gebhart/patrepeval huggingface dataset:
Proteasome inhibition by lactacystin in primary neuronal cells induces both potentially neuroprotective and pro‐apoptotic transcriptional responses: a microarray analysis (2005)

Although inhibition of the ubiquitin proteasome system has been postulated to play a key role in the pathogenesis of neurodegenerative diseases, studies have also shown that proteasome inhibition can induce increased expression of neuroprotective heat-shock proteins (HSPs). The global gene expression of primary neurons in response to treatment with the proteasome inhibitor lactacystin was studied to identify the widest range of possible pathways affected. Our results showed changes in mRNA abundance, both at different time points after lactacystin treatment and at different lactacystin concentrations. Genes that were differentially up-regulated at the early time point but not when most cells were undergoing apoptosis might be involved in an attempt to reverse proteasome inhibitor-mediated apoptosis and include HSP70, HSP22 and cell cycle inhibitors. The up-regulation of HSP70 and HSP22 appeared specific towards proteasome inhibitor-mediated cell death. Overexpression of HSP22 was found to protect against proteasome inhibitor-mediated loss of viability by up to 25%. Genes involved in oxidative stress and the inflammatory response were also up-regulated. These data suggest an initial neuroprotective pathway involving HSPs, antioxidants and cell cycle inhibitors, followed by a pro-apoptotic response possibly mediated by inflammation, oxidative stress and aberrant activation of cell cycle proteins.
Major Histocompatibility Complex Binding, Eluted Ligands, and Immunogenicity: Benchmark Testing and Predictions (2020)

Antidrug antibody (ADA) responses impact drug safety, potency, and efficacy. It is generally assumed that ADA responses are associated with human leukocyte antigen (HLA) class II-restricted CD4+ T-cell reactivity. Although this review does not address ADA responses <i>per se</i>, the analysis presented here is relevant to the topic, because measuring or predicting CD4+ T-cell reactivity is a common strategy to address ADA and immunogenicity concerns. Because human CD4+ T-cell reactivity relies on the recognition of peptides bound to HLA class II, prediction, or measurement of the capacity of different peptides to bind or be natural ligands of HLA class II is used as a predictor of CD4+ T-cell reactivity and ADA development. Thus, three different interconnected variables are commonly utilized in predicting T-cell reactivity: major histocompatibility complex (MHC) binding, capacity to be generated as natural HLA ligands, and T-cell immunogenicity. To provide the scientific community with guidance in the relative merit of different approaches, it is necessary to clearly define what outcomes are being considered. Thus, the accuracy of HLA binding predictions varies as a function of what the outcome predicted is, whether it is binding itself, natural processing, or T-cell immunogenicity. Furthermore, it is necessary that the accuracy of prediction is based on rigorous benchmarking, grounded by fair, objective, transparent, and experimental criteria. In this review, we provide our perspective on how different variables and methodologies predict each of the various outcomes and point out knowledge gaps and areas to be addressed by further experimental work.
Mechanism and stereochemistry of the fluorination of uracil and cytosine using fluorine and acetyl hypofluorite (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism and stereochemistry of the fluorination of uracil and cytosine using fluorine and acetyl hypofluoriteGerard W. M. Visser, Saskia Boele, Bert W. Van Halteren, Gertrudis H. J. N. Knops, Jacobus D. M. Herscheid, Gerard A. Brinkman, and Arend HoekstraCite this: J. Org. Chem. 1986, 51, 9, 1466–1471Publication Date (Print):May 1, 1986Publication History Published online1 May 2002Published inissue 1 May 1986https://pubs.acs.org/doi/10.1021/jo00359a015https://doi.org/10.1021/jo00359a015research-articleACS PublicationsRequest reuse permissionsArticle Views573Altmetric-Citations48LEARN 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
In vitro activities of ceftriaxone and fusidic acid against 13 isolates of Coxiella burnetii, determined using the shell vial assay (1993)

The susceptibilities of 13 isolates of Coxiella burnetii to fusidic acid and ceftriaxone were determined by use of the recently described shell vial assay (D. Raoult, H. Torres, and M. Drancourt, Antimicrob. Agents Chemother, 35:2070-2077, 1991). At a concentration of 4 micrograms/ml, ceftriaxone was bacteriostatic for four isolates and slowed the multiplication of the other nine. Fusidic acid at a concentration of 2 micrograms/ml was bacteriostatic for six isolates and slowed the multiplication of three others. These results show that these compounds could be effective in the phagolysosome of C. burnetii-infected cells.
Imaging of human brain lesions with an ω<sub>3</sub> site radioligand (1988)

The topography and magnitude of increase in peripheral type benzodiazepine binding sites (omega 3 sites) was investigated autoradiographically in the brains of patients with ischemic cerebrovascular disease, with multiple sclerosis, and with malignant glioma. 3H-PK 11195, a selective omega 3 site ligand, was employed. A manyfold increase in omega 3 site density was observed in all these disease states; this increase reflects macrophage invasion or glial proliferation or both as demonstrated by neuropathological studies carried out in parallel. There was an excellent spatial correlation between increased omega 3 site densities and extent of the lesion histologically. Specifically, an elevated density of omega 3 sites was observed in the plaques of demyelination in multiple sclerosis patients, in the periphery of infarcted zones in stroke patients, and throughout tumor in patients with grade IV astrocytomas. As our approach is applicable to both tomographic (in vivo) and autoradiographic investigations, imaging of omega 3 sites may be considered for the detection and monitoring of the natural evolution of many disorders of the human central nervous system.
Dip Pen Nanolithography: a maturing technology for high-throughput flexible nanopatterning (2007)

Precision nanoscale deposition is a fundamental requirement for much of current nanoscience research. Further, depositing a wide range of materials as nanoscale features onto diverse surfaces is a challenging requirement for nanoscale processing systems. As a high resolution scanning probe-based direct-write technology, Dip Pen Nanolithography® (DPN®) satisfies and exceeds these fundamental requirements. Herein we specifically describe the massive scalability of DPN with two dimensional probe arrays (the 2D nano PrintArray). In collaboration with researchers at Northwestern University, we have demonstrated massively parallel nanoscale deposition with this 2D array of 55,000 pens on a centimeter square probe chip. (To date, this is the highest cantilever density ever reported.) This enables direct-writing flexible patterns with a variety of molecules, simultaneously generating 55,000 duplicates at the resolution of single-pen DPN. To date, there is no other way to accomplish this kind of patterning at this unprecedented resolution. These advances in high-throughput, flexible nanopatterning point to several compelling applications. The 2D nano PrintArray can cover a square centimeter with nanoscale features and pattern 10<sup>7</sup> &mgr;m<sup>2</sup> per hour. These features can be solid state nanostructures, metals, or using established templating techniques, these advances enable screening for biological interactions at the level of a few molecules, or even single molecules; this in turn can enable engineering the cell-substrate interface at sub-cellular resolution.
Analýza mutace K329E (A985) způsobující deficit acyl-CoA-dehydrogenasy mastných kyselin o středně dlouhém řetězci (MCAD) v české populaci (2000)

Deficit acyl-CoA dehydrogenazy o středně dlouhem řetězci (MCAD)
je nejběžnějsi dědicna porucha beta-oxidace mastných kyselin.
Větsina klinicky zjistěných připadů pochazejici z kavkazske
populace je způsobena bodovou mutaci K329E (A985G) v genu pro
MCAD. Cile studie byly: 1) stanovit frekvenci uvedene mutace a
upřesnit incidenci deficitu MCAD v nasi populaci, 2) zjistit v
jakem měřitku se tento defekt podili na nahlem umrti kojenců.
Podařilo se vyoptimalizovat DNA diagnostiku mutace K329E ze
suche kapky krve a z tkani zemřelých děti uchovavaných v
parafinových bloccich. Ze 4066 analyzovaných vzorků z oblasti
jižni Moravy jsme prokazali 16 heterozygotů - přenaseců mutace
K329E, homozygot nebyl nalezen žadný. Poměrně nizka frekvence
nosiců mutace K329E (1/254) nasvědcuje tomu, že se děti s
deficitem MCAD rodi v nasi populaci s incidenci vyssi než 1:100
000. Mutace K329E byla prokazana pouze u 3% tkani nahle
zemřelých děti. Nepotvrdila se domněnka, že by v nasi populaci
novorozenci, kteři zemřeli pod syndromem SIDS, trpěli v
převažne miře deficitem MCAD. Zavěrem lze zhodnotit, že oproti
původnimu ocekavani se bude deficit MCAD v nasi populaci řadit
k meně castým metabolickým porucham, s vyssi molekularni
heterogenitou, než je tomu ve větsině evropských zemi.
Inductively Compensated Parallel Coupled Microstrip Lines and Their Applications (2006)

A simple method using lumped inductors to compensate unequal even- and odd-mode phase velocities in parallel coupled microstrip lines is presented. The singly and doubly compensated cases are analyzed to enable the optimum inductor values and the electrical lengths of the compensated coupled lines to be calculated from closed-form expressions. The technique proposed not only improves the performance, but also yields a more compact design. To demonstrate the technique's broad range of applicability, the compensated coupled-line structure is used to enhance the performance of a 900-MHz Lange coupler, a 1-GHz multisection 10-dB coupler, a 900-MHz planar Marchand balun, and a 1.8-GHz parallel coupled bandpass filter.
Integration of ultra-low-loss silica waveguides with silicon photonics (2012)

We demonstrate an integrated silicon and ultra-low-loss silica waveguide platform. Coupling between layers is achieved with (0.4±0.2) dB of loss per transition and a 20 nm 3-dB bandwidth.
Contrasting fiber-optic-component-design requirements in telecommunications, analog, and local data communications applications (1980)

This paper contrasts the system requirements in the three major applications of fiber optics: digital telecommunications, analog, and local data communications. These comparisons reveal how differing system requirements result in very different architectural design for the fiber optics components, particularly the receiver design. Some alternative receiver architectures are discussed along with performance tradeoffs.
Design of battery and ultracapacitor multiple energy storage in hybrid electric vehicle (2009)

Combination of battery and ultracapacitor as energy storage of hybrid electric vehicles is considered a good way to improve overall vehicle efficiency and battery life. Coordinated power distribution and bi-directional DCDC converter control are challenges. Method to determine distribution of ultracapacitor and battery is proposed based on a specific hybrid electric bus. A bi-directional DCDC converter is interface of two energy storage to control power flow. Metrics of converter are determined from vehicle simulation. To downsize the converter and get high efficiency, bi-directional DCDC converter operates under complementary DCM condition and soft-switching.
Ion Binding Affinity in the Cavity of the KcsA Potassium Channel (2004)

The hydrophobic cell membrane interior presents a large energy barrier for ions to permeate. Potassium channels reduce this barrier by creating a water-filled cavity at the middle of their ion conduction pore to allow ion hydration and by directing the C-terminal "end charge" of four alpha-helices toward the water-filled cavity. Here we have studied the interaction of monovalent cations with the cavity of the KcsA K(+) channel using X-ray crystallography. In these studies, Tl(+) was used as an analogue for K(+) and the total ion-stabilization energy for Tl(+) in the cavity was estimated by measuring its binding affinity. Binding affinity for the Na(+) ion was also measured, revealing a weak selectivity ( approximately 7-fold) favoring Tl(+) over Na(+). The structures of the cavity containing Na(+), K(+), Tl(+), Rb(+), and Cs(+) are compared. These results are consistent with a fairly large (more negative than -100 mV) electrostatic potential inside the cavity, and they also imply the presence of a weak nonelectrostatic component to a cation's interaction with the cavity.
Human Neutrophils Kill Bacillus anthracis (2005)

Bacillus anthracis spores cause natural infections and are used as biological weapons. Inhalation infection with B. anthracis, the etiological agent of anthrax, is almost always lethal, yet cutaneous infections usually remain localized and resolve spontaneously. Neutrophils are typically recruited to cutaneous but seldom to other forms of anthrax infections, raising the possibility that neutrophils kill B. anthracis. In this study we infected human neutrophils with either spores or vegetative bacteria of a wild-type strain, or strains, expressing only one of the two major virulence factors. The human neutrophils engulfed B. anthracis spores, which germinated intracellularly and were then efficiently killed. Interestingly, neutrophil killing was independent of reactive oxygen species production. We fractionated a human neutrophil granule extract by high-performance liquid chromatography and identified alpha-defensins as the component responsible for B. anthracis killing. These data suggest that the timely recruitment of neutrophils can control cutaneous infections and possibly other forms of B. anthracis infections, and that alpha-defensins play an important role in the potent anti-B. anthracis activity of neutrophils.
<i>Introduction to Fourier Optics</i> (1969)

Share Icon Share Twitter Facebook Reddit LinkedIn Reprints and Permissions Cite Icon Cite Search Site Citation Joseph W. Goodman, Mary E. Cox; Introduction to Fourier Optics. Physics Today 1 April 1969; 22 (4): 97–101. https://doi.org/10.1063/1.3035549 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentPhysics Today Search Advanced Search
Reducing 3-D acquisition footprint for 3-D DMO and 3-D prestack migration (1998)

Abstract The acquisition patterns of 3-D surveys often have a significant effect on the results of dip moveout (DMO) or prestack migration. When the spatial distribution of input traces is irregular, results from DMO and migration are contaminated by artifacts. In many cases, the footprint of the acquisition patterns can be seen on the migrated section and may result in incorrect interpretation. This phenomena also has a very significant effect on the feasibility of conducting amplitude variation with offset (AVO) analysis after 3-D prestack migration or after 3-D DMO, and also may affect velocity analysis. We propose a simple enhancement to migration and DMO programs that acts to minimize acquisition artifacts.
Molecular and immunological characterization of a novel polymorphic lipoprotein of Borrelia burgdorferi (1993)

We describe the cloning, expression, and molecular characterization of a novel polymorphic Borrelia burgdorferi lipoprotein recognized by monoclonal antibody LA7. Sequence analysis revealed an open reading frame encoding a 21,866-Da polypeptide (IpLA7). Comparison with other known proteins indicated sequence similarity between IpLA7 signal peptides and those of other prokaryotic lipoproteins, including the immunodominant B. burgdorferi outer surface proteins OspA, OspB, pC, and OspD. Both natural IpLA-7 and recombinant IpLA-7 could be biosynthetically labeled with [3H]palmitate. Upon solubilization of intact B. burgdorferi with the nonionic detergent Triton X-114, IpLA7 was extracted together with other lipoproteins into the detergent phase. Indirect immunolabeling studies indicated that the epitope recognized by monoclonal antibody LA7 is mainly located in the periplasmic space. Two-dimensional gel electrophoresis and immunoblotting confirmed the calculated acidic pI of 5.7 for IpLA-7. The LA7 gene was shown to be species specific and to be located on the linear chromosome of B. burgdorferi. The analysis of 40 individual spirochetal isolates on the basis of restriction fragment length polymorphisms revealed considerable genotypic heterogeneity of LA7 corresponding to that previously found for ospA. Native IpLA-7 and recombinant IpLA-7 were recognized by immune sera from infected mice as well as some human sera derived from infected but healthy donors and may thus prove useful as an additional marker for the serodiagnosis of Lyme disease.
Aryl Hydrocarbon Receptor Expression and Activity in Cerebellar Granule Neuroblasts: Implications for Development and Dioxin Neurotoxicity (2004)

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent teratogen that produces neurobehavioral abnormalities associated with both cognitive and locomotor systems, yet the precise regional and cellular targets of developmental neurotoxicity remain largely unknown. Most, if not all, TCDD-induced pathology is mediated via binding to the aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor that belongs to the basic helix-loop-helix/Per-Arnt-Sim (bHLH/PAS) superfamily. Upon ligand binding, AhR translocates to the nucleus, dimerizes with the AhR nuclear translocator protein (Arnt), and regulates transcription by interaction with dioxin-response elements (DREs) in target genes, most notably specific cytochrome P450 (CYP) family members. To assess whether developing cerebellar granule neuroblasts are potential direct targets for TCDD toxicity, AhR expression and transcriptional activity were examined. AhR and Arnt proteins were present in mouse cerebellum from birth throughout postnatal development. AhR protein levels peaked between postnatal day (PND) 3-10, a critical period for granule neuroblast growth and maturation. Transcriptionally active AhR was detected in immature cerebellar granule cells in a transgenic dioxin-responsive lacZ mouse model after acute TCDD exposure. AhR and Arnt were also expressed in cerebellar granule neuroblast cultures. AhR localized to the nucleus in granule cells 15 min after TCDD treatment. TCCD elicited time-dependent and concentration-dependent increases in CYP1A1 and 1B1 mRNA and protein levels. Moreover, TCDD treatment reduced both thymidine incorporation and granule neuroblast survival in a concentration-dependent manner. These data suggest that (1) granule neuroblasts are direct targets for developmental AhR-mediated TCDD neurotoxicity and (2) TCDD exposure may disrupt granule cell neurogenesis.
Spin transfer into an inhomogeneous magnetization distribution (2001)

Based on specific examples, we examine the consequence of spin-polarized current injection into confined model micromagnetic configurations, namely a high remanence state known as the S state and a low, though nonzero, remanence state called the Leaf state. Magnetization dynamics is solved in the space and time domain owing to the Landau–Lifshitz–Gilbert equation. It is shown that, within model bounds, the S state is not propitious to fast switching under the sole influence of a polarized current, even if disregarding the current induced field, whereas Leaf state switching characteristics become extremely complex as soon as due account is made for the latter.
Characteristics of anti-Co <sup>b</sup> in vitro and in vivo: a case study (1996)

Serologic and biologic properties of an example of anti-Cob were investigated. The antibody was of the IgG class, and it bound small amounts of complement. It reacted optimally in the albumin-antiglobulin test with little or no enhancement of its reactivity in tests using enzymes. Additional experiments indicated that the Cob antigen is resistant to treatment with chemicals known to destroy other antigens. The antibody caused shortened survival of radiolabeled Co(b+) donor red cells in our patient. At 24 hours, nearly 50 percent of the red cells were no longer detectable in the circulation. It is concluded that anti-Cob is a clinically relevant antibody, a fact that must be taken into account when transfusing patients with anti-Cob.
Low Efficiency of Ca <sup>2+</sup> Entry Through the Na <sup>+</sup> -Ca <sup>2+</sup> Exchanger as Trigger for Ca <sup>2+</sup> Release From the Sarcoplasmic Reticulum (1997)

It has been proposed that Ca2+ entry through the Na(+)-Ca2+ exchanger can contribute significantly to the trigger for Ca2+ release from the sarcoplasmic reticulum (SR). We have compared the characteristics of Ca2+ release triggered by reverse-mode Na(+)-Ca2+ exchange and by L-type Ca2+ current (ICaL) during depolarizing steps in single guinea pig ventricular myocytes (whole-cell voltage clamp, fluo 3 and fura-red as [Ca2+]i indicators, 36 +/- 1 degrees C, K(+)-based pipette solution with 20 mmol/L [Na+]). Conditioning pulses to +60 mV ensured comparable Ca2+ loading of the SR. In the presence of ICaL, [Ca2+]i transients typically have an early and rapid rising phase reflecting Ca2+ release, which has a bell-shaped voltage dependence with a peak at +10 mV. With Ca2+ entry through Na(+)-Ca2+ exchange only (20 mumol/L nisoldipine), Ca2+ release flux from the SR is decreased and directly related to the amplitude of the depolarizing step. Ca2+ release is preceded by a significant delay (81 +/- 21 ms at +20 mV, 24 +/- 4 ms at +70 mV) related to Ca2+ entry through the exchanger. Triggered release interrupts Ca2+ entry, as evidenced by reversal of the exchanger current. At potentials positive to +40 mV, Ca2+ influx through Na(+)-Ca2+ exchange, calculated from the outward exchange current, reaches magnitudes comparable to ICaL, but Ca2+ release due to reverse-mode Na(+)-Ca2+ exchange still has a significant delay. We calculated trigger efficiency as the ratio between the maximal rate of Ca2+ release and the Ca2+ influx preceding this release; efficiency of reverse-mode Na(+)-Ca2+ exchange is approximately four times less than that of ICaL. With both ICaL and reverse-mode Na(+)-Ca2+ exchange present, Ca2+ release is triggered by ICaL, and a contribution of reverse-mode Na(+)-Ca2+ exchange to the trigger could not be detected at potentials below +60 mV. These characteristics of reverse-mode Na(+)-Ca2+ exchange predict that its role as a trigger for Ca2+ release during the action potential is likely to be negligible.