gebhart/patrepeval huggingface dataset:
Genome‐free hepatitis B virion levels in patient sera as a potential marker to monitor response to antiviral therapy (2014)

Complete virions of hepatitis B virus (HBV) contain a DNA genome that is enclosed in a capsid composed of the HBV core antigen (HBcAg), which is in turn surrounded by a lipid envelope studded with viral surface antigens (HBsAg). In addition, HBV-infected cells release subviral particles composed of HBsAg only (HBsAg 'spheres' and 'filaments') or HBsAg enveloping HBcAg but devoid of viral DNA ('empty virions'). The hepatitis B e antigen (HBeAg), a soluble antigen related to HBcAg, is also secreted in some HBV-infected patients. The goals of this study were to explore the levels of empty virions in HBV-infected patients before and during therapy with the nucleotide analog tenofovir disoproxil fumarate (TDF) that inhibits HBV DNA synthesis and the relationships of empty virions to complete virions, HBsAg and HBeAg. HBV DNA, HBcAg and HBsAg levels were determined in serum samples from 21 patients chronically infected with HBV and enrolled in clinical TDF studies. Serum levels of empty virions were found to exceed levels of DNA-containing virions, often by ≥ 100-fold. Levels of both empty and complete virions varied and were related to the HBeAg status. When HBV DNA replication was suppressed by TDF, empty virion levels remained unchanged in most but were decreased (to the limit of detection) in some patients who also experienced significant decrease or loss of serum HBsAg. In conclusion, empty virions are present in the serum of chronic hepatitis B patients at high levels and may be useful in monitoring response to antiviral therapy.
Replica plating of colonies from Listeria-selective agars to blood agar to improve the isolation of Listeria monocytogenes from foods (1990)

Bacterial colonies from Listeria-selective agars were replica plated to sheep blood agar to screen for beta-hemolysis. By using the replica plating method to test for the beta-hemolytic characteristic of all the colonies growing on Listeria-selective agars instead of picking 3 to 10 suspected colonies for further testing, we recovered Listeria monocytogenes from 59 of 142 Listeria-selective agar plates which contained colonies of hemolytic and nonhemolytic Listeria species and were negative when tested by conventional colony picks.
Photochemical cross-linking between rabbit skeletal troponin subunits. Troponin I-troponin T interactions. (1982)

The heterobifunctional photoaffinity probe, AGTC (N-(4-azidobenzoyl-[2-3H]glycyl)-S-(2-thiopyridyl) cysteine), was attached to cysteines 48 and 64 of troponin I to determine which component of rabbit skeletal troponin was in close proximity to these cysteines. The reconstituted troponin complex (AGC labeled CM-TnI, TnT, and TnC) was photolyzed and separated using DEAE-Sephadex chromatography in the presence of 8 M urea and absence of reducing agent. Radioactivity measurements indicated that 12% of the cross-linker reacted with solvent and 88% with protein. The percentage of radiolabel found in TnI, TnI-TnT, and TnI-TnC complexes was 35, 55, and 10%, respectively. These results have shown that both TnT and TnC are within 14 A of one or both cysteines 48 and 64 of TnI. Of the total radiolabel found in TnT, 33 and 23% was found in the two cyanogen bromide fragments, CB4 (residues 176-230) and CB2 (residues 71-151). The most likely interpretation of the cross-linking results is that one of the interaction sites between TnI and TnT is an ionic interaction involving the region around cysteines 48 and 64 of TnI (residues 28-82) with the CB5 region of TnT (residues 135-185).
Influence of intermediate-heat treatment on the structure and magnetic properties of iron-rich Sm(CoFeCuZr)Z sintered magnets (2015)

In this study, we investigated intermediate-heat treatment (IHT) at temperatures between those of sintering and solution treatment, and evaluated the effects on the macrostructure, microstructure, and magnetic properties of Sm(Cobal.Fe0.35Cu0.06Zr0.018)7.8. We found that squareness was clearly improved by adopting the IHT, which promotes grain growth. These results indicate that reducing the fraction of grain boundaries by increasing the grain size affects the behavior of domain-wall motion. Magnetic properties of Mr 1.22 T, HcJ 1580 kA/m, and (BH)max 282 kJ/m3 (&gt;35 MGOe) were obtained for Sm(Cobal.Fe0.35Cu0.06Zr0.018)7.8 subjected to IHT at 1453 K.
High-coercivity (NdDy)2(FeNb)14B–α–Fe nanocrystalline alloys (1997)

High coercivity, high remanence, and high energy product (NdDy)2(FeNb)14B–α–Fe nanocrystalline alloys containing 0 to 30 wt % α–Fe have been prepared by melt spinning and subsequent annealing. The best magnetic properties of remanence (Br), coercivity (Hci), and maximum energy product [(BH)max] are 1.02 T, 702 kA/m, and 134 kJ/m3, respectively, for Nd8.16Dy1Fe85.26Nb1B4.58. The microstructure consists of a two phase nanocomposite of hard magnetic (NdDy)2(FeNb)14B and soft magnetic α–Fe with an average size of about 30 nm. These small dimensions allow effective exchange coupling between hard and soft magnetic grains and result in the simultaneous enhancement of Br, Hci, and (BH)max. A systematic study on the effect of annealing temperature and time on the microstructure and magnetic properties has been carried out.
Molecular Origin of the Hierarchical Elasticity of Titin: Simulation, Experiment, and Theory (2011)

This review uses the giant muscle protein titin as an example to showcase the capability of molecular dynamics simulations. Titin is responsible for the passive elasticity in muscle and is a chain composed of immunoglobulin (Ig)-like and fibronectin III (FN-III)-like domains, as well as PEVK segments rich in proline (P), glutamate (E), valine (V), and lysine (K). The elasticity of titin is derived in stages of extension under increasing external force: Ig domain straightening occurs first (termed tertiary structure elasticity), followed by the extension of the disordered PEVK segments. At larger extension and force, Ig domains unfold one by one (termed secondary structure elasticity). With the availability of crystal structures of single and connected Ig domains, the tertiary and secondary structure elasticity of titin was investigated through molecular dynamics simulations, unveiling the molecular origin of titin's elasticity.
An update on recent patents on thrombin inhibitors (2010 – 2013) (2013)

Thrombin is a multifaceted, dynamic enzyme with both coagulant and anticoagulant functions. Newer DTIs are attempting to fine tune thrombin's activity by targeting allosteric sites or by site-specific targeting of clotting. The complexity of thrombin's functions is driving the design of complex anticoagulants. Advancements in formulations and production processes have attempted to make traditional DTIs more cost effective to produce. The literature reveals a trend to develop a thrombin 'modulator' rather than an 'inhibitor.'
ChemInform Abstract: STUDIES IN CLAISEN REARRANGEMENT. NOVEL THERMAL TRANSFORMATION OF α‐((ARYLOXY)METHYL)ACRYLIC ACIDS AND THEIR DERIVATIVES (1985)

Abstract Die thermische Umlagerung der Titelverbindungen (II) nach A) ergibt nicht, wie von den Autoren zuerst angenommen, Dimeren des Typs (I), sondern Dimere des Typs (III).
Anthrax lethal factor-cleavage products of MAPK (mitogen-activated protein kinase) kinases exhibit reduced binding to their cognate MAPKs (2004)

Anthrax lethal toxin is the major cause of death in systemic anthrax. Lethal toxin consists of two proteins: protective antigen and LF (lethal factor). Protective antigen binds to a cell-surface receptor and transports LF into the cytosol. LF is a metalloprotease that targets MKKs [MAPK (mitogen-activated protein kinase) kinases]/MEKs [MAPK/ERK (extracellular-signal-regulated kinase) kinases], cleaving them to remove a small N-terminal stretch but leaving the bulk of the protein, including the protein kinase domain, intact. LF-mediated cleavage of MEK1 and MKK6 has been shown to inhibit signalling through their cognate MAPK pathways. However, the precise mechanism by which this proteolytic cleavage inhibits signal transmission has been unclear. Here we show that the C-terminal LF-cleavage products of MEK1, MEK2, MKK3, MKK4, MKK6 and MKK7 are impaired in their ability to bind to their MAPK substrates, suggesting a common mechanism for the LF-induced inhibition of signalling.
Anterior Vertebral Body Screw Pullout Testing (1998)

The addition of a pullout-resistant nut to an anterior vertebral body screw improves the pullout strength by twofold and changes the mode of failure to rely ultimately on the inherent vertebral body strength rather than the screw's characteristics. The addition of a pullout-resistant nut may be applicable to multilevel implant constructs to prevent screw pullout at the top and bottom.
Peptidomimetic GnRH receptor antagonists for the treatment of reproductive and proliferative diseases (2006)

PKS Sarma*a, Atul Tiwarib, Atul Kondaskarc & Ian A Cliffeda Ranbaxy Research Laboratories, Department of Medicinal Chemistry, Plot No.20, Sector –18, Udyog Vihar Industrial Area, Gurgaon-122001 (Haryana), India. b Jubilant Biosys Ltd, Assay Development Group, Drug Discovery Unit, #96, 2nd stage, Industrial Area, Yashwantpura, Bangalore-560022, (Karnataka), India. c Ranbaxy Research Laboratories, Department of Medicinal Chemistry, Plot No.20, Sector –18, Udyog Vihar Industrial Area, Gurgaon-122001 (Haryana), India. d Ranbaxy Research Laboratories, Department of Medicinal Chemistry, Plot No.20, Sector –18, Udyog Vihar Industrial Area, Gurgaon-122001 (Haryana), India.
Role of oxygen vacancies in the high-temperature thermopower of indium oxide and indium tin oxide films (2009)

Thermopower measurements in a range of 300–650 K along with room temperature optical absorption and electrical resistivity studies were performed on indium oxide (IO) and indium tin oxide (ITO) thin films grown by reactive dc sputtering. The thermopower of as-grown and oxygen-annealed IO and ITO films measured in Ar ambient displayed characteristics attributable to oxygen loss. The observations were substantiated with optical absorption and electrical resistivity results.
Sequences upstream from the T-A-T-A box are required in vivo and in vitro for efficient transcription from the adenovirus serotype 2 major late promoter. (1982)

We show that sequences located upstream from the T-A-T-A box, between positions -97 and -34, are necessary for efficient in vivo transcription from the adenovirus serotype 2 major late promoter. The effect of these upstream sequences was also investigated in vitro using a whole cell or an S100 extract and circular or linear templates. With the whole cell extract, the in vivo effect of the upstream sequences was reproduced in vitro. With the S100 extract, some effect of the upstream sequences was observed with circular, but not with linear, templates.
Laboratory Evolution of Enantiocomplementary Candida antarctica Lipase B Mutants with Broad Substrate Scope (2013)

Candida antarctica lipase B (CALB) is a robust and easily expressed enzyme used widely in academic and industrial laboratories with many different kinds of applications. In fine chemicals production, examples include acylating kinetic resolution of racemic secondary alcohols and amines as well as desymmetrization of prochiral diols (or the reverse hydrolytic reactions). However, in the case of hydrolytic kinetic resolution of esters or esterifying kinetic resolution of acids in which chirality resides in the carboxylic acid part of the substrate, rate and stereoselectivity are generally poor. In the present study, directed evolution based on iterative saturation mutagenesis was applied to solve the latter problem. Mutants with highly improved activity and enantioselectivity relative to wild-type CALB were evolved for the hydrolytic kinetic resolution of p-nitrophenyl 2-phenylpropanoate, with the selectivity factor increasing from E = 1.2 (S) to E = 72 (S) or reverting to E = 42 (R) on an optional basis. Surprisingly, point mutations both in the acyl and alcohol pockets of CALB proved to be necessary. Some of the evolved CALB mutants are also efficient biocatalysts in the kinetic resolution of other chiral esters without performing new mutagenesis experiments. Another noteworthy result concerns the finding that enantiocomplementary CALB mutants for α-substituted carboxylic acid esters also show stereocomplementarity in the hydrolytic kinetic resolution of esters derived from chiral secondary alcohols. Insight into the source of stereoselectivity was gained by molecular dynamics simulations and docking experiments.
Habits without Values (2016)

Abstract Habits form a crucial component of behavior. In recent years, key computational models have conceptualized habits as arising from model-free reinforcement learning (RL) mechanisms, which typically select between available actions based on the future value expected to result from each. Traditionally, however, habits have been understood as behaviors that can be triggered directly by a stimulus, without requiring the animal to evaluate expected outcomes. Here, we develop a computational model instantiating this traditional view, in which habits develop through the direct strengthening of recently taken actions rather than through the encoding of outcomes. We demonstrate that this model accounts for key behavioral manifestations of habits, including insensitivity to outcome devaluation and contingency degradation, as well as the effects of reinforcement schedule on the rate of habit formation. The model also explains the prevalent observation of perseveration in repeated-choice tasks as an additional behavioral manifestation of the habit system. We suggest that mapping habitual behaviors onto value-free mechanisms provides a parsimonious account of existing behavioral and neural data. This mapping may provide a new foundation for building robust and comprehensive models of the interaction of habits with other, more goal-directed types of behaviors and help to better guide research into the neural mechanisms underlying control of instrumental behavior more generally.
Room temperature CW tunable green upconversion holmium fibre laser (1990)

CW tunable green laser emission between 540 and 553nm (5S2 → 5I8) has been achieved in Ho3+-doped fluorozirconate fibre by upconversion pumping at room temperature, with output powers in excess of 10mW. Laser emission at 0.75μm (3S2 → 5I7) was also observed at the same excited level.
Liquid water can slip on a hydrophilic surface (2011)

Understanding and predicting the behavior of water, especially in contact with various surfaces, is a scientific challenge. Molecular-level understanding of hydrophobic effects and their macroscopic consequences, in particular, is critical to many applications. Macroscopically, a surface is classified as hydrophilic or hydrophobic depending on the contact angle formed by a water droplet. Because hydrophobic surfaces tend to cause water slip whereas hydrophilic ones do not, the former surfaces can yield self-cleaning garments and ice-repellent materials whereas the latter cannot. The results presented herein suggest that this dichotomy might be purely coincidental. Our simulation results demonstrate that hydrophilic surfaces can show features typically associated with hydrophobicity, namely liquid water slip. Further analysis provides details on the molecular mechanism responsible for this surprising result.
Inhibition of platelet 12-lipoxygenase by hydroxy-fatty acids (1984)

Conference Article| October 01 1984 Inhibition of platelet 12-lipoxygenase by hydroxy-fatty acids PAUL D. MITCHELL; PAUL D. MITCHELL 1Department of Biochemistry and Physical Chemistry, Fisons plc, Pharmaceutical Division, Loughborough, Leics. LE11 0RH, U.K. Search for other works by this author on: This Site PubMed Google Scholar CATHERINE HALLAM; CATHERINE HALLAM 1Department of Biochemistry and Physical Chemistry, Fisons plc, Pharmaceutical Division, Loughborough, Leics. LE11 0RH, U.K. Search for other works by this author on: This Site PubMed Google Scholar PAUL E. HEMSLEY; PAUL E. HEMSLEY 1Department of Biochemistry and Physical Chemistry, Fisons plc, Pharmaceutical Division, Loughborough, Leics. LE11 0RH, U.K. Search for other works by this author on: This Site PubMed Google Scholar GARRY H. LORD; GARRY H. LORD 1Department of Biochemistry and Physical Chemistry, Fisons plc, Pharmaceutical Division, Loughborough, Leics. LE11 0RH, U.K. Search for other works by this author on: This Site PubMed Google Scholar DAVID WILKINSON DAVID WILKINSON 1Department of Biochemistry and Physical Chemistry, Fisons plc, Pharmaceutical Division, Loughborough, Leics. LE11 0RH, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1984) 12 (5): 839–841. https://doi.org/10.1042/bst0120839 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation PAUL D. MITCHELL, CATHERINE HALLAM, PAUL E. HEMSLEY, GARRY H. LORD, DAVID WILKINSON; Inhibition of platelet 12-lipoxygenase by hydroxy-fatty acids. Biochem Soc Trans 1 October 1984; 12 (5): 839–841. doi: https://doi.org/10.1042/bst0120839 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: g.c.–m.s., gas chromatography-mass spectrometry; 12-HETE, 12-ls-hydroxyeicosa-5z, 8z, 10e, 14z-tetraenoic acid; h.p.l.c., high-performance liquid chromatography This content is only available as a PDF. © 1984 Biochemical Society1984 Article PDF first page preview Close Modal You do not currently have access to this content.
Development and Field Testing of a Novel Fracturing Fluid (1991)

ABSTRACT A new polymer has been introduced into the oilfield for use in hydraulic fracturing. Its unique properties complement the wide range of polymers currently in use. This biopolymer was originally developed for enhanced oil recovery and is now also used for gravel packing and as a mud Viscosifier. The biopolymer causes minimal formation/proppant-pack permeability impairment - yielding the highest retained permeabilities of any polymer tested to date. It exhibits a constant viscosity up to a transition temperature (adjustable between 40°C and 100°C) beyond which the viscosity decreases to a level close to that of water. This eliminates the need for a breaker. The polymer is highly shear-thinning, resulting in the lowest tubing-head pressure of all fluids available. The good proppant-carrying capacity of the fluid is achieved without the addition of a crosslinker while fluid loss is similar to other polymers that are commonly used for fracturing. The formulation of a fully functional fracturing fluid for use at medium temperatures without the need for a breaker or crosslinker is unique. In particular, it can be used with resin-coated proppants where unwanted side reactions occur with conventional fracturing fluids The new fracturing fluid was successfully tested in combination with resin-coated proppant in the Southern North Sea.
A 0.84ps-LSB 2.47mW time-to-digital converter using charge pump and SAR-ADC (2013)

We propose a time-to-digital converter (TDC) using a charge pump and a SAR-ADC. With this architecture, high time resolution is attainable by increasing the charging current or reducing the sampling capacitance. Thus, the resolution limitation in a delay-chain TDC does not exist. We propose to use a SAR-ADC attributed to its characteristics of compact structure, scalability, low power consumption, and small area. The prototype chip was fabricated in 65nm CMOS, achieving 0.84ps LSB, 2.47mW power consumption, and 0.06mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> area occupation. With 8-bit outputs, the DNL and INL are −0.7/1.0 LSB and −2.7/1.7 LSB, respectively.
Tuning Hydrogel Mechanics Using the Hofmeister Effect (2015)

The mechanical properties of hydrogels are commonly modified by changing the concentration of the molecular components. This approach, however, does not only change hydrogel mechanics, but also the microstructure, which in turn alters the macroscopic properties of the gel. Here, the Hofmeister effect is used to change the thermoresponsiveness of polyisocyanide hydrogels. In contrast to previous Hofmeister studies, the effect is used to change the phase transition temperatures and to tailor the mechanics of the thermoresponsive (semiflexible) polymer gels. It is demonstrated that the gel stiffness can be manipulated over more than two orders of magnitude by the addition of salts. Surprisingly, the microstructure of the gels does not change upon salt addition, demonstrating that the Hofmeister effect provides an excellent route to change the mechanical properties without distorting other influential parameters of the gel.
The Essential Role of the Intestinal Microbiota in Facilitating Acute Inflammatory Responses (2004)

The restoration of blood flow, i.e., reperfusion, is the treatment of choice to save viable tissue following acute ischemia of a vascular territory. Nevertheless, reperfusion can be accompanied by significant inflammatory events that limit the beneficial effects of blood flow restoration. To evaluate the potential role of the intestinal microbiota in facilitating the development of tissue injury and systemic inflammation, germ-free and conventional mice were compared in their ability to respond to ischemia and reperfusion injury. In conventional mice, there was marked local (intestine) and remote (lung) edema formation, neutrophil influx, hemorrhage, and production of TNF-alpha, KC, MIP-2, and MCP-1. Moreover, there was an increase in the concentration of serum TNF-alpha and 100% lethality. In germ-free mice, there was no local, remote, or systemic inflammatory response or lethality after intestinal ischemia and reperfusion and, in contrast to conventional mice, germ-free animals produced greater amounts of IL-10. Similar results were obtained after administration of LPS, i.e., little production of TNF-alpha or lethality and production of IL-10 after LPS in germ-free mice. Blockade of IL-10 with Abs induced marked inflammation and lethality in germ-free mice after ischemia and reperfusion or LPS administration, demonstrating that the ability of these mice to produce IL-10 was largely responsible for their "no inflammation" phenotype. This was consistent with the prevention of reperfusion-associated injury by the exogenous administration of IL-10 to conventional mice. Thus, the lack of intestinal microbiota is accompanied by a state of active IL-10-mediated inflammatory hyporesponsiveness.
Collaborative genres for collaboration: genre systems in digital media (2002)

Using the concept of genre, we examined the use of Team Room to facilitate collaborative work in one organization. Team Room is a collaborative application built within Lotus Notes and designed specifically to support teams within organizational settings. We studied three teams' communication in Team Room over seven months and found that some of the genres they enacted formed sets of interdependent genres or "genre systems", which facilitated collaboration among team members. The teams' use of these genre systems (meeting documentation, collaborative repository, and collaborative authoring) varied in ways that reflected differences in team size, task, and orientation towards the new technology. The three genre systems observed in Team Room demonstrate different of electronic collaboration that both build on and vary from collaboration in traditional media. Based on the notion of collaborative genres, we suggest insights for research and practical implications for system designers and users.