gebhart/patrepeval huggingface dataset:
ChemInform Abstract: SYNTHETIC STUDIES ON ECHINULIN AND RELATED NATURAL PRODUCTS. IV. ISOLATION, STRUCTURE AND SYNTHESIS OF FLAVOGLAUCIN‐AUROGLAUCIN TYPE NATURAL PRODUCTS ISOLATED FROM ASPERGILLUS AMSTELODAMI (1977)

Abstract Isoliert werden die Verbindungen (I)‐(V), von denen (III)‐(V) entsprechend dem Formelschema dargestellt werden.
NCL Inhibition Exerts Antineoplastic Effects against Prostate Cancer Cells by Modulating Oncogenic MicroRNAs (2020)

Prostate cancer (PCa) is the most frequently diagnosed cancer in men and second most common cause of cancer-related deaths in the United States. Androgen deprivation therapy (ADT) is only temporarily effective for advanced-stage PCa, as the disease inevitably progresses to castration-resistant prostate cancer (CRPC). The protein nucleolin (NCL) is overexpressed in several types of human tumors where it is also mislocalized to the cell surface. We previously reported the identification of a single-chain fragment variable (scFv) immuno-agent that is able to bind NCL on the surface of breast cancer cells and inhibit proliferation both in vitro and in vivo. In the present study, we evaluated whether NCL could be a valid therapeutic target for PCa, utilizing DU145, PC3 (CRPC), and LNCaP (androgen-sensitive) cell lines. First, we interrogated the publicly available databases and noted that higher NCL mRNA levels are associated with higher Gleason Scores as well as with recurrent and metastatic tumors. Then, using our anti-NCL scFv, we demonstrated that NCL is expressed on the surface of all three tested cell lines and that NCL inhibition results in reduced proliferation and migration. We also measured the inhibitory effect of NCL targeting on the biogenesis of oncogenic microRNAs such as miR-21, -221 and -222, which was cell context dependent. Taken together, our data provide evidence that NCL targeting inhibits the key hallmarks of malignancy in PCa cells and may provide a novel therapeutic option for patients with advanced-stage PCa.
Origins and Diversity of the Aging Reaction in Phosphonate Adducts of Serine Hydrolase Enzymes: What Characteristics of the Active Site do They Probe? (1995)

Molecular mechanics and dynamics combined with semiempirical calculations were carried out for purposes of comparison of the active site characteristics of AChE, trypsin, and chymotrypsin as probed by their diastereomeric adducts with 2-(3,3-dimethylbutyl) methylphosphonofluoridate (soman), methylphosphonate monoester anions, and tetravalent carbonyl intermediates of the reactions of the natural substrates in each case. Glu199 is a key residue in the electrostatic catalytic mechanism of AChE, in removal of the leaving group, and possibly by acting as an alternate general base catalyst. "Pushing" of an alkoxy ligand by Glu199 and the numerous small van der Waals interactions promote dealkylation in phosphonate adducts of AChE much more effectively than any other enzyme. A high concentration of negative charge created by the phosphonate ester monoanion and Glu199 adjacent to it fully accounts for the resistance to the attack of even the strongest nucleophile applied for enzyme reactivation. Stabilization of the developing negative charge on the phosphonates in the soman-inhibited PSCS adducts of serine hydrolases is by electrophilic residues in the oxyanion hole (AChE) and the protonated catalytic His. PR diastereomers of soman-inhibited AChE can be accommodated in an orientation in which the oxyanion hole interactions are lost and for which the stabilizing interactions are 17-26 kcal/mol smaller than in the PS diastereomer. The dealkylation reaction is almost equally likely in all diastereomers of soman-inhibited AChE. The stabilizing interaction energies are approximately 4 kcal/mol greater in the PR than in the PS adducts of the soman-inhibited serine proteases. There is 0.60 unit greater partial negative charge on the phosphonyl fragment in the anion of phosphonate monoesters of Ser than at the oxygens of tetravalent carbonyl transients resulting in approximately 12-22 kcal/mol greater stabilization of the former than the latter.
Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, Diaphorina citri, reveals novel features (2021)

Hox genes and their cofactors are essential developmental genes that specify regional identity in animals, including insects. A particularly interesting feature of Hox genes is their conserved arrangement in clusters in the same order in which they specify identity along the anterior-posterior axis. Among insects, breaks in the cluster have been reported in a few species, but these seem to be the exception rather than the rule. We have annotated the ten Hox genes of the Asian citrus psyllid, Diaphorina citri, and determined that there is a split in its Hox cluster between the Deformed and Sex combs reduced genes. This is the first time a break at this position has been observed in an insect Hox cluster. We have also annotated the D. citri orthologs of the Hox cofactor genes homothorax, PKNOX and extradenticle. Interestingly, we found an additional copy of extradenticle in D. citri that appears to be a retrogene. Expression data and sequence conservation suggest that the extradenticle retrogene may have retained the original extradenticle function and allowed the parental extradenticle gene to diverge.
Architecture designs of a large-capacity abacus ATM switch (2002)

The abacus switch we proposed has a size limitation due to excessive routing delay in the switch fabric. Here, we suggest three different approaches to increase the capacity of the abacus switch to, for instance, 1 Tb/s with existing CMOS technology. The first approach uses a memoryless multistage concentration network (MMCN), which reduces the routing delay and increases the capacity of the Abacus switch. The second approach uses a buffered multistage concentration network (BMCN), which uses a funnel concept and an input-buffered concentration modules (CMs) to relax the memory speed constraint. A new priority assignment scheme is proposed for the input-buffered CM to maintain the cell sequence of a virtual connection. The third approach allows the arbitration cycle exceeding a cell slot and thus resequences cells at the output ports. It is proved that the maximum degree of out-of-sequence is bounded in the worst case.
Hepatitis C virus clearance correlates with HLA-DR expression on proliferating CD8+ T cells in immune-primed chimpanzees (2013)

Our data suggest that the appearance of proliferating HLA-DR+/CD8+ T cells can be used as a predictor of a successfully primed memory immune response against HCV and as a marker of effective vaccination in clinical trials.
Characterization of Materials Used as Face Coverings for Respiratory Protection (2021)

Use of masks is a primary tool to prevent the spread of the novel COVID-19 virus resulting from unintentional close contact with infected individuals. However, detailed characterization of the chemical properties and physical structure of common mask materials is lacking in the current literature. In this study, a series of commercial masks and potential mask materials, including 3M Particulate Respirator 8210 N95, a material provided by Oak Ridge National Laboratory Carbon Fiber Technology Facility (ORNL/CFTF), and a Filti Face Mask Material, were characterized by a suite of techniques, including scanning electron microscopy, X-ray diffraction, Raman spectroscopy, and X-ray photoelectron spectroscopy. Wetting properties of the mask materials were quantified by measurements of contact angle with a saliva substitute. Mask pass-through experiments were performed using a dispersed metal oxide nanoparticle suspension to model the SARS-CoV-2 virus, with quantification via spatially resolved X-ray fluorescence mapping. Notably, all mask materials tested provided a strong barrier against respiratory droplet breakthrough. The comparisons and characterizations provided in this study provide useful information when evaluating mask materials for respiratory protection.
Asymptotic bit error probabilities of some closed-loop transmit diversity schemes (2003)

Transmit diversity techniques have received a lot of attention recently, and open-loop and closed-loop downlink transmit diversity modes for two transmit antennas have been included in the 3GPP WCDMA Release 5. System capacity can be increased from that of open-loop modes if the transmitter can be provided additional side information of the downlink channel. In a frequency division duplex (FDD) system this requires a separate feedback channel. Quantization of the feedback messages in closed-loop transmit diversity schemes reduces the performance of the system. However, this effect has not been usually taken into account in the analysis. In this paper we analyze the effect of quantization and deduce an analytic formula for the asymptotic bit error probability of the closed-loop transmit diversity schemes defined in 3GPP WCDMA specification.
An efficient and practical layer-preference policy for routing in GMPLS networks (2008)

We address the problem of routing Label Switched Paths (LSPs) in multi-layer networks based on the Generalized MultiProtocol Label Switching (GMPLS) paradigm. In particular, we pursue strategies for choosing the appropriate layer to host a new LSP request, since choosing this policy has enormous impact on the eventual performance of the network. Therefore, we developed a mixed strategy, the Min-phys-hop routing and wavelength assignment algorithm, as a policy to govern the selection of the best layer of a multi-layer network in which to host new LSP requests. In this paper, we discuss the practical issues concerning the deployment of this algorithm in modern GMPLS networks. Firstly, we discuss the applicability of the algorithm with respect to the state-of-the-art GMPLS standards, above all, the GMPLS routing extensions to OSPF-TE. We also sketch two possible reference deployment scenarios. Secondly, we present simulation studies to demonstrate that (1) there does not exist a universally optimal static layer-preference policy and (2) the Min-phys-hop algorithm realizes an adequate heuristics even considering the realistic limitations of contemporary network devices. We found that the Min-phys-hop algorithm produces close-to-optimal blocking and resource consumption under almost all possible selections of input parameters, and this is regardless of the wavelength and Optical-Electrical-Optical (OEO) conversion capability present in the network.
Adenosine A2AReceptors in Bone Marrow-Derived Cells But Not in Forebrain Neurons Are Important Contributors to 3-Nitropropionic Acid-Induced Striatal Damage as Revealed by Cell-Type-Selective Inactivation (2006)

Endogenous adenosine acting at the adenosine A2A receptor (A2AR) can modify brain injury in a variety of neurological disorder models. However, both A2AR activation and inactivation have been shown to be neuroprotective in different situations, raising the intriguing possibility that A2ARs in distinct cellular elements may have different and even opposing effects. In this study, we developed three novel transgenic models to dissect out cell-type-specific actions of A2ARs on striatal damage by the mitochondrial toxin 3-nitropropionic acid (3-NP). Whereas global inactivation of A2ARs exacerbated 3-NP-induced neurological deficit behaviors and striatal damage, selective inactivation of A2ARs in forebrain neurons (using the Cre/loxP strategy) did not affect neurological deficit or striatal damage after the acute systemic treatment of 3-NP and intrastriatal injection of malonate. However, selective inactivation of A2ARs in bone marrow-derived cells (BMDCs) by transplanting bone marrow cells from global A2AR knock-out (KO) mice into wild-type C57BL/6 mice produced a similar phenotype of global A2AR KO mice, i.e., exacerbation of 3-NP-induced striatal damage. Thus, cell-type-selective inactivation of A2ARs reveals that A2ARs in BMDCs but not in forebrain neurons are an important contributor to striatal damage induced by mitochondrial dysfunction.
Elastography Assessment of Liver Fibrosis: Society of Radiologists in Ultrasound Consensus Conference Statement (2015)

The Society of Radiologists in Ultrasound convened a panel of specialists from radiology, hepatology, pathology, and basic science and physics to arrive at a consensus regarding the use of elastography in the assessment of liver fibrosis in chronic liver disease. The panel met in Denver, Colo, on October 21-22, 2014, and drafted this consensus statement. The recommendations in this statement are based on analysis of current literature and common practice strategies and are thought to represent a reasonable approach to the noninvasive assessment of diffuse liver fibrosis.
Assessment of the Mosquito-Pathogenic Fungus Culicinomyces Clavosporus as a Black Fly (Diptera: Simuliidae) Pathogen (1983)

Culicinomyces clavosporus, a highly virulent pathogen of mosquito larvae, was evaluated in the laboratory as a candidate for the biological control of black flies. Larvae of the black fly Simulium vittatum were not significantly affected by exposure to the Knight isolate of the fungus, even when exposed to more than 30 times the conidial concentration causing 100% mosquito (Aedes aegypti) mortality. These results, which are not in agreement with earlier studies, suggest that not all C. clavosporus isolates are black fly pathogens.
Multicomponent diffusion of hydrogen‐bonding solutes in a polymer (2002)

Abstract The diffusion of methyl ethyl ketone (MEK)/1‐butanol (BOH) mixtures in polyisobutylene (PIB) was studied using time‐resolved FTIR‐ATR spectroscopy at varying mixture compositions. Diffusion coefficients and hydrogen‐bonding interactions were quantitatively measured using this technique. In the MEK/BOH/PIB system, three species were identified from the infrared spectra, free MEK, an MEK‐BOH complex, and a self‐associated BOH cluster. The diffusion coefficient for the MEK‐BOH complex was less than that for free MEK, but larger than the values determined for the BOH cluster. These results were compared to a numerical solution of a multicomponent transport model that explicitly accounts for solute–solute interactions to determine individual diffusion coefficients for all the species identified. In addition, the MEK/BOH/PIB results were compared to those for an MEK/acetonitrile (ACN) mixture, a nonhydrogen‐bonding system, in PIB, to elucidate the differences between interacting and noninteracting systems.
Ruthenium Catalyzed Oxidation of 1,2‐Diols to 1,2‐Diketones Using Bromamine‐T as an Oxidizing Agent. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
The solution structure of bis(phenazine‐1‐carboxamide)‐DNA complexes: MLN 944 binding corrected and extended (2014)

MLN 944 is a bisintercalating DNA-binding antitumor agent known to be a template inhibitor of transcription. Previous (1) H NMR studies of its d(ATGCAT)2 complex concluded that its phenazine chromophores are protonated. However, we find that this is not so, which has important consequences for the charged state of the ligand, for the orientation of its 1-carboxamide group in the complex, and for the details of the interaction of its protonated interchromophore linker with the DNA base pairs. Here, we report a corrected solution structure of the MLN 944-d(ATGCAT)2 complex, and extend the study to complexes with d(TATGCATA)2 , and d(TACGCGTA)2 , using a variety of (1) H and (31) P NMR methods and molecular dynamics simulations employing the AMBER 12 force field. We find that for all three complexes MLN 944 binds as a dication, in which the chromophores are uncharged, in the DNA major groove spanning the central 2 GC base pairs in a manner that maintains the dyad symmetry of the DNA. The carboxamide group lies in the plane of the chromophore, its NH making hydrogen bonding interactions with the phenazine N10 nitrogen, and the protonated linkers form hydrogen bonds with the O6 atom of guanine. The dynamics simulations reveal extensive solvent interactions involving the linker amines, the carboxamide group, and the DNA bases.
Economic Analysis of High-Longevity Battery Capacity Fades for Electric Vehicles Supercharger Buffering Application (2020)

Current global trends show increasing numbers of electric vehicles on the road. The demand for fast charging is likely to keep pace with the adoption of electric vehicles. Fast charging places exceptionally high load demand on the electric utility infrastructure. These loads are beyond the capabilities of the existing infrastructure in many locations. The infrastructure power limitations can be offset by a high-power energy storage system (ESS). The crucial metrics for this system, in addition to meeting the peak load and energy demands of an EV battery, are cost and longevity. The main contribution of this article is to provide a methodology to assess the economic viability of an ESS solution for EVs supercharger buffering application. This methodology includes the model of aging effects on battery capacity, the overall efficiency, CAPEX, and OPEX of such system as well as the cost of the grid electricity purchased. This methodology is applied to two mature high-longevity lithium-ion battery technologies, namely, LFP and LTO. The results of this analysis suggest that there is no scenario where LFP is economically suitable. However, LTO shows the potential to be suitable in cases where there is a high demand from EV consumers for fast charging.
Capacitive silicon optical modulators for high-speed and high-efficiency operation (2021)

The silicon optical modulator is a key component in a high speed optical data link. To advance the modulator performance beyond the popular carrier depletion based devices, we have produced a capacitive device which is instead based upon the accumulation of free carriers either side of a thin insulating layer positioned in the middle of the waveguide. Such a device has a superior efficiency compared with the carrier depletion approach allowing compactness and improved power consumption whilst retaining high speed operation and CMOS compatibility.
Identification and characterization of recombinant plasmids carrying the complete qa gene cluster from Neurospora crassa including the qa-1+ regulatory gene. (1981)

The early reactions in the catabolism of quinic acid in Neurospora crassa are controlled by at least four genes which are clustered on linkage group VII. Three of the loci (qa-2, qa-4, and qa-3) encode enzymes that convert quinic acid to protocatechuic acid. The fourth gene (qa-1) encodes a positive regulatory protein which, in the presence of quinic acid, leads to the de novo synthesis of the other proteins in the qa cluster. This communication describes a series of recombinant plasmids that span 36.5 kilobases of linkage group VII and contain the coding sequences for qa-2, qa-4, qa-3, and the qa-1 regulatory protein. The plasmids were obtained by partial digestion of wild-type N. crassa DNA with EcoRI and ligation into the cosmid cloning vehicle pHC79. Two independently derived plasmids (pMSK331 and pMSK335), each containing 36.5-kilobase inserts, were shown by transformation back into N. crassa to contain the entire qa gene cluster. A preliminary physical organization of the gene cluster is presented. An improved procedure for the transformation of N. crassa with plasmid DNA is also described.
Online Channel Estimation for Hybrid Beamforming Architectures (2020)

Hybrid analog-/digital beamforming architectures are a promising means of reducing power consumption and hardware costs in large multi-antenna transceivers. However, channel estimation becomes more complicated compared with conventional (fully-digital) architectures because multiple measurements (pilots in subsequent time slots) are required to reconstruct the channel matrix. In this paper, we use variants of the adaptive projected subgradient method to devise online estimation algorithms that exploit temporal correlations of channel samples. Simulations show that these methods are competitive with conventional batch methods in terms of estimation error at a significantly reduced computational cost. We further improve the performance of the proposed methods by exploiting their potential to adapt the analog combiner at runtime.
Identification of Native Flavin Adducts from Fusarium oxysporum Using Accurate Mass Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (1997)

Accurate mass matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry is used to determine the identity of a naturally occurring substituted flavin adenine dinucleotide (FAD) of nitroalkane oxidase isolated from Fusarium oxysporum. Accurate mass measurements (1−2 ppm) combined with an elemental composition search identifies the unknown FAD substituent as nitrobutane. The use of internal and external calibration in accurate mass MALDI-TOF is discussed.
Aqueous citrato-oxovanadate(iv) precursor solutions for VO2: synthesis, spectroscopic investigation and thermal analysis (2014)

An aqueous precursor solution, containing citrato-VO(2+) complexes, is synthesized for the formation of monoclinic VO2. With regard to the decomposition of the VO(2+) complexes towards vanadium oxide formation, it is important to gain insights into the chemical structure and transformations of the precursor during synthesis and thermal treatment. Hence, the conversion of the cyclic [V4O12](4-) ion to the VO(2+) ion in aqueous solution, using oxalic acid as an acidifier and a reducing agent, is studied by (51)Vanadium nuclear magnetic resonance spectroscopy. The citrate complexation of this VO(2+) ion and the differentiation between a solution containing citrato-oxalato-VO(2+) and citrato-VO(2+) complexes are studied by electron paramagnetic resonance and Fourier transform infra-red spectroscopy. In both solutions, the VO(2+) containing complex is mononuclear and has a distorted octahedral geometry with a fourfold R-CO2(-) ligation at the equatorial positions and likely a fifth R-CO2(-) ligation at the axial position. Small differences in the thermal decomposition pathway between the gel containing citrato-oxalato-VO(2+) complexes and the oxalate-free gel containing citrato-VO(2+) complexes are observed between 150 and 200 °C in air and are assigned to the presence of (NH4)2C2O4 in the citrato-oxalato-VO(2+) solution. Both precursor solutions are successfully used for the formation of crystalline vanadium oxide nanostructures on SiO2, after thermal annealing at 500 °C in a 0.1% O2 atmosphere. However, the citrato-oxalato-VO(2+) and the oxalate-free citrato-VO(2+) solution result in the formation of monoclinic V6O13 and monoclinic VO2, respectively.