gebhart/patrepeval huggingface dataset:
Quantitative comparison of IMAC and TiO2 surfaces used in the study of regulated, dynamic protein phosphorylation (2007)

Protein phosphorylation regulates many aspects of cellular function, including cell proliferation, migration, and signal transduction. An efficient strategy to isolate phosphopeptides from a pool of unphosphorylated peptides is essential to global characterization using mass spectrometry. We describe an approach employing isotope tagging reagents for relative and absolute quantification (iTRAQ) labeling to compare quantitatively commercial and prototypal immobilized metal affinity chelate (IMAC) and metal oxide resins. Results indicate a prototype iron chelate resin coupled to magnetic beads outperforms either the Ga(3+)-coupled analog, Fe(3+), or Ga(3+)-loaded, iminodiacetic acid (IDA)-coated magnetic particles, Ga(3+)-loaded Captivate beads, Fe(3+)-loaded Poros 20MC, or zirconium-coated ProteoExtract magnetic beads. For example, compared with Poros 20MC, the magnetic metal chelate (MMC) studied here improved phosphopeptide recovery by 20% and exhibited 60% less contamination from unphosphorylated peptides. With respect to efficiency and contamination, MMC performed as well as prototypal magnetic metal oxide-coated (TiO(2)) beads (MMO) or TiO(2) chromatographic spheres, even if the latter were used with 2,5-dihydroxybenzoic acid (DHB) procedures. Thus far, the sensitivity of the new prototypes reaches 50 fmol, which is comparable to TiO(2) spheres. In an exploration of natural proteomes, tryptic (phospho)peptides captured from stable isotopic labeling with amino acids in cell culture (SILAC)-labeled immunocomplexes following EGF-treatment of 5 x 10(7) HeLa cells were sufficient to quantify stimulated response of over 60 proteins and identify 20 specific phosphorylation sites.
Integrated NFV/SDN Architectures: A Systematic Literature Review (2018)

Network Functions Virtualization (NFV) and Software-Defined Networking (SDN) are new paradigms in the move towards open software and network hardware. While NFV aims to virtualize network functions and deploy them into general purpose hardware, SDN makes networks programmable by separating the control and data planes. NFV and SDN are complementary technologies capable of providing one network solution. SDN can provide connectivity between Virtual Network Functions (VNFs) in a flexible and automated way, whereas NFV can use SDN as part of a service function chain. There are many studies designing NFV/SDN architectures in different environments. Researchers have been trying to address reliability, performance, and scalability problems using different architectural designs. This Systematic Literature Review (SLR) focuses on integrated NFV/SDN architectures, with the following goals: i) to investigate and provide an in-depth review of the state-of-the-art of NFV/SDN architectures, ii) to synthesize their architectural designs, and iii) to identify areas for further improvements. Broadly, this SLR will encourage researchers to advance the current stage of development (i.e., the state-of-the-practice) of integrated NFV/SDN architectures, and shed some light on future research efforts and the challenges faced.
COMPRESSIVE PRELOAD IMPROVES THE STABILITY OF ANTERIOR LUMBAR INTERBODY FUSION CAGE CONSTRUCTS (2003)

The study suggests that the segment treated with an anterior lumbar interbody fusion cage is relatively less stable under conditions of low external compressive preload. The magnitude of preload required to achieve stabilization with stand-alone cages may be only partially achieved by anular pretensioning. Since the magnitude of the preload across the disc space due to muscle activity can vary with activities of daily living, supplemental stabilization of the cage construct may provide a more predictably stable environment for lumbar spine fusion.
High Performance 800-1000nm single mode lasers using an asymmetric waveguide (2007)

We report on the design and fabrication of high performance 800-1000 nm high power lasers using an asymmetric waveguide structure. The structure offers lower beam divergence, improved power kink and reduced resistively.
Scale Stain: Multi-Resolution Feature Enhancement in Pathology Visualization (2016)

Digital whole-slide images of pathological tissue samples have recently become feasible for use within routine diagnostic practice. These gigapixel sized images enable pathologists to perform reviews using computer workstations instead of microscopes. Existing workstations visualize scanned images by providing a zoomable image space that reproduces the capabilities of the microscope. This paper presents a novel visualization approach that enables filtering of the scale-space according to color preference. The visualization method reveals diagnostically important patterns that are otherwise not visible. The paper demonstrates how this approach has been implemented into a fully functional prototype that lets the user navigate the visualization parameter space in real time. The prototype was evaluated for two common clinical tasks with eight pathologists in a within-subjects study. The data reveal that task efficiency increased by 15% using the prototype, with maintained accuracy. By analyzing behavioral strategies, it was possible to conclude that efficiency gain was caused by a reduction of the panning needed to perform systematic search of the images. The prototype system was well received by the pathologists who did not detect any risks that would hinder use in clinical routine.
Source number estimation in reverberant conditions via full-band weighted, adaptive fuzzy c-means clustering (2014)

We introduce a novel approach for source number estimation through an adaptive fuzzy c-means clustering. Spatial feature vectors are extracted from microphone observations, weighted for reliability and then clustered in a full-band manner using an adaptive variation on the fuzzy c-means. A number of quality measures are combined to produce a weighted sum which is used to find the optimal number of clusters at each iteration of the clustering algorithm. Experimental evaluations using real-world recordings from a reverberant room (RT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> = 390 ms) demonstrated encouraging performance in both even- and under-determined conditions.
A new water disinfectant; a comparative study (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleA new water disinfectant; a comparative studyShelby D. Worley, Walter B. Wheatley, Herbert H. Kohl, Herman D. Burkett, Johnathon A. Van Hoose, and Nicholas BodarCite this: Ind. Eng. Chem. Prod. Res. Dev. 1983, 22, 4, 716–718Publication Date (Print):December 1, 1983Publication History Published online1 May 2002Published inissue 1 December 1983https://pubs.acs.org/doi/10.1021/i300012a038https://doi.org/10.1021/i300012a038research-articleACS PublicationsRequest reuse permissionsArticle Views180Altmetric-Citations20LEARN 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 options Get e-Alerts
Abatacept for Delay of Type 1 Diabetes Progression in Stage 1 Relatives at Risk: A Randomized, Double-Masked, Controlled Trial (2023)

&lt;p&gt; &lt;/p&gt; &lt;p&gt;&lt;strong&gt;Objective&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Previous studies showed that inhibiting lymphocyte costimulation reduces declining beta cell function in individuals newly-diagnosed with type 1 diabetes. We tested whether abatacept would delay or prevent progression of type 1 diabetes from normal (NGT) to abnormal (AGT) glucose tolerance or to diabetes and the effects of treatment on immune and metabolic responses. &lt;/p&gt; &lt;p&gt;&lt;strong&gt;Research Design and Methods&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;We conducted a phase-2, randomized, placebo-controlled, double-masked trial of abatacept&lt;/p&gt; &lt;p&gt;in antibody-positive participants with NGT who received monthly abatacept/placebo infusions for 12 months. The endpoint was AGT or diabetes, assessed by oral glucose-tolerance tests. &lt;/p&gt; &lt;p&gt;&lt;strong&gt;Results&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;101 participants received abatacept and 111 placebo. Eighty-one (35 abatacept/46 placebo) met the endpoint of AGT or type 1 diabetes diagnosis (HR=0.702 (0.452, 1.09)(p=0.11) The C-peptide responses to OGTTs were higher in the abatacept arm (p&lt;.03) . Abatacept reduced the frequency of ICOS+PD1+ T-follicular helper (Tfh) cells during treatment (p&lt;0.0001), increased naïve CD4+ T cells, and also reduced the frequency of CD4+ Tregs from the baseline (p=0.0067). Twelve months after treatment, the frequency of ICOS+ Tfh, naïve CD4+ T, and Treg cells returned to baseline. &lt;/p&gt; &lt;p&gt;&lt;strong&gt;Conclusions&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Although abatacept treatment for one year did not significantly delay progression to glucose intolerance in at-risk individuals, it impacted immune cell subsets and preserved insulin secretion suggesting that costimulation blockade may modify progression of type 1 diabetes.&lt;/p&gt;
Antagonistic Interactions between Yeast Chaperones Hsp104 and Hsp70 in Prion Curing (1999)

The maintenance of [PSI], a prion-like form of the yeast release factor Sup35, requires a specific concentration of the chaperone protein Hsp104: either deletion or overexpression of Hsp104 will cure cells of [PSI]. A major puzzle of these studies was that overexpression of Hsp104 alone, from a heterologous promoter, cures cells of [PSI] very efficiently, yet the natural induction of Hsp104 with heat shock, stationary-phase growth, or sporulation does not. These observations pointed to a mechanism for protecting the genetic information carried by the [PSI] element from vicissitudes of the environment. Here, we show that simultaneous overexpression of Ssa1, a protein of the Hsp70 family, protects [PSI] from curing by overexpression of Hsp104. Ssa1 protein belongs to the Ssa subfamily, members of which are normally induced with Hsp104 during heat shock, stationary-phase growth, and sporulation. At the molecular level, excess Ssa1 prevents a shift of Sup35 protein from the insoluble (prion) to the soluble (cellular) state in the presence of excess Hsp104. Overexpression of Ssa1 also increases nonsense suppression by [PSI] when Hsp104 is expressed at its normal level. In contrast, hsp104 deletion strains lose [PSI] even in the presence of overproduced Ssa1. Overproduction of the unrelated chaperone protein Hsp82 (Hsp90) neither cured [PSI] nor antagonized the [PSI]-curing effect of overproduced Hsp104. Our results suggest it is the interplay between Hsp104 and Hsp70 that allows the maintenance of [PSI] under natural growth conditions.
Transient grating measurement of surface acoustic waves in thin metal films with extreme ultraviolet radiation (2006)

The authors demonstrate the use of coherent extreme ultraviolet (EUV) light in laser induced transient grating spectroscopy. In this work, the authors study the dispersion of pulsed laser induced surface acoustic waves in a thin uniform nickel film by monitoring the diffraction of 30nm EUV light from the surface. Transient deformation of the sample surface leads to absolute diffracted intensities approaching 10−3 for 1Å displacement, an ∼700-fold increase in sensitivity compared with optical probing. EUV probing provides a convenient geometry for observing short wavelength acoustic propagation.
Perfluoroalkyl‐Substituted Arylphosphanes as Ligands for Homogenous Catalysis in Supercritical Carbon Dioxide (1997)

The solubility of complexes is one decisive factor for their use as homogeneous catalysis in supercritical carbon dioxide (scCO2). Complexes with perfluoroalkyl-substituted arylphosphane ligands (shown schematically on the right), which can be prepared by a straightforward and variable synthetic methodology, exhibit high solubility in scCO2 in contrast to unsubstituted parent compounds.
American College of Radiology White Paper on MR Safety: 2004 Update and Revisions (2004)

American College of Radiology White Paper on MR Safety: 2004 Update and RevisionsEmanuel Kanal1, James P. Borgstede2, A. James Barkovich3, Charlotte Bell4, William G. Bradley5, Shawn Etheridge6, Joel P. Felmlee7, Jerry W. Froelich8, Jeffrey Hayden9, Ellisa M. Kaminski10, James W. Lester, Jr.11, Elizabeth A. Scoumis12, Loren A. Zaremba13 and Marie D. Zinninger14Audio Available | Share
Sparsity maximization under a quadratic constraint with applications in filter design (2010)

This paper considers two problems in sparse filter design, the first involving a least-squares constraint on the frequency response, and the second a constraint on signal-to-noise ratio relevant to signal detection. It is shown that both problems can be recast as the minimization of the number of non-zero elements in a vector subject to a quadratic constraint. A solution is obtained for the case in which the matrix in the quadratic constraint is diagonal. For the more difficult non-diagonal case, a relaxation based on the substitution of a diagonal matrix is developed. Numerical simulations show that this diagonal relaxation is tighter than a linear relaxation under a wide range of conditions. The diagonal relaxation is therefore a promising candidate for inclusion in branch-and-bound algorithms.
A Styrene-alt-Maleic Acid Copolymer Is an Effective Inhibitor of R5 and X4 Human Immunodeficiency Virus Type 1 Infection (2010)

An alternating copolymer of styrene and maleic acid (alt-PSMA) differs from other polyanionic antiviral agents in that the negative charges of alt-PSMA are provided by carboxylic acid groups instead of sulfate or sulfonate moieties. We hypothesized that alt-PSMA would have activity against human immunodeficiency virus type 1 (HIV-1) comparable to other polyanions, such as the related compound, poly(sodium 4-styrene sulfonate) (PSS). In assays using cell lines and primary immune cells, alt-PSMA was characterized by low cytotoxicity and effective inhibition of infection by HIV-1 BaL and IIIB as well as clinical isolates of subtypes A, B, and C. In mechanism of action assays, in which each compound was added to cells and subsequently removed prior to HIV-1 infection ("washout" assay), alt-PSMA caused no enhancement of infection, while PSS washout increased infection 70% above control levels. These studies demonstrate that alt-PSMA is an effective HIV-1 inhibitor with properties that warrant further investigation.
Managing Biological Emergencies: A New Approach (2001)

Biological emergencies can be defined as events which occur infrequently to a biological system and that are usually caused by a biological entity. Examples include pest invasion, disease outbreaks in humans, plants and animals and food poisoning outbreaks. The complexity of the biological emergency management response required may involve more conventional emergency services, however this involvement is not routine and their roles are often unfamiliar.
Effect of Aluminum Alkyls on a Homogeneous and Silica-Supported Phenoxy-Imine Titanium Catalyst for Ethylene Trimerization (2015)

A phenoxy-imine titanium catalyst (FI-catalyst) for selective ethylene trimerization was immobilized on methyl aluminoxane (MAO) pretreated silica and its activity and selectivity was compared with that of the corresponding homogeneous catalyst system. The homogeneous and heterogeneous ethylene oligomerization was conducted in the presence of different aluminum alkyls, commonly used as scavengers during olefin polymerization to remove residual oxygen and moisture from the reaction medium. Both the homogeneous and heterogeneous catalysts were strongly affected by the presence of scavenger in the reaction medium. Upon activation with R3Al/MAO (R= Et, nOct, iBu), the homogeneous catalyst switches selectivity from ethylene trimerization to polymerization. NMR spectroscopic investigations indicate that this change of selectivity can be attributed to ligand exchange between the precatalyst and the aluminum alkyl and reduction of the titanium species. The thereby formed ligand-free and/or reduced titanium alkyls act as polymerization catalysts and are responsible for the increasing polymer formation. Using the heterogeneous catalyst, the scavenger employed during ethylene trimerization was found to be of crucial influence regarding the activity of the catalyst and the occurrence of reactor fouling. Employing aluminum alkyls like iBu3Al and nOct3Al resulted in catalyst leaching and homogeneous polymer formation. The latter was prevented using Me3Al or Et3Al as scavengers; however, in general the supported catalyst was poisoned by aluminum alkyls, resulting in a low overall activity. It was found to be beneficial for the heterogeneous trimerization system to employ silica-supported scavengers. By physical separation of the catalyst and the scavenger this poisoning effect was effectively prevented, resulting in a highly active heterogeneous catalyst.
Efficacy of Oral APX001 in a Murine Model of Cryptococcal Meningitis (2017)

APX001 is a first-in-class intravenous and orally available broad spectrum antifungal inhibitor of Gwt1, a protein involved in glycosylphosphatidylinositol anchor biosynthesis. This study evaluated efficacy of APX001, alone and in combination with fluconazole (FCN), in a mouse model of cryptococcal meningitis. Mice (10/group) infected via tail vein with Cryptococcus neoformans received APX001, FCN, both, or neither, for 7 days. APX001 was given orally as 390mg/kg thrice daily. FCN was given intraperitoneally as 80mg/kg/day. Brain and lung were cultured to determine tissue burden. Data were evaluated by unpaired t-test. In brain, the burden of C. neoformans in mice receiving combined therapy was 3.52 log lower than in untreated control mice. The burden in mice receiving APX001 alone was 0.78 log lower than in untreated mice. The burden in mice receiving FCN alone was 1.04 log lower than in untreated mice. In lung, the burden in mice receiving combined therapy was 1.84 log lower than in untreated control mice. The tissue burden for mice receiving APX001 alone was 1.58 log lower than in untreated mice. The tissue burden in mice receiving FCN alone was 1.3 log lower than untreated mice. Activity in murine brain: (i) Combined therapy of APX001 with FCN significantly inhibited growth of C. neoformans H99 compared with untreated control mice (P < 0.0001), and was significantly more active than monotherapy with APX001 or FCN (P < 0.0001 and P < 0.0003, respectively). (ii) APX001 and FCN each, alone, significantly inhibited growth of C. neoformans H99 in brain tissue compared with untreated control mice (P < 0.0001). Activity in murine lung: (i) Combined therapy of APX001 with FCN performed somewhat better than FCN alone (P = 0.0297), but no better than APX001 alone (P = 0.2500). (ii) APX001 and FCN each, alone, significantly inhibited growth of C. neformans H99 in lung tissue compared with untreated control mice (P < 0.0001). (iii) Significant potentiation of APX001 in combination with FCN in this model with C. neoformans H99 was observed within the brain, and further investigation is warranted to determine whether APX001 in combination with FCN has potential to be an effective oral regimen for treating cryptococcal meningitis. K. J. Shaw, Amplyx Pharmaceuticals Inc.: Employee, Salary
Analysis of Fyn function in hemostasis and αIIbβ3-integrin signaling (2008)

Recent studies have shown that Src-family kinases (SFKs) play an important role in mediating integrin signalling, and the beta3 subunit of alphaIIbbeta3 integrin has been shown to interact with multiple SFK members. Here, we analyzed the interactions and functional consequences of Fyn and Src binding to alphaIIbbeta3. Fyn associated with the beta3 subunit in resting and thrombin-aggregated platelets, whereas interaction between Src and alphaIIbbeta3 was seen predominantly in resting but not in thrombin-aggregated platelets. We have also observed that Fyn but not Src localized to focal adhesions in CHO cells adherent to fibrinogen through alphaIIbbeta3. On the basis of these differences, we wanted to determine the sequence requirements for the interaction of Fyn and Src within the beta3-cytoplasmic domain. Whereas Src association required the C-terminal region of beta3, Fyn continued to interact with mutants that could no longer associate with Src and that contained as few as 13 membrane-proximal amino acids of the beta3-cytoplasmic tail. Using deletion mutants of beta3-cytoplasmic tails expressed as GST-fusion proteins, we narrowed down the Fyn-binding site even further to the amino acid residues 721-725 (IHDRK) of the beta3-cytoplasmic domain. On the basis of these observations, we explored whether Fyn-/- mice exhibited any abnormalities in hemostasis and platelet function. We found that Fyn-/- mice significantly differed in their second bleeding times compared with wild-type mice, and platelets from Fyn-/- mice exhibited delayed spreading on fibrinogen-coated surfaces. Using mutant forms of Fyn, it appears that its kinase activity is required for its localization to focal adhesions and to mediate alphaIIbbeta3-dependent cell spreading. Our results suggest that Fyn and Src have distinct requirements for interaction with alphaIIbbeta3; and, consequently, the two SFK can mediate different functional responses.
A Versatile Chemical Strategy for Ultrafine AlN and Al−O−N Powders (2000)

A versatile low-temperature chemical approach utilizing an alkoxide-based hydrazide process was developed for the synthesis of nanometer-size aluminum nitride, oxynitride, and composite powders. The process consists of reacting aluminum tri-sec-butoxide and anhydrous hydrazine in acetonitrile at 80 °C to yield solid precipitates, which, when dried and heated in argon, nitrogen, or ammonia, yielded nanosize powders of the desired chemistry. The precursors and products of the reactions were identified by gas chromatography (GC), chemical analyses, and X-ray diffraction (XRD), while the morphology and particle size of the powders were determined by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). GC revealed the release of butyl alcohol due to the reaction of the alkoxide with anhydrous hydrazine, suggesting the partial replacement (56.5%) of alkoxy groups by hydrazide groups (i.e., formation of Al−NHNH2 species). Fourier transform infrared (FTIR) and 27Al magic-angle-spinning−nuclear-magnetic-resonance (MAS−NMR) spectroscopy provided structural insights regarding the changes in molecular linkages during heating of the precursor and the role of hydrazine in the subsequent nitridation reaction. Hydrazine's critical function as a nitride former in the initial stages of formation of the precursor, as well as during heat treatment, was further confirmed by studying its reaction with the alkoxide in the presence of controlled amounts of deionized (DI) water. Hydrolysis of the alkoxide while limiting the hydrazide reaction was found to promote the formation of versatile precursors that lead to oxide, oxynitride, or composite powders containing nanoparticles of the nitride phase in an oxynitride matrix.