gebhart/patrepeval huggingface dataset:
Comparative Biology and Pathogenesis of AIDS and Hepatitis B Viruses: Related but Different (1994)

AIDS (HIV) and hepatitis B viruses are remarkably similar in their sharing of reverse transcription, in their ancestral origins and common genetic elements, and in their modes of transmission. Both are hypermutable and exist as quasispecies due primarily to errors in reverse transcription, though there is severe restriction in the replicative competence of most hepatitis B mutants. They differ in the lack of an integrase in hepatitis B virus and in their pathogenesis in the infected host. HIV survives mainly by antigenic variability, immune evasion, and impairment of immune function though viral regulatory control elements seek to restrict fatal damage to the host. Hepatitis B virus survives primarily by mutation of e antigen/core genes that directly obviates cytotoxic T cell destruction of infected liver cells, or indirectly limits destruction of infected cells through induction of anergy in the cytotoxic T cell response. Most persons infected with hepatitis B virus recover completely while recovery from HIV infection is rare if ever. Hepatitis B is highly preventable by vaccine while HIV vaccine is still seeking a meaningful immunoprophylactic target. AIDS and hepatitis B represent an extreme example, among the viruses of man, in their close similarities but distinct differences. In depth details and perspectives are presented in this review.
Faculty Opinions recommendation of Time course of isotonic shortening and the underlying contraction mechanism in airway smooth muscle. (2011)

Although the structure of the contractile unit in smooth muscle is poorly understood, some of the mechanical properties of the muscle suggest that a sliding-filament mechanism, similar to that in striated muscle, is also operative in smooth muscle. To test the applicability of this mechanism to smooth muscle function, we have constructed a mathematical model based on a hypothetical structure of the smooth muscle contractile unit: a side-polar myosin filament sandwiched by actin filaments, each attached to the equivalent of a Z disk. Model prediction of isotonic shortening as a function of time was compared with data from experiments using ovine tracheal smooth muscle. After equilibration and establishment of in situ length, the muscle was stimulated with ACh (100 μM) until force reached a plateau. The muscle was then allowed to shorten isotonically against various loads. From the experimental records, length-force and force-velocity relationships were obtained. Integration of the hyperbolic force-velocity relationship and the linear length-force relationship yielded an exponential function that approximated the time course of isotonic shortening generated by the modeled sliding-filament mechanism. However, to obtain an accurate fit, it was necessary to incorporate a viscoelastic element in series with the sliding-filament mechanism. The results suggest that a large portion of the shortening is due to filament sliding associated with muscle activation and that a small portion is due to continued deformation associated with an element that shows viscoelastic or power-law creep after a step change in force. PMID: 21636567 Funding information This work was supported by: Canadian Institutes of Health Research, Canada Grant ID: MOP-37924 Canadian Institutes of Health Research, Canada Grant ID: MOP-13271
Synchronization method employing a cyclic redundancy check in an asynchronous transport system (1990)

Abstract This paper proposes a synchronization method in an asynchronous transport system. In this method, the cyclic redundancy check (CRC) code inserted in each cell for error control is also used for cell alignment recovery. Then frame alignment is established using cell alignment signals. The analyses include CRC detection probability in an out‐of‐synchronization mode, and cell/frame alignment recovery performance. The analyses also include the performance for an extended frame structure in which frame length is not divisible by cell length. This method has the following advantages: (a) this system shows good synchronization performance without using additional synchronization patterns; (b) frame alignment recovery time is reduced considerably using cell alignment signals; (c) this technique is also applicable to the forementioned extended frame structure and performs well.
Explaining the Bias in the 23S rRNA Gene Mutations Associated with Clarithromycin Resistance in Clinical Isolates of Helicobacter pylori (1998)

A single point mutation in the 23S rRNA gene of Helicobacter pylori is known to confer resistance to clarithromycin. Most prevalent among clarithromycin-resistant clinical H. pylori isolates are the mutations from A-2142 to G and A-2143 to G in the 23S rRNA gene. The bias in the 23S rRNA gene mutations conferring clarithromycin resistance may result from the higher MIC, stability of resistance, and growth rate found for the strains with the above-mentioned mutations.
Sensing microscopic directional noise baths with an optically cooled and levitated nanoparticle (2023)

Optomechanical devices are being harnessed as sensors of ultraweak forces for applications ranging from inertial sensing to the search for the elusive dark matter. For the latter, there is a focus on detection of either higher energy single recoils or ultralight, narrowband sources; a directional signal is expected. However, the possibility of searching for a stochastic stream of weak impulses, or more generally a directional broadband signal, need not be excluded; with this and other applications in mind, we investigate the experimental signature of Gaussian white noise impulses with a well defined direction $Ψ$ on a levitated nanosphere, trapped and 3D cooled in an optical tweezer. We find that cross-correlation power spectra offer a calibration-free distinctive signature of the presence of a directional but stochastic microscopic force and its orientation quadrant, unlike normal power spectral densities (PSDs). We obtain excellent agreement between theoretical and experimental results. With calibration we are able to measure the angle $Ψ$, akin to a force compass in a plane. We discuss prospects for extending this technique into quantum regime and compare the expected behaviour of quantum baths and classical baths.
Points, Paths, and Playscapes: Large-scale Spatial Language Understanding Tasks Set in the Real World (2018)

Jason Baldridge, Tania Bedrax-Weiss, Daphne Luong, Srini Narayanan, Bo Pang, Fernando Pereira, Radu Soricut, Michael Tseng, Yuan Zhang. Proceedings of the First International Workshop on Spatial Language Understanding. 2018.
Compressibility Effects in the Analysis and Interpretation of Neutron Scattering Data from Polymer Blends (1996)

A thermodynamically consistent procedure, based on statistical mechanical fluctuation theory, has been developed for the analysis and interpretation of small-angle neutron scattering (SANS) data for compressible polymer blends. The development was motivated by inconsistencies between the interaction parameter obtained with an analysis based on the incompressible Flory−Huggins model, which is a function of composition, and the Flory−Huggins model itself, in which the interaction parameter is independent of composition. An expression is obtained that connects the forward scattering intensity with the curvature of the Gibbs energy for a binary blend of arbitrary compressibility. This expression, which forms the basis of the data analysis procedure, permits the contributions of various effects of compressibility to be estimated without the introduction of specific models. We show that contributions from both density fluctuations and excess volumes of mixing can safely be neglected in the analysis of SANS data for polymer blends. We illustrate the methodology with the lattice fluid model, which expresses the Gibbs energy curvature in terms of microscopic properties, thereby relating to the SANS intensity. A parameter characterizing system interactions can then be defined in terms of three energetic quantities, two of which can be evaluated from pure component PVT data. The remaining quantity, when treated as a system-specific constant, independent of temperature and blend composition, can quantitatively and self-consistently describe SANS data for weakly interacting blends, such as mixtures of saturated hydrocarbon polymers and isotopically substituted species.
Creating secondary spectrum usage opportunity for D2D communication with interference cancellation (2015)

In this demonstration, we consider secondary spectrum usage by D2D users in cellular network. Secondary usage is allowed if primary users are not impacted. We show how a Base Station (BS) creates new D2D communication opportunities on uplink resources by enabling Interference Cancellation (IC). BS can apply single-state IC when the D2D signal is strong enough. This can occur when the D2D transmitter is located near to the BS or when the BS explicitly orders D2D transmitter to increase its transmission power. This demonstration shows that D2D user successfully streams a video without influencing the cellular user's live video streaming on the same spectrum resource. The demonstration is based on software defined radio platform with Universal Software Radio Peripherals (USRP) as the hardware front-ends.
bwtool: a tool for bigWig files (2014)

The C source code is freely available under the GNU public license v3 at http://cromatina.crg.eu/bwtool.
Realization Of A Driver's Warning Assistant For Intersections (1993)

A driver's warning assistant (DWA) is an automatic copilot system that is designes to support the driver in actual traffic situations. In contrast to systems that concentrate on autonomous driving, a DWA presents warning message to a driver instead of acting directly upon the vehicle or the environment. In order to study the feasibility of a DWA's functions and the acceptance of DWA's warning messages, we investigated urban traffic situations, especially approaching an intersection. Based on a system architecture of a DWA, experimental results obtained with a DWA implemented in a passenger car (BMW 735 iL) will be discussed. The experimental car has been equipped with on board facilities to evaluate image sequences and vehicle data in real-time on a transputer network.
Evolution of Technology for Continuous Renal Replacement Therapy: Forty Years of Improvements (2016)

Continuous arteriovenous hemofiltration (CAVH) was proposed in 1977 as an alternative treatment for acute renal failure in patients in whom peritoneal dialysis or hemodialysis was clinically or technically precluded. In the mid-1980s, this technique was extended to infants and children. CAVH presented important advantages in the areas of hemodynamic stability, control of circulating volume, and nutritional support. However, there were serious shortcomings such as the need for arterial cannulation and limited solute clearance. These problems were solved by the introduction of continuous arteriovenous hemodiafiltration and continuous arteriovenous hemodialysis, where uremic control could be achieved by increasing countercurrent dialysate flow rates to 1.5 or 2 L/h as necessary, or by venovenous techniques utilizing a double-lumen central venous catheter for vascular access. Thus, continuous venovenous hemofiltration replaced CAVH because of its improved performance and safety. From the initial adoptive technology, specific machines have been designed to permit safe and reliable performance of the therapy. These new machines have progressively undergone a series of technological steps that have resulted in the evolution of highly sophisticated equipment utilized today. A significant number of advances have taken place since the time continuous renal replacement therapy was initiated. In particular, there have been successful experiments with high-volume hemofiltration and high-permeability hemofiltration. The additional and combined use of sorbent has also been tested successfully. Progress has been made in the technology as well as the understanding of the pathophysiology of acute kidney injury. Today, new biomaterials and new devices are available and new frontiers are on the horizon. Although improvements have been made, a lot remains to be done. Critical care nephrology is expected to further evolve in the near future, especially in the area of information and communication technology, utilization of big data and large database registries, biofeedback, and assisted prescription and treatment delivery, with high potential for improvement in morbidity and mortality of the most severely ill patients.
In-Space Production of Storable Propellants (2016)

Our exploration of the feasibility of in-space production of storable propellants from resourcesavailable on asteroids, and also on Mars and the Moon, has considered the process of sampleacquisition; the energy requirements for heating and volatile release; the thermodynamic behaviorof gas release from minerals and organic polymers containing hydrogen, oxygen, carbon, sulfur,and nitrogen; purification of the released water and carbon dioxide; the storage and transportation of these materials in the condensed state; synthesis of fuels including methanol and dimethyl ether(DME); and the co-production, concentration, stability, and storage of the complementary oxidizer high-test hydrogen peroxide (HTP). We call attention to the ability of the storable propellant/oxidizer combination of DME and HTP to carry out deep-space missions and to perform retrieval and relocation of any and all space-derived resources, such as retrieving asteroidal metal to high Earth orbit. This study's analyses are based on returning resources to a storage/processing/dispensing facility in a Highly Eccentric Earth Orbit (HEEO) with a perigee above geosynchronous orbit and an apogee approach or beyond the Moon's orbit.The methane/LOX option, notable for good engine performance, has not been included in this study because our scope includes only fully storable propellants.
Induction of IRAK-M in melanoma induces caspase-3 dependent apoptosis by reducing TRAF6 and calpastatin levels (2020)

Melanoma represents the most serious type of skin cancer. Although recent years have seen advances using targeted and immunotherapies, most patients remain at high risk for tumor recurrence. Here we show that IRAK-M, a negative regulator of MyD88 signaling, is deficient or low in melanoma and expression levels correlate with patient survival. Inducing IRAK-M expression using genetic approaches or epigenetic modifiers initiates apoptosis by prompting its interaction with TRAF6 via IRAK-M's C-terminal domain. This complex recruits and degrades calpastatin which stimulates calpain activity and triggers caspase-3-dependent but caspase-8,-9-independent apoptosis. Using a drug screen, we identified compounds that induced IRAK-M expression. Administration of IRAK-M-inducing drugs reduced tumor growth in mice but was ineffective against IRAK-M knock-down tumors. These results uncover a previously uncharacterized apoptosis pathway, emphasize IRAK-M as a potential therapeutic target and suggest that the anticancer activity of certain drugs could do so through their ability to induce IRAK-M expression.
Thermal Isomerization of Substituted 5-Aminotetrazoles1 (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermal Isomerization of Substituted 5-Aminotetrazoles1Ronald A. Henry, William G. Finnegan, and Eugene LieberCite this: J. Am. Chem. Soc. 1954, 76, 1, 88–93Publication Date (Print):January 1, 1954Publication History Published online1 May 2002Published inissue 1 January 1954https://pubs.acs.org/doi/10.1021/ja01630a024https://doi.org/10.1021/ja01630a024research-articleACS PublicationsRequest reuse permissionsArticle Views248Altmetric-Citations51LEARN 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
Modeling of transfer phenomena on heterogeneous Ziegler catalysts. III. Modeling of intraparticle mass transfer resistance (1997)

International audience
Isolation, characterization, and inactivation of the APA1 gene encoding yeast diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase (1989)

The gene encoding diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) phosphorylase from yeast was isolated from a lambda gt11 library. The DNA sequence of the coding region was determined, and more than 90% of the deduced amino acid sequence was confirmed by peptide sequencing. The Ap4A phosphorylase gene (APA1) is unique in the yeast genome. Disruption experiments with this gene, first, supported the conclusion that, in vivo, Ap4A phosphorylase catabolizes the Ap4N nucleotides (where N is A, C, G, or U) and second, revealed the occurrence of a second Ap4A phosphorylase activity in yeast cells. Finally, evidence is provided that the APA1 gene product is responsible for most of the ADP sulfurylase activity in yeast extracts.
Paraoxonases (PON) 1, 2, and 3 Polymorphisms and PON-1 Activities in Patients with Sickle Cell Disease (2019)

(1) Background: Oxidative stress, chronic inflammation, vasoocclusion, and free iron are all features present in sickle cell disease. Paraoxonases (PON) are a family (PON-1, PON-2, PON-3) of antioxidant enzymes with anti-inflammatory action. Here, for the first time, we described PON-1 activities and PON-1, PON-2, PON-3 polymorphisms in patients with sickle cell disease, homozygous for HbSS, compared with healthy controls. (2) Methods: The groups were matched for age and gender. PON-1 activities (arylesterase and paraoxonase) were determined by enzymatic hydrolysis of phenylcetate and paraoxon, respectively. Polymorphisms were determined by Restriction Fragment Length Polymorphism- Polymerase Chain Reaction (RFLP-PCR). (3) Results: Plasma cholesterol and fractions, ApoA1 and ApoB levels were all decreased in sickle cell disease patients, while anti-oxidized low-density lipoprotein (LDL) antibodies and C-reactive protein were increased. Serum arylesterase activity was lower in sickle cell disease patients when compared with healthy controls. In patients, paraoxonase activity was higher in those with PON-1 RR Q192R polymorphism. In these patients, the increase of serum iron and ferritin levels and transferrin saturation were less pronounced than those observed in patients with QQ or QR polymorphism. No differences were observed with PON-1 L55M, and PON-2 and PON-3 polymorphisms. Multivariate regression analysis showed that transferrin and ferritin concentrations correlated with arylesterase and paraoxonase activities. (4) Conclusions: Both transferrin and ferritin were the main predictors of decreased arylesterase and paraoxonase activities in patients with sickle cell disease. LDL oxidation increased, and RR PON-1 Q192R polymorphism is likely to be a protective factor against oxidative damage in these patients.
A novel hydrophobically associating water-soluble polymer used as constant rheology agent for cement slurry (2022)

During the process of well cementing in deep water, the cement slurry experiences a wide range of temperature variation from low temperature at seabed to high temperature in downhole. The elevated temperature affects the rheology of cement slurry. The change of rheology of cement slurry could influence the safety of cementing operation. The aim of this paper is to develop a new kind of hydrophobically associating water-soluble polymer (NHAWP) as an additive to prepare a constant rheology oil well cement slurry, which can be used at temperature range from 4°C to 90°C. The acrylamide, 2-acrylamide-2-methylpropionic acid and stearyl methylacrylate were applied to synthesize the NHAWP by the inverse microemulsion polymerization. Test results indicate that the critical association temperature of NHAWP is 45°C. The critical association temperature is independent of NHAWP concentration, salt concentration and alkalinity of solution. When the temperature is below 45°C, NHAWP shows little influence on the viscosity of solution. When the temperature is above 45°C, the NHAWP forms spatial network structure by intermolecular hydrophobic association and thus increases the viscosity of solution significantly. The NHAWP also displays good thermal stability and excellent salt and alkali resistance properties. In addition, the NHAWP shows nearly no negative influence on the basic properties of cement slurry, which indicates that the NHAWP can be used as a constant rheology agent to prepare a cement slurry with constant rheology in the temperature range of 4°C to 90°C.
Hierarchical Path Views: A Model Based on Fragmentation and Transportation Road Types. (1995)

Efficient path query processing necessary for route guidance has been identified as one of the key requirements for Intelligent Transportation Systems (ITS) applications. While precomputing the view of all shortest paths provides the most efficient path retrieval, the view maintenance and storage costs become unrealistic for large ITS networks. Based on ITS road type classification, we propose a hierarchical path view approach, in which the path view maintenance and storage costs are dramatically reduced at the cost of negligible loss of path optimality. Comparing with the traditional ITS path finding approaches that use A or hierarchical A , our hierarchical approach is superior in three areas: 1) path search is more efficient, 2) the connecting point from the low-level roads to the high-level roads and vice versa are dynamically determined based on the most recent traffic, 3) within one region, the high-level traffic can be dynamically rerouted through the low-level roads. In ...
Computer simulation of wayside energy storage substations in DC traction power systems (2010)

This paper describes a computer simulation technique that has been used to evaluate the effectiveness of wayside energy storage substations (WESS). Possible benefits afforded by a WESS, such as train voltage support and energy saving, are presented through the simulation results of a sample light rail transit system. (5 pages)
Study on Solid Cooling by Low-pressure Gas of Normal Temperature (1st report) (2005)

45nmルール以降の次世代リソグラフィ露光装置に搭載が有力視されている低圧ガス冷却方式ウェハチャックシステムの構築を目指し, 新規に伝熱特性評価装置を開発, その装置性能評価を行った. 得られた実験データに有限要素解析によるフィッティングを行う事で, 常温低圧ヘリウムガスの伝熱特性を明らかにする手法を確立した.