gebhart/patrepeval huggingface dataset:
Temozolomide: a novel oral alkylating agent (2001)

Temozolomide is an imidazotetrazine with a mechanism of action and efficacy similar to dacarbazine (DTIC). However, it differs from DTIC in that it can be taken orally, degrades spontaneously to an active metabolite and penetrates the blood-brain barrier. It is well tolerated, making it a suitable candidate for combination chemotherapy. Trials to date have focussed on its activity in advanced metastatic melanoma and high-grade malignant glioma. Investigations into other indications, in particular solid tumors with central nervous system metastases, are ongoing. Studies of new drug schedules and of drugs to ameliorate temozolomide resistance offer the prospect of increased efficacy.
Combined Cardiac Resynchronization and Implantable Cardioversion Defibrillation in Advanced Chronic Heart Failure (2003)

ContextCardiac resynchronization therapy (CRT) through biventricular pacing is an effective treatment for heart failure (HF) with a wide QRS; however, the outcomes of patients requiring CRT and implantable cardioverter defibrillator (ICD) therapy are unknown.ObjectiveTo examine the efficacy and safety of combined CRT and ICD therapy in patients with New York Heart Association (NYHA) class III or IV congestive HF despite appropriate medical management.Design, Setting, and ParticipantsRandomized, double-blind, parallel-controlled trial conducted from October 1, 1999, to August 31, 2001, of 369 patients with left ventricular ejection fraction of 35% or less, QRS duration of 130 ms, at high risk of life-threatening ventricular arrhythmias, and in NYHA class III (n = 328) or IV (n = 41) despite optimized medical treatment.InterventionsOf 369 randomized patients who received devices with combined CRT and ICD capabilities, 182 were controls (ICD activated, CRT off) and 187 were in the CRT group (ICD activated, CRT on).Main Outcome MeasuresThe primary double-blind study end points were changes between baseline and 6 months in quality of life, functional class, and distance covered during a 6-minute walk. Additional outcome measures included changes in exercise capacity, plasma neurohormones, left ventricular function, and overall HF status. Survival, incidence of ventricular arrhythmias, and rates of hospitalization were also compared.ResultsAt 6 months, patients assigned to CRT had a greater improvement in median (95% confidence interval) quality of life score (–17.5 [–21 to –14] vs –11.0 [–16 to –7], P = .02) and functional class (–1 [–1 to –1] vs 0 [–1 to 0], P = .007) than controls but were no different in the change in distance walked in 6 minutes (55 m [44-79] vs 53 m [43-75], P = .36). Peak oxygen consumption increased by 1.1 mL/kg per minute (0.7-1.6) in the CRT group vs 0.1 mL/kg per minute (–0.1 to 0.8) in controls (P = .04), although treadmill exercise duration increased by 56 seconds (30-79) in the CRT group and decreased by 11 seconds (–55 to 12) in controls (P&lt;.001). No significant differences were observed in changes in left ventricular size or function, overall HF status, survival, and rates of hospitalization. No proarrhythmia was observed and arrhythmia termination capabilities were not impaired.ConclusionsCardiac resynchronization improved quality of life, functional status, and exercise capacity in patients with moderate to severe HF, a wide QRS interval, and life-threatening arrhythmias. These improvements occurred in the context of underlying appropriate medical management without proarrhythmia or compromised ICD function.
Molecular basis of glyphosate resistance – different approaches through protein engineering (2011)

Glyphosate (N-phosphonomethyl-glycine) is the most widely used herbicide in the world: glyphosate-based formulations exhibit broad-spectrum herbicidal activity with minimal human and environmental toxicity. The extraordinary success of this simple, small molecule is mainly attributable to the high specificity of glyphosate for the plant enzyme enolpyruvyl shikimate-3-phosphate synthase in the shikimate pathway, leading to the biosynthesis of aromatic amino acids. Starting in 1996, transgenic glyphosate-resistant plants were introduced, thus allowing application of the herbicide to the crop (post-emergence) to remove emerged weeds without crop damage. This review focuses on mechanisms of resistance to glyphosate as obtained through natural diversity, the gene-shuffling approach to molecular evolution, and a rational, structure-based approach to protein engineering. In addition, we offer a rationale for the means by which the modifications made have had their intended effect.
Levetiracetam in the treatment of childhood epilepsy. (2007)

Epilepsy is a common pediatric neurologic disorder that is difficult to manage in a substantial portion of children. Levetiracetam (LEV) is a novel antiepileptic drug (AED) that has recently been approved as add-on treatment for various seizure types in epilepsy populations that include children: for refractory partial seizures in epilepsy patients >/=4 years old, for myoclonic seizures in juvenile myoclonic epilepsy patients >/=12 years old, and for primary generalized tonic-clonic seizures in idiopathic generalized epilepsy patients (>/=6 years old with FDA approval; >/=12 years old with EMEA approval). A review of published pediatric studies indicates that the efficacy of LEV is best established for partial seizures; however, results from recent double-blind and open-label trials indicate that adjunctive LEV also controls generalized seizures - particularly myoclonic and generalized tonic-clonic - in children and adolescents with primary generalized epilepsy. LEV was well-tolerated in pediatric studies. The most common adverse events (AEs) reported were sedation related. Behavioral AEs were among the most commonly reported events in some trials; conversely, improvements in behavior and cognition were also frequently reported. LEV appears to be a safe and effective AED with unique characteristics that benefit the treatment of children with epilepsy.
Involvement of the V1/V2 variable loop structure in the exposure of human immunodeficiency virus type 1 gp120 epitopes induced by receptor binding (1995)

The binding of human immunodeficiency virus type 1 (HIV-1) to the cellular receptor CD4 has been suggested to induce conformational changes in the viral envelope glycoproteins that promote virus entry. Conserved, discontinuous epitopes on the HIV-1 gp120 glycoprotein recognized by the 17b, 48d, and A32 antibodies are preferentially exposed upon the binding of soluble CD4 (sCD4). The binding of the 17b and 48d antibodies to the gp120 glycoprotein can also be enhanced by the binding of the A32 antibody. Here we constructed HIV-1 gp120 mutants in which the variable segments of the V1/V2 and V3 structures were deleted, individually or in combination, while the 17b, 48d, and A32 epitopes were retained. The effects of the variable loop deletions on the function of the HIV-1 envelope glycoproteins and on the exposure of epitopes induced by sCD4 or A32 binding to the monomeric gp120 glycoprotein were examined. The variable-loop-deleted envelope glycoproteins were able to mediate virus entry, albeit at lower efficiencies than those of the wild-type glycoproteins. Thus, the V1/V2 and V3 variable sequences contribute to the efficiency of HIV-1 entry but are not absolutely required for the process. Neither the V1/V2 nor V3 loops were necessary for the increase in exposure of the 17b/48d epitopes induced by binding of the A32 monoclonal antibody. By contrast, induction of the 17b, 48d, and A32 epitopes by sCD4 binding apparently involves a movement of the V1/V2 loops, which in the absence of CD4 partially mask these epitopes on the native gp120 monomer. The results obtained with a mutant glycoprotein containing a deletion of the V1 loop alone indicated that the contribution of the V2 loop to these phenomena was more significant than that of the V1 sequences. These results suggest that the V1/V2 loops, which have been previously implicated in CD4-modulated, postattachment steps in HIV-1 entry, contribute to CD4-induced gp120 conformational changes detected by the 17b, 48d, and A32 antibodies.
Chromatin remodeling in nuclear cloning (2002)

Nuclear cloning is a procedure to create new animals by injecting somatic nuclei into unfertilized oocytes. Recent successes in mammalian cloning with differentiated adult nuclei strongly indicate that oocyte cytoplasm contains unidentified remarkable reprogramming activities with the capacity to erase the previous memory of cell differentiation. At the heart of this nuclear reprogramming lies chromatin remodeling as chromatin structure and function define cell differentiation through regulation of the transcriptional activities of the cells. Studies involving the modification of chromatin elements such as selective uptake or release of binding proteins, covalent histone modifications including acetylation and methylation, and DNA methylation should provide significant insight into the molecular mechanisms of nuclear dedifferentiation and redifferentiation in oocyte cytoplasm.
Interpretation of Leaching Data for Cementitious WasteForms Using Analytical Solutions Based on Mass Transport Theory and Empiricism (2024)

Despite the demonstrated importance of diffusion control in leaching, other mechanisms have been observed to play a role and leaching from porous solid bodies is not simple diffusion. Only simple diffusion theory has been developed well enough for extrapolation, as yet. The well developed diffusion theory, used in data analysis by ANSI/ANS-16.1 and the NEWBOX program, can help in trying to extrapolate and predict the performance of solidified waste forms over decades and centuries, but the limitations and increased uncertainty must be understood in so doing. Treating leaching as a semi-infinite medium problem, as done in the Cote model, results in simpler equations, but limits, application to early leaching behavior when less than 20% of a given component has been leached.
CD40 Ligand/Trimer DNA Enhances Both Humoral and Cellular Immune Responses and Induces Protective Immunity to Infectious and Tumor Challenge (1998)

CD40/CD40 ligand interactions have a central role in the induction of both humoral and cellular immunity. In this study, we examined whether a plasmid expressing CD40 ligand/trimer (CD40LT) could enhance immune responses in vivo. BALB/c mice were injected with plasmid expressing beta-galactosidase DNA with or without CD40LT DNA or IL-12 DNA, and immune responses were assessed. Mice vaccinated with beta-gal DNA plus CD40LT DNA or IL-12 DNA had a striking increase in Ag-specific production of IFN-gamma, cytolytic T cell activity, and IgG2a Ab. The mechanism by which CD40LT DNA enhanced these responses was further assessed by treating vaccinated mice with anti-IL-12 mAb or CTLA-4 Ig (CTLA4Ig). Production of IFN-gamma and CTL activity was abrogated by these treatments, suggesting that CD40LT DNA was mediating its effects on IFN-gamma and CTL activity through induction of IL-12 and enhancement of B7 expression, respectively. Physiologic relevance for the ability of CD40LT DNA to enhance immune responses by the aforementioned pathways was shown in two in vivo models. First, with regard to CTL activity, mice vaccinated with CD40LT DNA did not develop metastatic tumor following challenge with lethal dose of tumor. Moreover, in a mouse model requiring IL-12-dependent production of IFN-gamma, mice vaccinated with soluble Leishmania Ag and CD40LT DNA were able to control infection with Leishmania major. These data suggest that CD40LT DNA could be a useful vaccine adjuvant for diseases requiring cellular and/or humoral immunity.
An analysis of temporal-difference learning with function approximation (1997)

We discuss the temporal-difference learning algorithm, as applied to approximating the cost-to-go function of an infinite-horizon discounted Markov chain. The algorithm we analyze updates parameters of a linear function approximator online during a single endless trajectory of an irreducible aperiodic Markov chain with a finite or infinite state space. We present a proof of convergence (with probability one), a characterization of the limit of convergence, and a bound on the resulting approximation error. Furthermore, our analysis is based on a new line of reasoning that provides new intuition about the dynamics of temporal-difference learning. In addition to proving new and stronger positive results than those previously available, we identify the significance of online updating and potential hazards associated with the use of nonlinear function approximators. First, we prove that divergence may occur when updates are not based on trajectories of the Markov chain. This fact reconciles positive and negative results that have been discussed in the literature, regarding the soundness of temporal-difference learning. Second, we present an example illustrating the possibility of divergence when temporal difference learning is used in the presence of a nonlinear function approximator.
Physicochemical Properties of the Nucleoside Prodrug R1626 Leading to High Oral Bioavailability (2008)

The nucleoside analog R1479 is a potent and highly selective inhibitor of NS5b-directed hepatitis C virus (HCV) RNA polymerase in vitro. Because of its limited permeability, lipophilic prodrugs of R1479 were screened. Selection of the prodrug involved optimization of solubility, permeability, and stability parameters. R1626 has dissociation constant, intrinsic solubility, log partition coefficient (n-octanol water), and Caco-2 permeability of 3.62, 0.19 mg/mL, 2.45, and 14.95 x 10(-6) cm/s, respectively. The hydrolysis of the prodrug is significantly faster in the Caco-2 experiments than in hydrolytic experiments, suggesting that the hydrolysis is catalyzed by enzymes in the cellular membrane. Using GastroPlus, the physical properties of R1626 successfully predict the dose dependence of the pharmacokinetics in humans previously studied. The program predicts that if the particle size of R1626 is less than 25 microm, it will be well absorbed. Prodrugs with a solubility of greater than 100 microg/mL and permeability in the Caco-2 assay greater than 3 x 10(-6) cm/s are expected to achieve a high fraction absorbed.
The Anti-neuroinflammatory Activity of Tectorigenin Pretreatment via Downregulated NF-κB and ERK/JNK Pathways in BV-2 Microglial and Microglia Inactivation in Mice With Lipopolysaccharide (2018)

The activation of microglia is decisively involved with the neurodegeneration observed in many neuroinflammatory pathologies, such as multiple sclerosis, Parkinson's disease, and Alzheimer's disease. Tectorigenin (TEC) is an isoflavone isolated from various medicinal plants, such as <i>Pueraria thunbergiana</i> Benth, <i>Belamcanda chinensis</i>, and <i>Iris unguicularis</i>. In the present study, the neuroinflammatory effects of TEC were evaluated in both lipopolysaccharide (LPS)-treated BV-2 microglial and mouse models. TEC remarkably inhibited reactive oxygen species (ROS) generation. TEC also inhibits the production and expression of nitric oxide (NO), prostaglandin E<sub>2</sub> (PGE<sub>2</sub>), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) in LPS-stimulated BV-2 cells. In addition, TEC suppressed the LPS-induced activation of nuclear factor-κB (NF-κB), phosphorylation of extracellular signal-regulated kinase (ERK), and c-Jun N-terminal kinase (JNK) to regulate the inflammatory mediators, such as inducible NO synthase (iNOS), cyclooxygenase-2 (COX-2), TNF-α, and IL-6. These results indicate that TEC may inhibit neuronal inflammation through the downregulation of inflammatory mediators, including iNOS, COX-2, TNF-α, and IL-6 by suppressing NF-κB/ERK/JNK-related signaling pathways. Furthermore, cotreatment with TEC and ERK inhibitor SCH772984 or JNK inhibitor SP600125 suppressed the overproduction of LPS-induced NO production in BV-2 cells. Consistent with the results of <i>in vitro</i> experiments, an LPS-induced brain inflammation mouse model, administration of TEC effectively decrease the levels of malondialdehyde, iNOS in hippocampus, and prevented increases in the levels of TNF-α and IL-6 in the serum. TEC showed marked attenuation of microglial activation. Finally, TEC inhibited protein expression of toll-like receptor 4 and myeloid differentiation factor 88 in LPS-activated BV-2 microglia and mouse models. Taken altogether, the cumulative findings suggested that TEC holds the potential to develop as a neuroprotective drug for the intervention of neuroinflammatory disorders.
Inhibition of the angiogenesis by the MCP‐1 (monocyte chemoattractant protein‐1) binding peptide (2005)

The CC chemokine, monocyte chemoattractant protein-1 (MCP-1), plays a crucial role in the initiation of atherosclerosis and has direct effects that promote angiogenesis. To develop a specific inhibitor for MCP-1-induced angiogenesis, we performed in vitro selection employing phage display random peptide libraries. Most of the selected peptides were found to be homologous to the second extracellular loops of CCR2 and CCR3. We synthesized the peptide encoding the homologous sequences of the receptors and tested its effect on the MCP-1 induced angiogenesis. Surface plasmon resonance measurements demonstrated specific binding of the peptide to MCP-1 but not to the other homologous protein, MCP-3. Flow cytometry revealed that the peptide inhibited the MCP-1 binding to THP-1 monocytes. Moreover, CAM and rat aortic ring assays showed that the peptide inhibited MCP-1 induced angiogenesis. Our observations indicate that the MCP-1-binding peptide exerts its anti-angiogenic effect by interfering with the interaction between MCP-1 and its receptor.
Oxygen-regulated isoforms of cytochrome c oxidase have differential effects on its nitric oxide production and on hypoxic signaling (2008)

Recently, it has been reported that mitochondria possess a novel pathway for nitric oxide (NO) synthesis. This pathway is induced when cells experience hypoxia, is nitrite (NO(2)(-))-dependent, is independent of NO synthases, and is catalyzed by cytochrome c oxidase (Cco). It has been proposed that this mitochondrially produced NO is a component of hypoxic signaling and the induction of nuclear hypoxic genes. In this study, we examine the NO(2)(-)-dependent NO production in yeast engineered to contain alternative isoforms, Va or Vb, of Cco subunit V. Previous studies have shown that these isoforms have differential effects on oxygen reduction by Cco, and that their genes (COX5a and COX5b, respectively) are inversely regulated by oxygen. Here, we find that the Vb isozyme has a higher turnover rate for NO production than the Va isozyme and that the Vb isozyme produces NO at much higher oxygen concentrations than the Va isozyme. We have also found that the hypoxic genes CYC7 and OLE1 are induced to higher levels in a strain carrying the Vb isozyme than in a strain carrying the Va isozyme. Together, these results demonstrate that the subunit V isoforms have differential effects on NO(2)(-)-dependent NO production by Cco and provide further support for a role of Cco in hypoxic signaling. These findings also suggest a positive feedback mechanism in which mitochondrially produced NO induces expression of COX5b, whose protein product then functions to enhance the ability of Cco to produce NO in hypoxic/anoxic cells.
Substituent Effects in the Extraction of Cesium from Acidic Nitrate Media With Macrocyclic Polyethers* (1996)

ABSTRACT A variety of dibenzocrown ethers have been evaluated for the extraction of cesium from acidic nitrate media. Compounds incorporating a 21-crown-7 moiety are shown to exhibit greater cesium/sodium selectivity, superior functional stability, and better compatibility with PUREX-like diluents than dibenzocrown ethers with other ring sizes. The cesium distribution ratios obtained with these compounds, however, are generally not large enough to be of practical value. Higher Dcs values are achieved with several dibenzo-18-crown-6 derivatives. Of these, the best results are achieved with 4,4'(5')-di-[(l-hydroxy-2-ethylhexyl)benzo]-18-crown-6. The distribution ratios obtained with this compound in undiluted tri-n-butyl phosphate (TBP) compare favorably with those reported for synergistic systems combining a crown ether with the anion of a lipophilic organic acid.
Characterization of acceptance angles of  small circular apertures (2009)

We characterize the acceptance angles of small circular apertures for light collection by simulations and experimental measurements. By examining the full width half maximum acceptance angle as a function of the aperture size, we show that the acceptance angle of a circular aperture reaches a minimum of 67 deg before rebounding around the transition between single mode and multimode transmission (approximately 400 nm). This behavior can be explained by the change of mode-coupling efficiency during the transition from single mode to multimode propagation regime. This work in understanding of the behavior of light transmission through subwavelength apertures will guide the design of better aperture based imaging devices where apertures are used as light collection units.
Scalable Production of Sensor Arrays Based on High-Mobility Hybrid Graphene Field Effect Transistors (2016)

We have developed a scalable fabrication process for the production of DNA biosensors based on gold nanoparticle-decorated graphene field effect transistors (AuNP-Gr-FETs), where monodisperse AuNPs are created through physical vapor deposition followed by thermal annealing. The FETs are created in a four-probe configuration, using an optimized bilayer photolithography process that yields chemically clean devices, as confirmed by XPS and AFM, with high carrier mobility (3590 ± 710 cm<sup>2</sup>/V·s) and low unintended doping (Dirac voltages of 9.4 ± 2.7 V). The AuNP-Gr-FETs were readily functionalized with thiolated probe DNA to yield DNA biosensors with a detection limit of 1 nM and high specificity against noncomplementary DNA. Our work provides a pathway toward the scalable fabrication of high-performance AuNP-Gr-FET devices for label-free nucleic acid testing in a realistic clinical setting.
The First Phosphine Oxide Ligand Precursors for Transition Metal Catalyzed Cross-Coupling Reactions: C−C, C−N, and C−S Bond Formation on Unactivated Aryl Chlorides (2001)

Rapid and regioselective oxidative addition of unactivated aryl chlorides in the presence of bases can be achieved by using metal complexes of phosphinous acid (RR′POH), for which air-stable phosphine oxides (RR′P(O)H) serve as ideal ligand precursors. Such processes can be incorporated into efficient catalytic cycles for a variety of C−C, C−N, and C−S bond-forming processes (see scheme, Ar=aryl).