gebhart/patrepeval huggingface dataset:
mTFE3, an X-linked transcriptional activator containing basic helix-loop-helix and zipper domains, utilizes the zipper to stabilize both DNA binding and multimerization. (1992)

Southwestern (DNA-protein) screening of a murine L-cell cDNA library by using a probe for the microE3 site in the immunoglobulin heavy-chain enhancer yielded a clone, mTFE3, which is a member of the subset of basic helix-loop-helix (BHLH) proteins that also contain a leucine zipper (ZIP). Since the individual contribution of these domains is not well understood for proteins which contain them both, mutational analyses were performed to assess the functional roles of the HLH and ZIP regions for DNA binding and multimerization. The HLH region is stringently required for DNA binding but not for multimerization. The ZIP region is not stringently required for binding or multimerization, but stabilizes both multimer formation and DNA binding. A high degree of conservation at both the amino acid and nucleotide levels between the human transcription factor TFE3 and mTFE3 suggests that mTFE3 is the murine homolog of human TFE3. By using fluorescent in situ hybridization, mTFE3 was mapped to mouse chromosome X in band A2, which is just below the centromere. We show that in addition to the immunoglobulin heavy-chain microE3 site, mTFE3 binds to transcriptional elements important for lymphoid-specific, muscle-specific, and ubiquitously expressed genes. Binding of mTFE3 to DNA induces DNA bending.
Pollen Developmental Arrest: Maintaining Pollen Fertility in a World With a Changing Climate (2019)

During evolution of land plants, the haploid gametophytic stage has been strongly reduced in size and the diploid sporophytic phase has become the dominant growth form. Both male and female gametophytes are parasitic to the sporophyte and reside in separate parts of the flower located either on the same plant or on different plants. For fertilization to occur, bi-cellular or tri-cellular male gametophytes (pollen grains) have to travel to the immobile female gametophyte in the ovary. To survive exposure to a hostile atmosphere, pollen grains are thought to enter a state of complete or partial developmental arrest (DA). DA in pollen is strongly associated with acquisition of desiccation tolerance (DT) to extend pollen viability during air travel, but occurrence of DA in pollen is both species-dependent and at the same time strongly dependent on the reigning environmental conditions at the time of dispersal. Several environmental stresses (heat, drought, cold, humidity) are known to affect pollen production and viability. Climate change is also posing a serious threat to plant reproductive behavior and crop productivity. It is therefore timely to gain a better understanding of how DA and pollen viability are controlled in plants and how pollen viability can be protected to secure crop yields in a changing environment. Here, we provide an overview of how DA and pollen viability are controlled and how the environment affects them. We make emphasis on what is known and areas where a deeper understanding is needed.
Isomotive dielectrophoresis for parallel analysis of individual particles (2017)

Two dielectrophoresis systems are introduced where the induced dielectrophoretic force is constant throughout the experimental region, resulting in uniform (isomotive) microparticle translation. Isomotive dielectrophoresis (isoDEP) is accomplished through a unique geometry where the gradient of the field-squared (∇Erms2) is constant, a characteristic that is otherwise highly nonuniform in traditional DEP platforms. The governing isoDEP equations were derived herein and applied to two different isoDEP prototypes: (i) one fabricated from deep reactive ion etching (DRIE) of a conductive silicon wafer (1-10 Ω-cm) whose patterned features served as electrodes and microchannel sidewalls simultaneously; (ii) a second where the electric field is applied lengthwise through a PDMS microchannel whose geometry follows a specific curvature. Both positive and negative dielectrophoresis was demonstrated with the isoDEP devices using silver-coated hollow glass spheres and polystyrene particles, respectively. Particle tracking was used to compare particle trajectory with the expected dielectrophoretic response; further, particle velocity was used to measure the Clausius-Mossotti factor of individual polystyrene particles (18-24.9 μm) in both devices with a value of -0.40 ± 0.063 (n = 110) and -0.48 ± 0.055 (n = 18) for the DRIE and PDMS isoDEP platforms, respectively. The isoDEP platform is capable of analyzing multiple particles simultaneously, providing greater throughput than traditional electrorotation platforms.
Stimulation of TLRs by LMW‐HA induces self‐defense mechanisms in vaginal epithelium (2010)

The innate immune system is present throughout the female reproductive tract and functions in synchrony with the adaptive immune system to provide protection in a way that enhances the chances for fetal survival, while protecting against potential pathogens. Recent data show that activation of Toll-like receptor (TLR)2 and 4 by low-molecular weight hyaluronic acid (LMW-HA) in the epidermis induces secretion of the antimicrobial peptide β-defensin 2. In the present work, we show that LMW-HA induces vaginal epithelial cells to release different antimicrobial peptides, via activation of TLR2 and TLR4. Further, we found that LMW-HA favors repair of vaginal epithelial injury, involving TLR2 and TLR4, and independently from its classical receptor CD44. This wound-healing activity of LMW-HA is dependent from an Akt/phosphatidylinositol 3 kinase pathway. Therefore, these findings suggest that the vaginal epithelium is more than a simple physical barrier to protect against invading pathogens: on the contrary, this surface acts as efficient player of innate host defense, which may modulate its antimicrobial properties and injury restitution activity, following LMW-HA stimulation; this activity may furnish an additional protective activity to this body compartment, highly and constantly exposed to microbiota, ameliorating the self-defense of the vaginal epithelium in both basal and pathological conditions.
HIV-1 Tat transactivator recruits p300 and CREB-binding protein histone acetyltransferases to the viral promoter (1998)

In cells infected with HIV type 1 (HIV-1), the integrated viral promoter is present in a chromatin-bound conformation and is transcriptionally silent in the absence of stimulation. The HIV-1 Tat protein binds to a stem-loop structure at the 5' end of viral mRNA and relieves this inhibition by inducing a remodeling of the nucleosome arrangement downstream of the transcription-initiation site. Here we show that Tat performs this activity by recruiting to the viral long terminal repeat (LTR) the transcriptional coactivator p300 and the closely related CREB-binding protein (CBP), having histone acetyltransferase (HAT) activity. Tat associates with HAT activity in human nuclear extracts and binds to p300 and CBP both in vitro and in vivo. Integrity of the basic domain of Tat is essential for this interaction. By a quantitative chromatin immunoprecipitation assay we show that the delivery of recombinant Tat induces the association of p300 and CBP with the chromosomally integrated LTR promoter. Expression of human p300 in both human and rodent cells increases the levels of Tat transactivation of the integrated LTR. These results reinforce the evidence that p300 and CBP have a pivotal function at both cellular and viral promoters and demonstrate that they also can be recruited by an RNA-targeted activator. Additionally, these findings have important implications for the understanding of the mechanisms of HIV-1 latency and reactivation.
Proteomics of Hepatocellular Carcinoma: Present Status and Future Prospects (2006)

Proteome analysis of HCC is an emerging area of research in the discovery of novel proteins as early biomarkers for diagnosis and potential therapeutic targets for the treatment of HCC. Although numerous publications have appeared on the gene expression analysis of HCC by cDNA microarrays, there is still a need to analyze the differentially expressed proteins in the cellular proteome as many protein modifications are not reflected by changes at the RNA level. New and improved proteomic technologies such as DIGE, and ICAT labelling in combination with mass spectrometric analysis will drive and accelerate the next phase of expression profiling of HCC. There will also be a concerted effort in performing proteome analysis at the subcellular level (subproteomics) in order to detect and identify low abundance proteins which may be missed at the global expression profile of the whole cell. In addition the localization sites of these identified proteins will provide clues to their functions. Finally, it is hoped that integration of proteome-based approaches with data from genomic profiling will lead to a better understanding of hepatocarcinogenesis which will then contribute to the direct translation of the research findings into clinical practice (Selinger and Kellner, 2002).
cDNA cloning and characterization of human Δ5-desaturase involved in the biosynthesis of arachidonic acid (2000)

Two human expressed sequence tag (EST) cDNA sequences with identity with ∆5- and ∆6-desaturases from a filamentous fungus, Mortierella alpina, were identified from the LifeSeq® database of Incyte Pharmaceuticals, Inc. (Palo Alto, CA, U.S.A.). An oligonucleotide complementary to the 3ʹ EST cDNA sequences was used to screen human liver cDNA using rapid amplification of cDNA ends (RACE)-PCR. The amplified DNA fragment had 98% identity with a putative open reading frame (ORF) predicted from a human genomic sequence, and encoded 444 amino acids. Expression of this ORF in mouse fibroblast cells demonstrated that the encoded protein was a ∆5-desaturase, as determined by the conversion of dihomo-γ-linolenic acid (C20:3,n-6) into arachidonic acid (C20:4,n-6). The human ∆5-desaturase contained a predicted N-terminal cytochrome b5-like domain, as well as three histidine-rich domains. A tissue expression profile revealed that this gene is highly expressed in fetal liver, fetal brain, adult brain and adrenal gland. A search of the existing databases led to localization of this ORF within a 14 kb interval flanked by the flap endonuclease-1 (FEN1) and vitelliform macular dystrophy (Best's disease; VMD2) loci of chromosome 11q12.
Diagnosis of Lyme Borreliosis (2005)

A large amount of knowledge has been acquired since the original descriptions of Lyme borreliosis (LB) and of its causative agent, Borrelia burgdorferi sensu stricto. The complexity of the organism and the variations in the clinical manifestations of LB caused by the different B. burgdorferi sensu lato species were not then anticipated. Considerable improvement has been achieved in detection of B. burgdorferi sensu lato by culture, particularly of blood specimens during early stages of disease. Culturing plasma and increasing the volume of material cultured have accomplished this. Further improvements might be obtained if molecular methods are used for detection of growth in culture and if culture methods are automated. Unfortunately, culture is insensitive in extracutaneous manifestations of LB. PCR and culture have high sensitivity on skin samples of patients with EM whose diagnosis is based mostly on clinical recognition of the lesion. PCR on material obtained from extracutaneous sites is in general of low sensitivity, with the exception of synovial fluid. PCR on synovial fluid has shown a sensitivity of up to >90% (when using four different primer sets) in patients with untreated or partially treated Lyme arthritis, making it a helpful confirmatory test in these patients. Currently, the best use of PCR is for confirmation of the clinical diagnosis of suspected Lyme arthritis in patients who are IgG immunoblot positive. PCR should not be used as the sole laboratory modality to support a clinical diagnosis of extracutaneous LB. PCR positivity in seronegative patients suspected of having late manifestations of LB most likely represents a false-positive result. Because of difficulties in direct methods of detection, laboratory tests currently in use are mainly those detecting antibodies to B. burgdorferi sensu lato. Tests used to detect antibodies to B. burgdorferi sensu lato have evolved from the initial formats as more knowledge on the immunodominant antigens has been collected. The recommendation for two-tier testing was an attempt to standardize testing and improve specificity in the United States. First-tier assays using whole-cell sonicates of B. burgdorferi sensu lato need to be standardized in terms of antigen composition and detection threshold of specific immunoglobulin classes. The search for improved serologic tests has stimulated the development of recombinant protein antigens and the synthesis of specific peptides from immunodominant antigens. The use of these materials alone or in combination as the source of antigen in a single-tier immunoassay may someday replace the currently recommended two-tier testing strategy. Evaluation of these assays is currently being done, and there is evidence that certain of these antigens may be broadly cross-reactive with the B. burgdorferi sensu lato species causing LB in Europe.
Increased 2-Hydroxylation of Estradiol as a Possible Mechanism for the Anti-Estrogenic Effect of Cigarette Smoking (1986)

Epidemiologic data indicate that cigarette smoking is associated with an important anti-estrogenic effect, and increased hepatic metabolism has been suggested as a possible mechanism. We examined the hypothesis that cigarette smoking in women induces an increase in estradiol 2-hydroxylation. This irreversible metabolic pathway yields 2-hydroxyestrogens, which possess minimal peripheral estrogenic activity and are cleared rapidly from the circulation. We found a significant increase in estradiol 2-hydroxylation in premenopausal women who smoked at least 15 cigarettes per day. The extent of the reaction (mean +/- SEM) was 53.6 +/- 2.2 percent among 14 smokers and 35.1 +/- 1.8 percent among 13 nonsmoking controls--an increase of approximately 50 percent (P less than 0.001). The extent of 2-hydroxylation among five smokers did not vary during the follicular and luteal phases of their menstrual cycles. In addition, urinary excretion of estriol relative to estrone was significantly decreased among smokers (P less than 0.01), providing evidence that the smoking-induced increase in 2-hydroxylation diminishes the competing metabolic pathway involving 16 alpha-hydroxylation. This study demonstrates that smoking exerts a powerful inducing effect on the 2-hydroxylation pathway of estradiol metabolism, which is likely to lead to decreased bioavailability at estrogen target tissues. Elucidation of the mechanism responsible for smoking-induced changes in 2-hydroxylation may be useful in the development of strategies to reduce the risk of hormone-dependent tumors.
Differential Inhibition of mRNA Degradation Pathways by Novel Cap Analogs (2005)

mRNA degradation predominantly proceeds through two alternative routes: the 5'-->3' pathway, which requires deadenylation followed by decapping and 5'-->3' hydrolysis; and the 3'-->5' pathway, which involves deadenylation followed by 3'-->5' hydrolysis and finally decapping. The mechanisms and relative contributions of each pathway are not fully understood. We investigated the effects of different cap structure (Gp(3)G, m(7)Gp(3)G, or m(2)(7,3'-O) Gp(3)G) and 3' termini (A(31),A(60), or G(16)) on both translation and mRNA degradation in mammalian cells. The results indicated that cap structures that bind eIF4E with higher affinity stabilize mRNA to degradation in vivo. mRNA stability depends on the ability of the 5' terminus to bind eIF4E, not merely the presence of a blocking group at the 5'-end. Introducing a stem-loop in the 5'-UTR that dramatically reduces translation, but keeping the cap structure the same, does not alter the rate of mRNA degradation. To test the relative contributions of the 5'-->3' versus 3'-->5' pathways, we designed and synthesized two new cap analogs, in which a methylene group was substituted between the alpha- and beta-phosphate moieties, m(2)(7,3'-O)Gpp(CH2)pG and m(2)(7,3'-O)Gp(CH2)ppG, that are predicted to be resistant to cleavage by Dcp1/Dcp2 and DcpS, respectively. These cap analogs were recognized by eIF4E and conferred cap-dependent translation to mRNA both in vitro and in vivo. Oligonucleotides capped with m(2)(7,3'-O)Gpp(CH2)pG were resistant to hydrolysis by recombinant human Dcp2 in vitro. mRNAs capped with m(2)(7,3'-O)Gpp(CH2)pG, but not m(2)(7,3'-O)Gp(CH2)ppG, were more stable in vivo, indicating that the 5'-->3' pathway makes a major contribution to overall degradation. Luciferase mRNA containing a 5'-terminal m(2)(7,3'-O)Gpp(CH2)pG and 3'-terminal poly(G) had the greatest stability of all mRNAs tested.
Transurethral Ultrasound-Guided Laser-Induced Prostatectomy (Tulip Procedure): A Canine Prostate Feasibility Study (1991)

We describe the TULIP procedure, a new system to relieve bladder outlet obstruction caused by benign prostatic hyperplasia. This device is composed of a real-time 7.5 MHz ultrasound transducer coupled to a Nd:YAG laser with a 1.064 microns wavelength that fires through an intact intraprostatic balloon. A series of feasibility studies in 21 canine prostate glands was performed with a follow-up time to 3 months. Results indicate that the Nd:YAG laser in the 20 to 40 W range at a pull rate of approximately 1 mm. per second is an effective means of removing substantial amounts of canine benign prostatic hyperplasia. Transurethral ultrasonography was a reliable means of identifying essential landmarks and of controlling the laser. Prostatectomy by laser coagulation necrosis resulted in no bleeding or postoperative obstruction. Intraoperative irrigation fluids were not required, eliminating systemic volume related problems.
Nature of the addition of dienophiles to the acridizinium ion (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNature of the addition of dienophiles to the acridizinium ionCharles K. Bradsher and John Arthur StoneCite this: J. Org. Chem. 1968, 33, 2, 519–523Publication Date (Print):February 1, 1968Publication History Published online1 May 2002Published inissue 1 February 1968https://doi.org/10.1021/jo01266a009RIGHTS & PERMISSIONSArticle Views101Altmetric-Citations14LEARN 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 (673 KB) Get e-Alertsclose Get e-Alerts
Expression of laminin receptor in normal and carcinomatous human tissues as defined by a monoclonal antibody. (1985)

It has been hypothesized that epithelial and endothelial cells interact with the laminin component of basement membranes via a cell surface laminin receptor molecule. It has also been proposed that the expression of this molecule may be involved in the invasion of carcinoma cells from their tissue of origin and their subsequent penetration through blood vessel basement membranes. We report here the use of a monoclonal antibody, LR-3, to define the expression of laminin receptor in normal, dysplastic, and carcinomatous human tissues. Monoclonal antibody LR-3 is shown by immunoblotting to recognize the Mr 67,000 laminin receptor protein, to bind to the carcinoma cells, and to constitute approximately 0.1% of total cellular protein. Numerous normal human epithelial and endothelial cell types, as well as pulmonary macrophages, are shown to express laminin receptor to varying degrees. Selected human mammary carcinomas and colon carcinomas are shown to bind more monoclonal antibody LR-3 than normal or dysplastic counterparts. A monoclonal antibody to laminin receptor now makes possible the study of the role of laminin receptor in tumor cell metastases and in the differentiation and function of various normal human epithelial and endothelial cell types.
Characterization of Cell Lysis in Pseudomonas putida Induced upon Expression of Heterologous Killing Genes (1998)

Active biological containment systems are based on the controlled expression of killing genes. These systems are of interest for the Pseudomonadaceae because of the potential applications of these microbes as bioremediation agents and biopesticides. The physiological effects that lead to cell death upon the induction of expression of two different heterologous killing genes in nonpathogenic Pseudomonas putida KT2440 derivatives have been analyzed. P. putida CMC4 and CMC12 carry in their chromosomes a fusion of the PA1-04/03 promoter to the Escherichia coli gef gene and the phiX174 lysis gene E, respectively. Expression of the killing genes is controlled by the LacI protein, whose expression is initiated from the XylS-dependent Pm promoter. Under induced conditions, killing of P. putida CMC12 cells mediated by phiX174 lysis protein E was faster than that observed for P. putida CMC4, for which the Gef protein was the killing agent. In both cases, cell death occurred as a result of impaired respiration, altered membrane permeability, and the release of some cytoplasmic contents to the extracellular medium.
Pain following spinal cord injury: animal models and mechanistic studies (2000)

Vierck, Charles J. Jr.a,b,*; Siddall, Phillipc; Yezierski, Robert P.d,e,f Author Information
The length of homology required for gene targeting in embryonic stem cells. (1991)

Homologous recombination has been used to introduce site-specific mutations into murine embryonic stem (ES) cells with both insertion and replacement vectors. In this study, we compared the frequency of gene targeting with various lengths of homology and found a dramatic increase in targeting with an increase in homology from 1.3 to 6.8 kb. We examined in detail the relationship between the length of homology and the gene-targeting frequency for replacement vectors and found that a critical length of homology is needed for targeting. Adding greater lengths of homology to this critical length has less of an effect on the targeting frequency. We also analyzed the lengths of homology necessary on both arms of the vector for gene replacement events and found that 472 bp of homology is used as efficiently as 1.2 kb in the formation and resolution of crossover junctions.
Effects of Noninvasive Transcutaneous Electrical Stimulation via Concentric Ring Electrodes on Pilocarpine‐induced Status Epilepticus in Rats (2007)

Noninvasive TcES, applied 5 min after SE onset via novel concentric ring electrodes on the scalp, reduced, or abolished electrographic and behavioral seizure activity in pilocarpine-induced SE in rats. These findings suggest that TcES may have a role in the treatment of SE.