gebhart/patrepeval huggingface dataset:
Cloning, sequencing, and expression of the genes encoding subunits of Paracoccus denitrificans electron transfer flavoprotein. (1993)

The genes encoding the two subunits of Paracoccus denitrificans electron transfer flavoprotein (ETF) were identified by screening a genomic library constructed in pBluescript II SK+ with probes generated by amplification of genomic sequences by the polymerase chain reaction. Primers for the polymerase chain reaction were designed based on peptide sequences from purified Paracoccus ETF subunits. The genes are arranged in tandem in the genomic DNA with the deoxyadenylic acid residue in the TGA termination codon of the small subunit providing the deoxyadenylic acid residue for the ATG initiating codon of the large subunit. The deduced amino acid sequences of the ETF subunits exhibits extensive sequence identity with the human ETF subunits. The Paracoccus ETF is expressed from the pBluescript vector in Escherichia coli, yielding 30 mg of purified, catalytically active protein per liter of culture.
M Channel KCNQ2 Subunits Are Localized to Key Sites for Control of Neuronal Network Oscillations and Synchronization in Mouse Brain (2001)

Mutations in the potassium channel subunit KCNQ2 lead to benign familial neonatal convulsions, a dominantly inherited form of generalized epilepsy. In heterologous cells, KCNQ2 expression yields voltage-gated potassium channels that activate slowly (tau, approximately 0.1 sec) at subthreshold membrane potentials. KCNQ2 associates with KCNQ3, a homolog, to form heteromeric channels responsible for the M current (I(M)) in superior cervical ganglion (SCG) neurons. Muscarinic acetylcholine and peptidergic receptors inhibit SCG I(M), causing slow EPSPs and enhancing excitability. Here, we use KCNQ2N antibodies, directed against a conserved N-terminal portion of the KCNQ2 polypeptide, to localize KCNQ2-containing channels throughout mouse brain. We show that KCNQ2N immunoreactivity, although widespread, is particularly concentrated at key sites for control of rhythmic neuronal activity and synchronization. In the basal ganglia, we find KCNQ2N immunoreactivity on somata of dopaminergic and parvalbumin (PV)-positive (presumed GABAergic) cells of the substantia nigra, cholinergic large aspiny neurons of the striatum, and GABAergic and cholinergic neurons of the globus pallidus. In the septum, GABAergic, purinergic, and cholinergic neurons that contribute to the septohippocampal and septohabenular pathways exhibit somatic KCNQ2 labeling. In the thalamus, GABAergic nucleus reticularis neurons that regulate thalamocortical oscillations show strong labeling. In the hippocampus, many PV-positive and additional PV-negative interneurons exhibit strong somatic staining, but labeling of pyramidal and dentate granule somata is weak. There is strong neuropil staining in many regions. In some instances, notably the hippocampal mossy fibers, evidence indicates this neuropil staining is presynaptic.
Fabrication of palladium-based microelectronic devices by microcontact printing (2002)

This letter demonstrates the patterning of thin films of metallic palladium by microcontact printing (μCP) of octadecanethiol, and the use of the patterned films in the fabrication of a functional sensor. This technique was also used to prepare templates of palladium for the electroless deposition of copper. The resistivity of the palladium and copper microstructures was 13.8 and 2.8 μΩ cm, respectively; these values are approximately 40% larger than the values for the pure bulk metals. Palladium patterned into serpentine wires using μCP functioned as a hydrogen sensor with sensitivity of 0.03 vol % H2 in N2, and a response time of ∼10 s (at room temperature).
A Versatile Strategy for Quantum Dot Ligand Exchange (2006)

A new and efficient procedure for ligand exchange on core−shell fluorescent nanocrystals is reported. The process involves the reaction of carbon disulfide with a ligand containing an amino group. The resulting dithiocarbamate is strongly bound to the surface of the quantum dots leading to a secure coating of the nanoparticle. The strategy was applied to the aqueous transfer of quantum dots.
Activity, expression, and transcription rate of the cathepsins B, D, H, and L in cutaneous malignant melanoma (2001)

It may be relevant for the malignant potential of the lesion whether the increase in activity is accompanied by an increase in the mRNA level. Two different mechanisms-the existence of different mRNAs and the higher transcription rate of the cathepsin gene-have been proposed for the regulation of cathepsin B activity in tumor cells. The current data suggest that, depending on the thickness of the melanoma, cathepsin activity is regulated by different mechanisms. The up-regulation of cathepsin gene transcription appears to be characteristic for more invasive tumor cells.
Engineered glucagon-like peptide-1-producing hepatocytes lower plasma glucose levels in mice (2009)

Glucagon-like peptide (GLP)-1 is an incretin hormone with well-characterized antidiabetic properties, including glucose-dependent stimulation of insulin secretion and enhancement of beta-cell mass. GLP-1 agonists have recently been developed and are now in clinical use for the treatment of type 2 diabetes. Rapid degradation of GLP-1 by enzymes including dipeptidyl-peptidase (DPP)-IV and neutral endopeptidase (NEP) 24.11, along with renal clearance, contribute to a short biological half-life, necessitating frequent injections to maintain therapeutic efficacy. Gene therapy may represent a promising alternative approach for achieving long-term increases in endogenous release of GLP-1. We have developed a novel strategy for glucose-regulated production of GLP-1 in hepatocytes by expressing a DPP-IV-resistant GLP-1 peptide in hepatocytes under control of the liver-type pyruvate kinase promoter. Adenoviral delivery of this construct to hepatocytes in vitro resulted in production and secretion of bioactive GLP-1 as measured by a luciferase-based bioassay developed to detect the NH2-terminally modified GLP-1 peptide engineered for this study. Transplantation of encapsulated hepatocytes into CD-1 mice resulted in an increase in plasma GLP-1 levels that was accompanied by a significant reduction in fasting plasma glucose levels. The results from this study demonstrate that a gene therapy approach designed to induce GLP-1 production in hepatocytes may represent a novel strategy for long-term secretion of bioactive GLP-1 for the treatment of type 2 diabetes.
Refractive Keratoplasty (1982)

We performed routine microkeratome and freehand lamellar keratectomies in 65 canine eyes and 24 human eye-bank eyes. The microkeratome technique produced more predictable resections compared with the freehand technique and at the same time produced a wound that would allow for better wound coaptation. Neither technique damaged the corneal endothelium. We conclude that one of the reasons for the success of the refractive keratoplasty procedures is the refined microkeratome technique.
The PROSITE database, its status in 1995 (1996)

The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of proteins (if any) a new sequence belongs or which known domain(s) it contains.
Cellular Immune Responses of Healthy Individuals to Intradermal Administration of an E1 - E3 - Adenovirus Gene Transfer Vector (1999)

In animals, Ad-mediated gene transfer initiates anti-Ad host immune responses that vary, depending on vector design, dose, host, and transgene. To begin to understand whether the anti-Ad vector responses in humans simulate those in animals, Ad(GV)CD.10, an E1-E3- Ad5 vector encoding the E. coli cytosine deaminase gene, was administered by the intradermal route to six normal individuals (8 x 10(7) to 8 x 10(9) particle units, each dose administered to two sites; n = 2 per group). No adverse events were observed. Polymerase chain reaction/Southern analysis demonstrated vector genome in the skin through 28 days in all individuals except one of two at the lowest dose. Local induration, independent of vector dose and baseline systemic anti-Ad5 neutralizing antibodies, developed in all subjects (6 to 17 mm, peak by day 3). Biopsies revealed a mild to moderate T cell (CD3+, CD4+, CD8+), B cell, and macrophage infiltrate at day 3, all decreased by day 28. Langerhans cells accumulated primarily in the papillary dermis. The day 3 cellular response was dose independent. On day 28, CD4+ and CD8+ T lymphocytes and macrophages showed dose dependency. There was minimal systemic Ad5-specific lymphocyte proliferation induced by Ad vector administration in three individuals studied, and no Ad5-specific cytotoxic T lymphocytes (evaluated in two subjects) could be detected. Thus, intradermal administration of an E1-E3- Ad vector to normal subjects induces mild/moderate local cellular responses, even in Ad-immunized individuals. These observations provide a baseline to determine if these human anti-Ad vector host responses can be circumvented by using "stealth" vectors and/or immunosuppression.
Auxin Biosynthesis and Its Role in Plant Development (2010)

Indole-3-acetic acid (IAA), the main auxin in higher plants, has profound effects on plant growth and development. Both plants and some plant pathogens can produce IAA to modulate plant growth. Although the genes and biochemical reactions for auxin biosynthesis in some plant pathogens are well understood, elucidation of the mechanisms by which plants produce auxin has proven to be difficult. So far, no single complete pathway of de novo auxin biosynthesis in plants has been firmly established. However, recent studies have led to the discoveries of several genes in tryptophan-dependent auxin biosynthesis pathways. Recent findings have also determined that local auxin biosynthesis plays essential roles in many developmental processes including gametogenesis, embryogenesis, seedling growth, vascular patterning, and flower development. In this review, I summarize the recent advances in dissecting auxin biosynthetic pathways and how the understanding of auxin biosynthesis provides a crucial angle for analyzing the mechanisms of plant development.
Direct Interaction of Pericentrin with Cytoplasmic Dynein Light Intermediate Chain Contributes to Mitotic Spindle Organization (1999)

Pericentrin is a conserved protein of the centrosome involved in microtubule organization. To better understand pericentrin function, we overexpressed the protein in somatic cells and assayed for changes in the composition and function of mitotic spindles and spindle poles. Spindles in pericentrin-overexpressing cells were disorganized and mispositioned, and chromosomes were misaligned and missegregated during cell division, giving rise to aneuploid cells. We unexpectedly found that levels of the molecular motor cytoplasmic dynein were dramatically reduced at spindle poles. Cytoplasmic dynein was diminished at kinetochores also, and the dynein-mediated organization of the Golgi complex was disrupted. Dynein coimmunoprecipitated with overexpressed pericentrin, suggesting that the motor was sequestered in the cytoplasm and was prevented from associating with its cellular targets. Immunoprecipitation of endogenous pericentrin also pulled down cytoplasmic dynein in untransfected cells. To define the basis for this interaction, pericentrin was coexpressed with cytoplasmic dynein heavy (DHCs), intermediate (DICs), and light intermediate (LICs) chains, and the dynamitin and p150(Glued) subunits of dynactin. Only the LICs coimmunoprecipitated with pericentrin. These results provide the first physiological role for LIC, and they suggest that a pericentrin-dynein interaction in vivo contributes to the assembly, organization, and function of centrosomes and mitotic spindles.
Heterogenous Catalysis Mediated by Plasmon Heating (2009)

We introduce a new method for performing and miniaturizing many types of heterogeneous catalysis involving nanoparticles. The method makes use of the plasmon resonance present in nanoscale metal catalysts to provide the necessary heat of reaction when illuminated with a low-power laser. We demonstrate our approach by reforming a flowing, liquid mixture of ethanol and water over gold nanoparticle catalysts in a microfluidic channel. Plasmon heating of the nanoparticles provides not only the heat of reaction but the means to generate both water and ethanol vapor locally over the catalysts, which in turn allows the chip and the fluid lines to remain at room temperature. The measured products of the reaction, CO(2), CO, and H(2), are consistent with catalytic steam reforming of ethanol. The approach, which we refer to as plasmon-assisted catalysis, is general and can be used with a variety of endothermic catalytic processes involving nanoparticles.
Conservation of a Gliding Motility and Cell Invasion Machinery in Apicomplexan Parasites (1999)

Most Apicomplexan parasites, including the human pathogens Plasmodium, Toxoplasma, and Cryptosporidium, actively invade host cells and display gliding motility, both actions powered by parasite microfilaments. In Plasmodium sporozoites, thrombospondin-related anonymous protein (TRAP), a member of a group of Apicomplexan transmembrane proteins that have common adhesion domains, is necessary for gliding motility and infection of the vertebrate host. Here, we provide genetic evidence that TRAP is directly involved in a capping process that drives both sporozoite gliding and cell invasion. We also demonstrate that TRAP-related proteins in other Apicomplexa fulfill the same function and that their cytoplasmic tails interact with homologous partners in the respective parasite. Therefore, a mechanism of surface redistribution of TRAP-related proteins driving gliding locomotion and cell invasion is conserved among Apicomplexan parasites.
Cancers predispose neutrophils to release extracellular DNA traps that contribute to cancer-associated thrombosis (2012)

Cancer-associated thrombosis often lacks a clear etiology. However, it is linked to a poor prognosis and represents the second-leading cause of death in cancer patients. Recent studies have shown that chromatin released into blood, through the generation of neutrophil extracellular traps (NETs), is procoagulant and prothrombotic. Using a murine model of chronic myelogenous leukemia, we show that malignant and nonmalignant neutrophils are more prone to NET formation. This increased sensitivity toward NET generation is also observed in mammary and lung carcinoma models, suggesting that cancers, through a systemic effect on the host, can induce an increase in peripheral blood neutrophils, which are predisposed to NET formation. In addition, in the late stages of the breast carcinoma model, NETosis occurs concomitant with the appearance of venous thrombi in the lung. Moreover, simulation of a minor systemic infection in tumor-bearing, but not control, mice results in the release of large quantities of chromatin and a prothrombotic state. The increase in neutrophil count and their priming is mediated by granulocyte colony-stimulating factor (G-CSF), which accumulates in the blood of tumor-bearing mice. The prothrombotic state in cancer can be reproduced by treating mice with G-CSF combined with low-dose LPS and leads to thrombocytopenia and microthrombosis. Taken together, our results identify extracellular chromatin released through NET formation as a cause for cancer-associated thrombosis and unveil a target in the effort to decrease the incidence of thrombosis in cancer patients.
Differential production of cytokines, reactive oxygen and nitrogen by bovine macrophages and dendritic cells stimulated with Toll‐like receptor agonists (2003)

Toll-like receptors (TLR) have been described as partially sharing signalling pathways but showing unique ligand specificity and tissue distribution. Here, the response of bovine macrophages (Mphi) and dendritic cells (DC), both derived from monocytes, was compared by exposing them to the TLR-specific ligands lipopolysaccharide, poly(I:C)-double-stranded RNA, and CpG-DNA, as well as inactivated Gram-negative and Gram-positive bacteria, shown to bind to TLR. The production of NO, superoxide anion, interleukin-10 (IL-10), IL-12 and tumour necrosis factor (TNF) was determined. Compared to monocytes, Mphi expressed more TLR2 and similar levels of TLR4 mRNA transcripts, as analysed by quantitative polymerase chain reaction, whereas DC expressed reduced amounts. Although both DC and Mphi recognized the TLR ligands, dramatic differences were seen in their reaction pattern to them. Both cell types responded with the production of TNF, but DC produced more IL-12, whereas Mphi produced more IL-10, regardless of the TLR agonist used. Co-stimulation with interferon-gamma influenced the amount of cytokine production, but did not alter the cell type-specific response pattern. Compared to Mphi, DC produced > 10 times less NO upon triggering with TLR ligands. In addition, DC produced superoxide anion to opsonized and non-opsonized zymosan, but not to phorbol 12-myristate 13-acetate, a response pattern confirmed for human Mphi and DC, respectively. Different protein kinase C isoforms and extracellular signal-regulated kinase patterns were detected in cell lysates of resting and stimulated Mphi and DC. Collectively, our results point to profound differences in pathogen-derived signal-response coupling occurring commensurate with distinct functions carried out by Mphi or DC.
Sequence-specific binding of luzopeptin to DNA (1988)

We have examined the binding of luzopeptin, an antitumor antibiotic, to five DNA fragments of varying base composition. The drug forms a tight, possibly covalent, complex with the DNA causing a reduction in mobility on nondenaturing polyacrylamide gels and some smearing of the bands consistent with intramolecular cross-linking of DNA duplexes. DNAase I and micrococcal nuclease footprinting experiments suggest that the drug binds best to regions containing alternating A and T residues, although no consensus di- or trinucleotide sequence emerges. Binding to other sites is not excluded and at moderate ligand concentrations the DNA is almost totally protected from enzyme attack. Ligand-induced enhancement of DNAase I cleavage is observed at both AT and GC-rich regions. The sequence selectivity and characteristics of luzopeptin binding are quite different from those of echinomycin, a bifunctional intercalator of related structure.
The Pall Ultipor Breathing Circuit Filter???An Efficient Heat and Moisture Exchanger (1984)

The Pall bacterial filter was tested as a potential heat and moisture exchanger on a model patient, placed on a circle absorber system, and clinically. The laboratory study was conducted during mechanical ventilation at a V of 6 L/min with fresh gas inflows of 1, 3 and 6 L/min. The model patient introduced carbon dioxide into the circuitry at a rate of 200 ml/min. The resistance of the filter was tested before and after each experiment. With all fresh gas inflows , absolute humidity increased from around 19 mg H2O/L at the start of experimentation to about 27 mg H2O/L within 30 min. Maximum humidities reached were 28 +/- 0.7 mg H2O/L, 27.6 +/- 0.5 mg H2O/L, and 27.7 +/- 0.5 mg H2O/L within 3 hr, with fresh gas inflows of 1, 3, and 6 L/min, respectively. Variations in inspired humidity were also assessed at minute volumes of 4 and 5 L/min with fresh gas inflows of 6 and 3 L/min. Increases in percent dead space were negligible when the filter was inserted between the model patients (assumed to weigh between 70-40 kg) and the circuit. There was no statistically significant increase in pressure with gas flows of 50 L/min when the instrument was dry (0.02 +/- 0.001 cm H2O/L X min-1) or when it was wet (0.02 +/- 0.002 cm H2O/L X min-1). The clinical study was conducted on ten adult anesthetized patients breathing through the bacterial filter and ten controls. The loss of body temperature was 0.2 degrees C when the filter was used and 1.5 degrees C when the filter was not used. Arterial blood gas tensions were within normal limits when the bacterial filter was used as a humidifier.
Chronic hypoxia induces right heart failure in caveolin-1−/− mice (2012)

Caveolin-1 (Cav-1)-/- mice develop mild pulmonary hypertension as they age. In this study, we sought to determine the effect of chronic hypoxia, an established model of pulmonary hypertension, on young Cav-1-/- mice with no measurable signs of pulmonary hypertension. Exposure of Cav-1-/- mice to chronic hypoxia resulted in an initial rise in right ventricular (RV) systolic pressure (RVSP) similar to wild-type (WT) mice. By three weeks RVSP decreased in the Cav-1-/- mice, whereas it was maintained in WT mice. The drop in RVSP in Cav-1-/- mice was accompanied by decreased cardiac output, increased RV hypertrophy, RV interstitial fibrosis, decreased RV sarco(endo)plasmic reticulum Ca(2+)-ATPase 2a mRNA and decreased RV function compared with WT mice. Importantly, minimal differences were noted in pulmonary vascular remodeling between WT and Cav-1-/- mice, and left ventricular function was normal in hypoxic Cav-1-/- mice. Mechanistically, increased endothelial nitric oxide synthase uncoupling and increased tyrosine nitration of protein kinase G were detected in the RV of Cav-1-/- mice. These hemodynamic, histological, and molecular changes were prevented in Cav-1-/- mice expressing an endothelial-specific Cav-1 transgene or by nitric oxide synthase inhibition. These data suggest that, in Cav-1-/- mice, increased oxidative/nitrosative stress due to endothelial nitric oxide synthase uncoupling modifies the response of the RV to pressure overload, accelerating the deterioration of RV function.
The Perils of Academic Administration: Gatekeeping, Academic Freedom, and Corporatization (2006)

The following narrative is an account of one social work educators experiences in higher education administration. Three areas of concern are explored: gatekeeping, academic freedom, and the corporatization of academia. The author diseusses issues unique to educational administration, given the challenges for growth and funding, and the organizational weaknesses imbedded in such institutions.
Properties of memory T lymphocytes isolated from the mixed leukocyte reaction. (1985)

During the primary mixed leukocyte reaction, T lymphocytes of the lyt-2- helper subclass proliferate in response to transplantation antigens on allogeneic dendritic cells. We have isolated populations of antigen-specific proliferating lymphoblasts and recultured them in fresh medium. Within 2 days, the blasts become smaller in size, lose responsiveness to T-cell growth factor or interleukin 2, but retain vigorous reactivity to the original alloantigen. Two new biologic properties of these "memory" lymphocytes have been noted. First, they primarily respond to alloantigen on dendritic cells, whereas freshly sensitized lymphoblasts react to allogeneic dendritic cells, macrophages, and B lymphocytes. Second, the memory lymphocytes quickly aggregate with dendritic cells that are either syngeneic or allogeneic, but not with B cells. The aggregates that form with syngeneic dendritic cells disassemble within hours and do not release interleukin 2 or proliferate. The aggregates that form with allogeneic dendritic cells remain intact, release large amounts of interleukin 2 on the first day of culture, and synthesize DNA on the second day. Therefore, dendritic cells actively cluster memory lymphocytes by an antigen-independent mechanism, and this may underlie the heightened functional activity of each cell type.