gebhart/patrepeval huggingface dataset:
Short Communication on Umbilical Cord Blood Stem Cells (2020)

Umbilical cord blood was once thought of as a waste product. Now, years after the first successful umbilical cord blood transplant, more families seek information about whether or not to save their newborn’s cord blood. Umbilical cord blood collected at birth is a rich source of stem cells that can be used in research and in the clinic to treat diseases of the blood and immune system. With the consent of the parents, blood can be collected from the umbilical cord of a newborn baby shortly after birth.
Screening self-peptides for recognition by mouse alloreactive CD8+ T cells using direct ex vivo multimer staining (2022)

Here, we present a protocol to identify immunogenic self-peptide/allogeneic major histocompatibility complex (MHC) epitopes. We describe the generation of enriched alloreactive CD8+ T cells by priming mice with a skin graft expressing the allogeneic MHC class I molecule of interest, followed by boosting with a liver-specific AAV vector encoding the heavy chain of that donor MHC allomorph. We then use a peptide-exchange approach to assemble a range of peptide-MHC (pMHC) multimers for measuring recognition of the various epitopes by these alloreactive T cells. For complete details on the use and execution of this protocol, please refer to Son et al. (2021).<sup>1</sup>.
Nanomechanical Infrared Spectroscopy with Vibrating Filters for Pharmaceutical Analysis (2017)

Abstract Standard infrared spectroscopy techniques are well‐developed and widely used. However, they typically require milligrams of sample and can involve time‐consuming sample preparation. A promising alternative is represented by nanomechanical infrared spectroscopy (NAM‐IR) based on the photothermal response of a nanomechanical resonator, which enables the chemical analysis of picograms of analyte directly from a liquid solution in only a few minutes. Herein, we present NAM‐IR using perforated membranes (filters). The method was tested with the pharmaceutical compound indomethacin to successfully perform a chemical and morphological analysis on roughly 100 pg of sample. With an absolute estimated sensitivity of 109±15 fg, the presented method is suitable for ultrasensitive vibrational spectroscopy.
Unraveling Radical and Oxygenate Routes in the Oxidative Dehydrogenation of Propane over Boron Nitride (2023)

Oxidative dehydrogenation of propane (ODHP) is an emerging technology to meet the global propylene demand with boron nitride (BN) catalysts likely to play a pivotal role. It is widely accepted that gas-phase chemistry plays a fundamental role in the BN-catalyzed ODHP. However, the mechanism remains elusive because short-lived intermediates are difficult to capture. We detect short-lived free radicals (CH<sub>3</sub><sup>•</sup>, C<sub>3</sub>H<sub>5</sub><sup>•</sup>) and reactive oxygenates, C<sub>2-4</sub> ketenes and C<sub>2-3</sub> enols, in ODHP over BN by <i>operando</i> synchrotron photoelectron photoion coincidence spectroscopy. In addition to a surface-catalyzed channel, we identify a gas-phase H-acceptor radical- and H-donor oxygenate-driven route, leading to olefin production. In this route, partially oxidized enols propagate into the gas phase, followed by dehydrogenation (and methylation) to form ketenes and finally yield olefins by decarbonylation. Quantum chemical calculations predict the >BO dangling site to be the source of free radicals in the process. More importantly, the easy desorption of oxygenates from the catalyst surface is key to prevent deep oxidation to CO<sub>2</sub>.
Developing New Multicolor Protein MRI Contrast Agents (2006)

where: kA,ref, kB,ref , and kW,ref are the acid, base and water rate constants for the appropriate reference peptide, A is the specific acid rate factor for the neighboring peptides, and B is the specific base factor for the neighbor. This equation can be used for both backbone amide protons (HN) and sidechain exchangeable groups (NH2, OH, SH), by adjusting the reference rates. The temperature dependence of these rates can be added as well, by
Nanoparticles for diagnostics and laser medical treatment of cartilage in orthopaedics (2013)

Laser reconstruction of intervertebral disc (LRD) is a new technique which uses local, non-destructive laser irradiation for the controlled activation of regenerative processes in a targeted zone of damaged disc cartilage. Despite pronounced advancements of LRD, existing treatments may be substantially improved if laser radiation is absorbed near diseased and/or damaged regions in cartilage so that required thermomechanical stress and strain at chondrocytes may be generated and non-specific injury reduced or eliminated. The aims of the work are to study possibility to use nanoparticles (NPs) to provide spatial specificity for laser regeneration of cartilage. Two types of porcine joint cartilage have been impregnated with magnetite NPs: 1) fresh cartilage; 2) mechanically damaged cartilage. NPs distribution was studied using transition electron microscopy, dynamic light scattering and analytical ultracentrifugation techniques. Laser radiation and magnetic field have been applied to accelerate NPs impregnation. It was shown that NPs penetrate by diffusion into the mechanically damaged cartilage, but do not infiltrate healthy cartilage. Temperature dynamics in cartilage impregnated with NPs have been theoretically calculated and measurements using an IR thermo vision system have been performed. Laser-induced alterations of cartilage structure and cellular surviving have been studied for cartilage impregnated with NPs using histological and histochemical techniques. Results of our study suggest that magnetite NPs might be used to provide spatial specificity of laser regeneration. When damaged, the regions of cartilage impreganted with NPs have higher absorption of laser radiation than that for healthy areas. Regions containing NPs form target sites that can be used to generate laser-induced thermo mechanical stress leading to regeneration of cartilage of hyaline type.
An Assessment of Fixed-Mobile Convergence (2007)

FMC (fixed-mobile convergence) is introduced as an approach for converging wireless and wireline networks. Even though it has a number of appealing aspects, it also has significant technical, political and competitive problems.
Optical properties of InGaN/GaN nanopillars fabricated by postgrowth chemically assisted ion beam etching (2010)

The optical properties of InGaN/GaN quantum wells, which were nanopatterned into cylindrical shapes with diameters of 2 μm, 1 μm, or 500 nm by chemically assisted ion beam etching, were investigated. Photoluminescence (PL) and time-resolved PL measurements suggest inhomogeneous relaxation of the lattice-mismatch induced strain in the InGaN layers. By comparing to a strain distribution simulation, we found that partial stain relaxation occurs at the free side wall, but strain remains in the middle of the pillar structures. The strain relaxation leads to an enhanced radiative recombination rate by a factor of 4–8. On the other hand, nonradiative recombination processes are not strongly affected, even by postgrowth etching. Those characteristics are clearly reflected in the doughnut-shape emission patterns observed by optical microscopy.
Integrated Catadioptric Pickup with Ferrofluidic Cooling Structure (2006)

Integrated Catadioptric Pickup with Ferrofluidic Cooling Structure, Onozawa, Kazutoshi, Yamanaka, Kazuhiko, Okuda, Takuya, Tojo, Tomoaki, Iijima, Shinichi, Ueda, Daisuke, Kubo, Junichi, Kitagawa, Seiichro
Combining the benefits of 3D acquisitions and spiral readouts in VASO fMRI (2022)

VASO fMRI has been shown to provide benefits compared to the commonly used BOLD contrast. Previous work has also shown the benefits of using spiral readouts compared to Cartesian ones. In this work, we explore the benefits of 3D stack of spirals readouts for VASO and compare it with the current state of the art 3D EPI readouts for VASO fMRI. The sequence implementation is done using Pulseq, images were reconstructed using gpuNUFFT; functional analysis with an openly available pipeline. We find that a tSNR efficiency improvement of a factor of 3 over EPI is achieved using the proposed spiral implementation.
MIGS: miRNA‐induced gene silencing (2011)

Gene silencing is an important tool in the study of gene function. Virus-induced gene silencing (VIGS) and hairpin RNA interference (hpRNAi), both of which rely on small interfering RNAs, together with artificial microRNAs (amiRNA), are amongst the most popular methods for reduction of gene activity in plants. However, all three approaches have limitations. Here, we introduce miRNA-induced gene silencing (MIGS). This method exploits a special 22-nucleotide miRNA of Arabidopsis thaliana, miR173, which can trigger production of another class of small RNAs called trans-acting small interfering RNAs (tasiRNAs). We show that fusion of gene fragments to an upstream miR173 target site is sufficient for effective silencing of the corresponding endogenous gene. MIGS can be reliably used for the knockdown of a single gene or of multiple unrelated genes. In addition, we show that MIGS can be applied to other species by co-expression of miR173.
Conformational changes at polymer gel interfaces upon saturation with various liquids studied by infrared-visible sum frequency generation vibrational spectroscopy (2006)

Molecular restructuring at the free surface of poly(2-hydroxyethyl methacrylate) (PHEMA) films and the buried interface with a sapphire substrate due to submersion into deuterated water (D2O) and acetonitrile (d3ACN) was investigated by infrared-visible sum frequency generation (SFG) vibrational spectroscopy. Film hydration by saturation with D2O and d3ACN resulted in polymer swelling. Because of the amphiphilic nature of PHEMA, direct information about polymer restructuring was obtained due to the existence of hydrophilic and hydrophobic moieties. SFG results provided insight into the restructuring behavior at the PHEMA surface and buried interface upon swelling due to the diffusion of the two different liquids.
Test of Higher-Order Nonlinearity via Low-Order Harmonic Generation Revisited (2014)

We measure the ratio between fifth- and third-harmonic signals from air as a function of the laser intensity determined by mode measurements. Our results do not support the presence of a higher-order Kerr nonlinearity.
Hydrogen Bonding and Solvent Structure in an Antigen−Antibody Interface. Crystal Structures and Thermodynamic Characterization of Three Fv Mutants Complexed with Lysozyme<sup>,</sup> (1996)

Using site-directed mutagenesis, X-ray crystallography, and titration calorimetry, we have examined the structural and thermodynamic consequences of removing specific hydrogen bonds in an antigen-antibody interface. Crystal structures of three antibody FvD1.3 mutants, VLTyr50Ser (VLY50S), VHTyr32Ala (VHY32A), and VHTyr101Phe (VHY101F), bound to hen egg white lysozyme (HEL) have been determined at resolutions ranging from 1.85 to 2.10 A. In the wild-type (WT) FvD1.3-HEL complex, the hydroxyl groups of VLTyr50, VHTyr32, and VHTyr101 each form at least one hydrogen bond with the lysozyme antigen. Thermodynamic parameters for antibody-antigen association have been measured using isothermal titration calorimetry, giving equilibrium binding constants Kb (M-1) of 2.6 x 10(7) (VLY50S), 7.0 x 10(7) (VHY32A), and 4.0 x 10(6) (VHY101F). For the WT complex, Kb is 2.7 x 10(8) M-1; thus, the affinities of the mutant Fv fragments for HEL are 10-, 4-, and 70-fold lower than that of the original antibody, respectively. In all three cases entropy compensation results in an affinity loss that would otherwise be larger. Comparison of the three mutant crystal structures with the WT structure demonstrates that the removal of direct antigen-antibody hydrogen bonds results in minimal shifts in the positions of the remaining protein atoms. These observations show that this complex is considerably tolerant, both structurally and thermodynamically, to the truncation of antibody side chains that form hydrogen bonds with the antigen. Alterations in interface solvent structure for two of the mutant complexes (VLY50S and VHY32A) appear to compensate for the unfavorable enthalpy changes when protein-protein interactions are removed. These changes in solvent structure, along with the increased mobility of side chains near the mutation site, probably contribute to the observed entropy compensation. For the VHY101F complex, the nature of the large entropy compensation is not evident from a structural comparison of the WT and mutant complexes. Differences in the local structure and dynamics of the uncomplexed Fv molecules may account for the entropic discrepancy in this case.
Synthesis of Carboxamides by LDA‐Catalyzed Haller—Bauer and Cannizzaro Reactions. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
All- <i>trans</i> Retinoic Acid Enhances Murine Dendritic Cell Migration to Draining Lymph Nodes via the Balance of Matrix Metalloproteinases and Their Inhibitors (2007)

Cancers escape immune surveillance through the manipulation of the host's immune system. Sequestration of dendritic cells (DCs) within tumor tissues and the subsequent inhibition of their migration is one of the several mechanisms by which tumors induce immunosuppression. In view of recent findings depicting the improvement of tumor immune responses in cancer patients following all-trans retinoic acid (ATRA) treatment, we sought to identify the effects of ATRA on DC mobility in the context of tumor immunotherapy. Our results demonstrate that ATRA, added to differentiating murine bone marrow progenitor cells, enhances the invasive capacity of the resulting DCs. Immature DCs injected intratumorally in mice show increased accumulation in draining lymph nodes, but not in nondraining lymph nodes and spleens, when differentiated in the presence of ATRA. The in vitro migration of mature DCs through the basement membrane matrix toward the lymphoid chemokines CCL19 and CCL21 is enhanced in these cells, albeit not in the presence of a matrix metalloproteinase (MMP) inhibitor. An increase in MMP production with a simultaneous decrease in the production of their inhibitors (tissue inhibitors of matrix metalloproteinase or TIMPs) is provoked by ATRA. This affects the MMP/TIMP balance in DCs, in particular that of MMP-9 and TIMP-1, favoring protease activity and thus allowing for enhanced DC mobilization. In conclusion, this study demonstrates that ATRA is capable of improving DC trafficking in a tumor milieu and, in view of the encouraging results obtained in the clinic, further supports the notion that ATRA might be a valuable chemical adjuvant to current immunotherapeutic strategies for cancer.
Enhancement of the reactivity by chaotic mixing (1997)

We report an experimental study of chaotic mixing of chemically reacting species, for first- and second-order reactions, in a system composed of a pair of like-sign vortices, oscillating periodically in time. For the second-order reaction, we find that the overall reactivity is enhanced compared to homogeneous mixing. This provides experimental evidence that chaotic mixing may increase the overall reaction rate for second-order reactions. We offer a method to estimate the global reactivity, which underlines the role of the concentration filaments formed, in the system, by the chaotic process.
Sensor image augmentation to avoid saturation (2011)

A method to enhance the legibility of FLIR (Forward-Looking Infra Red) images was invented and evaluated by flight test. The method intends to avoid image saturation when a pilot is looking for low temperature objects of interest in an image dominated by high temperature areas, such as searching for objects on a cooler land area in an image mostly filled with a warmer sea area. The method utilizes a 2D mask generated from 3D object of interest data, and overlays the raw image. The effectiveness of the method was evaluated by flight tests in which the processed image was presented on a HMD (Helmet Mounted Display). The flight tests confirmed the enhanced image legibility brought by the method.
Rolling Contact Fatigue Property of Sintered and Carburized Compacts Made of Molybdenum Hybrid-Alloyed Steel Powder (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Disk drive pivot nonlinearity modeling. II. Time domain (2005)

For pt. I see ibid. p.2600-3. This paper describes studies done at HP Labs on the actuator pivot bearing nonlinearity of a small disk drive. It presents several models and discusses a time-domain approach, comparing simulated and lab measured torque versus displacement hysteresis curves. Using the measured and simulated time and frequency responses as a guide, the designer can iteratively improve the model of the system and verify the correctness of the measurements.
Response to Liang&amp; colon; Responsiveness in Quality-of-Life Assessment (2000)

From the Department of Medical Affairs, Merck-Medco Managed Care, LLC, Franklin Lakes, New Jersey. Address correspondence to: Robert S. Epstein, MD, MS, 100 Parsons Pond Drive, Franklin Lakes, NJ 07417. E-mail: [email protected]
New mixed organic-inorganic polymers: hydrolysis and polycondensation of bis(trimethoxysilyl)organometallic precursors (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew mixed organic-inorganic polymers: hydrolysis and polycondensation of bis(trimethoxysilyl)organometallic precursorsRobert J. P. Corriu, Joel J. E. Moreau, Philippe Thepot, and Michel Wong Chi ManCite this: Chem. Mater. 1992, 4, 6, 1217–1224Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://pubs.acs.org/doi/10.1021/cm00024a020https://doi.org/10.1021/cm00024a020research-articleACS PublicationsRequest reuse permissionsArticle Views1398Altmetric-Citations252LEARN 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
The role of Stewartson and Ekman layers in turbulent rotating Rayleigh–Bénard convection (2011)

Abstract When the classical Rayleigh–Bénard (RB) system is rotated about its vertical axis roughly three regimes can be identified. In regime I (weak rotation) the large-scale circulation (LSC) is the dominant feature of the flow. In regime II (moderate rotation) the LSC is replaced by vertically aligned vortices. Regime III (strong rotation) is characterized by suppression of the vertical velocity fluctuations. Using results from experiments and direct numerical simulations of RB convection for a cell with a diameter-to-height aspect ratio equal to one at $\mathit{Ra}\ensuremath{\sim} 1{0}^{8} \text{{\ndash}} 1{0}^{9} $ ( $\mathit{Pr}= 4\text{{\ndash}} 6$ ) and $0\lesssim 1/ \mathit{Ro}\lesssim 25$ we identified the characteristics of the azimuthal temperature profiles at the sidewall in the different regimes. In regime I the azimuthal wall temperature profile shows a cosine shape and a vertical temperature gradient due to plumes that travel with the LSC close to the sidewall. In regimes II and III this cosine profile disappears, but the vertical wall temperature gradient is still observed. It turns out that the vertical wall temperature gradient in regimes II and III has a different origin than that observed in regime I. It is caused by boundary layer dynamics characteristic for rotating flows, which drives a secondary flow that transports hot fluid up the sidewall in the lower part of the container and cold fluid downwards along the sidewall in the top part.
Intrahepatic <scp>B</scp>‐cell follicles of chronically hepatitis <scp>C</scp> virus‐infected individuals lack signs of an ectopic germinal center reaction (2014)

Chronic infection with hepatitis C virus ( HCV ) often affects the B ‐cell compartment, leading to the occurrence of autoimmunity and B ‐cell lymphoproliferation, in particular mixed cryoglobulinemia and B ‐cell lymphomas. HCV presumably causes these lymphoproliferations by chronic antigenic stimulation and/or direct mutagenic effects on B cells. It has been speculated that the interaction of HCV with B cells and the expansion of antigen‐triggered B cells happens in germinal center‐like structures in the livers of HCV carriers. We studied rearranged immunoglobulin V H genes from seven B ‐cell follicles microdissected from the livers of three unselected chronic HCV patients. The follicles consisted of polyclonal naive and memory B ‐cell populations with only rare indication of minor clonal expansions and no evidence for active somatic hypermutation. Frequent detection of V H rearrangements using the VH 1‐69 gene segment nevertheless indicated that at least a fraction of the B cells is HCV ‐specific and/or autoreactive. Thus, the typical intrahepatic B‐cell follicles in chronic HCV carriers do not function as ectopic germinal centers for clonal expansion and affinity maturation of B cells. Hence, autoreactive and HCV ‐specific B ‐cell clones might either develop in secondary lymphoid organs or in intrahepatic follicles only under particular, yet undefined, circumstances.
Prognostic factors for survival in amyotrophic lateral sclerosis patients treated with riluzole (2005)

The objective of this study was to identify prognostic factors for survival in amyotrophic lateral sclerosis from a large prospective observational study performed in France. The study included a cohort of 2069 patients fulfilling broad entry criteria treated with riluzole. Over 100 demographic, biological, clinical and quality-of-life variables were monitored and assessed for their effect on survival. Patients were randomized post hoc into two groups: one group (two-thirds of the patients) to generate the prognostic models and one group (one-third of the patients) to validate the resulting models. Thirteen variables were found to affect survival independently and were used to construct a survival prediction score, RL401. These included age, disease duration, slow vital capacity, intensity of tiredness (visual analogue scale), number of body levels with spasticity, atrophy and/or fasciculations, cough, distal muscle strength, household income, depression and two biological parameters, plasma creatinine levels and neutrophil counts. A simplified score, RL401S, was constructed, designed to be easy to use and interpret. The predictive powers of the two scores were similar.