gebhart/patrepeval huggingface dataset:
Liquid‐crystal photoaligning by azo dyes (Invited Paper) (2008)

Abstract— Liquid‐crystal (LC) photoalignment using azo dyes is described. It will be shown that this photoaligning method can provide a highly uniform alignment with a controllable pretilt angle and strong anchoring energy of the LC cell, as well as a high thermal and UV stability. The application of LC photoalignment to the fabrication of various types of liquid‐crystal displays, such as VAN‐LCDs, FLCDs, TN‐LCDs, and microdisplays, on glass and plastic substrates is also discussed. Azo‐dye photoaligned super‐thin polarizers and phase retarders are considered as new optical elements in LCD production, in particular for transflective displays.
CC chemokine receptor 1 enhances susceptibility to Leishmania major during early phase of infection (2003)

CC chemokine receptor 1 (CCR1) is expressed on the surfaces of monocytes, lymphocytes, neutrophils and eosinophils. CC chemokine receptor 1 not only regulates leucocyte chemotaxis, but also plays a role in the regulation of Th1/Th2 cytokine responses. To determine the role of CCR1 in regulation of immune response during Leishmania major infection, we analysed the course of cutaneous L. major infection in CCR1-deficient C57BL/6 mice (CCR1-/-) and compared with similarly infected wild-type mice (CCR1+/+). Following L. major infection, CCR1-/- mice developed significantly smaller lesions containing fewer parasites than CCR1+/+ mice. Furthermore, the severity of the inflammation as assessed by the degree of leucocyte infiltration at the site of infection was similar in CCR1+/+ and CCR1-/- mice. Although both groups developed significant antibody responses following L. major infection, CCR1-/- mice produced significantly lower IgE. On day 20 postinfection, LmAg-stimulated lymph node cells from L. major-infected CCR1+/+ and CCR1-/- mice produced comparable levels of IL-12 and IFN-gamma, but those from CCR1-/- mice produced significantly less IL-4 and IL-10. By day 70, lymph node cells from both CCR1+/+ and CCR1-/- mice produced significant amounts of IL-12 and IFN-gamma but low IL-4. At both time points, the draining lymph nodes from CCR1+/+ and CCR1-/- mice contained similar number of leucocytes. These results demonstrate that CCR1 plays a role in pathogenesis of cutaneous L. major infection. Moreover, they also indicate that CCR1 exacerbates L. major infection in C57BL/6 mice by up-regulating Th2-like response rather than inhibiting Th1 development or/and influencing leucocyte chemotaxis.
Coupled continuous-time random walks for fluid stretching in two-dimensional heterogeneous media (2016)

We study the relation between flow structure and fluid deformation in steady flows through two-dimensional heterogeneous media, which are characterized by a broad spectrum of stretching behaviors, ranging from sub- to superlinear. We analyze these behaviors from first principles, which uncovers intermittent shear events to be at the origin of subexponential stretching. We derive explicit expressions for Lagrangian deformation and demonstrate that stretching obeys a coupled continuous-time random walk, which for broad distributions of flow velocities becomes a Lévy walk. The derived model provides a direct link between the flow and deformation statistics, and a natural way to quantify the impact of intermittent shear events on the stretching behavior.
Accelerating the Coupling of Maleated Polyolefins with Polyesters via Tin Compounds (2019)

Poly(ethylene terephthalate) (PET) and polyethylene (PE) are two of the most commonly used polymers in the packaging industry, and they make up a large portion of the recycling stream. Adhesion between these two immiscible polymers is poor without compatibilization. Maleic anhydride (MAH) grafted PE is a popular compatibilizer for PET/PE but is limited by the slow rate of reaction. In this study, we propose tin additives for improving adhesion and explore the mechanism of that improvement. We demonstrate that either dibutyltin oxide (DBTO) or di-n-octyltin oxide (DOTO) can dramatically enhance adhesion with only 60 s of contact time during lamination. A range of MAH and DOTO concentrations are examined, yielding adhesion up to 1300 J/m2. Possible reactions at the interface are investigated with small molecule model compounds, namely 1-hexadecanol, octylsuccinic anhydride (OSA), and ethylene glycol dibenzoate. DOTO does not improve the reaction rate in the hexadecanol–OSA system. This suggests that another reaction is responsible for the adhesion improvement. We provide evidence that tin oxides can open the ring of alkylsuccinic anhydrides and form complexes that can interesterify PET. This overall reaction appears to be third order with an activation energy of 100 kJ/mol. Extrapolating these kinetic results to 270 °C, the lamination temperature, we estimate that interfacial interesterification is very fast. Thus, adhesion development is limited by diffusion of the tin additives.
Roles of Ti in Electrode Materials for Sodium-Ion Batteries (2019)

Sodium-ion batteries offer a promising alternative to lithium-ion batteries due to the low cost, environmental friendliness, high abundance of sodium and established electrochemical process. However, problems, such as low capacity, low storage voltage and capacity fade of electrode materials for sodium-ion batteries must be resolved. Many Ti-containing compounds were reported as cathode and anode materials, but very few studies focused on the role of Ti in electrodes used in sodium-ion batteries. This paper systemically reviews the roles of Ti in electrodes of sodium ion batteries. The Ti4+/Ti3+ redox couple is a good choice for anodes due to its low potential and it exhibits different storage voltages in different structures. Although Ti4+ does not participate in charge transfer in cathodes, it can indirectly enhance the capacity, cycling life and rate performance via structure change, cation order-disorder transition and its interaction with the crystal lattice structure. This review will provide a new insight in designing and understanding novel high-performance electrodes.
[Isolation and characterization of the hematopoietic stem cell]. (1995)

When one hundred of c-Kit+Sca-1+Lin- cells obtained from B6. Ly 5.1 mouse were injected into lethally irradiated B6. Ly 5.2, 100% of the mice injected survived. Sequential analyses of recipient's peripheral blood leukocytes revealed presence of Ly 5.1+ myeloid and lymphoid cells even 12 months after the injection. We also examined the fate of these cells in the recipient mouse after transplantation. Time course analyses of the mouse injected with 500 FACS-purified c-Kit+Sca-1+L- cells revealed that spleen is the primary site for expansion of the injected c-Kit+Sca-1+Lin- cells. By day 28 s/p transplantation, more than 50,000 donor type c-Kit+Sca-1+Lin- cells were found in the spleen and over 15,000 cells in the bone marrow. By day 60, number of c-Kit+Sca-1+Lin- cells decreased in the spleen and returned to normal level in the bone marrow. Stem cell activity of the donor derived c-Kit+Sca-1+Lin- cells in the primary recipient was confirmed by in vitro and in vivo colony formation as well as transplantation to the secondary recipient. These results provide evidence that c-Kit+Sca-1+Lin- cells in the bone marrow have capability of self-renew as well as multilineage differentiation potential and that spleen is the primary site of stem cell expansion after bone marrow transplantation in mouse.
Patient-specific untreated virtual imaging controls for [18F]-FMISO PET imaging of glioblastoma (2012)

1259 Objectives Glioblastoma multiforme (GBM) is a class of primary brain tumours characterized by their ability to rapidly proliferate and diffusely infiltrate surrounding brain tissue. The aggressive growth of GBM leads to the development of regions of hypoxia, which can be clinically assessed through [18F]-fluoromisonidazole (FMISO) PET. PET imaging is challenged by image resolution and reconstruction artifact, therefore there is great utility for an integrative tool for predicting patient-specific hypoxic tumor burden beyond the obscuring lens of molecular imaging. Methods Our bio-mathematical model characterizes gliomas into distinct cellular phenotypes including normoxic, hypoxic and necrotic cells that interact with themselves and the microenvironment (vasculature). A pharmacokinetic model for the FMISO-PET tracer is applied throughout the brain and an analytical simulator (ASIM) for image acquisition and reconstruction is applied to the resultant tracer activity map. This combination produces a patient-specific virtual PET image that reproduces the image characteristics of the clinical PET scan. For a wide range of tumor growth and invasion kinetics, we simulated tumor growth for 6 GBM patients, producing maps of tumor cell density, hypoxia and virtual FMISO-PET images to allow comparison with clinical FMISO-PET images. Results Overall hypoxic burden, pixel intensity distribution as well as spatial location of hypoxia relative to MRI abnormalities are compared and demonstrate excellent agreement between the virtual and real FMISO-PET images for all 6 patients. Conclusions The ability to produce simulated PET images from MRI data using the our bio-mathematical model provides a better dynamic understanding of the biological connection between anatomical changes seen on MRI and biochemical activity seen on PET of GBM in vivo. This result provides a novel means for distinguishing hyper activity from hyper density of hypoxic cells on a FMISO-PET image on a patient-specific basis. Research Support NIH grants R01 CA164371, U54 CA14397
An optimized, synthetic DNA vaccine encoding the toxin A and toxin B receptor binding domains of Clostridium difficile induces protective antibody responses in vivo (VAC7P.958) (2014)

Abstract Clostridium difficile-associated disease (CDAD) constitutes a large majority of nosocomial diarrhea cases within industrialized nations and is mediated by the effects of two secreted toxins, toxin A (TcdA) and toxin B (TcdB). Key toxin-neutralizing epitopes have been discovered within the carboxy-terminal receptor-binding domain (RBD) of the toxins, which has generated interest in developing the RBD as a vaccine target. While numerous platforms have been studied, very few data describe the potential of DNA vaccination against CDAD. Therefore, we created highly optimized plasmids encoding the RBD from TcdA and TcdB and immunized C57BL/6 mice and rhesus macaques intramuscularly followed by in vivo electroporation. In these animal models, vaccination induced significant levels of anti-RBD antibodies within the serum and feces that could neutralize toxins in an in vitro cytotoxicity assay. Moreover, mice that were either immunized with plasmids or given non-human primate immune sera were protected from a lethal intraperitoneal challenge of purified C. difficile toxins. Finally, immunized mice were significantly protected when challenged with strains of C. difficile spores that were homologous (VPI 10463; n=10/10) and heterologous (UK1; n=4/8) to our vaccine antigens. These data demonstrate the robust immunogenicity and efficacy of a TcdA/B RBD-based DNA vaccine in preclinical models of acute toxin-associated disease.
Thio Sol–Gel Process for the Synthesis of Titanium Disulfide (1994)

A thio sol–gel process for the synthesis of titanium disulfide using titanium alkoxide as the metal source is demonstrated. The alkoxide reacts at room temperature with H 2 S to form a precipitate which is a precursor to the sulfide. Through infrared spectroscopy and chemical analysis of the powder and gas chromatographic analysis of the liquid byproducts of the reaction, it is shown that a partially sulfidized alkoxide precursor forms through the displacement of alkoxy groups from the alkoxide by sulfur‐bearing thiol groups. This thiolysis reaction is very similar to that which occurs in the case of sol–gel reactions to form oxides. The alkoxy–thiol species then undergo condensation–polymerization by the liberation of H 2 S. When it is heat‐treated in H 2 S, this precursor transforms to TiS 2 at ∼700°C. Systematic heat treatments have been performed and the formation of TiS 2 has been observed using X‐ray diffractometry. The change in the morphology has also been studied using scanning electron microscopy.
Sequential enrichment of sulfated glycans by strong anion-exchange chromatography prior to mass spectrometric measurements (2009)

Structural characterization of sulfated glycans through mass spectrometry (MS) has been often limited by their low abundance in biological materials and inefficient ionization in the positive-ion mode. Here, we describe a microscale method for sequentially enriching sulfated glycans according to their degree of sulfation. This method is based on modifying the binding ability of strong anion-exchange material through the use of different sodium acetate concentrations, thus enabling fairly selective binding and a subsequent elution of different glycans according to their degree of sulfation. Before this enrichment, the negative charge on the sialic acid, which is commonly associated with such glycans, was eliminated through permethylation that is used to enhance the positive-ion mode matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-MS) signal for all glycans. This enrichment approach minimizes competitive ionization between sulfated and neutral glycans, as well as that between sulfated species with a different degree of sulfation. The described method was initially optimized using sulfated oligosaccharide standards, while its potential has been verified for the sulfated N-glycans originated from the bovine thyroid-stimulating hormone (bTSH), a glycoprotein possessing mono- and disulfated N-glycans. This enhancement of the MALDI-MS signal facilitates analysis of some otherwise undetected components.
Vaccine Breakthrough Infections with SARS-CoV-2 Variants (2021)

Vaccine Breakthrough Infections with SARS-CoV-2 VariantsTo the Editor: The article by Hacisuleyman et al. (published online on April 21) 1 reinforces concerns about SARS-CoV-2 variants and vaccine breakthrough.The authors describe two fully vaccinated women older than 50 years of age in whom subsequent vaccine breakthrough infection occurred with variants.The authors did not report on the measurement of SARS-CoV-2-specific T-cell responses.T-cell immunity is important in the control of SARS-CoV-2 2 and may be critical for potential cross-reactive protection against variants.SARS-CoV-2 messenger RNA (mRNA) vaccines generate weaker T-cell responses than other vaccine platforms. 3Although several mix-and-match vaccine studies are ongoing or planned, the effect of a vector boost of an mRNA vaccine prime on T-cell responses is currently unknown.Since Covid-19 vaccines vary with regard to immunogenicity and immune specificity, we would encourage consideration of a vaccine boost from a T-cell-skewed vaccine after mRNA vaccination to boost T-cell responses and potentially to reduce the chance of breakthrough infection through the generation of cross-protective T-cell immunity.The prevention of vaccine failure due to variants is a critical part of pandemic management.
High-frequency ducted broadband acoustic mode detection in the swirling flows (2022)

This paper presents a theoretical and numerical investigation into the broadband (BB) modal analysis in complex swirling flows, typical of the aeroengine interstage. Asymptotic (high-frequency limit) wavenumber distribution approaches, measuring the BB modal amplitudes as a continuous distribution over the normalised modal axial wavenumber (ζ) , have previously been developed and validated under uniform axial flow conditions. In the swirling flows, however, the use of ζ as a modal analysis parameter was previously shown to result in an ambiguous region of modal overlap, the ζ values within which correspond to both the upstream and the downstream propagating modes and are therefore indistinguishable. In this paper, the potential significance of this wavenumber overlap on the BB modal analysis has been studied in detail. It has been shown that at the higher mean swirl levels (typical of the cutback/sideline), this modal overlap region is consequential in terms of the proportion of the total modal power (as well as pressure) it obscures, rendering the existing 1-D mode detection techniques (based on ζ) unreliable for estimating the relative modal levels of the upstream and the downstream side sources. Using a simple analytical model, the distinctive features of the multi-modal sound field in a swirling flow have been elucidated, with the ambiguous phenomenon of the modal overlap explained through an order-of-magnitude analysis. Based on the resulting inferences, a new phased array technique (called here as the two-ring method) has been developed, which employs two close-by wall-microphone rings to separately estimate the BB mode amplitude distribution for the co-rotating and the contra-rotating spinning modes. The 2-D wavenumber distribution approach (based on the azimuthal number, m, and ζ) of the new technique has been shown to effectively separate the dominant overlapping modes at the higher mean swirl levels, resulting in an enhanced and reliable prediction of the relative source contribution in complex swirling flow conditions.
SPATIAL FILTERING OPTIMISATION IN MOTOR IMAGERY EEG-BASED BCI (2013)

Common spatial pattern (CSP) is becoming a standard way to combine linearly multi-channel EEG data in order to increase discrimination between two motor imagery tasks. We demonstrate in this article that the use of robust estimates allows improving the quality of CSP decomposition and CSP-based BCI. Furthermore, a scheme for electrode subset selection is proposed. It is shown that CSP with such subset of electrodes provides better results with the ones obtained with CSP over large multi-channel recordings.
Rapid 3D light-sheet microscopy with a tunable lens (2013)

The in-vivo investigation of highly dynamic biological samples, for example the beating zebrafish heart, requires high-speed volume imaging techniques. Light-sheet microscopy is ideal for such samples as it records high-contrast images of entire planes within large samples at once. However, in order to obtain images of different planes, it has been necessary to move the sample relative to the fixed focal plane of the detection objective lens. This mechanical movement limits speed, precision and may be harmful to the sample. We have built a light-sheet microscope that uses remote focusing with an electrically tunable lens (ETL). Without moving specimen or objective we have thereby achieved flexible volume imaging at much higher speeds than previously reported. Our high-speed microscope delivers 3D snapshots of sensitive biological samples. As an example, we imaged 17 planes within a beating zebrafish heart at 510 frames per second, equivalent to 30 volume scans per second. Movements, shape changes and signals across the entire volume can be followed which has been impossible with existing reconstruction techniques.
The Centers for Mendelian Genomics: A new large‐scale initiative to identify the genes underlying rare Mendelian conditions (2012)

Next generation exome sequencing (ES) and whole genome sequencing (WGS) are new powerful tools for discovering the gene(s) that underlie Mendelian disorders. To accelerate these discoveries, the National Institutes of Health has established three Centers for Mendelian Genomics (CMGs): the Center for Mendelian Genomics at the University of Washington; the Center for Mendelian Genomics at Yale University; and the Baylor-Johns Hopkins Center for Mendelian Genomics at Baylor College of Medicine and Johns Hopkins University. The CMGs will provide ES/WGS and extensive analysis expertise at no cost to collaborating investigators where the causal gene(s) for a Mendelian phenotype has yet to be uncovered. Over the next few years and in collaboration with the global human genetics community, the CMGs hope to facilitate the identification of the genes underlying a very large fraction of all Mendelian disorders; see http://mendelian.org.
Anisotropy of Rotational Diffusion, Dipole–Dipole Cross-Correlated NMR Relaxation and Angles between Bond Vectors in Proteins (2001)

Cross correlations between the fluctuations of dipolar 13Cα–1Hα interactions yield information about the relative orientation of successive 13Cα–1Hα bond vectors in proteins, in turn providing a direct handle on their structure and dynamics in solution. However, overall anisotropic reorientation must be taken into account in the interpretation of cross-correlation rates. The protein shown, human ubiquitin, has amino acid residues in white where the cross-correlation rates deviate from those predicted for a rigid structure.
Runtime Parameterizable Regular Expression Operators for Databases (2016)

Relational databases execute user queries through operator trees, where each operator has a well defined interface and a specific task (e.g., arithmetic function, pattern matching, aggregation, etc.). Hardware acceleration of compute intensive operators is a promising prospect but it comes with challenges. Databases execute tens of thousands of different queries per second. Thus, if only one specific instantiation of an operator is supported by the accelerator, it will have little effect on the overall workload. In this paper we explore the tradeoff between resource efficiency and expression complexity for an FPGA accelerator targeting string-matching operators (LIKE and REGEXP_LIKE in SQL). This tradeoff is complex. For instance, the FPGA not always wins: simple queries that can be answered from indexes run faster on the CPU. On complex regular expressions, the FPGA is faster but needs to be parametrized at runtime to be able to support different queries. For very long patterns, the entire expression might not fit into the FPGA circuit and a combined mode CPU-FPGA must be chosen. We evaluate our design on a heterogeneous multi-core machine in which the FPGA has cache coherent access to the CPU memory. In addition to the string matching circuit, we also show how to implement database page parsing logic so as to be able to work directly on the same memory data structures as the database engine.
Estimation of the time-course of dopamine D2 receptor occupancy in living human brain from plasma pharmacokinetics of antipsychotics (2004)

Although the kinetic profile of antipsychotics at dopamine D2 receptor sites has been suggested to be important for antipsychotic action and dosing schedule, the kinetic profiles of the respective antipsychotic drugs in the brain have not yet been clearly defined. We aimed to estimate the time-course of dopamine D2 receptor occupancy from plasma pharmacokinetics and the apparent in-vivo affinity parameter (ED50; concentration required to induce 50% occupancy). Dopamine D2 receptor occupancies and plasma concentrations of risperidone were measured in five patients with schizophrenia using positron emission tomography with [11C]FLB 457. Measured dopamine D2 occupancies were compared with those estimated from plasma kinetics and in-vivo ED50. The time-course of dopamine D2 receptor occupancy was simulated with altered plasma kinetics or apparent in-vivo affinity parameters of the drug. Mean half-life of dopamine D2 receptor occupancy of risperidone was 80.2 h while that of the plasma concentration was 17.8 h. Dopamine D2 receptor occupancy estimated from plasma pharmacokinetics and in-vivo ED50 was within 1 S.D. of the mean measured occupancy. When the ED50 value was changed to one-tenth and 10-fold, the simulated half-life of receptor occupancy changed to 117.6 h and 27.3 h respectively. Using plasma pharmacokinetics and in-vivo ED50, the time-course of receptor occupancy could be calculated. Simulation of drug kinetics at receptors would provide useful information for the evaluation of antipsychotics.