gebhart/patrepeval huggingface dataset:
Probing the structure of monomers and dimers of the bacterial virus phi29 hexamer RNA complex by chemical modification (2000)

All dsDNA viruses multiply their genome and assemble a procapsid, a protein shell devoid of DNA. The genome is subsequently inserted into the procapsid. The bacterial virus phi29 DNA translocating motor contains a hexameric RNA complex composed of six pRNAs. Recently, we found that pRNA dimers are building blocks of pRNA hexamers. Here, we report the structural probing of pRNA monomers and dimers by chemical modification under native conditions and in the presence or absence of Mg2+. The chemical-modification pattern of the monomer is compared to that of the dimer. The data strongly support the previous secondary-structure prediction of the pRNA concerning the single-stranded areas, including three loops and seven bulges. However, discrepancies between the modification patterns of two predicted helical regions suggest the presence of more complicated, higher-order structure in these areas. It was found that dimers were formed via hand-in-hand and head-to-head contact, as the interacting sequence of the right and left loops and all bases in the head loop were protected from chemical modification. Cryoatomic force microscopy revealed that the monomer displayed a check-mark shape and the dimer exhibited an elongated shape. The dimer was twice as long as the monomer. Direct observation of the shape and measurement of size and thickness of the images strongly support the conclusion from chemical modification concerning the head-to-head contact in dimer formation. Our results also suggest that the role for Mg2+ in pRNA folding is to generate a proper configuration for the right and head loops, which play key roles in this symmetrical head-to-head organization. This explains why Mg2+ plays a critical role in pRNA dimer formation, procapsid binding, and phi29 DNA packaging.
Entity Search with NECESSITY (2009)

Loosely structured heterogeneous information spaces are typically created by merging data from a variety of different applications and information sources. A common problem these information spaces need to address is that various data describe the same real-word entities (e.g., conferences, organizations). In this demo, we introduce necessity, an efficient and scalable entity store. necessity is able to handle a large number of entities and at the same time provide an efficient and highly accurate entity search functionality for heterogeneous and partially structured queries that follow the vision of dataspaces. 1.
Enantiomerically pure quaternary ammonium salts with a chiral alkyl chain N(CH<sub>3</sub>)(<i>n</i>‐C<sub>3</sub>H<sub>7</sub>)<sub>2</sub>(<i>sec</i>‐C<sub>4</sub>H<sub>9</sub>)I: Synthesis and physical studies (2008)

A pair of enantiomerically pure quaternary ammonium salts with a chiral side chain, methyl-(R)-(1-methylpropyl)di(n-propyl)ammonium iodide 1 and methyl-(S)-(1-methylpropyl)di(n-propyl)ammonium iodide 2, and the related racemate, methyl-(rac)-(1-methylpropyl)di(n-propyl)ammonium iodide 3, were synthesized through a reductive alkylation procedure, starting from enantiomerically pure and, also, racemic forms of (rac)-(1-methylpropyl)amine. A spectroscopic chiroptical signature in solution was provided by the Raman optical activity spectra of compounds 1 and 2. The crystallographic structures of 1, 2, and 3 were examined by single crystal X-ray diffraction. 1 crystallizes in the tetragonal space group P4(3)2(1)2 (no. 96), a = b = 12.826 (2) A, c = 17.730 (2) A, V = 2916.9 (5) A(3), Z = 8, Flack coefficient 0.04 (2). 2 crystallizes in the tetragonal space group P4(1)2(1)2 (no. 92), a = b = 12.842 (1) A, c = 17.749 (2) A, V = 2927.0 (5) A(3), Z = 8, Flack coefficient 0.05 (2). The crystal structures and space groups for 1 and 2 are enantiomorphs and the crystallographic investigation confirmed the absolute configuration of the stereocenter in both compounds. 3 crystallizes in the monoclinic space group P2(1)/n(no. 14), a = 8.178 (1) A, b = 14.309 (2) A, c = 12.328 (2) A, beta = 96.811 (6) degrees, V = 1432.4 (2) A(3), Z = 4.
Cost of Medical Care for Chronic Kidney Disease and Comorbidity among Enrollees in a Large HMO Population (2004)

Chronic kidney disease (CKD) afflicts up to 20 million people in the United States, but little is known about their health care costs. The authors analyzed costs and resource use associated with CKD by using National Kidney Foundation staging definitions. Patients insured through a large health maintenance organization with a laboratory finding of CKD (defined as estimated GFR between 15 and 90 ml/min per 1.73 m(2) in 1996 followed by a second GFR below 90 at the next creatinine measurement occurring at least 90 d later) were followed from 1996 for up to 66 mo. The final cohort included 13,796 persons with CKD and their age- and gender-matched controls; 1741 in stage 2; 11,278 in stage 3; and 777 in stage 4. Depending on stage, cases had 1.9 to 2.5 times more prescriptions, 1.3 to 1.9 times more outpatient visits, were 1.6 to 2.2 times more likely to have had an inpatient stay, and had 1.8 to 3.1 more stays than did controls. Total per patient follow-up costs were [$total, (95% CI) cases and controls, respectively] $38,764 (95% CI, 37,033 to $40,496) and $16,212 (95% CI, $15,644 to $16,780) in stage 2; $33,144 (95% CI, $32,578 to $33,709) and $18,964 (95% CI, $18,730 to $19,197) in stage 3; and $41,928 (95% CI, $39,354 to $44,501) and $19,106 (95% CI, $18,212 to $20,000) in stage 4. Cases with no CKD-related comorbidities had costs double that of controls with no CKD-related comorbidities, and comorbidities related to CKD were more costly to manage than CKD alone. Future research in this area could be usefully directed toward analyzing the clinical and economic consequences of better managing or preventing comorbidities in patients with CKD.
Effets de la double couche électrique sur un écoulement de Poiseuille (2006)

International audience
ChemInform Abstract: Synthesis and in vitro Cytotoxic Activity of Aza‐ and Diazaanthraquinone Derivatives. (1995)

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.
Deposit Control in Modern Diesel Fuel Injection Systems (2010)

<div class="section abstract"><div class="htmlview paragraph">Modern diesel Fuel Injection Equipment (FIE) systems are susceptible to the formation of a variety of deposits. These can occur in different locations, e.g. in nozzle spray-holes and inside the injector body. The problems associated with deposits are increasing and are seen in both Passenger Car (PC) and Heavy Duty (HD) vehicles. Mechanisms responsible for the formation of these deposits are not limited to one particular type.</div><div class="htmlview paragraph">This paper reviews FIE deposits developed in modern PC and HD engines using a variety of bench engine testing and field trials. Euro 4/ IV and Euro 5/V engines were selected for this programme. The fuels used ranged from fossil only to distillate fuels containing up to 10% Fatty Acid Methyl Ester (FAME) and then treated with additives to overcome the formation of FIE deposits.</div><div class="htmlview paragraph">It was observed that engine performance was significantly impacted by the formation of deposits which may lead to increased fuel consumption, loss in power, poor driveability and failure to start.</div><div class="htmlview paragraph">The selection of appropriate fuel additive technology allows control of all deposit types, either by preventing their formation or restoring engine performance.</div></div>
Eddy current induction in a solid conducting cylinder with a transverse magnetic field (1978)

Quasistatic magnetic field solutions for a right circular cylinder of arbitrary conductivity and permeability immersed in a uniform transverse magnetic field are considered. The cases of a rotating cylinder in a dc magnetic field and a stationary cylinder in an ac magnetic field are included. The solutions are described in terms of the magnetic Reynolds number, a dimensionless quantity which indicates the effect of dynamics on the magnetic field inside the conducting cylinder. The field distributions are plotted over the complete range of dynamic behavior using known approximations to ber and bei functions. To verify the theoretical results, experiments are performed to measure changes in the magnetic field outside a conducting shaft as a function of shaft rotation speed or magnetic field frequency. These measurements are correlated with the calculated solutions for the magnetic flux density outside the conducting cylinder. An external magnetic Reynolds number is found to be an appropriate indication of the change in magnetic field outside the conducting cylinder.
Ring‐Ketten‐Tautomerie bei 2‐Phenyl‐semicarbazonen (1969)

Abstract 2‐Phenyl‐semicarbazone des Acetons und Acetophenons können außer in der normalen Semicarbazon‐Struktur 1 bzw. 5 auch in der Triazolidon‐Struktur 2 bzw. 6 vorliegen. Die Isomeren werden dargestellt und ihre Strukturen diskutiert.
Enhanced Electron Transfer Dissociation through Fixed Charge Derivatization of Cysteines (2009)

Electron transfer dissociation (ETD) has proven to be a promising new ion activation method for proteomics applications due to its ability to generate c- and z-type fragment ions in comparison to the y- and b-type ions produced upon the more conventional collisional activation of peptides. However, low precursor charge states hinder the success of electron-based activation methods due to competition from nondissociative charge reduction and incomplete sequence coverage. In the present report, the reduction and alkylation of disulfide bonds prior to ETD analysis is evaluated by comparison of three derivatization reagents: iodoacetamide (IAM), N,N-dimethyl-2-chloro-ethylamine (DML), and (3-acrylamidopropyl)-trimethyl ammonium chloride (APTA). While both the DML and APTA modifications lead to an increase in the charge states of peptides, the APTA-peptides provided the most significant improvement in percent fragmentation and sequence coverage for all peptides upon ETD, including formation of diagnostic ions that allow characterization of both the C- and N-termini. In addition, the formation of product ions in multiple charge states upon ETD is minimized for the APTA-modified peptides.
Package embedded decoupling capacitor impact on core power delivery network for ARM SoC application (2014)

In this paper, a BGA package having a ARM SoC chip is introduced, which has component-type embedded decoupling capacitors (decaps) for good power integrity performance of core power. To evaluate and confirm the impact of embedded decap on core PDN (power distribution network), two different packages were manufactured with and without the embedded decaps. The self impedances of system-level core PDN were simulated in frequency-domain and On-chip DvD (Dynamic Voltage Drop) simulations were performed in time-domain in order to verify the system-level impact of package embedded decap. There was clear improvement of system-level core PDN performance in middle frequency range when package embedded decaps were employed. In conclusion, the overall system-level core PDN for ARM SoC could meet the target impedance in frequency-domain as well as the target On-chip DvD level by having package embedded decaps.
Preactivation: An Alternative Strategy in Stereoselective Glycosylation and Oligosaccharide Synthesis (2013)

Abstract The multifaceted biological importance of carbohydrates has made them very popular targets in modern synthetic chemistry. Great progress has been made in stereoselective glycosylation methods and the construction of complex oligosaccharides. This Focus Review highlights the versatile applications of preactivation strategies in stereoselective glycosylation and oligosaccharide synthesis. Recent advances in synthetic methods, such as 4,6‐ O ‐benzylidene‐acetal‐directed β‐mannosylation, the 1,2‐ cis ‐glycosylation mediated by a chiral auxiliary, the use of an oxazolidinone or carbonate protecting group, and glycosylation with participating additives, are described. Various examples of sequential glycosylation based on preactivation protocols for efficient oligosaccharide assembly are also summarized.
Antiviral activity obtained from aqueous extracts of the Chilean soapbark tree (Quillaja saponaria Molina) (2006)

Natural, aqueous extracts of Quillaja saponaria , the Chilean soapbark tree, contain several physiologically active triterpenoid saponins that display strong adjuvant activity when used in either human or animal vaccines. In this paper, we describe studies that demonstrate a novel antiviral activity of Quillaja extracts against six viruses: vaccinia virus, herpes simplex virus type 1, varicella zoster virus, human immunodeficiency viruses 1 and 2 (HIV-1, HIV-2) and reovirus. We demonstrate that microgram amounts of extract, while exhibiting no cell cytotoxicity or direct virucidal activity, prevent each of the six viruses tested from infecting their host cells. In addition, the presence of residual amounts of extract continue to block virus infection and render cells resistant to infection for at least 16 h after the removal of the extract from the cell culture medium. We demonstrate that a Quillaja extract possesses strong antiviral activity at concentrations more than 100-fold lower than concentrations that exhibit cell cytotoxicity. Extract concentrations as high as 100 μg ml −1 are not cytotoxic, but concentrations as low as 0.1 μg ml −1 are able to block HIV-1 and HIV-2 virus attachment and infection.
Dilatometric Studies of High Polymers. II. Crystallization of Aromatic Polyesters (1949)

By means of both a density balance and gradient tube, experimental density data are obtained to illustrate the thermal crystallization behavior of 3 aromatic polyesters at temperatures from 90°C to 150°C. The data are discussed with reference to both amount and rate of crystallization and density curves are presented to show qualitative similarity between kinetics of polymer crystallization and the kinetics of chemical reactions. From the experimental data, a temperature, for convenience labeled the minimum crystallization temperature, is described and is shown to be 30° to 50° above the second-order transition temperature for the polyesters. In addition to thermal crystallization, data are presented to show that immersion media may initiate crystallization below the minimum temperature associated with thermal crystallization of polymers. Liquids used as immersion media for polyethylene terephthalate were water, methyl alcohol, acetone, benzene, nitromethane, and nitric acid. The last four liquids initiate crystallization of the polymer at room temperature.
General & applied toxicology (1994)

Volume I General aspects. Part 1 Introductory and basic material: fundamentals of toxicology, B. Ballantyne et al statistics for toxicology, P.N. Lee principles of testing for acute toxic effects, C. Rhodes et al biotransformation of xenobiotics, J. Timbrell toxicokinetics, A.G. Renwick physiologically-based pharmacokinetic modeling, Hon-Wing Leung biochemical mechanisms of toxicology, J. Caldwell alternatives to in vivo studies in toxicology, S.C. Gad acute non-specific toxicity, J.A. Henry and S.L. Cassidy information resources for toxicology, J. Deschamps and Morgan. Part 2 Techniques in toxicity: design of toxicology studies, A. Paine pathological techniques in toxicology, P. Greaves haematology in toxicology studies, D. Woodman and J. Fuller clinical chemistry in toxicology studies, M. Stonard and Evans antidotal studies, N. Bateman and T.C. Marrs quality assurance in toxicology studies, T.R. Stiles hazards in the toxicology laboratory, B. Ballantyne evaluation of toxicity in human subjects, P.N. Bennett. Part 3 Toxicity by routes: parental toxicity, D. Walker peroral toxicity, T.R. Tyler percutaneous toxicity, Hon-Wing Leung inhalation toxicity, P. Hext and I.P. Bennett. Volume II Organ and special toxicity - applied toxicology. Part 1 Target organ toxicity: neurotoxicity, J.N. LeFauconnier peripheral sensory irritation, B. Ballantyne nephrotoxicity, B.A. Lock systemic pulmonary toxicity, J.P. Kehrer pulmonary hypersensitivity reactions, H.C. Lewinsohn and H.D. Burleigh-Flayer ophthalmic toxicology, B. Ballantyne cardiovascular toxicity, S.I. Baskin heptotoxicity, P. Grasso and R.H. Hinton toxicity of the pancreas, J.M. Braganza toxicology of skeletal muscle, K.E. Misulis et al toxicology of bone, A.G.B. Lansdowne cutaneous toxicity, S.J. Hermansky ototoxicity, Forge and E.S. Harper, toxicology of the adrenal, thyroid and endocrine pancreas, J.A. Thomas immunotoxicology, K. Miller and C. Neredith haematotoxicology, J. Amess. Part 2 Special toxicology: mutagenicity, A. Tweats cytogenetics, D. Anderson chemical carcinogenesis (genotoxic), D.B. McGregor chemical carcinogenesis (epigenetic), C. Berry Reproductive toxicology, J.N. Ratcliffe and F. Sullivan developmental toxicology, R.W. Tyl neonatal toxicology, S. Kacew. Part 3 Regulatory tocicology: overview of regulatory agencies, G. Diggle regulation of drugs in Europe and the United Kingdom, R.D. Mann regulation of drugs on the North American continent, M.B. Vernoy regulation of veterinary product in Europe and the United Kingdom, K. Woodward regulation of veterinary products in the United States, K. Woodward regulation of industrial chemicals and pesticides in Europe and the United Kingdom, R. Fielder and Martin regulation of food additives and food contact materials on the North American continent, M.B. Vernoy. Part 4 Toxicology in special situations: pharmaceutical toxicology, P.F. D'Arcy medical devices, Adams. Part contents.
Thaxtomin A Production and Virulence Are Controlled by Several <i>bld</i> Gene Global Regulators in <i>Streptomyces scabies</i> (2014)

Streptomyces scabies is the main causative agent of common scab disease, which leads to significant annual losses to potato growers worldwide. The main virulence factor produced by S. scabies is a phytotoxic secondary metabolite called thaxtomin A, which functions as a cellulose synthesis inhibitor. Thaxtomin A production is controlled by the cluster-situated regulator TxtR, which activates expression of the thaxtomin biosynthetic genes in response to cello-oligosaccharides. Here, we demonstrate that at least five additional regulatory genes are required for wild-type levels of thaxtomin A production and plant pathogenicity in S. scabies. These regulatory genes belong to the bld gene family of global regulators that control secondary metabolism or morphological differentiation in Streptomyces spp. Quantitative reverse-transcriptase polymerase chain reaction showed that expression of the thaxtomin biosynthetic genes was significantly downregulated in all five bld mutants and, in four of these mutants, this downregulation was attributed to the reduction in expression of txtR. Furthermore, all of the mutants displayed reduced expression of other known or predicted virulence genes, suggesting that the bld genes may function as global regulators of virulence gene expression in S. scabies.
Prognostic Markers and Targeted Therapies for Renal Cell Carcinoma (2009)

Management of advanced renal cell carcinoma remains a persistent clinical challenge with high morbidity and mortality for a large proportion of patients. Until recently, available medical immunotherapy regimens yielded a therapeutic response in only 20% of patients. Advances in the understanding of molecular mechanisms of renal cell carcinoma have led to a rapidly expanding body of work exploring biomarkers for the disease and targeted therapeutics. We review current investigations into biomarkers and novel therapies for renal cell carcinoma, discuss the concept of anticancer vaccines, and propose a novel target for anticancer vaccine development.
The Interconnectability Of Neuro-Optic Processors (1986)

The inherent parallelism, great processing speed, and massive interconnectability of optical systems have made the latter natural candidates for realizing various neural net models of associative memory, feature extraction, novelty filtering and problem optimization. Moreover, through the use of nonlinear thresholding and feedback techniques, such systems (hereafter referred to as neuro-optic processors or NOPs) appear to achieve the degree of operational accuracy long sought after in analog optical processor systems. Key elements of a typical NOP architecture include an optical interconnect network, an array of nonlinear optical processing elements, and a suitable means for providing optical feedback. In this paper we address ourselves to the optical interconnect network. Specifically we present practical design and information storage capacity analyses of the covariance matrix operator, = Emni=ilvm, >< Vmd, which characterizes this interconnect network. Here > is Hilbert-space object (state) vector in discrete or continuous 2D configuration space (in Dirac notation) and M represents the extent of NOP exposure to a particular object domain (within the context of pattern recognition, for example, M is the number of elements in a training pattern set). Central to our analyses is a discussion of the holographic technique which may be used to make R in hardware form.
What obama gets right (2017)

he editor of the journal presents his thoughts concerning the success of U.S. foreign policy during the administration of U.S. president Barack Obama. It examines what the author terms Obama's appreciation for the liberal international order nurtured by the U.S., Obama's determination to reverse the foreign policy approach by the administration of former U.S. president George W. Bush, and Obama's role in the nuclear weapons accord signed with Iran in 2015. It also discusses Obama's policies concerning Russia's conflict with Ukraine, the Middle East, and Asia, in addition to Obama's record concerning U.S. national security, the role of the organization the North Atlantic Treaty Organization (NATO), and the rise of the Islamic militant group Islamic State (ISIS)
Explosive Compaction of Metal Powders (1978)

transmit a shock pulse into the powder so as to effect its compaction. The controlling parameter of the process is assumed to be the ratio of the powder mass to the explosive mass, Mp/ME, and values of this ratio necessary to fully compact various powders have been quoted· for specified explosives. Apart from an attempt by Leonard4 to relate the Mp/ME ratio for full compaction to the compressive yield strength of five powder materials, no definite relationship has been established between this ratio and any measurable. property of a metal powder. Although details of the powder container are not normally included in the literature, initial work by Ludlow,S subsequently verified by Bhalla,6 showed that compacted density was dependent on the container tube wall thickness and material, even when Mp/ME was maintained constant. Bhalla subsequently found that a rel(~tionship existed between the compacted density Dc and the kinetic energy per unit area of the tube E immediately after detonation of the explosive charge. This relationship took the form: