gebhart/patrepeval huggingface dataset:
Multiplex Assay Detection of Immunoglobulin G Antibodies That Recognize Babesia microti Antigens (2012)

Human babesiosis, a blood-borne infection caused by several species of Babesia, including B. microti, is an emerging disease that is endemic in the Northeast, upper Midwest, and Pacific Northwest regions of the United States. Risk factors for babesiosis include exposure to the infected tick vector and blood transfusions from infected donors. In this work, we cloned and expressed two of the immunodominant antigens from B. microti and used them in a multiplex bead format assay (MBA) to detect parasite-specific IgG responses in human sera. The MBA using recombinant B. microti secreted antigen 1 (BmSA1) protein was more specific (100%) and slightly more sensitive (98.7%) than the assay using a truncated recombinant BMN1-17 construct (97.6% and 97.4%, respectively). Although some antibody reactivity was observed among sera from confirmed-malaria patients, only one Plasmodium falciparum sample was simultaneously positive for IgG antibodies to both antigens. Neither antigen reacted with sera from babesiosis patients who were infected with Babesia species other than B. microti. Both positive and negative MBA results were reproducible between assays and between instruments. Additional studies of these recombinant antigens and of the multiplex bead assay using blood samples from clinically defined babesiosis patients and from blood donors are needed to more clearly define their usefulness as a blood screening assay.
Rapid Differentiation of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus by Flow Cytometry after Brief Antibiotic Exposure (2011)

We noticed that methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) isolates yielded side-scatter (SSC) and fluorescence intensity (FI) differences on flow cytometry (FCM) following incubation in oxacillin broth. The purpose of this study was to determine whether MRSA and MSSA could be reliably differentiated by FCM. S. aureus isolates were incubated in oxacillin-containing Mueller-Hinton broth, stained using the FASTEST total viable organisms kit, and analyzed by FCM in the MicroPRO instrument. SSC versus FI were examined, and gates 1 and 2 were defined to encompass the majority of MSSA and MRSA signal events, respectively. A count ratio (CR) was defined as the ratio of counts in gate 2 to those in gate 1. Initially, 33 isolates were tested after 4 h of incubation for proof-of-concept. Twenty others were then tested after incubation intervals ranging from 30 min to 4 h to determine the earliest possible time for differentiation. Next, 100 separate isolates were tested to determine the best CR cutoff value. Finally, the CR was validated by using an independent cohort of 121 isolates. We noted that MRSA isolates had higher SSC and FI readings than did MSSA isolates after 2 h of incubation. The receiver-operator characteristics curve showed that a CR cutoff of 0.0445 reliably differentiated MRSA from MSSA. In the validation cohort, this cutoff had a sensitivity of 100% and a specificity of 98.7% for identifying MRSA from among S. aureus isolates, following 2 h of incubation. This study demonstrates that MRSA and MSSA can be accurately differentiated by FCM after 2 h of incubation in an oxacillin-containing liquid culture medium.
Engineering of papain: selective alteration of substrate specificity by site-directed mutagenesis (1991)

The S2 subsite specificity of the plant protease papain has been altered to resemble that of mammalian cathepsin B by site-directed mutagenesis. On the basis of amino acid sequence alignments for papain and cathepsin B, a double mutant (Val133Ala/Ser205Glu) was produced where Val133 and Ser205 are replaced by Ala and Glu, respectively, as well as a triple mutant (Val133Ala/Val157Gly/Ser205Glu), where Val157 is also replaced by Gly. Three synthetic substrates were used for the kinetic characterization of the mutants, as well as wild-type papain and cathepsin B: CBZ-Phe-Arg-MCA, CBZ-Arg-Arg-MCA, and CBZ-Cit-Arg-MCA. The ratio of kcat/KM obtained by using CBZ-Phe-Arg-MCA as substrate over that obtained with CBZ-Arg-Arg-MCA is 8.0 for the Val133Ala/Ser205Glu variant, while the equivalent values for wild-type papain and cathepsin B are 904 and 3.6, respectively. This change in specificity has been achieved by replacing only two amino acids out of a total of 212 in papain and with little loss in overall enzyme activity. However, further replacement of Val157 by Gly as in Val133Ala/Val157Gly/Ser205Glu causes an important decrease in activity, although the enzyme still displays a cathepsin B like substrate specificity. In addition, the pH dependence of activity for the Val133Ala/Ser205Glu variant compares well with that of cathepsin B. In particular, the activity toward CBZ-Arg-Arg-MCA is modulated by a group with a pKa of 5.51, a behavior that is also encountered in the case of cathepsin B but is absent with papain.(ABSTRACT TRUNCATED AT 250 WORDS)
ChemInform Abstract: Asymmetric Friedel—Crafts Reactions with Fluoral, Catalyzed by Chiral Binaphthol‐Derived Titanium Catalysts (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Riboswitch-mediated control of gene expression in eukaryotes (2010)

The discovery of metabolite-sensing RNA domains with gene regulatory functions, so-called riboswitches, has greatly expanded our view of the structural and functional complexity of RNA. Hitherto, more than 20 distinct riboswitch classes have been identified, which respond to a variety of small molecules and perform sophisticated gene regulatory tasks. Riboswitches are typically positioned in the 5' untranslated region of bacterial mRNAs, where they control gene expression by transcriptional or translational attenuation. However, the recent investigation of additional riboswitch classes has revealed a more complex repertoire of regulatory mechanisms. This also includes splicing control in filamentous fungi, green algae and higher plants by thiamin pyrophosphate-binding riboswitches, the only class of metabolite-sensing RNAs identified in eukaryotes so far. All eukaryotic riboswitches characterized to date modulate, in a first step, splicing, but the downstream processes under control vary fundamentally among different species further highlighting the versatility of this gene regulatory mechanism.
Preparation of mesoporous tin oxide for electrochemical applications (1999)

F. Chen and M. Liu, Chem. Commun., 1999, 1829 DOI: 10.1039/A904142G
Regenerative Therapy for Stress Urinary Incontinence (2008)

In anatomical and functional studies of the human and animal urethra, the middle urethral contained rhabdosphincter is critical for maintaining continence. Transplanted muscle and/or stem cells may have the ability to undergo self-renewal and multipotent differentiation, leading to sphincter regeneration. In addition, such cells may release, or be engineered to release, neurotrophins with subsequent paracrine recruitment of endogenous host cells to concomitantly promote a regenerative response of nerve-integrated muscle. Cell-based therapies include the use of autologous multipotent stem cells, such as the bone marrow stromal cells. However, harvesting bone marrow stromal stem cells is difficult, painful, and may yield low numbers of stem cells upon processing. In contrast, alternative autologous adult stem cells such as muscle-derived stem cells and adipose-derived stem cells can be easily obtained in large quantities and with minimal discomfort. We will review the neurophysiology of stress urinary incontinence (highlighting the importance of the middle urethra); current injectable cell sources for cystoscopic treatment; and the potential of muscle-derived cells.
Generation of a double-ring perfect optical vortex by the Fourier transform of azimuthally polarized Bessel beams (2019)

The perfect optical vortex (POV), the ring size being independent of its topological charge, has found potential applications in optical tweezers and optical communications. In this Letter, we report a new kind of POV, termed as double-ring POV (DR-POV), whose diameters of the two rings are independent of topological charge. We theoretically demonstrate that such a vortex is the Fourier transform of an azimuthally polarized Bessel beam. Experimental results agree well with theoretical prediction. We further investigate the vortex nature of the DR-POV through an interferometric method, showing that the two rings of the vortex have the same topological charge value (magnitude and sign). The specular properties of the DR-POV may find application in optical tweezers, such as trapping and rotating of low-refractive-index particles in the dark region between the two rings.
ChemInform Abstract: SYNTHESES OF 2‐ AND 4‐SUBSTITUTED THIENO(2,3‐D)PYRIMIDINES. II (1976)

Abstract Die aus 2‐Amino‐3‐ thenoesäureamid durch Acylierung erhältlichen Säureamide (I) cyclisieren zu den Thienopyrimidinen (II) (Tautomeriegleichgewicht), die in die Chlorderivate (III) übergeführt werden.
Effect of Inhalation Flow Rate on the Dosing Characteristics of Dry Powder Inhaler (DPI) and Metered Dose Inhaler (MDI) Products (1996)

Both the dose delivered from the device and the particle size of the medication are important parameters for inhalation products because they influence the amount of drug that is delivered to the patient's lung. The inspiratory flow rate may vary from dose to dose in a given patient and between patients. The Marple-Miller Cascade Impactor, a new multistage inertial impactor that operates at two flow rates (30 and 60 liters/min) with comparable particle size cut-offs, provides a means to study the effect of inhalation flow rate on the particle size distributions of inhalation products. The medication delivery, mass median aerodynamic diameter (MMAD), and fine particle mass were determined, in a randomized fashion, for albuterol, beclomethasone, budesonide, and terbutaline in both metered dose inhaler (MDI) and dry powder inhaler (DPI) products as a function of flow rate. In all cases, independent of drug or device used, the MDI products had a more reproducible respirable dose than the breath-actuated DPI products tested as a function of inhalation flow rate.
Parameter extraction framework for DUV lithography simulation (1999)

As the semiconductor industry moves into the deep submicron range, the costs associated with wafer processing are increasing rapidly. This calls for improved simulation capabilities that provide information for meaningful 'what if' analysis. This work proposes a common methodology for extracting information from FTIR, dissolution rate monitor and ellipsometry measurements, to be ultimately used for the calibration of commercial lithography simulation tools. Using global optimization techniques, this approach uses cross-section CD data available in fabs to tune the simulation engine, thus giving it the predictive capabilities that could potentially improve yield ramp rates and hence reduce development costs. Results of this framework for a commercial Shipley resist are presented.
Anaerobic Digestion of Distillery Wastewater in a Two-Phase UASB System (1992)

A two-phase UASB system was operated for high-rate treatment of concentrated distillery wastewater. The phase separation was obtained by adjusting pH in each reactor. When influent SS concentration was 4.1 g/l, the first phase UASB reactor was effectively operated up to the loading rate of 16.5 kg COD/m3.day, producing 3.9 g HAc/l.day. In the methanogenic UASB reactor, loading rates up to 44 kg COD/m3.day could be applied while removing 80 % of influent COD with a specific gas production of 16.5 l/l.day. After the formation of granular sludge in both reactors, it was possible to maintain the appropriate pH in the first phase only by recirculating the effluent from the methanogenic phase without the addition of alkaline chemicals. The morphological study on the granular sludge consortia was made with both scanning and transmission electron microscopes. It was interesting to find the granules of different color and shape in the acidogenic phase in 90 days and in the methanogenic phase in 120 days after start-up. The acidogenic granular sludge mainly consisted of long chains of large rods, short plump rods, and various size of cocci, which have a different shape and cytoplasmic appearance from common methanogenic bacteria. Whereas the long multicellular filaments of Methanothrix spp. were prevalent in the methanogenic granule, diverse bacteria were entrapped therein.
Attenuation of sound in a low Mach Number nozzle flow (1979)

This paper examines the energy conversion mechanisms which govern the emission of low frequency sound from an axisymmetric jet pipe of arbitrary nozzle contraction ratio in the case of low Mach number nozzle flow. The incident acoustic energy which escapes from the nozzle is partitioned between two distinct disturbances in the exterior fluid. The first of these is the free-space radiation, whose directivity is equivalent to that produced by monopole and dipole sources. Second, essentially incompressible vortex waves are excited by the shedding of vorticity from the nozzle lip, and may be associated with the large-scale instabilities of the jet. Two linearized theoretical models are discussed. One of these is an exact linear theory in which the boundary of the jet is treated as an unstable vortex sheet. The second assumes that the finite width of the mean shear layer of the real jet cannot be neglected. The analytical results are shown to compare favourably with recent attenuation measurements.
Thermochemical studies of carbonyl compounds. 5. Enthalpies of reduction of carbonyl groups (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermochemical studies of carbonyl compounds. 5. Enthalpies of reduction of carbonyl groupsKenneth B. Wiberg, Louis S. Crocker, and Kathleen M. MorganCite this: J. Am. Chem. Soc. 1991, 113, 9, 3447–3450Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://doi.org/10.1021/ja00009a033Request reuse permissionsArticle Views1046Altmetric-Citations151LEARN 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 InReddit PDF (435 KB) Get e-Alertsclose Get e-Alerts
IL-15Rα expression on CD8<sup>+</sup>T cells is dispensable for T cell memory (2003)

The generation and maintenance of immunological memory requires the activation, expansion, and persistent proliferation of antigen-specific T cells. Recent work suggests that IL-15 may be important for this process. Surprisingly, we now find that expression of the high-affinity receptor for IL-15, IL-15R alpha, on T cells is dispensable for the generation or maintenance of memory CD8(+) T cells. By contrast, IL-15R alpha expression on cells other than T cells is absolutely critical for this function. These findings may be related to IL-15R alpha's ability to present IL-15 in trans to low-affinity IL-15R beta gamma(c) receptors on memory CD8(+) T cells. These unexpected results provide insights into how IL-15R alpha supports memory CD8(+) T cells.
Convolutional Neural Networks for Font Classification (2017)

Classifying pages or text lines into font categories aids transcription because single font Optical Character Recognition (OCR) is generally more accurate than omni-font OCR. We present a simple framework based on Convolutional Neural Networks (CNNs), where a CNN is trained to classify small patches of text into predefined font classes. To classify page or line images, we average the CNN predictions over densely extracted patches. We show that this method achieves state-of-the-art performance on a challenging dataset of 40 Arabic computer fonts with 98.8% line level accuracy. This same method also achieves the highest reported accuracy of 86.6% in predicting paleographic scribal script classes at the page level on medieval Latin manuscripts. Finally, we analyze what features are learned by the CNN on Latin manuscripts and find evidence that the CNN is learning both the defining morphological differences between scribal script classes as well as overfitting to class-correlated nuisance factors. We propose a novel form of data augmentation that improves robustness to text darkness, further increasing classification performance.
High-Level Expression and Secretion of Methyl Parathion Hydrolase in <i>Bacillus subtilis</i> WB800 (2005)

The methyl parathion hydrolase (MPH)-encoding gene mpd was placed under the control of the P43 promoter and Bacillus subtilis nprB signal peptide-encoding sequence. High-level expression and secretion of mature, authentic, and stable MPH were achieved using the protease-deficient strain B. subtilis WB800 as the host.
Iris liveness detection based on quality related features (2012)

A new liveness detection scheme for iris based on quality related measures is presented. The novel anti-spoofing technique is tested on a database comprising over 1,600 real and fake (high quality printed images) iris samples proving to have a very high potential as an effective protection scheme against direct attacks. Furthermore, the liveness detection method presented has the added advantage over previously studied techniques of needing just one iris image (the same used for verification) to decide whether it comes from a real or fake eye.
Specific Tryptophan UV-Absorbance Changes Are Probes of the Transition of Rhodopsin to Its Active State (1996)

The difference of rhodopsin and metarhodopsin II (MII) absorption spectra exhibits a characteristic pattern in the UV wavelength range, consisting of peaks at 278, 286, 294, 302 nm. These difference bands are thought to result from the perturbation of the environments of tryptophan and/or tyrosine residues. We used site-directed mutagenesis to investigate the contribution of tryptophan absorption to these spectral features. Each of the five tryptophan residues in bovine rhodopsin was replaced by either a phenylalanine or a tyrosine. The mutant pigments (W35F, W126F, W161F, W175F, W265F/Y) were prepared and studied by UV-visible photobleaching difference spectroscopy. The difference spectra of the W35F and W175F mutants were identical to that of rhodopsin, whereas in the W161F mutant, the magnitudes of the 294- and 302-nm bands were slightly lowered. The differential absorbance at 294 nm was reduced by over 50% in the W126F and W265F/Y mutants. The difference peak at 302 nm was reduced in the W265F/Y mutants, but was almost completely absent in the W126F mutant. These data indicate that the difference bands at 294 and 302 nm originate from the perturbations of Trp126 and Trp265 environments resulting from a general conformational change concomitant with MII formation and receptor activation. Model studies on tryptophan absorption indicate that the difference peak at 294 nm is due to the differential shift of the Lb absorption of the indole side chain as a result of decreased hydrophobicity or polarizability of the Trp126 and Trp265 environments. The resolution of the 302-nm band, assigned to the differential shift of the indole La absorption, is consistent with hydrogen-bonding interactions of the indole N-H groups of Trp126 and Trp265 becoming weaker in MII. These results suggest that the photoactivation of rhodopsin involves a change in the relative disposition of transmembrane helices 3 and 6, which contain Trp126 and Trp265 respectively, within the alpha-helical bundle of the receptor.
Inversion of azimuthal velocity and amplitude variations for seismic anisotropy (2017)

Natural fractures can play a key role in production of hydrocarbon in the form of increased porosity and permeability for efficient fluid flow especially for unconventional reservoirs of low matrix permeability. Thus, knowledge related to fracture orientation and intensity is vital for the development of unconventional hydrocarbon reservoirs, such as tight sand oil and shale gas reservoirs. The most productive horizontal wells are those crossing the most vertical fractures. A pattern of vertical fractures causes the seismic wavefield to exhibit azimuthal anisotropy. The best way known to detect fractures, at large scales, is by recognizing the effect of them on seismic data in attempt of inversing it. The Altamont-Bluebell play is within the Uinta Basin in northeast Utah, and is considered an unconventional play in the sense that natural fractures act as fluid storage and conduits in mostly the tight sandstones and partially in the tight carbonates. Consequently, analyzing the azimuthal variation in the observed amplitudes and velocities of the 3D seismic data acquired over the Altamont-Bluebell field is of great value in ascertaining important and relevant reservoir conditions in terms of porosity and permeability. In the Altamont-Bluebell field, azimuthal anisotropy was analysed using two types of data (3D surface seismic and VSP) and using three different methods (inversion of azimuthal amplitude, inversion of azimuthal travel times, and S-wave splitting). To use the VSP data, several types of VSPs were processed from field files to final products (P and S wavefield images and velocities). All results of different methods and data types were correlated to each other where similarities were pointed out and differences were explained. Numerical seismic modeling provides a valuable tool for geophysicists to test and validate their methodologies. Fractures make numerical modeling more complicated and introduce complexities that might even require geophysicists to validate their numerical models before using them to assess their methods. Scaled-down physical modeling of seismic surveys provides a unique opportunity to test, validate, and develop methods for characterizing fractured reservoirs, because it can produce experimental data from known physical properties and geometries that can be comparable with both numerical and field seismic data. Therefore, physical modeling is utilized to determine stiffness coefficients associated with the anisotropic material and validate techniques used for anisotropy, such as S-wave splitting.
Reduced Silent Occlusions with a Novel Catheter Infusion Set (BD FlowSmart): Results from Two Open-Label Comparative Studies (2015)

A novel side-ported insulin infusion set demonstrated significant reductions in flow interruptions, including silent occlusions, versus a leading marketed set, which may improve insulin delivery.