gebhart/patrepeval huggingface dataset:
Synthesis and Biological Evaluation of New 5,6-dichlorobenzimidazole Nucleoside Derivatives (1994)

Novel 5,6-dichlorobenzimidazole nucleoside analogues structurally related to the well-known riboside DRB have been synthesized. The 1′,2′- trans nucleosides were prepared by condensation of peracylated sugars with 5,6-dichlorobenzimidazole, whereas the 1′,2′- cis β-D-arabinofuranosyl and β-D-lyxofuranosyl nucleosides were obtained by inversion of configuration on the sugar moiety. Chiral acyclic derivatives were stereospecifically prepared by ring-opening of furano- or pyrano-nucleosides by means of periodate oxidation, followed by borohydride reduction. The in vitro activities against a range of DNA and RNA viruses, as well as the cytotoxicities in human T-lymphocyte MT-4 cells, have been determined for these novel compounds and for DRB. No truly selective activity (i.e. clearly below the cytotoxic concentration) was observed against any of the viruses used. Some of the compounds, including DRB, were cytotoxic to MT-4 cells at CC 50 values of less than 10 μg ml −1 .
Combination of a Brief Irrigation With Tissue Factor Pathway Inhibitor (TFPI) and Adenovirus-Mediated Local TFPI Gene Transfer Additively Reduces Neointima Formation in Balloon-Injured Rabbit Carotid Arteries (2001)

A combination of rTFPI irrigation and TFPI gene transfer overcomes the shortcomings shown by each method when used alone and achieves a full coverage of TF activity suppression, thereby enhancing their therapeutic effects without systemic side effects. This combination may be an effective strategy for the prevention of thrombosis and proliferative changes after angioplasty in humans.
Phospholipid (diacyl, alkylacyl, alkenylacyl) and fatty acyl chain composition in murine mastocytoma cells. (1985)

The phospholipids from murine mastocytoma FMA3 and P-815 clone cells were quantitatively analyzed, and the major glycerophospholipids were examined for their fatty acyl chain distribution. In these cells, the content of histamine was less than 1/100 of normal mouse mast cells, and FMA3 cells had 1.5-fold as much histamine content as P-815 cells. The predominant phospholipid species of both mastocytoma FMA3 and P-815 were choline-containing glycerophospholipids (48%) and ethanolamine-containing glycerophospholipids (29%). The remaining minor constituents were sphingomyelin (6%, 7%), phosphatidylinositol (7%, 5%), phosphatidylserine (2%, 5%), cardiolipin (4%, 3%), and phosphatidic acid (2%, 1% for FMA3 and P-815, respectively). The choline-containing glycerophospholipids consisted of high amounts of 1-O-alkyl-2-acyl type (31%, 25%) and 1,2-diacyl type (63%, 66%) and a smaller amount of 1-O-alk-1'-enyl-2-acyl type (7%, 8%). In contrast, ethanolamine-containing glycerophospholipids were characterized by high contents of 1-O-alk-1'-enyl-2-acyl type (36%, 31%) and 1,2-diacyl type (55%, 58%), and a lower level of 1-O-alkyl-2-acyl type (12% and 11% for FMA3 and P-815, respectively). Unlike choline-containing glycerophospholipids and sphingomyelin that were rich in palmitic acid, ethanolamine-containing glycerophospholipids, phosphatidylserine and phosphatidylinositol showed a high proportion of stearic acid in the overall fatty acid composition. The content of arachidonic acid was highest in phosphatidylinositol. Sphingomyelin had a large amount of long chain and polyunsaturated fatty acids. In both choline- and ethanolamine-containing glycerophospholipids, the predominant fatty acids in the sn-1-position were palmitic, stearic, and oleic acid.(ABSTRACT TRUNCATED AT 250 WORDS)
The Raf/MEK/ERK pathway can govern drug resistance, apoptosis and sensitivity to targeted therapy (2010)

The effects of the Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR signaling pathways on proliferation, drug resistance, prevention of apoptosis and sensitivity to signal transduction inhibitors were examined in FL/DeltaAkt-1:ER*(Myr(+)) + DeltaRaf-1:AR cells which are conditionally-transformed to grow in response to Raf and Akt activation. Drug resistant cells were isolated from FL/DeltaAkt-1:ER*(Myr(+)) + DeltaRaf-1:AR cells in the presence of doxorubicin. Activation of Raf-1, in the drug resistant FL/DeltaAkt-1:ER*(Myr(+)) + DeltaRaf-1:AR cells, increased the IC(50) for doxorubicin 80-fold, whereas activation of Akt-1, by itself, had no effect on the doxorubicin IC50. However, Akt-1 activation enhanced cell proliferation and clonogenicity in the presence of chemotherapeutic drugs. Thus the Raf/MEK/ERK pathway had profound effects on the sensitivity to chemotherapeutic drugs, and Akt-1 activation was required for the long term growth of these cells as well as resistance to chemotherapeutic drugs. The effects of doxorubicin on the induction of apoptosis in the drug resistant cells were enhanced by addition of either mTOR and MEK inhibitors. These results indicate that targeting the Raf/MEK/ERK and PI3K/Akt/mTOR pathways may be an effective approach for therapeutic intervention in drug resistant cancers that have mutations activating these cascades.
Murine malaria parasite sequestration: CD36 is the major receptor, but cerebral pathology is unlinked to sequestration (2005)

Sequestration of malaria-parasite-infected erythrocytes in the microvasculature of organs is thought to be a significant cause of pathology. Cerebral malaria (CM) is a major complication of Plasmodium falciparum infections, and PfEMP1-mediated sequestration of infected red blood cells has been considered to be the major feature leading to CM-related pathology. We report a system for the real-time in vivo imaging of sequestration using transgenic luciferase-expressing parasites of the rodent malaria parasite Plasmodium berghei. These studies revealed that: (i) as expected, lung tissue is a major site, but, unexpectedly, adipose tissue contributes significantly to sequestration, and (ii) the class II scavenger-receptor CD36 to which PfEMP1 can bind is also the major receptor for P. berghei sequestration, indicating a role for alternative parasite ligands, because orthologues of PfEMP1 are absent from rodent malaria parasites, and, importantly, (iii) cerebral complications still develop in the absence of CD36-mediated sequestration, dissociating parasite sequestration from CM-associated pathology. Real-time in vivo imaging of parasitic processes may be used to evaluate the molecular basis of pathology and develop strategies to prevent pathology.
One‐Dimensional Nanostructures: Synthesis, Characterization, and Applications (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Adversarial Variational Optimization of Non-Differentiable Simulators (2017)

Complex computer simulators are increasingly used across fields of science as generative models tying parameters of an underlying theory to experimental observations. Inference in this setup is often difficult, as simulators rarely admit a tractable density or likelihood function. We introduce Adversarial Variational Optimization (AVO), a likelihood-free inference algorithm for fitting a non-differentiable generative model incorporating ideas from generative adversarial networks, variational optimization and empirical Bayes. We adapt the training procedure of generative adversarial networks by replacing the differentiable generative network with a domain-specific simulator. We solve the resulting non-differentiable minimax problem by minimizing variational upper bounds of the two adversarial objectives. Effectively, the procedure results in learning a proposal distribution over simulator parameters, such that the JS divergence between the marginal distribution of the synthetic data and the empirical distribution of observed data is minimized. We evaluate and compare the method with simulators producing both discrete and continuous data.
Interaction of Zinc Oxide Nanoparticles with Water: Implications for Catalytic Activity (2019)

Novel technological applications in catalysis and bactericidal formulation have emerged for zinc oxide (ZnO) nanoparticles owing to their ability to generate reactive oxygen species by fostering H2O dissociation. Rational improvement of those properties requires a mechanistic understanding of ZnO nanoparticle reactivity, which is currently lacking. Here, we determine the structural and electronic properties of nanometer-sized ZnO, determine the binding energetics of H2O adsorption, and compare to an extended macroscopic surface. We show that the electronic density of states of ZnO nanoparticles is size-dependent, exhibiting a decreasing bandgap with the increase of nanoparticle diameter. The electronic states near the Fermi energy dominantly arise from O 2p states, which are spatially localized on “reactive” surface O atoms on the nanoparticle edges that are doubly coordinated. The frontier electronic states localized at the low coordinated atoms induce a spontaneous dissociation of H2O at the nanoparticle edges. The surface Zn and O atoms have inhomogeneous electronic and geometrical/topological properties, thus providing nonequivalent sites for dissociative and molecular H2O adsorption. The free energy of H2O binding is dominated by the electronic DFT interaction energy, which is site-dependent and correlated with the Bader charge of surface Zn atom. Entropy is found to stabilize the bound form, because the increase in the vibrational contribution is greater than the decrease in the translational and rotational contribution, whereas solvation stabilizes the unbound state. The absence of rough edges on an extended, macroscopic ZnO surface prevents spontaneous dissociation of a single H2O. This study underlies the importance of coupling geometrical and electronic degrees of freedom in determining the reactivity of nanoparticles and provides a simple elucidation of the superior catalytic activity of ZnO nanoparticles compared to ZnO in macroscopic forms.
T helper 17 cells play a critical pathogenic role in lung cancer (2014)

Lung cancer development is associated with extensive pulmonary inflammation. In addition, the linkage between chronic obstructive pulmonary disease (COPD) and lung cancer has been demonstrated in population-based studies. IL-17-producing CD4 helper T cells (Th17 cells) play a critical role in promoting chronic tissue inflammation. Although Th17 cells are found in human COPD and lung cancer, their role is not understood. We have thus used a mouse model of lung cancer, in which an oncogenic form of K-ras (K-ras(G12D)), frequently found in human lung cancer, is restrictedly expressed in lung epithelial cells [via Clara cell secretory protein (CCSP(cre))]. In this model, Th17 and Treg but not Th1 cells were found enriched at the tumor tissues. When CCSP(cre)/K-ras(G12D) mice were weekly challenged with a lysate of nontypeable Haemophilus influenza (NTHi), which induces COPD-type inflammation and accelerates the tumor growth, they showed greatly enhanced Th17 cell infiltration in the lung tissues. Lack of IL-17, but not IL-17F, resulted in a significant reduction in lung tumor numbers in CCSP(cre)/K-ras(G12D) mice and also those treated with NTHi. Absence of IL-17 not only resulted in reduction of tumor cell proliferation and angiogenesis, but also decreased the expression of proinflammatory mediators and reduced recruitment of myeloid cells. Depletion of Gr-1(+)CD11b(+) myeloid cells in CCSP(cre)/K-ras(G12D) mice suppressed tumor growth in lung, indicating Gr-1(+)CD11b(+) myeloid cells recruited by IL-17 play a protumor role. Taken together, our data demonstrate a critical role for Th17 cell-mediated inflammation in lung tumorigenesis and suggest a novel way for prevention and treatment of this disease.
Microbial production of gallic acid by modified solid state fermentation (1999)

Bioconversion of tannin to gallic acid from powder of teri pod (Caesalpinia digyna) cover was achieved by the locally isolated fungus, Rhizopus oryzae, in a bioreactor with a perforated float for carrying solid substrate and induced inoculum. Modified Czapek-Dox medium, put beneath the perforated float, with 2% tannic acid at pH 4.5, temperature 32C, 93% relative humidity, incubated for 3 days with 3-day-old inoculum was optimum for the synthesis of tannase vis-a `-vis gallic acid production. Conversion of tannin to gallic acid was 90.9%. Diethyl ether was used as the solvent for extraction of gallic acid from the fermented biomass.
Metabolism of proteoglycans in rat ovarian granulosa cell culture. Multiple intracellular degradative pathways and the effect of chloroquine. (1984)

The metabolism of endogenously labeled proteoglycans was studied in rat ovarian granulosa cell cultures by a series of pulse-chase experiments using [35S]sulfate as a precursor. More than 90% of the newly synthesized proteoglycans are transported to the cell surface (trypsin-accessible compartment) with a median transit time of 13 min. The membrane-bound heparan sulfate-proteoglycan (HS-PG) is lost from the cell surface either by release into the medium (30%, with t1/2 of 4 h) or by internalization (70%, with t1/2 of 4 h). Internalized HS-PG, which does not recycle to the cell surface, is degraded by two major pathways. In pathway 1, 60% of the internalized HS-PG migrates to lysosomes with a relatively short t1/2 of 30 min, where it is rapidly degraded, releasing free [35S]sulfate without detectable intermediate products. Chloroquine treatment inhibited degradation, resulting in the accumulation of intact proteoglycans inside the cell. In pathway 2, 40% of the internalized HS-PG is first subjected to extensive proteolysis and limited endoglycosidic degradation yielding single HS chains about 1/3 of their original size (t1/2 of 30 min). Chloroquine did not inhibit this step. The partially degraded HS is then degraded further by limited endoglycosidic activity to about 1/4-1/5 the original size (t1/2 of 30-60 min). This step is inhibited by chloroquine. These smaller fragments have a relatively long t1/2 of 3-4 h before rapid degradation in the lysosomes, releasing free [35S]sulfate. Approximately 7% of the newly synthesized HS-PG that is not transported to the cell surface is degraded directly by pathway 2. The larger dermatan sulfate proteoglycan (DS-I) is transported to the cell surface from which it is quantitatively released into the medium with a t1/2 of 4-6 h. The smaller DS-PG (DS-II) is metabolized similarly to the HS-PG. Most (greater than 90%) is transported to the cell surface from which it is lost either by release into the medium (40%) or by internalization (60%). About 60% of the internalized DS-II is degraded by pathway 1 (t1/2 of 30 min), while the remainder appears to be degraded by pathway 2 with an overall t1/2 of 4 h. However, in contrast to the degradation of HS-PG by pathway 2, no endoglycosidic degradation of the DS chains occurred.
J-Sim: A Simulation Environment for Wireless Sensor Networks (2005)

Wireless sensor networks (WSNs) have gained considerable attention in the past few years. As such, there has been an increasing need for defining and developing simulation frameworks for carrying out high-fidelity WSN simulation. In this paper, the authors presented a modeling and simulation framework for WSNs in J-Sim - an open-source, component-based compositional network simulation environment that is developed entirely in Java. This framework is built upon the autonomous component architecture (ACA) and the extensible internetworking framework (INET) of J-Sim, and provides an object-oriented definition of (i) target, sensor and sink nodes, (ii) sensor and wireless communication channels, and (iii) physical media such as seismic channels, mobility model and power model (both energy-producing and energy-consuming components). Application-specific models can be defined by sub-classing classes in the simulation framework and customizing their behaviors. The use of the proposed WSN simulation framework was demonstrated by implementing several well-known localization, geographic routing, and directed diffusion protocols. In addition, performance comparisons were performed (in terms of execution time incurred, and the memory used) in simulating several typical WSN scenarios in J-Sim and ns-2. The simulation study indicates that the proposed WSN simulation framework in J-Sim is much more scalable than ns-2 (especially in memory usage).
Electrochemical measurements of electron transfer rates through zirconium 1,2-ethanediylbis(phosphonate) multilayer films on gold electrodes (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrochemical measurements of electron transfer rates through zirconium 1,2-ethanediylbis(phosphonate) multilayer films on gold electrodesHun Gi Hong and Thomas E. MalloukCite this: Langmuir 1991, 7, 10, 2362–2369Publication Date (Print):October 1, 1991Publication History Published online1 May 2002Published inissue 1 October 1991https://pubs.acs.org/doi/10.1021/la00058a065https://doi.org/10.1021/la00058a065research-articleACS PublicationsRequest reuse permissionsArticle Views433Altmetric-Citations68LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Antiallergic and Anti-Inflammatory Effects of a Novel IκB Kinase β Inhibitor, IMD-0354, in a Mouse Model of Allergic Inflammation (2008)

A specific IKK beta inhibitor, IMD-0354, improved allergic airway inflammation and hyperresponsiveness in mice. IMD-0354 may have therapeutic potential for bronchial asthma.
Synthesis of suicide inhibitors of monoamine oxidase: Carbon‐11 labeled clorgyline, L‐deprenyl and D‐deprenyl (1988)

Abstract The suicide inhibitors of monoamine oxidase type A and B, clorgyline and L‐deprenyl have been labeled with carbon‐11 by [ 11 C]methylation of the norbases with [ 11 C]H 3 I. The less active enantiomer of deprenyl (D‐deprenyl) was also labeled using this procedure. The synthesis time was 35 minutes, the radiochemical yield was 25–40% and the specific activity was 0.8–2.0 Ci/μmol (calculated to EOB). Procedures for synthesis of the precursor norbases as well as the synthesis of unlabeled clorgyline, L‐deprenyl and D‐deprenyl are given.
YKL‐40 in type 2 diabetic patients with different levels of albuminuria (2010)

This is the first report of a significant elevation of YKL-40 in type 2 diabetic patients with albuminuria. In addition, we observed a significant association with macrovascular disease. Because we detected an association between YKL-40 with renal, micro- and macrovascular disease, this protein could play an important for the increased risk of type 2 diabetic patients with albuminuria for the development of cardiovascular disease.
Therapeutic effects of the angiogenesis inhibitor TNP-470 against carcinomatous peritonitis in mice (1995)

The therapeutic effects of the new anti-angiogenesis factor TNP-470 were examined against carcinomatous peritonitis in mice. In the first experiment using carcinomatous peritonitis caused by i.p. inoculation of 10(6) M5076 tumor cells, TNP-470 solution was injected i.p. in a bolus of 50 mg/kg body weight into two groups of 10 mice either 1 or 8 days after the i.p. inoculation. The administration of TNP-470 on day 1 extended the survival time of the mice compared with 10 control mice receiving no treatment, whereas TNP-470 given on day 8 did not affect the survival time. In the next experiment on the M5076 tumor, TNP-470 solutions at 100 or 300 mg/kg were injected i.p. in a bolus into two groups of 20 mice 1 day after the inoculation 10(6) tumor cells, respectively. The administration of TNP-470 at 100 mg/kg also had an inhibitory effect. However, TNP-470 at 300 mg/kg caused toxic death in half of the mice. Next, we examined the effects of TNP-470 on another type of carcinomatous peritonitis model, which was caused by i.p. inoculation of 10(6) B16 melanoma cells. In this experiment, TNP-470 solutions in a bolus of 150 mg/kg were injected i.p. into six groups of 10 mice each on day 1 only (group 1), on days 1 and 4 (group 2), on days 1, 4 and 7 (group 3), on day 8 only (group 4), on days 8 and 11 (group 5), or on days 8, 11 and 14 (group 6), respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Analysis of epidermal growth factor receptor gene expression in stained smears and formalin-fixed, paraffin-embedded cell pellets by reverse transcription intron differential polymerase chain reaction. (1993)

Previous studies have demonstrated quantitation of epidermal growth factor receptors (EGFR) to be of prognostic significance in breast, bladder, esophageal and other neoplasms. However, the relatively large quantity of unfixed tissue required for epidermal growth factor radioligand binding assays (RLBA) has precluded its application to cytologic specimens and small biopsy specimens. For this reason we evaluated reverse transcription intron differential polymerase chain reaction (RTIDPCR) as an assay of EGFR gene expression. Squamous cell carcinoma (A431 and SiHa), transitional cell carcinoma (HT1376, T24, RT4), mammary (MCF7) and endocervical (HeLa) adenocarcinoma, and leukemia (K562) cell lines were used to compare RTIDPCR and RLBA. RTIDPCR involved reverse transcription of RNA and amplification of cDNA using primers for beta-actin and EGFR. Good agreement was observed between the RLBA and RTIDPCR results. RNA extracted from fresh cells, Diff-Quik-stained smears and formalin-fixed, paraffin-embedded cell pellet sections yielded similar results. These data suggest that RTIDPCR may be useful in evaluating gene expression by cells processed as cytologic specimens.
Digital Predistortion for Joint Mitigation of I/Q Imbalance and MIMO Power Amplifier Distortion (2016)

This paper analyzes the joint effects of in-phase and quadrature (I/Q) imbalance and power amplifier (PA) distortion for RF multiple input multiple output (MIMO) transmitters in the presence of crosstalk. This paper proposes candidate models for the digital predistortion of static I/Q imbalanced sources exciting a dynamic MIMO Volterra system. The proposed models are enhanced using a novel technique based on subsample resolution to account for dynamic I/Q imbalance distortions. Finally, the computational complexity of the proposed models is analyzed for implementation suitability in digital platforms. It is shown that the error spectrum for the proposed models in subsample resolution reaches the noise floor of the measurements. The proposed models achieve a normalized mean squared error of -50 dB and an adjacent channel power ratio of -57 dB for signal bandwidths upto 65 MHz and crosstalk levels ranging to -10 dB. These results demonstrate the effectiveness of the proposed techniques in the joint mitigation of I/Q imbalance and PA distortion with crosstalk for a typical 2 x 2 MIMO telecommunication setup.