gebhart/patrepeval huggingface dataset:
Synthesis of 5-membered Heteroaryl-substituted Benzyloxy-benzaldehydes by theSuzuki-Miyaura Coupling Reaction (2022)

Abstract: In medicinal chemistry, benzyloxy-benzaldehyde is a valuable intermediate, to which the attachment of a five membered heterocycle may be advantageous from the point of view of drug design. The starting iodo-benzyloxy-benzaldehydes were synthesized by the O-benzylation of o-, m- and p-hydroxybenzaldehydes with 2-, 3- and 4-iodobenzylbromides in refluxing acetone or acetonitrile in the presence of potassium carbonate and potassium iodide. Starting from the corresponding iodo-benzyloxy-benzaldehydes, the Suzuki-Miyaura carbon-carbon cross-coupling reaction was utilized to get five membered heteroaryl-substituted benzyloxy-benzaldehydes. Various methods for Suzuki cross-coupling were studied. The applied boronic acids were 2- and 3-thiophene-boronic acids, as well as 2- and 3-furan-boronic acids. The reactions were followed by TLC and HPLC-UV-MS analysis. The products were purified by column chromatography. The original Suzuki method comprising NaOEt/EtOH, tetrakis(triphenylphosphine)palladium, in toluene was applied only in a few cases, resulting in poor yields. In several cases, the Suzuki coupling of substituted aryl iodides with 2-furanboronic acid failed to result in the formation of the expected products using the palladium acetate/tri(o-tolyl)phosphine/aqueous tripotassium phosphate/dimethoxyethan system. But reacting 3-thiophene-boronic acids with the corresponding iodo-benzyloxybenzaldehydes, this method afforded the products in 76-99 % yields. The more powerful tetrakis(triphenylphosphine)palladium/ aqueous cesium carbonate/dimethylformamide system seemed to be more successful in cases of 2-thiophene boronic acid as well as 2- and 3-furan-boronic acids, providing the desired products in 75-93% yield. Twenty-six new compounds were synthesized.
microRNA-200c/141 upregulates SerpinB2 to promote breast cancer cell metastasis and reduce patient survival (2017)

The microRNA-200 (miR-200) family is associated with tumor metastasis and poor patient prognosis. We found that miR-200c/141 cluster overexpression upregulated SerpinB2 in the MDA-MB-231 triple-negative (TN) breast cancer cell line. We observed transcription factor (c-Jun, c-Fos, and FosB) upregulation, nuclear localization of c-Jun, and increased SerpinB2 promoter-directed chloramphenicol acetyltransferase activity in miR-200c/141 cluster-overexpressing cells relative to controls. Additionally, miR-124a and miR-26b, which directly target SepinB2, were downregulated compared to controls. In mouse xenograft models, miR-200c/141 cluster overexpression promoted lymph node and lung metastasis, and siRNA-mediated SerpinB2 knockdown decreased lung metastasis, suggesting that SerpinB2 mediates miR-200c/141-induced lung metastasis. We also explored the clinical significance of SerpinB2 protein status through analysis of primary breast tumor samples and The Cancer Genome Atlas (TCGA) data. High SerpinB2 levels were associated with reduced survival and increased lymph node metastasis in breast cancer patients. SerpinB2 was overexpressed in the TN breast cancer subtype as compared to the luminal subtype. The present study demonstrates that SerpinB2 promotes miR-200c/141 cluster overexpression-induced breast cancer cell metastasis, and SerpinB2 overexpression correlates with increased metastatic potential and unfavorable outcomes in breast cancer patients. SerpinB2 may be a useful biomarker for assessing metastasis risk in breast cancer patients.
ASLA: reverse engineering approach for software license information retrieval (2006)

Software maintenance and reuse require identification of the applied software licenses. The information needs of maintainers and reusers can be supported by reverse engineering tools at different information retrieval levels. The paper presents a reverse engineering approach called ASLA for retrieving license information typically used in OSS. User needs, system architecture, tool features, and tool evaluation are presented. The implemented tool features include support for identifying source file dependencies and licenses in source files. The tool is evaluated against another tool for license information extraction. ASLA supports the same programming languages as GCC. License identification coverage is good and the tool is extendable
Cysteuze nierafwijkingen (2005)

Cysten in de nieren ontstaan bij een aantal verschillende aandoeningen, waaronder erfelijke ziekten of sporadisch voorkomende afwijkingen. De cysten ontstaan ofwel door verwijding van tubuli ofwel door verwijding van de ruimte van Bouwman in de glomeruli of als dysplastische ontwikkeling van de nier.
Ligand-Activation of the Adenosine A2a Receptors Inhibits IL-12 Production by Human Monocytes (2000)

Adenosine (ADO) exerts potent anti-inflammatory and immunosuppressive effects. In this paper we address the possibility that these effects are partly mediated by inhibition of the secretion of IL-12, a proinflammatory cytokine and a major inducer of Th1 responses. We demonstrate that 5'-N-ethylcarboxamidoadenosine (NECA), a nonspecific ADO analogue, and 2-p-(2-carbonyl-ethyl)phenylethylamino-5'-N-ethylcarboxamidoadenos ine (CGS-21680), a specific A2a receptor agonist, dose-dependently inhibited, in whole blood ex vivo and monocyte cultures, the production of human IL-12 induced by LPS and Stapholococcus aureus Cowan strain 1. However, the A1 receptor agonist 2-Chloro-N6-cyclopentyladenosine and the A3 receptor agonists N6-Benzyl-NECA and 1-deoxy-1-[6-[[(3-iodophenyl)methyl]amino]-9H-purin-9-yl]-N-methyl-be ta-d -ribofuranuronamide expressed only weak inhibitory effects. On the other hand, NECA and CGS-21680 dose-dependently potentiated the production of IL-10. The differential effect of these drugs on monocyte IL-12 and IL-10 production implies that these effects are mediated by A2a receptor signaling rather than by intracellular toxicity of ADO analogue's metabolites. Moreover, CGS-21680 inhibited IL-12 production independently of endogenous IL-10 induction, because anti-IL-10 Abs failed to prevent its effect. The selective A2a antagonist 8-(3-Chlorostyryl) caffeine prevented the inhibitory effect of CGS-21680 on IL-12 production. The phosphodiesterase inhibitor Ro 20-1724 dose-dependently potentiated the inhibitory effect of CGS-21680 and, furthermore, Rp-cAMPS, a protein kinase A inhibitor, reversed the inhibitory effect of CGS-21680, implicating a cAMP/protein kinase A pathway in its action. Thus, ligand activation of A2a receptors simultaneously inhibits IL-12 and stimulates IL-10 production by human monocytes. Through this mechanism, ADO released in excess during inflammatory and ischemic conditions, or tissue injury, may contribute to selective suppression of Th1 responses and cellular immunity.
Table S5 from Dual Inhibition of GLUT1 and the ATR/CHK1 Kinase Axis Displays Synergistic Cytotoxicity in <i>KRAS</i>-Mutant Cancer Cells (2023)

&lt;p&gt;Table S5 contains data of the GSEA analysis.&lt;/p&gt;
Combustion-assisted plasma in fuel conversion (2011)

The long history of plasma application for fuel conversion shows that reasonably low specific energy requirement has been achieved in most cases using non-equilibrium systems with relatively high local temperature (‘warm’ plasmas). Analysis of reasons for this trend presented in this paper indicates that transitional warm plasma discharge systems are optimal for large-scale fuel processing. This analysis also reveals one specific feature of warm discharges that was not discussed earlier: warm discharge-based plasma-chemical systems are very sensitive to gas temperature and chemical reactions. When temperature reaches the level that is high enough to support chemical reactions in a particular system (ignition temperature), chemical reactions produce high concentration of excited molecules, and these molecules form a basis for stepwise ionization. This results in a significant drop in the energy necessary to support electric discharge in the system for two reasons. First, stepwise ionization that requires relatively low electron energy overcomes direct ionization that is typical for low-temperature non-equilibrium plasmas and requires much higher ionization energy. Second, high temperature of surrounding gas reduces heat losses from the discharge channel, while a significant portion of the discharge energy in warm plasma systems should be spent to compensate these losses. Thus, an intensive chemical reaction, e.g. combustion, supports the existence of a warm electric discharge.
Electric-field-induced exciton-linewidth broadening in short-period GaAs/GaxAl1−xAs superlattices (1993)

We have investigated the Wannier-Stark effect in GaAs/${\mathrm{Ga}}_{\mathit{x}}$${\mathrm{Al}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$As superlattices under electric fields by photocurrent spectroscopy measurements in the range of temperatures 10--300 K. The linewidth of the 0h Stark-ladder exciton was found to increase significantly along with an increase in peak intensity when the electric field increases. We present a mechanism based on an enhanced interface roughness scattering of electronic states due to Wannier-Stark localization in order to explain this increased broadening with electric field. This electric-field-related scattering mechanism will weaken the negative differential conductance effects in superlattices predicted by Esaki and Tsu.
Plastid Genome Instability Leads to Reactive Oxygen Species Production and Plastid-to-Nucleus Retrograde Signaling in Arabidopsis (2013)

The plastid genome is highly conserved among plant species, suggesting that alterations of its structure would have dramatic impacts on plant fitness. Nevertheless, little is known about the direct consequences of plastid genome instability. Recently, it was reported that the plastid Whirly proteins WHY1 and WHY3 and a specialized type-I polymerase, POLIB, act as safeguards against plastid genome instability in Arabidopsis (Arabidopsis thaliana). In this study, we use ciprofloxacin, an organelle double-strand break-inducing agent, and the why1why3polIb-1 variegated mutant to evaluate the impact of generalized plastid DNA instability. First, we show that in why1why3polIb-1 and ciprofloxacin-treated plants, plastid genome instability is associated with increased reactive oxygen species production. Then, using different light regimens, we show that the elevated reactive oxygen species production correlates with the appearance of a yellow-variegated phenotype in the why1why3polIb-1 population. This redox imbalance also correlates to modifications of nuclear gene expression patterns, which in turn leads to acclimation to high light. Taken together, these results indicate that plastid genome instability induces an oxidative burst that favors, through nuclear genetic reprogramming, adaptation to subsequent oxidative stresses.
Publisher’s Note: Fluctuation Mediated Interaction and Phase Separation of Nanoparticles in a Liquid Crystal Solvent [Phys. Rev. Lett.PRLTAO0031-900791, 085704 (2003)] (2003)

Received 16 September 2003DOI:https://doi.org/10.1103/PhysRevLett.91.139901©2003 American Physical Society
Prophylactic Urokinase in the Management of Long-Term Venous Access Devices in Children: A Children's Oncology Group Study (2004)

Urokinase administration every 2 weeks significantly affects the rate of occlusive events in ports and tunneled catheters and of infectious events in external catheters compared with heparin administration.
Protein Corona Composition and Dynamics on Carbon Nanotubes in Blood Plasma and Cerebrospinal Fluid (2020)

Abstract When a nanoparticle enters a biological environment, the surface is rapidly coated with proteins to form a “protein corona”. Presence of the protein corona surrounding the nanoparticle has significant implications for applying nanotechnologies within biological systems, affecting outcomes such as biodistribution and toxicity. Herein, we measure protein corona formation on single-stranded DNA wrapped single-walled carbon nanotubes (ssDNA-SWCNTs), a high-aspect ratio nanoparticle ideal for sensing and delivery applications, and polystyrene nanoparticles, a model nanoparticle system. The protein corona of each nanoparticle is studied in human blood plasma and cerebrospinal fluid. We characterize corona composition by proteomic mass spectrometry to determine abundant and differentially enriched vs. depleted corona proteins. High-binding corona proteins on ssDNA-SWCNTs include proteins involved in lipid binding and transport (clusterin and apolipoprotein A-I), complement activation (complement C3), and blood coagulation (fibrinogen). Of note, albumin is the most common blood protein (55% w/v), yet exhibits low-binding affinity towards ssDNA-SWCNTs, displaying 1300-fold lower bound concentration relative to native plasma. We investigate the role of electrostatic and entropic interactions driving selective protein corona formation, and find that hydrophobic interactions drive inner corona formation, while shielding of electrostatic interactions allows for outer corona formation. Lastly, we study real-time binding of proteins on ssDNA-SWCNTs and find relative agreement between proteins that are enriched and bind strongly, such as fibrinogen, and proteins that are depleted and bind marginally, such as albumin. Interestingly, certain proteins express contrary behavior in single-protein experiments than within the whole biofluid, highlighting the importance of cooperative mechanisms driving selective corona adsorption on the SWCNT surface. Knowledge of the protein corona composition, dynamics, and structure informs translation of engineered nanoparticles from in vitro design to effective in vivo application.
The Hemopump-a new cardiac prothesis device (1990)

A unique cardiac prothesis device is currently undergoing clinical trials. Called the Hemopump, this device is a radical new design of a temporary left ventricular assist blood pump. It uses a miniature (7 mm diameter) axial flow pump placed transvalvular across the aortic valve which pumps blood from the left ventricle to the aorta. Mechanical power from an external motor is transmitted percutaneously to the pump by a flexible cable contained within a catheter-like sheath. This arrangement allows the pump to be placed through a femoral artery cutdown without requiring major surgery. Development of the Hemopump concept presented significant challenges in pump hydraulic design, bearing, and seal design, as well as materials selection and miniature parts fabrication. Clinical trial results thus far indicate these challenges have been well met and that the Hemopump has the potential to become a widely used safe and effective clinical device.
Eigenvectors of a Raman Medium (2000)

We show the existence of discrete sets of Raman sidebands which self-consistently establish a Raman coherence and propagate without change in amplitude and relative phase. Equivalently, there exist periodic femtosecond-time-scale, temporal pulse shapes which propagate without change in shape.
Binding of ethidium to DNA measured using a 2D diffusion‐modulated gradient COSY NMR experiment (2000)

The binding of ethidium bromide to a DNA hairpin (dU(5)-hairpin) was investigated using a novel 2D diffusion-modulated gradient correlation spectroscopy (DMG-COSY) experiment to evaluate the applicability of this technique for studying the binding of drugs to DNA. The DMG-COSY experiment includes a preparation period during which coherent magnetization is attenuated due to molecular self-diffusion. Magnetization then evolves due to scalar coupling during an evolution delay, and is detected using gradient pulses for coherence selection. The time-domain data are processed in an analogous manner as for gradient-selected COSY experiments. The diffusion coefficient for uridine in DMSO solution was determined from the H5-H6 crosspeak intensities for a series of 2D DMG-COSY experiments that differed in the magnitude of the gradient pulses applied during the preparation period of the DMG-COSY experiment. The diffusion coefficient for uridine calculated from the DMG-COSY experiments was identical (within experimental error) to that determined from 1D diffusion experiments (5.24x10(-6) cm(2)/s at 26 degrees C). The diffusion coefficients for ethidium bromide and for the dU(5)-hairpin were first measured separately using the DMG-COSY experiment, and then measured in the putative complex. The diffusion coefficient for free ethidium bromide (4.15x10(-6) cm(2)/s at 26 degrees C) was considerably larger than for the dU(5)-hairpin (1. 60x10(-6) cm(2)/s at 26 degrees C), as expected for the smaller molecule. The diffusion coefficient for ethidium was markedly decreased upon addition of the dU(5)-hairpin, consistent with complex formation (1.22x10(-6) cm(2)/s at 26 degrees C). Complex formation of 1:1 stoichiometry between ethidium and the stem of the dU(5)-hairpin was verified independently by fluorescence spectroscopy. These results demonstrate the utility of the DMG-COSY experiment for investigating the binding of drugs to DNA in aqueous solution.
Clinical outcome measures in SPMS trials: An analysis of the IMPACT and ASCEND original trial data sets (2019)

Our analyses inform the selection of primary outcome measures as well as inclusion criteria for clinical trials in SPMS.
The ISO/LWS spectrum of the Egg nebula, AFGL 2688 (1996)

We present an ISO Long Wavelength Spectrometer (LWS) grating spectrum of the carbon-rich proto-planetary nebula AFGL 2688 between 43 and 194μm. The far-infrared spectrum of AFGL 2688 is dominated by strong rotational transitions of CO which are detected from J=14-13 up to J=23-22. The atomic fine structure lines [O I] and [C II] are not detected. This is consistent with the cool central star of AFGL 2688 not having yet photodissociated the molecular gas ejected during the AGB phase. The far-infrared CO emission in AFGL 2688 appears to originate in shocked dense gas at a temperature of ~400K.
Infrared studies on the conformation of synthetic alamethicin fragments and model peptides containing .alpha.-aminoisobutyric acid (1980)

Infrared studies of synthetic alamethicin fragments and model peptides containing alpha-aminoisobutyric acid (Aib) have been carried out in solution. Tripeptides and larger fragments exhibit a strong tendency to form beta turns, stabilized by 4 leads to 1 10-atom hydrogen bonds. Dipeptides show less well-defined structures, though C5 and C7 conformations are detectable. Conformational restrictions imposed by Aib residues result in these peptides populating a limited range of states. Integrated intensities of the hydrogen-bonded N-H stretching band can be used to quantitate the number of intramolecular hydrogen bonds. Predictions made from infrared data are in excellent agreement with nuclear magnetic resonance and X-ray diffraction studies. Assignments of the urethane and tertiary amide carbonyl groups in the free state have been made in model peptides. Shifts to lower frequency on hydrogen bonding are observed for the carbonyl groups. The 1--6 segment of alamethicin is shown to adopt a 3(10) helical structure stabilized by four intramolecular hydrogen bonds. The fragments Boc-Leu-Aib-Pro-Val-Aib-OMe (12--16) and Boc-Gly-Leu-Aig-Pro-Val-Aib-OMe (11--16) possess structures involving 4 leads to 1 and 5 leads to 1 hydrogen bonds. Supporting evidence for these structures is obtained from proton nuclear magnetic resonance studies.
A Peristaltic Meso-Scale Mixer (2000)

Abstract We consider incompressible, viscous fluid confined in a rectangular cavity. One or more of the cavity walls are made of a thin membrane. Traveling waves are transmitted in a cavity’s wall and induce peristaltic motion. The induced velocity profiles are determined analytically for small amplitude waves (ε) and numerically for waves of arbitrary amplitude. The analysis consists of a perturbation expansion in terms of the wave amplitude (ε). Solutions for large amplitude oscillations are obtained through the use of a finite element code that employs a moving grid. The effect of the peristaltic motion on the stretching and deformation of material lines is discussed. The study is relevant to the analysis and design of micro and meso-scale mixers and stirrers.
Building a standards-based and collaborative e-prescribing tool: MyRxPad (2011)

MyRxPad (rxp.nlm.nih.gov) is a prototype application intended to enable a practitioner-patient collaborative approach towards e-prescribing: patients play an active role by maintaining up-to-date and accurate medication lists. Prescribers make well-informed and safe prescribing decisions based on personal medication records contributed by patients. MyRxPad is thus the vehicle for collaborations with patients using MyMedicationList (MML). Integration with personal medication records in the context of e-prescribing is thus enabled. We present our experience in applying RxNorm in an e-prescribing setting: using standard names and codes to capture prescribed medication as well as extracting information from RxNorm to support medication-related clinical decision.
Issues and Challenges in Using Existing Data and Tools for Performance Measurement (2005)

Many transportation agencies seek to improve business processes by expanding the use of performance measurement without making significant additional investments in data collection and analysis tools. The purpose of this resource paper is to highlight technical issues associated with the use of existing data and tools for performance measurement in a transportation agency. Common challenges are identified and recommendations are included so that agency staff can anticipate and address the challenges in a proactive manner.
Contemporary pacemaker and ICD lead management: techniques for lead extraction (2012)

With the increasing utilization of cardiac implantable electronic devices, the ability to extract leads using the transvenous approach has become important. Devices that are infected and leads that pose a risk to the patient by causing damage to cardiovascular structures, interference with device function or life-threatening arrhythmias should be removed. While the majority of extractions are performed through the vein of implantation, other approaches, such as the femoral approach, are required in some circumstances. Simple traction may be successful in removing the lead in relatively new (<1 year) implants. Older devices invariably require devices such as locking stylets and simple or powered sheaths. With current techniques, complete lead extraction can be achieved in >90% of cases with a major complication rate of <2% and mortality rate of <1%. Transvenous lead extraction should be performed only by experienced operators with the resources to address life-threatening complications.
GTLS algorithms in the frequency domain system identification using noise information out of a finite number of repeated independent realizations (1997)

This paper gives an overview of the stochastic properties of frequency domain total least squares estimators for rational transfer function models of linear time-invariant systems. The generalized total least squares (GTLS) and the bootstrapped total least squares (BTLS) methods require the exact knowledge of the noise covariance matrix. The paper studies the asymptotic behavior for the GTLS and the BTLS estimator when the covariance matrix is replaced by the sample covariance matrix obtained from a small number of independent repeated observations. The GTLS estimates remain consistent and do not loose any asymptotic efficiency when replacing the exact covariance matrix with the sample covariance matrix. The BTLS estimator, whose efficiency approaches the maximum likelihood efficiency, needs to be adapted slightly to produce consistent estimates.