gebhart/patrepeval huggingface dataset:
Antibodies against Tumor Cell Glycolipids and Proteins, but Not Mucins, Mediate Complement-Dependent Cytotoxicity (2005)

One of several effector mechanisms thought to contribute to Ab efficacy against cancer is complement-dependent cytotoxicity (CDC). Serological analysis of a series of clinical trials conducted over a 10-year period suggested that six vaccines containing different glycolipids induced Abs mediating CDC whereas four vaccines containing carbohydrate or peptide epitopes carried almost exclusively by mucin molecules induced Abs that did not mediate CDC. To explore this further, we have now compared cell surface reactivity using flow cytometry assays (FACS), complement-fixing ability, and CDC activity of a panel of mAbs and immune sera from these trials on the same two tumor cell lines. Abs against glycolipids GM2, globo H and Lewis Y, protein KSA (epithelial cell adhesion molecule, also known as EpCAM) and mucin Ags Tn, sialylated Tn, Thomsen Friedenreich (TF), and MUC1 all reacted comparably by FACS with tumor cells expressing these Ags. Compared with the strong complement binding and CDC with Abs against glycolipids and KSA, complement binding was diminished with Abs against mucin Ags and no CDC was detected. A major difference between these two groups of Ags is proximity to the cell membrane. Glycolipids and globular glycoproteins extend less than 100 A from the cell membrane while mucins extend up to 5000 A. Although complement activation at sites remote from the cell membrane has long been known as a mechanism for resistance from complement lysis in bacteria, it is identified here for the first time as a factor which may contribute to resistance from CDC against cancer cells.
Nitric Oxide Mimetic Molecules as Therapeutic Agents in Alzheimers Disease (2005)

Nitric oxide is multifunctional messenger molecule in the brain, playing important roles including in learning and memory and in regulating the expression of trophic factors that may be reduced with aging. Small molecules that mimic the biological activity of NO, NO mimetics, will bypass cholinergic receptor activation and are anticipated to provide multiple pathways of treating and circumventing dementia in Alzheimer's disease. Activation of soluble guanylyl cyclase and cGMP formation in the brain represents one element of effective neuroprotective pathways mediated by NO. Substantial evidence suggests that NO mimetics may display cGMP-dependent and cGMP-independent activity and may operate via multiple biochemical signaling pathways, both to ensure the survival of neurons subjected to stress and also to provide cognition-enabling pathways to circumvent dementia. GT 1061 is an NO mimetic compound currently in clinical trials for Alzheimer's. A survey of current research indicates that NO mimetics will provide a combined neuroprotective and cognition-enabling approach to anti-neurodegenerative therapy.
A phosphonate monoester hydrolase from Burkholderia caryophilli PG2982 is useful as a conditional lethal gene in plants (1996)

A bacterial phosphonate monoester hydrolase was evaluated in plants as a conditional lethal gene useful for cell ablation and negative selection. Glyphosate is a potent herbicide whereas its phosphonate monoester derivative, glyceryl glyphosate, is approximately 50-fold less active. A phosphonate monoesterase gene (pehA) encoding an enzyme that hydrolyzes phosphonate esters including glyceryl glyphosate to glyphosate and glycerol was cloned from the glyphosate metabolizing bacterium, Burkholderia caryophilli PG2982. Constitutive expression of the pehA gene in Escherichia coli and Arabidopsis thaliana RLD had no observable phenotypic effects on growth and development. However, cells and plants expressing the pehA gene were killed when treated with glyceryl glyphosate. The phytotoxicity resulted from the hydrolysis of glyceryl glyphosate to glyphosate and subsequent inhibition of aromatic amino acid biosynthesis. As an example of tissue-specific cell ablation, floral sterility without vegetative toxicity was demonstrated by expressing the pehA gene using a tapetal-specific promoter and treating the mature plants with glyceryl glyphosate. A chromogenic phosphonate ester substrate, 5-bromo-4-chloro-indolyl phenylphosphonate, was used to monitor in situ expression of the pehA gene. The general utility of the pehA gene as a heterologous conditional lethal gene in plants is discussed.
Synthesis, characterization, and crystal structures of M(DO3A) (M = iron, gadolinium) and Na[M(DOTA)] (M = Fe, yttrium, Gd) (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, characterization, and crystal structures of M(DO3A) (M = iron, gadolinium) and Na[M(DOTA)] (M = Fe, yttrium, Gd)C. Allen Chang, Lynn C. Francesconi, Mary F. Malley, Krishan Kumar, Jack Z. Gougoutas, Michael F. Tweedle, Daniel W. Lee, and Lon J. WilsonCite this: Inorg. Chem. 1993, 32, 16, 3501–3508Publication Date (Print):August 1, 1993Publication History Published online1 May 2002Published inissue 1 August 1993https://pubs.acs.org/doi/10.1021/ic00068a020https://doi.org/10.1021/ic00068a020research-articleACS PublicationsRequest reuse permissionsArticle Views2626Altmetric-Citations223LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Heat shock proteins and cardiac protection (2001)

The heat shock proteins (hsps) are expressed in normal cells but their expression is enhanced by a number of different stresses including heat and ischaemia. They play important roles in chaperoning the folding of other proteins and in protein degradation. In the heart a number of studies have shown that prior induction of the hsps by a mild stress has a protective effect against a more severe stress. Moreover, over-expression of an individual hsp in cardiac cells in culture or in the intact heart of either transgenic animals or using virus vectors, also produces a protective effect, directly demonstrating the ability of the hsps to produce protection. These findings indicate the potential importance of developing procedures for elevating hsp expression in a safe and efficient manner in human individuals using either pharmacological or gene therapy procedures.
Effects of galactose depletion from oligosaccharide chains on immunological activities of human IgG. (1989)

We previously reported a decrease in the content of galactose residues in oligosaccharide chains of serum IgG from patients with rheumatoid arthritis, which was presumed to affect the 3 dimensional structure of CH2 domain. In the present study, we prepared the galactose depleted IgG (agalacto IgG) and characterized its immunological activities. Significant reduction in Clq binding and Fc receptor binding was observed in agalacto IgG. However, IgM rheumatoid factor binding and protein A binding were the same as with intact IgG. Our results implied the biological function of the carbohydrate moiety of human IgG.
A 3 GHz Fractional All-Digital PLL With a 1.8 MHz Bandwidth Implementing Spur Reduction Techniques (2009)

Digital implementation of analog functions is becoming attractive in CMOS ICs, given the low supply voltage of ultra-scaled processes. Particularly, all-digital PLLs are being considered for RF frequency synthesis. However, they suffer from intrinsic deficiencies making them inferior to traditional analog solutions. The investigation in this paper shows that in-band output spurs, the major shortcoming of wideband divider-less ADPLLs with respect to analog fractional PLLs, are intrinsic and due to the finite resolution of the time-to-digital converter (TDC), even assuming perfect quantization and linearity. Moreover, even if the conceptual spur level is arbitrarily reduced by increasing the TDC resolution, TDC nonlinearities can cause a significant spur re-growth. This paper proposes two techniques to reduce the gap between all-digital and analog implementations of wideband fractional PLLs. These techniques have been applied to a 3 GHz ADPLL, whose bandwidth is programmable from 300 kHz to 1.8 MHz, operating from a 25 MHz reference signal. The test chip features more than 10 dB of worst in-band spur reduction when both corrections are active, for a worst-case in-band spur of -45 dBc at a bandwidth of 1.8 MHz and an in-band noise floor of -101 dBc/Hz. The chip core occupies 0.4 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in 65 nm CMOS technology, and consumes less than 10 mW from a 1.2 V supply.
Behavioral clustering of HTTP-based malware and signature generation using malicious network traces (2010)

We present a novel network-level behavioral malware clustering system. We focus on analyzing the structural similarities among malicious HTTP traffic traces generated by executing HTTP-based malware. Our work is motivated by the need to provide quality input to algorithms that automatically generate network signatures. Accordingly, we define similarity metrics among HTTP traces and develop our system so that the resulting clusters can yield high-quality malware signatures.We implemented a proof-of-concept version of our network-level malware clustering system and performed experiments with more than 25,000 distinct malware samples. Results from our evaluation, which includes real-world deployment, confirm the effectiveness of the proposed clustering system and show that our approach can aid the process of automatically extracting network signatures for detecting HTTP traffic generated by malware-compromised machines.
Molecular modulation of calcium oxalate crystallization (2006)

Calcium oxalate monohydrate (COM) is the primary constituent of the majority of renal stones. Osteopontin (OPN), an aspartic acid-rich urinary protein, and citrate, a much smaller molecule, are potent inhibitors of COM crystallization at levels present in normal urine. Current concepts of the role of site-specific interactions in crystallization derived from studies of biomineralization are reviewed to provide a context for understanding modulation of COM growth at a molecular level. Results from in situ atomic force microscopy (AFM) analyses of the effects of citrate and OPN on growth verified the critical role of site-specific interactions between these growth modulators and individual steps on COM crystal surfaces. Molecular modeling investigations of interactions of citrate with steps and faces on COM crystal surfaces provided links between the stereochemistry of interaction and the binding energy levels that underlie mechanisms of growth modification and changes in overall crystal morphology. The combination of in situ AFM and molecular modeling provides new knowledge that will aid rationale design of therapeutic agents for inhibition of stone formation.
Characterization of recombinant human glucuronyltransferase I involved in the biosynthesis of the glycosaminoglycan‐protein linkage region of proteoglycans (1999)

We characterized the recombinant glucuronyltransferase I (GlcAT-I) involved in the glycosaminoglycan-protein linkage region biosynthesis. The enzyme showed strict specificity for Galbeta1-3Galbeta1-4Xyl, exhibiting negligible incorporation into other galactoside substrates including Galbeta1-3Galbeta1-O-benzyl, Galbeta1-4GlcNAc and Galbeta1-4Glc. A comparison of the GlcAT-I with another beta1,3-glucuronyltransferase involved in the HNK-1 epitope biosynthesis revealed that the two beta1,3-glucuronyltransferases exhibited distinct and no overlapping acceptor substrate specificities in vitro. Nevertheless, the transfection of the GlcAT-I cDNA into COS-1 cells induced the significant expression of the HNK-1 epitope. These results suggested that the high expression of the GlcAT-I gene rendered the cells capable of synthesizing the HNK-1 epitope.
Dielectrophoresis and Chemically Mediated Directed Self‐Assembly of Micrometer‐Scale Three‐Terminal Metal Oxide Semiconductor Field‐Effect Transistors (2005)

Micrometer-scale metal oxide semiconductor field-effect transistors (MOSFETs) self-assemble from a fluid onto a substrate, and are held in place during drying by application of a dielectrophoretic force or by interactions with a self-assembled monolayer. The assembled devices (see Figure) are fully functional. This approach might be used to assemble devices on flexible plastic or other substrates, or for 3D integration of silicon devices on chips.
Racial differences in the incidence of gout (1995)

The approximately 2-fold excess risk for gout among black men is explained, in part, by a greater risk of incident hypertension.
KDM2b/JHDM1b, an H3K36me2-specific demethylase, is required for initiation and maintenance of acute myeloid leukemia (2011)

The histone H3 lysine 36 dimethyl-specific demethylase KDM2b/JHDM1b, which is highly expressed in various human leukemias, was previously found to be important in regulating cell proliferation and cellular senescence. However, its functions in leukemia development and maintenance are unclear. Here, we demonstrate that ectopic expression of Kdm2b/Jhdm1b is sufficient to transform hematopoietic progenitors. Conversely, depletion of Kdm2b/Jhdm1b in hematopoietic progenitors significantly impairs Hoxa9/Meis1-induced leukemic transformation. In leukemic stem cells, knockdown of Kdm2b/Jhdm1b impairs their self-renewing capability in vitro and in vivo. The functions of Kdm2b/Jhdm1b are mediated by its silencing of p15(Ink4b) expression through active demethylation of histone H3 lysine 36 dimethyl. Thus, our study suggests that Kdm2b/Jhdm1b functions as an oncogene and plays a critical role in leukemia development and maintenance.
Transfer of synthetic sialic acid analogs to N- and O-linked glycoprotein glycans using four different mammalian sialyltransferases (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTransfer of synthetic sialic acid analogs to N- and O-linked glycoprotein glycans using four different mammalian sialyltransferasesHans Juergen Gross, Ursula Rose, Jean Michel Krause, James C. Paulson, Karl Schmid, Robert E. Feeny, and Reinhard BrossmerCite this: Biochemistry 1989, 28, 18, 7386–7392Publication Date (Print):September 1, 1989Publication History Published online1 May 2002Published inissue 1 September 1989https://pubs.acs.org/doi/10.1021/bi00444a036https://doi.org/10.1021/bi00444a036research-articleACS PublicationsRequest reuse permissionsArticle Views299Altmetric-Citations63LEARN 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
Content-based video retrieval and compression: a unified solution (2002)

Video compression and retrieval have been treated as separate problems in the past. We present an object-based video representation that facilitates both compression and retrieval. Typically in retrieval applications, a video sequence is subdivided in time into a set of shorter segments each of which contains similar content. These segments are represented by 2-D representative images called "key-frames" that greatly reduce amount of data that is searched. However, key-frames do not describe the motions and actions of objects within the segment. We propose a representation that extends the ideas of the key-frame to further include what we define as "key-objects". These key-objects consist of regions within a key-frame that move with similar motion. Thus our key-objects allow a retrieval system to more efficiently present information to users and assist them in browsing and retrieving relevant video content.
Differential Production of IL-12, IFN-α, and IFN-γ by Mouse Dendritic Cell Subsets (2001)

Dendritic cells (DC) not only stimulate T cells effectively but are also producers of cytokines that have important immune regulatory functions. In this study we have extended information on the functional differences between DC subpopulations to include differences in the production of the major immune-directing cytokines IL-12, IFN-alpha, and IFN-gamma. Splenic CD4(-)8(+) DC were identified as the major IL-12 producers in response to microbiological or T cell stimuli when compared with splenic CD4(-)8(-) or CD4(+)8(-) DC; however, all three subsets of DC showed similar IL-12 regulation and responded with increased IL-12 p70 production if IL-4 was present during stimulation. High level CD8 expression also correlated with extent of IL-12 production for DC isolated from thymus and lymph nodes. By using gene knockout mice we ruled out any role for CD8alpha itself, or of priming by T cells, on the superior IL-12-producing capacity of the CD8(+) DC. Additionally, CD8(+) DC were identified as the major producers of IFN-alpha compared with the two CD8(-) DC subsets, a finding that suggests similarity to the human plasmacytoid DC lineage. In contrast, the CD4(-)8(-) DC produced much more IFN-gamma than the CD4(-)8(+) or the CD4(+)8(-) DC under all conditions tested.
Thermal Decomposition Study of Isolated Lignin Using Temperature Modulated TGA (2008)

Abstract Temperature modulated TGA (MTGA) was utilized to study the kinetics of lignin pyrolysis. Three industrial lignin preparations were investigated: softwood kraft lignin, hardwood kraft lignin, and Alcell lignin. Unlike conventional TGA, MTGA provides apparent activation energy (E a ) distribution curve using a single experimental run in a relatively short experimental time. Under Hi-Res conditions using a dynamic heating rate, the activation energies were higher than those determined using a constant heating rate. Likewise, small sample masses provided higher activation energies than those run with large sample mass. These effects can be eliminated by using a relatively large sample mass, > 10 mg. In this study, we discuss the effect of MTGA conditions on calculating E a distribution curves for lignin pyrolysis.
Anion and Cation Mixed-Bed Ion Exchange for Enhanced Multidimensional Separations of Peptides and Phosphopeptides (2007)

Shotgun proteomics typically uses multidimensional LC/MS/MS analysis of enzymatically digested proteins, where strong cation-exchange (SCX) and reversed-phase (RP) separations are coupled to increase the separation power and dynamic range of analysis. Here we report an on-line multidimensional LC method using an anion- and cation-exchange mixed bed for the first separation dimension. The mixed-bed ion-exchange resin improved peptide recovery over SCX resins alone and showed better orthogonality to RP separations in two-dimensional separations. The Donnan effect, which was enhanced by the introduction of fixed opposite charges in one column, is proposed as the mechanism responsible for improved peptide recovery by producing higher fluxes of salt cations and lower populations of salt anions proximal to the SCX phase. An increase in orthogonality was achieved by a combination of increased retention for acidic peptides and moderately reduced retention of neutral to basic peptides by the added anion-exchange resin. The combination of these effects led to approximately 100% increase in the number of identified peptides from an analysis of a tryptic digest of a yeast whole cell lysate. The application of the method to phosphopeptide-enriched samples increased by 94% phosphopeptide identifications over SCX alone. The lower pKa of phosphopeptides led to specific enrichment in a single salt step resolving acidic phosphopeptides from other phospho- and non-phosphopeptides. Unlike previous methods that use anion exchange to alter selectivity or enrich phosphopeptides, the proposed format is unique in that it works with typical acidic buffer systems used in electrospray ionization, making it feasible for online multidimensional LC/MS/MS applications.
Neural control of the lower urinary tract: Peripheral and spinal mechanisms (2009)

This review deals with individual components regulating the neural control of the urinary bladder. This article will focus on factors and processes involved in the two modes of operation of the bladder: storage and elimination. Topics included in this review include: (1) The urothelium and its roles in sensor and transducer functions including interactions with other cell types within the bladder wall ("sensory web"), (2) The location and properties of bladder afferents including factors involved in regulating afferent sensitization, (3) The neural control of the pelvic floor muscle and pharmacology of urethral and anal sphincters (focusing on monoamine pathways), (4) Efferent pathways to the urinary bladder, and (5) Abnormalities in bladder function including mechanisms underlying comorbid disorders associated with bladder pain syndrome and incontinence.
Decreased type II/type I TGF-beta receptor ratio in cells derived from human atherosclerotic lesions. Conversion from an antiproliferative to profibrotic response to TGF-beta1. (1995)

Atherosclerosis and postangioplasty restenosis may result from abnormal wound healing. The present studies report that normal human smooth muscle cells are growth inhibited by TGF-beta1, a potent wound healing agent, and show little induction of collagen synthesis to TGF-beta1, yet cells grown from human vascular lesions are growth stimulated by TGF-beta1 and markedly increase collagen synthesis. Both cell types increase plasminogen activator inhibitor-1 production, switch actin phenotypes in response to TGF-beta1, and produce similar levels of TGF-beta activity. Membrane cross-linking of 125I-TGF-beta1 indicates that normal human smooth muscle cells express type I, II, and III receptors. The type II receptor is strikingly decreased in lesion cells, with little change in the type I or III receptors. RT-PCR confirmed that the type II TGF-beta1 receptor mRNA is reduced in lesion cells. Transfection of the type II receptor into lesion cells restores the growth inhibitory response to TGF-beta1, implying that signaling remains responsive. Because TGF-beta1 is overexpressed in fibroproliferative vascular lesions, receptor-variant cells would be allowed to grow in a slow, but uncontrolled fashion, while overproducing extracellular matrix components. This TGF-beta1 receptor dysfunction may be relevant for atherosclerosis, restenosis and related fibroproliferative diseases.