gebhart/patrepeval huggingface dataset:
An Efficient Process for Synthesis of 3-(R)-3-(2,3-Dihydrobenzofuran-5-yl)- 1,2,3,4-tetrahydropyrrolo[3,4-b]quinolin-9-one (2005)

3-(R)-3-(2,3-Dihydrobenzofuran-5-yl)-1,2,3,4-tetrahydropyrrolo[3,4-b]quinolin-9-one (1) is a key intermediate in the synthesis of pyrroloquinolone analogues, a series of highly potent and selective phosphodiesterase 5 (PDE5) inhibitors. Racemic 1-(2,3-dihydrobenzofuran-5-yl)-2,3,4,9-tetrahydro-1H-β-carboline (6, Scheme 2) was prepared by Pictet−Spenger condensation in 84% isolated yield with >97% chemical purity. The desired intermediate, 1-(R)-1-(2,3-dihydrobenzofuran-5-yl)-2,3,4,9-tetrahydro-1H-β-carboline N-acetyl-d-leucine salt (8), was obtained in 35% isolated yield with high chiral purity (≥ 97% ee) from the chemical resolution of 6 with N-acetyl-d-leucine (7). A racemization step was developed for recycling enriched 1-(S)-β-carboline 9 freebase (8/9, 25 ± 3%/75 ± 3%) to a near racemic mixture (8/9, 47 ± 1%/53 ± 1%). Furthermore, the resolving reagent 7 was recovered in >76% yield, which, together with the recycled racemic mixture (8/9, 47 ± 1%/53 ± 1%), afforded 35% more salt 8 after two recycles (≥97.0% ee). The salt 8 was converted to 1-(R)-1-(2,3-dihydrobenzofuran-5-yl)-2-benzyl-2,3,4,9-tetrahydro-1H-β-carboline (10) in excellent yield (94%). A modified Winterfeldt oxidation of compound 10 using Aliquat 175 as a phase transfer catalyst produced 3-(R)-2-benzyl-3-(2,3-dihydrobenzofuran-5-yl)-1,2,3,4-tetrahydropyrrolo[3,4-b]quinolin-9-one (12) in moderate 42% yield. Hydrogenolysis of compound 12 gave the desired compound 1 in quantitative yield with retention of chiral purity (≥97.0% ee). This efficient, reproducible, economical, and nonchromatography scale-up process could be used to make multikilogram quantities of compound 1.
Genetically Engineered Microorganisms for Biodegradation of Recalcitrant Compounds (2002)

Abstract The mineralization of organic molecules by microbes is essential for the carbone cycle to operate. The massive mobilization of compounds stored in natural resources or the introduction of xenobiotics into the biosphere produces unidirectional fluxes that result in the persistence of many chemicals in the biosphere, where they are a source of pollution. Molecular biology offers the tools to optimize the biodegradative capacities of microorganisms, accelerate the evolution of new metabolic activities, and construct totally new pathways through the assemblage of catabolic segments from different microbes.
Multiscale Progressive Failure Analysis of 3D Woven Composites (2022)

Application of three-dimensional (3D) woven composites is growing as an alternative to the use of ply-based composite materials. However, the design, analysis, modeling, and optimization of these materials is more challenging due to their complex and inherently multiscale geometries. Herein, a multiscale modeling procedure, based on efficient, semi-analytical micromechanical theories rather than the traditional finite element approach, is presented and applied to a 3D woven carbon-epoxy composite. A crack-band progressive damage model was employed for the matrix constituent to capture the globally observed nonlinear response. Realistic microstructural dimensions and tow-fiber volume fractions were determined from detailed X-ray computed tomography (CT) and scanning electron microscopy data. Pre-existing binder-tow disbonds and weft-tow waviness, observed in X-ray CT scans of the composite, were also included in the model. The results were compared with experimental data for the in-plane tensile and shear behavior of the composite. The tensile predictions exhibited good correlations with the test data. While the model was able to capture the less brittle nature of the in-plane shear response, quantitative measures were underpredicted to some degree.
BING-2: a layered tin–oxalate potassium fluoride, KSn(C2O4)F (2001)

The title compound, KSn(C2O4)F, is a two-dimensional material related to our previously reported three-dimensional framework, Na4Sn4(C2O4)3F6. Both are alkali-metal tin–oxalate materials, but here the compound is layered and has potassium in place of sodium. The material was synthesized solvothermally at 423 K and crystallized in the monoclinic space group P21/c. The structure consists of potassium fluoride layers in the bc plane, which are sandwiched on both sides by tin–oxalate chains that extend along the c axis.
Si–InAs heterojunction Esaki tunnel diodes with high current densities (2010)

Si–InAs heterojunction p-n diodes were fabricated by growing InAs nanowires in oxide mask openings on silicon substrates. At substrate doping concentrations of 1×1016 and 1×1019 cm−3, conventional diode characteristics were obtained, from which a valence band offset between Si and InAs of 130 meV was extracted. For a substrate doping of 4×1019 cm−3, heterojunction tunnel diode characteristics were obtained showing current densities in the range of 50 kA/cm2 at 0.5 V reverse bias. In addition, in situ doping of the InAs wires was performed using disilane to further boost the tunnel currents up to 100 kA/cm2 at 0.5 V reverse bias for the highest doping ratios.
Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species (2009)

The extent by which different cellular components generate phenotypic diversity is an ongoing debate in evolutionary biology that is yet to be addressed by quantitative comparative studies. We conducted an in vivo mass-spectrometry study of the phosphoproteomes of three yeast species (Saccharomyces cerevisiae, Candida albicans, and Schizosaccharomyces pombe) in order to quantify the evolutionary rate of change of phosphorylation. We estimate that kinase-substrate interactions change, at most, two orders of magnitude more slowly than transcription factor (TF)-promoter interactions. Our computational analysis linking kinases to putative substrates recapitulates known phosphoregulation events and provides putative evolutionary histories for the kinase regulation of protein complexes across 11 yeast species. To validate these trends, we used the E-MAP approach to analyze over 2,000 quantitative genetic interactions in S. cerevisiae and Sc. pombe, which demonstrated that protein kinases, and to a greater extent TFs, show lower than average conservation of genetic interactions. We propose therefore that protein kinases are an important source of phenotypic diversity.
Functional Metamaterials for Wireless Phase Conjugation (2013)

Functional metamaterials provide useful properties for the design of electromagnetic devices. In this work we demonstrate that functions including high nonlinearity and amplification can be included in metamaterials to realize time reversal imaging.
A constant-Q spectral transformation with improved frequency response (2004)

This paper introduces a new transform intended for audio processing. The proposed transform exhibits two interesting features in the frequency domain, namely: a constant-Q characteristic and a steep response for each output channel. Constant-Q implies that the spectral description of the transformed signal is performed along a log-like scale, as opposed to the linear scale of standard transforms, such as the discrete Fourier transform (DFT). The consequent variable resolution makes the new transform especially suited for the analysis of musical audio signals. The improved frequency response, as compared also to the DFT, is achieved by its implementation as a bank of very selective filters based on the frequency-response masking (FRM) approach. Such selectivity results in higher isolation between adjacent channels of the overall transform. Application of the new transform to the analysis of musical signals is illustrated through a computer experiment.
New Metabolites with Nematicidal and Antimicrobial Activities from the Ascomycete Lachnum papyraceum(Karst.) Karsts. VI. Structure Determination of Non-halogenated Metabolites Structurally Related to Mycorrhizin A. (1995)

The structure determination of four new biologically active non-halogenated metabolites isolated from submerged cultures of the ascomycete Lachnum papyraceum is described. The compounds are structurally related to the antibiotic mycorrhizin A: (l'Z)-Dechloromycorrhizin A (12), a stereoisomer of dechloromycorrhizin A (5) previously isolated from the same fungus, as well as papyracon A (13), papyracon B (14) and papyracon C (15) containing an exocyclic double bond. The amounts of the latter three increased significantly when CaBr2 was added to the culture medium. The structures were determined by spectroscopic methods.
DNA and recombinant adenovirus serotype 35 and 5 preventive HIV-1 vaccines with Env A inserts elicit cross-clade binding and V1V2 antibodies (2012)

High frequency responses were elicited against clade A (T1 95.8%, T2 100%, T3 97.4%, T4 100%), clade B (T1 95.8%, T2 95.0%, T3 92.1%, T4 96.3%), clade C (T1 92%, T2 76%, T3 76%, T4 78%), and Con S (T1-4 100%). There were no significant between-group differences in response frequency or magnitude. The majority also had responses to V1V2 clade A (T1 100%, T2 87.8%, T3 83.8%, T4 85.2%) and clade B (T1 58.3%, T2 65.9%, T3 54.1%, T4 51.9%). The mean fluorescent intensity was higher in T2 vs T1 (p=0.005) for clade A V1V2. No significant differences were observed between other groups.
Dependence of Regioregular Poly(3-hexylthiophene) Film Morphology and Field-Effect Mobility on Molecular Weight (2005)

Morphological characterization has been used to explain the previously observed strong correlation between charge carrier mobility measured with thin-film transistors and the number-average molecular weight (MW) of the conjugated polymer regioregular poly(3-hexylthiophene). Atomic force microscopy and X-ray diffraction show that the low-mobility, low-MW films have a highly ordered structure composed of nanorods and the high-mobility, high-MW films have a less ordered, isotropic nodule structure. Modifying the morphology for a constant MW by changing the casting conditions or annealing the samples strongly affects the charge transport and morphology in the low-mobility, low-MW films, but has little effect on the high-MW films. In-plane grazing incidence X-ray scattering shows the in-plane π-stacking peak increases when the mobility increases for a constant MW. When the MW is changed, this correlation breaks down, confirming that in-plane π-stacking does not cause the mobility−MW relationship. We believe a combination of disordered domain boundaries and inherent effects of chain length on the electronic structure cause the mobility−MW relationship.
In vitro and in vivo evaluation of cerium oxide nanoparticles in respiratory syncytial virus infection (2022)

Respiratory syncytial virus (RSV) is the most common cause of viral bronchiolitis among children worldwide, yet there is no vaccine for RSV disease. This study investigates the potential of cube and sphere-shaped cerium oxide nanoparticles (CNP) to modulate reactive oxygen (ROS) and nitrogen (RNS) species and immune cell phenotypes in the presence of RSV infection <i>in vitro</i> and <i>in vivo</i>. Cube and sphere-shaped CNP were synthesized by hydrothermal and ultrasonication methods, respectively. Physico-chemical characterization confirmed the shape of sphere and cube CNP and effect of various parameters on their particle size distribution and zeta potential. <i>In vitro</i> results revealed that sphere and cube CNP differentially modulated ROS and RNS levels in J774 macrophages. Specifically, cube CNP significantly reduced RSV-induced ROS levels without affecting RNS levels while sphere CNP increased RSV-induced RNS levels with minimal effect on ROS levels. Cube CNP drove an M1 phenotype in RSV-infected macrophages <i>in vitro</i> by increasing macrophage surface expression of CD80 and CD86 with a concomitant increase in TNFα and IL-12p70, while simultaneously decreasing M2 CD206 expression. Intranasal administration of sphere and cube-CNP were well-tolerated with no observed toxicity in BALB/c mice. Notably, cube CNP preferentially accumulated in murine alveolar macrophages and induced their activation, avoiding enhanced uptake and activation of other inflammatory cells such as neutrophils, which are associated with RSV-mediated inflammation. In conclusion, we report that sphere and cube CNP modulate macrophage polarization and innate cellular responses during RSV infection.
Evaluation of Platelet Function by PFA-100TM (1994)

Journal Article Evaluation of Platelet Function by PFA-100TM Get access Sourav Kundu, Sourav Kundu Baxter Diagnostics, 10555 W. Flagler St., Miami, FL 33174 Search for other works by this author on: Oxford Academic Google Scholar Reynaldo Sio, Reynaldo Sio Baxter Diagnostics, 10555 W. Flagler St., Miami, FL 33174 Search for other works by this author on: Oxford Academic Google Scholar Angela Mitu, Angela Mitu Baxter Diagnostics, 10555 W. Flagler St., Miami, FL 33174 Search for other works by this author on: Oxford Academic Google Scholar Roy Ostgaard Roy Ostgaard Baxter Diagnostics, 10555 W. Flagler St., Miami, FL 33174 Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 40, Issue 9, 1 September 1994, Pages 1827–1828, https://doi.org/10.1093/clinchem/40.9.1827 Published: 01 September 1994
Parkinsonism and vigilance: alteration in neural oscillatory activity and phase-amplitude coupling in the basal ganglia and motor cortex (2017)

Oscillatory neural activity in different frequency bands and phase-amplitude coupling (PAC) are hypothesized to be biomarkers of Parkinson's disease (PD) that could explain dysfunction in the motor circuit and be used for closed-loop deep brain stimulation (DBS). How these putative biomarkers change from the normal to the parkinsonian state across nodes in the motor circuit and within the same subject, however, remains unknown. In this study, we characterized how parkinsonism and vigilance altered oscillatory activity and PAC within the primary motor cortex (M1), subthalamic nucleus (STN), and globus pallidus (GP) in two nonhuman primates. Static and dynamic analyses of local field potential (LFP) recordings indicate that <i>1</i>) after induction of parkinsonism using the neurotoxin MPTP, low-frequency power (8-30 Hz) increased in the STN and GP in both subjects, but increased in M1 in only one subject; <i>2</i>) high-frequency power (~330 Hz) was present in the STN in both normal subjects but absent in the parkinsonian condition; <i>3</i>) elevated PAC measurements emerged in the parkinsonian condition in both animals, but in different sites in each animal (M1 in one subject and GPe in the other); and <i>4</i>) the state of vigilance significantly impacted how oscillatory activity and PAC were expressed in the motor circuit. These results support the hypothesis that changes in low- and high-frequency oscillatory activity and PAC are features of parkinsonian pathophysiology and provide evidence that closed-loop DBS systems based on these biomarkers may require subject-specific configurations as well as adaptation to changes in vigilance.<b>NEW & NOTEWORTHY</b> Chronically implanted electrodes were used to record neural activity across multiple nodes in the basal ganglia-thalamocortical circuit simultaneously in a nonhuman primate model of Parkinson's disease, enabling within-subject comparisons of electrophysiological biomarkers between normal and parkinsonian conditions and different vigilance states. This study improves our understanding of the role of oscillatory activity and phase-amplitude coupling in the pathophysiology of Parkinson's disease and supports the development of more effective DBS therapies based on pathophysiological biomarkers.
Continuous Monitoring of IgG using Immobilized Fluorescent Reporters (2022)

In the manufacture of therapeutic monoclonal antibodies (mAbs), the clarified cell culture fluid is typically loaded onto an initial protein A affinity capture column. Imperfect mass transfer and loading to maximum capacity can risk antibody breakthrough and loss of valuable product, but conservative underloading wastes expensive protein A resin. In addition, the effects of column fouling and ligand degradation require the frequent optimization of IgG loading to avoid wastage. Therefore, continuous real-time monitoring of IgG flowthrough is of great interest. We previously developed a fluorescence-based monitoring technology that allows mix-and-read mAb detection in cell culture fluid. Here we report the use of reporters immobilized on CNBr-activated Sepharose 4B resin for continuous detection of IgG in column breakthrough. The column effluent is continuously contacted with immobilized fluorescein-labeled Fc-binding ligands to produce an immediately detectable change in fluorescence intensity. The technology allows rapid and reliable monitoring of IgG in a flowing stream of clarified cell culture fluid emerging from a Protein A column, without prior sample preparation. We observed a significant change in fluorescence intensity at 0.5 g/L human IgG, sufficient to detect a 5% breakthrough of a 10 g/L load, within 2 minutes at a flow rate of 0.5 mL/min.
Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives (2004)

This article shows that any single-step or stepwise multiple testing procedure (asymptotically) controlling the family-wise error rate (FWER) can be augmented into procedures that (asymptotically) control tail probabilities for the number of false positives and the proportion of false positives among the rejected hypotheses. Specifically, given any procedure that (asymptotically) controls the FWER at level alpha, we propose simple augmentation procedures that provide (asymptotic) level-alpha control of: (i) the generalized family-wise error rate, i.e., the tail probability, gFWER(k), that the number of Type I errors exceeds a user-supplied integer k, and (ii) the tail probability, TPPFP(q), that the proportion of Type I errors among the rejected hypotheses exceeds a user-supplied value 0<q<1. Existing approaches for control of the proportion of false positives typically rely on the assumption that the test statistics are independent, while our proposed augmentation procedures control the gFWER and TPPFP for general data generating distributions, with arbitrary dependence structures among variables. Applying the augmentation methods to step-down multiple testing procedures that control the FWER asymptotically exactly at level alpha (van der Laan et al., 2004), yields procedures that also provide exact asymptotic control of the gFWER and TPPFP at level alpha. The adjusted p-values for the gFWER and TPPFP-controlling augmentation procedures are shown to be simple functions of the adjusted p-values for the original FWER-controlling procedure. Finally, two simple conservative procedures are proposed for controlling the false discovery rate.
Unsupervised cleansing of noisy text (2010)

In this paper we look at the problem of cleansing noisy text using a statistical machine translation model. Noisy text is produced in informal communications such as Short Message Service (SMS), Twitter and chat. A typical Statistical Machine Translation system is trained on parallel text comprising noisy and clean sentences. In this paper we propose an unsupervised method for the translation of noisy text to clean text. Our method has two steps. For a given noisy sentence, a weighted list of possible clean tokens for each noisy token are obtained. The clean sentence is then obtained by maximizing the product of the weighted lists and the language model scores.
Dynamic Electron Paramagnetic Resonance Imaging: Modern Technique for Biodistribution and Pharmacokinetic Imaging (2020)

The imaging of the biodistribution and pharmacokinetics is critical in understanding the complexity of drug delivery mechanisms, the status of the disease, and the monitoring of the treatment progress. The imaging techniques, such as magnetic resonance imaging, computed tomography, and positron emission tomography, are suitable for clinical applications. However, with regards to the biodistribution and pharmacokinetics, their availability is often limited due to the requirements of ionizing radiation or high magnetic fields, low spatial and temporal resolution (applicable for animals), and high maintenance costs. Electron paramagnetic resonance (EPR) imaging is a technique that allows for the minimal invasive mapping of unique parameters, such as the oxygen concentration, the redox state, the thiol concentration, or the pH level, in vivo. In this work, a high temporal resolution 3D EPR imaging technique was used for assessing the trityl spin probe pharmacokinetics in mice. The results demonstrate the preliminary outcomes in the application of EPR imaging for the comparison of the trityl spin probe pharmacokinetics between that of a healthy mouse and a tumor-bearing mouse. This study will stimulate further investigation into the use of imaging strategies, such as EPR imaging, to analyze pharmacokinetics.
HMGB1 in Systemic Lupus Erythematosus (2020)

The high-mobility group box 1 (HMGB1) has been shown to exert proinflammatory effects on many cells of the innate immune system. Originally identified as a nuclear protein, HMGB1 has been found to play an important role in mediating inflammation when released from apoptotic or necrotic cells as a damage-associated molecular pattern (DAMP). Systemic lupus erythematosus (SLE) is a disease of non-resolving inflammation, characterized by the presence of autoantibodies and systemic inflammation involving multiple organ systems. SLE patients have impaired clearance of apoptotic debris, which releases HMGB1 and other DAMPs extracellularly. HMGB1 activity is implicated in multiple disease phenotypes in SLE, including lupus nephritis and neuropsychiatric lupus. Elucidating the various properties of HMGB1 in SLE provides a better understanding of the disease and opens up new opportunities for designing potential therapeutics.
Attempts to programme ovulation with exogenous oestrogens and LH-RH analogue. (1975)

An attempt was made to programme ovulation in women on a predetermined day of the menstrual cycle by treatment used to induce ovulation in anovulatory sterility. At laparotomy for elective sterilization the ovaries were observed to assess the occurrence of ruptured follicles and ovulation. Histological analysis of ovaries and endometrium was performed, and ova were recovered from some women. Several regimens were tested but ovulation seldom occurred as planned. Clomiphene citrate, human chorionic gonadotrophin (HCG), synthetic luteinizing hormone releasing hormone (LH-RH), and ethinyloestradiol were ineffective. Human menopausal gonadotrophin followed by HCG was more effective, but multiple ovulations occurred. When one single injection of a potent long-acting LH-RH analogue was given on day 13 of the cycle to 10 women pretreated with ethinyloestradiol signs of recent ovulation were observed on day 15 in seven and on day 16 in two.
Statistical approach to channel state reporting for URLLC (2022)

For 5G New Radio services with the requirement of high reliability and low latency, the HARQ loop can only afford one or a couple of retransmissions within the latency bound, or none at all, depending on the system configuration. In response to such stringent demand on the link adaptation algorithm, improved algorithms for predicting or estimating downlink channel conditions are desired. This paper describes the problem and proposes a solution where channel state statistics are reported by user equipment to aid the base station for more accurate downlink scheduling. Simulation results are provided to demonstrate the benefit of the new approach.