gebhart/patrepeval huggingface dataset:
Structure of E. coli Glutaminyl-tRNA Synthetase Complexed with tRNA Gln and ATP at 2.8 Å Resolution (1989)

The crystal structure of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) complexed with its cognate glutaminyl transfer RNA (tRNA(Gln] and adenosine triphosphate (ATP) has been derived from a 2.8 angstrom resolution electron density map and the known protein and tRNA sequences. The 63.4-kilodalton monomeric enzyme consists of four domains arranged to give an elongated molecule with an axial ratio greater than 3 to 1. Its interactions with the tRNA extend from the anticodon to the acceptor stem along the entire inside of the L of the tRNA. The complexed tRNA retains the overall conformation of the yeast phenylalanine tRNA (tRNA(Phe] with two major differences: the 3' acceptor strand of tRNA(Gln) makes a hairpin turn toward the inside of the L, with the disruption of the final base pair of the acceptor stem, and the anticodon loop adopts a conformation not seen in any of the previously determined tRNA structures. Specific recognition elements identified so far include (i) enzyme contacts with the 2-amino groups of guanine via the tRNA minor groove in the acceptor stem at G2 and G3; (ii) interactions between the enzyme and the anticodon nucleotides; and (iii) the ability of the nucleotides G73 and U1.A72 of the cognate tRNA to assume a conformation stabilized by the protein at a lower free energy cost than noncognate sequences. The central domain of this synthetase binds ATP, glutamine, and the acceptor end of the tRNA as well as making specific interactions with the acceptor stem.2+t is
Distinct cellular and regional localization of immunoreactive protein kinase C in rat brain. (1987)

Monoclonal antibodies raised against highly purified protein kinase C were used to localize protein kinase C in the rat brain. Using various monoclonal antibodies, at least three distinct antibody-staining patterns were found. One monoclonal antibody exclusively labeled astroglial elements, including astrocytes, tanycytes, and cerebellar radial glia. Another monoclonal antibody exclusively labeled neural cells, including cortical and hippocampal pyramidal dendrites and Purkinje cells of the cerebellum. A third monoclonal antibody (which inhibited protein kinase C activity) intensely stained more limited brain regions, particularly thalamic neurons, and also stained astroglial structures in brain, spinal cord, and cerebellum. The possibility that the three staining patterns reflect the differential regional and cellular localization of related, but distinct, enzymes of protein kinase C is discussed.
Optical path cross-connect systems transport experimentwith simulated five-node network (1995)

The authors describe an optical path cross-connect systems transport experiment performed by simulating a five-node network. Eight wavelength-division multiplexing signals, directly modulated at 2.5 Gbit/s, are confirmed to be transported over 330 km from the origination to the termination node via a cross-connection node. Optical path cross-connection is successfully performed with a crosstalk level of better than –35 dB.
Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage λ-Infected Escherichia coli Cells (1998)

Fluctuations in rates of gene expression can produce highly erratic time patterns of protein production in individual cells and wide diversity in instantaneous protein concentrations across cell populations. When two independently produced regulatory proteins acting at low cellular concentrations competitively control a switch point in a pathway, stochastic variations in their concentrations can produce probabilistic pathway selection, so that an initially homogeneous cell population partitions into distinct phenotypic subpopulations. Many pathogenic organisms, for example, use this mechanism to randomly switch surface features to evade host responses. This coupling between molecular-level fluctuations and macroscopic phenotype selection is analyzed using the phage lambda lysis-lysogeny decision circuit as a model system. The fraction of infected cells selecting the lysogenic pathway at different phage:cell ratios, predicted using a molecular-level stochastic kinetic model of the genetic regulatory circuit, is consistent with experimental observations. The kinetic model of the decision circuit uses the stochastic formulation of chemical kinetics, stochastic mechanisms of gene expression, and a statistical-thermodynamic model of promoter regulation. Conventional deterministic kinetics cannot be used to predict statistics of regulatory systems that produce probabilistic outcomes. Rather, a stochastic kinetic analysis must be used to predict statistics of regulatory outcomes for such stochastically regulated systems.
3,7-Bis(dialkylamino)phenothiazin-5-ium Derivatives: Biomedical Applications and Biological Activity (2003)

The light-induced reactions of 3,7-bis(dialkylamino)phenothiazin-5-ium compounds with biological substrates are briefly discussed. Their biomedical applications, in particular those related with biological staining, interaction with proteins and antiviral, antibacterial and antitumour activity are reviewed.
Effects of Adjuvants to Local Anaesthetics on Their Duration (1985)

The effects of addition of hyaluronic acid (sodium hyaluronate, Healon) to different local anaesthetics of the amide type on the duration of sensory or motor blocks following various regional anaesthetic procedures were studied in animal experiments. In the rat infra-orbital nerve block model, the addition of 0.1-0.5% hyaluronic acid (HA) to 2% prilocaine increased the duration of sensory block of varying degrees in a dose-dependent way by up to 500% of values obtained with plain prilocaine. The duration of degree 5 blocks produced by 0.5% etidocaine and 0.5% bupivacaine was also significantly prolonged when 0.4% HA was included to 206% and 282% of control, respectively, while blocks induced by 2% lidocaine were prolonged to 123% of control. The duration of motor block following spinal anaesthesia in the mouse was prolonged in a dose-dependent way when HA was added to prilocaine, bupivacaine and etidocaine. For solutions containing 0.4% HA, prolongations to 254%, 166% and 134% of control, respectively, were obtained. A concomitant increase of latency to onset of block and failure rate occurred with increasing concentrations of HA. The duration of corneal anaesthesia in the rabbit increased by 57% and 44% when 0.3% HA was added to prilocaine and bupivacaine, respectively. The duration of infiltration anaesthesia was not affected by the addition of HA to the local anaesthetic solutions. Addition of HA had no effect on the onset, depth and duration of prilocaine-induced block of the nervous transmission in vitro. The duration of infra-orbital nerve block and spinal anaesthesia shows a significant relation to the relative viscosity of the local anaesthetic solution.
Endothelium and haemostasis (2015)

The endothelium is a widely distributed organ system that plays an important role in health and disease. The endothelium is remarkably heterogeneous in structure and function. One vital function of the endothelium is to maintain blood in its fluid state, and to provide controlled haemostasis at sites of vascular injury. In keeping with the theme of endothelial cell heterogeneity, endothelial cells from different sites of the vascular employ different strategies to mediate local haemostatic balance. These differences are sufficient to explain why systemic imbalances of haemostatic components invariably lead to local thrombotic phenotypes. An important goal for the future is to identify diagnostic markers that reflect phenotypic changes at the level of individual vascular beds, and to develop therapies that target one or another site of the vasculature.
Dose-response effect of oxygen on hyperinflation and exercise endurance in nonhypoxaemic COPD patients (2001)

Dynamic hyperinflation contributes to exertional breathlessness and reduced exercise tolerance in chronic obstructive pulmonary disease (COPD) patients. This study examined whether oxygen supplementation results in a dose-dependent decrease in hyperinflation associated with functional and symptomatic improvement. Ten severe COPD patients without clinically significant oxygen (O2) desaturation during exercise, and seven healthy subjects, performed five exercise tests at 75% of maximally tolerated work rate. Inspired oxygen fraction (FI,O2) was varied (0.21, 0.3, 0.5, 0.75 and 1.0) among tests in a randomized order. Ventilation (V'E) was measured, and end-inspiratory (EILV) and end-expiratory (EELV) lung volume changes were assessed from inspiratory capacity manoeuvres. In the patients, compared to room air, endurance time increased with FI,O2=0.3 (mean+/-SEM 92+/-20%) and increased further with FI,O2=0.5 (157+/-30%). At isotime, compared to room air, there were significant reductions in dyspnoea score, EELV, EILV, V'E and respiratory frequency (fR) with FI,O2=0.3. Improved endurance time negatively correlated with change in EELV (r=0.48, p=0.002) and EILV (r=0.43, p=0.005). The dyspnoea rating decrease correlated with fR decrease. In healthy subjects, smaller V'E and fR decreases were observed at FI,O2=0.5, accompanied by more modestly increased endurance. Oxygen supplementation during exercise induced dose-dependent improvement in endurance and symptom perception in nonhypoxaemic chronic obstructive pulmonary disease patients, which may be partly related to decreased hyperinflation and slower breathing pattern. This effect is maximized at an inspired oxygen fraction of 0.5.
Potent 11β-Hydroxylase Inhibitors with Inverse Metabolic Stability in Human Plasma and Hepatic S9 Fractions To Promote Wound Healing (2014)

Topical application of CYP11B1 inhibitors to reduce cutaneous cortisol is a novel strategy to promote healing of chronic wounds. Pyridyl substituted arylsulfonyltetrahydroquinolines were designed and synthesized resulting in a strong inhibitor 34 (IC50 = 5 nM). It showed no inhibition of CYP17 and CYP19 and no mutagenic effects. It exhibited inverse metabolic stability in plasma (t1/2 ≫ 150 min), which is similar to wound fluid in composition, and in liver S9 fractions (t1/2 = 16 min).
Monitoring SAGD Steam Injection Using Microseismicity and Tiltmeters (2007)

Abstract A combination of microseismic and surface deformation monitoring with an array of tiltmeters was used to monitor the warm-up phase of a SAGD well pair. A sequence of microseismic events was recorded with signal characteristics suggesting deformation associated with thermal expansion of the wellbore, in addition to events apparently associated with induced fracturing in the reservoir. Integration of the microseismic data with volumetric strain, inverted from the measured surface deformation, indicates a discrete deforming region near the toe of the well. The volumetric strain also shows another region near the heel of the well, although the area is too far from the microseismic observation well for any associated microseismicity to be recorded. The central portion of the well pair did not have significant deformation, indicating poor steam conformance during this warm-up phase. A comparison of the temporal response of the microseismic deformation with the surface uplift, suggests a lag between periods of accelerated seismic deformation followed by an associated period of accelerated uplift a few days later. This timing suggests the creation of a fracture network and related seismic deformation, which then fills with steam and starts to expand over a period of a few days. In a related paper9, stress changes associated with the volumetric strain are used to examine potential geomechanical failure zones that match the observed locations of microseisms. Together the volumetric strain, computed stress changes, and failure zones could be used to calibrate a geomechanically linked reservoir simulator.
Plasmon‐polariton transport in hybrid semiconductor–metal–nanoparticle structures with gain (2006)

Abstract Plasmon‐polariton transport in noble‐metal nanoparticle chains embedded in an optical‐gain medium are considered theoretically. We show that short‐wavelength modes can acquire gain to counter loss. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Assembly, structural characterization, and thermal behavior of layer-by-layer deposited ultrathin films of poly(vinyl sulfate) and poly(allylamine) (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAssembly, structural characterization, and thermal behavior of layer-by-layer deposited ultrathin films of poly(vinyl sulfate) and poly(allylamine)Yuri Lvov, Gero Decher, and Helmuth MoehwaldCite this: Langmuir 1993, 9, 2, 481–486Publication Date (Print):February 1, 1993Publication History Published online1 May 2002Published inissue 1 February 1993https://pubs.acs.org/doi/10.1021/la00026a020https://doi.org/10.1021/la00026a020research-articleACS PublicationsRequest reuse permissionsArticle Views3651Altmetric-Citations839LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Etched-wall bent-guide structure for integrated optics in the III-V semiconductors (1984)

Bent-guide structures will undoubtedly play an important role in increasing packing density in future integrated optical circuits. A method for forming bends in waveguides in III-V semiconductors by reflection off an etched vertical wall is proposed for providing wave-guiding through 90° with negligible loss.
Examination of HIV-1 protease secondary structure specificity using conformationally constrained inhibitors (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExamination of HIV-1 protease secondary structure specificity using conformationally constrained inhibitorsMichael Kahn, Hiroshi Nakanishi, R. Alan Chrusciel, Dennis Fitzpatrick, and Michael E. JohnsonCite this: J. Med. Chem. 1991, 34, 12, 3395–3399Publication Date (Print):December 1, 1991Publication History Published online1 May 2002Published inissue 1 December 1991https://pubs.acs.org/doi/10.1021/jm00116a009https://doi.org/10.1021/jm00116a009research-articleACS PublicationsRequest reuse permissionsArticle Views223Altmetric-Citations14LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Load balancing a cluster of web servers: using distributed packet rewriting (2002)

We present and evaluate an implementation of a prototype scalable web server consisting of a load-balanced cluster of hosts that collectively accept and service TCP connections. The host IP addresses are advertised using round robin DNS (RR-DNS) technique, allowing any host to receive requests from any client. Once a client attempts to establish a TCP connection with one of the hosts, a decision is made as to whether or not the connection should be redirected to a different host-namely, the host with the lowest number of established connections. We use the low-overhead Distributed Packet Rewriting (DPR) technique to redirect TCP connections. In our prototype, each host keeps information about the remaining hosts in the system. Load information is maintained using periodic multicast amongst the cluster hosts. Performance measurements suggest that our prototype outperforms both pure RR-DNS and the stateless DPR solutions.
Viral and Cellular Determinants of Hepatitis C Virus RNA Replication in Cell Culture (2003)

Studies on the replication of hepatitis C virus (HCV) have been facilitated by the development of selectable subgenomic replicons replicating in the human hepatoma cell line Huh-7 at a surprisingly high level. Analysis of the replicon population in selected cells revealed the occurrence of cell culture-adaptive mutations that enhance RNA replication substantially. To gain a better understanding of HCV cell culture adaptation, we characterized conserved mutations identified by sequence analysis of 26 independent replicon cell clones for their effect on RNA replication. Mutations enhancing replication were found in nearly every nonstructural (NS) protein, and they could be subdivided into at least two groups by their effect on replication efficiency and cooperativity: (i). mutations in NS3 with a low impact on replication but that enhanced replication cooperatively when combined with highly adaptive mutations and (ii). mutations in NS4B, -5A, and -5B, causing a strong increase in replication but being incompatible with each other. In addition to adaptive mutations, we found that the host cell plays an equally important role for efficient RNA replication. We tested several passages of the same Huh-7 cell line and found up to 100-fold differences in their ability to support replicon amplification. These differences were not due to variations in internal ribosome entry site-dependent translation or RNA degradation. In a search for cellular factor(s) that might be responsible for the different levels of permissiveness of Huh-7 cells, we found that replication efficiency decreased with increasing amounts of transfected replicon RNA, indicating that viral RNA or proteins are cytopathic or that host cell factors in Huh-7 cells limit RNA amplification. In summary, these data show that the efficiency of HCV replication in cell culture is determined both by adaptation of the viral sequence and by the host cell itself.
Enhanced expression of genes involved in initial xylose metabolism and the oxidative pentose phosphate pathway in the improved xylose-utilizing Saccharomyces cerevisiae through evolutionary engineering (2013)

Fermentation of xylose in lignocellulosic hydrolysates by Saccharomyces cerevisiae has been achieved through heterologous expression of the xylose reductase (XR)-xylitol dehydrogenase (XDH) pathway. However, the fermentation efficiency is far from the requirement for industrial application due to high yield of the byproduct xylitol, low ethanol yield, and low xylose consumption rate. Through evolutionary engineering, an improved xylose-utilizing strain SyBE005 was obtained with 78.3 % lower xylitol production and a 2.6-fold higher specific ethanol production rate than those of the parent strain SyBE004, which expressed an engineered NADP(+)-preferring XDH. The transcriptional differences between SyBE005 and SyBE004 were investigated by quantitative RT-PCR. Genes including XYL1, XYL2, and XKS1 in the initial xylose metabolic pathway showed the highest up-regulation in SyBE005. The increased expression of XYL1 and XYL2 correlated with enhanced enzymatic activities of XR and XDH. In addition, the expression level of ZWF1 in the oxidative pentose phosphate pathway increased significantly in SyBE005, indicating an elevated demand for NADPH from XR. Genes involved in the TCA cycle (LAT1, CIT1, CIT2, KGD1, KGD, SDH2) and gluconeogenesis (ICL1, PYC1) were also up-regulated in SyBE005. Genomic analysis revealed that point mutations in transcriptional regulators CYC8 and PHD1 might be responsible for the altered expression. In addition, a mutation (Y89S) in ZWF1 was identified which might improve NADPH production in SyBE005. Our results suggest that increasing the expression of XYL1, XYL2, XKS1, and enhancing NADPH supply are promising strategies to improve xylose fermentation in recombinant S. cerevisiae.
Cloning and Sequence Analysis of the Mercury Resistance Operon of Streptomyces sp. Strain CHR28 Reveals a Novel Putative Second Regulatory Gene (2000)

A DNA library of pRJ28, a large linear plasmid encoding mercury resistance, was constructed, and the mercury resistance genes were cloned. The 5,921-bp sequence was analyzed and showed a high degree of similarity to the Streptomyces lividans 1326 mercury resistance operon. Genes merR, merT, merP, and orfIV were found in a similar order and in a single transcription unit. merA and merB were found to be transcribed in the opposite direction to genes merR, merT, merP, and orfIV, as in S. lividans 1326. A novel putative regulatory gene, orfX, was found 22 bp downstream of merA. orfX encodes a 137-amino acid protein with a potential helix-turn-helix motif in the N-terminal domain, characteristic of the MerR family of transcriptional regulators. Transcriptional studies showed that orfX is cotranscribed with merA and merB. It is hypothesized that orfX plays a role in the regulation of the mercury resistance operon, probably by binding at the MerR operator site.
Preparation of Cell Cultures and Vaccinia Virus Stocks (1998)

This unit describes the maintenance of cell lines used with vaccinia virus, both in monolayer cultures and in suspension. The suspended cell culture is then used in the preparation of vaccinia virus stocks. The preparation of chick embryo fibroblasts (CEF) is also presented for use in the production of the highly attenuated and host range-restricted modified vaccinia virus Ankara (MVA) strain of vaccinia virus. Additionally, support protocols are presented for the titration of standard and MVA vaccinia virus stocks.
De NovoSCN8A Mutation Identified by Whole-Exome Sequencing in a Boy With Neonatal Epileptic Encephalopathy, Multiple Congenital Anomalies, and Movement Disorders (2013)

Epileptic encephalopathies represent a clinically and genetically heterogeneous group of disorders, majority of which are of unknown etiology. We used whole-exome sequencing of a parent-offspring trio to identify the cause of early infantile epileptic encephalopathy in a boy with neonatal seizures, movement disorders, and multiple congenital anomalies who died at the age of 17 months because of respiratory illness and identified a de novo heterozygous missense mutation (c.3979A>G; p.Ile1327Val) in SCN8A (voltage-gated sodium-channel type VIII alpha subunit) gene. The variant was confirmed in the proband with Sanger sequencing. Because the clinical phenotype associated with SCN8A mutations has previously been identified only in a few patients with or without epileptic seizures, these data together with our results suggest that mutations in SCN8A can lead to early infantile epileptic encephalopathy with a broad phenotypic spectrum. Additional investigations will be worthwhile to determine the prevalence and contribution of SCN8A mutations to epileptic encephalopathies.