gebhart/patrepeval huggingface dataset:
Regulation of RNA Polymerase III Transcription during Cell Cycle Entry (2001)

Increased rates of RNA polymerase (pol) III transcription constitute a central feature of the mitogenic response, but little is known about the mechanism(s) responsible. We demonstrate that the retinoblastoma protein RB plays a major role in suppressing pol III transcription in growth-arrested fibroblasts. RB knockout cells are compromised in their ability to down-regulate pol III following serum withdrawal. RB binds and represses the pol III-specific transcription factor TFIIIB during G(0) and early G(1), but this interaction decreases as cells approach S phase. Full induction of pol III coincides with mid- to late G(1) phase, when RB becomes phosphorylated by cyclin D- and E-dependent kinases. TFIIIB only associates with the underphosphorylated form of RB, and overexpression of cyclins D and E stimulates pol III transcription in vivo. The RB-related protein p130 also contributes to the repression of TFIIIB in growth-arrested fibroblasts. These observations provide insight into the mechanisms responsible for controlling pol III transcription during the switch between growth and quiescence.
MicroRNA: Potential for Cancer Detection, Diagnosis, and Prognosis (2007)

The Cancer Diagnosis Program of the National Cancer Institute sponsored a workshop entitled “MicroRNA: Potential for Cancer Detection, Diagnosis, and Prognosis” in Rockville, Maryland on November 28 and 29, 2006. The purpose of this workshop was to bring together leaders in the microRNA (miRNA)
A novel family of Ig-like receptors for HLA class I molecules that modulate function of lymphoid and myeloid cells (1999)

We review what is presently known about structure, cellular distribution, biochemical characteristics, and function of a new family of human cell-surface receptors referred to as immunoglobulin-like transcripts (ILTs), leukocyte Ig-like receptors (LIRs), or monocyte/macrophage Ig-like receptors (MIRs). These receptors are genetically, structurally, and functionally related to a group of natural killer (NK) cell receptors for HLA class I molecules known as killer cell Ig-like receptors (KIRs). Distinct ILT/LIR/MIR isotypes are differentially expressed on lymphocytes, monocytes, macrophages, dendritic cells, and granulocytes; at least some of them recognize HLA class I molecules. Whereas some isotypes either inhibit or induce cell activation, others may be secreted as soluble receptors. ILT/LIR/MIR receptors may allow all immune cells to monitor class I expression on other cells and to respond in its absence, just as NK cells do. In addition, they may contribute to homeostasis by establishing activation thresholds that can be overcome only by relevant triggering stimuli and not by bystander cells.
Effect of mutations affecting the p6 gag protein on human immunodeficiency virus particle release. (1991)

Mutations in sequences at the C terminus of the capsid precursor protein of human immunodeficiency virus type 1 that affect the viral p6 protein prevent release of budded virus particles from the cell surface. The experiments reported here define an important step in the life cycle of the virus, the release of the budded particle from a tether that binds the assembled particle to the cell surface. Inhibition of the release of the viral capsid proteins by interferon alpha indicates that this step of virus maturation may be sensitive to inhibition by antiviral drugs.
Serotonin transporter mRNA levels are associated with the methylation of an upstream CpG island (2006)

The serotonin reuptake transporter (5HTT) is thought to be the principal regulator of serotonergic activity and epigenetic effects at this locus are thought to be important moderators of vulnerability to neuropsychiatric illness. In attempt to understand the basis of this regulation, several gene polymorphisms that affect 5HTT mRNA levels have been described. But to date, no clear mechanism linking these polymorphisms to vulnerability to epigenetic effects have been described. In this communication, we describe a CpG island in the 5' region of the 5HTT gene that contains an alternative exon 1 and possible promoter for 5HTT. We then confirm the existence of this transcript and ascertain the methylation status of this CpG island in 49 lymphoblast cell lines and analyze the relationship between methylation and 5HTT mRNA levels. We demonstrate that methylation at this CpG island is associated with decreased levels of 5HTT mRNA, but that this effect is evident only when 5HTTLPR genotype is taken into account. We suggest that these findings have significant implications for the understanding of the role of this locus in behavioral illness.
Molecular Models of Hydroxide, Oxyhydroxide, and Clay Phases and the Development of a General Force Field (2004)

The fate of chemical and radioactive wastes in the environment is related to the ability of natural phases to attenuate and immobilize contaminants through chemical sorption and precipitation processes. Our understanding of these complex processes at the atomic level is provided by a few experimental and analytical methods such as X-ray absorption and NMR spectroscopies. However, due to complexities in the structure and composition of clay and other hydrated minerals, and the inherent uncertainties of the experimental methods, it is important to apply theoretical molecular models for a fundamental atomic-level understanding, interpretation, and prediction of these phenomena. In this effort, we have developed a general force field, CLAYFF, suitable for the simulation of hydrated and multicomponent mineral systems and their interfaces with aqueous solutions. Interatomic potentials were derived from parametrizations incorporating structural and spectroscopic data for a variety of simple hydrated compounds. A flexible SPC-based water model is used to describe the water and hydroxyl behavior. Metal−oxygen interactions are described by a Lennard-Jones function and a Coulombic term with partial charges derived by Mulliken and ESP analysis of DFT results. Bulk structures, relaxed surface structures, and intercalation processes are evaluated and compared to experimental and spectroscopic findings for validation. Our approach differs from most others in that we treat most interatomic interactions as nonbonded. This allows us to effectively use the force field for a wide variety of phases and to properly account for energy and momentum transfer between the fluid phase and the solid, while keeping the number of parameters small enough to allow modeling of relatively large and highly disordered systems. Simulations of clay, hydroxide, and oxyhydroxide phases and their interfaces with aqueous solutions combine energy minimization and molecular dynamics methods to describe the structure and behavior of water, hydroxyl, surface species, and intercalates in these systems. The results obtained to date demonstrate that CLAYFF shows good promise to evolve into a widely adaptable and broadly effective force field for molecular simulations of fluid interfaces with clays and other clay-related phases, as well as other inorganic materials characterized by complex, disordered, and often ill-determined structure and composition.
Bionectins A−C, Epidithiodioxopiperazines with Anti-MRSA Activity, from Bionectra byssicola F120 (2006)

Three new epidithiodioxopiperazine compounds, bionectins A (1), B (2), and C (3), along with a known compound, verticillin D (4), have been isolated from the mycelium of liquid fermentation cultures of the fungus Bionectra byssicola F120. The structures of compounds 1−3 were assigned on the basis of MS and NMR data. Compounds 1 and 2 incorporate a dioxopiperazine moiety with a disulfide bridge in their molecules, while 3 contains a dioxopiperazine ring with two methylsulfanyl groups. Compounds 1 and 2 exhibited antibacterial activity against S. aureus including methicillin-resistant S. aureus (MRSA) and quinolone-resistant S. aureus (QRSA), with MIC values of 10−30 μg/mL, while 3 showed no antibacterial activity even at 100 μg/mL.
Risk factors associated with development of postoperative ileus in horses (2001)

Results suggest that by evaluating certain factors, horses at increased risk of postoperative ileus may be recognized before the condition develops. Preventative treatment and early intervention may be instituted in these horses. Shortening surgery time and performing an enterotomy may decrease the probability of horses developing postoperative ileus.
Performance Assessment and Authentic Assessment: A Conceptual Analysis of the Literature (2020)

Performance assessment and authentic assessment are recurrent terms in the literature on education and educational research. They have both been given a number of different meanings and unclear definitions and are in some publications not defined at all. Such uncertainty of meaning causes difficulties in interpretation and communication and can cause clouded or misleading research conclusions. This paper reviews the meanings attached to these concepts in the literature and describes the similarities and wide range of differences between the meanings of each concept. Accessed 54,055 times on https://pareonline.net from April 11, 2008 to December 31, 2019. For downloads from January 1, 2020 forward, please click on the PlumX Metrics link to the right.
In Vitro Differentiation of Neural Precursors From Human Embryonic Stem Cells (2006)

We describe a procedure for efficient and reproducible differentiation of neuroectodermal cells from human embryonic stem (ES) cells using an adherent colony culture. ES cell colonies are detached intact from the fibroblast feeder layer using dispase or collagenase. The ES cell aggregates, after 4-6 d in suspension culture, are adhered to the culture surface and form colonies of monolayer in a chemically defined medium. Under this culture condition, columnar neuroectodermal cells appear in the center of each colony and organize into neural tube-like rosettes after 14 d of differentiation culture. These neuroectodermal cells in the rosettes can be effectively isolated through differential enzymatic and adhesion treatment and the neural population accounts for at least 70% of the total differentiated progenies. Thus, our system not only provides a source of synchronized neuroectodermal cells, but also offers a paradigm to dissect mechanisms of neural induction and cell lineage specification during early human development.
gp330 on type ii pneumocytes mediates endocytosis leading to degradation of pro-urokinase, plasminogen activator inhibitor-1 and urokinase-plasminogen activator inhibitor-1 complex (1995)

Glycoprotein 330 (gp330) is a member of a family of receptors related to the low density lipoprotein receptor (LDLR). Although several ligands have been shown to bind gp330 in solid-phase assays, the ability of gp330 to mediate ligand endocytosis has not been demonstrated. To develop a cellular model for gp330 function we screened a variety of cultured cell lines and identified several that expressed this protein, including immortalized rat type II pneumocytes and a human and two rodent tumor cell lines. Using type II pneumocytes, endocytosis of a previously described gp330 ligand, urokinase (uPA) complexed with plasminogen activator inhibitor-1 (uPA:PAI-1) and two new ligands, PAI-1 and pro-uPA, was demonstrated. RAP, the 39 kDa receptor-associated protein known to antagonize ligand binding to gp330 in solid-phase binding assays, completely inhibited both internalization and degradation of the radiolabeled ligands by type II pneumocytes. This suggested that the clearance of these ligands was dependent on either gp330 or the LDLR-related protein (LRP), which shares several ligand-binding characteristics with gp330. By using polyclonal antibodies to gp330, the cellular internalization and degradation of the ligands were inhibited by 30-50%; remaining ligand internalization and degradation activity could be partially inhibited by polyclonal antibodies against LRP. These findings indicate that gp330, like other LDLR family members, mediates endocytosis of its ligands. In addition, gp330 acts in concert with LRP in type II pneumocytes to mediate clearance of a variety of proteins involved in plasminogen activation, including uPA:PAI-1 complexes PAI-1 and pro-uPA.(ABSTRACT TRUNCATED AT 250 WORDS)
Successful treatment of advanced murine renal cell cancer by bicompartmental adoptive chemoimmunotherapy. (1987)

The most challenging aspect of cancer treatment remains the management of invasive and metastatic tumor growth. Recent progress in the development and use of biologic response modifiers for immunomodulation has raised the possibility that the immune system can be used as an additional antitumor treatment modality in conjunction with surgery, chemotherapy, and/or radiotherapy for the treatment of established tumors and their metastases. As a model for adoptive chemoimmunotherapy (ACIT) of renal cancer we have used a murine renal cancer (Renca) of spontaneous origin that mimics the tumor progression characteristically observed for human renal cell carcinoma. In the present study, we demonstrate that broadly cytotoxic lymphocytes, generated by in vitro culture with human recombinant interleukin 2, and used in conjunction with the chemotherapeutic drug doxorubicin hydrochloride, are effective in treating invasive and metastatic renal cell cancer. Administration of ACIT i.v. or i.p., alone, or after nephrectomy of the tumor-bearing kidney, did not cure mice with stage II (locoregional invasive tumor) or stage III (lymph node metastases) disease. In contrast, nephrectomy followed by simultaneous bicompartmental i.v. and i.p. ACIT administration cured 80% of mice with either stage II or stage III Renca. These data demonstrate that simultaneous bicompartmental ACIT affords dramatically improved cure rates for advanced and metastatic Renca. This effect most likely results from efficient control of both locoregional and metastatic tumor growth.
Inhibition of nitric oxide synthesis protects the isolated working rabbit heart from ischaemia-reperfusion injury (1995)

These results suggest that: (1) the recovery of mechanical function of hearts subjected to ischaemia-reperfusion injury can be improved by modulation of myocardial NO synthesis, (2) inhibition of NO synthesis (with L-NAME or L-NMMA) may offer prolonged protection whereas its stimulation (with L-arginine) provides only brief protection, and (3) the reasons for the pharmacological effectiveness of these divergent strategies may be due to the formation of peroxynitrite from NO and superoxide anion during reperfusion.
Adsorption losses from urine-based cannabinoid calibrators during routine use (1993)

The major metabolite of cannabis found in urine, 11-nor-delta 9-tetrahydrocannabinol-9-carboxylic acid (delta 9-THC), is the compound most often used to calibrate cannabinoid immunoassays. The hydrophobic delta 9-THC molecule is known to adsorb to solid surfaces. This loss of analyte from calibrator solutions can lead to inaccuracy in the analytical system. Because the calibrators remain stable when not used, analyte loss is most probably caused by handling techniques. In an effort to develop an effective means of overcoming adsorption losses, we quantified cannabinoid loss from calibrators during the testing process. In studying handling of these solutions, we found noticeable, significant losses attributable to both the kind of pipette used for transfer and the contact surface-to-volume ratio of calibrator solution in the analyzer cup. Losses were quantified by immunoassay and by radioactive tracer. We suggest handling techniques that can minimize adsorption of delta 9-THC to surfaces. Using the appropriate pipette and maintaining a minimum surface-to-volume ratio in the analyzer cup effectively reduces analyte loss.
Cloned Mice from Fetal Fibroblast Cells Arrested at Metaphase by a Serial Nuclear Transfer1 (2001)

Cloning using G0-arrested somatic cells has led to the suggestion that this stage of the cell cycle is necessary for the success of cloning. In this study we report that cloned mice can be generated from fetal fibroblasts arrested at metaphase of the cell cycle. The procedure involves fusing a metaphase-arrested fetal fibroblast to an enucleated oocyte. After parthenogenetic activation a polar body and single diploid pronucleus were formed. Some of these were allowed to develop to the blastocyst stage, while others were enucleated and the nucleus was transferred to an enucleated fertilized 1-cell embryo. After the single transfer technique, 2 out of 164 developed to late stages of gestation were dead with gross abnormalities. However, after the serial nuclear transfer, 5 out of 272 embryos were recovered live at Day 19.5, and 2 of these went on to develop into apparently normal adults. All of the cloned embryos showed severe placental hypertrophy and defective differentiation of placental tissues. This study illustrates that reprogramming can occur after nuclear transfer at metaphase of the cell cycle.
Impaired brain glucose metabolism leads to Alzheimer neurofibrillary degeneration through a decrease in tau O-GlcNAcylation (2006)

Neurofibrillary degeneration characterized by abnormal hyperphosphorylation and aggregation of tau in affected neurons is directly associated with dementia symptoms and plays a pivotal role in the pathogenesis of Alzheimer disease (AD) and related tauopathies. It is well established that brain glucose uptake/metabolism is impaired in AD, but how this impairment contributes to the disease is unknown. We recently found that tau in human brain is also modified by O-GlcNAcylation in addition to phosphorylation and that the former negatively regulates the latter. On the basis of these findings, we propose a novel hypothesis that the impaired glucose uptake/metabolism contributes to AD by facilitating abnormal hyperphosphorylation of tau. Further studies of this mechanism are likely to offer a novel therapeutic target for preventing and treating AD.
Long‐acting recombinant factor IX Fc fusion protein (rFIXFc) for perioperative management of subjects with haemophilia B in the phase 3 B‐LONG study (2014)

In the phase 3 B-LONG (Recombinant Factor IX Fc Fusion Protein [rFIXFc] in Subjects With Haemophilia B) study, rFIXFc demonstrated a prolonged half-life compared with recombinant factor IX (rFIX), and safety and efficacy for prophylaxis and treatment of bleeding in subjects with moderately-severe to severe haemophilia B. In this B-LONG sub-analysis, rFIXFc was evaluated for efficacy in subjects requiring major surgery. Dosing was investigator-determined. Assessments included dosing, consumption, bleeding, transfusions and haemostatic response. A population pharmacokinetics model of rFIXFc was used to predict FIX activity. Twelve subjects underwent 14 major surgeries (including 11 orthopaedic surgeries); most subjects (11/12) received rFIXFc prophylaxis before surgery (range, ~2 weeks-12 months). Investigators/surgeons rated haemostatic responses as excellent (n = 13) or good (n = 1). In most surgeries (85·7%), haemostasis from the pre-surgical dose until the end of surgery was maintained with a single rFIXFc infusion. Blood loss was consistent with similar surgeries in subjects without haemophilia. The strong correlation (R(2) = 0·9586, P < 0·001) between observed and population pharmacokinetic model-predicted FIX activity suggests surgery did not impact rFIXFc pharmacokinetics. No unique safety concerns or inhibitors were observed. In conclusion, rFIXFc was safe and efficacious, with prolonged dosing intervals and low consumption, when used perioperatively in haemophilia B. Surgery did not appear to alter rFIXFc pharmacokinetics.
Topological median filters (2002)

This paper describes the definition and testing of a new type of median filter for images. The topological median filter implements some existing ideas and some new ideas on fuzzy connectedness to improve, over a conventional median filter, the extraction of edges in noise. The concept of alpha-connectivity is defined and used to create an algorithm for computing the degree of connectedness of a pixel to all the other pixels in an arbitrary neighborhood. The resulting connectivity map of the neighborhood effectively disconnects peaks in the neighborhood that are separated from the center pixel by a valley in the brightness topology. The median of the connectivity map is an estimate of the median of the peak or plateau to which the center pixel belongs. Unlike the conventional median filter, the topological median is relatively unaffected by disconnected features in the neighborhood of the center pixel. Four topological median filters are defined. Qualitative and statistical analyses of the four filters are presented. It is demonstrated that edge detection can be more accurate on topologically median filtered images than on conventionally median filtered images.
Transgenic mouse model for synergistic effects of nuclear oncogenes and growth factors in tumorigenesis: interaction of c-myc and transforming growth factor alpha in hepatic oncogenesis. (1993)

Double transgenic mice bearing fusion genes consisting of mouse albumin enhancer/promoter-mouse c-myc complementary DNA and mouse metallothionein 1 promoter-human transforming growth factor alpha complementary DNA were generated to investigate the interaction of these genes in hepatic oncogenesis and to provide a general paradigm for characterizing the interaction of nuclear oncogenes and growth factors in tumorigenesis. Coexpression of c-myc and transforming growth factor alpha as transgenes in the mouse liver resulted in a tremendous acceleration of neoplastic development in this organ as compared to expression of either of these transgenes alone. The two distinct cellular reactions that occurred in the liver of the double transgenic mice prior to the appearance of liver tumors were dysplastic and apoptotic changes in the existing hepatocytes followed by emergence of multiple focal lesions composed of both hyperplastic and dysplastic cell populations. These observations suggest that the interaction of c-myc and transforming growth factor alpha, and possibly other combinations of nuclear oncogenes and growth factors, during development of hepatic neoplasia contributes to the selection and expansion of the preneoplastic cell populations which consequently increases the probability of malignant conversion.
Analytical Centrifugation: Equilibrium Approach (1999)

The specific interaction of biological molecules with one another is fundamental to the biochemistry of all living things. Equilibrium sedimentation is a classic method of biochemistry that provides first-principle thermodynamic information about the molar mass, association energy, association stoichiometry, and thermodynamic nonideality of molecules in solution. It is one of the most rigorous, powerful, and readily adapted methods for characterizing solution interactions.