gebhart/patrepeval huggingface dataset:
Cross-reactive antibodies facilitate innate sensing of dengue and Zika viruses (2022)

The Aedes aegypti mosquito transmits both dengue virus (DENV) and Zika virus (ZIKV) . Individuals in endemic areas are at risk for infection with both viruses, as well as for repeated DENV infection. In the presence of anti-DENV antibodies, outcomes of secondary DENV infection range from mild to life threatening. Furthermore, the role of cross-reactive antibodies on the course of ZIKV infection remains unclear. We assessed the ability of cross-reactive DENV mAbs or polyclonal immunoglobulin isolated after DENV vaccination to upregulate type I IFN production by plasmacytoid DCs (pDCs) in response to both heterotypic DENV- and ZIKV-infected cells. We found a range in the ability of antibodies to increase pDC IFN production and a positive correlation between IFN production and the ability of an antibody to bind to the infected cell surface. Engagement of Fc receptors on the pDC and engagement of epitope on the infected cell by the Fab portion of the same antibody molecule was required to mediate increased IFN production by providing specificity to and promoting pDC sensing of DENV or ZIKV. This represents a mechanism independent of neutralization by which preexisting cross-reactive DENV antibodies could protect a subset of individuals from severe outcomes during secondary heterotypic DENV or ZIKV infection.
Comparison of Time–Frequency Responses and the Event-Related Potential to Auditory Speech Stimuli in Human Cortex (2009)

We recorded the electrocorticogram directly from the exposed cortical surface of awake neurosurgical patients during the presentation of auditory syllable stimuli. All patients were unanesthetized as part of a language-mapping procedure for subsequent left-hemisphere tumor resection. Time-frequency analyses showed significant high-gamma (gammahigh: 70-160 Hz) responses from the left superior temporal gyrus, but no reliable response from the left inferior frontal gyrus. Alpha suppression (alpha: 7-14 Hz) and event-related potential responses exhibited a more widespread topography. Across electrodes, the alpha suppression from 200 to 450 ms correlated with the preceding (50-200 ms) gammahigh increase. The results are discussed in terms of the different physiological origins of these electrocortical signals.
3-D simulations of rigid microwave-propelled sails including spin (2001)

This paper discusses the three-dimensional (3-D) stability of carbon fiber sail structures (beam riders) that are being studied in a series of experiments at the Jet Propulsion Laboratory (JPL) and U.C. Irvine by a team led by Microwave Sciences, Inc. The stability analysis is developed for a limited set of conical sail configurations, and the code described in this paper has been developed at JPL by one of the coauthors. The assumptions in the model and the principles behind the simulation, in addition to their relationship to earlier experiments utilizing disk configurations are discussed. Results of stability analyses for several beam rider configurations will be presented at the Forum.
Land‐Atmosphere Interactions at a Semi‐Arid Region in the Deccan Plateau (2022)

Abstract Comprehensive characterization of turbulent fluxes and land‐atmosphere interactions at a semi‐arid region in the Deccan Plateau of peninsular India is presented using 2‐year eddy covariance measurements. Contrary to previously reported results over the Indian region, surface energy partitioning is more into sensible heat flux than latent heat flux, even during the monsoon season. Irrespective of the seasons, the soil moisture and its response to rainfall drive the land‐atmosphere interactions and along with the net radiation, play crucial roles in deciding the surface fluxes and its partitioning. Time series comparison with ERA5 reanalysis data reveals the inadequate representation of land‐atmosphere interactions in ERA5 reanalysis over the peninsular Indian region, particularly the intensity and duration of rainfall and the feedbacks of soil moisture to the atmosphere. The surface energy balance closure improves by ∼3% when the soil heat storage term is considered and is the highest when the height and scatter of the roughness elements around the measurement site are the lowest. The influence of rainfall on energy balance closure is lower as compared to land surface heterogeneity. The present study also fills an existing gap of validating the surface fluxes and its partitioning in ERA5 reanalysis in the tropics and will provide deeper insights on the land‐atmosphere interactions in tropical semi‐arid regions.
On the Arctic climate paradox and the continuing role of atmospheric circulation in affecting sea ice conditions (2007)

The reduction in ice cover observed in the late 1980s and early 1990s has been attributed to the strongly positive Arctic Oscillation (AO) phase during that time. However, despite a change in the AO to more neutral conditions since then, ice extent and the fraction of old ice have continued to decrease. This mismatch between the AO index and loss of ice can be explained by the frequency of three main sea level pressure (SLP) patterns that yield overall variability in SLP, rather than the presence of a single, coherent physical pattern of SLP reduction associated with the positive mode of the AO. These three patterns were in phase during the peak AO period but their frequency has varied differently since then, with two of the patterns continuing to contribute to reduced ice cover in the western Arctic. Hence, regional atmospheric circulation remains a significant factor in recent reductions in ice cover.
Reaction of Azides with Tetrathiomolybdate: Reduction and Imine Formation (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of Azides with Tetrathiomolybdate: Reduction and Imine FormationA. R. Ramesha, Shridhar Bhat, and Srinivasan ChandrasekaranCite this: J. Org. Chem. 1995, 60, 23, 7682–7683Publication Date (Print):November 1, 1995Publication History Published online1 May 2002Published inissue 1 November 1995https://doi.org/10.1021/jo00128a048RIGHTS & PERMISSIONSArticle Views1281Altmetric-Citations50LEARN 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 InReddit PDF (277 KB) Get e-AlertscloseSupporting Info (3)»Supporting Information Supporting Information Get e-Alerts
Repression of Retinoic Acid-Induced Transactivation by Embryonal LTR Binding Protein1 (1994)

The mechanism of repression of transcription by ELP, the embryonal long terminal repeat binding protein, was investigated. ELP represses the Moloney murine leukemia virus long terminal repeat by binding to a site which overlaps with a sequence element for retinoic acid receptor binding. This suggests possible competition of ELP with retinoic acid receptor for the same sequence elements. Oligonucleotides corresponding to ELP and/or retinoic acid receptor binding elements were placed upstream of the SV40 promoter and their effect on gene expression was analyzed by CAT assay. Elements which have affinity to both ELP and retinoic acid receptor were activated by retinoic acid receptor and these activations were repressed by ELP. An ELP binding element without affinity to retinoic acid receptor was insensitive to both activation by retinoic acid receptor and repression by ELP. Furthermore, cellular ELP binding elements and the Moloney leukemia virus long terminal repeat were activated by retinoic acid. These data suggest that one of the mechanism of transcriptional repression by ELP is competition for binding sites with transactivators such as retinoic acid receptors.
Cryptographic hash functions from expander graphs. (2006)

Abstract. We propose constructing provable collision resistant hash functions from expander graphs. As examples, we investigate two specific families of optimal expander graphs for provable hash function constructions: the families of Ramanujan graphs constructed by Lubotzky-Phillips-Sarnak and Pizer respectively. When the hash function is constructed from one of Pizer’s Ramanujan graphs, (the set of supersingular elliptic curves over Fp2 with ℓ-isogenies, ℓ a prime different from p), then collision resistance follows from hardness of computing isogenies between supersingular elliptic curves. We estimate the cost per bit to compute these hash functions, and we implement our hash function for several members of the LPS graph family and give actual timings. 1
A Self‐Immolative Reporter For β‐Galactosidase Sensing (2007)

A dual fluorogenic and chromogenic probe, Gal-2SBPO, has been developed based on a synthesized water-soluble dye, 9-di-3-sulfonyl-propylaminobenzo[a]phenoxazonium perchloride (2SPBO, lambda(ex/em)=630/670 nm). beta-D-Galactopyranoside, the substrate of beta-galactosidase, was conjugated to 2SBPO through a para-substituted benzyloxycarbonyl group and a glycine residue, which serve as a self-immolative spacer and as a molecular blocker to mask the optical signal of 2SBPO, respectively. Gal-2SBPO was soluble and stable under physiological conditions. Enzymatic cleavage of the beta-D-galactopyranoside triggered a series of spontaneous reactions that resulted in a release of optically active 2SBPO. The beta-galactosidase activity was assayed by monitoring the absorbance at 630 nm and fluorescence at 670 nm.
E-process design and assurance using model checking (2000)

Trust in e-commerce is difficult to establish and maintain. Almost daily, news headlines cover some incident, causing users to question e-commerce systems' trustworthiness. Strong e-process design and implementation is the first line of defense against errors, fraud and hacking. Minimizing program faults in business operations is critical for an e-business's survival. Carefully designed and implemented code can handle most expected situations, so these e-processes often function well within their defined boundaries, but guaranteeing correct processing under all circumstances is extremely difficult, if not impossible. Hidden flaws and errors, triggered only under unexpected, hard-to-anticipate scenarios, lead to subtle mistakes and even catastrophic failures. The authors use an online ticket sales example to illustrate the potential of model checking (an advanced formal method) for economically finding certain flaws. Model checking is a powerful verification method that determines whether a system model satisfies certain specifications under all circumstances. It can locate subtle but critical flaws that conventional design and assurance methods, such as testing and simulation, often miss.
Effect of dimensionality on the percolation threshold of overlapping nonspherical hyperparticles (2013)

We study the effect of dimensionality on the percolation threshold η(c) of identical overlapping nonspherical convex hyperparticles in d-dimensional Euclidean space R(d). This is done by formulating a scaling relation for η(c) that is based on a rigorous lower bound [Torquato, J. Chem. Phys. 136, 054106 (2012)] and a conjecture that hyperspheres provide the highest threshold, for any d, among all convex hyperparticle shapes (that are not a trivial affine transformation of a hypersphere). This scaling relation also exploits the recently discovered principle that low-dimensional continuum percolation behavior encodes high-dimensional information. We derive an explicit formula for the exclusion volume v(ex) of a hyperparticle of arbitrary shape in terms of its d-dimensional volume v, surface area s, and radius of mean curvature R[over ¯] (or, equivalently, mean width). These basic geometrical properties are computed for a wide variety of nonspherical hyperparticle shapes with random orientations across all dimensions, including, among other shapes, various polygons for d=2, Platonic solids, spherocylinders, parallepipeds, and zero-volume plates for d=3 and their appropriate generalizations for d≥4. Using this information, we compute the lower bound and scaling relation for η(c) for this comprehensive set of continuum percolation models across dimensions. We demonstrate that the scaling relation provides accurate upper-bound estimates of the threshold η(c) across dimensions and becomes increasingly accurate as the space dimension increases.
A clock skew absorbing flip-flop (2003)

A 0.11/spl mu/m 1.2V CMOS flip-flop absorbs up to 50ps of clock skew. Measured results confirm 27% delay and 33% energy-delay product improvement over previously reported flip-flops, regardless of clock skew.
Dendritic cells focus CTL responses toward highly conserved and topologically important HIV-1 epitopes (2021)

Background: During early HIV-1 infection, immunodominant T cell responses to highly variable epitopes lead to the establishment of immune escape virus variants. Here we assessed a type 1-polarized monocyte-derived dendritic cell (MDC1)-based approach to selectively elicit cytotoxic T lymphocyte (CTL) responses against highly conserved and topologically important HIV-1 epitopes in HIV-1-infected individuals from the Thailand RV254/SEARCH 010 cohort who initiated antiretroviral therapy (ART) during early infection (Fiebig stages I-IV). Methods: Autologous MDC1 were used as antigen presenting cells to induce in vitro CTL responses against HIV-1 Gag, Pol, Env, and Nef as determined by flow cytometry and ELISpot assay. Ultra-conserved or topologically important antigens were respectively identified using the Epigraph tool and a structure-based network analysis approach and compared to overlapping peptides spanning the Gag proteome. Findings: MDC1 presenting either the overlapping Gag, Epigraph, or Network 14–21mer peptide pools consistently activated and expanded HIV-1-specific T cells to epitopes identified at the 9–13mer peptide level. Interestingly, some CTL responses occurred outside known or expected HLA associations, providing evidence of new HLA-associated CTL epitopes. Comparative analyses demonstrated more sequence conservation among Epigraph antigens but a higher magnitude of CTL responses to Network and Gag peptide groups. Importantly, CTL responses against topologically constrained Gag epitopes contained in both the Network and Gag peptide pools were selectively enhanced in the Network pool-initiated cultures. Interpretation: Our study supports the use of MDC1 as a therapeutic strategy to induce and focus CTL responses toward putative fitness-constrained regions of HIV-1 to prevent immune escape and control HIV-1 infection. Funding: A full list of the funding sources is detailed in the Acknowledgment section of the manuscript.
Step-by-Step Uncoordination of the Pyrazolyl Rings of Hydrotris(pyrazolyl)borate Ligands in Complexes of RhI and RhIII (2001)

Compounds of rhodium(I) and rhodium(III) that contain ancillary hydrotris(pyrazolyl)borate ligands (Tp') react with monodentate and bidentate tertiary phosphanes in a step-wise manner, with incorporation of P-donor atoms and concomitant replacement of the Tp' pyrazolyl rings. Accordingly, [Rh(kappa3-TpMe2)(C2H4)(PMe3)] (1b), converts initially into [Rh(kappa2-TpMe2)-(PMe3)2] (3), and then into [Rh(kappa1-TpMe2)-(PMe3)3] (2) upon interaction with PMe3 at room temperature, in a process which can be readily reversed under appropriate experimental conditions. Full disengagement of the Tp' ligand is feasible to give Tp' salts of rhodium(I) complex cations, for example, [Rh(CO)(dppp)2]-[TpMe2,4-Cl] (5; dppp = Ph2P(CH2)3PPh2), or [Rh(dppp)2][TpMe2,4-Cl] (6). Bis(hydride) derivatives of rhodium(III) exhibit similar substitution chemistry, for instance, the neutral complex [Rh(Tp)-(H)2(PMe3)] reacts at 20 degrees C with an excess of PMe3 to give [Rh(H)2-(PMe3)4][Tp] (9b). Single-crystal X-ray studies of 9b, conducted at 143 K, demonstrate the absence of bonding interactions between the [Rh(H)2(PMe3)4]+ and Tp ions, the closest Rh...N contact being at 4.627 A.
Concise Palladium-Catalyzed Synthesis of Dibenzodiazepines and Structural Analogs (2011)

A general and highly efficient protocol for the synthesis of dibenzodiazepines and their structural analogues is reported. In the presence of catalytic quantities of palladium, readily accessible precursors are cross-coupled with ammonia and then spontaneously undergo an intramolecular condensation to form the corresponding dibenzodiazepines in one step. This new strategy is applicable to the construction of a wide variety of dibenzooxazepines and other structurally related heterocycles.
Multifunctional Mesoporous Ionic Gels and Scaffolds Derived from Polyhedral Oligomeric Silsesquioxanes (2017)

A new methodology for fabrication of inorganic-organic hybrid ionogels and scaffolds is developed through facile cross-linking and solution extraction of a newly developed ionic polyhedral oligomeric silsesquioxane with inorganic core. Through design of various cationic tertiary amines, as well as cross-linkable functional groups on each arm of the inorganic core, high-performance ionogels are fabricated with excellent electrochemical stability and unique ion conduction behavior, giving superior lithium ion battery performance. Moreover, through solvent extraction of the liquid components, hybrid scaffolds with well-defined, interconnected mesopores are utilized as heterogeneous catalysts for the CO<sub>2</sub>-catalyzed cycloaddition of epoxides. Excellent catalytic performance, as well as highly efficient recyclability are observed when compared to other previous literature materials.
Microbial Production of Plant‐Derived Pharmaceutical Natural Products through Metabolic Engineering: Artemisinin and beyond (2011)

This chapter contains sections titled: The Case for Microbial Production of Plant-Derived Pharmaceuticals Using Artemisinin to Establish an Isoprenoid Biosynthesis Platform Terpene Indole Alkaloids: Expanding upon the Mevalonate Pathway Benzylisoquinoline Alkaloids (BIAs): Revisiting Plant-Derived Enzyme Overexpression Conclusions References
In vivo role of ER-associated peptidase activity in tailoring peptides for presentation by MHC class Ia and class Ib molecules (2006)

Endoplasmic reticulum (ER)-associated aminopeptidase (ERAP)1 has been implicated in the final proteolytic processing of peptides presented by major histocompatibility complex (MHC) class I molecules. To evaluate the in vivo role of ERAP1, we have generated ERAP1-deficient mice. Cell surface expression of the class Ia molecules H-2Kb and H-2Db and of the class Ib molecule Qa-2 was significantly reduced in these animals. Although cells from mutant animals exhibited reduced capacity to present several self- and foreign antigens to Kb-, Db-, or Qa-1b-restricted CD8+ cytotoxic T cells, presentation of some antigens was unaffected or significantly enhanced. Consistent with these findings, mice generated defective CD8+ T cell responses against class I-presented antigens. These findings reveal an important in vivo role of ER-associated peptidase activity in tailoring peptides for presentation by MHC class Ia and class Ib molecules.
Ultra-Low Phase Noise Measurement of Microwave Sources Using Carrier Suppression Enabled by a Photonic Delay Line (2021)

We propose and demonstrate a photonic delay line based carrier suppression interferometer system for measuring the phase noise of microwave sources. We show both theoretically and experimentally for the first time that carrier suppression is capable of suppressing the effects of the residual phase noise of the microwave amplifiers and the relative intensity noise of light in the system by up to 70 dB, and therefore effectively eliminates the contributions of these noise sources to the noise floor of the phase noise measurement system. Using a 2-km photonic delay line, we achieved phase noise measurement floors of −126 dBc/Hz at 1 kHz and −152 dBc/Hz at 10 kHz around a 10 GHz carrier, respectively, which are 15 and 20 dB lower than those of a frequency discriminator based phase noise measurement system using the same length of fiber delay and the same optical and microwave components. The noise floor of −152 dBc/Hz at 10 kHz is also 8 dB and 17 dB lower than those of a Keysight E5052B phase noise measurement system with 100-times cross-correlation and without cross-correlation, respectively. Even lower phase noise floors are expected for such a carrier suppression system if microwave phase shifters with lower residual phase noise or a longer photonics delay line are used.
Fabrication of metal nanorod arrays using anodic porous alumina mask with elliptical apertures prepared by lattice conversion process (2020)

Abstract Highly ordered Au nanorod arrays were fabricated using anodic porous alumina with elliptical nanoholes as an evaporation mask and applied as a substrate for measurements of surface-enhanced Raman scattering (SERS) spectra. Shape of nanoholes in anodic porous alumina obtained by self-ordering anodization process is usually circular. In the present study, elliptical nanoholes ordered in rectangular lattice were successfully fabricated by lattice conversion process using naturally ordered anodic porous alumina. The Au nanorod arrays were fabricated by thermal evaporation using the obtained anodic porous alumina. The SERS activity of the Au nanorods were higher than that of a circular Au nanodots.
A positron-probe system for arterial input function quantification for positron emission tomography in humans (2008)

We developed an intra-arterial positron-probe (beta(+)-probe) system to measure the arterial time-activity concentration in humans for quantitative compartmental modeling of positron emission tomography studies. Performance was characterized in vitro, by using a uniform phantom to calculate dead time, linearity, and absolute detector sensitivity. In vitro evaluations in a uniform phantom showed a system dead time of 2.5 micros, linear regression between measured and true count rates with R(2)=0.999, and detector sensitivity of 6.9-7.0 counts/s kBq(-1) ml. These met or exceeded values of previously reported systems.
Screening soft materials for their effect on skin barrier function by high throughput experimentation (2005)

Some of the challenges in applying high throughput experimentation (HTE) to materials in contact with natural media or tissues are outlined, with an emphasis on soft materials applied to biological surfaces, such as skin. We overview approaches to soft materials development and to assaying, in high throughput, how such soft materials affect skin barrier properties and skin irritation. The efficacy of an HTE approach in this area is already evidenced in the recent discovery of SCOPE formulations, synergistic combinations of chemical penetration enhancers (CPE) that dramatically improve skin permeability for hydrophilic and larger molecules. SCOPE formulations were discovered in a screening program that has, to date, evaluated more than 5000 distinct CPE-containing formulations.