gebhart/patrepeval huggingface dataset:
The Patch Clamp Technique (1995)

The introduction of the patch clamp technique less than two decades ago revolutionized the study of cellular physiology by providing a high-resolution method of observing the function of individual ionic channels in a variety of normal and pathological cell types. By the use of variations of the basic recording methodology, cellular function and regulation can be studied at a molecular level by observing currents through individual ionic channels. At a cellular level, processes such as signaling, secretion, and synaptic transmission can be examined. In addition, by combining the information from high-resolution electrophysiological recordings obtained by the patch clamp method with modern molecular biological techniques, further insight can be gained into the gene expression and protein structure of ionic channels. Given the ubiquity and importance of ionic channels, it is not surprising that their study has led to a new understanding of the mechanisms of certain disease processes and has given insight into treatments for these diseases. This review gives an historical perspective of the development of the patch clamp technique and an overview of the methodologies currently in use. Examples are shown to illustrate typical uses of the patch clamp technique with emphasis on the variety of recording configurations available and the advantages and drawbacks of each method.
<title>Hyperspectral Raman imaging of bone growth and regrowth chemistry</title> (1998)

Hyperspectral Raman microscopic imaging of carbonated hydroxyapatite (HAP) is used to follow the chemistry of bone growth and regrowth. Deep red excitation is employed to minimize protein fluorescence interference. A passive line generator based on Powell lens optics and a motorized translation stage provide the imaging capabilities. Raman image contrast is generated from several lines of the HAP Raman spectrum, primarily the PO<SUB>4</SUB><SUP>-3</SUP>. Factor analysis is used to minimize the integration time needed for acceptable contrast and to explore the chemical species within the bone. Bone age is visualized as variations in image intensity. High definition, high resolution images of newly formed bone and mature bone are compared qualitatively. The technique is currently under evaluation for study of experimental therapies for fracture repair.
Comparability and Monitoring Immunogenic N-linked Oligosaccharides from Recombinant Monoclonal Antibodies from Two Different Cell Lines using HPLC with Fluorescence Detection and Mass Spectrometry (2008)

One of the most important structural features of recombinant monoclonal antibodies produced in mammalian cells is the N-linked oligosaccharide profile. These profiles impact recombinant therapeutics in a multitude of ways affecting distribution, efficacy, and immunogenicity. High mannose, alpha-gal and other oligosaccharide species are highly immunogenic and in most cases should be minimized during manufacturing. A recombinant monoclonal antibody, h5G1.1, was produced in NS0 and CHO cell lines and tested to identify changes in the N-linked oligosaccharide profiles caused from a change in cell line. Traditional peak analysis using HPLC with fluorescence detection was augmented by mass spectrometric analysis. Nano LC-MS following tryptic digestion corroborated HPLC findings of the presence of several alpha-gal oligosaccharide species in the recombinant IgG (rIgG) from NS0 cell line. Both cell lines possessed rIgGs with complex and small amounts of high mannose glycans.
Binding of a pea nuclear protein to promoters of certain photoregulated genes is modulated by phosphorylation. (1989)

There have been numerous recent reports documenting phosphorylation of DNA-binding proteins [Montminy and Bilezikjian (1987); Sorger, Lewis, and Pelham (1987); Hoeffler, Kovelman, and Roeder (1988); Jones et al. (1988); Prywes et al. (1988); Sorger and Pelham (1988); Yamamoto et al. (1988)], and the transcriptional regulatory activity of at least one of these proteins appears to be modulated by this modification [Montminy and Bilezikjian (1987); Yamamoto et al. (1988)]. We report here on a plant nuclear protein, the DNA-binding activity of which is strongly affected by phosphorylation. This protein, AT-1, binds to specific AT-rich elements (the AT-1 box) within promoters of certain nuclear genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase and the polypeptide components of the light-harvesting chlorophyll a/b protein complex. A consensus sequence of AATATTTTTATT was derived for the AT-1 box. We demonstrate that the DNA-binding ability of AT-1, from nuclear extracts of pea, can be reversibly modulated by phosphorylation. AT-1 is active in the nonphosphorylated form and loses all DNA-binding ability as a result of phosphorylation. The kinase that phosphorylates AT-1 uses both Mg-ATP and Mg-GTP as a substrate and is inhibited by heparin and spermine, indicative of an NII-type casein kinase.
Phylogenetic specificity of cholinergic ligands: .alpha.-conotoxin SI (1988)

The alpha-conotoxins are small peptide neurotoxins from the venom of fish-hunting cone snails which block nicotinic acetylcholine receptors (nAChRs). We describe the purification, characterization, and chemical synthesis of a new alpha-conotoxin from Conus striatus, alpha-conotoxin SI. In contrast to other AChR ligands, alpha-SI discriminates between different vertebrate nAChRs. The sequence of alpha-conotoxin SI is Ile-Cys-Cys-Asn-Pro5-Ala-Cys-Gly-Pro-Lys10-Tyr-Ser-Cys-NH2. This sequence was confirmed by chemical synthesis. A des-Ile-alpha-SI derivative was also synthesized and is biologically active. Although alpha-conotoxin SI is highly homologous to previously described alpha-conotoxins, it has one noteworthy sequence feature which may account for its novel biological specificity. In all other alpha-conotoxins, there is a positively charged amino acid at residue 9; in alpha-conotoxin SI, this is replaced by proline. The discovery that different alpha-conotoxins can vary by orders of magnitude in their apparent affinity for different vertebrate receptors demonstrates that alpha-conotoxins will be useful probes for investigating phylogenetic differences between vertebrate nAChRs.
Serum-Derived Immunoglobulins Neutralize Adverse Effects of Amyloid-β Peptide on the Integrity of a Blood-Brain Barrier In Vitro Model (2010)

A disrupted blood-brain barrier (BBB) might have major effects on the progression of Alzheimer's disease (AD). This supports the theory of blood as a chronic source of exogenous amyloid-beta (Abeta) peptide as well as other neurotoxic substances in the brain, which would normally be excluded by an intact BBB. In addition to Abeta, neuroinflammation is suggested to contribute to the pathological conditions in AD and is a known disruptor of BBB integrity. Consequently, new therapeutic approaches to stabilize the BBB should be developed. Serum derived immunoglobulins, also called intravenous immunoglobulins (IVIG), are gained from plasma of healthy individuals and were found to induce positive effects in some patients with AD, but mechanisms of action are unclear by now. Moreover, there are no data on how IVIG affects the BBB itself. Therefore, we examined the potency of Abeta peptides as well as neuroinflammatory mediators (TNF-alpha and LPS) either alone or after simultaneous application of IVIG to disintegrate the BBB by evaluating the transport rate of carboxyfluorescein, a marker of paracellular leakage. Our results showed beneficial effects of IVIG on a disrupted BBB, which could positively influence diseases outcome in AD. With a stabilized BBB the brain is prevented from systemic Abeta entry, as well as from entry of other toxic substances from the blood.
Cyclin D1-negative mantle cell lymphoma: a clinicopathologic study based on gene expression profiling (2005)

Cyclin D1 overexpression is believed to be essential in the pathogenesis of mantle cell lymphoma (MCL). Hence, the existence of cyclin D1-negative MCL has been controversial and difficult to substantiate. Our previous gene expression profiling study identified several cases that lacked cyclin D1 expression, but had a gene expression signature typical of MCL. Herein, we report the clinical, pathologic, and genetic features of 6 cases of cyclin D1-negative MCL. All 6 cases exhibited the characteristic morphologic features and the unique gene expression signature of MCL but lacked the t(11;14)(q13; q32) by fluorescence in situ hybridization (FISH) analysis. The tumor cells also failed to express cyclin D1 protein, but instead expressed either cyclin D2 (2 cases) or cyclin D3 (4 cases). There was good correlation between cyclin D protein expression and the corresponding mRNA expression levels by gene expression analysis. Using interphase FISH, we did not detect chromosomal translocations or amplifications involving CCND2 and CCND3 loci in these cases. Patients with cyclin D1-negative MCL were similar clinically to those with cyclin D1-positive MCL. In conclusion, cases of cyclin D1-negative MCL do exist and are part of the spectrum of MCL. Up-regulation of cyclin D2 or D3 may substitute for cyclin D1 in the pathogenesis of MCL.
Civil Society: The Unanswered Question of Where Power Resides (2003)

Proponents of civil society assume that where association lies, power follows. Yet, power resides in social and cultural sites that have little to do with formal institutions of political power and the political functions of voluntary associations. The Aristotelian virtue of participation (at the heart of the literature extolling the democratic benefits of association) guards against tyranny in public institutions; but power also moves along cultural grids which have little attachment to public or governmental structure, power that works on the self in everyday life, power that ministers to the body, its regulation and treatment, its containment and confinement. That kind of power, with sites deep in cultural and social practice, supported by strong belief and entrenched knowledge, scrutinizes and disciplines individual and group behavior. It is power that rarely appears in the deliberations and programs of those secondary associations de Tocqueville found critical to the vibrant democratic life of America.
Subsection V (2015)

Cyanobacteria / Subsection V / Incertae Sedis / Subsection V Genera of this subsection exhibit the highest degree of morphological complexity and differentiation within the cyanobacteria; the few available 16S rDNA sequence data analyses suggest that it is a monophyletic group, arising from within an assemblage of filamentous heterocystous cyanobacteria that divide in a single plane (Turner, 1997; “Phylogenetic relationships amongst the Cyanobacteria ,” p. 487). Longitudinal and oblique cell divisions occur in addition to transverse cell divisions. This results in periodic true branching in all genera and in multiseriate trichomes (two or more rows of cells) in some genera. Three major types of true branchings, named “T”, “V”, and “Y”, can be distinguished (Golubic et al., 1996). T‐branching is a lateral, nearly perpendicular branching originating from the change of division plane from transverse to longitudinal (Figure 1), V‐branching is a dichotomous or pseudodichotomous bifurcation originating from a change in division plane at, or close to, the trichome tip (Figure 2), and Y‐branching arises from the displacement of an intercalary branch‐point cell by surrounding meristematic growth (Figure 3). False branching also occurs in some genera. Pit‐like synapses or pore channels occur between the cells of trichomes in some of these genera. Heterocysts are both intercalary and terminal. Although reproduction occurs by random breakage of trichomes, hormogonia are also formed in most strains. Akinetes or akinete‐ like cells are produced by some genera.
Clinical significance, biochemical features, and susceptibility patterns of sporadic isolates of the Mycobacterium chelonae-like organism (1993)

Mycobacterium chelonae-like organisms are nonpigmented rapidly growing mycobacteria whose clinical significance is unknown. We evaluated 87 sporadic isolates encountered in a clinical laboratory. Most isolates (62%) were respiratory; only 2 of 54 (4%) (both from patients with AIDS) were clinically significant. Among 33 nonrespiratory isolates, 20 of 33 (or 61%) were clinically significant. Clinical diseases included posttraumatic wound infections and catheter-related sepsis. Routine biochemical features included growth inhibition by 5% NaCl (100%), a smooth colony morphology (94%), positive 3-day arylsulfatase reaction (84%), no color or a light tan color on iron uptake (100%), and variable nitrate reduction (45%). Additional characteristics that helped to separate this group from M. chelonae and Mycobacterium abscessus were susceptibility to cephalothin (90%) and ciprofloxacin (100%), utilization of mannitol (94%) and citrate (83%) as carbon sources, and unique patterns of mycolic acid esters by high-performance liquid chromatography. This group was quite drug susceptible, with 100% of isolates inhibited by amikacin, imipenem, cefoxitin, cefmetazole, and the newer quinolones ciprofloxacin and ofloxacin. Three examples of this group, including a proposed type strain, have been deposited in the American Type Culture Collection.
Graphene for CMOS and Beyond CMOS Applications (2010)

Owing in part to complementary metal–oxide–semiconductor (CMOS) scaling issues, the semiconductor industry is placing an increased emphasis on emerging materials and devices that may provide a solution beyond the 22-nm node. Single and few layers of carbon sheets (graphene) have been fabricated by a variety of techniques including mechanical exfoliation and chemical vapor deposition, and field-effect devices have been demonstrated with room temperature field-effect mobilities close to 10 000 cm <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX"> $^{2}$</tex></formula> /Vs. But since graphene is a gapless semiconductor, these transistors have high off-state leakage and nonsaturating drive currents. This is problematic for digital logic, but is acceptable for analog device applications such as low-noise amplifiers and radio-frequency (RF)/millimeter-wave field-effect transistors (FETs). The remarkable transport physics of graphene due to its linear bandstructure have led to novel beyond CMOS logic devices as well, such as “pseudospin” devices.
Theory of error in factor analysis (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheory of error in factor analysisEdmund R. MalinowskiCite this: Anal. Chem. 1977, 49, 4, 606–612Publication Date (Print):April 1, 1977Publication History Published online1 May 2002Published inissue 1 April 1977https://pubs.acs.org/doi/10.1021/ac50012a026https://doi.org/10.1021/ac50012a026research-articleACS PublicationsRequest reuse permissionsArticle Views612Altmetric-Citations206LEARN 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
Alkaline liquid chromatography/electrospray ionization skimmer collision‐induced dissociation mass spectrometry for phosphopeptide screening (2001)

Abstract A rapid on‐line method for the identification of phosphorylated peptides in enzymatic protein digests by specific marker ion signals is described. In our study we investigated the use of alkaline conditions together with a previously described method for selective and sensitive detection of phosphopeptide ions combining high‐performance capillary liquid chromatography (LC) and electrospray ionization mass spectrometry (ESI‐MS)., Phosphorylation‐specific marker ions ( m/z 79, PO 3 − , and m/z 97, H 2 PO 4 − ) were generated by skimmer collision‐induced dissociation (sCID) in the negative‐ion mode. The method was evaluated and validated for mono‐phosphorylated synthetic peptides using different alkaline pH values and CID offsets. Alkaline conditions (pH 10.5) enhance the generation of phosphopeptide‐specific fragment ions from serine‐ and tyrosine‐phosphorylated peptides, and enable the use of m/z 79 (PO 3 − ) and m/z 97 (H 2 PO 4 − ) as phosphorylation‐specific marker traces. Note that HPLC separation in trifluoroacetic acid containing solvents impairs the use of m/z 97 (C 2 F 3 O − fragment ion at m/z 97) as a phosphorylation‐specific marker. The optimized method was applied for the detection of phosphorylated peptides in a tryptic β‐casein digest. The expected mono‐ and tetra‐phosphorylated peptides were detected and rapidly identified by µLC/ESI‐sCID‐MS and µLC/ESI‐MS analysis. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Covalent and Selective Immobilization of Fusion Proteins (2003)

A general method for the covalent immobilization of fusion proteins is presented. The approach is based on the unusual mechanism of the human O6-alkylguanine-DNA alkyltransferase, which irreversibly transfers the alkyl group from its substrate, alkylated or benzylated guanine, to a reactive cysteine residue. By attaching the benzyl group to a surface, hAGT fusion proteins immobilize themselves in a specific and covalent manner. The specificity of the reaction of hAGT with its substrate even allows the specific immobilization of hAGT fusion proteins directly out of cell extracts, making the approach an attractive alternative to currently used immobilization procedures.
Enhancing effect of pyrrolidone derivatives on transdermal penetration of phenolsulfonphthalein and indomethacin from aqueous vehicle. (1990)

We investigated the enhancing effect of three alkyl-2-pyrrolidones on transdermal penetration of phenolsulfonphthalein (phenol red) and indomethacin from an aqueous vehicle by using an in vitro technique with excised rat skin. The enhancers included 1-methyl- (I), 1-hexyl- (II) and 1-lauryl-2-pyrrolidone (III). These derivatives effectively enhanced the penetration and skin accumulation of phenol red and indomethacin. Lipophilic enhancers such as II and III showed particularly high enhancing effects. The penetration profiles of phenol red and indomethacin showed a lag phase followed by a linear increase. Compounds II and III showed long lag times. The enhancer penetration was also determined. Compounds I and II showed a slight penetration. Compound III showed little penetration but high skin accumulation.
Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression (2004)

Signaling by the transcription factor nuclear factor kappa B (NF-kappaB) involves its release from inhibitor kappa B (IkappaB) in the cytosol, followed by translocation into the nucleus. NF-kappaB regulation of IkappaBalpha transcription represents a delayed negative feedback loop that drives oscillations in NF-kappaB translocation. Single-cell time-lapse imaging and computational modeling of NF-kappaB (RelA) localization showed asynchronous oscillations following cell stimulation that decreased in frequency with increased IkappaBalpha transcription. Transcription of target genes depended on oscillation persistence, involving cycles of RelA phosphorylation and dephosphorylation. The functional consequences of NF-kappaB signaling may thus depend on number, period, and amplitude of oscillations.
[Biological properties study and animal experiment of polylactide/polytrimethylene carbonate blends membrane]. (2006)

Polylactide is a biodegradable and biocompatible biomaterial. Based on the PLA (Polylactide) membrane, we have produced a new PLA/PTMC (Polytrimethylene carbonate) blends membrane. The biological properties of this membrane were studied by cell toxicity experiment, acute toxicity experiment, skin irritant experiment, sensitization test, hemolytic test, micronucleus test and subcutaneous implantation test. The results demonstrated that the blends membrane has no toxicity and it does not cause skin irritation, hypersensitive reaction and hemolysis. The micronucleus ratio of the membrane is 1.3% +/- 1.0%, being less than 3%. The result of medullary micronucleus test was reported negative. The wounds were free from suppuration and necrosis after subcutaneous implantation in all periods. In the experimental application of this member to preventing adhesion after rabbit intestine operation, the membrane demonstrated good effect. In conclusion, PLA/PTMC blends membrane is a material with good biocompatibility.
Using ultrasonic spray nozzles to coat drug-eluting stents. (2007)

Polymer coatings containing drugs released over time are used to inhibit restenosis in bare-metal stents; however applying coatings to stents, which have intricate geometries, is challenging. Ultrasonic atomising spray nozzles can be effective in achieving continuous and uniform coatings. This article describes unique nozzle designs, the methodology and the results obtained.
Serum lysyl oxidase-like 2 levels and idiopathic pulmonary fibrosis disease progression (2013)

We evaluated whether lysyl oxidase-like 2 (LOXL2), which promotes cross-linking of collagen in pathological stroma, was detectable in serum from idiopathic pulmonary fibrosis (IPF) patients, and assessed its relationship with IPF disease progression. Patients from the ARTEMIS-IPF (n=69) and the Genomic and Proteomic Analysis of Disease Progression in IPF (GAP) (n=104) studies were analysed. Baseline serum LOXL2 (sLOXL2) levels were compared with baseline clinical and physiological surrogates of disease severity, and the association with IPF disease progression was assessed using a classification and regression tree (CART) method. sLOXL2 correlated weakly with forced vital capacity and carbon monoxide diffusion capacity (r -0.24-0.05) in both cohorts. CART-determined thresholds were similar: ARTEMIS-IPF 800 pg·mL(-1) and GAP 700 pg·mL(-1). In ARTEMIS-IPF, higher sLOXL2 (>800 pg·mL(-1)) was associated with increased risk for disease progression (hazard ratio (HR) 5.41, 95% CI 1.65-17.73). Among GAP subjects with baseline spirometric data (n=70), higher sLOXL2 levels (>700 pg·mL(-1)) were associated with more disease progression events (HR 1.78, 95% CI 1.01-3.11). Among all GAP subjects, higher sLOXL2 levels were associated with increased risk for mortality (HR 2.28, 95% CI 1.18-4.38). These results suggest that higher sLOXL2 levels are associated with increased risk for IPF disease progression. However, due to multiple limitations, these results require validation.