gebhart/patrepeval huggingface dataset:
YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling (2006)

We previously discovered that yliH and yceP are induced in Escherichia coli biofilms (D. Ren, L. A. Bedzyk, S. M. Thomas, R. W. Ye, and T. K. Wood, Appl. Microbiol. Biotechnol. 64:515-524, 2004). Here, it is shown that deletion of yceP (b1060) and yliH (b0836) increases biofilm formation in continuous-flow chambers with minimal glucose medium by increasing biofilm mass (240- to 290-fold), surface coverage (16- to 31-fold), and mean thickness (2,800-fold). To determine the genetic basis of the increase in biofilm formation, we examined the differential gene expression profile in biofilms for both the mutants relative to the wild-type strain in rich medium with glucose and found that 372 to 882 genes were induced and that 76 to 337 were repressed consistently >2-fold (P < or = 0.05). The increase in biofilm formation was related to differential expression of genes related to stress response (8 to 64 genes) for both mutants, including rpoS and sdiA. More importantly, 42 to 130 genes related to autoinducer 2 cell signaling were also differentially expressed, including gadAB and flgBCEGHIJLMN, as well as signaling through indole, since 17 to 26 indole-related genes were differentially expressed, including phoAER, gltBD, mtr (encodes protein for indole import), and acrEF (encodes proteins for indole export). Increased biofilm formation in the yliH and yceP mutants in LB supplemented with 0.2% glucose (LB glu) occurred through a reduction in extracellular and intracellular indole concentrations in both mutants (50- to 140-fold), and the addition of indole to the culture restored the wild-type biofilm phenotype; hence, indole represses biofilms. Additionally, both mutants regulate biofilms through quorum sensing, since deletion of either yliH or yceP increased extracellular autoinducer 2 concentrations 50-fold when grown in complex medium (most notably in the stationary phase). Both proteins are involved in motility regulation, since YliH (127 amino acids) and YceP (84 amino acids) repressed motility two to sevenfold (P < or = 0.05) in LB, and YceP repressed motility sevenfold (P < or = 0.05) in LB glu. Heightened motility in the yceP mutant occurred, due to increased transcription of the flagella and motility loci, including fliC, motA, and qseB (3- to 86-fold). We propose new names for these two loci: bssR for yliH and bssS for yceP, based on the phrase "regulator of biofilm through signal secretion."
Apparent clinical resolution of pinnal actinic keratoses and squamous cell carcinoma in a cat using topical imiquimod 5% cream (2008)

Imiquimod is a topical immune response modifier and stimulator used in humans to treat a number of cutaneous neoplasms. This case report describes a cat with actinic keratoses and squamous cell carcinoma of the pinnae. The pinnal lesions were treated with topical 5% imiquimod three times per week. Treatment was discontinued after 82 days of therapy. Twelve weeks of topical imiquimod application resulted in clinical resolution of the pinnal lesions. Although no post-treatment biopsies were performed, there was no relapse of the pinnal lesions in 5 months of clinical follow-up. Expected side effects were limited to erythema, crusting, alopecia, and mild discomfort at the sites of application during the first 3 weeks of application. These results suggest that topical imiquimod, although unproven, might be a therapeutic option or adjunct to therapy for cats with actinic keratoses and squamous cell carcinoma, especially those cats for whom surgery and radiation therapy are not an option.
Anticancer Antibodies (2003)

The recent clinical and commercial success of anticancer antibodies such as rituximab and trastuzumab has created great interest in antibody-based therapeutics for hematopoietic malignant neoplasms and solid tumors. Given the likelihood of lower toxic effects of antibodies that target tumor cells and have limited impact on nonmalignant bystander organs vs small molecules, the potential increased efficacy by conjugation to radioisotopes and other cellular toxins, and the ability to characterize the target with clinical laboratory diagnostics to improve the drug’s clinical performance, current and future antibody therapeutics are likely to find substantial roles alone and in combination therapeutic strategies for treating patients with cancer. It also is likely that conjugation strategies will add new radiolabeled and toxin-linked products to the market to complement the recent approvals of ibritumomab tiuxetan and gemtuzumab ozogamicin. This review considers the structure of anticancer therapeutic antibodies and the techniques used to reduce their antigenicity. Efficacy and toxic effects, conjugation with isotopes and toxins, and validation of the antibody targets also are discussed. Antibodies approved by the Food and Drug Administration are described in detail, as are antibodies in late and early stages of clinical development.
In Vivo Identification of Glycolipid Antigen–Specific T Cells Using Fluorescent Cd1d Tetramers (1999)

The CD1 family of major histocompatibility complex (MHC)-like molecules specializes in presenting lipid and glycolipid antigens to alpha/beta T lymphocytes, but little is known about the size of the CD1-restricted T cell population or the frequency of T lymphocytes specific for a given glycolipid antigen. Here, we report the generation and use of mouse CD1d1-glycolipid tetramers to visualize CD1d-restricted T cells. In contrast with previous BIAcore-based estimates of very short half-lives for CD1d-glycolipid complexes, we found that the dissociation rate of several different CD1d-glycolipid complexes was very slow. Fluorescent tetramers of mouse CD1d1 complexed with alpha-galactosylceramide (alphaGalCer), the antigen recognized by mouse Valpha14-Jalpha281/Vbeta8 and human Valpha24-JalphaQ/Vbeta11 natural killer T (NKT) cell T cell receptors (TCRs), allowed us for the first time to accurately describe, based on TCR specificity, the entire population of NKT cells in vivo and to identify a previously unrecognized population of NK1.1-negative "NKT" cells, which expressed a different pattern of integrins. In contrast, natural killer (NK) cells failed to bind the tetramers either empty or loaded with alphaGalCer, suggesting the absence of a CD1d-specific, antigen-nonspecific NK receptor. Mouse CD1d1-alphaGalCer tetramers also stained human NKT cells, indicating that they will be useful for probing a range of mouse and human conditions such as insulin-dependent diabetes mellitus, tumor rejection, and infectious diseases where NKT cells play an important role.
An Intuitive Look at the Relationship of Ki and IC50: A More General Use for the Dixon Plot (2003)

To compare the relative potencies of a variety of enzyme-inhibiting compounds, a quantitative measure must be employed. IC50 values and Ki values are often reported in the literature, but direct comparison of these values is not possible. The relationship of Ki and IC50 for a given compound varies depending on the assay conditions and the compound’s mechanism of inhibition. The Cheng–Prusoff equations describe this relationship mathematically, and an intuitive description of this relationship is presented. Although there are currently a number of means to graphically determine IC50 values, there is not a biochemically intuitive linear method. A novel use of the Dixon plot will aid students in the determination of IC50 values. While the Dixon plot has been traditionally used to determine Ki in limited cases, a more widely applicable use is in IC50 determination. A new convention for presenting IC50 values is suggested.
Exome Sequencing: Current and Future Perspectives (2015)

The falling cost of DNA sequencing has made the technology affordable to many research groups, enabling researchers to link genomic variants to observed phenotypes in a range of species. This review focusses on whole exome sequencing and its applications in humans and other species. The exome has traditionally been defined to consist of only the protein coding portion of the genome; a region where mutations are likely to affect protein structure and function. There are several commercial kits available for exome sequencing in a number of species and, owing to the highly conserved nature of exons, many of these can be applied to other closely related species. The data set produced from exome sequencing is many times smaller than that of whole genome sequencing, making it more easily manageable and the analysis less complex. Exome sequencing for disease gene discovery in humans is well established and has been used successfully to identify mutations that are causative of complex and rare diseases. Exome sequencing has also been used in a number of domesticated and companion species. The successful application of exome sequencing to crops has yielded results that may be used in selective breeding to improve production in these species, and there is potential for exome sequencing to provide similar advances in livestock species that have not yet been realized.
EFFECTS OF MONOSODIUM GLUTAMATE‐INDUCED OBESITY IN MICE ON CARBOHYDRATE METABOLISM IN INSULIN SECRETION (1978)

1. The syndrome of obesity induced by neonatal injection of monosodium glutamate (MSG) has been further studied in mice. In confirmation of previous studies stunting and decreased pituitary and gonadal weights were observed. 2. After weaning food intake was consistently less in MSG-treated than control mice. Body lipid stores were significantly elevated in MSG-treated mice by 2 weeks of age and increased progressively up to 4 months. 3. Plasma glucose was comparable between MSG-treated and control mice in the fed state whereas after an overnight fast MSG-treated mice exhibited relative hypoglycaemia. 4. Obese MSG-treated mice did not exhibit resistance to exogenous insulin and disposed of an intravenous glucose load more rapidly than control mice. 5. Hyperinsulinaemia was present inconsistently in both fed and fasted mice and in response to administered glucose. 6. Neonatal administration of MSG provides a useful additional model for studying the role of the hypothalamus in obesity.
DAC-MACS: Effective Data Access Control for Multiauthority Cloud Storage Systems (2013)

Data access control is an effective way to ensure data security in the cloud. However, due to data outsourcing and untrusted cloud servers, the data access control becomes a challenging issue in cloud storage systems. Existing access control schemes are no longer applicable to cloud storage systems, because they either produce multiple encrypted copies of the same data or require a fully trusted cloud server. Ciphertext-policy attribute-based encryption (CP-ABE) is a promising technique for access control of encrypted data. However, due to the inefficiency of decryption and revocation, existing CP-ABE schemes cannot be directly applied to construct a data access control scheme for multiauthority cloud storage systems, where users may hold attributes from multiple authorities. In this paper, we propose data access control for multiauthority cloud storage (DAC-MACS), an effective and secure data access control scheme with efficient decryption and revocation. Specifically, we construct a new multiauthority CP-ABE scheme with efficient decryption, and also design an efficient attribute revocation method that can achieve both forward security and backward security. We further propose an extensive data access control scheme (EDAC-MACS), which is secure under weaker security assumptions.
A 25-kilodalton fraction from Mycobacterium tuberculosis that inhibits hexose monophosphate shunt activity, lysozyme release, and H2O2 production: reversal by gamma interferon (1989)

This study examined the effects of a 25-kilodalton (kDa) glycolipoprotein derived from Mycobacterium tuberculosis on phagocyte functions associated with antimicrobial activity. The 25-kDa fraction inhibited the ability of both polymorphonuclear cells and cultured monocytes to release lysozyme and produce hydrogen peroxide. In addition, the glycolipoprotein was capable of reducing hexose monophosphate shunt activity and interfered with the ability of polymorphonuclear cells to reduce Nitro Blue Tetrazolium. Inhibition of these antimicrobial systems was optimal at a 50-micrograms/ml concentration of the 25-kDa fraction. Gamma interferon, but not alpha interferon, partially reversed the inhibitory effect of the mycobacterial component in all of the systems assessed. These studies indicate important mechanisms in the understanding of the pathogenesis of tuberculosis and suggest that gamma interferon may have a therapeutic role in mycobacterial diseases.
Induction of α-Helix in the β-Sheet Protein Tumor Necrosis Factor-α:  Thermal- and Trifluoroethanol-Induced Denaturation at Neutral pH (1996)

The unfolding and refolding of alpha-helical proteins has been extensively studied, demonstrating formation of intermediate structures which retain the native-like alpha-helix but lack the tertiary structure. Studies on the folding of proteins consisting primarily of beta-sheet are interesting since, unlike the alpha-helix, the beta-sheet requires the formation of peptide hydrogen bonds between two or more polypeptide segments which may be far apart in the linear sequence. Here we have studied the unfolding of the beta-sheet-containing protein tumor necrosis factor-alpha (TNF-alpha). This protein exists as a symmetric trimer in solution. Murine TNF-alpha begins to melt at 60 degrees C and unfolds to a soluble structure with a transition midpoint of 66 degrees C. This reaction is irreversible. This unfolded form contains a considerable amount of (approximately 30%) alpha-helix, as determined by circular dichroism. Human TNF-alpha begins to melt at 60 degrees C and precipitates concurrently with unfolding, such that there is no soluble protein present by 70 degrees C. The secondary and tertiary structures of murine TNF-alpha unfold simultaneously, suggesting that unfolding from the native to the unfolded state occurs cooperatively. The thermal-induced denaturation is very insensitive to protein concentration, indicating that trimer to monomer conversion, if it occurs, is not rate-limiting. Trifluoroethanol induces alpha-helix in both human and murine TNF-alpha, further demonstrating the propensity of TNF-alpha to form alpha-helix. The different behavior of human versus murine TNF-alpha upon thermal unfolding is due to differences in the solubility of the unfolded protein, the murine form being more soluble. These results indicate that TNF-alpha can form alpha-helix when the long range interactions conferred by the native structure are removed during unfolding.
The Src family of protein tyrosine kinases: regulation and functions (1993)

ABSTRACT Most of the nine members of the Src family of tyrosine kinases are restricted in their expression, often to cells of the haematopoietic lineage, while some, particularly Src, Fyn and Yes, are more ubiquitously expressed. We have been studying the functions of Src, Fyn and Yes in fibroblasts. We have shown that stimulation of quiescent fibroblasts with platelet-derived growth factor (I’DGF) causes Src, Fyn and Yes to become activated, and to associate transiently with the I’DGF receptor. To address the role of Src, Fyn and Yes in the response to I’DGF, we have used a dominant negative approach, in which cells were engineered to express catalytically inactive forms of Src kinases. These cells were unable to enter S phase in response to I’DGF, and we therefore conclude that Src family tyrosine kinases are required in order for the I’DGF receptor to transmit a mitogenic signal. It has previously been shown that the kinase activity of Src is negatively regulated by phosphorylation of tyr 527 in its carboxy-terminal tail. A kinase, Csk, that phosphorylates tyr 527 has recently been identified. We expressed Src in yeast to test the model that phosphorylation of tyr 527 represses activity by promoting intramolecular association between the tail and the SH2 domain. Inducible expression of Src in .S’. pombe caused cell death. Co-expression of Csk counteracted this effect. Src proteins mutated in the SH2 domain were as lethal as wild-type Src, but were insensitive to Csk. We interpret these results in favour of an SH2 domain : phosphorylated tail interaction repressing Src activity. However, we have also found that Src molecules containing mutations in the SH3 domain are not regulated by Csk. suggesting that the SH3 domain also functions in the intramolecular regulation of Src activity.
Evidence for association of schizophrenia with genetic variation in the 8p21.3 gene,PPP3CC, encoding the calcineurin gamma subunit (2003)

Schizophrenia is a severe psychiatric disorder characterized by a complex mode of inheritance. Forebrain-specific CNB knockout mice display a spectrum of behavioral abnormalities related to altered behaviors observed in schizophrenia patients. To examine whether calcineurin dysfunction is involved in schizophrenia etiology, we undertook studies of an initial subset of calcineurin-related genes, prioritizing ones that map to loci previously implicated in schizophrenia by linkage studies. Transmission disequilibrium studies in a large sample of affected families detected association of the PPP3CC gene, which encodes the calcineurin gamma catalytic subunit, with disease. Our results identify PPP3CC, located at 8p21.3, as a potential schizophrenia susceptibility gene and support the proposal that alterations in calcineurin signaling contribute to schizophrenia pathogenesis.
Expression of IL‐27 in human Th1‐associated granulomatous diseases (2004)

Interleukin (IL)-27 is a newly described member of the IL-12 family. It is a heterodimeric cytokine composed of two subunits, p28 and Epstein-Barr virus-induced gene 3 (EBI3). In vitro studies have shown that IL-27 is mainly produced by activated monocytes and dendritic cells. It induces the proliferation of naïve CD4-positive T cells and synergizes with IL-12 for interferon-gamma (IFN-gamma) production. Knock-out mice for the IL-27 receptor (WSX-1/TCCR) have impaired Th1 responses and form abnormal granulomas when injected with bacillus Calmette-Guérin. However, the expression profile of IL-27 in vivo is currently unknown. To investigate the potential role of IL-27 in the development of a Th1 response in humans in vivo, this study has analysed the in situ expression of IL-27 subunits in three types of granulomatous disease (tuberculosis, sarcoidosis, and Crohn's disease), each characterized by a Th1 response. Tissue sections from patients with tuberculosis (n = 9), sarcoidosis (n = 8), or Crohn's disease (n = 7) were analysed by immunohistochemistry with anti-EBI3 and anti-p28 antibodies, in parallel with control tissues (control reactive lymph nodes, n = 14, and control intestinal tissues, n = 11). In granulomatous tissues, EBI3 and p28 co-expression was detected in epithelioid and multinucleate giant cells in granulomas. In addition, sinus or tissue macrophages, endothelial cells, and plasma cells were found to co-express EBI3 and p28. These data support a possible role for IL-27 in human Th1 responses.
Reciprocal Velocity Obstacles for real-time multi-agent navigation (2008)

In this paper, we propose a new concept - the "Reciprocal Velocity Obstacle"- for real-time multi-agent navigation. We consider the case in which each agent navigates independently without explicit communication with other agents. Our formulation is an extension of the Velocity Obstacle concept [3], which was introduced for navigation among (passively) moving obstacles. Our approach takes into account the reactive behavior of the other agents by implicitly assuming that the other agents make a similar collision-avoidance reasoning. We show that this method guarantees safe and oscillation- free motions for each of the agents. We apply our concept to navigation of hundreds of agents in densely populated environments containing both static and moving obstacles, and we show that real-time and scalable performance is achieved in such challenging scenarios.
Syncytium Formation and Destruction of Bystander CD4+ Cells Cocultured with T Cells Persistently Infected with Human Immunodeficiency Virus as Demonstrated by Flow Cytometry (1989)

We have developed a flow cytometric method for demonstrating cell fusion between human immunodeficiency virus type 1 (HIV-1)- or HIV-2-infected HUT-78 cells and uninfected CD4-bearing MOLT-4 cells. Syncytium formation due to an interaction between the gp120 glycoprotein expressed on HIV-infected HUT-78 cells and the CD4 receptor present on MOLT-4 cells, resulted in an immediate decrease in the number of MOLT-4 cells; after a 24 h incubation period almost all MOLT-4 cells had disappeared from the culture. To show that the target MOLT-4 cells and not the aggressor HUT-78 cells were destroyed, specific monoclonal antibodies (MAbs) that reacted with antigens expressed on either MOLT-4 or HUT-78 cells were used. The formation of giant cells and the concomitant disappearance of MOLT-4 cells was blocked by MAbs specific for OKT4A and Leu3a, and, to a much lower level, by the MAbs specific of OKT4 and gp120. MAbs specific for OKT3, Leu2a, HLA-DR, Leu18 and LeuM3 did not prevent the disappearance of MOLT-4 cells. Sera from two AIDS patients containing antibodies to the HIV envelope glycoproteins did not protect MOLT-4 cells against the destructive effect of the HIV-infected HUT-78 cells. The fusion index, the percentage fusion inhibition and the 50% fusion inhibitory concentration of the MAbs can be accurately determined with the flow cytometric assay. The method can be readily implemented to evaluate any therapeutic treatment by examining its capacity to block cell-to-cell fusion, and hence destruction of the target bystander cells. Five anti-HIV compounds which have been previously shown to interfere with HIV binding to cells (namely pentosan polysulphate, heparin, suramin, aurintricarboxylic acid and Evans Blue) were further evaluated by this new method. With the exception of heparin, all of these compounds were found to inhibit cell-to-cell fusion and the concomitant destruction of the target bystander cells. Azidothymidine failed to inhibit fusion or bystander T cell destruction.