gebhart/patrepeval huggingface dataset:
Chemical Synthesis and Antigenicity Evaluation of <i>Shigella dysenteriae</i> Serotype 10 O-Antigen Tetrasaccharide Containing a (<i>S</i>)-4,6-<i>O</i>-Pyruvyl Ketal (2022)

<i>Shigella</i> is the second most common etiologic pathogen responsible for childhood acute diarrhea. An anti-<i>Shigella</i> vaccine is still eagerly awaited due to the increasing drug resistance of this pathogen. The <i>Shigella</i> O-antigen is a promising vaccine target. To identify the immune epitopes of the glycan, the first total synthesis of <i>Shigella dysenteriae</i> serotype 10 O-antigen tetrasaccharide containing a (<i>S</i>)-4,6-<i>O</i>-pyruvyl ketal was completed. The 1,2-<i>trans</i>-β-glycosylation & C2 epimerization and conformational locking strategies facilitated the construction of two 1,2-<i>cis</i>-β-glycosidic linkages. The reactivities of both the glycosyl donor and acceptor were improved by adding electron-donating benzyl groups, enabling an efficient assembly of the tetrasaccharide. The (<i>S</i>)-4,6-<i>O</i>-pyruvyl ketal was introduced at the final stage due to its influence on the glycosylation stereospecificity and efficiency. In addition, (<i>R</i>)-4,6-<i>O</i>-pyruvylated and nonpyruvylated tetrasaccharides and three further fragments were synthesized. Glycan microarray screening revealed that the tetrasaccharide repeating unit is the key antigenic epitope of the O-antigen. Moreover, the (<i>S</i>)-4,6-<i>O</i>-pyruvyl ketal is an essential structural feature of this antigen for designing carbohydrate-based vaccines against <i>S. dysenteriae</i> serotype 10. The comparison of the (<i>S</i>)-4,6-<i>O</i>-pyruvylated glycan and its (<i>R</i>)-epimer will set an example for biological evaluation of other bacterial glycans containing pyruvyl ketals.
Development and Optimization of a Hydrophobic Interaction Chromatography-Based Method of AAV Harvest, Capture, and Recovery (2020)

With many ongoing clinical trials utilizing adeno-associated virus (AAV) gene therapy, it is necessary to find scalable and serotype-independent primary capture and recovery methods to allow for efficient and robust manufacturing processes. Here, we demonstrate the ability of a hydrophobic interaction chromatography membrane to capture and recover AAV1, AAV5, AAV8, and AAV "Mutant C" (a novel serotype incorporating elements of AAV3B and AAV8) particles from cell culture media and cell lysate with recoveries of 76%-100% of loaded material, depending on serotype. A simple, novel technique that integrates release and recovery of cell-associated AAV capsids is demonstrated. We show that by the addition of lyotropic salts to AAV-containing cell suspensions, AAV is released at an equivalent efficiency to mechanical lysis. The addition of the lyotropic salt also promotes a phase separation, which allows physical removal of large amounts of DNA and insoluble cellular debris from the AAV-containing aqueous fraction. The AAV is then captured and eluted from a hydrophobic interaction chromatography membrane. This integrated lysis and primary capture and recovery technique facilitates substantial removal of host-cell DNA and host-cell protein impurities.
An analytical approach to determine the optimal duration of continuous glucose monitoring data required to reliably estimate time in hypoglycemia (2020)

Diabetes is a chronic metabolic disease that causes blood glucose (BG) concentration to make dangerous excursions outside its physiological range. Measuring the fraction of time spent by BG outside this range, and, specifically, the time-below-range (TBR), is a clinically common way to quantify the effectiveness of therapies. TBR is estimated from data recorded by continuous glucose monitoring (CGM) sensors, but the duration of CGM recording guaranteeing a reliable indicator is under debate in the literature. Here we framed the problem as random variable estimation problem and studied the convergence of the estimator, deriving a formula that links the TBR estimation error variance with the CGM recording length. Validation is performed on CGM data of 148 subjects with type-1-diabetes. First, we show the ability of the formula to predict the uncertainty of the TBR estimate in a single patient, using patient-specific parameters; then, we prove its applicability on population data, without the need of parameters individualization. The approach can be straightforwardly extended to other similar metrics, such as time-in-range and time-above-range, widely adopted by clinicians. This strengthens its potential utility in diabetes research, e.g., in the design of those clinical trials where minimal CGM monitoring duration is crucial in cost-effectiveness terms.
Applications of a cell culture system for studying the interaction of<i>Anaplasma</i>marginale with tick cells (2002)

A cell culture system for the tick-borne rickettsia Anaplasma marginale offers new opportunities for research on this economically important pathogen of cattle. A. marginale multiplies in membrane-bound inclusions in host cells. Whereas erythrocytes appear to be the only site of infection in cattle, A. marginale undergoes a complex developmental cycle in ticks and transmission occurs via the salivary glands during feeding. We recently developed a cell culture system for A. marginale using a cell line derived from embryos of Ixodes scapularis. Here we review the use of this cell culture system for studying the interaction of A. marginale with tick cells. Several assays were developed using the A. marginale/tick cell system. An adhesion assay was developed for the identification of proteins required by A. marginale for adhesion to tick cells. The effect of antibodies against selected major surface proteins in inhibiting A. marginale infection was tested in an assay that allowed further confirmation of the role of surface proteins in the infection of tick cells. A drug screening assay for A. marginale was developed and provides a method of initial drug selection without the use of cattle. The culture system was used to test for enhancing effects of tick saliva and saliva components on A. marginale infection. The tick cell culture system has proved to be a good model for studying A. marginale-tick interactions. Information gained from these studies may be applicable to other closely related tick-borne pathogens that have been propagated in the same tick cell line.
RTCP for inter-destination media synchronization (2011)

This document gives information on an RTCP Packet Type and RTCP XR
Block Type including associated SDP parameters for inter-destination
media synchronization (IDMS). The RTCP XR Block Type, registered with
IANA based on an ETSI specification, is used to collect media play-
out information from participants in a group playing-out (watching,
listening, etc.) a specific RTP media stream. The RTCP packet type
specified by this document is used to distribute a summary of the
collected information so that the participants can synchronize play-
out. Typical applications for IDMS are social TV, shared service
control (i.e. applications where two or more geographically separated
users are watching a media stream together), distance learning,
network quiz shows, multi-playing online games, etc.
Measuring the group velocity dispersion of higher order modes in hollow core photonic bandgap fibre (2015)

We present for the first time the group velocity dispersion of multiple distinguishable modes propagating in 3, 7 and 19 cell hollow core photonic bandgap fibres. Measurements are made by direct phase extraction from spectral domain low coherence interferometry.
Wyner-Ziv Coding for the Half-Duplex Relay Channel (2006)

Cover and El Gamal derived the tightest bounds on the capacity of the relay channel using random coding and proposed two coding strategies, namely decode-and-forward (DF) and compress-and-forward (CF), to provide the best known lower bounds of the achievable rate region. Depending on transmission parameters, either DF or CF could be superior. Several practical code designs based on DF have appeared recently. We present the first practical CF design for the half-duplex Gaussian relay channel based on Wyner-Ziv coding of the received source signal at the relay. Assuming ideal source and channel coding, our design achieves the lower bound of CF. It thus realizes the performance gain of CF over DF promised by the theory when the relay is close to the destination. Our practical implementation based on LDPC codes for error protection at the source and nested scalar quantization and IRA (irregular repeat-accumulate) codes for Wyner-Ziv coding at the relay comes as close as 0.76 dB to the theoretical limit of CF.
Progressive collapse risk of steel framed building considering column buckling (2022)

Steel buildings are generally susceptible to the risk of progressive collapse in case one or a few load-carrying members are lost in an extreme event such as blast, impact, or fire. Thus, to avoid the catastrophic collapse of steel structures, it is imperative to investigate and learn from the performance of existing steel buildings for progressive collapse potential. The Ohio Union building, a multi-story steel-framed building that existed on the campus of Ohio State University, was tested earlier before its demolition by one of the co-authors for progressive collapse assessment under the successive removal of four columns located at the first-story level. The aim of this study is to conduct NLD (nonlinear dynamic) analysis for the building considering buckling of columns to numerically assess its potential for progressive collapse and then compare it with test observations. The calibrated finite element (FE) model was then extended to incorporate more hypothetical sequential and simultaneous column-loss scenarios. As one of the most widely accepted documents used among practicing engineers for numerical assessment of progressive collapse potential of buildings, the 2003 GSA (General Services Administration) guidelines were also applied. The simplified LS (linear static) analysis approach of the GSA guidelines was used for assessing the progressive collapse risk of the building, and the results were then compared with both test observations and NLD analysis. New dynamic increase factors (DIFs) are recommended for both force- and deformation-controlled actions to be used with the LS analysis.
Single photon nonlinear optics in photonic crystals (2009)

We coherently probe a quantum dot that is strongly coupled to a photonic crystal nano-cavity by scattering of a resonant laser beam. The coupled system's response is highly nonlinear as the quantum dot saturates with nearly one photon per cavity lifetime. This system enables large amplitude and phase shifts of a signal beam via a control beam, both at single photon levels. We demonstrate photon-photon interactions with short pulses in a system that is promising for ultra-low power switches and two-qubit quantum gates.
Optimal Cluster Mill Pass Scheduling With an Accurate and Rapid New Strip Crown Model (2007)

Besides the requirement to roll coiled sheet at high levels of productivity, the optimal pass scheduling of cluster‐type reversing cold mills presents the added challenge of assigning mill parameters that facilitate the best possible strip flatness. The pressures of intense global competition, and the requirements for increasingly thinner, higher quality specialty sheet products that are more difficult to roll, continue to force metal producers to commission innovative flatness‐control technologies. This means that during the on‐line computerized set‐up of rolling mills, the mathematical model should not only determine the minimum total number of passes and maximum rolling speed, it should simultaneously optimize the pass‐schedule so that desired flatness is assured, either by manual or automated means. In many cases today, however, on‐line prediction of strip crown and corresponding flatness for the complex cluster‐type rolling mills is typically addressed either by trial and error, by approximate deflection models for equivalent vertical roll‐stacks, or by non‐physical pattern recognition style models. The abundance of the aforementioned methods is largely due to the complexity of cluster‐type mill configurations and the lack of deflection models with sufficient accuracy and speed for on‐line use. Without adequate assignment of the pass‐schedule set‐up parameters, it may be difficult or impossible to achieve the required strip flatness. In this paper, we demonstrate optimization of cluster mill pass‐schedules using a new accurate and rapid strip crown model. This pass‐schedule optimization includes computations of the predicted strip thickness profile to validate mathematical constraints. In contrast to many of the existing methods for on‐line prediction of strip crown and flatness on cluster mills, the demonstrated method requires minimal prior tuning and no extensive training with collected mill data. To rapidly and accurately solve the multi‐contact problem and predict the strip crown, a new customized semi‐analytical modeling technique that couples the Finite Element Method (FEM) with classical solid mechanics was developed to model the deflection of the rolls and strip while under load. The technique employed offers several important advantages over traditional methods to calculate strip crown, including continuity of elastic foundations, non‐iterative solution when using predetermined foundation moduli, continuous third‐order displacement fields, simple stress‐field determination, and a comparatively faster solution time.
Antimicrobial peptides: key components of the innate immune system (2011)

Life-threatening infectious diseases are on their way to cause a worldwide crisis, as treating them effectively is becoming increasingly difficult due to the emergence of antibiotic resistant strains. Antimicrobial peptides (AMPs) form an ancient type of innate immunity found universally in all living organisms, providing a principal first-line of defense against the invading pathogens. The unique diverse function and architecture of AMPs has attracted considerable attention by scientists, both in terms of understanding the basic biology of the innate immune system, and as a tool in the design of molecular templates for new anti-infective drugs. AMPs are gene-encoded short (<100 amino acids), amphipathic molecules with hydrophobic and cationic amino acids arranged spatially, which exhibit broad spectrum antimicrobial activity. AMPs have been the subject of natural evolution, as have the microbes, for hundreds of millions of years. Despite this long history of co-evolution, AMPs have not lost their ability to kill or inhibit the microbes totally, nor have the microbes learnt to avoid the lethal punch of AMPs. AMPs therefore have potential to provide an important breakthrough and form the basis for a new class of antibiotics. In this review, we would like to give an overview of cationic antimicrobial peptides, origin, structure, functions, and mode of action of AMPs, which are highly expressed and found in humans, as well as a brief discussion about widely abundant, well characterized AMPs in mammals, in addition to pharmaceutical aspects and the additional functions of AMPs.
Antineoplastic Agents. 545. Isolation and Structure of Turbostatins 1−4 from the Asian Marine Mollusk<i>Turbo stenogyrus</i><sup>,1</sup> (2005)

The cancer cell line bioassay-guided separation of an extract from the marine mollusk Turbo stenogyrus led to the isolation of four new cerebrosides designated turbostatins 1-4 (1-4). The structure of each glycolipid was determined by interpreting results of a series of HR-APCI-MS and NMR (1D and 2D) spectral analyses. All four turbostatins exhibited significant (GI50 0.15-2.6 microg/mL) cancer cell growth inhibition against the murine P388 lymphocytic leukemia and a panel of human cancer cell lines.
A facile synthesis of substituted 3-amino-1<i>H</i>-quinazoline-2,4-diones (2005)

A new synthesis of a series of 3-amino-1H-quinazoline-2,4-diones is described. The 1H-quinazoline-2,4-dione 10 was made starting with fluorobenzoic acid in three high yielding steps. The key step of this synthesis involved the generation of the dianion of urea 7 and the subsequent intramolecular nucleophilic displacement of the 2-fluoro to form the quinazolinedione ring. The 3-amino moiety was incorporated using (2,4-dinitro-phenyl)-hydroxylamine as the aminating reagent.
Kerr nonlinearity induced optical frequency comb generation in microcavities (2007)

It is shown that the optical sidebands generated via optical parametric oscillations in a monolithic microcavity are equidistant thus overcoming the intrinsic cavity dispersion. This leads to the generation of optical frequency combs at input powers < 10 mW.
Nonlinear weighted feedback control of groundwater remediation under uncertainty (1993)

Differential dynamic programming is used to compute optimal time‐varying pumping policies for a pump and treat strategy for groundwater remediation. The feedback law generated by a constrained differential dynamic programming algorithm with penalty functions is used as the basis of feedback laws tested in cases where there is uncertainty in the hydraulic conductivity. Confined transient aquifer flow and transport are modeled using a two‐dimensional Galerkin finite element scheme with implicit time differencing. Optimal policies are calculated using a given or “measured” set of hydraulic conductivities and initial conditions. The optimal policies (with and without feedback) are applied using the same finite element model with a second or “true” set of conductivities. The “true” sets of conductivities are generated randomly from an autocorrelated lognormal distribution by the spectral method. The approach used here has an advantage over other uncertainty approaches because it is not necessary to specify precisely which parameters are considered uncertain and which are certain. Also no single probability distribution need be assumed for each uncertain parameter. By adjusting the relative weight assigned each penalty function, robust feedback laws were obtained that perform equally well under nine different assumed error distributions. In our examples, well‐designed feedback policies cost between 4% and 51% less than the cost of applying the calculated optimal policies without using a feedback law.
Rate-Adaptive Irregular QC-LDPC Codes from Pairwise Balanced Designs for Ultra-High-Speed Optical Transport (2013)

A rate-adaptive, software-defined, coded-modulation scheme based on irregular quasi-cyclic LDPC codes designed using the concept of pairwise balanced designs is proposed. The proposed scheme outperforms the corresponding scheme based on regular LDPC codes, and eliminates the error floor phenomenon of regular LDPC codes.
Preparation and properties of stacked oligomeric and polymeric metallocenes (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and properties of stacked oligomeric and polymeric metallocenesRegina Arnold, Stephen A. Matchett, and Myron RosenblumCite this: Organometallics 1988, 7, 11, 2261–2266Publication Date (Print):November 1, 1988Publication History Published online1 May 2002Published inissue 1 November 1988https://pubs.acs.org/doi/10.1021/om00101a002https://doi.org/10.1021/om00101a002research-articleACS PublicationsRequest reuse permissionsArticle Views501Altmetric-Citations49LEARN 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
Miniature, sub-nanometer resolution Talbot spectrometer (2016)

Miniaturization of optical spectrometers has a significant practical value as it can enable compact, affordable spectroscopic systems for chemical and biological sensing applications. For many applications, the spectrometer must gather light from sources that span a wide range of emission angles and wavelengths. Here, we report a lens-free spectrometer that is simultaneously compact (<0.6 cm<sup>3</sup>), of high resolution (<1 nm), and has a clear aperture (of 10×10 mm). The wavelength-scale pattern in the dispersive element strongly diffracts the input light to produce non-paraxial mid-field diffraction patterns that are then recorded using an optimally matched image sensor and processed to reconstruct the spectrum.
Discovery of Face-Centered-Cubic Ruthenium Nanoparticles: Facile Size-Controlled Synthesis Using the Chemical Reduction Method (2013)

We report the first discovery of pure face-centered-cubic (fcc) Ru nanoparticles. Although the fcc structure does not exist in the bulk Ru phase diagram, fcc Ru was obtained at room temperature because of the nanosize effect. We succeeded in separately synthesizing uniformly sized nanoparticles of both fcc and hcp Ru having diameters of 2-5.5 nm by simple chemical reduction methods with different metal precursors. The prepared fcc and hcp nanoparticles were both supported on γ-Al2O3, and their catalytic activities in CO oxidation were investigated and found to depend on their structure and size.
Spatially Multiplexed Bioparticle Detection Using Multi-mode Interference (2016)

On-chip fluorescence multiplexed detection of bioparticles is achieved by using a single multi-mode interference waveguide and a single wavelength light source to create different number of spots on three liquid-core waveguides in an optofluidic platform.
ChemInform Abstract: Induced Helical Backbone Conformations of Self‐Organizable Dendronized Polymers (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53 (2013)

The tumour suppressor p53 is the most frequently mutated gene in human cancer. Reactivation of mutant p53 by small molecules is an exciting potential cancer therapy. Although several compounds restore wild-type function to mutant p53, their binding sites and mechanisms of action are elusive. Here computational methods identify a transiently open binding pocket between loop L1 and sheet S3 of the p53 core domain. Mutation of residue Cys124, located at the centre of the pocket, abolishes p53 reactivation of mutant R175H by PRIMA-1, a known reactivation compound. Ensemble-based virtual screening against this newly revealed pocket selects stictic acid as a potential p53 reactivation compound. In human osteosarcoma cells, stictic acid exhibits dose-dependent reactivation of p21 expression for mutant R175H more strongly than does PRIMA-1. These results indicate the L1/S3 pocket as a target for pharmaceutical reactivation of p53 mutants.
Characterization of HydH5 lytic activity, the virion-associated peptidoglycan hydrolase of Staphylococcus aureus bacteriophage vB_SauS-philPLA88 (2011)

Microbial viruses: genomics, evolution and application in ecology, biotechnology and medicine. April 19-20 2011, Queen's University Belfast.