gebhart/patrepeval huggingface dataset:
Structural characterization of idiotopes by using antibody variants generated by site-directed mutagenesis. (1990)

Four anti-idiotopic mAB, 107, MB, AI, and AD8, react with mouse hybridoma protein 36-65 specific for the hapten p-azophenylarsonate. The four antiidiotypic antibodies do not react with hybridoma protein 36-71, a somatically mutated variant of 36-65 whose H and L chain V region sequence differs at 19 amino acid positions. To determine which regions of 36-65 are important for the interaction with each of the four anti-idiotypic antibodies, variants of 36-65 containing one or more of the 36-71 substitutions were generated by oligonucleotide-directed mutagenesis of the rearranged 36-65 H chain V region gene, followed by expression of mutant proteins containing either the 36-65 or the 36-71 L chain in transfected hybridoma cells. Idiotypic characterization of the mutant proteins showed that reactivity correlates with the 36-65 H chain, but some contributions from the 36-65 L chain come into play. In the 36-65 H chain V region, idiotopes were mapped to the first and third complementarity-determining regions for anti-idiotypic antibodies 107, MB, and AI, and to all three complementarity-determining regions for anti-idiotypic antibody AD8. The binding of all four anti-idiotypic antibodies to hybridoma protein 36-65 was hapten inhibitable. However, a comparison between the effect of individual 36-71 substitutions on idiotope expression and their effect on Ag-binding affinity suggests that none of the four anti-idiotypic antibodies bodies mimics the structure of Ag.
Development of a nano-electrospray mass spectrometry source for nanoscale liquid chromatography and sheathless capillary electrophoresis (1998)

A Fisons Quattro I electrospray ionization (ESI) source has been modified to produce stable electrospray ion currents at flow rates as low as 50 nL/min. The original counter electrode and skimmer cone lens of the Fisons ESI source have been replaced with a spherical cone lens. This improved source provides a greater range of x,y,z positioning of a stainless steel tip resulting in a stable ion signal for flow rates of 50 nL/min to 2 μL/min. A tapered stainless steel electrospray tip (50 μm i.d.) was evaluated for mass spectrometry using nano-liquid chromatography (50 μm i.d., flow rate = 120 nL/min) and sheathless capillary electrophoresis. The analysis of a nonionic surfactant, octylphenol ethoxylate, was accomplished with both nanoscale separation techniques. © 1998 John Wiley & Sons, Ltd.
Flagellar elongation and shortening in Chlamydomonas. III. structures attached to the tips of flagellar microtubules and their relationship to the directionality of flagellar microtubule assembly. (1977)

Two structures on the distal ends of Chlamydomonas flagellar microtubules are described. One of these, the central microbutule cap, attaches the distal ends of the central pair microtubules to the tip of the flagellar membrane. In addition, filaments, called distal filaments, are observed attached to the ends of the A-tubules of the outer doublet microtubules. Inasmuch as earlier studies suggested that flagellar elongation in vivo occurs principally by the distal addition of sublnits and because it has been shown that brain tubulin assembles in vitro primarily onto the distal ends of both central and outer doublet microtubules, the presence of the cap and distal filaments was quantitated during flagellar resorption and elongation. The results showed that the cap remains attached to the central microtubules throughout flagellar resorption and elongation. The cap was also found to block the in vitro assembly of neurotubules onto the distal ends of the central microtubules. Conversely, the distal filaments apparently do not block the assembly of neurotubules onto the ends of the outer doublets. During flagellar elongation, the distal ends of the outer doublets are often found to form sheets of protofilaments similar to those observed on the elongating ends of neurotubules being assembled in vitro. These results suggest that the outer doublet microtubules elongate by the distal addition of subunits, whereas the two central microtubules assemble by the addition of subunits to the proximal ends.
Asymmetric hydroformylation catalyzed by homogeneous and polymer-supported platinum complexes containing chiral phosphine ligands (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric hydroformylation catalyzed by homogeneous and polymer-supported platinum complexes containing chiral phosphine ligandsGiovanni Parrinello and J. K. StilleCite this: J. Am. Chem. Soc. 1987, 109, 23, 7122–7127Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November 1987https://pubs.acs.org/doi/10.1021/ja00257a036https://doi.org/10.1021/ja00257a036research-articleACS PublicationsRequest reuse permissionsArticle Views2053Altmetric-Citations273LEARN 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
Egg-white lysozyme as a food preservative: an overview (1991)

AbstractThe use of lysozyme as a food preservative and the factors affecting lysozyme activity (temperature, chemicals, processing and complexes) is reviewed. Lysozyme inhibits the growth of deleterious organisms thus prolonging shelf life. Chemicals used to improve the preservative effect of lysozyme and those that inhibit the enzyme are discussed along with the stability of lysozyme in various chemical environments. Lysozyme has been used to preserve fresh fruits and vegetables, tofu bean curd, seafoods, meats and sausages, potato salad, cooked burdock with soy sauce, and varieties of semi-hard cheeses such as Edam, Gouda and some Italian cheeses. Lysozyme added to infant feeding formulae makes them more closely resemble human milk.Keywords:: Egg-whitefood productslysozymepreservative
Nanosecond Pulsed Electric Field (nsPEF) Ablation as an Alternative or Adjunct to Surgery for Treatment of Cancer (2013)

Surgery as resection or transplantation remains a fundamental means for cancer treatment and often offers an opportunity for a cure. However, surgery is not always possible because of tumor proximity to blood vessels or ducts or when a patient is not healthy enough to undergo surgery. Application of nanosecond pulsed electric fields (nsPEFs) is a new approach to treat cancer using pulse power technology that was originally designed for military purposes. This novel approach deposits extremely short pulses of high power, low energy electric fields into malignant tissues using electrodes to encompass tumors. Pre-clinical studies show that treatments are effective and without local or systemic side effects, including absences of scarring. Pre-clinical trials for basal cell carcinoma are completed, but results have not been published. For treating internal tumors, electric fields can be delivered by catheter electrodes and laparoscopy procedures. Here we present a review of the literature using nsPEFs for cancer ablation and present some recent work from the author's laboratory. We demonstrate efficacy for treatment of an ectopic mouse (Hepa-1-6) and an orthotopic rat (N1-S1) Hepatocellular Carcinoma (HCC). NsPEFs eliminate tumors by mechanisms in the presence of active caspases (apoptosis) as well as in absences of active caspases (necrosis/necroptosis). Treatment also breaches small vessels, but spares larger vessels and ducts. NsPEF treatments also reduce angiogenesis as determined by decreases in Vascular Endothelia Growth Factor (VEGF). Microvascular density markers (CD-31, CD-34 and CD-105) are significantly decreased after treatment, limiting new blood vessel formation and reinforcing tumor cell demise. Furthermore, initial challenge studies show that mice are resistant to re-introduction of the same tumor cells after treatment, suggesting that nsPEFs induces immunogenic cell death and possible host cell immune responses after treatment. NsPEF ablation of cancer targets at least three hallmarks of cancer (evasion of apoptosis, angiogenesis maintenance and immune surveillance) and provides an effective alternative or adjunct therapy for cancers in skin and internal organs.
Understanding Blind Deconvolution Algorithms (2011)

Blind deconvolution is the recovery of a sharp version of a blurred image when the blur kernel is unknown. Recent algorithms have afforded dramatic progress, yet many aspects of the problem remain challenging and hard to understand. The goal of this paper is to analyze and evaluate recent blind deconvolution algorithms both theoretically and experimentally. We explain the previously reported failure of the naive MAP approach by demonstrating that it mostly favors no-blur explanations. We show that, using reasonable image priors, a naive simulations MAP estimation of both latent image and blur kernel is guaranteed to fail even with infinitely large images sampled from the prior. On the other hand, we show that since the kernel size is often smaller than the image size, a MAP estimation of the kernel alone is well constrained and is guaranteed to succeed to recover the true blur. The plethora of recent deconvolution techniques makes an experimental evaluation on ground-truth data important. As a first step toward this experimental evaluation, we have collected blur data with ground truth and compared recent algorithms under equal settings. Additionally, our data demonstrate that the shift-invariant blur assumption made by most algorithms is often violated.
Time Series Mining Approach for Noninvasive Intracranial Pressure Assessment: An Investigation of Different Regularization Techniques (2009)

A data mining framework has been proposed to estimate intracranial pressure (ICP) non-invasively in our previous work. In the corresponding approach, the feature vector extracted from arterial blood pressure (ABP) and flow velocity (FV) is translated to the estimated errors by the mapping function for each entry in the database. In this paper, three different mapping function solutions, linear least squares (LLS), truncated singular value decomposition (TSVD) and standard Tikhonov regularization (STR) are systemically tested to compare the possible effects of different solutions on the non-invasive ICP estimation. The conducted comparison demonstrated that the selection of mapping function solution actually influences the estimation. Among the tested three solutions for mapping function, TSVD and STR show better ICP estimation performance with smaller ICP errors than LLS.
Protein microarrays: A new tool for profiling antibody cross-reactivity (2006)

Antibody cross-reactivity can compromise interpretation of experiments and derail therapeutic antibody development. Standard techniques such as immunohistochemistry or Western analysis provide important but often inadequate approaches to assess antibody specificity. Protein microarrays are providing a new approach to rapidly characterize antibody cross-reactivity against 1,000s of proteins simultaneously. This review will focus on reported examples of antibody cross-reactivity, methods used to characterize them, and the recent development and use of protein microarrays for assessing antibody specificity.
Emerging Significance of NLRs in Inflammatory Bowel Disease (2014)

Pattern recognition receptors are essential mediators of host defense and inflammation in the gastrointestinal system. Recent data have revealed that toll-like receptors and nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) function to maintain homeostasis between the host microbiome and mucosal immunity. The NLR proteins are a diverse class of cytoplasmic pattern recognition receptors. In humans, only about half of the identified NLRs have been adequately characterized. The majority of well-characterized NLRs participate in the formation of a multiprotein complex, termed the inflammasome, which is responsible for the maturation of interleukin-1β and interleukin-18. However, recent observations have also uncovered the presence of a novel subgroup of NLRs that function as positive or negative regulators of inflammation through modulating critical signaling pathways, including NF-κB. Dysregulation of specific NLRs from both proinflammatory and inhibitory subgroups have been associated with the development of inflammatory bowel disease (IBD) in genetically susceptible human populations. Our own preliminary retrospective data mining efforts have identified a diverse range of NLRs that are significantly altered at the messenger RNA level in colons from patients with IBD. Likewise, studies using genetically modified mouse strains have revealed that multiple NLR family members have the potential to dramatically modulate the immune response during IBD. Targeting NLR signaling represents a promising and novel therapeutic strategy. However, significant effort is necessary to translate the current understanding of NLR biology into effective therapies.
Cross-linking of GPI-80, a possible regulatory molecule of cell adhesion, induces up-regulation of CD11b/CD18 expression on neutrophil surfaces and shedding of L-selectin (2002)

Previously, we described a novel glycosylphosphatidyl inositol (GPI)-anchored glycoprotein (designated GPI-80) on human neutrophils and monocytes that may regulate beta(2) integrin-dependent neutrophil adherence and migration. However, the mechanism regulating beta(2) integrin remains to be clarified. To study this, we examined changes in beta(2) integrin expression and function caused by cross-linking GPI-80. GPI-80 cross-linking induced up-regulation of CD11b/CD18 (Mac-1) expression on neutrophil surfaces and shedding of L-selectin, which depends on tyrosine phosphorylation and cytoskeleton remodeling. Furthermore, the cross-linking enhanced fMLP-induced human neutrophil adherence. These results suggest that GPI-80 may be a regulator of beta(2) integrin in neutrophils.
Always on, always connected mobile computing (2002)

We discuss an always on, always connected (AOAC) usage model for notebook PCs, and how it is enabled by the availability of ubiquitously deployed wireless data infrastructures. An experimental wide area information filtering and delivery system was used to identify missing technologies required by AOAC PCs. We present three findings: the critical role of narrowband data messaging (such as paging) in making data pushing applications financially viable; modifications to the Windows/sup */ communications infrastructure to integrate wireless data pipes with existing PC APIs; and a new transport protocol which adds advanced data capabilities to narowband wireless messaging networks, as well as providing a familiar sockets interface that hides applications from the differences in networks (e.g. 2 way paging and GSMs SMS appear the same to the application). Some other interesting aspects of the experimental system are also described, including the use of cell level location information for information filtering.
Soluble Ig-Like Transcript 3 Inhibits Tumor Allograft Rejection in Humanized SCID Mice and T Cell Responses in Cancer Patients (2007)

Attempts to enhance patients' immune responses to malignancies have been largely unsuccessful. We now describe an immune-escape mechanism mediated by the inhibitory receptor Ig-like transcript 3 (ILT3) that may be responsible for such failures. Using a humanized SCID mouse model, we demonstrate that soluble and membrane ILT3 induce CD8(+) T suppressor cells and prevent rejection of allogeneic tumor transplants. Furthermore, we found that patients with melanoma, and carcinomas of the colon, rectum, and pancreas produce the soluble ILT3 protein, which induces the differentiation of CD8(+) T suppressor cells and impairs T cell responses in MLC. These responses are restored by anti-ILT3 mAb or by depletion of soluble ILT3 from the serum. Immunohistochemical staining of biopsies from the tumors and metastatic lymph nodes suggests that CD68(+) tumor-associated macrophages represent the major source of soluble ILT3. Alternative splicing, resulting in the loss of the ILT3 transmembrane domain, may contribute to the release of ILT3 in the circulation. These data suggest that ILT3 depletion or blockade is crucial to the success of immunotherapy in cancer. In contrast, the inhibitory activity of soluble ILT3 on T cell alloreactivity in vitro and in vivo suggests the potential usefulness of rILT3 for immunosuppressive treatment of allograft recipients or patients with autoimmune diseases.
The effect of sodium selenite on chondrocytes in monolayer culture (1986)

The effect of sodium selenite on DNA and sulfated proteoglycan synthesis by cultured rabbit articular and growth plate chondrocytes was studied as an in vitro model for Kashin-Beck disease. The selenium content of a defined medium (DMEM, fibroblast growth factor, insulin, and dexamethasone) was below the limit of detection by isotope dilution mass spectrometry. The chondrocytes were viable in the Se-free basal medium. Selenite over a range of 5 X 10(-9) M to 5 X 10(-7) M had no stimulatory effect on DNA or sulfated proteoglycan synthesis by either type of chondrocyte or skin fibroblasts. Proliferation of bovine endothelial cells was enhanced by 5 X 10(-7) M Se. At Se concentrations of greater than or equal to 10(-6) M, there was progressive inhibition of cell growth and radiosulfate incorporation of the connective tissue cells; bovine endothelial cells were more resistant. Twice equimolar concentrations of vitamins C and E exerted no protective effect against the cytotoxicity of higher concentrations of Se. Se supplementation also failed to stimulate growth of human infant chondrocytes. The model enabled simulation of conditions of hyposelenosis below those encountered in nature. The data provide no evidence that chondrocytes have idiosyncratic requirements for Se, and do not support the hypothesis that Se deficiency is a major etiologic factor in Kashin-Beck disease.
Secretor phenotype and genotype are novel predictors of severe outcomes in premature infants (2010)

Background The secretor gene ( FUT2 ) and its products have important role in mucosal maturation, immunity, and host susceptibility to pathogens. We conducted the first investigation of secretor phenotype and genotype of premature infants in relation to their risk of death, necrotizing enterocolitis (NEC; Bell's stage II and III), and confirmed sepsis. Methods Secretor phenotype was measured in infant saliva samples by enzyme immunoassay of H antigen, the primary antigen produced by transferases of secretor gene. The optimal cut‐point in salivary H values was identified and confirmed by computerized algorithms (CART and ROC analysis). Results Of the 410 study infants, 14% with low salivary H died, compared to 2% of infants with high salivary H (p&lt;0.001). Modeled with clinical covariates, low H remained significant, and the overall model highly predicted death. Low H antigen was also associated with 10‐fold or greater odds of NEC and sepsis deaths, 3‐fold higher odds of surgical NEC and 2‐fold higher odds of NEC. Similarly, secretor genotype was a significant predictor: 13% of non‐secretors, 5% of heterozygotes, and 2% of secretor dominant infants died (p=0.01). Conclusions Lack of secretor antigen predicts adverse outcomes in prematurity. Sponsorship NICHD HD13021, HD059140
Conus geographus toxins that discriminate between neuronal and muscle sodium channels. (1985)

We describe the properties of a family of 22-amino acid peptides, the mu-conotoxins, which are useful probes for investigating voltage-dependent sodium channels of excitable tissues. The mu-conotoxins are present in the venom of the piscivorous marine snail, Conus geographus L. We have purified seven homologs of the mu-conotoxin set and determined their amino acid sequences, as follows, where Hyp = trans-4-hydroxyproline. GIIIA R.D.C.C.T.Hyp.Hyp.K.K.C.K.D.R.Q.C.K.Hyp.Q.R.C.C.A-NH2 [Pro6]GIIIA R.D.C.C. T.P.Hyp.K.K.C.K.D.R.Q.C.K.Hyp.Q.R.C.C.A-NH2 [Pro7]GIIIA R.D.C.C.T.Hyp.P.K.K.C.K.D.R.Q.C.R.Hyp.Q.R.C.C.A-NH2 GIIIB R.D.C.C.T.Hyp.Hyp.R.K.C.K.D.R.R.C.K.Hyp.M.K.C.C.A-NH2 [Pro6]GIIIB R.D.C.C.T.P.Hyp.R.K.C.K.D.R.R. C.K.Hyp.M.K.C.C.A-NH2 [Pro7]GIIIB R.D.C.C.T.Hyp.P.R.K.C.K.D.R.R.C.K.Hyp.M.K.C.C.A-NH2 GIIIC R.D.C.C.T.Hyp.Hyp.K.K.C.K.D.R.R.C.K.Hyp.L.K.C.C.A-NH2. Using the major peptide (GIIIA) in electrophysiological studies on nerve-muscle preparations and in single channel studies using planar lipid bilayers, we have established that the toxin blocks muscle sodium channels, while having no discernible effect on nerve or brain sodium channels. In bilayers the blocking kinetics of GIIIA were derived by statistical analysis of discrete transitions between blocked and unblocked states of batrachotoxin-activated sodium channels from rat muscle. The kinetics conform to a single-site, reversible binding equilibrium with a voltage-dependent binding constant. The measured value of the equilibrium KD for GIIIA is 100 nM at OmV, decreasing e-fold/34 mV of hyperpolarization. This voltage dependence of blocking is similar to that of tetrodotoxin and saxitoxin as measured by the same technique. The tissue specificity and kinetic characteristics suggest that the mu-conotoxins may serve as useful ligands to distinguish sodium channel subtypes in different tissues.
A developmentally regulated member of the sialyltransferase family (ST8Sia II, STX) is a polysialic acid synthase (1995)

We found polysialic acid synthase activity of ST8Sia II (STX) in vitro and in vivo. Previously, we showed that mouse ST8Sia II exhibits alpha 2,3-sialylated N-glycan alpha 2,8-sialyltransferase activity, but the polysialic acid synthase activity of ST8Sia II was not detected at that time [Kojima, N. et al. (1995) FEBS Lett. 360, 1-4]. When fetuin was [14C]sialylated with ST8Sia II and then its N-linked oligosaccharides were analyzed, a part of the N-linked oligosaccharides was eluted in the void volume from a Sephadex G-50 column, and was eluted in the void volume from a Sephadex G-50 column, and was eluted from the DEAE-Toyopearl column at almost the same salt concentration as that where colomic acid was eluted. In addition, a series of 14C-labeled oligo-sialic acids were obtained from the oligosaccharides on partial mild acid hydrolysis. These results indicated that a part of N-linked oligosaccharides of fetuin were polysialylated with ST8Sia II. Transfection of ST8Sia II gene into several cell lines including NIH3T3 led to the expression of polysialic acids on the cell surface. Thus, ST8Sia II can directly synthesize polysialic acid chains on alpha 2,3-sialylated N-linked oligosaccharides of glycoproteins without any initiator sialytransferase.