition. The sizes and morphologies of the catalytic sites on the TaN layers were found to be a function of catalyzation conditions, including solution temperature, immersion time, and the surface oxides. The appropriate formula for catalyzation was obtained by considering both the quality and efficiency. The catalytic sites were composed of Sn and Pd, and the ratio of Sn/Pd was about 1.3. During electroless Cu deposition on the catalyzed substrates, Cu nuclei first formed at the catalytic sites in the early stage, gradually agglomerated into dense islands, and finally merged to continuous deposition films. The Cu films were uniformly and smoothly deposited with a surface roughness of 6.2 nm under a film thickness of 210 nm. The lowest electrical resistivity of the Cu films was 2.5 μΩ cm, and the residual resistivity contributed to the participation of Sn-Pd catalyst and internal defects. Good gap-filling capability of electroless Cu deposition on Sn/Pd catalyzed, patterned substrates exhibited its high potential to act as a seed layer for Cu electrodeposition and even to completely fill submicrometer gaps in ultralarge-scale integrated metallization. © 2002 The Electrochemical Society. All rights reserved.
Screening Tool for Hollow‐Fiber Bioreactor Process Development (1998)

Fundamental research of factors affecting cell growth in hollow-fiber bioreactors is hindered by the lack of an efficient screening tool. To address this issue, a hollow-fiber micro-bioreactor has been developed. Hollow fibers with 10 kDa molecular weight cutoffs are housed within a piece of silicone tubing. Cells are inoculated within the hollow fibers which provides a 0.2-mL culture volume. The space between the fibers and silicone tubing (5 or 16 mL) is used as a medium reservoir sufficient to feed the cells for at least 24 h. Oxygenation is provided directly through the silicone tubing so that a pump for medium recirculation is not required. As a result, many conditions can be tested simultaneously in a single incubator. Three days after inoculation at 5 x 10(6) cells/mL in the micro-bioreactor, the rho 1D4 murine hybridoma cell line reached 2.8 x 10(7) cells/mL with an antibody concentration of 0.17 mg/mL. When inoculated at 5 x 10(7) cells/mL, the cell concentration reached 1.8 x 10(8)/mL after 3 days with an antibody concentration of 1.0 mg/mL. Results from a series of experiments with the micro-bioreactor suggested that the initial growth phase of this cell line in a hollow-fiber system is dependent on the serum concentration in the medium reservoir. This prediction was tested by simultaneously inoculating two production-scale hollow-fiber bioreactor systems. The cell side of the membrane for each bioreactor contained 10% serum, but serum was added to the reservoir side of only one of the bioreactors. The cells with only basal medium in the reservoir died after a few days, while the cells with 10% serum in the medium reservoir grew rapidly. These results demonstrate that the micro-bioreactor developed here can support good cell growth and that it can be used as a research tool to predict the performance of large-scale hollow-fiber systems.
Controlling electromagnetic fields at boundaries of arbitrary geometries (2016)

Rapid developments in the emerging field of stretchable and conformable photonics necessitate analytical expressions for boundary conditions at metasurfaces of arbitrary geometries. Here, we introduce the concept of conformal boundary optics: a design theory that determines the optical response for designer input and output fields at such interfaces. Given any object, we can realize coatings to achieve exotic effects like optical illusions and anomalous diffraction behavior. This approach is relevant to a broad range of applications from conventional refractive optics to the design of the next-generation of wearable optical components. This concept can be generalized to other fields of research where designer interfaces with nontrivial geometries are encountered.
Flueggenines A and B, Two Novel C,C-Linked Dimeric Indolizidine Alkaloids from <i>Flueggea </i><i>v</i><i>irosa</i> (2006)

[structure: see text] Two unprecedented C,C-linked dimeric indolizidine alkaloids, flueggenines A (1) and B (2), as well as their biosynthetic precursor (-)-norsecurinine, were isolated from the roots of Flueggea virosa. Their structures and absolute configurations were elucidated by spectroscopic methods, especially 2D NMR and CD spectral analyses, and supported by their unique biosynthetic pathway as proposed. Both 1 and 2 were tested against two tumor cell lines, and alkaloid 1 showed weak activity against the P-388 cell line.
Strategies for mucosal vaccine development. (1999)

Vaccines able to induce both secretory IgA for protection of mucosal surfaces and systemic immunity to pathogens invading the host are of great interest in the war against infectious diseases. Mucosal vaccines trigger immune cells in mucosal inductive sites and thus can induce immunity in both the mucosal and systemic compartments. This review presents a critical survey of adjuvants and delivery systems currently being tested for mucosal immunization. A better understanding of cellular and molecular factors involved in the regulation of mucosal immunity will help in the design of safer mucosal vaccines to elicit the appropriate protective immune response to a given pathogen.
Role of serotonergic neurons in L-DOPA-derived extracellular dopamine in the striatum of 6-OHDA-lesioned rats (1999)

The effect of L-dihydroxyphenylalanine (L-DOPA) on extracellular dopamine (DA) in the striatum was determined by microdialysis in 6-hydroxydopamine (6-OHDA)-lesioned rats treated with and without the serotonergic neurotoxin 5,7-dihydroxytryptamine (5,7-DHT). At the same time the intensity of L-DOPA-induced rotational behavior was assessed. In 6-OHDA-lesioned rats treated with 5,7-DHT, L-DOPA (50 mg/kg, i.p.) increased extracellular DA only to 20% of that measured in animals not treated with 5,7-DHT. Likewise, 6-OHDA-lesioned rats treated with 5,7-DHT exhibited a significantly lower number of L-DOPA-induced rotations. These results suggest that serotonergic terminals in the striatum can convert exogenously administered L-DOPA into DA that can be released into the extracellular space.
Contractile Function and Response to Agonists in Myocytes from Failing Human Heart (1994)

Ventricular myocytes from failing human hearts have a similar maximum contraction amplitude in high Ca2+ to those from non-failing heart at low stimulation rates (0.2 Hz, 32 degrees C), but do not exhibit the same positive frequency-interval relationship. At higher stimulation rates (1 Hz) therefore, the amplitude is depressed in cells from failing hearts compared to controls. Slow relaxation is seen in myocytes from failing ventricle at all stimulation rates, and contraction velocity is also slightly reduced. beta-adrenoceptor desensitization is evident, and increases with severity of disease. There is also a post-receptor defect in myocytes from failing heart since responses to forskolin and cyclic AMP analogues are reduced, and this is accompanied by decreased cyclic AMP levels in myocardium from patients in end-stage disease. Pertussis toxin treatment, which inactivates Gi, reverses most of the alterations in the beta-adrenoceptor pathway. The role of the sympathetic system is indicated by the parallels between myocytes from failing human heart and those from the noradrenaline-treated guinea-pig, which show beta-adrenoceptor desensitization, a post-receptor defect and reduced basal cyclic AMP levels. However, relaxation velocities are not slowed in these guinea-pig myocytes, indicating that basal cyclic AMP does not have a tonic role in speeding relaxation.
Inverse silica opal photonic crystals for optical sensing applications (2007)

This work reports fabrication of inverse silica opal photonic crystal structures from direct polystyrene micro sphere opals using low-temperature sol-gel infiltration of silica, and examines performance of these photonic crystals as environmental refractive index sensors. Sensitivity of the spectral position and optical attenuation of photonic stop gaps is found to allow detection of the index changes by the amount of ~10(-3). The high value of sensitivity, which is comparable with those of other optical sensing techniques, along with simplicity of the optical detection setup required for sensing, and the low-temperature, energy-efficient fabrication process make inverse silica opals attractive systems for optical sensing applications.
GLIS1-3: emerging roles in reprogramming, stem and progenitor cell differentiation and maintenance (2017)

Recent studies have provided evidence for a regulatory role of GLI-similar (GLIS) transcription factors in reprogramming, maintenance and differentiation of several stem and progenitor cell populations. GLIS1, in conjunction with several other reprogramming factors, was shown to markedly increase the efficiency of generating induced pluripotent stem cells (iPSC) from somatic cells. GLIS2 has been reported to contribute to the maintenance of the pluripotent state in hPSCs. In addition, GLIS2 has a function in regulating self-renewal of hematopoietic progenitors and megakaryocytic differentiation. GLIS3 plays a critical role during the development of several tissues. GLIS3 is able to promote reprogramming of human fibroblasts into retinal pigmented epithelial (RPE) cells. Moreover, GLIS3 is essential for spermatogonial stem cell renewal and spermatogonial progenitor cell differentiation. During pancreas development, GLIS3 protein is first detectable in bipotent pancreatic progenitors and pro-endocrine progenitors and plays a critical role in the generation of pancreatic beta cells. Here, we review the current status of the roles of GLIS proteins in the maintenance and differentiation of these different stem and progenitor cells.
Use of the Integration Elements Encoded by the Temperate Lactococcal Bacteriophage TP901-1 To Obtain Chromosomal Single-Copy Transcriptional Fusions in <i>Lactococcus lactis</i> (1999)

Previously we showed that only one phage-expressed protein (Orf1), a 425-bp region upstream of the orf1 gene (presumably encoding a promoter), and the attP region are necessary and also sufficient for integration of the bacteriophage TP901-1 genome into the chromosome of Lactococcus lactis subsp. cremoris (B. Christiansen, L. Brondsted, F. K. Vogensen, and K. Hammer, J. Bacteriol. 178:5164-5173, 1996). In this work, a further analysis of the phage-encoded elements involved in integration was performed. Here we demonstrate that even when the orf1 gene is separated from the attP region, the Orf1 protein is able to promote site-specific integration of an attP-carrying plasmid into the attB site on the L. lactis subsp. cremoris chromosome. Furthermore, the first detailed deletion analysis of an attP region of a phage infecting lactic acid bacteria was carried out. We show that a fragment containing 56 bp of the attP region, including the core, is sufficient for the site-specific integration of a nonreplicating plasmid into the chromosome of L. lactis subsp. cremoris when the orf1 gene is donated in trans. The functional 56-bp attP region of TP901-1 is substantially smaller than minimal attP regions identified for other phages. Based on the deletion analysis, several repeats located within the attP region seem to be necessary for site-specific integration of the temperate bacteriophage TP901-1. By use of the integrative elements (attP and orf1) expressed by the temperate lactococcal bacteriophage TP901-1, a system for obtaining stable chromosomal single-copy transcriptional fusions in L. lactis was constructed. Two promoter-reporter integration vectors containing the reporter gene gusA or lacLM, encoding beta-glucuronidase or beta-galactosidase, respectively, were constructed. Immediately upstream of both genes are found translational stop codons in all three reading frames as well as multiple restriction enzyme sites suitable for cloning of the promoter of interest. By transformation of L. lactis subsp. cremoris MG1363 containing the integrase gene on a replicating plasmid, the promoter-reporter integration vectors integrated with a high frequency site specifically into the chromosomal attachment site attB used by bacteriophage TP901-1.
Experimental therapy of epilepsy with transcranial magnetic stimulation: lack of additional benefit with prolonged treatment (2004)

Although prolonged rTMS treatment is safe and moderately decreases MDNS in a group of patients with intractable epilepsy, individual patient responses were mostly subtle and clinical relevance of this method is probably low. Our data suggest, however, that patients with focal cortical lesions may indeed benefit from this novel treatment. Further studies should concentrate on that patient subgroup.