gebhart/patrepeval huggingface dataset:
Functions of the Periplasmic Loop of the Porin MspA from Mycobacterium smegmatis (2009)

MspA is the major porin of Mycobacterium smegmatis and mediates diffusion of small and hydrophilic solutes across the outer membrane. The octameric structure of MspA, its sharply defined constriction zone, and a large periplasmic loop L6 represent novel structural features. L6 consists of 13 amino acids and is directly adjacent to the constriction zone. Deletion of 3, 5, 7, 9, and 11 amino acids of the L6 loop resulted in functional pores that restored glucose uptake and growth of a porin mutant of M. smegmatis. Lipid bilayer experiments revealed that all mutant channels were noisier than wild type (wt) MspA, indicating that L6 is required for pore stability in vitro. Voltage gating of the Escherichia coli porin OmpF was attributed to loops that collapse into the channel in response to a strong electrical field. Here, we show that deletion mutants Delta7, Delta9, and Delta11 had critical voltages similar to wt MspA. This demonstrated that the L6 loop is not the primary voltage-dependent gating mechanism of MspA. Surprisingly, large deletions in L6 resulted in 3-6-fold less extractable pores, whereas small deletions did not alter expression levels of MspA. Pores with large deletions in L6 were more permissive for glucose than smaller deletion mutants, whereas their single channel conductance was similar to that of wt MspA. These results indicate that translocation of ions through the MspA pore is governed by different mechanisms than that of neutral solutes. This is the first study identifying a molecular determinant of solute translocation in a mycobacterial porin.
Detection of antibody IgG to HIV‐1 in urine by ultrasensitive enzyme immunoassay (immune complex transfer enzyme immunoassay) using recombinant p24 as antigen for diagnosis of HIV‐1 infection (1994)

Abstract Anti‐HIV‐1 IgG in urine was detected by an ultrasensitive enzyme immunoassay (immune complex transfer enzyme immunoassay) using recombinant p24 gag protein (p24) of HIV‐1 as antigen and β‐D‐galactosidase from Escherichia coli as label. Anti‐HIV‐1 IgG in urine was reacted simultaneously with 2, 4‐dinitrophenyl‐bovine serum albumin‐recombinant p24 conjugate and recombinant p24‐β‐D‐galactosidase conjugate. The complex formed, consisting of the three components, was trapped onto polystyrene balls coated with affinity‐purified (anti‐2, 4‐dinitrophenyl group) IgG, eluted with ϵN‐2, 4‐dinitrophenyl‐L‐lysine, and transferred to polystyrene balls coated with affinity‐purified (anti‐human IgG γ‐chain) IgG. Bound γ‐D‐galactosidase activity was assayed by fluorometry. This assay was at least 3, 000‐fold more sensitive than conventional methods. The lowest signal among 49 asymptomatic carriers was 3.1‐fold higher than the highest nonspecific signal among 100 seronegative subjects. The sensitivity and specificity were both 100%. The positivity could be confirmed by preincubation of urine samples with excess of the antigen. Thus, this assay would be a powerful tool for detecting IgG antibody to HIV‐1 in urine. © 1994 Wiley‐Liss, Inc.
The Role of Actin Polymerization in Cell Motility (1991)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
Structural Analysis of Arabidopsis thaliana Chromosome 5. V. Sequence Features of the Regions of 1,381,565 bp Covered by twenty one Physically assigned P1 and TAC Clones (1998)

Sixteen P1 and TAC clones assigned to Arabidopsis thaliana chromosome 5 were sequenced, and their sequence features were analyzed using various computer programs. The total length of the sequences determined was 1,013,767 bp. Together with the nucleotide sequences of 109 clones previously reported, the regions of chromosome 5 sequenced so far now total 9,072,622 bp, which presumably covers approximately one-third of the chromosome. A similarity search against the reported gene sequences predicted the presence of a total of 225 protein-coding genes and/or gene segments in the newly sequenced regions, indicating an average gene density of one gene per 4.5 kb. Introns were identified in 72.4% of the potential protein genes for which the entire gene structure was predicted, and the average number per gene and the average length of the introns were 3.3 and 163 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
Bacterial cell division: regulating Z‐ring formation (2001)

The earliest stage of cell division in bacteria is the formation of a Z ring, composed of a polymer of the FtsZ protein, at the division site. Z rings appear to be synthesized in a bi-directional manner from a nucleation site (NS) located on the inside of the cytoplasmic membrane. It is the utilization of a NS specifically at the site of septum formation that determines where and when division will occur. However, a Z ring can be made to form at positions other than at the division site. How does a cell regulate utilization of a NS at the correct location and at the right time? In rod-shaped bacteria such as Escherichia coli and Bacillus subtilis, two factors involved in this regulation are the Min system and nucleoid occlusion. It is suggested that in B. subtilis, the main role of the Min proteins is to inhibit division at the nucleoid-free cell poles. In E. coli it is currently not clear whether the Min system can direct a Z ring to the division site at mid-cell or whether its main role is to ensure that division inhibition occurs away from mid-cell, a role analogous to that in B. subtilis. While the nucleoid negatively influences Z-ring formation in its vicinity in these rod-shaped organisms, the exact relationship between nucleoid occlusion and the ability to form a mid-cell Z ring is unresolved. Recent evidence suggests that in B. subtilis and Caulobacter crescentus, utilization of the NS at the division site is intimately linked to the progress of a round of chromosome replication and this may form the basis of achieving co-ordination between chromosome replication and cell division.
Targeting and localized signalling by small GTPases (2006)

Polarized cellular responses, for example, cell migration, require the co-ordinated assembly of signalling complexes at a particular subcellular location, such as the leading edge of cells. Small GTPases of the Ras superfamily play central roles in many (polarized) responses to growth factors, chemokines or integrin ligands. These small GTPases are functionally distinct, yet remarkably homologous in their primary sequence and especially in their effector domains. Therefore it has long been unclear how GTPase signalling specificity is regulated. Small GTPases carry a lipid anchor, in the context of a hypervariable region, which mediates membrane association. However, whereas the lipid has long been proposed to be the critical regulator of subcellular GTPase targeting, there is now increasing evidence that specific protein-protein interactions are important as well. This review discusses recent findings on GTPase targeting and proposes a revised model for GTPase signalling. In this model, the hypervariable domain acts in conjunction with the lipid tail to target the GTPase to specific membrane-associated protein complexes. Here, local GTPase activation occurs, leading to subsequent exposure of the effector domain, binding to effector proteins and the initiation of downstream signalling.
Hierarchical Mixtures of Experts and the EM Algorithm (1994)

We present a tree-structured architecture for supervised learning. The statistical model underlying the architecture is a hierarchical mixture model in which both the mixture coefficients and the mixture components are generalized linear models (GLIM's). Learning is treated as a maximum likelihood problem; in particular, we present an Expectation-Maximization (EM) algorithm for adjusting the parameters of the architecture. We also develop an on-line learning algorithm in which the parameters are updated incrementally. Comparative simulation results are presented in the robot dynamics domain.
Hyperexpression of mitogen-activated protein kinase in human breast cancer. (1997)

Mitogen-activated protein (MAP) kinases act as transducers of extracellular signaling via tyrosine kinase-growth factor receptors and G-protein-linked receptors to elements regulating transcription. The activity, abundance, and localization of MAP kinase was investigated in normal and malignant neoplasia of the breast. In carcinoma of the breast, MAP kinase was heavily phosphorylated on tyrosyl residues and its activity elevated 5-10-fold over benign conditions, such as fibroadenoma and fibrocystic disease. By in situ reverse transcription-polymerase chain reaction, hyperexpression of MAP kinase mRNA can be localized to malignant, epithelial cells. Metastatic cells within involved lymph nodes of patients with breast cancer also display hyperexpression of MAP kinase. In spite of persistent activation via phosphorylation, MAP kinase expression is upregulated 5-20-fold and this hyperexpression may be a critical element to initiation as well as the metastatic potential of various forms of human breast cancer.
Purification and characterization of a cyclic GMP-stimulated cyclic nucleotide phosphodiesterase from bovine tissues. (1982)

A cGMP-stimulated cyclic nucleotide phosphodiesterase has been purified to near homogeneity from bovine adrenal and heart tissues. The purification procedure utilizes chromatography on DEAE-cellulose and cGMP affinity resin. The procedure can be completed within 2 days and is easily adapted to large scale. To obtain pure enzyme, an 8,000-9,000-fold increase in specific activity was required in adrenal tissues and 15,000-30,000-fold in cardiac muscle. A single band of protein having an apparent Mr = 105,000-107,000 was seen on sodium dodecyl sulfate gel electrophoresis. At equilibrium, native polyacrylamide gradient gel electrophoresis revealed a single major band having an apparent Mr = 240,000. Cyclic GMP binding and phosphodiesterase activity co-migrated with the protein band on native polyacrylamide gradient gels. The enzyme bound cGMP with high affinity reaching a maximum binding of 1.02 mol of cGMP bound/mol of enzyme dimer. Titration curves of the binding data indicated at least two classes of binding sites with 10% maximal binding occurring at 7 nM and 90% maximal binding at 4 microM cGMP. Kinetic analysis indicated the enzyme can hydrolyze both cAMP and cGMP with similar maximal rates. The nucleotide concentration at half-maximal velocity were 30 and 10 microM for cAMP and cGMP, respectively. The hydrolyses of both nucleotides exhibit positive homotropic cooperativity with Hill coefficients of 1.9 for cAMP and 1.3 for cGMP. The rate of cAMP hydrolysis by the purified enzyme when measured at 10 microM cAMP was enhanced 5- to 6-fold by low levels of cGMP.
Novel Palladium(0)-Catalyzed Coupling Reaction of Dialkoxyborane with Aryl Halides:  Convenient Synthetic Route to Arylboronates (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTNovel Palladium(0)-Catalyzed Coupling Reaction of Dialkoxyborane with Aryl Halides: Convenient Synthetic Route to ArylboronatesMiki Murata, Shinji Watanabe, and Yuzuru MasudaView Author Information Department of Materials Science, Kitami Institute of Technology, Kitami 090, JapanCite this: J. Org. Chem. 1997, 62, 19, 6458–6459Publication Date (Web):September 19, 1997Publication History Received2 June 1997Published online19 September 1997Published inissue 1 September 1997https://pubs.acs.org/doi/10.1021/jo970963phttps://doi.org/10.1021/jo970963prapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views7967Altmetric-Citations272LEARN 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 SUBJECTS:Anions,Aromatic compounds,Catalysts,Coupling reactions,Palladium Get e-Alerts
Comparative antimycobacterial activities of rifampin, rifapentine, and KRM-1648 against a collection of rifampin-resistant Mycobacterium tuberculosis isolates with known rpoB mutations (1996)

A collection of 24 rifampin-resistant clinical isolates of Mycobacterium tuberculosis with characterized RNA polymerase beta-subunit (rpoB) gene mutations was tested against the antimycobacterial agents rifampin, rifapentine, and KRM-1648 to correlate levels of resistance with specific rpoB genotypes. The results indicate that KRM-1648 is more active in vitro than rifampin and rifapentine, and its ability to overcome rifampin resistance in strains with four different genetic alterations may prove to be useful in understanding structure-function relationships.
Spectrum efficiency of multilevel modulation schemes in mobile radio communications (1995)

Lee (1989) has produced equations describing spectrum efficiency for modulation schemes operating in cellular environments. The present authors consider the performance of a range of multilevel modulation schemes when these spectrum efficiency equations are applied. They then proceed to adapt these efficiency equations for use in microcells before considering the performance of multilevel modulation within this environment. The results show that the preferred modulation scheme depends on the BER required, with 4 level PSK being preferred in conventional cells, and variable 16 level QAM, or 32 or 64 level QAM being suitable in microcells, particularly when a high SNR is available.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Acyl homoserine-lactone quorum-sensing signal generation (1999)

Acyl homoserine lactones (acyl-HSLs) are important intercellular signaling molecules used by many bacteria to monitor their population density in quorum-sensing control of gene expression. These signals are synthesized by members of the LuxI family of proteins. To understand the mechanism of acyl-HSL synthesis we have purified the Pseudomonas aeruginosa RhlI protein and analyzed the kinetics of acyl-HSL synthesis by this enzyme. Purified RhlI catalyzes the synthesis of acyl-HSLs from acyl-acyl carrier proteins and S-adenosylmethionine. An analysis of the patterns of product inhibition indicated that RhlI catalyzes signal synthesis by a sequential, ordered reaction mechanism in which S-adenosylmethionine binds to RhlI as the initial step in the enzymatic mechanism. Because pathogenic bacteria such as P. aeruginosa use acyl-HSL signals to regulate virulence genes, an understanding of the mechanism of signal synthesis and identification of inhibitors of signal synthesis has implications for development of quorum sensing-targeted antivirulence molecules.
[Short-term results of reconstruction of elbow under arthroscopy in patients with elbow osteoarthritis]. (2011)

The arthroscopy is an effective technique to reconstruct the function of stiff elbow, which can obviously improve the range of motion and the function of elbow joint, and has good short-term results.
Mutations of the Rous sarcoma virus env gene that affect the transport and subcellular location of the glycoprotein products. (1984)

The envelope glycoproteins of Rous sarcoma virus (RSV), gp85 and gp37, are anchored in the membrane by a 27-amino acid, hydrophobic domain that lies adjacent to a 22-amino acid, cytoplasmic domain at the carboxy terminus of gp37. We have altered these cytoplasmic and transmembrane domains by introducing deletion mutations into the molecularly cloned sequences of a proviral env gene. The effects of the mutations on the transport and subcellular localization of the Rous sarcoma virus glycoproteins were examined in monkey (CV-1) cells using an SV40 expression vector. We found, on the one hand, that replacement of the nonconserved region of the cytoplasmic domain with a longer, unrelated sequence of amino acids (mutant C1) did not alter the rate of transport to the Golgi apparatus nor the appearance of the glycoprotein on the cell surface. Larger deletions, extending into the conserved region of the cytoplasmic domain (mutant C2), resulted in a slower rate of transport to the Golgi apparatus, but did not prevent transport to the cell surface. On the other hand, removal of the entire cytoplasmic and transmembrane domains (mutant C3) did block transport and therefore did not result in secretion of the truncated protein. Our results demonstrate that the C3 polypeptide was not transported to the Golgi apparatus, although it apparently remained in a soluble, nonanchored form in the lumen of the rough endoplasmic reticulum; therefore, it appears that this mutant protein lacks a functional sorting signal. Surprisingly, subcellular localization by internal immunofluorescence revealed that the C3 protein (unlike the wild type) did not accumulate on the nuclear membrane but rather in vesicles distributed throughout the cytoplasm. This observation suggests that the wild-type glycoproteins (and perhaps other membrane-bound or secreted proteins) are specifically transported to the nuclear membrane after their biosynthesis elsewhere in the rough endoplasmic reticulum.
IEEE 802.16 TG4 OFDM PHY Proposal for the 802.16b PHY Layer Date Submitted (2001)

TG4 process of defining the PHY layer. Abstract This document contains a structure for the TG4 PHY development, it contains various PHY modes and describes the common structure between them. Purpose This proposal should be used for the PHY specification of the TG4. Notice This document has been prepared to assist 802.16. It is offered as a basis for discussion and is not binding on the contributing individual(s) or organization(s). The material in this document is subject to change in form and content after further study. The contributor(s) reserve(s) the right to add, amend or withdraw material contained herein. Release The contributor grants a free, irrevocable license to the to incorporate text contained in this contribution, and any modifications thereof, in the creation of an Standards publication; to copyright in the IEEE's name any Standards publication even though it may include portions of this contribution; and at the IEEE's sole discretion to permit others to reproduce in whole or in part the resulting Standards publication. The contributor also acknowledges and accepts that this contribution may be made public by 802.16. Patent Policy and Procedures The contributor is familiar with the 802.16 Patent Policy and Procedures (Version 1.0) , including the statement IEEE standards may include the known use of patent(s), including patent applications, if there is technical justification in the opinion of the standards-developing committee and provided the receives assurance from the patent holder that it will license applicants under reasonable terms and conditions for the purpose of implementing the standard.
Hybridoma Technology for the Generation of Monoclonal Antibodies (2012)

Hybridoma technology has long been a remarkable and indispensable platform for generating high-quality monoclonal antibodies (mAbs). Hybridoma-derived mAbs have not only served as powerful tool reagents but also have emerged as the most rapidly expanding class of therapeutic biologics. With the establishment of mAb humanization and with the development of transgenic-humanized mice, hybridoma technology has opened new avenues for effectively generating humanized or fully human mAbs as therapeutics. In this chapter, an overview of hybridoma technology and the laboratory procedures used routinely for hybridoma generation are discussed and detailed in the following sections: cell fusion for hybridoma generation, antibody screening and characterization, hybridoma subcloning and mAb isotyping, as well as production of mAbs from hybridoma cells.
Dnases in health and disease (2017)

DNA degradation is critical to healthy organism development and survival. Two nuclease families that play key roles in development and in disease are the Dnase1 and Dnase2 families. While these two families were initially characterized by biochemical function, it is now clear that multiple enzymes in each family perform similar, non-redundant roles in many different tissues. Most Dnase1 and Dnase2 family members are poorly characterized, yet their elimination can lead to a wide range of diseases, including lethal anemia, parakeratosis, cataracts and systemic lupus erythematosus. Therefore, understanding these enzyme families represents a critical field of emerging research. This review explores what is currently known about Dnase1 and Dnase2 family members, highlighting important questions about the structure and function of family members, and how their absence translates to disease.
Interaction between Synovial Inflammatory Tissue and Bone Marrow in Rheumatoid Arthritis (2005)

Rheumatoid arthritis (RA) leads to destruction of cartilage and bone. Whether rheumatoid arthritis also affects the adjacent bone marrow is less clear. In this study, we investigated subcortical bone marrow changes in joints from patients with RA. We describe penetration of the cortical barrier by synovial inflammatory tissue, invasion into the bone marrow cavity and formation of mononuclear cell aggregates with B cells as the predominant cell phenotype. B cells expressed common B cell markers, such as CD20, CD45RA, and CD79a, and were mature B cells, as indicated by CD27 expression. Plasma cells were also present and were enriched in the regions between aggregates and inflammatory tissue. Moreover, molecules for B cell chemoattraction, such as BCA-1 and CCL-21, homing, mucosal addressin cell adhesion molecule-1 and survival, BAFF, were expressed. Endosteal bone next to subcortical bone marrow aggregates showed an accumulation of osteoblasts and osteoid deposition. In summary, we show that synovial inflammatory tissue can reach the adjacent bone marrow by fully breaking the cortical barrier, which results in formation of B cell-rich aggregates as well as increased formation of new bone. This suggests that bone marrow is an additional compartment in the disease process of RA.
Scanning the literature. (2001)

Johnston SC, Gress DR, Browner WS, et al. Short-term prognosis after emergency department diagnosis of TIA. JAMA 2000; 284:2901–2906.

### Comments

This cohort study involved over 1700 patients managed by primary Care Physicians after a first diagnosis of TIA in the emergency room. The mean age
Tumor‐induced angiogenesis: Lack of inhibition by irradiation (1975)

The effect of irradiation of tumors on their ability to induce vascular responses (angiogenesis) was studied. Rat Walker carcino-sarcoma 256, rabbit V2 carcinoma, mouse (C57B1) melanoma and mouse (129) teratoma (OTT 6050, 100K) were irradiated with up to 5000R, then grafted either to the chicken chorioallantoic membrane or intracorneally into adult rabbits to assess competence to provoke angiogenesis. For all tumors and both assay systems the results were similar: irradiation did not interfere with tumor-induced vascular responses.