gebhart/patrepeval huggingface dataset:
Correlation of plasma viral loads and presence of Chikungunya IgM antibodies with cytokine/chemokine levels during acute Chikungunya virus infection (2014)

Chikungunya (CHIKV) is an emerging arboviral infection of public health concern in India contributing to widespread morbidity. The precise molecular events occurring early in the infection have not been well understood. Cytokines/chemokines are suspected to play a key role in its pathogenesis. Very few studies have correlated the plasma levels of cytokines/chemokines with diagnostic markers such as viral loads and presence of CHIKV IgM antibodies. Understanding these dynamics in the early phase of CHIKV infection is likely to provide an insight into the evolution of the immune response, identify biomarkers for assessing severity, and for development of newer therapeutic strategies. This study was therefore undertaken to estimate the levels of various cytokines/chemokines in plasma samples of patients infected with CHIKV and correlate to viral load and CHIKV IgM antibodies. Cytokine/chemokine levels and viral loads in plasma were measured using cytometric bead array and TaqMan real time PCR assay, respectively. The findings revealed that acute phase of CHIKV infection is characterized by predominant inflammatory responses mediated by IL-6, IL-8, IP-10, MCP-1, and MIG (P < 0.003). Plasma levels of IL-6 (r = 0.53, P < 0.05) and MCP-1 (r = 0.83, P < 0.05) emerged as reliable biomarkers of high viral loads in Chikungunya patients. Further, presence of elevated levels of MCP-1 and MIG during the chronic phase of the disease suggests that these chemokines may contribute to perpetuation of symptoms. Hence, these chemokines might serve as targets for the development of treatment to ameliorate the symptoms during the acute phase and prevent the development of chronic manifestations.
Urinary Porphyrin Excretion in Neurotypical and Autistic Children (2010)

These findings identify disordered porphyrin metabolism as a salient characteristic of autism. Hg exposures were comparable between diagnostic groups, and a porphyrin pattern consistent with that seen in Hg-exposed adults was not apparent.
Sortase B, a New Class of Sortase inListeria monocytogenes (2004)

Sortases are transamidases that covalently link proteins to the peptidoglycan of gram-positive bacteria. The genome of the pathogenic bacterium Listeria monocytogenes encodes two sortases genes, srtA and srtB. The srtA gene product anchors internalin and some other LPXTG-containing proteins to the listerial surface. Here, we focus on the role of the second sortase, SrtB. Whereas SrtA acts on most of the proteins in the peptidoglycan fraction, SrtB appears to target minor amounts of surface polypeptides. We identified one of the SrtB-anchored proteins as the virulence factor SvpA, a surface-exposed protein which does not contain the LPXTG motif. Therefore, as in Staphylococcus aureus, the listerial SrtB represents a second class of sortase in L. monocytogenes, involved in the attachment of a subset of proteins to the cell wall, most likely by recognizing an NXZTN sorting motif. The DeltasrtB mutant strain does not have defects in bacterial entry, growth, or motility in tissue-cultured cells and does not show attenuated virulence in mice. SrtB-mediated anchoring could therefore be required to anchor surface proteins involved in the adaptation of this microorganism to different environmental conditions.
Protein Quantitation in 2-D Gels Using Fluorescence with Water Raman as an Internal Standard (2007)

We have developed a method to enhance fluorescence quantification in two-dimensional gel electrophoresis using the inherent Raman scattering of water as an internal standard. We demonstrate this water internal standard (WIS) method using quantitative comparisons of commercially available protein standards that were either covalently tagged or passively stained with fluorescent tags. Thus, WIS opens up the possibility of enhancing intra- and intergel quantitative comparisons.
STAT3 is critical to promote inflammatory cytokines and RANKL expression in inflammatory arthritis (2012)

Rheumatology has pioneered in the study of autoantibodies by showing that they are not only involved in pathogenesis but are also highly useful as diagnostic biomarkers. The diagnostic biomarker aspect of autoimmunity has gained increasing importance in cancer and many of the insights gained in Rheumatology have contributed to understanding the significance of autoantibodies in cancer. Features of autoantibodies in rheumatic disorders: In rheumatic diseases no individual autoantibody-antigen system has sufficient combination of sensitivity and specificity to serve as a useful diagnostic biomarker. Instead, several antigen-antibody systems constructed as profiles of biomarkers are highly effective in distinguishing one disorder from another. In lupus, anti-double strand DNA and anti-Sm distinguishes it from scleroderma, where the profile is anti-DNA topoisomerase 1 and anti-centromere proteins. The autoantigensare cell components involved in universal and basic gene expression pathways, such as Sm in precursor mRNA splicing and DNA topoisomerase 1 in DNA replication and transcription [1]. Features of autoantibodies in cancer: Autoantibodies in cancer target intracellular molecules referred to as TAAs (tumor-associated antigens). As in rheumatic disorders, no individual autoantibody-antigen system has sensitivity and specificity to serve as a stand-alone diagnostic marker [2]. Most tumors show multiple antibody specificities and with panels of TAAanti-TAAs (analogous toprofiles) the cumulative sensitivity and specificity reaches diagnostic significance. Different tumorigenesis pathways are
A linear equation that describes the steady-state kinetics of enzymes and subcellular particles interacting with tightly bound inhibitors (1972)

When an enzyme exhibits a high affinity for an inhibitor, the steady-state analysis of the mechanism is complicated by the non-linearity of normal dose–response plots or of reciprocal replots. It is shown here that dose–response measurements generate a linear plot of inhibitor concentration divided by degree of inhibition against velocity without inhibitor divided by velocity with inhibitor; the concentration of enzyme may be derived from the extrapolated intercept of such plots, and the mechanism of inhibition from replots of the variation of the slope with substrate concentration. The limiting cases where virtually all inhibitor molecules are bound or virtually all are free are described, together with the situation when a significant proportion of the substrate becomes bound. This type of analysis indicates that the inhibitors of oxidative phosphorylation, rutamycin and bongkrekic acid, are tightly bound to rat liver mitochondria.
Nucleotide sequence of the gene ompA coding the outer membrane protein II*of Escherichia coli K-12 (1980)

A nucleotide sequence of 2271 basepairs has been determined from cloned E. coli DNA which contains ompA. Withing that sequence, starting at nucleotide 1037, an open translational reading frame encodes a protein of 367 amino acids which starting with amino acid 22 agrees with the primary structure of protein II. The preceeding 21 amino acids constitute a typical signal sequence. There is a non-translated region of 360 nucleotides in front of the translational start. The insertion point of an IS1 element 110 nucleotides upstream from the start codon and an amber codon at the position of amino acid residue 28 have been localized in the DNA from two ompA mutants.
Organized monolayers by adsorption. 1. Formation and structure of oleophobic mixed monolayers on solid surfaces (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganized monolayers by adsorption. 1. Formation and structure of oleophobic mixed monolayers on solid surfacesJacob SagivCite this: J. Am. Chem. Soc. 1980, 102, 1, 92–98Publication Date (Print):January 1, 1980Publication History Published online1 May 2002Published inissue 1 January 1980https://doi.org/10.1021/ja00521a016RIGHTS & PERMISSIONSArticle Views7362Altmetric-Citations1258LEARN 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 (2 MB) Get e-Alertsclose Get e-Alerts
Selecting Aptamers for a Glycoprotein through the Incorporation of the Boronic Acid Moiety (2008)

The first general method for the selection of boronic acid-based aptamers (boronolectins) that allows for glycan substructure focusing is described. Using fibrinogen as a model glycoprotein, we have selected boronic acid-modified DNA aptamers that have high affinities (low nM Kd) and the ability to recognize changes in the glycosylation site. The method developed should also be applicable to the development of aptamers for other glycoproducts, such as glycolipids and glycopeptides.
IFN-α and Bortezomib Overcome Bcl-2 and Mcl-1 Overexpression in Melanoma Cells by Stimulating the Extrinsic Pathway of Apoptosis (2008)

We hypothesized that IFN-alpha would enhance the apoptotic activity of bortezomib on melanoma cells. Combined treatment with bortezomib and IFN-alpha induced synergistic apoptosis in melanoma and other solid tumor cell lines. Apoptosis was associated with processing of procaspase-3, procaspase-7, procaspase-8, and procaspase-9 and with cleavage of Bid and poly(ADP-ribose) polymerase. Bortezomib plus IFN-alpha was effective at inducing apoptosis in melanoma cells that overexpressed Bcl-2 or Mcl-1, suggesting that this treatment combination can overcome mitochondrial pathways of cell survival and resistance to apoptosis. The proapoptotic effects of this treatment combination were abrogated by a caspase-8 inhibitor, led to increased association of Fas and FADD before the onset of cell death, and were significantly reduced in cells transfected with a dominant-negative FADD construct or small interfering RNA targeting Fas. These data suggest that bortezomib and IFN-alpha act through the extrinsic pathway of apoptosis via FADD-induced caspase-8 activation to initiate cell death. Finally, bortezomib and IFN-alpha displayed statistically significant antitumor activity compared with either agent alone in both the B16 murine model of melanoma and in athymic mice bearing human A375 xenografts. These data support the future clinical development of bortezomib and IFN-alpha for malignant melanoma.
[Intraoperative serum parathyroid hormone measurement in the surgical treatment of hyperparathyroidism]. (1997)

The decrement of serum PTH(1-84) concentrations to 20% of the preresection levels 120 minutes after an adenomectomy confirms the complete removal of all pathologic parathyroid tissue. A less sharp decrement must be investigated and may justify an early surgical revision.
Increased Association of ZO-1 With Connexin43 During Remodeling of Cardiac Gap Junctions (2002)

The intercellular geometry of connexin43 (Cx43) gap junctional coupling is key to coordinated spread of electrical activation through the ventricle of the mammalian heart. A progressive redistribution of electrical and mechanical junctions into intercalated discs occurs during postnatal development. Breakdown of disc-localized pattern in the adult heart, to recapitulate immature distributions, is thought to be key to the genesis of conduction disturbance and arrhythmia. Recently, ZO-1 (a PDZ-MAGUK protein), has been suggested to have a role in generating coupling geometries between myocytes. We therefore investigated the codistribution of ZO-1 with Cx43 and N-cadherin in the adult rat ventricle using quantitative immunoconfocal and immunoelectron microscopy. These analyses indicated that, whereas ZO-1 and Cx43 codistribute within discs, only low to moderate point-by-point colocalization of Cx43 and ZO-1 is found within these domains compared with the relatively high level of colocalization between N-cadherin and ZO-1. By contrast, levels of association between Cx43 and ZO-1 increased rapidly and significantly (P<0.001) after partial or complete enzymatic dissociation of myocytes from intact ventricle--a treatment known to induce gap junction endocytosis. Coimmunoprecipitation using Cx43- and ZO-1-specific antibodies confirmed that significantly (P<0.03) increased ZO-1 is precipitated relative to Cx43 in freshly dissociated myocytes as compared with intact ventricle. On immunoblots, decreases in Cx43 relative mobility, consistent with increased phosphorylation, were observed following myocyte dissociation. The increased ZO-1-Cx43 association that occurs after remodeling of myocyte intercellular contacts indicates the possibility of unanticipated roles for ZO-1 in gap junction turnover during cardiac development and disease processes.
Molecular Dynamics of Segmented Polyurethane Copolymers: Influence of Soft Segment Composition (2013)

Dielectric relaxation spectroscopy was used to investigate the molecular dynamics of model segmented polyurethane copolymers having identical hard segments and hard segment weight fractions, but with four different soft segment chemistries of particular interest in biomedical devices. All soft segments have molecular weight ∼1000 g/mol and are composed of either tetramethylene oxide, hexamethylene oxide, aliphatic carbonate, or dimethylsiloxane (PDMS) segments. These microphase-separated materials exhibit rich dielectric relaxation behavior: up to two relaxations in the glassy state, a segmental α relaxation (two for the polymer with predominately PDMS soft segments), and three slower relaxations. The slowest process arises from interfacial (MWS) polarization, and its strength decreases significantly with increasing temperature (over a few tens of degrees) and disappears at a temperature similar to that at which the small-angle X-ray scattering from the phase-separated microstructure disappears.
The Role of LOX and LOXL2 in Scar Formation After Glaucoma Surgery (2013)

Targeting LOXL2 with an inhibitory monoclonal antibody (GS-607601) reduced pathologic angiogenesis, inflammation, and fibrosis. These results suggest that LOXL2 could be an appealing target for treatment of scar formation after glaucoma surgery, and point to the potential therapeutic benefits of simtuzumab, a humanized monoclonal antibody derived from GS-607601.
High-capacity electrode materials for rechargeable lithium batteries: Li 3 NbO 4 -based system with cation-disordered rocksalt structure (2015)

Rechargeable lithium batteries have rapidly risen to prominence as fundamental devices for green and sustainable energy development. Lithium batteries are now used as power sources for electric vehicles. However, materials innovations are still needed to satisfy the growing demand for increasing energy density of lithium batteries. In the past decade, lithium-excess compounds, Li2MeO3 (Me = Mn(4+), Ru(4+), etc.), have been extensively studied as high-capacity positive electrode materials. Although the origin as the high reversible capacity has been a debatable subject for a long time, recently it has been confirmed that charge compensation is partly achieved by solid-state redox of nonmetal anions (i.e., oxide ions), coupled with solid-state redox of transition metals, which is the basic theory used for classic lithium insertion materials, such as LiMeO2 (Me = Co(3+), Ni(3+), etc.). Herein, as a compound with further excess lithium contents, a cation-ordered rocksalt phase with lithium and pentavalent niobium ions, Li3NbO4, is first examined as the host structure of a new series of high-capacity positive electrode materials for rechargeable lithium batteries. Approximately 300 mAh ⋅ g(-1) of high-reversible capacity at 50 °C is experimentally observed, which partly originates from charge compensation by solid-state redox of oxide ions. It is proposed that such a charge compensation process by oxide ions is effectively stabilized by the presence of electrochemically inactive niobium ions. These results will contribute to the development of a new class of high-capacity electrode materials, potentially with further lithium enrichment (and fewer transition metals) in the close-packed framework structure with oxide ions.
Conformation and circular dichroism of DNA (1979)

Abstract CD spectra of calf thymus, C. perfringens, E. coli , and M. luteus DNA have been measured in the vacuum‐uv region to about 168 nm for the A‐, B‐, and C‐forms. The positive band at about 187 nm and the negative band at about 170 nm found for each type and form of DNA are sensitive to the source of the DNA and the base–base interactions of the double‐stranded helix. The A‐form spectra confirm that these bands are indeed sensitive to secondary structure. In the near‐uv, the CD of B‐form DNA is well analyzed as a linear combination of 27% A‐form and 78% C‐form. However, an analysis of the extended spectrum demonstrates that the near‐uv analysis is not correct. The extended analysis shows that the base–base interactions are similar for B‐ and C‐forms in solution, which implies that these two forms have nearly the same number of base pairs per turn. Various types of CD difference spectra are also discussed.
Polar codes using dynamic kernels (2015)

In the standard polar coding construction, the same kernel is used for every channel transformation. In this paper we propose a new polar coding scheme in which the channel combining transformation is dynamically chosen based on the properties of the virtual channels. We show that for some cases it can improve the finite-length performance of codes. We also show that the dynamic scheme retains some of the main properties of the original polar code construction.
Macrophage Migration Inhibitory Factor Stimulates Angiogenic Factor Expression and Correlates With Differentiation and Lymph Node Status in Patients With Esophageal Squamous Cell Carcinoma (2005)

These results demonstrate, for the first time, that human esophageal carcinomas express and secrete large amounts of MIF. Through its effects on VEGF and IL-8, MIF may serve as an autocrine factor in angiogenesis and thus play an important role in the pathogenesis of ESCC.
Ethidium Monoazide for DNA-Based Differentiation of Viable and Dead Bacteria by 5′-Nuclease PCR (2003)

PCR techniques have significantly improved the detection and identification of bacterial pathogens. Even so, the lack of differentiation between DNA from viable and dead cells is one of the major challenges for diagnostic DNA-based methods. Certain nucleic acid-binding dyes can selectively enter dead bacteria and subsequently be covalently linked to DNA. Ethidium monoazide (EMA) is a DNA intercalating dye that enters bacteria with damaged membranes. This dye can be covalently linked to DNA by photoactivation. Our goal was to utilize the irreversible binding of photoactivated EMA to DNA to inhibit the PCR of DNA from dead bacteria. Quantitative 5'-nuclease PCR assays were used to measure the effect of EMA. The conclusion from the experiments was that EMA covalently bound to DNA inhibited the 5'-nuclease PCR. The maximum inhibition of PCR on pure DNA cross-linked with EMA gave a signal reduction of approximately -4.5 log units relative to untreated DNA. The viable/dead differentiation with the EMA method was evaluated through comparison with BacLight staining (microscopic examination) and plate counts. The EMA and BacLight methods gave corresponding results for all bacteria and conditions tested. Furthermore, we obtained a high correlation between plate counts and the EMA results for bacteria killed with ethanol, benzalkonium chloride (disinfectant), or exposure to 70 degrees C. However, for bacteria exposed to 100 degrees C, the number of viable cells recovered by plating was lower than the detection limit with the EMA method. In conclusion, the EMA method is promising for DNA-based differentiation between viable and dead bacteria.
Molecular cloning of a ligand for the inducible T cell gene 4‐1BB: a member of an emerging family of cytokines with homology to tumor necrosis factor (1993)

4-1BB is an inducible T cell antigen that shows sequence homology to members of an emerging family of cytokine receptors, including those for tumor necrosis factor and nerve growth factor. To aid in the analysis of the function of 4-1BB we have utilized a soluble form of the molecule as a probe to identify and clone the gene which encodes its ligand. The ligand for 4-1BB is a type II membrane glycoprotein that has homology to tumor necrosis factor, lymphotoxin, and the ligands for CD40 and CD27, all of which are themselves ligands to receptors in this superfamily. The gene for 4-1BB is on mouse chromosome 4 and maps close to the p80 form of the tumor necrosis factor receptor as well as the gene for CD30. The gene for 4-1BB ligand maps to mouse chromosome 17, but considerably distal to the tumor necrosis factor and lymphotoxin genes. Interaction of 4-1BB with its ligand induces the proliferation of activated thymocytes and splenic T cells, a response which is mimicked on similar cell populations stimulated with an antibody to 4-1BB.
Enhanced Targeting and Killing of Tumor Cells Expressing the CXC Chemokine Receptor 4 by Transducible Anticancer Peptides (2005)

Protein transduction domains (PTDs), such as the TAT PTD, have been shown to deliver a wide variety of cargo in cell culture and to treat preclinical models of cancer and cerebral ischemia. The TAT PTD enters cells by a lipid raft-dependent macropinocytosis mechanism that all cells perform. Consequently, PTDs resemble small-molecule therapeutics in their lack of pharmacologic tissue specificity in vivo. However, several human malignancies overexpress specific receptors, including HER2 in breast cancer, GnRH in ovarian carcinomas, and CXC chemokine receptor 4 (CXCR4) in multiple malignancies. To target tumor cells that overexpress the CXCR4 receptor, we linked the CXCR4 DV3 ligand to two transducible anticancer peptides: a p53-activating peptide (DV3-TATp53C') and a cyclin-dependent kinase 2 antagonist peptide (DV3-TAT-RxL). Treatment of tumor cells expressing the CXCR4 receptor with either the DV3-TATp53C' or DV3-TAT-RxL targeted peptides resulted in an enhancement of tumor cell killing compared with treatment with nontargeted parental peptides. In contrast, there was no difference between DV3 targeted peptide and nontargeted, parental peptide treatment of non-CXCR4-expressing tumor cells. These observations show that a multidomain approach can be used to further refine and enhance the tumor selectivity of biologically active, transducible macromolecules for treating cancer.