gebhart/patrepeval huggingface dataset:
Brugia malayi Gene Expression in Response to the Targeting of the Wolbachia Endosymbiont by Tetracycline Treatment (2009)

Upregulation of protein translation and amino acid synthesis may indicate a generalized stress response induced in B. malayi due to a shortage of essential nutrients/factors that are otherwise supplied by Wolbachia. Downregulation of transcripts involved in cuticle biosynthesis perhaps reflects a disruption in the normal embryogenic program. This is confirmed by the expression pattern of transcripts that may be representative of the worms' response to Wolbachia in different tissues; the early peak potentially reflects the effect of bacteria death on the embryogenic program while the second peak may be a manifestation of the adult worm response to the affected bacteria within the hypodermis.
Condition monitoring of excavated CIPP-liners to ensure lifespan (2020)

In Sweden there is a lack of knowledge on the expected service life of installed CIPP-liners and a general aim to request CIPP-liners with a 100-year lifespan. In cooperation with Swedish water uti ...
Replication of the extrachromosomal ribosomal RNA genes of Tetrahymena thermophilia (1981)

Cultures of Tetrahymena thermophila were deprived of nutrients and later refed with enriched medium to obtain partial synchrony of DNA replication. Preferential replication of the extrachromosomal, macronuclear ribosomal RNA genes (rDNA) was found to occur at 40-80 min after refeeding. The rDNA accounted for one half of the label incorporated into cellular DNA during this period. Electron microscopy of the purified rDNA showed 1% replicative intermediates. Their structure was that expected for bidirectional replication of the linear rDNA from an origin or origins located in the central nontranscribed region of the palindromic molecule. Similar forms had previously been observed for the rDNA of a related species, Tetrahymena pyriformis. The electron microscopic data was consistent with an origin of replication located approximatley 600 base pairs from the center of the rDNA of T. thermophila, in contrast to a more central location in the rDNA of T. pyriformis. One implication of an off-center origin of replication is that there are two such sequences per palindromic molecule.
Structure-Based Design of an Iminoheterocyclic β-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) Inhibitor that Lowers Central Aβ in Nonhuman Primates (2016)

We describe successful efforts to optimize the in vivo profile and address off-target liabilities of a series of BACE1 inhibitors represented by 6 that embodies the recently validated fused pyrrolidine iminopyrimidinone scaffold. Employing structure-based design, truncation of the cyanophenyl group of 6 that binds in the S3 pocket of BACE1 followed by modification of the thienyl group in S1 was pursued. Optimization of the pyrimidine substituent that binds in the S2'-S2″ pocket of BACE1 remediated time-dependent CYP3A4 inhibition of earlier analogues in this series and imparted high BACE1 affinity. These efforts resulted in the discovery of difluorophenyl analogue 9 (MBi-4), which robustly lowered CSF and cortex Aβ40 in both rats and cynomolgus monkeys following a single oral dose. Compound 9 represents a unique molecular shape among BACE inhibitors reported to potently lower central Aβ in nonrodent preclinical species.
Enantioselective intramolecular C–H amination of aliphatic azides by dual ruthenium and phosphine catalysis (2019)

The catalytic enantioselective intramolecular C(sp<sup>3</sup>)-H amination of aliphatic azides represents an efficient method for constructing chiral saturated cyclic amines which constitute a prominent structural motif in bioactive compounds. We report a dual catalytic system involving a chiral-at-metal bis(pyridyl-NHC) ruthenium complex and tris(4-fluorophenyl)phosphine (both 1 mol%), which facilitates the cyclization of aliphatic azides to chiral α-aryl pyrrolidines with enantioselectivities of up to 99% ee, including a pyrrolidine which can be converted to the anti-tumor alkaloid (<i>R</i>)-(+)-crispine. Mechanistically, the phosphine activates the organic azide to form an intermediate iminophosphorane and transfers the nitrene unit to the ruthenium providing an imido ruthenium intermediate which engages in the highly stereocontrolled C-H amination. This dual catalysis combines ruthenium catalysis with the Staudinger reaction and provides a novel strategy for catalyzing enantioselective C-H aminations of unactivated aliphatic azides.
Quantitative real-time PCR protocol for analysis of nuclear receptor signaling pathways (2003)

A major goal of the Nuclear Receptor Signaling Atlas (NURSA) is to elucidate the biochemical and physiological roles of nuclear receptors in vivo. Characterizing the tissue expression pattern of individual receptors and their target genes in whole animals under various pharmacological conditions and genotypes is an essential component of this aim. Here we describe a high-throughput quantitative, real-time, reverse-transcription PCR (QPCR) method for the measurement of both the relative level of expression of a particular transcript in a given tissue or cell type, and the relative change in expression of a particular transcript after pharmacologic or genotypic manipulation. This method is provided as a standardized protocol for those in the nuclear receptor field. It is meant to be a simplified, easy to use protocol for the rapid, high-throughput measurement of transcript levels in a large number of samples. A subsequent report will provide validated primer and probe sequence information for the entire mouse and human nuclear receptor superfamily.
Establishment of an H6N2 Influenza Virus Lineage in Domestic Ducks in Southern China (2010)

Multiple reassortment events between different subtypes of endemic avian influenza viruses have increased the genomic diversity of influenza viruses circulating in poultry in southern China. Gene exchange from the natural gene pool to poultry has contributed to this increase in genetic diversity. However, the role of domestic ducks as an interface between the natural gene pool and terrestrial poultry in the influenza virus ecosystem has not been fully characterized. Here we phylogenetically and antigenically analyzed 170 H6 viruses isolated from domestic ducks from 2000 to 2005 in southern China, which contains the largest population of domestic ducks in the world. Three distinct hemagglutinin lineages were identified. Group I contained the majority of isolates with a single internal gene complex and was endemic in domestic ducks in Guangdong from the late 1990s onward. Group II was derived from reassortment events in which the surface genes of group I viruses were replaced with novel H6 and N2 genes. Group III represented H6 viruses that undergo frequent reassortment with multiple virus subtypes from the natural gene pool. Surprisingly, H6 viruses endemic in domestic ducks and terrestrial poultry seldom reassort, but gene exchanges between viruses from domestic ducks and migratory ducks occurred throughout the surveillance period. These findings suggest that domestic ducks in southern China mediate the interaction of viruses between different gene pools and facilitate the generation of novel influenza virus variants circulating in poultry.
Improved device performance of InAs∕GaAs quantum dot solar cells with GaP strain compensation layers (2007)

We report optical, electrical, and spectral response characteristics of three-stack InAs∕GaAs quantum dot solar cells with and without GaP strain compensation (SC) layers. The short circuit current density, open circuit voltage, and external quantum efficiency of these cells under air mass 1.5G at 290mW∕cm2 illumination are presented and compared with a GaAs control cell. The cells with SC layers show superior device quality, confirmed by I-V and spectral response measurements. The quantum dot solar cells show an extended photoresponse compared to the GaAs control cell. The effect of the SC layer thickness on device performance is also presented.
ChemInform Abstract: Synthesis and Characterization of Peptide Libraries (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Phosphofructokinases A and B from Mycobacterium tuberculosis Display Different Catalytic Properties and Allosteric Regulation (2021)

Tuberculosis (TB) remains one of the major health concerns worldwide. <i>Mycobacterium tuberculosis</i> (Mtb), the causative agent of TB, can flexibly change its metabolic processes during different life stages. Regulation of key metabolic enzyme activities by intracellular conditions, allosteric inhibition or feedback control can effectively contribute to Mtb survival under different conditions. Phosphofructokinase (Pfk) is one of the key enzymes regulating glycolysis. Mtb encodes two Pfk isoenzymes, Pfk A/Rv3010c and Pfk B/Rv2029c, which are differently expressed upon transition to the hypoxia-induced non-replicating state of the bacteria. While <i>pfkB</i> gene and protein expression are upregulated under hypoxic conditions, Pfk A levels decrease. Here, we present biochemical characterization of both Pfk isoenzymes, revealing that Pfk A and Pfk B display different kinetic properties. Although the glycolytic activity of Pfk A is higher than that of Pfk B, it is markedly inhibited by an excess of both substrates (fructose-6-phosphate and ATP), reaction products (fructose-1,6-bisphosphate and ADP) and common metabolic allosteric regulators. In contrast, synthesis of fructose-1,6-bisphosphatase catalyzed by Pfk B is not regulated by higher levels of substrates, and metabolites. Importantly, we found that only Pfk B can catalyze the reverse gluconeogenic reaction. Pfk B thus can support glycolysis under conditions inhibiting Pfk A function.
Putting Auction Theory to Work: The Simultaneous Ascending Auction (2017)

The “simultaneous ascending auction” was first introduced in 1994 to sell licenses to use bands of radio spectrum in the United States. Much of the attention devoted to the auction came from its role in reducing federal regulation of the radio spectrum and allowing market values, rather than administrative fiat, to determine who would use the spectrum resource. Many observers were also fascinated by the then-novel use of weblike interfaces for bidders. The large amounts of money involved were yet another source of interest. The very first use of the auction rules was a $617 million sale of 10 paging licenses in July 1994. In the broadband personal communications services (PCS) auction, which began in December 1994, 99 licenses were sold for a total price of approximately $7 billion. Once the auctions had been conducted, it became much harder to ignore the tremendous value of the large amounts of spectrum allocated to uses such as high-definition television, for which Congress had demanded no compensation at all. Moreover, the perceived successes with the new rules inspired imitators to conduct similar spectrum auctions in various countries around the world and to recommend similar auctions for other applications.
Evaluation of immunodiagnostic potential of ESAT-6 synthetic peptides mixture in Egyptian pulmonary tuberculosis patients. (2012)

Identification of M. tuberculosis ESAT-6 proteins has enhanced research for developing new specific and reliable in vitro diagnostic tests for pulmonary tuberculosis. The aim of this study was to assess the diagnostic potential of ESAT-6 synthetic overlapping peptides mixture (Pepmix) for diagnosis of pulmonary M. tuberculosis infection in Egypt. IFN-gammaand IL-17 production was assessed in whole-blood culture assay after overnight stimulation with M. tuberculosis crude culture filtrate (CF), purified 38 kDa antigen, and ESAT-6 Pepmix. Concentration of IFN-gamma and IL-17 was evaluated in the culture supernatant by ELISA. Patients with active pulmonary TB patients (n = 37), Tuberculin Skin Test (TST) positive healthy subjects (n = 16) and TST negative healthy subjects (n = 16) were included. Results indicated that IFN-gammaproduction following stimulation with crude CF, and 38 kDa purified antigen was not significantly different between patients and TST+ healthy controls. In contrast, Pepmix clearly distinguished between patients and TST+ healthy subjects with sensitivity of 70.3 % and specificity 96.9 %. The concentration of secreted IL-17 was significantly lower than IFN-gamma, and no statistically significant difference was found between groups. It is concluded that IFN-gamma assay using ESAT-6 Pepmix, as antigenic stimulus, has the potential to rapidly diagnose pulmonary TB infection.
Impurity corrections to the thermodynamics in spin chains using a transfer-matrix DMRG method (1999)

We use the density-matrix renormalization group for transfer matrices to numerically calculate impurity corrections to thermodynamic properties. The method is applied to two impurity models in the spin-1/2 chain, namely a weak link in the chain and an external impurity spin. The numerical analysis confirms the field theory calculations and gives explicit results for the crossover behavior.
Prolonged Illness after Infectious Mononucleosis Is Associated with Altered Immunity but Not with Increased Viral Load (2006)

The resolution of symptomatic IM is not determined by control of viremia, nor is it easily explained by altered host responses to EBV infection. The detailed determinants of delayed recovery remain to be elucidated.
GaAs/AlGaAs multiquantum well resonant photorefractive devices fabricated using epitaxial lift-off (1994)

This letter deals with resonant photorefractive devices fabricated from multiquantum wells of GaAs/Al0.3Ga0.7As and operated in a quantum-confined Stark effect geometry. Details of the processing are presented. Epitaxial lift-off was used to remove the active device from the substrate. Low-temperature Al0.3Ga.07As was used as an insulator to form metal-insulator-semiconductor structures on both sides of the multiquantum wells. Proton implant damage was used to improve the fringe visibility. Photorefractive wave mixing with a diffraction efficiency of ∼0.03% was demonstrated. The incorporation of a nitride layer between the top electrode and the low-temperature AlGaAs increased the efficiency to 0.5%. The improvement is attributed to a reduction in the conduction of carriers across the low-temperature layer into the electrode.
Alane reduction of selenium and tellurium: tertiary amine stabilised dimeric chalcogenides, trans-[{Me3N(H)Al(µ-E)}2](E = Se, Te) (1995)

Elemental selenium or tellurium react with trimethylamine alane, [Me3NAlH3], in toluene affording the bis-trimethylamine adducts of the dimeric chalcogenidoalanes, [{HAl(µ-E)}2](E = Se, Te) isolated as the trans-isomers; ab initio molecular orbital calculations on model species show that N-donor Lewis-base solvated dimeric species are the energetically most favourable structures for these chalcogenidoalane species.
Brief Exposure of Skin to Near-Infrared Laser Modulates Mast Cell Function and Augments the Immune Response (2018)

The treatment of skin with a low-power continuous-wave (CW) near-infrared (NIR) laser prior to vaccination is an emerging strategy to augment the immune response to intradermal vaccine, potentially substituting for chemical adjuvant, which has been linked to adverse effects of vaccines. This approach proved to be low cost, simple, small, and readily translatable compared with the previously explored pulsed-wave medical lasers. However, little is known on the mode of laser-tissue interaction eliciting the adjuvant effect. In this study, we sought to identify the pathways leading to the immunological events by examining the alteration of responses resulting from genetic ablation of innate subsets including mast cells and specific dendritic cell populations in an established model of intradermal vaccination and analyzing functional changes of skin microcirculation upon the CW NIR laser treatment in mice. We found that a CW NIR laser transiently stimulates mast cells via generation of reactive oxygen species, establishes an immunostimulatory milieu in the exposed tissue, and provides migration cues for dermal CD103<sup>+</sup> dendritic cells without inducing prolonged inflammation, ultimately augmenting the adaptive immune response. These results indicate that use of an NIR laser with distinct wavelength and power is a safe and effective tool to reproducibly modulate innate programs in skin. These mechanistic findings would accelerate the clinical translation of this technology and warrant further explorations into the broader application of NIR lasers to the treatment of immune-related skin diseases.
Involvement of Adenosine Receptor, Potassium Channel and Protein Kinase C in Hypoxic Preconditioning of Isolated Cardiomyocytes of Adult Rat (1999)

A possible mechanism for hypoxic preconditioning of adult rat cardiomyocytes was pharmacologically investigated. Isolated cardiomyocytes in all experimental groups were incubated for 120 min under hypoxic conditions followed by 15-min reoxygenation (sustained H/R). Sustained H/R decreased rod-shaped cells. Exposure of the cardiomyocytes to 20-min of hypoxia/30-min reoxygenation (hypoxic preconditioning) attenuated the sustained H/R-induced decrease in rod-shaped cells. The effects of hypoxic preconditioning were abolished by treatment with the protein kinase C (PKC) inhibitor polymyxin B, but abolished by neither the adenosine A1/A2-antagonist sulfophenyl theophylline (SPT) nor the ATP-sensitive potassium channel (K(ATP) channel) blocker glibenclamide. In another series of experiments, cardiomyocytes were incubated without hypoxic preconditioning in the presence of either the PKC activator PMA, adenosine or K(ATP)-channel opener nicorandil and then subjected to sustained H/R. Treatment of the cells with PMA, adenosine or nicorandil mimicked the effects of hypoxic preconditioning. The effects of treatment with adenosine and nicorandil were abolished by polymyxin B treatment. Combined treatment with both SPT and glibenclamide abolished the effects of hypoxic preconditioning, whereas it failed to abolish PMA-induced cytoprotection. These results suggest that the activation of PKC in hypoxic preconditioned cardiomyocytes coupled independently with stimulation of adenosine receptor or opening of K(ATP) channel, either of which is fully enough to exert the cytoprotective effects.
Block Copolymer Assembly on Nanoscale Patterns of Polymer Brushes Formed by Electrohydrodynamic Jet Printing (2014)

Fundamental understanding of the self-assembly of domains in block copolymers (BCPs) and capabilities in control of these processes are important for their use as nanoscale templates in various applications. This paper focuses on the self-assembly of spin-cast and printed poly(styrene-block-methyl methacrylate) BCPs on patterned surface wetting layers formed by electrohydrodynamic jet printing of random copolymer brushes. Here, end-grafted brushes that present groups of styrene and methyl methacrylate in geometries with nanoscale resolution deterministically define the morphologies of BCP nanostructures. The materials and methods can also be integrated with lithographically defined templates for directed self-assembly of BCPs at multiple length scales. The results provide not only engineering routes to controlled formation of complex patterns but also vehicles for experimental and simulation studies of the effects of chemical transitions on the processes of self-assembly. In particular, we show that the methodology developed here provides the means to explore exotic phenomena displayed by the wetting behavior of BCPs, where 3-D soft confinement, chain elasticity, interfacial energies, and substrate's surface energy cooperate to yield nonclassical wetting behavior.
[Study on solid surface fluorescence characteristic of saline soils around lakes in arid and semiarid regions]. (2010)

Fluorescence spectroscopy relies on the fluorescence emitted by rigid conjugated systems and thus has been increasingly used to assess the soil organic matter (SOM) humification. This technique is widely applied to solution samples of humic substances, and so far no information exists about its applicability to solid-phase soil samples. Composite soil samples of different depths (0-20, 20-40 and 40-60 cm) were collected from four different halophyte communities along a saline-impact gradient, namely, Comm. Salicornia europaea (CSE), Comm. Suaeda glauca (CSG), Comm. Kalidium foliatum (CKF) and Comm. Sophora alopecuroides (CSA) located around Wuliangsuhai Lake. A humification index based on solid surface fluorescence spectroscopy (HIX(SSF)) was proposed, and compared with conventional humification indices I400/I360, I470/I360, I465/I399 and A4 /Al. There were close positive linear correlations between HIXass and 1400/1360, 145/I399 and A4/A1, but a poor positive linear correlation existed between the HIX(SSF) and I470/I360. The results indicated that HIX(SSF) can be taken as a tool to assess the soil humi fication. The HIX(SSF) of the CSE and CSG varied inappreciably within soil profiles and there was no trend with depth. However the HIX(SSF) varied appreciably in the CKF and CSA, and the HIX(SSF) of the bottom soil profile was higher than that of the other profiles. As a whole, the soil humification degree was low around Wuliangsuhai Lake, and the ecological environment was relatively fragile. The salinity showed a strong negative linear relationship with the I400/I360, I470/I360, I465/I399 and A4/A1, but a good negative linear relationship with the HIX(SSF). The results indicated that the degree of the SOM humification increased with the drop in the salinity. The HIX(SSF) can be an indicator not only of the degree of SOM humification, but also of the process of the salinisation.
Obtaining fully polarised amplitudes in gauge invariant form (2022)

We describe progress applying the \textit{Worldline Formalism} of quantum field theory to the fermion propagator dressed by $N$-photons to study multi-linear Compton scattering processes, explaining how this approach -- whose calculational advantages are well-known at multi-loop order -- yields compact and manifestly gauge invariant scattering amplitudes.
Kpn I family of long interspersed repeated DNA sequences in primates: polymorphism of family members and evidence for transcription. (1983)

An approximately equal to 2-kilobase-pair-long member (Kpn I-LS1) of the African green monkey Kpn I family of repeated sequences has been cloned, subjected to sequence analysis, and compared to other family members which are over 6 kilobase pairs (Kpn I-alpha 7) and 829 base pairs (Kpn I-RET) long. Both Kpn I-LS1 and Kpn I-RET lack sequences found at the ends of the longer family member and their structures resemble those of processed genes. Kpm I-LS1 sequences are colinear with part of the long family member, Kpn I-alpha 7. However, although all sequences in Kpn I-RET are represented in Kpn I-LS1, the two are not colinear; Kpn I-RET is missing 731 base pairs found in Kpn I-LS1 and one segment flanking the deletion is inverted. The results demonstrate that Kpn I family members are not only of different lengths but may also contain scrambled arrangements of common sequences. Sequences in Kpn I-LS1 hybridize to RNA from monkey and human cells, indicating that some family members are transcribed.