gebhart/patrepeval huggingface dataset:
Comparative study on kinetics of nonenzymatic deamidation of soy protein and egg white lysozyme (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComparative study on kinetics of nonenzymatic deamidation of soy protein and egg white lysozymeJie. Zhang, Tung Ching. Lee, and Chi Tang. HoCite this: J. Agric. Food Chem. 1993, 41, 12, 2286–2290Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://pubs.acs.org/doi/10.1021/jf00036a012https://doi.org/10.1021/jf00036a012research-articleACS PublicationsRequest reuse permissionsArticle Views301Altmetric-Citations23LEARN 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
Activation-induced Markers Detect Vaccine-Specific CD4+ T Cell Responses Not Measured by Assays Conventionally Used in Clinical Trials (2018)

Immunogenicity of T cell-inducing vaccines, such as viral vectors or DNA vaccines and Bacillus Calmette-Guérin (BCG), are frequently assessed by cytokine-based approaches. While these are sensitive methods that have shown correlates of protection in various vaccine studies, they only identify a small proportion of the vaccine-specific T cell response. Responses to vaccination are likely to be heterogeneous, particularly when comparing prime and boost or assessing vaccine performance across diverse populations. Activation-induced markers (AIM) can provide a broader view of the total antigen-specific T cell response to enable a more comprehensive evaluation of vaccine immunogenicity. We tested an AIM assay for the detection of vaccine-specific CD4⁺ and CD8⁺ T cell responses in healthy UK adults vaccinated with viral vectored Ebola vaccine candidates, ChAd3-EBO-Z and MVA-EBO-Z. We used the markers, CD25, CD134 (OX40), CD274 (PDL1), and CD107a, to sensitively identify vaccine-responsive T cells. We compared the use of OX40⁺CD25⁺ and OX40⁺PDL1⁺ in CD4⁺ T cells and OX40⁺CD25⁺ and CD25⁺CD107a⁺ in CD8⁺ T cells for their sensitivity, specificity, and associations with other measures of vaccine immunogenicity. We show that activation-induced markers can be used as an additional method of demonstrating vaccine immunogenicity, providing a broader picture of the global T cell response to vaccination.
Identification and functional analysis of bifunctional ent‐kaurene synthase from the moss Physcomitrella patens (2006)

ent-Kaurene is the key intermediate in biosynthesis of gibberellins (GAs), plant hormones. In higher plants, ent-kaurene is synthesized successively by copalyl diphosphate synthase (CPS) and ent-kaurene synthase (KS) from geranylgeranyl diphosphate (GGDP). On the other hand, fungal ent-kaurene synthases are bifunctional cyclases with both CPS and KS activity in a single polypeptide. The moss Physcomitrella patens is a model organism for the study of genetics and development in an early land plant. We identified ent-kaurene synthase (PpCPS/KS) from P. patens and analyzed its function. PpCPS/KS cDNA encodes a 101-kDa polypeptide, and shows high similarity with CPSs and abietadiene synthase from higher plants. PpCPS/KS is a bifunctional cyclase and, like fungal CPS/KS, directly synthesizes the ent-kaurene skeleton from GGDP. PpCPS/KS has two aspartate-rich DVDD and DDYFD motifs observed in CPS and KS, respectively. The mutational analysis of two conserved motifs in PpCPS/KS indicated that the DVDD motif is responsible for CPS activity (GGDP to CDP) and the DDYFD motif for KS activity (CDP to ent-kaurene and ent-16alpha-hydroxykaurene).
The human alpha‐1‐antitrypsin‐related sequence gene: isolation and investigation of its expression (1988)

A genomic sequence approximately 5 kb in length designated the alpha-1-antitrypsin-related gene (ATR), showing considerable homology to the human alpha-1-antitrypsin (AAT) gene, was identified 10 kb downstream of the authentic AAT gene. The AAT and ATR genes were introduced separately into L-cells by transfection in order to establish a method for distinguishing between expression of the two genes. RNA probes from the cloned ATR region were then used in a ribonuclease protection assay against RNA from a range of human adult and fetal tissues. No evidence of expression of ATR was found, indicating that this region is probably a pseudogene.
Peptides and Liposomes: From Biophysical to Immunogenic Studies (2003)

Synthetic peptide sequences constitute a useful tool to understand protein related diseases. A preliminary study consists of the analysis of peptide interaction with model membranes. The simplest one is based on monomolecular films of lipids spread at the air-water interface that imitate the interfacial environment in which some proteins function. Monolayer methodology provides a reliable screen of the extent to which hydrophobic interactions, charges, dipole potentials and subphase composition drive protein-lipid interaction. One step forward is based on the use of liposomes (lipid-based vesicles) that were originally introduced in 1965 as models of lipid bilayer membranes. Later, they have been widely studied as drug delivery systems mainly due to their safety, structural versatility, composition, fluidity and also because of their ability to incorporate almost any molecule regardless of its structure. In this sense, liposomes have been used as carriers of proteins and peptide antigens. Antigenic materials can be attached to the outer surface, encapsulated within the internal aqueous spaces or reconstituted within the lipid bilayers of the liposomes. In the present review we describe the steps going from the selection of peptides related to viral hepatitis proteins to its diagnostic and therapeutic application, with special emphasis on the use of model membranes to predict peptide mode of interaction with the target cell.
Hollow Spherical Nucleic Acids for Intracellular Gene Regulation Based upon Biocompatible Silica Shells (2012)

Cellular transfection of nucleic acids is necessary for regulating gene expression through antisense or RNAi pathways. The development of spherical nucleic acids (SNAs, originally gold nanoparticles functionalized with synthetic oligonucleotides) has resulted in a powerful set of constructs that are able to efficiently transfect cells and regulate gene expression without the use of auxiliary cationic cocarriers. The gold core in such structures is primarily used as a template to arrange the nucleic acids into a densely packed and highly oriented form. In this work, we have developed methodology for coating the gold particle with a shell of silica, modifying the silica with a layer of oligonucleotides, and subsequently oxidatively dissolving the gold core with I(2). The resulting hollow silica-based SNAs exhibit cooperative binding behavior with respect to complementary oligonucleotides and cellular uptake properties comparable to their gold-core SNA counterparts. Importantly, they exhibit no cytotoxicity and have been used to effectively silence the eGFP gene in mouse endothelial cells through an antisense approach.
A versatile and potentially general approach to the targeting of specific cell types by retroviruses: application to the infection of human cells by means of major histocompatibility complex class I and class II antigens by mouse ecotropic murine leukemia virus-derived viruses. (1989)

A technique for delivering genes carried by recombinant retroviruses into specific cell types could have numerous applications in oncology, developmental biology, and gene therapy. As a first step toward this remote goal we designed a procedure allowing in vitro cell targeting by retroviruses. Biotinylated antibodies against the viral envelope protein on one side, and against specific cell membrane markers on the other side, were bridged by streptavidin and used to link the virus to the host. The method was successfully used to infect human cells with ecotropic murine retroviruses by means of major histocompatibility complex class I and class II antigens and appears easily adaptable to other cell membrane markers. Moreover, the sequential protocol we designed, although allowing infection of human cells, requires less stringent safety constraints than would handling of amphotropic virus stocks.
Rigid model-based 3D segmentation of the bones of joints in MR and CT images for motion analysis (2008)

There are several medical application areas that require the segmentation and separation of the component bones of joints in a sequence of images of the joint acquired under various loading conditions, our own target area being joint motion analysis. This is a challenging problem due to the proximity of bones at the joint, partial volume effects, and other imaging modality-specific factors that confound boundary contrast. In this article, a two-step model-based segmentation strategy is proposed that utilizes the unique context of the current application wherein the shape of each individual bone is preserved in all scans of a particular joint while the spatial arrangement of the bones alters significantly among bones and scans. In the first step, a rigid deterministic model of the bone is generated from a segmentation of the bone in the image corresponding to one position of the joint by using the live wire method. Subsequently, in other images of the same joint, this model is used to search for the same bone by minimizing an energy function that utilizes both boundary- and region-based information. An evaluation of the method by utilizing a total of 60 data sets on MR and CT images of the ankle complex and cervical spine indicates that the segmentations agree very closely with the live wire segmentations, yielding true positive and false positive volume fractions in the range 89%-97% and 0.2%-0.7%. The method requires 1-2 minutes of operator time and 6-7 min of computer time per data set, which makes it significantly more efficient than live wire-the method currently available for the task that can be used routinely.
Activated Microglia Inhibit Axonal Growth through RGMa (2011)

By causing damage to neural networks, spinal cord injuries (SCI) often result in severe motor and sensory dysfunction. Functional recovery requires axonal regrowth and regeneration of neural network, processes that are quite limited in the adult central nervous system (CNS). Previous work has shown that SCI lesions contain an accumulation of activated microglia, which can have multiple pathophysiological influences. Here, we show that activated microglia inhibit axonal growth via repulsive guidance molecule a (RGMa). We found that microglia activated by lipopolysaccharide (LPS) inhibited neurite outgrowth and induced growth cone collapse of cortical neurons in vitro--a pattern that was only observed when there was direct contact between microglia and neurons. After microglia were activated by LPS, they increased expression of RGMa; however, treatment with RGMa-neutralizing antibodies or transfection of RGMa siRNA attenuated the inhibitory effects of microglia on axonal outgrowth. Furthermore, minocycline, an inhibitor of microglial activation, attenuated the effects of microglia and RGMa expression. Finally, we examined whether these in vitro patterns could also be observed in vivo. Indeed, in a mouse SCI model, minocycline treatment reduced the accumulation of microglia and decreased RGMa expression after SCI, leading to reduced dieback in injured corticospinal tracts. These results suggest that activated microglia play a major role in inhibiting axon regeneration via RGMa in the injured CNS.
Minimizing Variations in Functionality of Whey Protein Concentrates from Different Sources (2004)

Enhancement in processing technology has improved the nutritional and functional properties of whey protein concentrates by increasing the content and quality of the protein, leading to their increased use in different food products. The extent of heat treatment affects the quality of the whey protein concentrate, and wide variation in product quality exists due to the various means of manufacture and from the whey product history from farm to factory. The study was carried out with 6 commercial whey protein concentrates with 80% protein (WPC80) to determine variations in physical properties, particle size and density, and functional properties--solubility, gel strength, foam volume, and stability. Significant differences were observed among all the products for every property compared. Particulate size was the most important determinant of functional characteristics. Larger particulate WPC80 had significantly higher fat content and were less soluble with poor foam stability; but narrowing the particle size distribution through sieving, minimized variations. We determined that sieving all products within the particle size distribution range of 100 to 150 microns minimized variation in physical composition, making functionality uniform. WPC80 from different manufacturers can be made to perform uniformly within a narrow functionality range by reducing the particle size distribution through sieving.
Evaluation of Spike-Detection Algorithms for a Brain-Machine Interface Application (2004)

Real time spike detection is an important requirement for developing brain machine interfaces (BMIs). We examined three classes of spike-detection algorithms to determine which is best suited for a wireless BMI with a limited transmission bandwidth and computational capabilities. The algorithms were analyzed by tabulating true and false detections when applied to a set of realistic artificial neural signals with known spike times and varying signal to noise ratios. A design-specific cost function was developed to score the relative merits of each detector; correct detections increased the score, while false detections and computational burden reduced it. Test signals both with and without overlapping action potentials were considered. We also investigated the utility of rejecting spikes that violate a minimum refractory period by occurring within a fixed time window after the preceding threshold crossing. Our results indicate that the cost-function scores for the absolute value operator were comparable to those for more elaborate nonlinear energy operator based detectors. The absolute value operator scores were enhanced when the refractory period check was used. Matched-filter-based detectors scored poorly due to their relatively large computational requirements that would be difficult to implement in a real-time system.
An Artificial Gene for Human Porphobilinogen Synthase Allows Comparison of an Allelic Variation Implicated in Susceptibility to Lead Poisoning (2000)

Porphobilinogen synthase (PBGS) is an ancient enzyme essential to tetrapyrrole biosynthesis (e.g. heme, chlorophyll, and vitamin B(12)). Two common alleles encoding human PBGS, K59 and N59, have been correlated with differential susceptibility of humans to lead poisoning. However, a model for human PBGS based on homologous crystal structures shows the location of the allelic variation to be distant from the active site with its two Zn(II). Previous microbial expression systems for human PBGS have resulted in a poor yield. Here, an artificial gene encoding human PBGS was constructed by recursive polymerase chain reaction from synthetic oligonucleotides to rectify this problem. The artificial gene was made to resemble the highly expressed homologous Escherichia coli hemB gene and to remove rare codons that can confound heterologous protein expression in E. coli. We have expressed and purified recombinant human PBGS variants K59 and N59 in 100-mg quantities. Both human PBGS proteins purified with eight Zn(II)/octamer; Zn(II) binding was shown to be pH-dependent; and Pb(II) could displace some of the Zn(II). However, there was no differential displacement of Zn(II) by Pb(II) between K59 and N59, and simple Pb(II) inhibition studies revealed no allelic difference.
Oxazolidinones Mechanism of Action: Inhibition of the First Peptide Bond Formation (2001)

Oxazolidinones are potent inhibitors of bacterial protein biosynthesis. Previous studies have demonstrated that this new class of antimicrobial agent blocks translation by inhibiting initiation complex formation, while post-initiation translation by polysomes and poly(U)-dependent translation is not a target for these compounds. We found that oxazolidinones inhibit translation of natural mRNA templates but have no significant effect on poly(A)-dependent translation. Here we show that various oxazolidinones inhibit ribosomal peptidyltransferase activity in the simple reaction of 70 S ribosomes using initiator-tRNA or N-protected CCA-Phe as a P-site substrate and puromycin as an A-site substrate. Steady-state kinetic analysis shows that oxazolidinones display a competitive inhibition pattern with respect to both the P-site and A-site substrates. This is consistent with a rapid equilibrium, ordered mechanism of the peptidyltransferase reaction, wherein binding of the A-site substrate can occur only after complex formation between peptidyltransferase and the P-site substrate. We propose that oxazolidinones inhibit bacterial protein biosynthesis by interfering with the binding of initiator fMet-tRNA(i)(Met) to the ribosomal peptidyltransferase P-site, which is vacant only prior to the formation of the first peptide bond.
Pseudo-Prolines as a Solubilizing, Structure-Disrupting Protection Technique in Peptide Synthesis (1996)

Serine-, threonine-, and cysteine-derived cyclic building blocks (pseudo-prolines, ΨPro) serve as reversible protecting groups for Ser, Thr, and Cys and prove to be versatile tools for overcoming some intrinsic problems in the field of peptide chemistry. The presence of ΨPro within a peptide sequence results in the disruption of β-sheet structures considered as a source of intermolecular aggregation during chain elongation, thus increasing solvation and coupling kinetics in peptide assembly. Due to their easy synthetic access and variability in the chemical stability by modifications introduced in the C-2 position of the oxazolidine/thiazolidine ring system, this protection technique is adaptable to all common strategies in peptide synthesis. We describe new types of ΨPro building blocks suitable for standard Fmoc/tBu-based solid phase peptide synthesis, convergent strategies, and chemoselective ligation techniques as well as their use as a structure-disrupting, solubilizing protection technique for the example of peptides generally considered as “difficult sequences”.
Fraud Detection Using the Fraud Triangle Theory and Data Mining Techniques: A Literature Review (2021)

Fraud entails deception in order to obtain illegal gains; thus, it is mainly evidenced within financial institutions and is a matter of general interest. The problem is particularly complex, since perpetrators of fraud could belong to any position, from top managers to payroll employees. Fraud detection has traditionally been performed by auditors, who mainly employ manual techniques. These could take too long to process fraud-related evidence. Data mining, machine learning, and, as of recently, deep learning strategies are being used to automate this type of processing. Many related techniques have been developed to analyze, detect, and prevent fraud-related behavior, with the fraud triangle associated with the classic auditing model being one of the most important of these. This work aims to review current work related to fraud detection that uses the fraud triangle in addition to machine learning and deep learning techniques. We used the Kitchenham methodology to analyze the research works related to fraud detection from the last decade. This review provides evidence that fraud is an area of active investigation. Several works related to fraud detection using machine learning techniques were identified without the evidence that they incorporated the fraud triangle as a method for more efficient analysis.
Trimming of critical current in niobium Josephson devices by laser annealing (2008)

The authors report a new thermal annealing technique for Nb/Al-AlOx/Nb Josephson devices based on laser heating. This technique allows to "locally" modify the Josephson critical current density. In fact, it is possible the heating of a single circuit element with a good spatial resolution using a focused Ar+ laser beam which is aligned by an optical system on a selected junction of the sample. During the procedure, performed at room temperature, a thermal camera provides a monitoring of the temperature distribution on the whole chip. A continuous reduction of the critical current density up to about 40% has been observed on high quality Josephson junction measured in liquid helium. Neighbouring junctions have not exhibited any measurable change ensuring the effective capability to locally modify the Josephson critical current density. The new technique has been employed to recover noisy dc SQUID magnetometers with non optimal critical current values obtaining a reduction of the spectrum density of magnetic field noise from about 30 to 2.5 fT/Hz1/2.
MR arthrography of the shoulder with gadopentetate dimeglumine: influence of concentration, iodinated contrast material, and time on signal intensity. (1994)

For MR arthrography performed within 1 hr after injection, protocol 2 is sufficient. The optimal time frame for protocol 3 is between 1.5 and 3 hr after joint puncture. Protocol 3 allows the prior performance of conventional and CT arthrography. Therefore, the addition of 1 ml of a 500 mmol/l solution of gadopentetate dimeglumine to 10 ml of iodinated contrast material is advisable if a subsequent MR study is anticipated.