gebhart/patrepeval huggingface dataset:
Design and Implementation of a New Electrodynamic Ion Funnel (2000)

A new electrodynamic (rf) ion funnel has been developed and evaluated for use in the interface regions (at ∼1−10 Torr) of atmospheric pressure ion sources (e.g., electrospray ionization (ESI) for mass spectrometry). The ion funnel consists of a ring electrode ion guide with decreasing i.d. and with a superimposed dc potential gradient along the ring stack. The thicknesses of the ring electrodes and the spacings between them were reduced to 0.5 mm from 1.59 mm compared to those used for previous designs. The new ion funnel displays a significant improvement in low-mass transmission (m/z >200) and sensitivity compared to previous designs. The transmission efficiencies for electrosprayed peptides and proteins (ranging in mass from 200 to 17 000 Da) were typically 50−60% of total incoming currents from a heated capillary inlet. The transmitted ion currents were a factor of 30−56 greater than those of the standard interface for peptide samples and a factor of 18−22 greater than those for protein samples. The sensitivity gains realized at the MS detector were somewhat lower, possibly due to space charge effects in the octapole ion beam guide following the ion funnel. The improved ion transmission properties result primarily from the use of reduced spacings between ring electrodes. We also show that the ion funnel can be operated in two different modes, one using low-rf-amplitude scans, allowing fragile noncovalent complexes (as well as generally undesired adducts) to be transmitted, and the other using high-rf-amplitude scans, providing greater collisional activation and more effective adduct removal (or the dissociation of lower m/z species).
An electrically switchable visible to infra-red dual frequency cholesteric liquid crystal light shutter (2018)

Herein, an electrically switchable cholesteric liquid crystal (LC) shutter from visible to infrared light was prepared using a dual frequency LC (DFLC).
Synthesis of Novel Derivatives of (1S,4S)‐2,5‐Diazabicyclo[2.2.1]heptane and Their Evaluation as Potential Ligands in Asymmetric Catalysis (2007)

Abstract Thirty‐seven (most of them novel) chiral derivatives of (1 S ,4 S )‐2,5‐diazabicyclo[2.2.1]heptane ( 2 – 36 , 38 , 39 ) were prepared from ( S )‐ trans ‐4‐hydroxyproline. A selection of these chiral ligands were examined as potential ligands in the preparation of catalysts for the enantioselective addition of diethylzinc to aldehydes and as chiral Lewis acid activators in the asymmetric Diels–Alder reaction. In the former system, diamine 30 induced up to 92 % enantiomeric excess in the formation of ( S )‐phenyl ethyl carbinol, whereas in the case of the cycloaddition reaction between cyclopentadiene and 3‐acryloyloxazolidin‐2‐one the catalytic complex formed between dimeric derivative 8 and copper triflate [Cu(OTf) 2 ] afforded the expected product in a 95:5 endo / exo ratio and up to 72 % ee for the major diastereomeric product. Finally, some of the novel chiral diamines prepared in this work were also evaluated as potential organocatalysts in the asymmetric amination of ethyl α‐phenyl‐α‐cyano acetate. Bifunctional derivative 12 provided the aminated product in excellent yield and with up to 40 % ee .(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)
IL-13 Regulates the Immune Response to Inhaled Antigens (2005)

The large inhibitory effect of IL-13 blockers on the asthma phenotype prompted us to ask whether IL-13 would play a role in regulating the allergic immune response in addition to its documented effects on structural pulmonary cells. Because IL-13 does not interact with murine T or B cells, but with monocytes, macrophages, and dendritic cells (DCs), we examined the role of IL-13 in the activation of pulmonary macrophages and DCs and in the priming of an immune response to a harmless, inhaled Ag. We found that a majority of cells called "alveolar or interstitial macrophages" express CD11c at high levels (CD11c(high)) and are a mixture of at least two cell types as follows: 1) cells of a mixed phenotype expressing DC and macrophage markers (CD11c, CD205, and F4/80) but little MHC class II (MHC II); and 2) DC-like cells expressing CD11c, CD205, MHC II, and costimulatory molecules. Endogenous IL-13 was necessary to induce and sustain the increase in MHC II and CD40 expression by pulmonary CD11c(high) cells, demonstrated by giving an IL-13 inhibitor as a measure of prevention or reversal to allergen-primed and -challenged mice. Conversely, IL-13 given by inhalation to naive mice increased the expression of MHC II and costimulatory molecules by CD11c(high) cells in an IL-4Ralpha-dependent manner. We found that exogenous IL-13 exaggerated the immune and inflammatory responses to an inhaled, harmless Ag, whereas endogenous IL-13 was necessary for the priming of naive mice with an inhaled, harmless Ag. These data indicate that blockade of IL-13 may have therapeutic potential for controlling the immune response to inhaled Ags.
Fundus Autofluorescence Imaging in Best's Vitelliform Dystrophy (2003)

Fundus autofluorescence imaging provides new information regarding the content and spatial distribution of RPE lipofuscin in eyes with Best's disease, which appears to correspond to retinal function. This may "in vivo" give important clues to the pathogenesis and progression of Best's disease in which non-invasive autofluorescence imaging may replace fluorescein angiography.
Elastic and macroporous agarose–gelatin cryogels with isotropic and anisotropic porosity for tissue engineering (2008)

The focus of this work was to design a macroporous scaffold with controlled porosity in isotropic and anisotropic manner for tissue-engineering applications. Agarose-gelatin scaffolds were synthesized by cryogelation method, in which agarose was used to improve the mechanical characteristics and gelatin-provided amiable property of elasticity, cell adhesion, and cell proliferation in the scaffold. Agarose-gelatin (8%) cryogels synthesized in two different solvent systems (i.e., water and 0.1% acetic acid) at subzero temperature (-12 degrees C) showed well-interconnected porous structure. The agarose-gelatin cryogel synthesized in water solvent system (WSS) showed gradient porosity with an average pore diameter of a monolith (four sections from bottom to top; height 5 mm and diameter 13 mm each) ranging from 76 to 187 microm. The monolith of agarose-gelatin synthesized in 0.1% acetic acid solvent system (0.1% ASS) did not show any remarkable difference in average pore diameter of a monolith to their whole column length as revealed by scanning electron microscopy (SEM). These cryogels swelled up to approximately 90% of their capacity within 1 min. The aggregate tensile modulus showed good elasticity of the cryogels, in which agarose-gelatin synthesized in WSS showed higher tensile modulus, that is, 380.23 +/- 63.97 kPa in comparison with agarose-gelatin synthesized in 0.1% ASS, i.e., 278.08 +/- 94.08 kPa. The unconfined fatigue observation with varying strain (10-40%) and varying frequencies (2 and 5 Hz) showed no deformation of cryogels. The fibroblast (Cos-7) cell line seeded on the scaffold displayed good cell attachment in both types of cryogels and MTT assay showed good cell compatibility and favorable conditions for cell proliferation. These results indicate that agarose-gelatin cryogels can be a promising material of choice for tissue-engineering applications.
Dendritic Molecular Capsules for Hydrophobic Compounds (2003)

Reichardt's dye, a highly solvatochromic dye, was encapsulated within poly (glycerol succinic acid) ([Gn]-PGLSA-OH) dendrimers to investigate the interior environment of these dendritic macromolecules. The absorption maximum for the encapsulated Reichardt's dye in water was indicative of a relatively high dielectric constant present within the dye/dendrimer complex. (1)H NMR of the encapsulated complex showed the presence of aromatic protons from Reichardt's dye along with the aliphatic protons of the dendrimer. Additionally, there were substantial changes in T(1) and T(2) times of the encapsulated dye when compared with the free dye, and (1)H NOESY spectra for the complex showed a significant number of intermolecular NOE cross-peaks. These data reveal the close through-space proximity of the dye to the dendrimer and the restricted motion of the encapsulated dye. To demonstrate the potential use of these macromolecules as drug delivery vehicles, the poorly water-soluble anticancer drug 10-hydroxycamptothecin (10HCPT) was encapsulated within a carboxylated PGLSA dendrimer ([G4]-PGLSA-COONa). Cytotoxicity assays with human breast cancer cells showed a significant reduction of cell viability, demonstrating that 10HCPT retains activity upon encapsulation.
Target recognition, resistance, immunity and genome mining of class II bacteriocins from Gram-positive bacteria (2011)

Due to their very potent antimicrobial activity against diverse food-spoiling bacteria and pathogens and their favourable biochemical properties, peptide bacteriocins from Gram-positive bacteria have long been considered promising for applications in food preservation or medical treatment. To take advantage of bacteriocins in different applications, it is crucial to have detailed knowledge on the molecular mechanisms by which these peptides recognize and kill target cells, how producer cells protect themselves from their own bacteriocin (self-immunity) and how target cells may develop resistance. In this review we discuss some important recent progress in these areas for the non-lantibiotic (class II) bacteriocins. We also discuss some examples of how the current wealth of genome sequences provides an invaluable source in the search for novel class II bacteriocins.
The roles of factor VII's structural domains in tissue factor binding (1995)

Factor VIIa binds to tissue factor in one of the initial steps of blood clotting. In order to determine the role of the various domains of the factor VII molecule in this interaction, we made several chimeric factor VII proteins using recombinant DNA techniques. The molecules have factor IX domains substituted into factor VII and vice versa. The domains exchanged were the 4-carboxyglutamic acid plus aromatic stack domain (gla), the first epidermal growth factor-like domain (Egf-1), the second epidermal growth factor-like domain (Egf-2), and the catalytic domain. Using tissue factor-coated microtiter wells, competition binding studies with 125I-labeled factor VIIa indicated factor VIIa's Kd is 4.2 nM. Employing the same microtiter plate assay, koff and kon were determined and yielded a Kd of 1.5 nM. The results of competitive binding experiments and activation assays using chimeric proteins indicated the interaction between factor VIIa and tissue factor involves direct contact between tissue factor and factor VIIa's Egf-1 domain and catalytic domain. On the other hand, the gla and Egf-2 domains, while necessary for optimal binding, may merely impart structure to the rest of the molecule. However, either one or both of the latter domains might contribute a relatively small amount of energy to direct binding.
Preinfection Treatment of Resistant Mice with CpG Oligodeoxynucleotides Renders Them Susceptible to Friend Retrovirus-Induced Leukemia (2003)

We recently reported that immunostimulatory oligodeoxynucleotides (CpG oligodeoxynucleotides [CpG-ODN]) were effective in postexposure treatment of retrovirus-induced disease (A. R. M. Olbrich et al., J. Virol. 76:11397-11404, 2002). We now show that the timing of treatment is a critical factor in treatment efficacy. In stark contrast to the success of postexposure treatments, we found that CpG treatment of susceptible mice prior to Friend retrovirus infection accelerated the development of virus-induced erythroleukemia. Furthermore, 70.8% of mice that were resistant to Friend virus-induced leukemia developed disease after inoculation of CpG-ODN before infection. The CpG pretreatment of these mice enhanced viral loads in their spleens and blood compared to controls that received ODN without CpG motifs. The main target cells of Friend virus, erythroid precursor cells and B cells, proliferated after CpG-ODN inoculation and provided an enlarged target cell population for viral infection. Our present findings together with our previous report demonstrate that CpG-ODN treatment of viral infections may be a double-edged sword that can result in an effective therapy but also in an acceleration of disease progression depending on the time point of treatment.
Mechanisms of Leukotriene B4–Triggered Monocyte Adhesion (2003)

Objective— Leukotriene B 4 (LTB 4 ) has been implicated in the trafficking of monocytes to inflammatory pathologic conditions, such as transplant rejection and atherosclerosis. The aim of this study was to determine the mechanisms by which LTB 4 contributes to monocyte capture from the circulation. Methods and Results— In in vitro and in vivo vascular models, the lipid chemoattractant LTB 4 was an equipotent agonist of monocyte adhesion compared with the chemokine monocyte chemoattractant protein-1 (MCP-1). Adenoviral gene transfer of specific endothelial adhesion molecules and blocking monoclonal antibody studies demonstrated that LTB 4 triggers both β 1 - and β 2 -integrin–dependent adhesion. Flow cytometry studies suggested that changes in integrin avidity or affinity, rather than alterations of integrin surface expression, were responsible for the chemoattractant-triggered arrest. Surprisingly, in contrast to the peptide chemokine MCP-1, LTB 4 did not activate the phosphoinositide 3-kinase pathway, which is a functionally critical step in chemokine-triggered effector functions. Conclusions— LTB 4 is a potent trigger of monocyte adhesion under flow yet mediates its effects via pathways that appear to differ from peptide chemoattractants. A better understanding of the mechanisms of LTB 4 -induced monocyte trafficking might shed insight into disease pathogenesis and pinpoint critical steps for therapeutic intervention for multiple human inflammatory pathologic conditions.
Eosinophilic Bronchitis, Eosinophilia Associated Genetic Variants, and Notch Signaling in Asthma (2010)

While much has indeed been learned about the biology and role of eosinophils, the paradigm of eosinophils has the pros and cons in development of asthma. To answer the questions in the black box, this review firstly discusses the biological and morphological differences between asthma and eosinophilic bronchitis (EB). EB is an interesting clinical manifestation of eosinophilic airway disease that does not involve airway hyperresponsiveness (AHR), demonstrating that airway eosinophilia alone is insufficient to merit a diagnosis of asthma. Secondly, I will describe and discuss the effect(s) of single-nucleotide polymorphisms (SNPs) in the genes CCR3, IL-5 RECEPTOR ALPHA (IL5RA), and IL1RL1, and finally the in vitro and in vivo effects of Notch inhibition on both eosinophil differentiation and experimental asthma. Eosinophilic airway inflammation is not as important in the pathogenesis and maintenance of asthma as had previously been thought. However, the role of eosinophils in other asthma subphenotypes, including refractory or severely remodeled asthma, needs to be evaluated further. High-throughput methodologies such as genomics will facilitate the discovery of new markers of inflammation; these, in turn, will aid in the evaluation of the role of eosinophils in asthma and its various subphenotypes.
Synergistic functions of protein phosphorylation and calcium mobilization in platelet activation. (1983)

When human platelets were stimulated by synthetic diacylglycerol such as 1-oleoyl-2-acetyl-glycerol, which was a potent activator in vitro of Ca2+-activated, phospholipid-dependent protein kinase (protein kinase C) (Mori, T., Takai, Y., Yu, B., Takahashi, J., Nishizuka, Y., and Fujikura, T. (1982) J. Biochem. (Tokyo) 91, 427-431), a protein having Mr approximately 40,000 (40-kilodalton protein) was rapidly phosphorylated, just as it was by natural extracellular messengers such as thrombin. Fingerprint analysis appeared to indicate that protein kinase C was indeed responsible for this 40-kilodalton protein phosphorylation in intact platelets. Under these conditions, neither inositol phospholipid breakdown nor endogenous diacylglycerol formation was observed, indicating that the synthetic diacylglycerol intercalated into the membrane and directly activated protein kinase C without interaction with cell surface receptors. During this process, the diacylglycerol was converted in situ to the corresponding phosphatidate, 1-oleoyl-2-acetyl-glyceryl-3-phosphoric acid. Experiments with the synthetic diacylglycerol and Ca2+ ionophore A23187 suggested that the protein phosphorylation catalyzed by protein kinase C was a prerequisite requirement for the release of serotonin, and that the receptor-linked protein phosphorylation and Ca2+ mobilization acted synergistically to elicit the full physiological cellular response.
Scalable Pattern Matching for High Speed Networks (2004)

In this paper, we present a scalable FPGA design methodology for searching network packet payloads for a large number of patterns, including complex regular expressions. The efficiency of the technique enables a current-generation FPGA device to support pattern-matching at network rates from 1 Gbps to 100 Gbps and beyond. It offers flexible trade-offs between character capacity, throughput, and data bus width and rate. This allows the approach to be used in a wide range of devices from low-end home network appliances to high-end backbone routers. Suitable network applications for the FPGA pattern-matcher include firewalls, network intrusion detection, email virus scanning, and junk-email identification. In this work, we use a standard set of patterns from an intrusion detection system to demonstrate the performance and scalability of our design with a real-world application.
Deep Learning Predicts Lung Cancer Treatment Response from Serial Medical Imaging (2019)

We demonstrate that deep learning can integrate imaging scans at multiple timepoints to improve clinical outcome predictions. AI-based noninvasive radiomics biomarkers can have a significant impact in the clinic given their low cost and minimal requirements for human input.
Geometric and electronic structures of fluorine bound silicon clusters (1998)

Geometries and energies of SinF− and SinF (n=1–7) were investigated with ab initio MO calculations; the Mo/ller–Plesset perturbation and coupled cluster methods were used to take into account the electron correlation. The F atom is bound to the apex atom in the Sin frame, and the electronic structures of the Sin part in SinF− and SinF are similar to those of the corresponding Sin and Sin+, respectively. The calculated electron affinities (EAs) of SinF are in agreement with the experimental values. The size dependence of EAs of SinF is similar to that of the ionization energies of Sin at n⩾5, whereas it is different at n⩽4. In the HOMO of SinF (n⩽4), the weak antibonding nature between F and Si greatly makes the SinF− anions unstable, resulting in small EA. The vibrationally resolved photoelectron spectra (PES) of SinF− (n=1–3) were measured, and were completely reproduced theoretically.
Rapamycin inhibits vascular smooth muscle cell migration. (1996)

Abnormal vascular smooth muscle cell (SMC) proliferation and migration contribute to the development of restenosis after percutaneous transluminal coronary angioplasty and accelerated arteriopathy after cardiac transplantation. Previously, we reported that the macrolide antibiotic rapamycin, but not the related compound FK506, inhibits both human and rat aortic SMC proliferation in vitro by inhibiting cell cycle-dependent kinases and delaying phosphorylation of retinoblastoma protein (Marx, S.O., T. Jayaraman, L.O. Go, and A.R. Marks. 1995. Circ. Res. 362:801). In the present study the effects of rapamycin on SMC migration were assayed in vitro using a modified Boyden chamber and in vivo using a porcine aortic SMC explant model. Pretreatment with rapamycin (2 ng/ml) for 48 h inhibited PDGF-induced migration (PDGF BB homodimer; 20 ng/ml) in cultured rat and human SMC (n = 10; P < 0.0001), whereas FK506 had no significant effect on migration. Rapamycin administered orally (1 mg/kg per d for 7 d) significantly inhibited porcine aortic SMC migration compared with control (n = 15; P < 0.0001). Thus, in addition to being a potent immunosuppressant and antiproliferative, rapamycin also inhibits SMC migration.
Dense array slab-coupled optical waveguide laser capable of 500W/bar (2014)

Dense array slab-coupled optical waveguide lasers (DASCOWLs) consist of several hundred single-mode SCOWL lasers on a monolithic bar. Near diffraction-limited output of the SCOWLs is preserved with spacing down to 40μm. Greater than 200W CW operation of a 4% FF, 100-element, 100μm-pitch, centimeter wide DASCOWL bar has been demonstrated, corresponding to <2W/emitter in array format. We have also demonstrated near 500W continuous wave (CW) operation from a 10% fill factor (FF) 1-cm wide, 1cm long DASCOWL bar which contains 250 emitters, with a 40μm pitch. The goal of 2W/emitter, 500W/bar represents a 5X increase above the conventional 10-emitter, 10% FF broad area laser diode bar that operates at 10W/100μm-emitter. Some of the reported DASCOWL performance benefits from SRL's low thermal resistance EPIC heat sinks.
Multiple Comparisons Using Rank Sums (1964)

This paper considers the use of rank sums from a combined ranking of k independent samples in order to decide which populations differ. Such a procedure is suggested as a convenient alternative to making separate rankings for each pair of samples, and the two methods are compared. Asymptotic use of the normal tables is given and the treatment of ties is discussed. A numerical example is given.
Making Blind Robots See: The Synergy Between Fluorescent Dyes and Imaging Devices in Automated Proteomics (2000)

Proteomics investigations endeavor to provide a global understanding of gene product synthesis rate, degradation rate, functional competence, posttranslational modification, subcellular distribution and physical interactions with other cell components. Protein expression encompasses an enormous dynamic range. Since rare proteins cannot be amplified by any type of PCR method, sensitive detection is critical to proteome projects. Fluorescence methods deliver streamlined detection protocols, superior detection sensitivity, broad linear dynamic range and excellent compatibility with modern microchemical identification methods such as mass spectrometry. Two general approaches to fluorescence detection of proteins are currently practiced: the covalent derivatization of proteins with fluorophores or noncovalent interaction of fluorophores either via the SDS micelle or through direct electrostatic interaction with proteins. One approach for quantifying fluorescence is to use a photomultiplier tube detector combined with a laser light scanner. In addition, fluorescence imaging is performed using a charge-coupled device camera combined with a UV light or xenon arc source. Fluorescent dyes with bimodal excitation spectra may be broadly implemented on a wide range of analytical imaging devices, permitting their widespread application to proteomics studies and incorporation into semiautomated analysis environments.
Extramedullary Hematopoiesis Generates Ly-6C high Monocytes That Infiltrate Atherosclerotic Lesions (2011)

Our findings indicate that extramedullary sites supplement the hematopoietic function of the bone marrow by producing circulating inflammatory cells that infiltrate atherosclerotic lesions.